Crystalline Molecular Complexes and Compounds: Structure and Principles 2 Volume Set (International Union of Crystallography Monographs on Crystallography)

INTERNATIONAL UNION OF CRYSTALLOGRAPHY BOOK SERIES IUCr BOOK SERIES COMMITTEE E. N. Baker, New Zealand J. Bernstein, I...

Author: Frank H. Herbstein

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INTERNATIONAL UNION OF CRYSTALLOGRAPHY BOOK SERIES

IUCr BOOK SERIES COMMITTEE E. N. Baker, New Zealand J. Bernstein, Israel P. Coppens, USA G. R. Desiraju, India E. Dodson, UK A. M. Glazer, UK J. R. Helliwell, UK P. Pauﬂer, Germany H. Schenk (Chairman), The Netherlands IUCr Monographs on Crystallography 1 Accurate molecular structures A. Domenicano, I. Hargittai, editors 2 P.P. Ewald and his dynamical theory of X-ray diffraction D.W.J. Cruickshank, H.J. Juretschke, N. Kato, editors 3 Electron diffraction techniques, Vol. 1 J.M. Cowley, editor 4 Electron diffraction techniques, Vol. 2 J.M. Cowley, editor 5 The Rietveld method R.A. Young, editor 6 Introduction to crystallographic statistics U. Shmueli, G.H. Weiss 7 Crystallographic instrumentation L.A. Aslanov, G.V. Fetisov, J.A.K. Howard 8 Direct phasing in crystallography C. Giacovazzo 9 The weak hydrogen bond G.R. Desiraju, T. Steiner 10 Defect and microstructure analysis by diffraction R.L. Snyder, J. Fiala and H.J. Bunge 11 Dynamical theory of X-ray diffraction A. Authier 12 The chemical bond in inorganic chemistry I.D. Brown 13 Structure determination from powder diffraction data W.I.F. David, K. Shankland, L.B. McCusker, Ch. Baerlocher, editors 14 Polymorphism in molecular crystals J. Bernstein

15 16 17 18

Crystallography of modular materials G. Ferraris, E. Makovicky, S. Merlino Diffuse x-ray scattering and models of disorder T.R. Welberry Crystallography of the polymethylene chain: an inquiry into the structure of waxes D.L. Dorset Crystalline molecular complexes and compounds: structures and principles F.H. Herbstein

IUCr Texts on Crystallography 1 The solid state A. Guinier, R. Julien 4 X-ray charge densities and chemical bonding P. Coppens 5 The basics of crystallography and diffraction, second edition C. Hammond 6 Crystal structure analysis: principles and practice W. Clegg, editor 7 Fundamentals of crystallography, second edition C. Giacovazzo, editor

Crystalline Molecular Complexes and Compounds Structures and Principles Volume 1

F RA N K H . H E R B S T E I N Emeritus Professor of Chemistry, Technion-Israel Institute of Technology, Israel

1

1

Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With ofﬁces in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York # Oxford University Press 2005 The moral rights of the author have been asserted Database right Oxford University Press (maker)

First published 2005 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Data available Typeset by Newgen Imaging Systems (P) Ltd., Chennai, India Printed in Great Britain on acid-free paper by Biddles Ltd., King’s Lynn ISBN 0–19–856893–2 (Vol 1) 978–0–19–856893–3 ISBN 0–19–856894–0 (Vol 2) 978–0–19–856894–0 ISBN 0–19–852660–1 (Set) 978–0–19–852660–5 10 9 8 7 6 5 4 3 2 1

TWENTY: Give up learning and put an end to your troubles. From TAO TE CHING by Lao Tsu (A new translation by Gia-fu Feng and Jane English Wildwood House, London 1973)

OR How charming is divine philosophy, Not harsh and crabbed as dull fools suppose, But musical as Apollo’s lute, And a perpetual feast of nectared sweets, Where no crude surfeit reigns, John Milton (1608–74): Comus, 476.

This book has been written in many places and over too many years. It would never have been completed without the help and support of my wife Any. It is dedicated to her and to four teachers and friends: R. W. James, FRS, formerly Professor of Physics in the University of Cape Town G. M. J. Schmidt, formerly Professor of Chemistry in the Weizmann Institute of Science J. D. Dunitz FRS, emeritus Professor of Chemical Crystallography in the Eidgeno¨ssische Technische Hochschule, Zu¨rich Sir Aaron Klug P-PRS, OM, NL. MRC Laboratory of Molecular Biology, Cambridge, UK

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Preface My intention is to give an account of the structure and properties of crystalline binary adducts, perhaps better known as molecular compounds and complexes, which are a broad group of materials whose several members are of interest to chemists (e.g. separations via crown ethers and identiﬁcations via charge transfer compounds), physicists (e.g. high-conductivity organics), biologists (is not DNA an excellent example of a hydrogenbonded molecular compound?) and technologists (zeolites for separations and as catalysts). I have tried to cater to them all; extensive inclusion of chemical formulae (for the nonchemists) and stereodiagrams (for the noncrystallographers) will hopefully make it easier to assimilate some of the unavoidable complexities. Most emphasis will be given to geometrical structures derived from crystal structure analyses for here lies the bulk of the available information. I refer to interactions between the components wherever this is possible, including both thermodynamic and electronic aspects. Consideration of the relation between structure and properties will be principally conﬁned to the solid state and the implications of solid state results for understanding chemical reactivity in other phases will not be pursued. I restrict myself to crystalline materials because the results, and their meanings, are least unequivocal for this state of matter. Interactions between components in the ﬂuid states are undoubtedly important but I leave these aspects to others. The word ‘‘molecular’’ appears in the title because most of the relevant materials are indeed molecular, but many contain charged entities and I have licensed myself to include what seems relevant, regardless of the formal restrictions of the title. Most of the substances considered are organic, some are inorganic and many have both organic and inorganic parts. I discuss representatives of many of the various types of molecular compound and complex, but I early realized that any attempt to cover all examples of all types would be self-defeating. The problems of choice beset us all, at all levels of our lives, and an author, struggling to compress the vast expanses of knowledge into a practical physical conﬁne, is no exception. I have given preference to mature areas, where what is known presents a model for the treatment of those regions as yet unexplored, and I have emphasized the fundamentals – structure and thermodynamics. I guess (no other word seems realistic) that I have managed to include about 20% of what is available in the literature. The series Inclusion Complexes, dealing with less than half the topics covered here runs to ﬁve volumes and over two thousand pages. The series Comprehensive Supramolecular Chemistry, again with half the present coverage, stretches to eleven volumes and ﬁve thousand pages. Perhaps the most serious of my many acts of omission is exclusion of material on ‘‘Zeolites’’. This is not because of any lack of importance of the subject but because it is adequately covered in a number of books and an on-going journal. There is also little said about complexes between large biomolecules – this would have required a separate book.

viii

PREFACE

An overall theory is hardly possible but some areas have had sophisticated theories applied to them, e.g. the quantum-mechanical treatments of charge transfer interactions and the statistical mechanical treatments of some phase diagrams. In order to provide some unifying factors, I have given special emphasis to structural relationships and the classiﬁcation scheme used is structural rather than chemical in nature. The classiﬁcation scheme proposed here should not be regarded as more than a convenient framework – Nature is too complex and subtle for the imposition of straitjackets. Titles of books and review articles have been included in the (close to 4000) references, which are attached to each chapter for the convenience of the reader. Much of the information is conveyed through tables, some 200 in number. The tabulated material shows that considerable systematization is possible, but also that considerable variety remains as exceptions to those rules that I (and many others) have succeeded in developing. Crystal packing and other diagrams (some 600) are a challenge to author and reader alike. Colour would have helped but was ruled out as impractical. I am most grateful to authors, editors and publishers for permission to use published material. Some more detailed acknowledgments are made in the text. My thanks go to many friends and to Caltech, Northwestern, Cambridge (U.K.), The Royal Institution, the Universities of Cape Town and Witwatersrand and, last but not least, Technion for help and facilities. Needless to say, the responsibility for the contents is entirely mine. Haifa, November 2004

Frank H. Herbstein

Contents Volume 1 PART I

SOME PRELIMINARIES

1 Structural principles in the classiﬁcation of binary adducts 1.1 Introduction 1.2 Structural classiﬁcation of binary adducts 1.2.1 General considerations 1.2.2 Molecular complexes 1.2.2.1 Inclusion complexes 1.2.2.2 Moieties within molecules 1.2.2.3 Frameworks with guest participation and/or linkage 1.2.2.4 Segregated stack charge transfer complexes 1.2.2.5 Packing complexes 1.2.3 Molecular compounds 1.3 Other classiﬁcations 1.4 How many binary adducts are there? 1.5 Organic and inorganic supramolecular chemistry References

3 4 5 5 6 6 9 9 9 10 10 10 11 12 12

2 Historical outline References

15 19

PART II

MOIETIES WITHIN MOLECULES

Introduction to Part II 3 The enclosure species – crown ethers, cryptands and related molecules – as hosts 3.1 Introduction 3.2 Doubly bridged cyclophanes and analogous molecules as hosts for intramolecular guests 3.3 Cleft molecules as hosts 3.3.1 Single-cleft hosts 3.3.2 Double-cleft hosts 3.4 Container molecules as hosts 3.4.1 Introduction

27 28 30 44 44 47 48 48

x

CONT ENTS

3.4.2 Cavitands and caviplexes 3.4.3 Hemispherands and hemispheraplexes 3.4.4 Triply bridged cyclophanes and analogous molecules as three-dimensional hosts for intramolecular guests 3.4.5 Spherands and spheraplexes 3.4.6 Carcerands and carceplexes 3.5 Hemicarcerands and hemicarceplexes 3.5.1 Overview 3.5.2 The taming of cyclobutadiene, and of o-benzyne 3.5.3 Molecular mechanics and dynamics studies on the complexation and decomplexation processes 3.6 Comparisons of concepts References

48 50

4 Cyclodextrins, and some analogs, as hosts 4.1 Introduction 4.2 -Cyclodextrins as host 4.2.1 -Cyclodextrin as host in clathrate inclusion complexes 4.2.2 -Cyclodextrin as host in tunnel inclusion complexes 4.2.3 Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes 4.3 -Cyclodextrins as host 4.3.1 -Cyclodextrin as host in clathrate inclusion complexes 4.3.2 -Cyclodextrin as host in tunnel inclusion complexes 4.3.3 Exceptional -cyclodextrin structures 4.3.4 Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes 4.4 Rotaxanes and catenanes of cyclodextrins 4.5 -Cyclodextrins as host 4.5.1 -Cyclodextrin as host in clathrate inclusion complexes 4.5.2 -Cyclodextrin as host in tunnel inclusion complexes 4.5.3 Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes 4.6 Larger cyclodextrins 4.7 Cyclic oligosaccharides as cyclodextrin analogs References

73 74 79 80 84

5 Crystal chemistry of some DNA oligonucleotides and their complexes 5.1 Introduction 5.2 Fundamentals of oligonucleotide structure 5.2.1 General aspects 5.2.2 Single crystal x-ray diffraction studies of oligonucleotides 5.3 Crystal chemistry of oligonucleotides and oligonucleotide-guest structures 5.3.1 Polymorphism, isomorphism, and heteromorphism

51 59 59 61 61 64 66 67 68

90 95 97 100 114 114 117 118 118 119 122 123 123 124

133 134 136 136 140 142 142

CONTENTS

5.4

5.5 5.6

5.7

5.3.2 Phase rule relationships 5.3.3 Applications of these concepts Intercalated hexanucleotide-drug complexes with B-DNA structures 5.4.1 The anthracycline drugs 5.4.2 Nogalamycin and derivatives 5.4.3 The 9-aminoacridine drugs 5.4.4 Native hexanucleotides and comparison of crystal structures Isomorphism and polymorphism of A-DNA octanucleotides and the binding of spermine 5.5.1 Octameric oligonucleotides Minor groove binders 5.6.1 Drug molecules that enter the minor groove 5.6.2 Decameric oligonucleotides 5.6.3 Polymorphs or intermediate phases? An example from the decanucleotides 5.6.4 Dodecameric oligonucleotides General survey of the crystal chemistry of oligonucleotide and oligonucleotide-drug complexes References

PART III

xi

143 144 145 145 151 154 156 158 158 167 167 171 178 183 187 189

HOST–GUEST INCLUSION COMPLEXES

Introduction to Part III 6 Tunnel inclusion complexes formed by hosts of lesser versatility 6.1 Introduction 6.2 Tunnel inclusion complexes with directionally bonded hosts 6.2.1 Urea, thiourea and selenourea as hosts 6.2.1.1 Introduction 6.2.1.2 Types of guest in hexagonal urea inclusion complexes 6.2.1.3 Guests which give rhombohedral urea inclusion complexes 6.2.1.4 Guests which give rhombohedral thiourea inclusion complexes 6.2.1.5 Hermann’s comprehensive structural model 6.2.1.6 Diffraction patterns from tunnel inclusion complexes 6.2.1.7 Hexagonal urea tunnel inclusion complexes 6.2.1.8 Determination of guest molecule conformation from diffuse x-ray scattering

203 204 206 206 206 207 208 209 210 212 215 218

CONT ENTS

xii

6.2.1.9

Variation of structure with temperature, with particular reference to {3(urea)[1/4(n-hexadecane)]} 6.2.1.10 Interruption of urea framework by host–guest hydrogen bonding 6.2.1.11 Rhombohedral urea, thiourea and selenourea tunnel inclusion complexes 6.2.1.12 Monoclinic complexes derived from the rhombohedral complexes 6.2.1.13 Behavior of some rhombohedral inclusion complexes on cooling 6.2.1.14 The orthorhombic Type 4 urea tunnel inclusion complexes 6.2.1.15 The hypothetical Type 5 orthorhombic tunnel inclusion complexes 6.2.1.16 The crystal structure of selenourea and its relation to the structures of its tunnel inclusion complexes 6.2.1.17 Thermodynamics of the formation of the tunnel inclusion complexes 6.2.2 The Bishop–Dance hosts – exo-2,exo-6-dihydroxy-2,6dimethylbicyclo[3.3.1]nonane and analogs 6.2.2.1 Introduction 6.2.2.2 The helical tubuland structures 6.2.2.3 The ellipsoidal tetragonal clathrate complexes of some Bishop–Dance hosts 6.2.2.4 Derived structures 6.2.3 Ta4P4S29 – an inorganic framework containing sulphur chains 6.2.4 The tunnel hydrates 6.2.4.1 Tunnel hydrates with several water molecules per tunnel cross-section 6.2.4.2 Tunnel hydrates with one water molecule per tunnel cross-section 6.3 Tunnel inclusion complexes with van der Waals bonded hosts 6.3.1 Tunnel inclusion and other complexes of deoxycholic acid and related compounds 6.3.2 Substituted spirocyclophosphazenes as hosts 6.3.3 Tritriptycene – a C62H38 hydrocarbon of D3h symmetry with three U-shaped bays 6.3.4 trans-anti-trans-anti-trans-Perhydrotriphenylene as host 6.3.5 N-(p-tolyl)tetrachloro-phthalimide as host 6.4 Comparison of the various types of tunnel inclusion complexes References 7 Clathrate inclusion complexes formed by hosts of lesser versatility 7.1 Introduction 7.2 Directionally bonded hosts

219 227 231 235 236 245 245 247 247 251 251 251 264 267 268 269 269 271 272 272 291 297 298 307 310 311 321 323 323

CONTENTS

7.2.1 Quinol (hydroquinone, 1,4-dihydroxybenzene) as host 7.2.1.1 Crystal structures of quinol polymorphs and -quinol clathrates 7.2.1.2 Low temperature phase transitions in -quinol clathrates 7.2.1.3 Introduction to statistical thermodynamics of clathrate structures and application to the quinol clathrates 7.2.2 Crystal structure of {(6H2O)[hexamethylene tetramine]} 7.2.3 Clathrates derived from existing structures 7.2.3.1 Helium hexahydrate 7.2.3.2 Cadmium cyanide clathrates 7.2.4 Overview of the polyhedral clathrates (including metalloid structures, clathrasils, gas hydrates, clathrate and semiclathrate hydrates) 7.2.4.1 Historical and general introduction 7.2.4.2 Restrictions on the shapes of the polyhedra 7.2.4.3 Packing of pentagonal dodecahedra 7.2.5 Metalloid structures 7.2.6 Clathrasils 7.2.7 Gas hydrates (structures with pentagonal dodecahedra) 7.2.7.1 Relation between guest type and structure type in the gas hydrates 7.2.7.2 Stoichiometry and thermodynamics of the gas hydrates 7.2.7.3 Prototype CS-I and CS-II crystal structures at low temperatures 7.2.7.4 Br286H2O is the only bromine hydrate, and the implications of this result 7.2.7.5 Gas hydrates with charged frameworks (ionic clathrate hydrates) 7.2.8 Peralkylonium hydrates and related structures 7.2.8.1 Introduction 7.2.8.2 Structures based on the CS-I structure 7.2.8.3 Structures based on the CS-II structure 7.2.8.4 Structures based on the HS-II structure 7.2.8.5 Structures based on the HS-I structure and its superstructure SHS-I 7.2.8.6 Structures based on the OS-I structure 7.2.8.7 Structures based on the TS-I structure 7.2.8.8 The effectiveness of the alkyl substituents in forming hydrates 7.2.9 Varieties of structures formed by a particular guest 7.2.10 The alkylamine hydrates 7.2.11 Structures without pentagonal dodecahedra (some with charged frameworks)

xiii

323 323 331

333 345 346 346 347

348 348 353 355 360 363 370 370 372 379 381 383 383 383 384 385 385 385 387 387 389 389 389 392

xiv

CONT ENTS

7.3 Hosts with a combination of directional bonds and van der Waals interactions 7.3.1 Phenol (and related compounds) as hosts 7.3.1.1 Phenol 7.3.1.2 Guayacanin as host 7.3.2 Dianin’s compound (4-p-hydroxyphenyl-2,2,4trimethylchroman) and related compounds as hosts 7.4 Van der Waals linked hosts 7.4.1 Tetraphenylene as host 7.5 Hexahosts and related compounds 7.6 Conclusions and a perspective view References 8 Inclusion complexes formed by versatile hosts 8.1 Introduction 8.2 Tri-o-thymotide and analogs as hosts 8.2.1 Crystallography of tri-o-thymotide and its complexes 8.2.1.1 The trigonal clathrate inclusion complexes 8.2.1.2 The hexagonal tunnel inclusion complexes 8.2.1.3 Tunnel inclusion complexes with organometallic guests 8.2.1.4 Crossed tunnel triclinic inclusion complexes 8.2.1.5 Miscellaneous inclusion complexes 8.2.2 Analogs of tri-o-thymotide 8.3 Trimesic acid and analogs as hosts 8.3.1 Introduction 8.3.2 Host–guest tunnel inclusion complexes based on noncatenated unary hexagonal networks 8.3.2.1 TMA as host 8.3.2.2 Two coordination complexes as potential hosts 8.3.3 Host–guest tunnel inclusion complexes based on catenated hexagonal unary networks 8.3.4 Host–guest clathrate interstitial inclusion complexes based on catenated hexagonal unary networks 8.3.5 Generalization of the concept of ‘‘interruption’’ to give binary networks 8.3.5.1 TMAH2O networks 8.3.5.2 Catenated neutral binary networks 8.3.5.3 Ionic binary networks 8.3.6 Hydrogen-bonded TMA binary complexes 8.4 The Heilbron complexes 8.5 Gossypol and its inclusion complexes 8.6 Tris(5-acetyl-3-thienyl)methane (TATM) as host 8.6.1 Introduction 8.6.2 Chemistry of TATM and its inclusion complexes 8.6.3 Conformations taken up by the TATM molecule in the various crystallographic structure types 8.6.4 Crystallography of the inclusion complexes of TATM

396 396 396 398 399 406 406 408 410 411 421 423 423 423 425 429 431 433 435 436 437 437 437 437 443 446 448 448 449 450 450 452 456 459 469 469 469 470 474

CONTENTS

8.6.5 Formation of the inclusion complexes 8.6.6 Dynamics of guest molecules in the complexes 8.6.7 Other examples 8.6.8 Summary 8.7 (5,10,15,20)-Tetraphenylmetalloporphyrins and complexes 8.7.1 Introduction 8.7.2 Crystallography of (5,10,15,20)tetraphenylmetalloporphyrin coordination complexes 8.7.2.1 Introduction 8.7.2.2 The four-coordinate coordination complexes 8.7.2.3 The ﬁve-coordinate coordination complexes 8.7.2.4 The six-coordinate coordination complexes 8.7.3 Crystallography of (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.3.1 Crystallography of four-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.3.2 Crystallography of ﬁve-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.3.3 Crystallography of six-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.4 Comparative crystallography of the (5,10,15,20)tetraphenylmetalloporphyrin coordination and inclusion complexes 8.7.5 Questions of nomenclature and description 8.7.6 Can ‘‘sponge’’ structures be inferred from the chemical nature of the second component? References 9 Intercalation complexes 9.1 Introduction 9.2 Intercalation complexes of graphite (GICs) 9.2.1 Introduction 9.2.2 Alkali metals as guests (preparation at atmospheric pressure) 9.2.3 Alkali metals as guests (preparation at high pressures) 9.2.4 Alkaline earth and lanthanide metals as guests 9.2.5 Halogens as guests 9.2.6 Uses, actual and potential, of GICs 9.2.7 Summary for GICs 9.3 Intercalation complexes of inorganic hosts 9.3.1 Introduction 9.3.2 2H--TaS2 as host 9.3.3 Zirconium phosphates and phosphonates as hosts

xv

476 477 477 477 478 478 480 480 481 483 486 493

493

500

502

505 506 507 508 515 516 517 517 520 532 533 533 539 539 540 540 540 546

CONT ENTS

xvi

9.4 Concluding summary References

PART IV

552 552

PACKING COMPLEXES

Introduction to Part IV 10 Packing complexes 10.1 Introduction 10.2 Components are isomers of various types 10.3 The (stereoisomeric) components are enantiomers 10.3.1 Background 10.3.2 Types of binary phase diagram found with enantiomers as components 10.3.3 Formation of conglomerates 10.3.4 Comparing the stability of enantiomorphs and racemic compounds 10.3.5 The structural chemistry of systems with isolatable enantiomers 10.3.5.1 Components are rigid molecules 10.3.5.2 Complications due to conformational isomerism of component molecules 10.3.6 Enantiomorphs and racemic compounds of nonisolatable conformers 10.3.7 Racemic enantiomorphs 10.3.8 Solid solutions of enantiomers 10.4 The (stereoisomeric) components are diastereoisomers 10.4.1 Background 10.4.2 Diastereoisomers as components 10.4.3 Conformers as components 10.4.4 Cis-trans isomers as components 10.4.5 Cocrystallization of tautomers 10.4.6 Interallogon complexes 10.5 Components are positional isomers 10.6 Components have different chemical compositions 10.6.1 Substitutional solid solutions 10.6.1.1 Conditions for formation 10.6.1.2 The information desired 10.6.2 Systems with complete (or a wide range of ) mutual miscibility 10.6.3 Some binary phase diagrams involving phases (primary and intermediate) with extensive composition ranges 10.6.3.1 Dibenzyl – trans-stilbene 10.6.3.2 Diphenyl sulphoxide–diphenyl sulfone 10.6.3.3 p-Dibromobenzene–p-diiodobenzene 10.6.3.4 p-Dibromobenzene–p-chloronitrobenzene

563 564 565 566 566 568 569 571 574 574 577 582 584 585 590 590 590 592 597 600 603 605 605 605 605 607 608 615 615 615 617 617

CONTENTS

10.6.3.5 Benzoic acid–p-ﬂuorobenzoic acid 10.6.3.6 1,2-4,5-Tetrachlorobenzene–1,2-4,5tetrabromobenzene 10.6.4 Evidence for nonrandom substitution in primary solid solutions 10.6.4.1 (trans-Stilbene)–diphenylmercury and tolane–diphenylmercury 10.6.4.2 2,3-Dimethylnaphthalene–anthracene 10.6.5 Inhomogeneity of some solid solution crystals 10.7 Interblock solid solubility 10.8 Primary interstitial solid solutions 10.9 Ordered packing complexes 10.9.1 Metal coordination complexes 10.9.1.1 Components of different composition and conﬁguration but in the same oxidation state 10.9.1.2 Components with different compositions, conﬁgurations and oxidation states 10.9.1.3 The components are oligomers 10.9.2 Complexes in which a moiety plays more than one structural role 10.9.3 Miscellaneous packing complexes 10.9.3.1 Packing complexes without speciﬁc interactions 10.9.3.2 Packing complexes with incipient speciﬁc interactions 10.9.3.3 Packing complexes of the fullerenes C60-Ih, 6 C70-d5h and C76 References Book index

xvii

617 617 618 618 620 620 622 622 623 623 624 624 624 625 628 628 634 634 667 [1]

Volume 2 PART V

MOLECULAR COMPOUNDS WITH LOCALIZED INTERACTIONS

Introduction to Part V 11 Donor–acceptor molecular compounds (essentially localized interactions) 11.1 Introduction and classiﬁcation

683 684

Part 1: Pure acceptors 11.2 n-Donors and s-acceptors 11.2.1 N, O, S containing ligands as donors and AgI salts as acceptors

687 687

CONT ENTS

xviii

11.3

11.4 11.5 11.6

11.7

11.8

n-Donors and *-acceptors 11.3.1 N, O, S or Se containing donors and dihalogens or halogenated molecules as acceptors 11.3.2 S containing molecules as donors and iodine molecules as acceptors (the polyiodines) 11.3.3. Physical measurements on molecular compounds of the type discussed above 11.3.4 Halogenated molecules as donors and dihalogens as acceptors 11.3.5 Self-complexes – N, O, S, Se to halogen interactions in one-component systems n-Donors and p-acceptors 11.4.1 N, O or S containing ligands as donors and Group VA metal halides as acceptors n-Donors and *-acceptors -Donors and *-acceptors 11.6.1 Aromatic molecules as donors and dihalogens as acceptors 11.6.2 Aromatic molecules as donors and polyhalogenated methanes as acceptors -Donors and p-acceptors 11.7.1 Aluminum tribromide as an acceptor 11.7.2 Miscellany-mainly MX3 (M ¼ As, Sb; X ¼ Cl, Br) as acceptors and aromatic molecules as donors -Donors and (localized) *-acceptors

688 688 706 708 712 713 717 717 723 727 727 731 733 733 734 736

Part 2: Self-interacting acceptors 11.9

n-Donors and s-acceptors 11.9.1 N, O, S containing ligands as donors and AgI salts as acceptors 11.9.2 N, O, S containing ligands as donors and HgX2 (X ¼ Cl, Br, I) as acceptors 11.10 n-Donors and p-acceptors 11.10.1 N, O, S containing ligands as donors and MX3 (M ¼ As, Sb; X ¼ Cl, I) as acceptors 11.11 -Donors and s-acceptors 11.11.1 Aromatics as donors and Ag(I) salts as acceptors; also {benzene CuAlCl4} 11.11.2 Oleﬁns as donors and Ag(I) salts as acceptors 11.11.3 Some general structural principles emerging from Sections 11.11.1 and 11.11.2 11.11.4 Acetylides as donors and Ag(I) salts as acceptors 11.11.5 Acetylides as donors and Cu(I) salts as acceptors 11.11.6 Aromatics as donors and Hg(II) salts as acceptors 11.12 -Donors and p-acceptors n n n

737 737 739 761 761 764 765 777 783 784 784 786 788

CONTENTS

11.12.1 Aromatics as donors and MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) as acceptors 11.12.2 Aromatics as donors and np3 metal ions (GaI, InI, TlI, SnII, PbII) as acceptors 11.13 Summary References 12 Hydrogen bonded molecular complexes and compounds 12.1 Introductory survey 12.1.1 Introduction 12.1.2 The characteristic features of hydrogen bonds 12.2 Application of graph theory to the description of hydrogen bond patterns 12.3 Statistics of hydrogen bond patterns 12.3.1 Methodology 12.3.2 Statistics of ring formation 12.4 Appendage structures (one component forms a hydrogen bonded framework, to which the second component is appended by hydrogen bonding) 12.5 Alternating framework structures (the components, in hydrogen-bonded alternating array, form a mixed framework) 12.5.1 Zero-dimensional frameworks 12.5.1.1 Structures with discrete pairs (A–B) of components 12.5.1.2 Structures with discrete triples (B–A–B) of components 12.5.1.3 Larger discrete groupings of components 12.5.2 One-dimensional frameworks (linear chains of alternating components) 12.5.2.1 Component A has two donor groups and the single acceptor of component B can accept two hydrogen bonds 12.5.2.2 Component A has two hydrogen bond donor groups and component B two acceptor groups 12.5.2.3 Both components have both hydrogen bond donor and acceptor functions 12.5.3 Two-dimensional frameworks (layer arrangements of alternating components) 12.5.4 Three-dimensional frameworks (arrangements of alternating components in space) 12.5.5 Accounting for formation of a molecular compound 12.6 Crystal engineering with hydrogen bonds 12.7 Charged or neutral moieties – when is there hydrogen transfer between the components? References

xix

788 822 836 836 851 852 852 853 861 862 863 864

864

867 867 867 877 881 884

885 889 893 896 901 904 905 908 911

CONT ENTS

xx

PART VI

MOLECULAR COMPOUNDS WITH DELOCALIZED INTERACTIONS

Introduction to Part VI 13 Charge transfer molecular compounds with delocalized –* interactions – introduction and general survey 13.1 Introduction and historical development 13.2 Classiﬁcation 13.2.1 General considerations 13.2.2 Intramolecular -compounds and self-complexes 13.3 Chemical nature of donors and acceptors 13.3.1 Introduction 13.3.2 Donors 13.3.3 Acceptors 13.3.4 Quasi-acceptors 13.3.5 Ionization potentials of donors and electron afﬁnities of acceptors 13.3.6 Determination of degree of charge transfer 13.4 Binary and quasi-binary donor–acceptor systems 13.4.1 Phase diagrams 13.4.2 Component ratios in binary donor–acceptor systems 13.5 Ternary -molecular compounds References 14 Layered molecules with intra-molecular donor–acceptor interactions 14.1 Introduction 14.2 Molecules of the paracyclophane type 14.2.1 Molecules derived from [n.n]paracyclophanes 14.2.2 Systems related to [n.n]paracyclophanes 14.2.3 Multi-layered systems 14.3 Molecules of the metaparacyclophane type 14.4 Molecules of the metacyclophane type 14.5 Some other systems 14.6 Concluding summary References 15 Crystal chemistry of mixed-stack –* molecular compounds 15.1 Introduction 15.2 Nonstacked structures containing structural groups of limited size 15.3 The crystallochemical families found for 1:1 –* molecular compounds

925 926 927 927 930 932 932 933 935 939 940 944 948 948 952 953 954

959 959 961 961 972 974 976 980 984 986 986 989 990 993 994

CONTENTS

15.4 Packing arrangements in n : m –* molecular compounds 15.5 Some special features of packing arrangements in –* molecular compounds 15.5.1 Crystals where one of the components is also found in interstitial positions 15.5.2 Noncentrosymmetric crystals of -molecular compounds 15.5.3 Acceptors based on polynitroﬂuorene 15.5.4 Resolution of helicenes by formation of diastereoisomeric charge transfer molecular compounds with enantiomeric acceptors 15.6 Structurally important interactions between polarizable and polar groups 15.7 Mixed-stack crystals with both charge transfer and hydrogen bonding interactions 15.7.1 The quinhydrones as a crystallochemical family 15.7.2 Molecular compounds of the ﬂavins 15.7.3 Other crystals with both charge transfer and hydrogen bonding interactions 15.8 Mixed-stack crystals with both delocalized and localized charge transfer interactions 15.9 Donors and acceptors with special chemical features 15.9.1 Fluorinated aromatics as quasi-acceptors 15.9.2 1,3,5,7-tetramethyluric acid (TMU) as quasi-acceptor 15.9.3 Acceptor is a metal coordination complex 15.9.4 Donor is a metal coordination complex 15.9.5 Donors based on phenazine 15.10 Mixed-stack donor–acceptor molecular compounds with ionized ground states 15.10.1 Mixed-stack closed-shell charge transfer salts 15.10.2 Ion-radical salts 15.11 Isomeric (polymorphic) molecular compounds 15.11.1 Type 1 – isomerism due to different types of interaction without change of moiety structure 15.11.2 Type 2 – isomerism due to electron transfer 15.11.3 Type 3 – isomerism due to proton transfer or to –* electron transfer 15.11.4 Isomerism stabilized by both charge (–*) and proton transfer (CPT compounds) 15.12 Self-complexes 15.13 Conclusions 15.13.1 Structural variety in –* molecular compounds 15.13.2 How should the packing arrangements in –* molecular compounds be described?

xxi

1001 1005 1005 1007 1009

1010 1011 1013 1013 1022 1026 1030 1032 1032 1040 1040 1042 1044 1047 1047 1048 1052 1052 1054 1055 1058 1059 1064 1064 1065

CONT ENTS

xxii

15.13.3 Structural consequences of –* interactions References (Note. The components in the ground states of these molecular compounds are taken to be neutral unless explicitly stated otherwise). 16 Crystal (structural) physics of mixed stack –* molecular compounds 16.1 Introduction 16.2 Thermodynamic parameters 16.3 Spectroscopic measurements on the excited state 16.4 Crystals with disorder ) order transformations on cooling – modern treatments of second order phase transitions 16.4.1 General introduction 16.4.2 The Ehrenfest order of a phase transition 16.4.3 Landau theory of phase transitions 16.4.4 The critical exponents 16.4.5 The permitted symmetries of a low symmetry phase derived from a particular high symmetry phase 16.4.6 Temperature dependence of the order parameter 16.4.7 Pressure dependence of the critical temperature for ordering 16.5 Thermodynamic, structural and kinetic investigations of various systems showing second order transitions on cooling 16.5.1 The crystal structure of {Pyrene PMDA}(PYRPMA) and evidence for an order , disorder phase transition at 160K 16.5.2 The crystal structure of {Naphthalene TCNB} and evidence for an order , disorder phase transition at 72K 16.5.3 The crystal structure of {Anthracene TCNB} and evidence for an order , disorder phase transition at 213K 16.5.4 Other examples of second order transitions 16.6 Crystals with ﬁrst order transformations on cooling 16.6.1 {Cycl[3.2.2]azine TNB} 16.6.2 Other examples 16.7 Physical nature of the disordered phase 16.8 Transformation to quasi-plastic phase(s) on heating 16.9 Transformation of the ground state from neutral ) ionic on cooling and/or application of pressure (NI transitions) 16.9.1 Introduction 16.9.2 {TTF chloranil} 16.9.3 {DMTTF chloranil} 16.9.4 Other examples 16.9.5 Concluding summary References

1066 1068

1081 1082 1083 1086 1090 1090 1091 1092 1093 1094 1096 1097 1097

n n n

1097

n n n

1105

n n n

n n n

n n n

n n n

1115 1119 1120 1120 1122 1122 1126 1128 1128 1129 1137 1139 1142 1142

CONTENTS

17 Segregated stack -molecular complexes 17.1 Introduction 17.2 Chemistry of donors and acceptors that participate in segregated stacks 17.2.1 Introduction 17.2.2 Donors 17.2.3 Acceptors 17.2.4 Preparation of crystals 17.3 Structures of cation-radical salts 17.3.1 Introduction 17.3.2 Cations are polycyclic aromatic hydrocarbons 17.3.3 TTF and related compounds as cations 17.3.4 TMPD salts containing -dimerized cation radicals 17.4 Structures of TCNQ anion-radical salts 17.4.1 Mutual arrangements of approximately plane-parallel TCNQ moieties 17.4.2 Structures with stacks of limited length 17.4.3 TCNQ anion radical salts in which the cations are metals 17.4.4 Stacked structures with –e average charge on the TCNQ moieties 17.4.5 Stacked structures with –0.8e average charge on the TCNQ moieties 17.4.6 Stacked structures with –2/3e average charge on the TCNQ moieties 17.4.7 Stacked structures with –0.5e average charge on the TCNQ moieties 17.4.8 Stacked structures with –0.4e average charge on the TCNQ moieties 17.4.9 Systems studied over a wide range of temperatures 17.4.10 Conclusions drawn from a survey of structural results for TCNQ anion radical salts 17.5 Other anion-radical salts 17.5.1 Alkali-metal chloranil salts 17.5.2 M(dmit)2 and M(mnt)2 as anion radicals in various guises 17.6 Structures of cation-radical anion-radical salts 17.6.1 General survey 17.6.2 Cation : anion ratio 1 : 1; monad stacks 17.6.3 Cation : anion ratio 1 : 1; diad stacks 17.6.4 Cation : anion ratio 2 : 1 or 1 : 2; monad stacks 17.6.5 Cation : anion ratio 2 : 1 or 1 : 2; diad stacks 17.7 Electron density studies of segregated stack complexes

xxiii

1147 1148 1151 1151 1152 1157 1161 1162 1162 1163 1167 1175 1177 1177 1180 1187 1189 1192 1193 1196 1202 1205 1211 1214 1214 1215 1220 1220 1220 1227 1229 1230 1232

xxiv

CONT ENTS

17.8

Theoretical studies of some segregated stack complexes 17.9 Studies of {[TTF][TCNQ]} and some related materials 17.10 Concluding summary References Appendix Book index

1234 1235 1252 1253 1267 [1]

Acknowledgements The author wishes to thank the following for permission to reproduce published material. Academic Press: Inclusion Compounds. Figs. 6.39, 6.65, 7.1, 7.24(a), 7.24(b), 7.38, 7.39, 7.40, 7.42, 7.43, 9.19, 9.22. Non-Stoichiometric Compounds: Fig. 8.4. American Association for the Advancement of Science Science. Fig. 10.24. American Chemical Society Accts. Chem. Res. Figs. 7.36, 10.15. Biochemistry. Figs. 5.7, 5.8, 5.9, 5.12. Chemistry of Materials: Figs. 6.3(b), 6.14, 6.20, 6.30, 8.6. Cryst. Growth & Design: Figs. 12.35, 12.36. Inorg. Chem. Figs. 9.18, 9.21, 10.19, 11.41, 11.58, 11.59, 11.71, 11.100, 11.119, 15.27, 17.38. J. Am. Chem. Soc. Figs. 3.4(a), (b), 3.8, 3.9, 3.17, 3.19, 3.25, 3.26, 3.28, 4.4, 4.15, 6.55, 6.60, 6.61, 6.62, 6.69, 7.5, 7.6, 7.32, 8.8, 8.53, 10.13, 11.16, 11.31, 11.43, 11.60, 11.63, 11.116, 12.6, 12.12, 12.14, 12.16, 12.18, 12.21, 12.27, 15.13, 15.32, 15.33, 16.43, 16.44, 17.9, 17.15, 17.19, 17.23, 17.42, 17.53. J. Chem. Educ. Figs. 4.1, 7.29. J. Med. Chem. Fig. 5.21. J. Org. Chem. Figs. 11.3, 11.72. J. Phys. Chem. Figs. 6.19, 6.26, 6.27, 6.28, 7.26, 17.22(b), 17.37. Organometallics: Figs.11.113, 11.121. American Crystallographic Association Fig. 3.13. American Institute of Physics J. Chem. Phys. Figs. 6.17, 6.25, 7.7, 7.15, 7.34, 7.35, 7.37, 15.29, 16.5, 16.20, 16.23. Sov. Phys. Crystallogr. Figs. 10.20, 10.22 American Physical Society Phys. Rev. Letts.: Figs. 13.4, 16.36, 17.46. Phys. Rev.: Fig. 16.38. Elsevier Adv. Organometall. Chem.: Fig. 9.6. CALPHAD: Fig. 10.21. Carbohydrate Research: Figs. 4.5(a), 4.11(a).

xxvi

ACKNOWLEDGEMENTS

Carbon: Figs. 9.10, 9.11. Chem. Phys. Letts: Fig. 6.11. Comp. Rend. Acad. Sci. (Paris), Ser. C,: Fig. 17.18. Coord. Chem. Revs. Fig. 10.40. FEBS Letters: Fig. 5.23. Inorg. Chim. Acta: Figs. 11.46, 11.53. J. Chromatography: Fig. 15.9. J. Mol. Biol. Figs. 5.6, 5.11, 5.17, 5.18, 5.20. J. Organometall. Chem.: Figs. 10.34, 11.120. J. Phys. Chem. Solids: Figs. 6.13, 17.52. Mater. Sci.: Fig. 16.14. Sol. State Comm. Fig. 16.39. Synth. Mets. Fig. 16.42. International Union of Crystallography Acta Crystallographica, Figs. 6.31, 6.51, 10.14, 10.16, 11.1, 11.15. Acta Crystallographica, B. Figs. 4.3, 4.16, 4.17, 4.19, 6.1, 6.3(a), 6.8, 6.50, 6.53, 6.58, 7.2, 7.25, 7.31, 7.41,10.7,10.8, 10.26, 11.40, 12.2, 12.5, 12.9, 12.10, 12.30, 12.31, 15.2, 15.3, 15.5, 15.7, 15.15, 15.18, 15.21, 16.4, 16.9, 16.10, 16.11, 16.12, 16.13, 16.22, 16.32, 17.17, 17.20, 17.22(a), 17.24, 17.27, 17.29, 17.32, 17.33, 17.43(a), 17.48, 17.49. Acta Crystallographica, C. Figs. 6.18, 8.7, 8.31, 8.37, 8.38, 10.4, 10.17, 10.17A, 10.32(a), 10.32(b), 12.24, 12.28, 15.6, 17.6, 17.7. Acta Crystallographica, D. Fig. 5.16. IUCr Monographs on Crystallography: Figs. 15.34, 15.35. J. Appl. Cryst. Fig. 7.27. Kluwer Academic Publishers J. Incl. Phenom. Figs. 3.11, 6.43, 7.13, 7.14, 7.24, 9.13. Macmillan Publishers Nature. Figs. 5.15, 7.16, 10.33. National Academy of Sciences U. S. A.: Proceedings. Figs. 5.13, 5.14, 5.22. NRC Research Press (Canada) Can. J. Chem.: Figs. 11.45, 11.52. Oldenbourg Verlag Z. Kristallogr. Fig. 6.21. Pergamon Comprehensive Supramolecular Chemistry. Figs. 4.2, 6.59 (Vol. 6). Tetrahedron Letters: Figs. 3.12, 3.22. Tetrahedron: Fig. 12.13. Plenum Water–a comprehensive treatise. Fig. 7.30. J. Cryst. Spectroscop. Res.: Fig. 10.31.

A C KN O W L E D G E M E NT S

xxvii

Professor M. Le Cointe. Ph.D. thesis, University of Rennes I: Figs. 16.35, 16.37, 16.40. RIA-Novosti, Paris La Recherche: Fig. 7.18 (I am grateful to Professor Rose Marx, Saclay, for her help in obtaining this ﬁgure). Springer: Monatshefte Chem.: Fig. 10.10. Springer Series in Materials Science No 18: Figs. 9.7, 9.8, 9.9. Topics in Current Chemistry. Figs. 6.41, 12.26. Taylor and Francis: Adv. Phys.: Fig. 9.2. Contemp. Phys.: Fig. 17.57. Mol. Cryst. Liq. Cryst. Figs. 6.12, 6.22, 6.23, 6.33, 10.2, 10.23, 11.25, 15.30, 16.29, 17.3. The Chemical Society of Japan Bull. Chem. Soc. Jpn. Figs. 4.5(b), 4.6(a), (b), 4.7, 4.9, 4.10, 4.13, 4.18, 11.42, 13.9, 13.10, 13.11, 16.33, 16.34, 17.10, 17.16. Chem. Letts. Figs. 7.17, 10.46, 14.6, 17.44. The Physical Society of Japan J. Phys. Soc. Jpn.: Figs. 13.7, 17.54, 17.55. The Royal Society of Chemistry Chemical Communications: Figs. 3.3, 3.4(c), 3.5, 3.16, 3.23, 6.47, 6.48, 8.21, 8.22, 10.30, 10.35, 10.41, 12.19. Chem. Soc. Revs.: Fig. 9.17. Chemistry in Britain, Fig. 1.2. J. Chem. Soc. A: Fig. 11.49. J. Chem. Soc. B: Figs. 6.67, 6.68. JCS Dalton. Figs. 8.15, 8.16, 8.17, 8.18, 9.23, 9.24, 11.12, 11.33, 11.39, 11.101, 17.11, 17.36. JCS Perkin II: Figs. 3.15, 6.40, 6.42, 7.3, 12.15, 15.14. JCS Trans. Farad. Soc. Figs. 6.4, 6.5, 6.6. J. Mater. Chem.: Figs. 17.39, 17.40. New J. Chem.: Fig. 12.3. The Royal Society of London: Proceedings, Ser. A: Figs. 8.19, 9.12, 15.4, 16.8, 16.30, 16.31. Verlag Chemie-Wiley Angew. Chem. Intl. Ed.: Figs. 3.27, 5.3, 10.36, 11.115, 14.2. Chem. Ber. Figs. 10.28, 11.35, 14.8, 14.12, 14.13, 14,14, 16.45. Chemistry Eur. J. Fig. 6.56. Prog. Inorg. Chem. Figs. 7.21, 7.23.

xxviii

ACKNOWLEDGEMENTS

Verlag Helvetica Chimica Acta: Helvetica Chimica Acta. Figs. 5.19, 7.4, 10.11. Verlag der Zeitschrift fu¨r Naturforschung Z. Naturforsch. (b): Figs. 11.110, 11.114, 11.118. Worth Publishers New York Lehninger Biochemistry, 2nd edition. Figs. 5.1, 5.2. Various Acta Chem. Scand.: Figs. 11.7, 11.8, 11.9, 11.30. Acta Chem. Scand A: Figs. 11.10. 11.11. J. Phys. D: Fig. 9.1. J. Struct. Chem. USSR: Figs. 6.2, 7.33. Liebigs Annalen: Fig. 15.20. Molecular Complexes: Fig. 13.8. Phys. Chem. Low-dimens. Materials: Fig. 9.15. I am grateful to Dr Moshe Kapon and Dr Mark Botoshansky for help of many kinds and to the staff of the Chemistry-Biology Library at Technion for their assistance in tracking down material.

Part I Some preliminaries

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Chapter 1 Structural principles in the classiﬁcation of binary adducts

The author . . . thereby extended an old chemical tradition, of calling complexes all those compounds which are in some way odd or unusual, and which do not readily ﬁt the line-for-every-electron-pair representations that are the hallmark of our language. Very often the term complex persists even after the nature of the species has been elucidated – thus we have the complex inorganic ions, the -complexes, s-complexes, charge-transfer complexes, organo-metallic complexes, clathrate complexes, hydrogen-bonded complexes, and so on. W. J. le Noble (1974). Highlights of Organic Chemistry, An Advanced Textbook, Dekker New York Chapter 23, ‘‘Complexes’’, pp. 841–842

Summary: When the properties of the individual components are largely conserved in the primary or intermediate crystalline phases of a two-component (A and B) system, then these phases are called ‘‘binary adducts’’, which is a more formal name for what are usually called ‘‘molecular compounds and complexes.’’ The various types of binary adduct are classiﬁed in terms of those interactions between the components that determine the component arrangement in the crystal. Thus A . . . A interactions dominate in inclusion complexes, A . . . A and B . . . B interactions are equally important in segregated-stack charge transfer complexes, all interactions are of roughly equal importance in packing complexes, and A . . . B interactions dominate in molecular compounds. This classiﬁcation is compared to other complementary schemes.

1.1 Introduction 1.2 Structural classification of binary adducts 1.2.1 General considerations 1.2.2 Molecular complexes 1.2.2.1 Inclusion complexes 1.2.2.2 Moieties within molecules 1.2.2.3 Frameworks with guest participation and/or linkage 1.2.2.4 Segregated stack charge transfer complexes 1.2.2.5 Packing complexes 1.2.3 Molecular compounds 1.3 Other classifications 1.4 How many binary adducts are there? 1.5 Organic and inorganic supramolecular chemistry References

4 5 5 6 6 9 9 9 10 10 10 11 12 12

4

1.1

PRINCIPLES IN THE CLASSIFICATION OF BINARY ADDUCTS

Introduction

The section at 1 bar through the pressure–temperature–composition (P–T–x) phase diagram of a binary (two component) system shows the conditions of stability of the various crystalline phases of composition AxBy. These phases may be primary solid solutions of B in A (or conversely), or AxBy compounds, with congruent or incongruent melting points, with crystal structures different from those of A and/or B. We deﬁne a ‘‘binary adduct’’ as a crystalline two-component phase, relatively easily separated into its components, in which the properties of the individual components are very largely conserved. In this deﬁnition, which is based on some comments of Ketelaar (1958), the words ‘‘binary,’’ ‘‘component’’ and ‘‘phase’’ have the meanings of the Phase Rule (Ricci, 1966). The phrase concerning the separation of the components refers to the status of intertwined species (see Chapter 3). The collective term ‘‘binary adduct’’ refers to all those chemical species which are the subject matter of this book. We shall be faithful to this deﬁnition after our own fashion for there are occasions when the advantages of a broader treatment justify some straying from the strait and narrow paths of excessive conformity. An immediate consequence of the conservation of the properties of the individual components is that there cannot be covalent bonding between the two components, although ionic and ion–dipole interactions are allowed. The binary adduct may have the same crystal structure as one of the components, when there will be solid solution of the minor (guest) component B in the major (host) component A, or it may have a different crystal structure and thus appear as a compound in the A–B phase diagram. This is an important distinction because the solid solution crystal maintains its structure on decomposition of the adduct into its components, while the phase diagram compound decomposes into separate crystals of one (when one component is a gas or liquid under ambient conditions) or both components. Harris (1997) has suggested that the two types of host should be called ‘‘hard’’ (solid solution) and ‘‘soft’’ (phase diagram compound) respectively. We prefer to keep the connection to well-established phase-diagram principles rather than adapt terms already used in other areas of chemistry. Not all phase diagram compounds are binary adducts in our present sense; for example, the phase KF2Al(C2H5)3 is composed of Kþ cations and [(C2H5)3Al-F-Al(C2H5)3] anions (Allegro and Perego, 1963), the properties of the individual components clearly not being ‘‘very largely conserved.’’ In contrast, the neutral molecule–salt complex [(C2H5)4NþBr]2(succinimide)] (Powell and Wait, 1958) could be included because the moieties1 of the individual components appear also in the complex, although with altered mutual arrangement. The principles governing binary adducts can be carried over without much change to ternary and higher adducts and some of these will also be discussed. There is a considerable resemblance between the phase diagrams and thermodynamics of molecular systems on the one hand and those of metal alloy systems on the other; in both instances the properties of the individual components are largely conserved. This is generally not so in purely inorganic systems, where rearrangement of the ions can occur. But the resemblance between molecular and metallic systems hardly extends to structural features and modes of interaction between the components. Metal atoms are 1 One dictionary deﬁnes moiety as a portion of indeﬁnite size; we use it as a convenient term for molecule and/or ion.

STRUCTURAL CLASSIFICATION OF BINARY ADDUCTS

5

approximately spherical while molecules usually have complicated shapes; indeed formation of some binary adducts can be ascribed to particular features of these complicated shapes. Interactions between metal atoms in alloys and intermetallic compounds are approximately isotropic and, at the simplest level, are ascribed to delocalisation of one (or a few) electrons per atom over the volume of the substance; interactions between the entities in binary molecular adducts are usually highly anisotropic and directional and are ascribed, to different extents in different adducts, to hydrogen bonding, to localized or delocalized charge transfer, to ionic and ion–dipole forces and to the ubiquitous dispersion forces, possibly all acting in combination. It will be immediately apparent that we have here formalized the deﬁnition of ‘‘molecular complexes and compounds,’’ restricting ourselves to the crystalline state. The interactions between the components of binary adducts that occur in solution (or in the vapor phase) are traditionally considered to be of a transient, contact nature which can affect physical properties but are difﬁcult to deﬁne in structural terms. However, over the past thirty years, there have been two important developments, one of which concerns us directly and immediately while the second is likely to be of great importance in the future. The ﬁrst of these developments is the synthesis of an important new group of adducts in which the propinquity of the components persists in solution; the crown ethers represent the ﬁrst examples of this type of adduct. We use the overall term ‘‘moieties within molecules’’ to deﬁne this group. The second concerns the explosive improvement in techniques of studying the structures of adducts formed in the gas phase. Earlier work had employed spectroscopic methods to infer structures of gas-phase adducts (Tamres and Strong, 1979) but the great advance has come from the use of supersonic beams to cool the adducts formed to very low effective temperatures. Most of this work has so far concerned adducts which exist only in the gas phase (Hutson, 1990) but this will surely be extended to adducts which also exist in the crystalline state, thus permitting inference of the importance of aggregation on structure and properties.

1.2 Structural classiﬁcation of binary adducts 1.2.1 General considerations The primary level of our classiﬁcation (Herbstein, 1993) is based on the relative structural importance of the interactions between the components A and B in determining the component arrangement in crystalline AxBy. The various hierarchies possible for A . . . A, B . . . B and A . . . B interactions can be completely listed as shown in Table 1.1. We distinguish between molecular compounds and complexes and deﬁne ‘‘molecular compounds’’ as those adducts in which A . . . B interactions determine the structure. The rest are ‘‘molecular complexes,’’ which are further subdivided into a number of groups. We distinguish three different types of molecular complex, in all of which the structural pattern in the crystal is not determined primarily by interactions between the two different components, although these may play some role. Le Noble (see above) has already drawn attention to the ambiguous way in which the term ‘‘complex’’ (from the Latin complectere, to entwine, braid, embrace) is used in chemical nomenclature. A material is ﬁrst called a complex when its structure is not known, but the term generally persists even

6

PRINCIPLES IN THE CLASSIFICATION OF BINARY ADDUCTS

Table 1.1. The classification of binary adducts into molecular complexes and molecular compounds Molecular complexes A . . . A dominant A . . . A dominant and A . . . B important A . . . A and B . . . B dominant A . . . A, A . . . B and B . . . B about equally important Molecular compounds A . . . B dominant

Inclusion complexes Inclusion complexes Segregated stack complexes Packing complexes Localized interactions Delocalized interactions

after the structure has been clariﬁed. Thus we have such disparate usages as complex inorganic ions, s-complexes, -complexes, organometallic complexes and so on. The word ‘‘complex’’ is so entrenched in the chemical literature that it seems impossible to banish it, but we shall try to use it only in a clearly deﬁned sense. The second level of our classiﬁcation refers to the type of interaction denoted by the three dots linking the two components in the A . . . A, etc. notation. This interaction can be due to hydrogen bonding, van der Waals forces, ion and ion–dipole interactions, localized or delocalized charge transfer interactions and perhaps other interactions yet to be identiﬁed; we shall use the symbol in later chapters to indicate localized or delocalized charge transfer interactions. Such a classiﬁcation scheme is summarized in Fig. 1.1. Our classiﬁcation is based on structural features rather than on the chemical nature of the components, because a particular chemical entity can form adducts of different kinds, dependent on the nature of the second component. Urea provides a simple example; hydrogen bonded urea molecules form spirals enclosing parafﬁn hydrocarbons (and other types of guest) in typical channel2 inclusion complexes, and can also hydrogen bond to other molecules to form hydrogen bonded molecular compounds, such as hyperol (urea . . . H2O2; structure by X-ray diffraction at 295K (Lu, Hughes and Giguere, 1941) and by neutron diffraction at 85K (Fritchie and McMullan, 1981)). The metal coordination complexes of urea are not binary adducts in our present sense. We shall now discuss the various categories in Fig. 1.1, proceeding from top to bottom. n n n

1.2.2 1.2.2.1

Molecular complexes Inclusion complexes

We use the term ‘‘inclusion complex’’ in a similar but somewhat broader sense than has been customary in the past; parenthetically we remark that Powell (1984) used both ‘‘inclusion’’ and ‘‘enclosure’’ in his comprehensive introduction to the multivolume series Inclusion Compounds, but we have resisted the temptation to introduce yet another term into this already confused ﬁeld. Thus ‘‘inclusion complexes’’ are all those crystalline twocomponent systems in which A . . . A interactions dominate and host (A) and guest (B) 2 Although the word ‘‘channel’’ has wide usage in the literature, ‘‘tunnel’’ is pictorially a far more appropriate term. The latter is beginning to replace the former in the recent literature, and we dare to join this trend.

STRUCTURAL CLASSIFICATION OF BINARY ADDUCTS

7

Binary adducts Moieties within molecules Zeolites

A…A dominant

Inclusion complexes

Clathrates Channel inclusion complexes Lamellar complexes

A … A dominant, A … B important A … A and B … B equally important

Frameworks with guest participation and/or linkage Segregated stack complexes Packing complexes

A…B dominant

Localized interactions

A … A, B … B and A … B all about equally important

H-bonded interactions

Molecular compounds

Charge transfer interactions

Delocalized interactions

Charge transfer interactions

Fig. 1.1. Classiﬁcation scheme for binary adducts, based on the hierarchy of A . . . A, etc. interactions in determining the arrangement of the A and B components in the crystalline adduct. Some second level aspects are also shown.

components can be distinguished without ambiguity; A . . . B and B . . . B interactions are of lesser importance. We denote the inclusion complexes by the symbolism {host[guest]} or {A[B]}. The terms ‘‘host’’ and ‘‘guest’’ have been used in a wider sense by Cram (see below) but we prefer to apply them only to inclusion complexes. These complexes are further subdivided on the basis of the dimensionality of the inclusion into clathrate (cage), tunnel and intercalation (layer) inclusion complexes. The dimensionality is neatly encapsulated in a diagram ﬁrst used in an article in Scientiﬁc American (Brown, 1962) and now used as the logo of the Journal of Inclusion Phenomena and Molecular Recognition (Davies, Kemula, Powell and Smith, 1983); we use the diagram as presented by Harris (1993). Most inclusion complexes have frameworks in which the host molecules are linked to one another by hydrogen bonds or van der Waals forces. More recent work has shown that it is convenient to add here hosts where primary chemical bonds play an important role.

8

PRINCIPLES IN THE CLASSIFICATION OF BINARY ADDUCTS

This occurs in one of two ways; either the host is an individual molecule that encloses a guest, (host plus guest) then crystallizing as an entity to form the crystal, or the host framework constitutes the whole crystal, the guests being enclosed in interstices. We call the ﬁrst of these types ‘‘moieties within molecules’’ and discuss them below. Zeolites (Barrer, 1983), in which speciﬁc host–guest interactions can be important, are an example of the second type. Usually, however, host–guest and guest–guest interactions are of the van der Waals type; guest–guest interactions are often neglected. The term ‘‘clathrate’’ was introduced by Powell (1948), who deﬁned such complexes as a ‘‘structural combination of two substances which remain associated not through strong attraction between them but because strong mutual binding of the molecules of one sort only makes possible the ﬁrm enclosure of the other (‘clathratus’ – enclosed or protected by cross bars of a grating).’’ Zeolites also ﬁt this deﬁnition. The guest molecules in clathrate complexes are enclosed by the framework of host molecules and are localized at or about points within the framework – thus these complexes can be assigned a dimensionality of ‘‘zero’’. In the tunnel inclusion complexes the guests are enclosed in (essentially) one-dimensional tunnels in the matrix of host molecules. There are inclusion complexes that cannot be assigned unambiguously between the tunnel and clathrate types because of the occurrence of constrictions in the tunnels. In the intercalation complexes the guest molecules are located between layers of host molecules, and hence are considered ‘‘two-dimensional’’; the complexes of graphite and alkali metals (Dresselhaus and Dresselhaus, 1981) are typical examples. The discerning reader will already have noticed that the graphite intercalation complexes, with covalent bonding within the quasi-inﬁnite graphite sheets, constitute two-dimensional analogs to the zeolites with their quasi-inﬁnite three-dimensional frameworks.

Isolated cages

Linear nonintersecting tunnels (channels)

Interconnected cages

Two-dimensional interlamellar regions

Intersecting tunnels

Fig. 1.2. Some typical topologies of inclusion cavities in crystalline host solids. The smallest dimension of each of these cavities is comparable with molecular dimensions. (Reproduced with permission from Harris (1993)).

STRUCTURAL CLASSIFICATION OF BINARY ADDUCTS

9

1.2.2.2 Moieties within molecules A very important development during the past twenty years, recognised by the award of the 1987 Nobel Prize in Chemistry to Cram (1988), Lehn (1988) and Pedersen (1988), is the purposeful synthesis of molecules designed to enclose (or include) other molecules or ions in which the propinquity of the components persists in solution; the crown ethers (Pedersen, 1988) represent the ﬁrst examples of this type of adduct and the fullerenes with appropriate guests perhaps the most recent (Shinohara, Sato, Ohkoohchi, Ando, Kodama, Shida, Kato and Saito, 1992). We use the overall term ‘‘moieties within molecules’’ to deﬁne this group; in the formal terms of our classiﬁcation these are molecular complexes because the A . . . A (host–host) interactions predominate, even though here the interactions are by covalent bonding. An additional emphasis stresses the relationship between ‘‘moieties within molecules’’ and ‘‘host–guest inclusion complexes’’ in the spirit of the development of inclusion chemistry, which has been broadly deﬁned as incorporating ‘‘all those chemical species, whether they be continuous solids or discrete molecules, having voids or cavities of molecular dimension, and all of the related chemical association and other reaction chemistry. Implicit in the name is the capability of including some other molecular entities within the cavities’’ (Ramprasad, Lin, Goldsby and Busch, 1988). This point of view is recognized by inserting ‘‘Moieties within molecules’’ and ‘‘Zeolites’’ in Fig. 1.1 together with the now-classical clathrate and tunnel inclusion complexes as parts of the broader category of ‘‘Inclusion Complexes.’’ As the guests are not entirely contained within the hosts in the crystal structures of some members of the ‘‘moieties within molecules’’ group (e.g. in some cyclodextrin inclusion complexes), classiﬁcation can sometimes be ambiguous. 1.2.2.3 Frameworks with guest participation and/or linkage Atoms or ions of guest moieties forming parts of frameworks, or linked to the framework by hydrogen bonding, were ﬁrst discovered by Jeffrey (1984) and coworkers when analyzing the crystal structures of the peralkylonium salt hydrates and alkylamine hydrates; the latter were called semiclathrate hydrates. A simpler example is provided by trimesic acid.dimethyl sulphoxide (Herbstein, Kapon and Wasserman 1978), where the oxygen atoms of the dimethyl sulphoxide ‘‘guests’’ are parts of the walls of tunnels formed by the hydrogen bonded trimesic acid molecules, while the methyl groups lie within the tunnels. In these examples A . . . A interactions dominate but A . . . B interactions are important. 1.2.2.4 Segregated stack charge transfer complexes The members of the next group have A . . . A and B . . . B interactions of approximately equal importance, with smaller A . . . B interactions. The only complexes known which ﬁt into this category have the components segregated into separate stacks. Although small in number, the group is of great interest and importance because most of its (organic) members have high electrical conductivities, with tetrathiafulvalene: tetracyanoquinodimethane (TTF–TCNQ) as the most famous example (crystal structure by Kistenmacher, Phillips and Cowan (1974)). There are many chemical and physical resemblances to the (delocalized) –* mixed-stack donor–acceptor molecular

10

PRINCIPLES IN THE CLASSIFICATION OF BINARY ADDUCTS

compounds (see below), and the two groups will be considered together in Part VI (as is usually done), but with retention of the designation ‘‘complexes.’’ 1.2.2.5 Packing complexes Proceeding among the hierarchical possibilities, the next group has A . . . A, A . . . B and B . . . B interactions all of approximately equal importance; in other words, no one of these interactions is dominant in determining the structure. These are known as ‘packing complexes’. A typical example is sym-tetrabromobenzene:hexabromobenzene (Gafner and Herbstein, 1964). 1.2.3

Molecular compounds

Finally we arrive at the ‘‘molecular compounds.’’ Here the dominant A . . . B interactions can be localized in nature (Hassel, 1972), as in the acetone – bromine charge transfer compound where there is an n–s* interaction (Hassel and Strømme, 1972), or as in the hydrogen-bonded purine and pyrimidine bases in the DNA double helix (Watson and Crick, 1953). Alternatively the A . . . B interaction can be delocalized, as in the –* interactions found in anthracene picric acid (Fritzsche, 1858; Herbstein and Kaftory, 1976). n n n

1.3

Other classiﬁcations

Many proposals have been made for the classiﬁcation and nomenclature of molecular compounds and complexes, and there is much confusion, overlapping and redundancy. We note here other approaches that complement the scheme set out above. It is perhaps too much to hope that any classiﬁcation and nomenclature scheme will be able to match the complexity of reality and undoubtedly many binary adducts will be found to straddle classiﬁcatory boundaries. The terms host, guest, complex and their binding forces were deﬁned in 1977 by Cram and coworkers in the following way: ‘‘Complexes are composed of two or more molecules or ions held together in unique structural relationships by electrostatic forces other than those of full covalent bonds . . . molecular complexes are usually held together by hydrogen bonding, by ion pairing, by -acid to -base interactions, by metal to ligand binding, by van der Waals attractive forces, by solvent reorganizing, and by partially made and broken covalent bonds (transition states) . . . high structural organization is usually produced only through multiple binding sites . . . a highly structured molecular complex is composed of at least one host and one guest component . . . a host–guest relationship involves a complementary stereoelectronic arrangement of binding sites in host and guest . . . the host component is deﬁned as an organic molecule or ion whose bonding sites converge in the complex . . . the guest component is deﬁned as any molecule or ion whose binding sites diverge in the complex (Kyba, Helgeson, Madan, Gokel, Tarnowski, Moore and Cram, 1977).’’ To which was added later: ‘‘In these deﬁnitions, hosts are synthetic counterparts of the receptor sites of biological chemistry, and guests the counterparts of substrates, inhibitors or co-factors.’’ The principle of complementarity

HOW MANY BINARY ADDUCTS ARE THERE?

11

was also emphasised: [in order] ‘‘to complex, hosts must have binding sites which cooperatively contact and attract binding sites of guests without generating strong nonbonded repulsions.’’ This very broad deﬁnition was directed towards complexes in solution but can well be extended towards crystalline complexes. Lehn (1988) has introduced the term ‘‘supramolecular chemistry . . . deﬁned as ‘chemistry beyond the molecule’ bearing on the organized entities of higher complexity that result from the association of two or more chemical species held together by intermolecular forces.’’ The partners of a supramolecular species are called ‘‘molecular receptor’’ and ‘‘substrate,’’ in analogy to Cram’s use of ‘‘host’’ and ‘‘guest.’’ The complementarity of a receptor for a given substrate, leading to molecular recognition, depends on energetic (electronic) as well as geometrical features, and extends the celebrated ‘‘lock and key’’ steric ﬁt concept enunciated by Emil Fischer (1894).3 A rather elaborate proposal for the classiﬁcation and nomenclature of ‘‘host–guest-type compounds’’ has been made by Weber and Josel (1983), based on criteria of host–guest type and interaction, the topology of the host–guest aggregate and the number of components in the aggregate. The nomenclature used by Weber and Josel is rather different from our present proposal; for example the urea-n-parafﬁn tunnel inclusion complex is a tubulato-clathrate and the graphite-potassium lamellar intercalate is an intercalatoclathrate. Although we have preferred not to adopt the complete Weber–Josel proposal, we have found it convenient to use some of its parts.

1.4 How many binary adducts are there? What proportion of reported crystal structures can be classiﬁed as ‘binary (or higher) adducts’? The available statistics are limited to organic (ORG) and metalloorganic (MORG) structures, and refer to the inclusion of water and solvent molecules in such structures (Go¨rbitz and Hersleth, 2000). Using the October, 1998 release of the Cambridge Structural Database, they found that 8% of the 77 000 (nonduplicated) entries for organic compounds could be classed as ‘hydrates’ and 7% as ‘solvates’; the corresponding ﬁgures for the 91 000 metalloorganic structures were 10.5 and 17%. Clathrates and other molecular compounds and complexes were excluded from the survey, which thus somewhat underestimates the proportion of structures relevant in the context of this book. The proportion of published structures containing co-crystallized organic molecules has risen from very low values before 1950 to 11% (ORG) and 23% (MORG) for the three year period 1995–1997. Which molecule is the most proliﬁc former of adducts? The principal contender appears to be sulfathiazole, which forms more than 100 solvates, plus many related two-component systems (Bingham et al., 2001). Two broad classes have been identiﬁed – inclusion phases, in which the main function of the guest is cavity ﬁlling, and co-crystals in which the partner molecule forms an essential part of the hydrogen-bonded framework. Some 60 crystals structures have been reported. Cyclotetramethylene tetranitramine (HMX) (George et al., 1965; Selig, 1982) has also been reported to form more than 100 solvates. 3 ‘‘The restricted action of the enzymes on glucosides may therefore be explained by the assumption that only in the case of similar geometrical structure can the molecules so closely approach each other as to initiate a chemical action. To use a picture I would like to say that enzyme and glucoside have to ﬁt together like lock and key in order to exert a chemical effect on each other.’’ (quoted from Lichtenthaler, 1994).

12

1.5

PRINCIPLES IN THE CLASSIFICATION OF BINARY ADDUCTS

Organic and inorganic supramolecular chemistry

In this book we have placed more emphasis on organic than on inorganic aspects of our subject, although the latter have not been ignored. Some redress of this imbalance can be obtained from the review article of Mu¨ller, Reuter and Dillinger (1995) that, presumably deliberately, has been placed adjacent to Desiraju’s (1995) classic article on Crystal Engineering. As in most of modern chemistry, the distinction between ‘‘organic’’ and ‘‘inorganic’’ will undoubtedly become more and more blurred in the future. References Allegra, G. and Perego, G. (1963). Acta Cryst., 16, 185–190. Barrer, R. M. (1983). J. Incl. Phenom., 1, 105–123. Bingham, A. L., Hughes, D. S., Hursthouse, M. B., Lancaster, R. W., Taverner, S. and Threfall, T. L. (2001). Chem. Commun., pp. 603–604. Brown, J. F., Jr. (1962). Scientiﬁc American, 207, pp. 82–92 (July, 1962). Cram, D. J. (1988). J. Incl. Phenom., 6, 397–413 (Nobel Lecture). Davies, J. E. D., Kemula, W., Powell, H. M. and Smith, N. O. (1983). J. Incl. Phenom., 1, 3–44. Desiraju, G. R. (1995). Angew. Chem. Int. Ed. Engl., 34, 2311–2327. Dresselhaus, M. S. and Dresselhaus, G. (1981). Adv. Phys., 30, 139–326. Fischer, E. (1894). Ber. Deutsch. Chem. Gesell., 27, 2985–2993. Fritchie, C. J., Jr. and McMullan, R. K. (1981). Acta Cryst., B37, 1086–1091. Fritzsche, J. v. (1858). J. prakt. Chem., 73, 282–292. Gafner, G. and Herbstein, F. H. (1964). J. Chem. Soc., pp. 5290–5302. George, R. S., Cady, H. H., Rogers, R. N. and Rohwer, R. K. (1965). Ind. Eng. Chem. Prod. Res. Dev. 4, 209–214. Go¨rbitz, C. H. and Hersleth, H.-P. (2000). Acta Cryst., B56, 526–534. Harris, K. D. M. (1993). Chem. Brit., 29, 132–136. Harris, K. D. M. (1997). Chem. Soc. Rev., 26, 279–290. Hassel, O. (1972). ‘‘Structural aspects of interatomic charge-transfer bonding.’’ Nobel Lectures in Chemistry 1963–1970, Elsevier, Amsterdam (1969 Nobel Lecture published in 1972). Hassel, O. and Strømme, K. O. (1959). Acta Chem. Scand., 13, 275–280. Herbstein, F. H. (1993). Acta Chim. Hung. Models in Chemistry, 130, 377–387. Herbstein, F. H. and Kaftory, M. (1976). Acta Cryst., B32, 387–396. Herbstein, F. H., Kapon, M. and Wasserman, S. (1978). Acta Cryst., B34, 1613–1617. Hutson, J. M. (1990). Ann. Rev. Phys. Chem., 41, 123–154. Jeffrey, G. A. (1984). ‘‘Hydrate inclusion compounds,’’ in Inclusion Compounds, edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Academic Press, London, Vol. 1, pp. 135–190. Ketelaar, J. A. A. (1958). Chemical Constitution. Elsevier, Amsterdam, p. 363. Kistenmacher, T. A., Phillips, T. E. and Cowan, D. O. (1974). Acta Cryst., B30, 763–768. Kyba, E. P., Helgeson, H. C., Madan, K., Gokel, G. W., Tarnowski, T. L., Moore, S. S. and Cram, D. J. (1977). J. Am. Chem. Soc., 99, 2564–2571. Lehn, J. M. (1988). J. Incl. Phenom., 6, 351–396 (Nobel Lecture). Lichtenthaler, F. W. (1994). Angew. Chem. Int. Ed. Engl., 33, 2364–2374. Lu, C.-S., Hughes, E. W. and Giguere, P. A. (1941). J. Am. Chem. Soc., 63, 1507–1513. Mu¨ller, A., Reuter, H. and Dillinger, S. (1995). Angew. Chem. Int. Ed. Engl., 34, 2328–2361. Pedersen, C. J. (1988). J. Incl. Phenom., 6, 337–350 (Nobel Lecture). Powell, H. M. (1948). J. Chem. Soc., pp. 61–73.

REFERENCES

13

Powell, H. M. (1984), ‘‘Introduction,’’ in Inclusion Compounds, edited by J. L. Atwood, J. E. D. Davies, and D. D. MacNicol, Academic Press, London, Vol. 1, pp. 1–28. Powell, H. M. and Wait, E. (1958). J. Chem. Soc., pp. 1866–1872. Ramprasad, D., Lin, W.-K., Goldsby, K. A. and Busch, D. H. (1988). J. Am. Chem. Soc., 110, 1480–1487. Ricci, J. E. (1966). The Phase Rule and Heterogenous Equilibrium. Dover, New York (1951, reprinted 1966), Chapter 1. Selig, W. (1982). Propell. Explos., 7, 70–77. Shinohara, H., Sato, H., Ohkoohchi, M., Ando, Y., Kodama, T., Shida, T., Kato, T. and Saito, Y. (1992). Nature, 357, 52–54. Tamres, M. L. and Strong, R. L. (1979). Mol. Assoc., 2, 331–456. Watson, J. D. and Crick, F. H. C. (1953). Nature, 171, 737–738. Weber, E. and Josel, H.-P. (1983). J. Incl. Phenom., 1, 79–85.

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Chapter 2 Historical outline

Fir’d at ﬁrst sight with what the Muse imparts, In fearless youth we tempt the heights of Arts, While from the bounded level of our mind, Short views we take, nor see the lengths behind; But more advanc’d, behold with strange surprize New distant scenes of endless science rise! So pleas’d at ﬁrst the tow’ring Alps we try, Mount o’er the vales, and seem to tread the sky, Th’ eternal snows appear already past, And the ﬁrst clouds and mountains seem the last: But, those attain’d, we tremble to survey The growing labours of the lengthened way, Th’ increasing prospect tries our wand’ring eyes, Hills peep o’er hills, and Alps on Alps arise. Alexander Pope: An Essay on Criticism

Summary: The history of our subject goes back to the beginning of the nineteenth century, although the compounds concerned remained curiosities, outside the main stream of the development of chemistry, until the ﬁrst structures were determined by X-ray diffraction in the 1940s. We are now immersed in an explosion of interest and application, ranging from condensed-matter physics to structural biology.

Having deﬁned our terms in Chapter 1, we can now sketch out the historical background. The ﬁrst molecular complexes to be reported had illustrious parentages. The hydrate of sulphur dioxide appears to have been prepared in 1777–1778 by Joseph Priestley, while chlorine hydrate was reported in the following terms by Sir Humphry Davy in 1811 ‘it is generally stated in chemical books, that oxymuriatic gas [the original name of chlorine – F.H.H.] is capable of being condensed and crystallized at low temperature; I have found by several experiments that this is not the case. The solution of oxymuriatic gas in water freezes more readily than pure water, but the pure gas dried by muriate of lime undergoes no change whatever, at a temperature of 40 below 0 of FAHRENHEIT. The mistake seems to have arisen from exposure of the gas to cold in bottles containing moisture’ (Davy, 1811).

The complex was assigned the composition 10H2OCl2 by Michael Faraday (1823); the currently preferred formulation is about 66H2OCl2, the exact composition depending on conditions of preparation (see Chapter 7).

16

HISTORICAL OUTLINE

The ﬁrst molecular compound to be reported was quinhydrone (hydroquinone: p-benzoquinone) by Wo¨hler (1844), who noted its unexpected colour. Continuation of these studies led Wo¨hler (1848) to the preparation of the ﬁrst clathrates, with quinol (hydroquinone) as host and H2S as guest; the reported compositions of 4(quinol)H2S and 3(quinol)H2S are close to modern values. The SO2 clathrate was reported 10 years later (Clemm, 1859); Mylius (1886), who prepared the CO, HCN and formic acid clathrates somewhat later, suggested possible enclosure of guests by quinol without chemical combination. The picrates of benzene, naphthalene and anthracene were also prepared in the middle of the nineteenth century (Fritzsche, 1858), at a time when the atomic weight of carbon was still taken as 6. The ﬁrst tunnel (channel) inclusion complex was perhaps the 2(thiourea)diethyl oxalate complex reported by Nencki (1874), although this would appear to require checking. There followed many disparate observations, unrelated to main currents of contemporary organic chemistry and perplexing from a structural point of view. The classical period of development culminated with the publication of the second edition of Paul Pfeiffer’s Organische Moleku¨lverbindungen (1927, First Edition 1921), which remains a mine of useful factual information although some of the structural ideas are fanciful in terms of current knowledge (Fig. 2.1). The modern period was inaugurated by the application of X-ray diffraction methods to the determination of key crystal structures. The ﬁrst of these appears to have been Phenochinon OH

O

H

H

H

H5C6O H

H H

H H5C6O

H H OC6H6

OC6H5

H O

OH

Enolformen

H

O

Ketoformen

H

O H

H

H

H

OH H

H

O H

H

H

HO

H

H

H

H

O H

O

H O Chinhydron

H

Bei dem heutigen Stand der Chromophortheorie bleibt aber – entgegen der Ansicht Posners – die tiefe Farbe der Chinhydrone bei dieser Formulierung ganz ra¨tselhaft; auch die leichte Spaltbarkeit der Chinhydrone in ihre Komponenten, schon durch sog. indifferente Lo¨sungsmittel, la¨ßt sich schwer mit der Posnerschen Theorie in Einklang bringen. Fig. 2.1. Pfeiffer’s representation of Posner’s (1904) suggestion for the structures of phenoquinone and quinhydrone. From the short quotation attached, it is clear that Pfeiffer was not an enthusiastic supporter of the proposal. The diagram has been copied from p. 276 of Pfeiffer’s book (1927).

HIS T OR I C AL OUT L IN E

17

{{[(CH3)3AsPdBr2]2}-[dioxane]} (Wells, 1938), which is a tunnel inclusion complex. However, the real breakthrough came during and soon after the end of the Second World War when H. M. Powell and coworkers at Oxford reported the structures of p-iodoaniline 1,3,5-trinitrobenzene (Powell, Huse and Cooke, 1943), and {{3(quinol)}[CH3OH]} (Palin and Powell, 1945; cf. Davies, 1998), representative of charge transfer molecular compounds and clathrate complexes respectively. Other important structural elucidations of about the same time were those of gas hydrates (Stackelberg, 1949a,b; Pauling and Marsh, 1952), urea and thiourea tunnel inclusion complexes (Smith, 1950; Hermann and Lenne, 1952), and n–s* (localized) charge transfer compounds of halogens with donors containing oxygen or nitrogen (Hassel and Rømming, 1962). The important theoretical studies of charge transfer compounds by Mulliken (1952a,b) were complemented by thermodynamic and statistical-mechanical studies of clathrates (van der Waals and Plateeuw, 1959). The current period is distinguished by a number of themes. Firstly, there is extensive activity in the area of crystal structure analysis, which is the major experimental tool. The adducts range in size and complexity from the combination of small organic molecules found in hyperol (urea:hydrogen peroxide) (Lu, Hughes and Giguere, 1941) to complexes of large biomolecules, with the complex of lysozyme and tri(N-acetylglucosamine) (Phillips, 1966) as an early example now far surpassed in complexity. Secondly, there is considerable study of interactions between components using a wide range of spectroscopic techniques. Thirdly, there has been renewed interest in physical properties, especially electrical conductivity, and in theoretical explanations for the various types of physical behaviour that have been found. A major gap in current knowledge, in regard to both theory and experimental data, relates to the energetics and thermodynamics of the interactions between the components. One must also note that an important new direction of investigation has developed with the explosive growth of the branch of host-guest chemistry which we have called ‘‘moieties within molecules,’’ the moieties being ions as well as molecules. As we noted in Chapter 1, the importance of these substances rests on their occurrence in solution as well as in the crystalline state. Perhaps the ﬁrst examples to be studied structurally as well as chemically were the cyclodextrin inclusion complexes (Cramer, 1954), which can enclose many different types of moiety within the hydrophobic interior of the doughnut-shaped molecule. The antibiotics such as enniatin constitute a somewhat similar group. These two sorts of host compound are natural in origin; the ﬁrst purely synthetic examples, the macrocyclic ‘‘crown’’ ethers, were reported by Pedersen (1967) and since then this has become one of the most rapidly growing areas in the general ﬁeld of inclusion complexes. The crown ethers were followed by the cryptands and many other variations on this theme and there seem to be few limits to the ingenuity of the organic chemist in the tailoring of particular hosts for the inclusion of speciﬁc guests. There have been many applications in analytical chemistry, synthetic organic chemistry and in biochemistry. The analogies to the behaviour of many biomolecules is striking and the phrases ‘‘molecular recognition’’ and ‘‘supramolecular chemistry’’ have become established in the literature (Lehn, 1995; Desiraju, 1995; Nangia and Desiraju, 1998). An important potential contribution of a study of crystalline supramolecular systems (‘‘binary adducts,’’ in a more old-fashioned language) is to provide detailed structural information, both static and dynamic, leading to an understanding of the interactions which are fundamental to molecular recognition, and n n n

18

HISTORICAL OUTLINE

thus hopefully, to the enhancement of our capabilities as molecular engineers, designing desired structures from ﬁrst principles. The ability to form binary adducts is not limited to small molecules and considerable progress has been made in preparing adducts of large biomolecules, an early example of which has already been mentioned (Phillips, 1966). An important application is in the area of design of drugs that have a capability of recognising receptors in proteins and DNA. Both small-molecule model compounds and biomolecule complexes are subjects of active study. Biomolecule complexes of various kinds are hardly mentioned in this book – their variety and importance demand a book in its own right. However, there is no reason to believe that the interactions involved are fundamentally different from those described here. Highlights in the historical development of the scientiﬁc study of binary adducts are summarized in Table 2.1 (references are given in the body of the text). The task of this book is to weave these varied themes into whole cloth in as coherent and cohesive a manner as possible. Table 2.1. Some highlights in the study of binary adducts. The dates are only approximate and have generally been chosen to indicate publication of a particularly significant paper or book, or to mark some special event. Usually the contributions of the authors cited (and their coworkers) extend over many years Approximate date

Author(s)

Achievement

1777–8 1811 1823 1841 1849 1858

Joseph Priestley Humphry Davy Michael Faraday C. Schaftha¨ult F. Wo¨hler J. von Fritzsche

1891

A. Villiers

1893 1897

H. W. Pickering A. W. Hofmann

1916

H. Wieland and H. Sorge

1926 1927

J. Martinet and L. Bornand P. Pfeiffer

1930

E. Hertel

1938

A. F. Wells

1940

M. F. Bengen

First observation of a gas hydrate (of SO2). Observation of the gas hydrate of Cl2. Analysis of the gas hydrate of Cl2. Preparation of graphite intercalates. Preparation of quinol clathrate of H2S. Preparation of ﬁrst mixed-stack donor–acceptor compounds (benzene, naphthalene and anthracene with picric acid). Preparation of cyclodextrin inclusion complexes. Preparation of alkylamine hydrates. Preparation of nickel ammonium cyanide inclusion complex of benzene. Preparation of choleic acid inclusion complexes. Qualitative donor–acceptor theory of –* molecular compounds. Second edition of Organische Moleku¨lverbindungen. Early crystallographic studies of molecular compounds. Crystal structure of {{[(CH3)3AsPdBr2]2} [dioxane]} tunnel inclusion complex. Preparation of urea-hydrocarbon tunnel inclusion complexes.

19

REFERENCES

Table 2.1. (Continued) Approximate date

Author(s)

Achievement

1943

H. M. Powell

1945

H. M. Powell

1949 1950–2

1964

G. Briegleb A. E. Smith; C. Herrman and H.-U. Lenne M. von Stackelberg; L. Pauling and R. E. Marsh; W. F. Claussen. G. A. Jeffery, Yu. A. Dyadin, and their schools J. D. Watson and F. H. C. Crick F. Cramer W. Saenger; K. Harata J. H. van der Waals and J. C. Plateeuw L. Mandelcorn (editor)

Crystal structure of p-iodoaniline 1,3,5trinitrobenzene. Crystal structure of quinol clathrate of CH3OH. Spectroscopic studies of binary adducts. Crystal structures of urea-hydrocarbon tunnel inclusion complexes. Crystal structures of gas hydrates.

1966

R. S. Mulliken

1966 1969

D. C. Phillips O. Hassel

1983

J. L. Atwood and J. E. D. Davies (editors) D. J. Cram, J.-M. Lehn, C. J. Pedersen. J.-M. Lehn (chair, editorial board)

1951

1953 1954

1959

1987 1996

n n n

Further development of crystal chemistry of gas hydrates and related complexes. Structure of DNA (purine/pyrimidine hydrogen-bonded molecular compound). Publication of Einschlussverbindungen. Crystallography of cyclodextrin complexes. Statistical mechanics of clathrates. Publication of Non-Stoichiometric Compounds. Nobel Prize in Chemistry (inter alia theory of charge transfer interactions). Crystallography of lysozyme complexes. Nobel Prize in Chemistry (crystal structures of localized donor–acceptor molecular compounds). First issue of J. Inclus. Phenom. Nobel Prize in Chemistry (development of supramolecular chemistry). Publication of Comprehensive Supramolecular Chemistry in 11 volumes.

References Clemm, A. (1859). Ann. Chem., 110, 345–349. Cramer, F. (1954). Einschlussverbindungen. Springer, Heidelberg. Davies, J. E. D. (1998). J. Incl. Phenom. and Mol. Recogn. Chem., 32, 499–504. Davy, H. (1811). Phil. Trans. Roy. Soc., 101, 1–35, (see p. 30). Desiraju. G. R. (1995). Angew. Chem. Int. Ed. Engl., 34, 2311–2327. Faraday, M. (1823). Quart. J. Sci. Lit. and Arts, 15, 71–74. Fritzsche, J. von, (1858). J. prakt. Chem., 73, 282–292.

20

HISTORICAL OUTLINE

Hassel, O. and Rømming, C. (1962). Quart. Rev., 16, 1–18. Hermann, C. and Lenne, H.-U. (1952). Naturwiss., 39, 234–235. Lehn, J.-M. (1995). Supramolecular Chemistry – Concepts and Perspectives, VCH, Weinheim. Lu, C.-S., Hughes, E. W. and Giguere, P. A. (1941). J. Am. Chem. Soc., 63, 1507–1513. Mulliken, R. S. (1952a). J. Am. Chem. Soc., 72, 600–608. Mulliken, R. S. (1952b). J. Phys. Chem., 56, 801–822. Mylius, F. (1886). Chem. Ber., 19, 999–1009. Nangia, A. and Desiraju, G. R. (1998). Acta Cryst., A54, 934–944. Nencki, M. (1874). Ber. Deut. Chem. Gesell., 7, 779–780. Palin, D. E. and Powell, H. M. (1945). Nature, 156, 334–335. Pauling, L. and Marsh, R. E. (1952). Proc. Nat. Acad. Sci., 38, 112–118. Pedersen, C. J. (1967). J. Am. Chem. Soc., 89, 7017–7036. Pfeiffer, P. (1927). Organische Moleku¨lverbindungen. Enke, Stuttgart, 2nd Edition. Phillips, D. C. (1966). Scientiﬁc American, pp. 78–90 (November, 1966). Powell, H. M., Huse, G. and Cooke, P. W. (1943). J. Chem. Soc., pp. 153–157. Smith, A. E. (1950). J. Chem. Phys., 18, 150–151. Stackelberg, M. von, (1949a). Naturwiss., 36, 327–333. Stackelberg, M. von, (1949b). Naturwiss., 36, 359–362. Waals, J. H. van der, and Platteeuw, J. C. (1959). Adv. Chem. Phys., 51, 1–59. Wells, A. F. (1938). Proc. Roy. Soc. Lond. A, 167, 169–189. Wo¨hler, F. (1844). Ann. Chem., 51, 145–163. Wo¨hler, F. (1849). Ann. Chem., 69, 294–300.

Part II Moieties within molecules

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Introduction to Part II Moieties within molecules

Chemistry is going to move into bigger molecules and new types of reactions. And the chemist is going to have to pay far more attention than he or she has done in the past to noncovalent bonding. Hitherto the chemist has grown accustomed to hydrogen bonding. But other forces will have to be considered, forces that make these big molecules adopt certain shapes . . . I think there is great hope for the future in work going on in the inclusion of small molecules in big ones. Lord Alexander Todd Chemical and Engineering News October, 1980

The unifying theme of Part II is that the binary adducts considered exist in solution as well as in the crystalline state – the guest moieties are enclosed within the conﬁnes of the host molecule and held in tight enough embrace to maintain the integrity of the combination despite the potentially disintegrative buffeting forces of the solvent molecules. Therefore our choice of title – moieties within molecules. Alternative terms, meeting with growing acceptance, are ‘‘supermolecule’’ (noun) and ‘‘supramolecular’’ (adjective). The difference between ‘‘supermolecules’’ and the ‘‘molecular compounds and complexes’’ considered in the later sections of this book is that the latter have at most a transient, if any, existence in solution. The supermolecules can have a variety of chemical forms, with the most useful distinction being made between two major geometrical groups – the rings and the threedimensional cages. However, even rings tend to wrap around guests as much as possible. Guests are chosen to match the geometrical shapes of the cavities of the hosts thus imparting selectivity to the systems. This is one aspect of another theme of currently growing importance – that of molecular recognition, which also ﬁnds its expression in the matched hydrogen-bonded systems discussed especially in Chapter 12. Perhaps 90% of the binary adducts described in this book have been obtained by chance rather than deliberate design, and this includes those dealt with in Chapters 4 and 5. Not so for the subjects of Chapter 3 – crown ethers, cryptands and other types of enclosure hosts – for these are adducts where the host molecule has been designed to fulﬁll the function of enclosing within its boundaries a guest of a particular kind. However, the ﬁrst steps in this direction taken by C. J. Pedersen in the 1960s were not designed but serendipitous, with chance favoring his prepared mind. Pedersen, investigating the effects of bi- and multidentate phenolic ligands on the catalytic properties of the vanadyl group VO, obtained a small quantity (0.4%) of an unknown material which trapped sodium ions. His conclusion – ‘‘thus did I discover dibenzo-18-crown-6, the ﬁrst crown ether and the ﬁrst neutral synthetic compound capable of complexing the alkali metal cations’’ – has an almost Biblical ring of triumph (Pedersen, 1988). This discovery sparked off many

24

MOIETIES WIT HIN MOLECULES

investigations, some deepening our knowledge and understanding of the crown ethers, and others, especially those of Lehn (1988) and Cram (1988), moving off in new directions. Formation of complexes is most efﬁcient if the host has a built-in conformation adapted to enclosure of the guest, but this is not a sine qua non for there are many examples showing considerable differences between the conformation of the neat host and that taken up in the complex. Thermodynamic measurements (generally carried out by NMR techniques) on the host–guest combination in solution provide fundamental information about the stability of the complexes formed, and the energetics of the formation and break-up of the host–guest combinations. Both rings and three-dimensional cages have been synthesized, and the guest species include metallic cations, a few anions, organic cations and anions and neutral molecules. We devote most attention to the latter. An informative survey of synthetic supramolecular chemistry has been given by Fyfe and Stoddart (1997). In Chapter 4 (Cyclodextrins and their complexes) we consider a particular group of host molecules – the , and g cyclodextrins – which have toroidal forms of three different sizes; these are natural products obtained from the degradation of starch. Because the host does not entirely enclose the guest, these complexes are less stable in solution than the enclosure species considered in Chapter 3 and we pay more attention to the varieties of arrangement found in the crystals. Cyclodextrins have found widespread use in the chemical and pharmaceutical industries. In Chapter 5 (DNA and its complexes) we consider a limited group of the inclusion complexes formed by another type of host molecule obtained from a natural product – DNA. The complexes of DNA with other biological molecules such as proteins constitute an area of research which seems at present to have limits neither to its size nor its importance but is too large for discussion in a single chapter of this book. For this reason we have limited ourselves to considering complexes of ‘‘small’’ molecules with DNA oligomers of limited length and various compositions. These complexes are essentially of two different kinds – those formed by intercalation of guests between the base pairs of the double helix, and those formed by inclusion of the guests in the small or large grooves on the periphery of the helical DNA fragment. Maverick and Cram (1996) have made some interesting remarks on the role of crystal structure analysis in the prosecution of the type of research described in these chapters (and elsewhere). We quote (with permission) an abbreviated version: ‘‘The . . . analyses presented many problems . . . the solvents used for isolation and puriﬁcation . . . tend to disorder in the crystals . . . Almost without exception, crystals of carcerands, empty or complexed, were weak diffracters, resulting in very poor data-to-parameter ratios. Often the symmetry of the host cavity and . . . of the guest were incompatible, resulting in inaccuracies just where the greatest accuracy is required. For these reasons, the structures presented . . . are crude by some crystallographic standards.’’ The reader will ﬁnd a comparison with the even more severe situation described in Chapter 9 (Intercalation Complexes) instructive. Nevertheless, ‘‘Crystal structure determinations . . . were of great importance [because] (i) . . . they were the . . . ﬁnal criteria for our success in synthesizing these new types of complexes. (ii) [they] provided a wealth of information about preferred conformations . . . [suggesting] explanations for some of the observed binding phenomena . . . (vi) Crystal structures provide a simple, direct and independent means of convincing yourself and skeptics that ‘you know what you are doing.’’’ Few changes are required to make these remarks applicable to many analogous situations described in this book.

REFERENCES

25

Most of the molecules considered in this section have been described in a review volume edited by Semlyen (1997).

References Cram, D. J. (1988). J. Incl. Phenom., 6, 397–413. Fyfe, M. C. T. and Stoddart, J. F. (1997). Accts. Chem. Res., 30, 393–401. Lehn, J.-M. (1988). J. Incl. Phenom., 6, 351–396. Maverick, E. Cram, D. J. (1996). ‘‘Carcerands and Hemicarcerands: Hosts that imprison molecular guests,’’ in Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Pergamon, Oxford, Vol. 2, pp. 367–418. Pedersen, C. J. (1988). J. Incl. Phenom., 6, 337–350. Semlyen, J. A. (Editor) (1997). Large Ring Molecules, Wiley, Bognor Regis.

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Chapter 3 The enclosure species – crown ethers, cryptands and related molecules – as hosts

‘‘A gentle guest, a willing host, Affection deeply planted – It’s strange how those we miss the most Are those we take for granted.’’ Sir John Betjeman ‘‘The Hon. Sec.’’ (1986)

Summary: Crown ethers are prototype examples of host molecules of the ring type where small ring sizes interact with metallic cations to form widely studied ion-molecule complexes, dealt with here only in passing, while the larger ring sizes interact with neutral molecules and organic cations of various types to form intramolecular inclusion complexes, rotaxanes and even catenanes. Although formally two-dimensional rings, the actual conformations taken up by the larger crown ethers are more complicated and include the formation of molecular clefts. The overall shapes of threedimensional cage molecules are approximately ellipsoidal; the cages are closed to lesser or greater extents, thus permitting ingress and egress of guest molecules tailored in size and shape to match the available portals and cavities. Thermodynamic measurements in solution, principally using NMR methods, provide insight into the energetics of these processes. Although considerable ingenuity has been expended in the synthesis of the hosts, these are more easily obtainable than might be imagined at ﬁrst thought, and this holds great promise for their widespread use in the future. A crowning achievement of this type of host–guest chemistry is the synthesis of stable but reactive cyclobutadiene incarcerated within the cavity of a hemicarcerand, followed by the analogous preparation of o-benzyne.

3.1 Introduction 3.2 Doubly bridged cyclophanes and analogous molecules as hosts for intramolecular guests 3.3 Cleft molecules as hosts 3.3.1 Single-cleft hosts 3.3.2 Double-cleft hosts 3.4 Container molecules as hosts 3.4.1 Introduction 3.4.2 Cavitands and caviplexes 3.4.3 Hemispherands and hemispheraplexes 3.4.4 Triply bridged cyclophanes and analogous molecules as three-dimensional hosts for intramolecular guests 3.4.5 Spherands and spheraplexes 3.4.6 Carcerands and carceplexes

28 30 44 44 47 48 48 48 50 51 59 59

28

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

3.5

Hemicarcerands and hemicarceplexes 3.5.1 Overview 3.5.2 The taming of cyclobutadiene, and of o-benzyne 3.5.3 Molecular mechanics and dynamics studies on the complexation and decomplexation processes 3.6 Comparisons of concepts References

3.1

61 61 64 66 67 68

Introduction

Intramolecular enclosure of guests by hosts, often speciﬁcally and purposefully designed, has progressed remarkably rapidly over the last thirty years, spearheaded by the efforts of Pedersen, Lehn, Cram and their coworkers, and formally recognized by the joint award of the Nobel Prize for Chemistry to the trio in 1987. Many different host systems have been synthesized and the strengths of host–guest interactions in solution have been measured, and an understanding developed of the factors contributing to these interactions. In parallel, the determination of a number of crystal structures has led to establishment of a sounder geometrical foundation for the assessment of the various contributions to host– guest interaction. All this has been accompanied by growth of a nomenclature and jargon, especially as the systematic names of most of the host compounds are very complicated. We ﬁrst introduce representatives of the main types of host (Fig. 3.1) and then discuss the structures of the complexes formed, emphasizing crystallographic results and noting synthetic methods and studies of solution thermodynamics only peripherally. The hosts are given the sufﬁx ‘‘-and’’ (corand – often still called ‘‘crown ethers’’ – cryptand, . . . etc.) and the corresponding complexes are sometimes given the sufﬁx ‘‘-ate’’ and are coronates, cryptates, . . . etc., or else the sufﬁx ‘‘-plex’’ and become caviplexes, hemispheraplexes, . . . etc.). A distinction has been made between cavitands, which are hosts containing enforced cavities, and speleands, where the host combines the elements of a rigid, lipophilic cavity with polar binding sites. The classical origins of these names is obvious: Latin corona wreath, crown; Greek krupto hide; Greek speliaon cave; Latin cavus hollow; Latin carcer prison. When considering the formation of complexes in solution, two important factors are generally taken into account. These are (i) the principle of stereo-electronic complementarity between host and guest, and (ii) the principle of preorganization of a binding site before complexation. The ﬁrst is often stated to be a modern formulation of Emil Fischer’s ‘‘lock and key’’ principle (Behr, 1994). It implies that there is some special interaction, perhaps charge transfer or hydrogen bonding, between host and guest, as well as geometrical complementarity. The second has been deﬁned by Cram and coworkers in a long series of elegant investigations which we describe in more detail below. Essentially this principle states that binding sites are best organized to be complementary in a stereoelectronic sense prior to complexation; if not, then reorganization is necessary on complexation and the price paid in free energy may outweigh the gain achieved by complexation. If so, then complexation will not take place. In general, complexation requires replacement of solvent molecules by guest molecules. Preorganization also enhances selectivity by introduction of particular chemical features into an host molecule enhancing

29

I NT RO D UC T I O N

O O

O

O

O

N O

H3C

O

O

H

H

N

O O

O Corand (crown ether; 18-crown-6)

n

O

CH3 Podand

Cryptand

O O O

N

O X

X

O O

X

X

H3C

CH3

X

N X

H3C

CH3

CH3

CH3

Hemispherand (X = OCH3)

Cryptaspherand (X = OCH3) X

(H2C)n

X

(CH2)n

X

Doubly bridged cyclophanes CH3 CH3

O S

CH3

Si O

O Si

O CH3

CH3

CH3

CH3

O

O

O

O Si

S O

O

O

O O

O

S

O

O

CH3

CH3

Cavitand

O

O

O

CH3

O

CH3

O

O CH3 Si

Triply bridged cyclophanes

O

S O

Carcerand

Fig. 3.1. Representatives of the main types of host classiﬁed in chemical terms. It is important to note that the types of complex formed depend on the nature of the guest and, most importantly, on the geometry as well as the chemistry of the host. The ﬁlled circles in the carcerand represent methyl groups.

its ability to form complexes with special guests. However, as we shall see below, there can often be a considerable change of shape in an host molecule as it changes from uncomplexed to complexed conformation. Such comparisons require crystal structures of the neat host as well as those of the complex, and some are indeed available. In crystalline complexes it is also necessary to consider the possibility of intermolecular complexation of guest and/or solvent as an additional stabilizing factor.

30

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

Analysis of a crystal structure shows in detail the host–guest relationship in the solid state but it is often not clear to what extent this geometrical situation persists in long-lived fashion in solution. Thermodynamic and spectroscopic (especially NMR methods) studies of the solutions provide evidence to probe these questions. Here we draw special attention to ﬁve massive compilations of solution thermodynamic data, which also provide an exhaustive listing of the structural formulae of macrocyclic hosts. These deal with intramolecular complexation of metallic cations and anions (Christensen, Eatough and Izatt, 1974; 217 references; Izatt, Bradshaw, Nielsen, Lamb, Christensen and Sen, 1985; 340 references), organic cations and anions (Izatt, Pawlak, Bradshaw and Bruening, 1991; 1173 references), and neutral molecules (Izatt, Bradshaw, Pawlak, Bruening and Tarbet, 1992; 307 references); this information has been revised and extended (Izatt, Pawlak, Bradshaw and Bruening, 1995; 478 references). There does not seem to be any comparable material dealing with the thermodynamics of the solid complexes and their components, which would be even more relevant here in the context of our emphasis on the solid state. It will be observed that we pay much more attention in this chapter to thermodynamic parameters derived from measurements in solution than we do in most other chapters, where the emphasis is placed on the thermodynamics of the crystalline complexes. The reason is that the thermodynamic measurements refer to the process of intramolecular complexation and this will, we presume, be little altered if it occurs in solution or in the solid state. We start this chapter by considering intramolecular enclosure systems where the host molecules are perhaps more nearly two- rather than three-dimensional; enclosure is often less complete with two-dimensional hosts. We then proceed to the complete enclosure found with three-dimensional hosts. Our classiﬁcation is largely based on the shapes taken up by the host molecules and thus crosses boundaries of chemical type. We use a mnemonic nomenclature – the supramolecular macrocyclic complex is denoted by parentheses{M[X]}, with the included guest within square brackets [X]. This hopefully lessens the confusion, especially when counterions and solvent molecules are present in the crystal but not included within the conﬁnes of the host. There are a number of excellent reviews (Cram and Cram, 1994; Jasat and Sherman, 1999; Hof, Craig, Nuckolls and Rebek, 2002; Rudkevich, 2002) which describe the historical development of the ﬁeld, the synthetic aspects and the solution chemistry; these are complementary to the material given in this chapter, where the crystal-chemical aspects are emphasized.

3.2

Doubly bridged cyclophanes and analogous molecules as hosts for intramolecular guests

Background to the use of cyclophanes as hosts for the enclosure of neutral molecules has been given (Diederich, 1988; Odashima and Koga, 1983). The necessary, but not always sufﬁcient, condition for intramolecular inclusion of a guest species within the internal cavity of a suitable host molecule is that the cavity should be large enough to accommodate the guest. The classical studies of crown ether complexes deal mostly with those having inorganic cations as guests (Dobler, 1981; Hilgenfeld and Saenger, 1982; Bradshaw, Izatt, Bordunov, Zhu and Hathaway, 1996); we shall not make more than passing reference to these for

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

31

reasons of space. Many complexes of the smaller crown ethers, especially 18-crown-6, with neutral molecules are known, but crystal structure analysis shows that these are intermolecular complexes with hydrogen bonding between the components and not intramolecular inclusion complexes; many are discussed in Chapter 12. From a consideration of the available crystallographic results, Uiterwijk et al. (1986) concluded that ‘‘urea and urea analogs like uronium and guanidinium cations can only form encapsulated complexes with complementary H-bonding schemes if the crown ether has at least 27 ring atoms. With smaller rings, perching complexes are formed.’’ It may well be posssible to generalize this conclusion to other potential guests. An example of complexation by a derivative of 18-crown-6 (3.1) presents a cautionary tale. This forms a highly stable 1 : 1 complex with nitromethane in which the methyl hydrogens are directed towards the emphasised N and O atoms of 3.1 (Weber, Franken, Puff and Ahrendt, 1986; DIZTIP). The difﬁculties of deﬁnition and interpretation appear when the stereoview of the nitromethane environment (Fig. 3.2) is examined. Firstly, the host molecule is not planar and indeed approximates to the cleft shape discussed in Section 3.3 below; secondly, the guest is not entirely enclosed within the host but rather between a group of four host molecules. One should beware of drawing conclusions from projections onto the mean plane of possibly nonplanar molecules. An interesting feature of {3.1[nitromethane]} is that spontaneous resolution has taken place on crystallization, the space group of the complex being P212121; spontaneous resolution does not occur in the two polymorphs of the neat host (TAFYOO, CARXOI), nor in the complexes with acetonitrile (FUCFOY), phenyl cyanide (YURROS), or in the bis(methanol) monohydrate complex (CARXOU). Chloroacetonitrile forms a 1 : 1 complex while the acetonitrile complex has a 1 : 2 host : guest ratio, both complexes being less stable than the nitromethane complex. Dimethylformamide, dimethyl sulphoxide, acetone, benzene and toluene do not form complexes.

N O

O

O

O O

O

3.1

Fig. 3.2. The formula of 3.1 (the N and two O atoms involved in bonding to the methyl hydrogens are emphasised) is shown, and a stereoview of the surroundings of the nitromethane molecule in the crystal of {3.1[nitromethane]}. The host molecules are shown as line drawings and the guest in space-ﬁlling representation. (Adapted from Weber, Franken, Puff and Ahrendt, 1986.)

32

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

The larger crown ethers1 can and do act as hosts in intramolecular inclusion complexes; a wide range of host shapes and degrees of ﬂexibility can be attained by choice of suitable compositions. Most of the published results refer to (PF6) salts in which the guests are the dications bipyridinium (3.2), diquat (3.3) and paraquat (3.4). One series of publications carries the intriguing title ‘‘Molecular Meccano’’ (Anelli et al., 1992; Part 2, Amabilino, Ashton et al., 1995) and another invokes the name of ‘‘Molecular Lego’’ (Kohnke, Mathias and Stoddart, 1989), both trade names of children’s toys in which complicated structures are constructed by combination of a limited number of simpler units. We shall summarize some of the structural results, starting with smaller host molecules such as bis-m-phenylene-32-crown-10 (C28H40O10; BMP32C10; 3.5; Allwood, Shahriari-Zavareh, Stoddart and Williams, 1987). Note that we shall often use the acronyms of the original papers instead of systematic names. The neat compound (FIKWAX) crystallizes in space group P21/a (Z ¼ 2) and the molecules are centrosymmetric, with ˚ 2. Minimal an open conformation having a free central passage of dimensions 7.8 4.9 A rotations about four single bonds are required to extend the central passage so that a diquat cation can be complexed intramolecularly; the crystals have composition {C28H40O10[C12H12N22þ]}(PF6)2(CH3)2CO (space group P1, Z ¼ 2; FIKWEB). The conformations of uncomplexed and complexed hosts are compared in Fig. 3.3; the two pyridinium rings of the diquat cation have a twist angle of 22 .

NH+

+HN

Bipyridinium (3.2)

N+

N+

Diquat (3.3)

N+–CH3

H3CN+

Paraquat (3.4)

Scheme 3.1

Bis-p-phenylene-34-crown-10 (BPP34C10; 3.6; the formula is shown in Fig. 3.4(a) below2) also forms intramolecular inclusion complexes (Allwood, Spencer, ShahriariZavareh, Stoddart and Williams, 1987a). The neat compound (FIKVEA) crystallizes in space group P21/c (Z ¼ 4), with two molecules of somewhat different conformation at independent centres of symmetry; both conformations are open rather than self-ﬁlling. This is in contrast to the self-ﬁlling conformation found in tetramethoxy-BPP34C10 (Owen, 1984; CIDLOQ, C2/c, Z ¼ 4). The second conformation (designated II) of the 1 The crown ethers are named as n-crown-m where ‘n’ is the number of atoms in the macrocycle and ‘m’ is the number of (ether) oxygen atoms. Thus 3.5 is 32-crown-10 (or 32C10 for short), the macrocycle having 22 carbons and 10 oxygens. 3.5 contains two m-phenylenes and thus the overall number of carbons is 22 þ (2 3) giving the composition as C28H40O10. The acronym is BMP32C10 where BMP represents bis(m-phenylene) and 32 is the number of atoms (C þ O) in the macrocycle. 2 Although BMP32C10 and BPP34C10 have the same composition (C28H40O10), their macrocycles have different sizes and connectivities.

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

61 173 173 –174

74 –67 –154

68

N

16 73 167

–63

N

22 –66

77

33

94

–62 –171 164 –168 –67

9

7

175

–154 175 18 –62 64 173

Fig. 3.3. Comparison of the centrosymmetric shape of BMP32C10 (3.5) in its neat crystals (on the right) and in its complex with diquat (on the left); the oxygens are darkened; diquat is twisted by 22 about the central bond. The considerable difference in the two conformations is shown by the torsion angles about the various bonds (only torsion angles differing by >5 from 0, 180 are shown). (Reproduced from Allwood, Shahriari-Zavareh, Stoddart and Williams, 1987.)

neat crystals is unusually open and remains so when it encloses a bipyridinium cation, the terminal N–H groups being hydrogen bonded to opposing oxygens of the crown ether (Ashton, Philp et al., 1991; KOLMAZ). When the para hydrogens of the bipyridinium cation are successively replaced by methyls, n-propyls and n-butyls, then a series of rotaxanes3 is obtained, exempliﬁed by the complex of composition {C28H40O10[C12H14N22þ]}(PF6)22[(CH3)2CO] (Fig. 3.4) in which the BPP34C10 macrocycle is threaded by a paraquat (PQT2þ) cation (P1, Z ¼ 2; Allwood, Spencer et al., 1987a; FIRXOT); the 4,4 0 -bi(2-hydroxyethylpyridinium) complex is KOLMED and the 4,4 0 -bi(2-(2-hydroxyethoxy)ethylpyridinium) complex is KOLMIH. As the conformation of the macrocycle hardly changes from one complex to the next, these macrocycles are examples of almost perfect preorganization. A rather similar arrangement and illustration of preorganization is found in the intramolecular paraquat inclusion complex of 1,5-dinaphtho-38-crown-10, which is stabilized by –* interactions between the electron-rich naphthalene and the electron-poor bipyridinium rings, possibly supplemented by weak electrostatic interactions (Ashton, Chrystal et al., 1987; FUVBAZ; 3 Rotaxanes (rota (L) ¼ wheel, axis (L) ¼ axle) have been deﬁned (Schill, 1971) as molecules in which a cyclic structure is threaded by a chain or other linear subunit having bulky ends that prevent the dissociation (unthreading) of the cyclic and linear components. Pseudorotaxanes (Stoddart, 1991) are supramolecules in which the wheel is free to dissociate from the axle – thus the components are held together by nonbonded interactions rather than the mechanical interference of true rotaxanes. Catenanes (L. catena, chain) are molecules which contain two or more interlocked rings which are inseparable without the breaking of a covalent bond. The number of catenated rings is designated by [n] where n 2. These are all examples of interlocked or intertwined species (Amabalino and Stoddart, 1995). Here we return to a point of nomenclature. In Chapter 1 we required ‘binary adducts’ to be relatively easily separable into their components. In terms of this requirement, pseudorotaxanes are binary adducts while rotaxanes and catenanes are not. However, it is convenient to include here some examples of the latter in order to illustrate particular points.

34

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

(a)

O O

O

(b)

O

N

O O

O

N O

N

O

O N

O

O

O

O

O

O

O O

O O (c) N

N

Fig. 3.4. Ball and stick (a) and space-ﬁlling representations (b) of the centrosymmetric rotaxane complex {BPP34C10[PQT2þ]}(PF6)22(CH3)2CO; the diagrams show two different orientations. The host crown ether 3.6 has an S-shape when viewed from a direction normal to that of (b); (c) the best least squares ﬁt is shown between conformation II of neat BPP34C10 and that found in the paraquat complex. (Parts (a) and (b) reproduced from Anelli et al. (1992) and part (c) from Allwood, Spencer et al., 1987b.)

{C36H44O10[C12H14N2]2þ2(PF6)-2((CH3)2CO)}). Other rotaxanes and pseudorotaxanes are discussed below. The diquat monohydrate complex of BPP34C10 introduces a new feature, with both cation and water molecule located within the torus of the host molecule (Allwood, Spencer, Shahriari-Zavareh, Stoddart and Williams, 1987b; FIKVIE); thus the composition is best represented as {BPP34C10[diquatH2O]}(PF6)2 and the conformation of the host crown ether is again similar to that of conformation II of neat BPP34C10. The crystal structure of {BPP31C9[diquat]}(PF6)2 also shows intramolecular inclusion of diquat by the crown ether host (Ashton, Slawin, Spencer, Stoddart and Williams, 1987; FIRXUZ). The diquat cations are both twisted, as noted above. The crystal structures of neat crown ethers of general formula BPP(3n þ 4)Cn have been determined (Slawin, Spencer, Stoddart and Williams, 1987) for n ¼ 7, 8, 10 (BPP34C10), 11 and 12, and some edge-on views are shown in Fig. 3.5 (analogous diagrams for BPP34C10 have been shown above). It is clear that considerable reorganization of the ring conformations is needed before complexes can be formed, except for the two conformations of BPP34C10 (especially conformation II). An important interaction in these complexes is the edge-to-face stacking between aromatic rings shown for BPP25C7 (Fig. 3.5(a)) and discussed theoretically by Burley and Pesko (1986). It is inferred that the edge-to-face disposition is a result of an electrostatic attraction between a partial positive charge on the intruding hydrogen and the negatively charged

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

(a)

(b)

(c)

(d)

35

Fig. 3.5. Edge-on views of the molecules BPP25C7 (FIKTIC), BPP28C8 (FIKTOI), BPP37C11 (FIKTUO) and BPP40C12 (FIKVAW) in their neat crystals. (Reproduced from Slawin, Spencer, Stoddart and Williams, 1987.)

-cloud of the aromatic ring; energies of 4–8 kJ/mol are involved. The molecule of bis(1,5-dihydroxynaphtho)-35-crown-9 in its neat crystals provides another example (Ashton, Chrystal et al., 1987; FUTZUP); the central cavity is ﬁlled by a T-disposition of the two naphtho moieties, with one in an edge-to-face relation to the other. Similar dispositions have also been observed in intermolecular arrangements. Another new feature is introduced when the host molecule is 1,5-dinaphtho-44-crown-12; the neat molecule crystallizes in space group P21/a, Z ¼ 2 (KEBLEI). A complex of 1 : 2 composition is formed with paraquat which can be represented as {1,5-DN44C12 [PQT2þ]}(PQT2þ)(PF6) 4 (CH3)2CO (KEBLAE; P1, Z ¼ 1). One of the paraquat cations is included within the macrocycle and the second is stacked between the macrocycles, the whole assembly forming an alternating arrangement of donor and acceptor groups (Fig. 3.6; Ortholand, Slawin, Spencer, Stoddart and Williams, 1989). This is very similar in overall form to the well-known . . . DADADA . . . stacking of alternating -donors and *-acceptors found in molecular compounds of polycyclic aromatic hydrocarbons and a variety of electron acceptor molecules (see Chapter 15). In the double or [3]catenane (Ashton, Brown, Chrystal et al., 1991) described below the donor and acceptor units have a . . . DADDAD . . . sequence. Many related examples are given by Amabilino and Stoddart, (1995). It was noted (Ashton, Reddington et al., 1988; Ashton, Goodnow et al., 1989; Bu¨hner, Geuder, Gries, Hu¨nig, Kock and Poll, 1988) that formation of intramolecular inclusion complexes stabilized by charge transfer interactions from a donor host to an acceptor guest, as in most of the examples described above, implied that the converse situation – acceptor host and donor guest – should also lead to formation of complexes. This is shown schematically in Fig. 3.7 and was realized in practice by using the bis(paraquat) derivative (formula 3.7, also shown on the right hand side of Fig. 3.7), abbreviated as

36

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

O B Paraquat within crown ether

N

Paraquat between crown ethers

Naphtho donor

Polyoxomethylene chain

O y z

A

C

x

y

z

Intramolecular paraquat acceptor

Naphtho donor

x

Fig. 3.6. The stacking arrangement of the paraquat moieties within and between the naphtho-crown ether rings in {DN44C12[PQT2þ]}(PQT2þ) (PF6)4(CH3)2CO is shown on the left of the diagram; an edge-on view of the arrangement within the {DN44C12[PQT2þ]} portion is shown on the right. (Data from Ortholand, Slawin, Spencer, Stoddart and Williams, 1989.)

[BBIPYBIXYCY][PF6]4. The systematic name of the cyclobis(paraquat-p-phenylene) tetracation is 5,12,19,26-tetraazoniaheptacyclo-[24.2.2.22,527,10212,15216,19221,24] tetraconta-1(28),2,4,7,9,12,14,16,18,21,23,26,29,31,33,35,-37,39-octadecaene (Odell, Reddington, Slawin, Spencer, Stoddart and Williams, 1988), which illustrates why abbreviations are preferred. 4+ N

N

N

N

[BBIPYBIXYCY] 3.7

Scheme 3.2

The host system is quite rigid and the conformation taken up in the solvated salt of composition (BBIPYBIXYCY)4þ(PF 6 )43CH3CN (VAFRID10) is rather strictly preserved in the 1,2- (Odell, Reddington et al., 1988) and 1,4-dimethoxybenzene inclusion complexes, the compositions of which were given as {BBIPYBIXYCY [C8H10O2]}4þ(PF 6 )43CH3CN (the solvent content can also be 2CH3NO2.H2O) (Ashton, Reddington et al., 1988); the 1,4-dimethoxybenzene inclusion complex is shown schematically on the right hand side of Fig. 3.7 and in space-ﬁlling mode on the left side of Fig. 3.8. The 1,2-dimethoxybenzene guest is disordered over two orientations and approximates in appearance in the crystal to 1,5-dimethoxynaphthalene, which also can be

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

O O

O

O

O CH3 N+

N+ CH3 O

37

O N+

O

OMe

O

N+

MeO N+

N+

O

Fig. 3.7. Schematic representation of the donor host–acceptor guest intramolecular inclusion complex dication {BPP34C10[PQT]2þ} on the left and the converse situation on the right with donor and acceptor roles interchanged; here the tetracation is {(BBIPYBIXYCY)4þ [C8H10O2]}, with the host designated 3.7. The donor benzene rings are hatched. Space-ﬁlling views of the tetracation are shown in Fig. 3.8. (Adapted from Fig. 1 of Ashton, Goodnow et al., 1989.) ˚ , deg, A ˚ 3) for some intramolecular inclusion complexes of formula Table 3.1. Cell dimensions (A 4þ {BBIPYBIXYCY* [guest]} (PF6 )43(solvent). The su’sy of the cell edges are 1 in 5000, and of 0.03 . The crystals all have space group P21/n, with Z ¼ 2; the host:guest ratios are all 1:1 except for the 1,3-bis(5-hydroxy-1-naphthyloxy)propane guest, where it is 1 : 0.5 Guest and refcode

a

b

c

Cell volume

No guest; MeCN solvate VAFRID10 No guest; monohydrate VAFROJ 1,2-dimethoxybenzene VAFSAW 1,4-dimethoxybenzene VAFRUP 1,5-dimethoxynaphthalene KIRTEK 1,3-bis(5-hydroxy-1-naphthyloxy)propane (1:0.5) KIRTIO

10.805 10.478 11.076 10.948 11.218 10.881

19.819 20.152 19.805 19.869 19.756 20.043

14.027 13.757 13.962 13.886 13.980 14.066

109.36 106.45 111.57 110.55 111.23 110.09

2834 2786 2848 2828 2888 2881

* CSD name cyclobis(paraquat-p-phenylene) y

su is standard uncertainty

included. Furthermore, the longer but analogous guest molecule 1,3-bis(5-hydroxy-1naphthyloxy)propane can also be included, with a host : guest ratio of 1 : 0.5 (Reddington, Slawin, Spencer, Stoddart, Vicent and Williams, 1991). All these crystals are essentially isomorphous, as is shown by their similar cell dimensions and identical space groups (Table 3.1). The conformation of [BBIPYBIXYCY]4þ is also maintained in its other complexes. An inclusion complex is also produced with tetrathiafulvalene, an easily oxidized electron donor (see Chapter 13; oxidation potential 0.4 V); the crystals have composition {BBIPYBIXYCY[C6H4S2]}4þ(PF 6 )44CH3CN but are triclinic (P1, Z ¼ 1; VOLMEO) and hence different from the group listed in Table 3.1. The guest is indeed inserted into the cavity of the host but anions and solvent molecules are differently disposed (Philp, Slawin, Spencer, Stoddart and Williams, 1991). All these crystals have an arrangement of rectangular doughnut (or ‘‘bagel’’) shaped host cations alternating with

38

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

OH O O

N O

O

N

N

O

O

O

O

O

N

N

N

OH

O

O

Fig. 3.8. Plan views of space-ﬁlling representations of the host–guest arrangement in the 1,4dimethoxybenzene intramolecular inclusion complex {BBIPYBIXYCY[C8H10O2]}(PF6)43CH3CN (on the left), and in the rotaxane {BBIPYBIXYCY[HOC6H4(CH2CH2O)4C6H4(OCH2CH2)4 C6H4OH]}(PF6)42CH3CN (on the right). (Reproduced from Anelli et al., 1992.)

layers of anions plus solvent molecules. The host cavity is empty in the parent structure and ﬁlled by the included guests in the supermolecules, with ‘‘threaded’’ as perhaps a more appropriate description for the last, and longest, of the guests. Hu¨bner et al. (1989) have shown that analogous hosts can include a variety of guests, among which are anthracene, phenanthrene, pyrene and a number of substituted naphthalenes; no crystal structures have been reported. The ‘‘threading’’ motif is also maintained in a variety of self-assembling rotaxane and pseudorotaxane complexes of [BBIPYBIXYCY]4þ, such as that illustrated on the right hand side of Fig. 3.8, and found as solvated salts. We give a number of guests with refcodes of the crystal structures (Anelli, Ashton, Spencer, Slawin, Stoddart and Williams, 1991; Anelli, Ashton, Ballardini et al., 1992): R

O

O

O

O

O

O

O

O

R

VOTPAV, as shown, with R ¼ Si(i-Pr)3 SOVLEU, as shown with R ¼ p-phenol SOVKOD, as shown, with R ¼ 2,5-dimethoxyphenyl VOTNUN, with three oxygens per chain, and R ¼ Si(i-Pr)3 SOVKOJ, with ﬁve oxygens per chain and R ¼ p-phenol VOTNEX, with three oxygens per chain and R ¼ H VOTNIB, as shown, and R ¼ H VOTNOH with ﬁve oxygens per chain and R ¼ H Scheme 3.3

We reproduce here two other structures, which lie on the borders of the subject matter of this book, but perhaps could be described as the ultimate in ‘‘molecule-within-molecule’’ inclusion complexes – the [2] catenane composed of the two host molecules BPP34C10

39

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

N

N

O

O

O

O O

O

O

N

N

O

O

O

O

O

O O

O

N N

N O

N

O

O

O

Fig. 3.9. The intertwined macrocyclic rings found in the catenane {[2]-[BPP34C10][BBIPYBIXYCY]}[PF6]45CH3CN (KEBKUX10). The ball-and-stick and space-ﬁlling views are from somewhat different orientations. The C atoms and rings in the cation have been shaded for clarity. (Reproduced from Anelli et al., 1992.)

Macrocyclic tetracation

Crown ether

Crown ether

y z x

Macrocyclic tetracation

Fig. 3.10. Double interlacing of two crown ether rings with the macrocyclic tetracation as found in the [3]catenane SOVLIY C28H40O10C48H40N44þC28H40O104(PF6). (Data from Ashton, Brown, Chrystal et al., 1991.)

and [BBIPYBIXYCY]4þ (Fig. 3.9) and the double or [3]catenane composed of BPP34C10 and the cation analogous to [BBIPYBIXYCY]4þ but made up of four bipyridyl units (Fig. 3.10). As noted above, in the double or [3]catenane (Ashton, Brown, Chrystal et al., 1991) the donor and acceptor units have a . . . DADDAD . . . sequence. One important crystallographic feature of the above group of complexes, perhaps considered trivial by chemists, is that they are all ternary complexes. In addition to the intramolecular inclusion of guests within the cavities of the host molecules, there is also intermolecular inclusion of solvent molecules in the interstices between the host molecules. These solvent molecules make an essential contribution to the cohesion of the crystals, as do the interactions between the ions. If there is disorder of the

40

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

anions, then this will have a stabilizing effect due to the additional conﬁgurational entropy. Crystal structures of pseudorotaxanes, rotaxanes and catenanes illustrating and extending the principles described above continue to be reported (e.g. Amabilino and Stoddart 1995; Ashton, Ballardini, Balzani, Be´loradsk’y, Gandolﬁ, Philp, Prodi, Raymo, Reddington, Spencer, Stoddart, Venturi and Williams, 1996; Asakawa, Brown, Menzer, Raymo, Stoddart and Williams, 1997 (RISSER, RISSIV, RISSOB, RISSUH, RISTAO, RISTES, RISTIW, TEYMAL10); Asakawa, Ashton, Hayes, Janssen, Meijer, Menzer, Pasini, Stoddart, White and Williams, 1998 (PUKNOY, PUKNUE, PUKPAM)). The crystals described above are all of salts but [2]catenanes with both partners neutral are also known (Hamilton, Feeder, Prodi, Teat, Clegg and Sanders, 1998; NIFLAP as the perdeuterodimethylsulfoxide solvate C34H32O7C32H12N4O6C2D6OS). N,N 0 ,N00 -tritosyl-5,8,14,17,23,26-hexamethyl-2,11,20-triaza[3.3.3]paracyclophane (formula not shown) forms a 1 : 1 intermolecular inclusion complex with dichloromethane (Bottino, Finocchiaro, Lipkowski, Mamo and Pappalardo, 1991; SOVKAP), whereas a number of different guests form a series of intramolecular inclusion complexes with 2,11,20,29–tetramethyl–2,11,20,29–tetraaza-[3333]-para-cyclophane (3.8) (Tabushi, Yamamura, Nonoguchi, Horotsu and Higuchi, 1984a, b). 3.8 is enantiomeric with exact or approximate C2-2 symmetry. The enantiomers are rapidly interconverted in solution but appear separately in the crystals, among which both racemates and enantiomorphs are found (Table 3.2). H3C

CH3

N

N

N

N

H3C

CH3 3.8

H2N+

(CH2)4

NH2+

H2N+

(CH2)4

NH2+

3.9

Scheme 3.4

Crystal structures have been reported for the complexes with dioxane (Abbott, Barrett, Godfrey, Kalindjian, Simpson and Williams, 1982), CHCl3, CO2, CH3CN and CH2Cl2, (Tabushi, Yamamura, Nonoguchi, Hirotsu and Higuchi, 1984a, b; Hirotsu, Kamitori, Higuchi, Tabushi, Yamamura and Nonoguchi, 1984) and CH2BrCl (Nonoguchi, Yamamura, Tabushi, Higuchi and Hirotsu, 1992). This information, together with that summarised in Table 3.2, shows some interesting features. The host molecule is found to have C2-2 symmetry in all the complexes (crystallographically imposed for the dioxane, CHCl3, CH3CN and CO2 complexes), and is therefore chiral in the solid state (also, of course, in solution, where racemization will be very rapid). A feature common to the unit cells of the complexes is the similarity of the values of [010]. The structure analyses show

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

41

Table 3.2. Crystal data for 2,11,20,29–tetramethyl–2,11,20,29–tetraaza[3.3.3.3]paracyclophane (3.8) and some of its 1 : 1 intramolecular inclusion complexes with various guests (the compositions were determined directly by NMR and/or GLPC methods for the chloroform, methylene chloride, bromochloromethane and acetonitrile complexes). This table was adapted from a summary of results given by Nonoguchi et al. (1992), and in earlier papers Guest

˚ a/A

˚ b/A

˚ c/A

None DERFIP

21.491

15.123

10.020

12.694 89.86 5.772

13.496 80.30 13.514

5.668

Vol./ asymmetric unit (A˚3)

Vol./ guest (A˚3)*

Space group

Z

807.6

–

P21/a

4

–

893.2

85.6

P1

1

112.41

898.6

91.0

P21

4

13.438

111.31

892.9

85.3

C2

2

5.691

13.440

112.06

889.3

81.7

C2

2

25.544

5.406

26.948

109.90

874.8

67.2

C2/c

4

25.590

5.420

26.900

109.86

877.3

69.7

C2/c

4

25.314

5.536

53.508

111.07

874.6

67.0

C2/c

8

25.373

5.486

53.759

111.00

873.3

65.7

C2/c

8

Enantiomorphs pyridinex 5.712 JOPVOZ 68.16 C6H6 49.846 JOPVIT 25.166 CHCl3 CEYHIX Dioxane 25.091 BIJJOT Racemates CH3CN DERFUB CO2 DERFOV CH2BrCl JOPVEP CH2Cl2 CEYHOD

ß/

97.26

x Reduced cell. ˚ 3 from the volume of the asymmetric unit; these volumes will * Nominal values obtained by subtracting 807.6 A be overestimated because of the difference in the shape of the host in its neat crystals and in those of the ˚ 3 in its crystals so the composition is probably nearer complexes. Note that benzene has a molar volume of 122 A 1:0.5, and this is also likely for the pyridine and dioxane complexes.

that all have stacks of homochiral host molecules along [010]. The structures in Table 3.2 can be divided into two groups (a) those with chiral space groups where spontaneous resolution has occurred on crystallization (the pyridine, CHCl3 and dioxane complexes, and, possibly the benzene complex), and (b) those with racemic space groups. The principal difference between the two groups lies in the mutual arrangements of the stacks, and how adjacent homochiral stacks interact, or stacks of different senses of chirality interact. The interactions within the stacks have been calculated by molecular mechanics (MM2) for the CH2Cl2 complex (Hirotsu et al., 1984); the total interaction energy of a column is 138 kJ/mol, with host–guest interaction amounting to 56 kJ/mol and guest–guest interaction to 4 kJ/mol. A further subdivision can be made in terms of unit cells and space groups: thus the CHCl3 and dioxane complexes belong together, as do the CH3CN and CO2 complexes, and the CH2Cl2 and CH2BrCl complexes. Comparison of the crystal structure of the neat host with those of the complexes shows that the host takes up a

42

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

Fig. 3.11. Comparison of the conformations of the macrocycle 3.8 in its complexes (on the left) and in its neat crystals (on the right). (Reproduced from Hirotsu, Kamitori, Higuchi, Tabushi, Yamamura and Nonoguchi, 1984.)

more compact form in its neat crystals than in the complexes, where its shape has to allow for inclusion of guests (Fig. 3.11). Guest exchange experiments show that about 40% of the guest in the CHCl3 complex can be replaced by CH2BrCl before there is a change in crystal structure. Weakness of host-guest binding is shown by the fact that guest exchange occurs. The 1,6,20,25-tetraammonium[6.1.6.1]paracyclophane cation 3.9 forms intra-molecular complexes with 1,3-dihydroxynaphthalene, 2,7-dihydroxynaphthalene, p-xylene and durene when crystallized from aqueous solutions at pH < 2 (Odashima, Itai, Iitaka and Koga, 1980). The crystal structure of the salt {3.9[durene]}4Cl4H2O has been reported ˚ , ¼ 97.23(4) , V ¼ 2360 A ˚ 3, space group (a ¼ 14.552(7), b ¼ 22.58(1), c ¼ 7.238(3) A P21/n, Z ¼ 2; ACPHDR); the durene is included within the torus of the cation while the anions and water molecules are situated between the cations. The cation is centrosymmetric, in contrast to 3.8. An analog to 3.9, 1 0 ,100 -dimethyldispiro-[1,6,20,25tetraoxa[6161]paracyclophane-13,4 0 : 32,400 -bispiperidine] (3.10, formula not shown), forms a complex of composition {3.10[C6H6]}C6H6H2O (DENFOR; P1, Z ¼ 1) in which one of the benzenes is enclosed within the host cavity while the other is located in tunnels between the host molecules. Other complexes of 3.10, with toluene and p-xylene (DENFUR), are intermolecular (Krieger and Diederich, 1985). The macrocyclic tetraimide shown in Fig. 3.12, which is composed of two 1,4,5,8naphthalenetetracarboxylic acid diimide subunits joined by two (CH2)8 chains, forms an ‘‘intercalative molecular cryptate’’ with nitrobenzene as guest (Jaswinski, Blacker, Lehn, Cesario, Guilhem and Pascard, 1987); here the polyether chains of crown ethers are replaced by aliphatic chains of methylene groups. The nitrobenzene takes up two orientations in the cavity 165 apart and the two aliphatic (CH2)8 chains have somewhat different conformations and types of disorder; hence the non-centrosymmetric space group P1 was assigned to the triclinic crystals. An example of the effects of the ﬂexibility of an host molecule is illustrated by a tantalizingly brief report (Itai, Tanaka and Iitaka, 1979) about [26]metacyclophane (3.11) and its intramolecular complexes; a full report appears not to have been published. The diagrams reproduced in Fig. 3.13 show that the host molecule is very ﬂexible; in the neat P 1 polymorph (there is a second polymorph, space group Pbca, about which no

DOUBLY BRIDGED CYCLOPHANES AND ANALOGOUS MOLECULES

O N O A O N O

43

O N O + O N – O O N O

A

Fig. 3.12. Three diagrams showing the host–guest relationship for the macrocyclic tetraimide composed of two 1,4,5,8-naphthalenetetracarboxylic acid diimide subunits joined by two (CH2)8 chains; the chemical formula (with A ¼ (CH2)8) is shown in the lower part of the diagram, a line outline at top left and a space-ﬁlling model at top right. Only one of the two orientations found for nitrobenzene is shown. (Reproduced from Jaswinski, Blacker, Lehn, Cesario, Guilhem and Pascard, 1987.)

information is available) the conformer has a squashed shape without an interior cavity (c); the p- and o-xylene inclusion complexes (space group Pnmn) have the guests parallel to the mean plane of the host (a), whereas the guests penetrate the host in the benzene, m-xylene, n-heptane, cyclohexane and geraniol complexes (b; space group I2/a). It is not known whether the crystals of the complexes in these groups are isomorphous.

(CH2)2

(CH2)2

(CH2)2

(CH2)2

(CH2)2

(CH2)2

[26] metacyclophane (3.11)

Scheme 3.5

44

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

(a)

(b)

(c)

Fig. 3.13. Mode of inclusion of the guests in (a) the p- and o-xylene inclusion complexes of [26]metacyclophane, and (b) of the benzene, m-xylene, n-heptane, cyclohexane and geraniol complexes; (c) the conformation of the neat host in its triclinic polymorph. (Reproduced from Itai, Tanaka and Iitaka, 1979.)

3.3

Cleft molecules as hosts

3.3.1

Single-cleft hosts

Most of the structures described above have doughnut (or ‘‘bagel’’) molecules as hosts, with the guest ﬁlling the central hole. The hosts in the structures to be described in this section have a tweezer (or U, cake-server, hairpin or horseshoe) shape with the guests enclosed between the two arms of the tweezer. Dibenzocrown ethers of the general type DB3nCn (n ¼ 6–12, with the phenyl groups linked 1,2 (ortho) to O) form stable adducts with [Pt(bpy)(NH3)2]2þ (bpy ¼ bipyridyl), [Rh(cod)(NH3)2]þ (cod ¼ 1,5-cyclooctadiene) and [Rh(nbd)(NH3)2]þ (nbd ¼ norbornadiene), the counterion being (PF6). One of the ﬁrst hosts studied was dibenzo-24-crown-8, which forms adducts with these three metal complexes. The unsymmetrical location of guest in the Pt adduct (Colquhoun, Doughty, Maud, Stoddart, Williams and Wolstenholme, 1985; DATNOB, P1, Z ¼ 24) compared to its symmetrical location in the Rh adducts (Colquhoun, Doughty, Stoddart and Williams, 1984; cod complex COCPEP, P21/c, Z ¼ 4; nbd complex, COCPIT, Pbca, Z ¼ 4) is evidence for different types of host–guest interaction – charge transfer interactions between the benzene ring of the crown ether and the bipyridyl ligand stabilize the adducts with the Pt complex while the Rh complexes interact with the crown ether through a substantial number of weak hydrogen bonds and electrostatic interactions and their additive effect leads to stabilization (cf. caption to Fig. 3.14). The 1 : 1 complexes of the smaller host dibenzo-18-crown (DB18C6) with pyridinium NEXLOR) and 1-aminopyridinium BF4 (NEXLUX) are isostructural (both Cc, Z ¼ 4, with similar cell dimemsions), and have the cations located within the cleft (La¨msa¨, Huuskonen, Rissanen and Pursiainen, 1998). Crystal structures have been reported (Bush and Truter, 1972) for DB30C10 itself (P21/c, Z ¼ 2, hence centrosymmetric; DBTCAD) and DB30C10KI (Pnna, Z ¼ 4, the [host. Kþ] moiety having a twofold axis; KIBDOT10) and for DB30C10 intramolecular inclusion complexes. DB30C10 has an elongated shape in its neat crystals but the host molecules have U-shapes in all the complexes, including that with KI (Fig. 3.15). Thus there is a remarkable conformational change on complexation, indicating considerable 4

There is also (loc. cit.) a [Pt(bpy)(NH3)2]2þ monohydrate complex of DB30C10 (P21/n, Z ¼ 4; BEFHUP10).

45

CLEFT MOLECUL ES AS HOST S

norbornadiene

2,2'bipypridyl

Pt

Rh O

NH3 x

z

y

N

z x

y dibenzo-crown ether

dibenzo-crown ether

Fig. 3.14. The intramolecular complexes of DB24C8 with two metal coordination-complex cations. The unsymmetrical disposition on the left (DATNOB) is indicative of charge transfer interactions between the components while the symmetrical disposition on the right (COCPIT) suggests the combined effect of a large number of weak hydrogen-bonding and electrostatic interactions. (Data from Colquhoun, Doughty, Maud, Stoddart, Williams and Wolstenholme, (1985) and Colquhoun, Doughty, Stoddart and Williams (1984).)

K

Fig. 3.15. Comparison of the centrosymmetric shape of DB30C10 in its neat crystals (on the left) with the shape found in its complex with potassium iodide (on the right); the molecule has a twofold axis, shown by the vertical line. Oxygens are darkened. The U-shaped conformation of DB30C10 in the KI complex is rather similar to those conformations found in the intramolecular inclusion complexes shown in Figs. 3.14 and 3.16. (Reproduced from Bush and Truter, 1972.)

ﬂexibility of DB30C10. The analogous di-(1,2)-benzo-30-crown-10 (Colquhoun, Goodings, Maud, Stoddart, Wolstenholme and Williams, 1985; CAKMEG10) and di-(2,3)-naphtho-30-crown-10 (3.13) hosts both take up a U-shape in their crystals. For example, in {dinaphtho-30-crown-10[diquat]2þ}(PF6)21/2H2O (Fig. 3.16) (Allwood, Colquhoun, Doughty, Kohnke, Slawin, Stoddart, Williams and Zarzycki, 1987; FIKVUG), both host and guest are located on a crystallographic twofold axis. The host-guest complex has much the same shape when diquat2þ is replaced by (Pt(bipyridyl)(NH3)2)2þ (FIKVOK; here the crystallographic results were of poorer quality because of disorder). The differences between the mutual arrangements of host and guest in the two complexes

46

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

Fig. 3.16. Edge-on view of space ﬁlling diagram of {DN30C10[Diquat]2þ} cation in its hexaﬂuorophosphate hemihydrate salt. The diquat moiety is enclosed by the jaws of the tweezer host 3.12. The arrangement in {dibenzo-30-crown-10[diquat]2þ}[PF6] 21/2H2O is very similar. (Reproduced from Allwood, Colquhoun et al., 1987.)

were ascribed, as above, to maximization of Coulomb interactions in the diquat complex and of overlap of -arene systems in the Pt complex. Structures have also been reported (Kohnke, Stoddart, Allwood and Williams, 1985) for {2,20-bisformyldibenzo-30-crown-10[diquat]2þ}(PF6)2 0.75CH3CN (CULCAN) and {2,20-bismethyldibenzo-30-crown-10[diquat.]2þ}(PF6) 2H2O (CULCIV), with results rather similar to those already described. {2,20-Bishydroxymethyldibenzo-30-crown-10 [diquat]2þ}(PF6) 2 (CULCER) was also prepared but the structure was not determined because of its complexity; the crystals are of interest because it is possible that spontaneous resolution of the crown ether had occurred on crystallization (the space group is P2221, Z ¼ 8). O O

O

O 3.13

Scheme 3.6

Another type of molecular tweezer 3.13 has been synthesized by Harmata and Barnes (1990); this molecule has a U-shape despite its planar representation. Although crystals of the neat compound were not obtained, it could be crystallized together with a molecule of 1,3,5-trinitrobenzene (JESCAL; P21/c, Z ¼ 4) to give a cleft structure analogous to that shown in Fig. 3.16, the TNB molecule being held within the jaws of the host. It was suggested that the face-to-face donor–acceptor interactions (see Chapter 15) were supplemented by a face-to-edge interaction between a positively charged hydrogen of TNB pointing towards the centre of the -system of the central benzene ring; such interactions have been proposed for analogous systems (Burley and Pesko, 1986). 3.13a has a similar behaviour; it could only be crystallized as a 1 : 1 complex with nitrobenzene, ‘‘probably because different conformations precipitated together so that a single crystalline product could not form.’’ The guest molecule was located within the cleft of

47

CLEFT MOLECUL ES AS HOST S

the ‘‘naphthalene-walled clip’’ (Reek, Engelkamp, Rowan, Elemans and Nolte, 1998; BIZRAD, P1, Z ¼ 2; no 3D coordinates), as shown on the right. nitrobenzene guest OMe O MeO N Ph N OMe

N Ph N

O

O

O MeO 3.13a

N1

C1

C21

C1⬘ N1⬘ C21⬘

Scheme 3.7

Related molecules have been used for the synthesis of belt and collar shaped potential hosts for intermolecular complex formation. Crystal structures have been reported for two cylindrical hosts but not, as yet, for any complexes (Ashton, Brown, Isaacs et al., 1992; FUJGOG10; GIJWIF10). 3.3.2 Double-cleft hosts Saddle-shaped hosts, with two approximately mutually perpendicular clefts, have been reported (Schwartz, Knobler and Cram, 1992). As an example we reproduce a stereodiagram (Fig. 3.17) of one of these hosts with two enclosed molecules of benzene (JUSXIE). The

Fig. 3.17. Stereodiagram of a double-cleft host with a benzene guest in each cleft. (Reproduced from Schwartz, Knobler and Cram, 1992.)

48

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

crystals are tetragonal, space group I41/a and each molecule has S4 symmetry, the two clefts thus being equivalent. 3.4 3.4.1

Container molecules as hosts Introduction

An appreciable portion of the rest of this chapter is concerned with the work of D. J. Cram and colleagues at the University of California at Los Angeles. This has been described recently (Cram and Cram, 1994) in more detail than we can accommodate here; the series ‘‘Host-Guest Complexation’’ had reached No. 68 by 1997. Cram and coworkers use the following abbreviation (X)G where (X) is the container molecule and G the encapsulated guest, and (X)[G where the guest is perching or accommodated between (rather than within) the host molecules; we shall use our own notation described earlier. We (again) brieﬂy summarise the nomenclature. The container molecule is given the sufﬁx ‘‘-and’’ and the complex the sufﬁx ‘‘-ate’’ or, more usually, ‘‘-plex.’’ Thus, at one extreme of the classiﬁcation, cavitands are bowl-shaped molecular vessels, essentially closed at one end but open at the other; they contain enforced concave interior surfaces of molecular dimensions (Cram, Karbach et al., 1988). They form caviplexes without steric inhibition to either the complexation or decomplexation processes. At the other extreme one has the carcerands, which entrap guest molecules permanently within their shells by constrictive binding; this implies that the guests are incorporated during synthesis and presumably also have some template role. The hemicarcerands are intermediate, and have portals through which the guest molecules can enter or escape the host cavity, with energy barriers large enough to allow isolation and characterization of the complexes at normal temperatures. Cram has described these quasi-spherical molecules as having polar caps, generally rigid, joined by chains of atoms which can be rigid or ﬂexible, and cover the temperate and equatorial zones. A generalized diagram is given in Fig. 3.20 below, where the polar caps are called ‘‘spacers’’ and the linking chains of atoms ‘‘connectors.’’ 3.4.2

Cavitands and caviplexes

A general formula for cavitands is shown in the insert (3.14, n ¼ 1, 2, 3; R ¼ CH3, Br, I); the overall dimensions can be changed by introducing methylene bridges of varying length while the solubility can be manipulated by replacement of the methyls by suitable groups. The methylene bridges have been replaced by quinoxaline (or analogous) ﬂaps; these can be all axial with respect to the rest of the molecule, giving a vase conformation, or all equatorial, giving a kite conformation (Moran, Ericson, Dalcanale, Bryant, Knobler and Cram, 1991). A remarkable result was obtained for a derivative of host 3.14 in which the methylene bridges were replaced by quinoxalines and the pendant methyl groups by menthoxy (OOC(–)menthyl). Complexes of this host with aromatic guests such as benzene and toluene were shown, by desorption chemical ionization (DCI) mass spectrometry, to exist in the gas phase provided the temperature of the ion source was below 100 C. It was suggested that these complexes were formed by complexation of neutral benzene and neutral cavitand molecules in the gas phase, followed by ionization (Vincenti, Dalcanale, Soncini and Guglielmetti, 1990).

49

C ONT AINE R M OL E C UL E S AS HOSTS

Crystal structures were determined for nine caviplexes with methylene bridges, and seven of these contain uncomplexed, intermolecular, guests in addition to complexed, intramolecular, guests (Cram, Karbach et al., 1988). The space groups of two of the caviplexes show that spontaneous resolution of the enantiomeric host has occurred on crystallization. The conical cavitands are supported on the four methyl groups. The nearly closed bases of the cavities are deﬁned by a 16-membered [1.1.1.1] metacyclophane ˚ , too small to allow passage of guest macroring, with an internal diameter of about 3 A molecules. The open tops are deﬁned by [mmmm] meta-cyclophane macrorings con˚. taining eight oxygens and from 24 to 35 ring atoms, with internal diameters of 9–10 A We note some special features: R ¼ H, n ¼ 1, guest CH2Cl2, C2/c, Z ¼ 8. The guest perches above the open end of the bowl. When the guest is CH3CN, the space group is the noncentrosymmetric P4. An additional CH3CN molecule is located interstitially between the host molecules. R ¼ CH3, n ¼ 1, intramolecular guest cyclohexane, intermolecular guest benzene, P212121, Z ¼ 4; spontaneous resolution (of the enantiomeric host) has occurred on crystallization. The cyclohexane, perched above the open end of the bowl, is said to be in the boat conformation but this requires conﬁrmation, especially as the R factor was 15%. R ¼ Br, n ¼ 1, inner methyls replaced by CH2CH2C6H5 (for solubilization), H2O present both as intramolecular and intermolecular guest, space group Pnma, Z ¼ 4 (the host molecule has a mirror plane) (Sherman, Knobler and Cram, 1991; JILZEJ). This caviplex is important in the synthesis of carceplexes (see Section 3.4.6).

R (CH2)n O

O (CH2)n

O

O CH3

H

H

R O

CH3

CH3 H

H

R

CH3

O

O

N

R'

O

N

R'

O (CH2)n

(CH2)n O R

Substituted quinoxaline

3.14

Scheme 3.8

A particularly rigid host is obtained by replacing the CH2 groups bridging the oxygens by Si(CH3)2 to give C40H48Si4O8 (5,10;12,17;19,24;26,3-tetrakis-(dimethylsiladioxa)1,8,15,22-tetramethyl[14]metacyclophane, the cavitand shown in Fig. 3.1). In the crystal structure of {C40H48Si4O8[CS2]}CS2 (Goldberg, 1986; CUYXEZ10) one guest molecule lies along the central, (approximately) fourfold axis of the host, while the second lies between adjacent host molecules in the [100] direction (Fig. 3.18), illustrating the delicacy of the balance between intra- and intermolecular enclosure. The enclosed guest is in a

50

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

x z y

x z

y

Fig. 3.18. Stereoviews, parallel (a) and perpendicular (b) to the cavity surface, of the 1 : 2 molecular inclusion complex of the cavitand C40H48Si4O8 with CS2. There is another CS2 molecule between adjacent hosts. (Data from Goldberg, 1986.)

lipophilic environment composed of phenyl groups within the cavity and methyl groups on and above its surface. The host has a dish-like shape, and is thus representative also of the cavitands described above. 3.4.3

Hemispherands and hemispheraplexes

Hemispherands are receptor molecules in which at least half of the binding sites for intramolecular complexation are pre-organized, and complexes are known with alkali metal and alkylammonium cations and neutral organic molecules. The factors governing the binding of malononitrile (CH2(CN)2) to four hemispherands have been studied by combining the results of crystal structure analyses, molecular mechanics calculations and solution thermodynamic measurements (Grootenhuis, van Eerden, Dijkstra, Harkema and Reinhoudt, 1987). We take one example (3.15, formula with n ¼ 1; C30H36O6). The crystal structures of 3.15 (at 113 K, P21/c, Z ¼ 4; MOMODT, Goldberg, 1980) and {3.15[CH2(CN)2]}0.60 (C2H5)2O (C2/m, Z ¼ 4; Grootenhuis, van Eerden, Dijkstra, Harkema and Reinhoudt, 1987; DUTDOL10) have been reported; the conformations of the host are compared in Fig. 3.19. Molecular mechanics calculations using these conformations give strain energies of 57 and 64 kJ/mol, indicating that the host is more strained when it has the conformation taken up in the complex. NMR measurements (240–320 K; in CDCl3 solution) give the association constant as 28 M1

51

C ONT AINE R M OL E C UL E S AS HOSTS

CH3 CH3

H 3C X

X

O X = OCH3

012

08

X O

01

04

O n

Fig. 3.19. Comparison of the conformations taken up by 3.15 (n ¼ 1) in its neat crystals (centre) and in its complex {3.15[CH2(CN)2]}0.60 (C2H5)2O (right). (Reproduced from Grootenhuis, van Eerden, Dijkstra, Harkema and Reinhoudt, 1987.)

at 298 K, H ¼ 35.1, TS ¼ 26.8 and G ¼ 8.4 kJ/mol. The complex is enthalpy-stabilized in solution and, presumably, also in the solid state. The interaction energy between host and guest must be about 42 kJ/mol (we have ignored any inﬂuence of solvent molecules in the crystals of the complex). This will be due to four bifurcated C–H . . . O hydrogen bonds from guest to host (Fig. 3.19), and van der Waals interactions. t-Butylammonium perchlorate ((CH3)3CNH3þClO4) forms a complex with 3.15 (n ¼ 1) in which there are three Nþ–H . . . O hydrogen bonds to the oxygens of the three methoxy groups; there is also a conformational change on complexation but the strain energy of the macrocycle does not seem to have been calculated. The free energy of formation of the complex is 32.1 kJ/mol (in CDCl3 solution) (Koenig, Lein, Stuckler, Kaneda and Cram, 1979), four times greater than that of the malononitrile complex; values of H and TS have not yet been reported.

3.4.4 Triply bridged cyclophanes and analogous molecules as three-dimensional hosts for intramolecular guests The ﬁrst enclosure (or container) molecule to be purposefully synthesized was that of the [2.2.2] cryptand (Dietrich, Lehn and Sauvage, 1968) shown in Fig. 3.20. For reasons of space, we shall discuss only some aspects of cryptand structural chemistry and refer the reader to the broader account given by Dietrich (1996). A general formulation of an enclosure molecule is shown in Fig. 3.20; the synthetic methods used for translating the schematic into real molecules have been summarised by Seel and Vo¨gtle (1992). A formally simple realization of the schematic of Fig. 3.20 (left) is shown in Fig. 3.20 (right) and has been achieved by O’Krongly, Denmeade, Chiang and Breslow (1985; R ¼ CH3) and Vo¨gtle, Berscheid and Schnick (1991; R ¼ H). We now consider crystallographic data on the modes of enclosure. The crystal structures of {C56H38O6.[CH3CN]} (P21/c, Z ¼ 4; JIHJEP, Vo¨gtle et al.) and {C57H40O6[C6H6]}2C6H6 (triclinic, P1, Z ¼ 2); DECWOX, O’Krongly et al.) have been reported in these two papers; the spacer is RC(p-C6H4O–)3 and the connector –C C–C C–. The shapes taken up by the host molecules are appreciably different in the two crystals; O’Krongly et al. (1985) noted that

52

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

O

O O N

O N O

O

[2.2.2]cryptand Spacer R

o

o o Connectors o

o

o

R

Spacer

Fig. 3.20. (above) Line diagram of [2.2.2]cryptand. (Below left) General formulation of an enclosure molecule. The spacers illustrated have three links, as in sym-C6H3(CH2NH2)3, but four and six link spacers have also been used successfully. The chemical nature of the connectors is matched to that of the spacers. The spacers can be different, as can the connectors. (Below right) Example of the translations of the general formulation into practice, as achieved by Breslow (R ¼ CH3) and Vo¨gtle (R ¼ H) and their coworkers. (Adapted from Seel and Vo¨gtle, 1992.)

their compound was ‘‘self-adjusting’’. One of the phenyl groups is twisted so as to interact with the included benzene molecule in a face-to-edge fashion, whereas the -acceptor acetonitrile molecule, disordered over two positions, has its nitrile -orbitals interacting with phenyl groups in both face-to-edge and face-to-face fashion. The spacer of an analogous host is 1,3,5-C6H3(O–)3; in this supramolecule, with acetonitrile as guest, it is the methyl group of the guest which interacts with a phenyl of the host (Berscheid, Nieger and Vo¨gtle, 1991; JODMOE, P21/c, Z ¼ 4). Two triply substituted aromatic rings, linked by poly(methylene ether) chains, form enclosures which can take up guests in intramolecular fashion. One example is 3.16 (shown schematically in the formula of Scheme 3.9 and in its correct shape in Fig. 3.21), which encloses diquat2þ in an hexaﬂuorophosphate salt (Allwood, Kohnke, Stoddart and Williams, 1985); here the two spacers are benzenes linked between 1- and 2- positions by two -O-[(CH2)2-O]- chains and between 5-positions by a -(CH2)-O-(C6H4)-O-(CH2)chain. The crystal structures of the neat neutral host (orthorhombic, Pcab, Z ¼ 8; DAXMOE) and of the salt {3.16[Diquat2þ]}(PF6)2 (triclinic P1, Z ¼ 2; DAXMUK) have been reported. Comparison of the host conformation in the two crystals shows that some reorganization occurs on complexation (Fig. 3.21).

C ONT AINE R M OL E C UL E S AS HOSTS

53

[Diquat]2+

y

x

z

y

z

x

Fig. 3.21. On the right is shown the host-guest arrangement in the salt {3.16[diquat]}(PF6)2 (DAXMUK) and on the left the somewhat different conformations of the host in the neat material. (Data from Allwood, Kohnke, Stoddart and Williams, 1985.)

R2 R1

R1 3.16 R1 = –O–(CH2)2–O-; R2 = –CH2–O–(C6H4)–O–CH2–

Scheme 3.9

The triply linked macrocyclic polyammonium receptor 3.17 binds dicarboxylate substrates (Lehn, Me´ric, Vigneron, Bkouche-Waksman and Pascard, 1991); linear substrates of formula O2C(CH2)nCO 2 (n ¼ 2–8) and fumarate and maleate have stability constants Ks ranging from 1400–4100 M1, while terephthalate has a Ks value more than an order of magnitude greater. Determination of the crystal structure of the terephthalate complex, which has space group Pnna, Z ¼ 4 (SIRZAU) shows that it indeed contains a ‘‘supramolecular species of cryptate nature in which two binding subunits of the ditopic coreceptor molecule cooperate in substrate binding,’’ but is in fact considerably more complicated, as is made clear by Lehn et al. (1991). The asymmetric unit consists of the intramolecular complex shown in Fig. 3.22, made up of the macrocycle and an enclosed terephthalate dianion (T(1)2), the complex having a two fold axis of symmetry normal to the N . . . N axis, a terephthalate dianion on a center of symmetry (T(2)2), another terephthalate dianion disordered over two orientations (T(3)2), ﬁve ordered water

54

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

Fig. 3.22. The intramolecular complex made up of the macrocycle 3.17 and enclosed terephthalate dianion, viewed from the side in outline (left) and space-ﬁlling (right) modes and, in the centre, along the N . . . N axis, which is normal to the complex’s crystallographic twofold axis of symmetry. O and N atoms are shaded. (Reproduced from Lehn, Me´ric, Vigneron, Bkouche-Waksman and Pascard, 1991.)

molecules and two more waters disordered over four sites. The asymmetric unit should thus be formulated as 1=2f3:176þ ½Tð1Þ2 g Tð2Þ2 Tð3Þ2 ð5 þ ð4X1=2ÞÞ H2 O, or 1=2fC57 H78 N8 6þ ½ O2 CðC6 H4 ÞCO2 g ð O2 CðC6 H4 ÞCO2 Þ ð O2 CðC6 H4 Þ CO2 Þ ð5 þ ð4X1=2ÞÞH2 O:

An intricate arrangement of hydrogen bonds links all these units. The four oxygens of the included terephthalate dianion are hydrogen bonded to the four ammonium groups, and also to neighboring water molecules; thus the intramolecular interaction is largely, but not entirely, one-dimensional. The view down the N . . . N axis reinforces the point made previously that it can be misleading to draw inferences about the shape of a complex from projections onto mean planes, as in the left- and right-hand parts of Fig. 3.22. Cavitand hosts capable of complexing small organic molecules have been synthesized using cyclotriveratrylene as spacer and –OCH2CH2CH2O– as connectors; these have been called cryptophanes (Collet, 1987). Cryptophane C (3.18; C54H51O9) has a stability constant Ks5 of 300 M1 for complexation with CH2Cl2 (Canceill, Cesario, Collet, Guilhem and Pascard, 1985) in CDCl3 solution, while that for Cryptophane D (3.19) is about twelve times smaller (both measured by 200 MHz NMR in solution) (Canceill, Cesario, Collet, Guilhem, Riche and Pascard, 1986); the values given in the earlier reports have been corrected by Collet (1987) following Canceill, Lacombe and Collet (1987). The energy barriers for inclusion and extrusion of the CH2Cl2 guest in both hosts were determined from the maximum broadening of the NMR signal (Table 3.3). CH2Cl2 seems 5 * The true stability constant is Ks ¼ Ks0(1 þ KsCDCl3[CDCl3]) where Ks0 is the apparent stability constant and KsCDCl3 is the stability constant of the CDCl3 cavitate ( 0.1 M1 for cryptophane C) and [CDCl3] ¼ 12.4 M. At high temperatures (310–330 K), Ks 2.1 Ks0 .

55

C ONT AINE R M OL E C UL E S AS HOSTS

Table 3.3. Energy barriers (kJ/mol) for inclusion and extrusion of CH2Cl2 guest in Cryptophane C and D hosts in CDCl3 solution Host molecule

G# (inclusion)

G# (extrusion)

Cryptophane C Cryptophane D

45.2 49.5

47.0 46.1

Table 3.4. Thermodynamic parameters for intramolecular complexes of Cryptophane E with various guests. G refers to 300K; units for G and H are kJ/mol and for S J/mol K. The volumes were described as ‘van der Waals’ volumes without further definition Guest

˚ 3) V (A

G

H

CH3I CH2Cl2 CH2Br2 CHCl3 CHCl2Br CH(CH3)3 CHClBr2 CHBr3 CCl4 C(CH3)Cl3 C(CH3)2Cl2 C(CH3)3Cl CH3COCH3

54.5 57.6 65.5 72.2 76.1 79.4 80.1 84.0 86.8 89.2 91.6 93.9 70.0

10.0 11.7 12.6 15.5 14.2 11.7 12.1 9.6 5.0 0.8 0.4 3.3 5.4

S

4.2

25

25.1 21.8 15.9 6.3 5.9

29 25 13 17 17

Type of stabilization entropy enthalpy enthalpy enthalpy enthalpy and entropy enthalpy and entropy

c⬘ b⬘ O O Me

O

O Me

O Me

O

O

O

O

O Me

O O Me

O

O

O

O Me

b

Cl 13 c Cl 23

O

Cryptophane C (3.18) ((–) enantiomer)

O

a⬘ a

Cryptophane D (3.19) ((+) enantiomer)

Fig. 3.23. Left – schematic formulae of 3.18 and 3.19. Right – {Cryptophane D[CH2Cl2]} cavitate, showing the view down the pseudo-C3 axis, with 50% probability anisotropic thermal ellipsoids for the guest molecule (radii of other atoms are ﬁxed arbitrarily). (Reproduced from Canceill, Cesario, Collet, Guilhem and Pascard, 1985.)

56

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

to enter the cavity of Cryptophane C more easily than that of Cryptophane D and is retained there more strongly. There is not much difference in the rates of leaving (extrusion). The crystal structures of these two isomeric intramolecular complexes have been reported. The crystals of {Cryptophane C[CH2Cl2]}2CH2Cl2 have two additional CH2Cl2 molecules located between the molecules of the complex and are monoclinic (P21/n, Z ¼ 4; CUSCEY) and racemic. The packing consists of alternate homochiral layers of ( þ ) and ( ) enantiomers of Cryptophane C. The cycloveratrylene spacers are mutually rotated by about 60 so the host has a pseudo-C3 axis (Fig. 3.23). The intermolecular dichloromethanes are accommodated in pairs in relatively large voids between groups of host molecules. The orthorhombic crystals of {( þ )-Cryptophane D[CH2Cl2]}1.25CH2Cl2 (space group P212121, Z ¼ 4; DIJJUB) have two additional dichloromethane sites located between the host molecules with occupation factors of 0.5 and 0.75; the space group shows that the macrocycle has resolved spontaneously on crystallization. The dichloromethane of the ‘‘supermolecule’’ shows no signs of disorder, but the interstitial dichloromethanes are loosely held in the crystal, which is efﬂorescent. Cryptophane E (three additional methoxy groups compared to C and D) forms a chloroform inclusion complex of composition {C57H60O12[CHCl3]}0.2CHCl30.2H2O (space group P21/n, Z ¼ 4; Canceill, Cesario, Collet, Guilhem, Lacombe, Lozach and Pascard, 1989; SEDPOG); this cryptophane also has a pseudo-C3 axis. Thermodynamic parameters have been measured for complexation of Cryptophane E and various guests (1H NMR measurements at 300 and 330 K, 1,1,2,2-tetrachloro-1,2-deuterioethane solvent); these parameters are listed against molecular volume in Table 3.4. A plot of G against volume for the various substituted methanes has a roughly parabolic shape, with a ˚ 3; the most stable complex is formed by chloroform, presumably minimum at 73 A because it ﬁts most snugly into the cavity. The type of stabilization is also listed for those molecular complexes where separate H and S values are available. The methylene chloride complex is exceptional in that it is entropy stabilized. The acetone complex does not ﬁt into the substituted methane series. Remarkably, Cryptophane E is easily oxidized þ to give a crystalline radical cation salt of composition {C57H60O12 [CHCl3]}PF6, the chloroform remaining included in the host cation (Renault, Talham, Canceill, Batail, Collet and Lajzerowicz, 1989; cf. Chapter 13). An isomeric pair of molecules analogous to the cryptophanes, with similar but not identical spacers and –OCH2–C C–C C–CH2O– connectors, has been synthesized, one of which is racemic (3.20; C66H54O62(CH2Cl2)) and the other (3.21; C66H54O6(CHCl3)) meso (Cram, Tanner, Keipert and Knobler, 1991; JOHGES, P1, Z ¼ 2). The crystal structure of 3.20 (space group Pbca, Z ¼ 8; JOHGAO) shows that the molecule has a compact form and near-spherical cavity capable of enclosing small molecules such as CHCl3, (CH3)3COH, CH2Cl2, cubane, propylene oxide and benzene. The value of Ks for benzene at 20 is 103 M1 and the activation free energy for decomplexation of benzene at 20 is 50 kJ/mol. Meso-3.21, which has an ellipsoidal cavity, does not complex the above guests in (CCl3)2CO solution, possibly because of competition from the solvent. There is also a more compact pair (3.22, 3.23) with shorter connectors (Tanner, Knobler and Cram, 1990; Fig. 3.24). Crystal structures have been determined (Tanner, Knobler and Cram, 1992). for {3.22[CH3CN]}CH3CN (triclinic, P1, Z ¼ 2; JORVER) and the isomorphous crystals of {3.23[CH3OH]}CH3OH (JORVIV) and {3.23[empty]}CH2Cl2 (JORVOB) (both rhombohedral, space group R 3, hexagonal cell dimensions for the

tosylate Ts

Ts

Ts

N

N

N

O

tosylate

S N

• CH3CN CH3CN CH3O

OCH3

methoxy

OCH3

tosylate

enclosed acetonitrile methoxy

acetonitrile of crystallization

methoxy

y

3.22. [CH3CN]·CH3CN (JORVER) z

x N

H

H

H

N

N

N

• CH3Cl2

N

methoxy methoxy

CH3O

OCH3

3.23. [empty]·CH2Cl2 (JORVIV)

methoxy

OCH3

disordered methylene chloride

x

y z

Fig. 3.24. Line formulae and molecular diagrams for the two hemicarceplexes 3.22 and 3.23. The CSD has erroneously interchanged the sets of coordinates given for isomorphous JORVIV and JORVOB. The former, labeled as containing both included methanol and methanol of crystallization, actually lists only methylene chloride of crystallization: the latter does not include coordinates for either type of methanol. (Data from Tanner, Knobler and Cram 1992.)

58

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

CH2Cl2 complex and (bracketed) the CH3OH complex: a ¼ 14.301(3) (14.262(2)), ˚ , V ¼ 7950 (7912) A ˚ 3, Z ¼ 6 (1/3 of a molecule in the asymc ¼ 44.65(1) (44.914(6)) A metric unit)). Stereodiagrams of the host – guest complexes are shown in Fig. 3.24. 3.23 in CDCl3 binds O2, N2 and H2O weakly and CH3OH with Ka 47 M1 (G295 ¼ 10 kJ/ mol, H 36 kJ/mol and S 88 J/mol K). Comparison of the two isomorphous rhombohedral structures shows that 3.23 is rigid enough for the presence or absence of a guest not to affect its shape. Very strong binding of p-nitrophenol in CD2Cl2 is shown by the triply linked hosts 3.24 and 3.25; the value of Kassoc is about 3.5 104 mol1 for 3.24 and about 10 104 mol1 for 3.25 (Cochran, Parrott, Whitlock and Whitlock, 1992). The crystal structures of the 1 : 1 intramolecular complexes of 3.24 and 3.25 with p-nitrophenol have been determined (as the bis(1,2-dichloroethane) (SUBZOE; C45H34N2O8C6H5NO32(C2H4Cl2); P21/a, Z ¼ 4) and 1,2-dichloroethane (SUBZIY; C45H34N2O8C6H5NO3(C2H4Cl2); P1, Z ¼ 2) solvates respectively), and show similar dispositions of guest to host (Fig. 3.25). NMR measurements conﬁrm that these dispositions are maintained in solution. Hydrogen bonding ˚ between the hydroxyl of the guest and the pyridinium N of the host (d(O–H . . . N) ¼ 2.69 A ˚ (3.24) and 2.77 A (3.25)), noted in earlier work on analogous compounds (Sheridan and Whitlock, 1986, 1988; Whitlock and Whitlock, 1990), was inexplicably not mentioned in a later claim (Cochran, Parrott, Whitlock and Whitlock, 1992) that the detailed

O

O

O

O

O

O

O N O

O

N O

O

O

O

O

O 3.24

∗

3.25

N N

∗

N

N O

CH3 ∗ N CH3

∗

N N

CH3 N CH3

{3.25·[p-nitrophenol]}

Fig. 3.25. Upper – line formulae of 3.24 and 3.25. Lower – stereodiagram showing the disposition of guest and host in the supramolecular complex of 3.25 with p-nitrophenol; the triple bonds of the host molecule are marked with asterisks and oxygens are shown by hatched circles. In terms of the nomenclature used in Fig. 3.20(a), the substituted naphthalenes are the spacers of the host molecules, which have three different connectors. (Reproduced from Cochran, Parrott, Whitlock and Whitlock, 1992.)

C ONT AINE R M OL E C UL E S AS HOSTS

59

geometry of these complexes is dominated by formation of a hydrogen bond involving the electron-rich p-xylene connector and the acidic o-nitro proton of the guest. As the OH . . . N hydrogen bonding has an energy of 30 kJ/mol, while the hydrogen bond contributes only about one-quarter of this to the intramolecular cohesion, it is clear that the former dominates.

3.4.5 Spherands and spheraplexes Spherands are macrocyclic or macropolycyclic systems where the ligands are organised, during synthesis and prior to complexation, in such a way that the unshared electron pairs of the binding sites line a roughly spherical cavity maintained by auxiliary covalent bonding (Cram, Kaneda et al., 1985; Cram and Trueblood, 1981; Cram, 1986). A comprehensive account, with some forty stereodiagrams of spherands, spheraplexes, hemispherands and hemispheraplexes, has been given by Maverick and Cram (1996a); we are perforce more modest. An essential requirement is that the spherand molecule should be rigid and not turned back on itself, with the interior cavity relatively unsolvated. A test of this concept is provided by comparing the geometrical structures of a neat spherand and those of the corresponding spheraplexes. This has been done for spherand 3.26 (C48H48O6; formula not shown), {3.26[Liþ]}Cl and {3.26[Naþ]}CH3SO4C6H5CH3 (Trueblood, Maverick and Knobler, 1991). The spherand moiety maintains nearly the same shape in all three crystals; the cavity is large enough to enclose only lithium or sodium ions. In one type of chemical modiﬁcation of the prototype spherand the six methoxy groups of the interior were replaced by ﬂuorines; the structure of an intermolecular complex of composition C42H30F62CH2Cl2, with interstitial disordered methylene chlorides, has been reported (Trueblood, Maverick and Knobler, 1991). In another type of modiﬁcation, augmented spherands were prepared by replacing two pairs of ‘‘meta’’ methoxy groups by –OXO– bridges, where X ¼ –CH2CH2OCH2CH2–, –CH2CH2CH2– or –CH2CH2CH2CH2–. Crystal structures were reported for C52H52O8 (VOWVOS), C52H52O8LiCl3H2O (CAWRIB20). C50H48O6LiFeCl40.5CH2Cl2 (CAWREX20), C52H52O6LiCl3(C6H6) (VOWWEJ) and C50H48LiOþ 6 Cl 3(toluene) (VOWWIN). (VOWWEJ (reported as C2/c) and VOWWIN (reported as I2/a) are isomorphous (similar reduced triclinic cells). Lithium ions are enclosed in the interiors of all these hosts. These structures are extremely rigid, and the aromatic rings are very deformed; ˚ , 10% less than the sum of some intramolecular oxygen . . . oxygen contacts are about 2.5 A the van der Waals radii (Knobler, Maverick and Trueblood, 1992).

3.4.6 Carcerands and carceplexes Carcerands are noncollapsible molecular cells whose interiors are large enough to contain molecules or ions as guests and whose closed surfaces contain pores that are too small to allow guest molecules to enter or depart from their interiors without making or breaking covalent bonds; the concept was ﬁrst proposed in 1983 (Cram, 1983) and a general account of the reduction of the idea to practice has been given by Maverick and Cram (1996b). A carceplex is composed of a carcerand containing at least one guest (prisoner)

60

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

molecule in its interior. The carceplexes were made by shell-closing two identical bowl-shaped cavitands, each containing on their rims four phenolic hydroxyls (Scheme 3.10; Sherman, Knobler and Cram, 1991). The cavitands also contain pendant functional groups for enhancement of their solubilities. In each synthesis, one molecule of solvent was incarcerated, the shell closure being templated by the guest ultimately enclosed. C4

H

HO O

2X

O

O

OH

O

O

OH

O

O

OH O

H

C CH2 CH2

C

H

CH2

H

C CH2

CH2

CH2

C

CH2 CH2 CH2 CH2 H C C

CH2 H

CH2

CH2

CH2

C

C

H

O O

CH2BrCl

H CH2

O

O C2 O

O

O

O

O

O G

CH2

O

CH2

O

O

CH2

O

O CH2

O O

O

O

CH2

O O

O

σh

O O

H

C CH2 CH2

3.27

C CH2 CH2

H

H

C

C

CH2

CH2

CH2

H

CH2

3.28

Scheme 3.10

Carceplexes containing (CH3)2NCOCH3, (CH3)2NCHO and dimethyl sulphoxide were prepared in solution; in earlier work with a different carcerand, insoluble complexes with (CH3)2NCHO, (CH2)4O, Csþ, argon and ClCF2CF2Cl had been prepared (Cram, Karbach, Kim, Baczynskyj and Kalleymeyn, 1985; Cram, Karbach, Kim, Baczynskyj, Marti, Sampson and Kalleymeyn, 1988). The crystal structure of {3.28.[(CH3)2NCOCH3]}0.5 CHCl3 (additional, but not fully identiﬁed, solvent molecules ˚, were present) has been determined (triclinic, a ¼ 16.302(3), b ¼ 18.940(3), c ¼ 23.182(4) A 1; R ¼ 0.184 at time of publication; ¼ 90.22(1), ¼ 93.97(1), g ¼ 102.38(1) , Z ¼ 2, P JILZIN). The {carcerand.[guest]} complex is shown in the stereodiagram of Fig. 3.26. ˚ and The cavity has the shape of a prolate ellipsoid of revolution with long axis 10.9 A ˚ . The upper half of the host is rotated by 15 with respect to the lower short axis 6.2 A half, thus making the molecule chiral. That the guest is well and truly incarcerated was demonstrated by heating the complex in C6D5NO2 solution to 160 , subsequent cooling producing no change in the NMR spectrum. In Cram’s view the interior of the carceplex is a deﬁnable mixture of free space and space-ﬁlling guests – ‘‘guest plus vacuum in varying proportions’’ – and thus constitutes a new phase of matter (see Cram and Cram (1994), p. 148). The two reacting tetrols (3.27) in Scheme 3.10 can be joined by hydrogen bonds rather than by covalent linkages. This has been done by carrying out the reaction in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene, which acts as a proton acceptor and forms cations (C9H17N2þ) while the two halves of the anionic carcerand are joined by charged hydrogen bonds (Chapman, Olovsson, Trotter and Sherman, 1998). Pyrazine was found to be the most strongly bound guest of those tried, and its complex (HIMJES; P4cc, Z ¼ 4; {C36H32O12(C36H28O12)4[C4H4N2]4(C9H17Nþ 2 )2(C6H5NO2)4H2O}) was about

HEMICARCERANDS AND HEMICARCEPLEXES

61

{3.28·[(CH3)2NCOCH3]}

Fig. 3.26. Stereoscopic side view of the {carcerand[guest]} complex {3.28[(CH3)2NCOCH3]} (JILZIN); the guest (dark outline) was not well enough deﬁned to allow distinction among C, N and O atoms. Hydrogens have been omitted in this diagram; if included, then it is clear that there is no chance of the guest escaping without breaking bonds. (Reproduced from Sherman, Knobler and Cram, 1991.)

2000 times more stable than that of benzene. Crystal structure analysis showed that the pyrazines (disordered over two orientations) had their nitrogens in the equatorial plane of the host; they were involved in weak hydrogen bonding to half of the hydrogens of the intrabowl methylenes.

3.5 Hemicarcerands and hemicarceplexes 3.5.1 Overview A hemicarcerand is a host molecule that combines an enforced inner cavity large enough to accommodate solvent molecules with a portal which allows guest entry and exit at temperatures above 100 . This deﬁnition has a functional rather than a chemical structural basis and two types have so far been synthesized. In the ﬁrst type, the reacting tetrols of Scheme 3.10 (above) are replaced by triols, with the consequence that the dimer product of the shell-closing reaction will have an opening at one corner of its waistband, the inner space of the cavity no longer being entirely cut off from its surroundings as happens in the carcerands. 3.29 is an example of a Type I hemicarcerand host molecule

62

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

(Cram, Tanner and Knobler, 1991). It was suggested that the term constrictive binding be used for the steric repulsions (decomplexation activation energy) that must be overcome in the decomplexation process.

H2C H

O

H2C

H2C CH2 CH2 H C

H

C

O O

O

C

O

CH2 Hb O

O

C H CH2 CH2 H2C H2C H

O O

G

Ha O

O

O

O

O O CH2

H2C CH2 CH2 H C C

O

O

O

O O CH2 O O

C C H CH2 CH2 H2C H2C H

3.29

Scheme 3.11

Type I hemicarceplexes with 3.29 as host and containing (CH3)2NCOCH3, (CH3)2NCHO, dimethyl sulphoxide, (CH3)CN, CH2Cl2, CH2Br2, CS2, Xe (Ks 200 M1) and Ar were prepared in solution, isolated and characterized. The crystal structure of {3.29[(CH3)2NCOCH3]}2CH3CN2CHCl3 was determined (orthorhombic, ˚ , Z ¼ 8, Pbna; R ¼ 0.168 at time of a ¼ 20.455(5), b ¼ 20.773(5), c ¼ 30.307(8) A publication; KEHDAC10; Cram, Tanner and Knobler, 1991). The {hemicarcerand[guest]} complex has an overall shape similar to that shown in the stereodiagram of Fig. 3.26. NMR studies showed the formation in solution of hemicarceplexes with nitrogen (Ks 180 M1), oxygen (Ks 44 M1) and H2O. Type II hemicarcerands have been prepared in which the relatively short equatorial linking –OCH2O– groups were replaced by the longer –CH2SCH2– groups (Bryant, Blanda, Vincenti and Cram, 1991). Enantiomerically pure analogs were made by using (R)- or (S)-2,2’-bis(bromomethyl)-1,10 -binaphthyl as linking groups. In somewhat later work analogs were produced in which the four linking groups were (1,3-CH¼N–C6H4– N¼CH–), which is rigid, and where portals and inner-space volume were large enough to permit entry and occupation by hosts such as [2.2]paracyclophane, ferrocene, adamantane and camphor (Quan and Cram, 1991). Other analogs have the semi-mobile o-xylyl {1,2–OCH2C6H4CH2O–)} as linking group (Cram, Blanda, Paek and Knobler, 1991; VURBUF; Pcan, Z ¼ 4; C160H136O2418(C4H9NO)) (hemicarcerand abbreviated as 3.30, formula not given; C4H9NO is dimethylacetamide); a more recent example encapsulates hydrocarbons with molecular weights greater than 200 (Cram, Jaeger and Deshayes, 1993). The hosts are all tetra-linked and hence are analogous, from the standpoint of chemical structure, to the carcerand 3.28. Nevertheless, they are named as hemicarcerands on the functional ground that entry and exit of the guest occurs without breaking covalent bonds. Qualitative information about structural recognition of guest by host 3.29 is provided by the facile incarceration of p-xylene compared to the nonincarceration of the other two

HEMICARCERANDS AND HEMICARCEPLEXES

63

Table 3.5. Thermodynamic parameters (solution in 1,2(CD3)2C6D4 at 100 ) of the 3.30 hemicarceplexes referred to in the text. The units of G and H are kJ/ mol and of S J/mol K. Data from Cram, Blanda, Paek and Knobler, 1991 Guest

G

H

S

(CH3)2NCOCH3 CH3CH2O2CCH3 CH3COCH2CH3 C6H5CH3

15.5 15.9 22.2 14.2

6.3 13.0 10.5 þ9.2

þ25 þ8 þ31 þ63

xylene isomers. Some interesting thermodynamic parameters have been measured for hemicarceplexes of the 3.30 host (Cram, Blanda, Paek and Knobler, 1991), using 500 Mhz 1 H NMR to measure equilibrium constants for complexation and their temperature dependences, giving free energies, enthalpies and entropies of complexation (Table 3.5). The ﬁrst three of these hemicarceplexes are both enthalpy and entropy stabilized; the toluene guest is entropy stabilized. The explanation advanced is that the positive carbons of the carbonyl groups of the ﬁrst three guest molecules are electronically complementary to the 16 inward-turned unshared electron pairs of the oxygens of the eight ArOCH2 groups of the host. The unfavourable enthalpy of the toluene complex was attributed to the lack of complementary binding between the ﬂat surface of the guest and the concave inner surfaces of the host. The positive entropies were attributed to two sources: ﬁrstly, solvated guest releases solvent molecules which become dispersed in the solvent, increasing the entropy, and, secondly, there is a contribution from the entropy of dilution of the empty space within the cavity – the large empty space of the cavity is broken up into many smaller empty spaces scattered among the solvent molecules. The kinetics of decomplexation, and their dependence on temperature were also measured by NMR and the free energies, enthalpies and entropies of activation for # ¼ disassociation determined. The constrictive binding free energy was deﬁned as Gassoc # Gdisassoc (G ) and is the free energy of the transition state for association (relative to the uncomplexed state). It appears to depend little on the nature of the guest and derives mostly from the change from the unwrapped state of the empty host to the wrapped state # taken up by the hemicarceplex with included guest. The values found for Gassoc were about 100 kJ/mol, about 3/4 of which could be ascribed to an enthalpic contribution and 1/4 to an entropic contribution. Perhaps the most versatile of the currently available hemicarcerands is 3.31 (formula not shown) which differs from 3.29 in that the equatorial belt has four (instead of one) CH2 groups in each of the four (instead of three) vertical linkages (Robbins, Knobler, Bellew and Cram, 1994); again the term ‘‘hemicarcerand’’ is used here for functional rather than structural reasons. 3.31 is the host used in the work described below on o-benzyne (Warmuth, 1997). Thirty complexes of 3.31 were isolated and characterised, and crystal structures reported for six of these. Five were isomorphous; the general formula was {3.31[guest]}2C6H5NO2, space group P21/c, cell dimensions (for p-I2C6H4 guest at ˚ , ¼ 98.199(4) , Z ¼ 2 (PIHYEK); 156 K) a ¼ 16.777(2), b ¼ 19.795(2), c ¼ 20.327(2) A the other guests in this group were C6H5NO2 (PIHYIO), o-BrC6H4OH (PIHYOU),

64

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

p-(CH3)2C6H4(PIHZAH) and (CH3)2NCOCH3(PIHZEL). The 3.31 host is here centrosymmetric, and guests lacking a centre must be disordered. The sixth crystal structure was of {3.31[6H2O]}4(o-xylene); these crystals were triclinic, with two formula units in space group P1 (is this a misprint for P 1?). There are no symmetry requirements on the 3.31 molecule and it was twisted by 15 about its polar axis; the water molecules apparently take up an octahedral arrangement within the cavity. Crystal structures of cavitands, caviplexes and hemicarcerands and hemicarceplexes with a variety of guests continue to be reported in illustration of the principles described above (e.g. Helgeson, Paek, Knobler, Maverick and Cram, 1996 (TENLED, TENLIH, TENLON, TENLUT, TENMAA). For example, TENLED is {C128H168O24[C2H6OS] 2(C6H5NO2)} and is described as a ‘‘dimethyl sulfoxide clathrate nitrobenzene solvate.’’ ˚ , ¼ 69.36, ¼ 88.81, The reduced triclinic cell is a ¼ 12.984, b ¼ 14.664, c ¼ 20.336 A g ¼ 65.18 , P1, Z ¼ 1. The host is centrosymmmetric with partial disorder of some n-pentyl groups; the DMSO is disordered over two sites related by a center. Other examples, given by Helgeson, Knobler, and Cram (1997), are RAGXAY, RAGXEC, RACXIG, and RAGXOM. A general survey of Carceplexes and Hemicarceplexes has been given by Jasat and Sherman (1999). 3.5.2

The taming of cyclobutadiene, and of o-benzyne

Sherman, Knobler and Cram (1991) closed their report on carcerands with the prescient remark that ‘‘the inner phases of carcerands are unusual and interesting places where chemical reactions might be carried out.’’ A sequel was not long delayed – cyclobutadiene (C4H4) was reported as tamed but reactive within the ‘‘inner space’’ of 3.29 (Cram, Tanner and Thomas, 1991). The cyclobutadiene was synthesized in situ (within the inner cavity of the hemicarcerand) by irradiation (75 W xenon lamp, 25 ) of the 1 : 1 hemicarcerplex of 3.29 with -pyrone. O O

O hν

hν O

–CO2

Scheme 3.12

The -pyrone guest decomposes to C4H4 and CO2, the latter escaping from the cavity. The (Z)-OHCCH¼CHCHO was produced by reaction of C4H4 with O2 gas. The reactions were followed by NMR (Fig. 3.27). The sharp singlet in the NMR spectrum at ¼ 2.3 is assigned to singlet state cyclobutadiene on the basis of the following evidence. The host’s inward-pointing Ha and Hb protons give sharp doublets in the NMR spectrum of {3.29[C4H4]} at ¼ 4.27, 4.36, whereas triplet C4H4 would broaden and shift these signals, as does triplet oxygen in the spectrum of {3.29[O2]}. The sharpness of the signals at ¼ 4.27, 4.36 shows that the cyclobutadiene is rotating rapidly on the 1H NMR time scale about all its axes. {3.29[C4H4]} heated in (D8)THF at 220 gave free cyclooctatetraene (identiﬁed, inter alia, by its ‘‘pungent and characteristic odor’’), through intermediate formation of the cyclobutadiene dimer.

65

HEMICARCERANDS AND HEMICARCEPLEXES

3.29

C2H2

O

O

H

H

3.29 H

7.0

6.5

6.0

5.5

5.0

H

4.5 d

4.0

3.5

3.0

2.5

2.0

Fig. 3.27. 1H NMR spectra (500 MHz, CDCl3, 60 ) of the hemicarcerplexes of 3.29 with cyclobutadiene (CH)4 and (Z)-OHCCH¼CHCHO. (Reproduced from Cram, Tanner and Thomas, 1991.)

This remarkable achievement has been followed by the synthesis of o-benzyne (C6H4; IUPAC name 1,2-didehydrobenzene) within the inner cavity of a hemicarcerand 3.31. The precursor was benzocyclobutendione, which was complexed with 3.31 through a molten phase and then photolysed ( > 400 nm) at 77K to give {3.31[benzocyclopropenone]} as the only product, the structure being conﬁrmed by (an as-yet unpublished) crystal structure analysis. This intermediate complex was then further photolysed (77K, < 297 nm, 88 hours, 300 W xenon arc lamp) to give incarcerated benzyne, identiﬁed by its 1H and 13C NMR spectra. If the {3.31[o-benzyne]} product complex is allowed to warm up above 77K, then a host–guest reaction occurs in which the nominal triple bond of the o-benzyne is added across one of the aryl ether bars of the host cage (Warmuth, 1998). O O O

Scheme 3.13

˚ Singlet cyclobutadiene has a rectangular shape, with bond lengths of 1.34 and 1.60 A (Dunitz et al., 1988). Current very high level calculations of the structure of o-benzyne suggest that there is no bond length alternation, a conclusion in conﬂict with deductions from the NMR spectra which suggest a cumulene-type structure. These geometrical

66

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

details could possibly be identiﬁed from diffraction measurements on the hemicarcerplexes at low temperature. Studies of ‘‘chemistry in the inner space’’ continue, e.g. Warmuth, 2001.

3.5.3

Molecular mechanics and dynamics studies on the complexation and decomplexation processes

There is a wealth of information available about which hosts will complex (or not) with which guests, including studies of the chemistry, thermodynamics and kinetics. One would wish to translate these qualitative and quantitative results into molecular R

R

R

R

rigid ‘polar’ region OO

O

O O

O O

O

OO

O

O

O

O

O

O

OO

O

O

R

O

O O O

O

R

O

R

flexible ‘temperate’ and ‘equatorial’ regions

OO

R

1. R = PHCH2CH2 2. R = H

(a)

(b)

(c)

Fig. 3.28. (Above) Schematic diagram of the hemicarcerand; the pendant groups R ¼ PhCH2CH2 act to increase the solubility of the host 3.32 #1 in the experimental studies, while R is set to H in the stripped-down version of the molecule 3.32 #2 used for the calculations. (Below) Side views of three low-energy conformations of a space-ﬁlling model of 3.32 #2. (Reproduced from Sheu and Houk, 1996.)

COMPARISONS OF CONCEPTS

67

terms – how do the guests enter the hosts, how are they enabled to remain in the cavities and how can they leave? The hemicarcerands are very suitable substrates for this sort of study – the molecules have both rigid and ﬂexible portions, and the portals have reasonably well deﬁned shapes and sizes. The methods of molecular mechanics and molecular dynamics have been applied by Sheu and Houk (1996) to answer these questions, using the ‘‘stripped down’’ hemicarcerand (3.32 #2) as host (Fig. 3.28). The global minimum conformation of the host (2a in Fig. 3.28) has D2h symmetry; 2b has C2h symmetry and is 31.8 kJ/mol higher in energy than 2a, while 2c has D2h symmetry and is 38.5 kJ/mol higher in energy than 2a. Structure 2b is very similar to the analogous hemicarcerand structures found by X-ray diffraction. Sheu and Houk (1996) quote twelve examples of mono- and bicyclic guests which form isolable complexes with 3.32 #1, and twenty-eight examples of similar molecules which do not; 1,2-dimethoxy-4-bromobenzene is an example from the ﬁrst group and 1,2-dimethoxybenzene from the second. It is the orientation of the intrahemispheric bridges (–OCH2CH2OCH2CH2O–) which is important in determining how easy it is for guest molecules to pass in and out through the portals of the host. Cram has pointed out that preorganization of the shape of the host and stereo-electronic complementarity between host and guest are the important factors determining the binding power of a particular host-guest combination. 3.32 is highly preorganized with two rigid polar caps, while the ﬂexibility of the four intrahemispheric bridges allows the shape of the portals and cavity to range from square to rhomboid to rectangular (conformers 2a, 2b, 2c). Three processes must be considered. Firstly, can potential guests bind within the cavities? Calculation showed that all 12 guests and 28 nonguests mentioned above could form complexes with binding energies of 50–100 kJ/mol. Thus there must be reasons other than thermodynamics that allow some of these potential guests to form isolable complexes, while others do not. The second factor is whether the potential guest can enter the cavity through the available portals, taking into account the ﬂexibility of the gates formed by the intrahemispheric bridges. For many guests, the barrier to entry is high even with the gates open. The third factor is possible escape of complexed guest during the puriﬁcation process. This is considered to be the reason why many guests with otherwise favourable properties do not form isolable complexes.

3.6 Comparisons of concepts The different types of enclosure molecules introduced in this chapter, their unfamiliar nomenclature and their resemblances to and differences from established concepts in host–guest solid state chemistry can be somewhat bewildering. We have used the succint comparison of concepts made by Sherman, Knobler and Cram (1991) (see also Cram and Cram (1994; pp. 147–148)) as the basis for a more extended comparison organised in parallel with the treatment of this and subsequent chapters. The crown ethers considered here are single-ring hosts which wrap around cations and form intermolecular hydrogen-bonded complexes with suitably substituted organic guests. True intramolecular enclosure occurs only when the crown ether is large enough to bend back on itself to form a cleft into which the guest enters; a number of hosts (not necessarily crown ethers) of this ‘‘molecular tweezer’’ type have been prepared. Larger crown ethers, particularly benzocrown ethers, can, in addition to the act of enclosure, interact

68

CROWN ETHERS, CRYPTANDS AND RE LATED MOLECUL ES AS HOST S

with suitable guests by charge–transfer forces familiar from the classical chemistry (solution and solid state) of polycyclic aromatic hydrocarbons. Stoddart’s inception and extension of these ideas may well be leading to a new era of supramolecular chemistry based on manipulation of smaller units. Cryptands have three rings (connectors) joined at two apexes (spacers) and form triangular baskets with open sides; four connectors would give baskets of rectangular cross section. Here entry and exit of guests will be relatively easy, and conformational reorganization can be expected during the complexation process. The especial contribution of the Cram group lies in synthesizing molecular baskets with much more varied shapes and, usually, with restricted possibilities of entry and exit. Spherands are hollow and rigid baskets with pole–dipole interactions with guests; so far only cations or relatively small organic molecules have been enclosed in spherands. Carcerplexes contain guests which cannot escape without breaking covalent bonds of the carcerand host molecule; these baskets have a very tight weave. Hemicarcerands are analogous baskets but contain portals which are ﬂexible enough to allow entry and exit of guests at higher temperatures and thus exchange between interior and exterior occurs without bond cleavage. To quote from Sherman et al. (1991) – ‘‘[The] existence and stability [of carciplexes] do not depend on host–guest attractions . . . other than gross size complementarity, but on physical envelopment of guests during [the] shell closures leading to [the formation] of carciplexes.’’ Cram contends that the interiors of carciplexes constitute a new form of matter. The comparison can be completed by considering the place of other types of enclosure. Clathrates are crystalline compounds where the guests are included in cavities left between host molecules linked by hydrogen bonds or van der Waals forces. Generally the sublattice of host molecules has a structure different from that of the neat host, and hence clathrates are secondary solid solutions of guest in host (if of variable composition), or ‘‘phase rule compounds’’ (if of ﬁxed composition). There are some rare examples of primary solid solution. There is no special interaction between host and guest in solution. Zeolites constitute a special case of clathrates where the host structural units are linked by rigid covalent (or ionic) bonds, leading to the crystal becoming a ‘‘giant molecule’’ with many interstices; the complex is then a primary solid solution of guest in host.

References Abbott, S. J., Barrett, A. G. M., Godfrey, C. R. A., Kalindjian, S. B., Simpson, G. W. and Williams, D. J. (1982). J. Chem. Soc., Chem. Commun., pp. 796–797. Allwood, B. L., Colquhoun, H. M., Doughty, S. M., Kohnke, F. H., Slawin, A. M. Z., Stoddart, J. F., Williams, D. J. and Zarzycki, R. (1987). J. Chem. Soc., Chem. Commun., pp. 1054 –1058. Allwood, B. L., Kohnke, F. H., Stoddart, J. F. and Williams, D. J. (1985). Angew. Chem. Int. Ed. Engl., 24, 581–583. Allwood, B. L., Shahriari-Zavareh, H., Stoddart, J. F. and Williams, D. J. (1987). J. Chem. Soc., Chem. Commun., pp. 1058–1061. Allwood, B. L., Spencer, N., Shahriari-Zavareh, H., Stoddart, J. F. and Williams, D. J. (1987a). J. Chem. Soc., Chem. Commun., pp. 1064–1067.

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Chapter 4 Cyclodextrins, and some analogs, as hosts

. . . The Gem, The Diadem, The Ring Enclosing All T.Traherne ((?)1636–1674) Summary: The -, - and -cyclodextrins are oligosaccharides containing respectively six, seven and eight glucose units linked between 1 and 4 positions to form macrocyclic rings of overall toroidal or truncated-cone shape; the secondary hydroxyl side is conventionally deﬁned as the ‘‘head’’ of the cone. The inner and outer surfaces of the toroids are hydrophobic while the upper and lower faces are hydrophilic. When crystallized from aqueous solutions the cyclodextrins form inclusion complexes with a large variety of guest molecules, ranging in type from inert gases through polyiodide salts to aromatics. The crystals contain an appreciable number of water molecules which are hydrogen bonded together and also to the host molecules; the amount of water varies from complex to complex. Two types of general structure can be distinguished – the clathrates and the tunnel inclusion complexes – and each of these types contains a number of isomorphous or isostructural classes; about two-thirds of the complexes of known structure are of the tunnel type. The guest molecules are generally enclosed within the cavities of the toroids in a variety of packings; there are sometimes water molecules within the cavities in addition to those located between the cyclodextrins, and guests are sometimes found between the host molecules. If the guest is a salt, linear anions such as polyiodides are found within the cavities while the counter cations are included in the water network. Formation of hydrogen-bonded cyclodextrin dimers is a feature of the tunnel inclusion complexes and these dimers are mainly head-to-tail in the -cyclodextrin complexes, predominantly head-to-head in the -cyclodextrin complexes and with all three possibilities in the (mostly isomorphous) -cyclodextrin complexes so far studied. The catalytic properties of cyclodextrins in organic reactions and their mimicry of enzyme behavior is ascribed to the manner in which the guest is held in a ﬁxed position and orientation by the host even in solution. Cyclodextrins have found wide use in the pharmaceutical industry because of their water solubility, the innocuous nature of their degradation products and, most importantly, their ability to encapsulate drug molecules and release these slowly. Analogs to the cyclodextrins are currently being developed.

4.1 Introduction 4.2 -Cyclodextrins as host 4.2.1 -Cyclodextrin as host in clathrate inclusion complexes 4.2.2 -Cyclodextrin as host in tunnel inclusion complexes 4.2.3 Chemically modified -cyclodextrins as hosts in inclusion complexes 4.3 -Cyclodextrins as host 4.3.1 -Cyclodextrin as host in clathrate inclusion complexes 4.3.2 -Cyclodextrin as host in tunnel inclusion complexes

74 79 80 84 90 95 97 100

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C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

4.3.3 Exceptional -cyclodextrin structures 4.3.4 Chemically modified -cyclodextrins as hosts in inclusion complexes 4.4 Rotaxanes and catenanes of cyclodextrins 4.5 -Cyclodextrins as host 4.5.1 -Cyclodextrin as host in clathrate inclusion complexes 4.5.2 -Cyclodextrin as host in tunnel inclusion complexes 4.5.3 Chemically modified -cyclodextrins as hosts in inclusion complexes 4.6 Larger cyclodextrins 4.7 Cyclic oligosaccharides as cyclodextrin analogs References

4.1

114 114 117 118 118 119 122 123 123 124

Introduction

Towards the end of the nineteenth century Villiers (1891) reported the isolation (in 3% yield) of a group of unusual nonreducing oligosaccharides from cultures containing Bacillus macerans grown on a medium rich in amylose; the enzymes involved are cyclodextrin glycosyltransferases (CGTases EC 2.4.1.19). The product compounds (now obtained in 25% yield) were shown by Schardinger (1904) to be cyclic oligosaccharides, of toroidal or doughnut shape, containing from six to twelve glucose units. They have been called Schardinger dextrins, cyclo[n]amyloses (CAn), cyclomalto-oligosaccharides and cyclodextrins ( for n ¼ 6, for n ¼ 7 and for n ¼ 8, often abbreviated as -, - and -CD). The enzymatic breakdown of starch to give cyclodextrins is illustrated in Fig. 4.1. We follow Chemical Abstracts in using the -, - and -cyclodextrin (CD) nomenclature, corresponding to cyclomaltohexaose, cyclomaltoheptaose and cyclomalto-octaose respectively. There are also some larger cyclodextrins, whose properties are now being explored (see Section 4.6 below); these are referred to by Greek letters or as CAn, with the latter system to be preferred. However, we have generally retained the CD system because of its familiarity. There is also currently an active development of synthetic cyclic oligosaccharides (Gattuso, Nepogodiev and Stoddart, 1998), which show similarities and differences to the cyclodextrins. The water solubility of the cyclodextrins is an important feature of their properties – 14.5 g/100 ml. water at 25 C, 1.85 and 23.2. All three show increasing solubility with temperature (0–90 C), with solubility at 85 C in the order > > (Diaz, Vargas-Baca and Gracia-Mora, 1994). The solubility is ascribed to dipole interactions between the hydrophilic upper and lower surfaces of the tori and bulk water molecules. Complexes (inclusion complexes of one kind or another, in which molecules of many kinds as well as salts can be found as guests) have been reported for -, - and -cyclodextrins and a considerable amount of structural work has been reported, in addition to much chemical and biochemical study, all of which has been accompanied by important industrial developments. Formation of the complexes is ascribed to replacement of water molecules within the hydrophobic inner surface of the torus by hydrophobic guest molecules. The guests in the cyclodextrin complexes are retained within the rings in the solid state and even in solution (at least on a dynamic basis) and this has made the complexes useful as catalysts in organic chemistry and as model systems for many enzyme reactions. The

I NT RO D UC T I O N

75

14.6 Å 5.3 Å

OH O

O

HO

O HO OH

OH O HO

OH

O OH O

O

HO

OH

7.8 Å

HO O

HO

OH O HO

O

HO OH O

OH

O

O HO

O O O

O

O

O

O O

O

O O O

OH O OH HO

OH O HO

O O

CGTase (Enzyme)

O

O

O HO

OH

O HO

HO O

O

O

OH

O HO

O

O

15.4 Å 6.5 Å

O

O

HO

O

HO

O

OH O

OH O

OH HO O

O

O

7.8 Å

HO OH

O

O

OH

OH

O O O

O

O

O O

O

O

O

OH O

O

O OH HO

O

OOH O

Starch

OH O

O

OH

HO

HO

HO

O OH

O OH

OH

HO

17.5 Å 8.3 Å

OH

HO

HO OH O OH

7.8 Å

O

OH O OH HO O

O

O

OH

HO

α– cyclodextrin (top) Molecular Weight 973 Glucose Units 6 Specific Rotation [a]D25 150.5 Cavity Volume mL/g 0.10 6 H2O molecules included (in solution)

β–cyclodextrin (center) Molecular Weight 1135 Glucose Units 7 Specific Rotation [a]D25 162.5 Cavity Volume mL/g 0.14 11 H2O molecules included (in solution)

γ–cyclodextrin (center) Molecular Weight 1297 Glucose Units 8 Specific Rotation [a]D25 177.8 Cavity Volume mL/g 0.20 17 H2O molecules included (in solution)

Fig. 4.1. Enzymatic breakdown of starch to give -, - and -cyclodextrins, together with a summary of their properties. (Reproduced from Diaz,Vargas-Baca and Gracia-Mora, 1994.)

cyclodextrins have been used as encapsulating agents for slow-release drugs and for other pharmaceutical purposes. Cramer (1954, 1987) played a key role in initiating many of these developments. We shall emphasise the structural chemistry of the crystalline complexes and not attempt to duplicate the coverage of other aspects in the extensive contemporary literature (Senti and Erlander, 1964; Bender and Komiyama, 1978; Saenger, 1980, 1984; Saenger, Jacob, Gessler, Steiner, Hoffmann, Sanbe, Koizumi,

76

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Smith and Takaha, 1998; Saenger and Steiner, 1998; Szejtli, 1982, 1988, 1998; Duche´ne, 1987; Stoddart and Zarycki, 1989; Harata, 1991, 1998). A whole volume (No. 3) of Comprehensive Supramolecular Chemistry, edited by Szejtli and Osa (1996), deals with ‘cyclodextrins’ in 22 chapters extending over 693 pages; there are 3 700 references. Szejtli (1998) mentions that over 15 000 publications had appeared by the end of 1997 (duplication has not been taken into account). An accompanying development has been the preparation of chemically modiﬁed cyclodextrins, generally by methylating or acetylating some or all of the hydroxyl groups (Bender and Komiyama, 1978; Tabushi, 1982); these derivatives also form inclusion complexes, which are discussed together with those of the parent compounds. One fundamental crystallographic aspect must be emphasized at the outset. Apart from a few exceptions among chemically modiﬁed cyclodextrins, all the crystals discussed below contain varying amounts of water molecules essential to their existence, and crystals of anhydrous cyclodextrins have not been found. In this sense they resemble most crystalline biomolecules such as proteins. This situation differs from that found in virtually all the other molecular complexes and compounds dealt with here, where anhydrous hosts (for complexes) or parent components (for compounds) are the species of reference. -, - and -cyclodextrins all form both clathrate and tunnel inclusion complexes. Saenger, Jacob et al. (1998) suggest that, for -CD complexes, small guest molecules form clathrates and larger guests tunnel complexes, i.e. there is a size selectivity. There are not yet analogous generalizations for the - and -CD complexes. Cell dimensions have been reported for more than 300 inclusion complexes of the cyclodextrins and their methylated derivatives and the crystal structures of most of these compounds have been determined. These structures are complicated because of the possibilities of conformational differences in the macrocycles due to interactions with the included guests and, especially because of the variety of hydrogen bonding arrangements possible, particularly at room temperature, and the accompanying disorder. Thus nonstoichiometric amounts of water are often found in the structures, with the water molecules distributed over a number of sites with partial occupancies. In structural terms this means that the arrangements in different unit cells are different, the crystal structure analysis giving only a picture averaged over the whole crystal. It would be desirable to determine crystal structures at the lowest possible temperatures (currently 10K) by neutron diffraction, preferably also on deuterated crystals and then study the changes that ensue on heating. Not much attention has yet been paid to possible phase changes. Such a programme has been started but results are available for only a few complexes; some disorder often remains even at 15K. We shall generally describe the room-temperature structures in broad terms and not attempt to enter into all the details of conformational differences and hydrogen bonding; Harata (1996; 1998) covers much the same material from a somewhat different point of view. Thus, in essence, we concentrate on showing how the complexes can be classiﬁed into various structural (crystallographic) groups, pointing out both the great similarities within each group and the subtle differences among its members. The variety, in a chemical sense, of guests in particular structural families is quite remarkable. The next stage in an overall structural analysis should be to compare in detail the host–guest–water arrangements and interactions. This vast task is on the verge of practicality (Le Bas, Rysanek et al. (1988)) but we leave its realization to future explorers.

I NT RO D UC T I O N

77

Secondary hydroxy O(2)-H, O(3)-H rim Head

Internal tunnel

Tail Primary hydroxy O(6)-H rim (a)

(c)

o

a

o

c

b b (b)

(d) o

a

c o

b c (e)

c

o

b

a

Fig. 4.2. Schematic diagram showing (above): form of the cyclodextrin truncated cone molecule, with conventional deﬁnitions; there are twice as many secondary hydroxyls as primary hydroxyls (below) : the broad ways of describing cyclodextrin inclusion complexes: (a) head-to-head tunnel type, showing dimers found particularly in -CD complexes; (b) head-to-tail tunnel type; (c) cage herringbone type; (d) cage brickwork-like or slipped tunnel type; (e) slipped tunnel type with headto-head dimers. (Adapted from Harata, 1996.)

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C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.1. Statistics of reported cyclodextrin inclusion complex structures (as of end 2002). The herringbone type of clathrate is denoted by A1 and the slipped tunnel or brickwork type by A2; the head-to-tail arrangement in the tunnel complexes is denoted by B1 and the head-to-head arrangement by B2 Type of cyclodextrin

Polymethyl- Polymethyl-

Cage structures

Tunnel structures

A1

A2

B1

B2

16 – 18 4 1

10 – 2 –

18 4 1 2

27 – 71 11 12(mixed)

Following Saenger (1984), the crystal structures can be classiﬁed, into two broad groups (Fig. 4.2), each of which can be further subdivided: Group A: Clathrate or cage structures, where the arrangement of cyclodextrin molecules is such that the cavities of the macrocyclic hosts are blocked off by neighboring host molecules and the guests are therefore enclosed in these cavities. The two subdivisions are: Group A1: herringbone arrangement of host molecules, Group A2: slipped-tunnel or brickwork-like arrangement of host molecules. This group can formally be considered to derive from the tunnel structures (see below) by mutual displacement of adjacent layers of host molecules. Group B: Tunnel structures, where the arrangement of cyclodextrin molecules is such that the toroidal cavities are lined up through the crystals to form approximately linear tunnels in which the guests are accommodated. The mutual arrangement of cyclodextrin molecules has been found to be either head-to-tail or head-to-head in the - and -cyclodextrin complexes studied, and a combination of both in the (mostly isomorphous) -cyclodextrin complexes studied. These two groups, in turn, can be further subdivided into smaller groups of isomorphous or isostructural complexes as has been illustrated by Caira (2002). Our emphasis in this chapter is on structures of CD complexes determined by single crystal methods but one should remember that many such complexes are only obtainable as microcrystalline powders. Here powder diffraction has an important role to play, especially for identiﬁcation, and Caira (2002) has collected together typical powder patterns for the various isostructural groups. One should also note progress in the capability to solve crystal structures from powder data alone (Pop, Goubitz et al., 2002), and this will undoubtedly also be a feature of future developments. The November 2002 version of the CSD gives 358 hits for ‘cyclodextrin’, of which 116 refer to ‘alpha-cyclodextrin’, 214 to ‘beta-cyclodextrin’ and 17 to ‘gamma-cyclodextrin’. A statistical breakdown of the isomorphous and isostructural structures (i.e. those in Tables 4.2–4.19) among the various categories is shown in Table 4.1; about two-thirds of these structures are of the tunnel type. A measure of the rate of development of the ﬁeld can be gleaned from the fact that Saenger listed 37 structures in his 1984 and 1985

-CYCLODEXTRIN AS HOST

79

reviews, while Dodds (1999) found 74 -CD structures in Version 5.12, (October, 1998) of the Cambridge Structural Database and 11 -CD structures. Our list of structures is representative but certainly not complete, nor can it be, with the continuing interest in cyclodextrin structures. 4.2 a-Cyclodextrin as host In -cyclodextrin (C36H60O30) the -D-glucose moieties are all in the pyranose staggered chair form with C1 conformation (1a 2e 3e 4e 5e); the glucose moieties are linked betwen 1- and 4-positions. The important structural features are the toroidal, truncatedcone shape of the macrocyclic molecule, its hydrophobic cavity and curved outer surfaces, and its hydrophilic upper and lower faces. The interior diameter of the cavity ˚ . The (primary) 6-hydroxyl face (deﬁned conventionally as the ‘‘tail’’ of is about 5.2 A the molecule) is somewhat narrower than the 2,3-hydroxyl face (the ‘‘head’’ of the molecule); this is illustrated schematically in Fig. 4.2.1 There are intramolecular hydrogen bonds O(3)H . . . O(2) and O(3) . . . HO(2) between the secondary hydroxyl groups around the macrocyclic ring and these play an important role in its stabilization. X-ray data show that the mean O(2) . . . O(3) distances in -, - and -cyclodextrins are ˚ respectively; the interactions in -CD are weaker and its macrocycle 3.00, 2.86 and 2.81 A is more ﬂexible than those of - and -CD. The C(6)-O(6) bonds are preferentially directed away from the centre of the ring (torsion angle O(5)-C(5)-C(6)-O(6) is ( )gauche; some of these bonds can turn inwards, the torsion angle becoming ( þ )gauche, with formation of hydrogen bonds between the O(6)H group and the guest molecule. These features are illustrated in the diagrams of the various structures given below. The solution thermodynamics of the formation of 1 : 1 inclusion complexes (predominantly in water at 298K) has been extensively studied. Rekharsky and Inoue (1998) have summarised and discussed values for the stability constants, standard free energies, enthalpy and entropy changes, and, for some examples, heat capacities. Some 600 values are given for -CD, 400 for -CD and 50 for -CD complexes. Many multiple values are given (for various temperatures, pHs and so on) so the number of guests involved for each cyclodextrin is about two-thirds of the number of separate values. There are also many values for chemically modiﬁed cyclodextrins. Corresponding measurements on crystalline complexes do not appear to have been reported, apart from an adiabatic calorimeter study of {-CD11H2O} over the range 13–300K (Hanabata, Matsuo and Suga, 1987), where a ﬁrst-order phase change occurs at 226K. The solid-state heat capacities at 298.15K of the three common cyclodextrins and some deﬁned hydrates have also been measured (Briggner and Wadso¨, 1990). 1 The secondary hydroxyls are at the broad end of the truncated cone, and the primary hydroxyls at the narrower end. However, the authorities do not agree on which is ‘‘head’’ and which ‘‘tail.’’ We follow Hamilton (Hamilton and Chen, 1988a), Tsoucaris (Mentzafos et al., 1991) and Harata (1996; see p. 290) in designating the broad end as ‘‘head’’ and the narrower end as ‘‘tail.’’ For example, the ﬁrst of these references has ‘‘ . . . a head-tohead dimer is formed by means of extensive hydrogen bonding across the secondary hydroxyl ends of two adjacent -CD monomers . . . ’’. We use the same deﬁnition for - and -CD. Saenger (e.g. Steiner and Saenger, 1998a; see p. 454) and Kamitori et al (1998) interchange ‘‘head’’ and ‘‘tail.’’

80

4.2.1

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

a-Cyclodextrin as host in clathrate inclusion complexes

The crystalline inclusion complexes of -cyclodextrin (C36H60O30) fall into a number of isomorphous or isostructural groups and it is thus quite a versatile host. The chemical compositions within a group are reasonably similar, but there are differences among groups, especially in regard to degree of hydration, and this may indicate one of the sources of the structural differences. In our classiﬁcation we largely follow Saenger (1985), discussing ﬁrst the clathrates (Tables 4.2 and 4.3) and then the tunnel inclusion complexes (Tables 4.4–4.9). References and crystal data for earlier work given in extenso by Saenger are summarised in Tables 4.2 to 4.8, and in the text. We ﬁnd that about two thirds of the structures reported in the CSD fall into the various isomorphous or isostructural groups detailed in the Tables. -Cyclodextrin forms clathrate inclusion complexes with smaller guests which are grouped together in Table 4.2; the gas molecules Cl2, O2, CO2, C2H4, CH4, propane and butane can be enclosed (Cramer and Henglein, 1957) in addition to the guests listed in Table 4.2. Herringbone arrangement of -CD moieties in clathrate inclusion complexes of -cyclodextrin;. Unit cell dimensions: a 9.5, b 14.3, c 37.5; space group P212121; Z ¼ 4; ˚ 3 ; compositions are given in the form {volume per asymmetric unit 1275 A CD[m(guest)]n(H2O)}, where ‘-CD’ is generally omitted for brevity Guest composition

Refcode; reference

a

b

c

V/FU

[7.6H2O] (form III) 0.48Kr58H2O 0.78Kr53H2O I24H2O n-propanol 48H2O CH3OH57H2O 0.8(CH3CN)57H2O CH3NO25H2O [butyric acid]43H2O; [1-butanol] 55H2O [3-iodopropionic acid]5H2O trans-2-butenoic acid5H2O pyrrole5H2O Acetic acid Propionic acid [60H2O] (form I) DMSO2CH3OH2H2O

BANXUJ; CS81 CYDXKR10; SN76 CDEXKR10; SN76 CDEXTI10; MSFM73b CDXPRO; SMFM74 CDEXME10; HS76 GEVTOQ; AJWH98 GULTUC; NILL00 MSFM73a MSFM73a BUPDEV; HUOH83a JECPEM; TSN90 QOHMEF; SRPG00 S85 S85 CHXAMH; MS74, KHS80* ACDMSM; H78 (P21; Z ¼ 2)*

9.400 9.470 9.446 9.558 9.393 9.465 9.479 9.452 9.45 9.44 9.685 9.43 9.404 9.427 9.46 9.529 9.505

14.356 14.299 14.377 14.240 14.292 14.339 14.323 14.299 14.29 14.382 13.508 14.406 14.293 14.34 14.29 14.858 14.150 102.88

37.536 37.489 37.402 36.014 37.515 37.365 37.397 37.380 38.11 37.99 39.581 38.174 37.265 37.62 38.11 34.038 19.738

1266 1261 1266 1225 1259 1268 1269 1263 1287 1289 1323 1296 1252 1272 1287 1205 1294

* These complexes are structurally related but not isomorphous. References: AJWH98 – Aree, Jacob, Saenger and Hoier, 1998; CS81 – Chacko and Saenger, 1981; H78 – Harata, 1978; HS76 – Hingerty and Saenger, 1976; HUOH83a – Harata, Uekama, Otagiri and Hirayama, 1983a; KSH80 – Klar, Hingerty and Saenger, 1980 (XRD and ND; CHXAMH02); MS74 – Manor and Saenger, 1974; MSFM73b – McMullan, Saenger, Fayos and Mootz, 1973b; NILL00 – Nakagawa et al., 2000; S85 – Saenger, 1985; SMFM74 – Saenger, McMullan, Fayos and Mootz, 1974; SN76 – Saenger and Noltemeyer, 1976; SPRG00 – Storsberg et al., 2000.

-CYCLODEXTRIN AS HOST

81

Table 4.2 but detailed crystallographic information is lacking. The crystal data show that these crystals are all isomorphous, despite small differences in water content. The small differences in cell dimensions depend on the nature of the guest and thus there is a fair degree of adaptability among the complexes of Table 4.2. The guest molecules are contained in the internal tunnels (tori) of the -CD molecules and the packing of the hosts is such that free exit of the guests from the tori is blocked by contiguous host molecules held together by an intricate network of hydrogen bonds between hydroxyl groups; the arrangement is shown rather well in the schematic diagram of Fig. 4.2(c). The water molecules lie between the host molecules and participate in the hydrogen bonding, small differences in water content leading to differences of detail in the hydrogen bonding schemes. In addition to the {-CD[I2]4H2O} clathrate complex, the detailed structure of which has been determined, there is a tunnel complex of composition {-CD0.5[I2]4H2O} (Table 4.6). The ternary complex {-CD[2(CH3)2SO.-(CH3OH)]}(CH3OH)2H2O (ACDMSM) also belongs to this group of slipped-tunnel structures; its monoclinic cell can be transformed to give a pseudo-orthorhombic unit cell with the monoclinic b axis coincident with the b axis of the orthorhombic cell of the other examples in Table 4.2. One methanol lies within the torus and the other outside, together with the water molecules. Perhaps surprisingly, the undecahydrate also belongs to this group of complexes. The complexes in Table 4.3 are clathrates, but derived from tunnels by mutual offset of adjacent layers, giving in Saenger’s phrase a ‘‘brickwork-like’’ layer arrangement (Fig. 4.3) or, in an alternative nomenclature, a ‘‘slipped tunnel’’ structure. In these complexes the rings (or methyl groups, for the dimethylformamide guest) are enclosed within the torus with the amino or hydroxyl group of the guest protruding from the 2,3-dihydroxyl face. The space between the -CD molecules is occupied by water molecules, some of which are disordered. There are four distinct -CD hydrates, two being hexahydrates (Form I (BANXUJ) is related to the group of isomorphous crystals of Table 4.2 while Form II (a ¼ 13.70, ˚ , space group P212121; Z ¼ 4; Lindner and Saenger, 1982a) is on its b ¼ 29.35, c ¼ 11.92 A Table 4.3. Clathrate structures, brickwork-like layers in the (001) plane; space group P212121; ˚ ; volume per formula unit 1280 A ˚3 Z ¼ 4. Unit cell dimensions: a 13.6 b 15.3, c 24.5 A Guest composition

Refcode; reference

a

b

c

V/FU

4-chlorophenol5H2O 4-bromophenol5H2O 4-iodophenol3H2O 4-nitrophenol3H2O 2-ﬂuoro-4-nitrophenol3H2O p-iodoaniline3H2O p-hydroxybenzoic acid3.0H2O N,N-dimethylformamide5H2O 2-pyrrolidone 5H2O 11H2O

WEXKOZ; MMKO99 MESYEO; KTM01 CHAIPL; H76 ACDPNP; H77b ZEJDEX; ShSe94 CDEXIA; SBM76, H75 ACDHBA; H77b ACDMFM; H79 ACDPRO; H79 GOQZUH; PMP98

13.447 13.456 13.477 13.431 13.431 13.681 13.356 13.750 13.852 13.839

15.299 15.317 15.373 15.299 15.299 15.475 15.342 15.318 15.373 15.398

24.795 24.733 24.573 24.788 24.780 24.569 24.896 24.544 24.353 24.209

1275 1274 1273 1273 1273 1300 1275 1293 1297 1290

References: H75 – Harata, 1975; H76a – Harata, 1976a; H77b – Harata, 1977b; H79 – Harata, 1979; H82a – Harata, 1982a; HNI96 – Harata, Nagano, Ikeda et al., 1996; KTM01 – Kamitori, Toyama and Matsuzaka, 2001; MMKO99 – Muraoka et al., 1999; PMP98 – Puliti et al., 1998; SBM76 – Saenger, Beyer and Manor, 1976; ShSe94 – Shibakami and Sekiya, 1994.

82

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

(a)

a

1/4 (b)

1/4

1/4

N

b

N 1/4 N

N

N

1/4 c

N a N

Fig. 4.3. A schematic drawing showing the packing in {-CD[p-iodoaniline]}3H2O, a representative of the slipped tunnel structures of Table 4.3. Two cages, one intra-torus and occupied by guest molecules, and the other intermolecular and occupied by waters of hydration, are indicated by light and dense hatching respectively. In (a) the outer contour circles represent the O(2), O(3) rim (‘‘head’’) of the -CD molecules while the middle circles represent the O(6) rim (‘‘tail’’). Circles and molecules drawn with heavier lines are closer to the observer than those with lighter lines. This is also the structure of {-CD11H2O}. (Reproduced from Saenger, Beyer and Manor, 1976.)

own); Form III, approximately an octahydrate, is a ‘‘full’’ member of the group of isomorphous crystals of Table 4.2, and Form IV (undecahydrate) is classiﬁed in Table 4.3. The -CD moieties in both hexahydrates have strained, high-energy conformations, different from those in the other two complexes; two of the primary O(6) hydroxyl groups are in the gauche, trans conformation directed towards the center of the doughnut shaped molecule (Fig. 4.4) and two of the O(2) . . . O(3) hydrogen bonds are broken, leading to a ‘‘dented’’ shape for the macrocycle. In contrast, in both Forms III and IV (and also in the isomorphous I2 complex) all the O(6) hydroxyl groups are in the gauche, gauche conformation directed away from the centre of the macrocyclic ring which has a ‘‘round,’’ unstrained shape. In the octahydrate there are 2.6 water molecules within the cavity disordered over 4 sites while in the undecahydrate ﬁve water molecules are disordered. In Form I two ordered water molecules are included within the torus, and one water molecule in Form II. This comparison can be extended beyond the hydrates to a number of other -CD complexes (Saenger, Noltemeyer, Manor, Hingerty and Klar, 1976). Thus Saenger

-CYCLODEXTRIN AS HOST

83

Form III

Form I (b)

(a)

0(4)4

0(4)4

0(4)5

0(4)5

0(4)6

0(4)6

0(4)3

)3

0(4

0(4)2

0(4)1 0(4)2

(d)

(c)

(f)

(e)

0(4)1

Fig. 4.4. PLUTO (Motherwell, 1978) space-ﬁlling computer-drawn diagrams showing the conformation of the -CD ring in the Form II hexahydrate on the left and the (so-called ‘‘Form III’’) octahydrate on the right. In (a) and (b) the molecules are viewed, from the head side (O(2) . . . O(3)), normal to the hexagon of O(4) atoms of the various glucose residues; in (c) and (d) from the side and in (e) and (f) from the tail of the molecule. In the octahydrate the molecule has a relaxed, round shape but there are distortions in Forms I and II of the hexahydrate especially in the vicinity of glucoses 1 and 6, where O(2) . . . O(3) hydrogen bonds are broken in Form I. In the hexahydrate Form I two O(6) hydroxyls point into the cavity, but not in the octahydrate. (Reproduced from Chacko and Saenger, 1981.)

(1984) contends that -CD also has the strained conformation in aqueous solution and that adduct formation takes place by displacement of the two intra-torus waters by the guest molecule, accompanied by change of the -CD molecule from a ‘‘tense’’ to a more ‘‘relaxed’’ conformation. This mechanism is similar to the ‘‘induced-ﬁt’’ mechanism

84

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

proposed for the interaction of enzymic proteins with their cofactors and substrates (Koshland, 1970), thus indicating that cyclodextrins and their complexes should provide appropriate models for study of enzyme behaviour. The structures of four 1 : 1 crystalline complexes of -CD with metal coordination complexes (and approximately six associated molecules of water) have been reported. Classiﬁcation presents problems as only one packing arrangement (as opposed to the host–guest relationships) has been described, and the cell dimensions do not show deﬁnite similarities to any of the other groups listed in Table 4.2. There is an isomorphous pair of structures [{-CD[Rh(cod)(NH3)2]-PF66H2O}, a ¼ 14.033(4), b ¼ 19.517(6), ˚ (Alston et al., 1985a; DAXTEB) and {-CD [Co(Hdmg)2 c ¼ 23.803(6) A (n-C4H9)H2O)]7H2O}, where H2dmg ¼ dimethylglyoxime, a ¼ 14.083(3), b ¼ 19.237(4), ˚ (Chen et al., 2000; LOVVAT)] and two individual structures {-CD. c ¼ 24.517(5) A ˚ (Luo [Co(Hdmg)2 (n-C3H7)H2O)]7H2O}, a ¼ 13.440(3), b ¼ 17.593(4), c ¼ 29.009(6) A et al., 1996; RAXPOV) and {-CD[C6H12N2O4Pt)]5.5H2O}, a ¼ 10.102(4), b ¼ 13.526(4), ˚ (Alston et al., 1985b; DEGTEO). All these structures crystallize in space c ¼ 41.971(9) A group P212121 with Z ¼ 4, and this suggests that they may all be clathrates. This has been conﬁrmed for the complex with [Co(Hdmg)2(n-C3H7)H2O)] as guest which is the only complex for which the crystal packing has been described. 4.2.2

a-Cyclodextrin as host in tunnel inclusion complexes

The tunnel inclusion complexes of -CD fall into a number of isomorphous or isostructural classes. An immediate distinction can be made between head-to-tail Table 4.4. Tunnel inclusion complexes of -CD with head-to-tail dimers. The space groups are all P21212; Z ¼ 2, and unit cells have been reoriented so as to make [001] the stack axis. Compositions as in Table 4.2, i.e. in the form {-CD[m(guest)]n(H2O)}, where ‘-CD’ is generally omitted for brevity. The square brackets indicate that the guest is included in the torus Guest composition

Refcode; reference

a

b

c

V/FU

[m-Nitrophenol]m-Nitrophenol6H2O* [Benzyl alcohol]Benzyl alcohol6H2O* Na-1-propanesulfonate97H2O [Methyl orange]Naþ9.8H2O [Methyl orange]Kþ9.8H2O [-aminobutyrate]Kþ10.0H2O] [1.5(acetate)]15Kþ9.8H2O [Benzenesulphonate] Naþ10.0H2O 2,5-dihydroxybenzoic acid3.5H2O [Hexanoate] Naþ11.0H2O (Z ¼ 4; see text)

ACDMNP; HUT78 WILJAC; SG94 ACDPRS; H77a CDXSOM; H76a CDXKOM; H76a CDKABA; TAM81 HRW65 CDXBZS; H76c WIZQEB; MM00 MSFM73a

22.231 22.189 21.608 22.099 22.120 21.861 21.89 21.832 21.939 21.94

16.865 16.602 16.700 16.359 16.419 16.624 16.54 16.529 16.786 16.53

8.152 8.265 8.302 8.296 8.292 8.279 8.30 8.356 8.273 16.56

1528 1527 1498 1500 1506 1504 1506 1508 1523 1503

* One guest within each -CD cavity, and one between the stacks. References: H76a – Harata, 1976a; H76c – Harata, 1976c; H77a – Harata, 1977a; HRW65 – Hybl, Rundle and Williams, 1965; HUT78 – Harata, Uedaira and Tanaka, 1978; MM00 – Mele and Malpezzi, 2000; MSFM73a – McMullan, Saenger, Fayos and Mootz, 1973a; SG94 – Steiner and Gessler, 1994; TAM81 – Tokuoka, Abe, Matsumoto, Shirakawa, Fujiwara and Tomita, 1981.

-CYCLODEXTRIN AS HOST

85

and head-to-head arrangements of the -CD molecules in a stack. The crystals of Table 4.4 are built up of -CD molecules stacked head-to-tail along [001], with the guest anions within the tori and the water molecules and cations outside (Fig. 4.5 (left)). The heads and tails of adjacent -CD molecules are hydrogen bonded together in these tunnel complexes, water molecules being located on the peripheries but not between the -CD’s (Fig. 4.6). The Class IIB structures (Fig. 4.5(right)) are lower symmetry variants of the Class IIA type, with differences of detail rather than of principle. The -CD molecules have exact or approximate C2-2 symmetry and closely similar conformations in all the complexes of Table 4.4, although there is some elliptical distortion in the benzenesulphonate and Methyl Orange complexes because of the ﬂattened cross-sections of these guest molecules. The hydrophobic anions are located within the hydrophobic portions of the cavities but are hydrogen bonded to the host molecule at its 6-hydroxyl end; there is disorder about the two-fold axes. There are some differences among the individual complexes; for example the long Methyl Orange anions extend through two -CD molecules (in a partially disordered arrangement, as can be inferred from diffuse scattering on appropriate diffraction photographs), while the acetate groups of the potassium acetate complex are so small that water molecules are accommodated within as well as outside the cavities (Fig. 4.5). The hexanoate anion also extends through two -CD molecules but here the arrangement must be ordered as ˚ . The m-nitrophenol complex shows one the periodicity along [001] is doubled to 16.5 A striking difference of arrangement from the rest of this group, already hinted at by the compositional difference; one guest molecule is found within the torus while the other is located between the host molecules. There are a few analogous examples among other complexes; one possible consequence is different physico-chemical behavior for the two guest molecules. (a)

(b)

(c)

(d)

O6 H C6 H C5 O4 H C3 O3 H

Fig. 4.5. A comparison of the arrangements of guest molecules in the tunnels of some complexes of Table 4.4. The van der Waals envelopes of the guest molecules are shown; broken lines denote hydrogen bonds. The guests are (a) Methyl Orange (H3C)2NC6H4-N¼N–C6H4SO3; (b) Sodium benzenesulphonate NaC6H5SO3; (c) Sodium propanesulphonate NaC3H7SO3; (d) Potassium acetate KCH3COO. Compare with the schematic arrangement shown on the left side of Fig. 4.6. (Reproduced from Harata, 1976a,b.)

86

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.5. Tunnel inclusion complexes of -CD with head-to-tail dimers. Space groups are all P21; Z ¼ 2, with stacks along [100] Guest composition

Refcode/reference

a

[m-Nitroaniline]6H2O

CDNOAN; H80

8.054

[Benzaldehyde]6H2O

BAJJAX; HUO81

7.932

[4-ﬂuorophenol]6H2O

JUMYOF; ShSe92

7.845

[2-ﬂuorophenol]5H2O

JUMYUL; ShSe92

7.842

Hydroquinone. 6H2O

PUPTEZ; StSa94

7.909

[p-cresol]6H2O

WEXLEQ; MMKO99

7.927

3-methyl-1-butanol7.1 H2O

S85

(R,S)-1-phenylethanol4H2O

BIJHOR; H82a

8.176

Mono(3-amino-3-deoxy-) -CD 5.5H2O

TOVLOF; HNI96

7.955

16.64

b/

c

V/FU

13.508 94.58 13.500 90.85 13.587 91.75 13.615 92.27 13.505 90.76 13.568 90.41 13.95 95.0 23.930 106.69 24.989 98.15

24.668

1338

24.704

1323

24.557

1308

24.550

1310

24.706

1319

24.54

1320

23.64

1368

13.853

1298

13.106

1290

Notes: BIJHOR has a head-to-tail arrangement in which -CD moieties are inclined at 17 to stack axis; guests sandwiched between -CD molecules. CSD gives p-benzoquinone diagram and formula for PUPTEZ; this is wrong. TOVLOF is a chemically-modiﬁed -CD. References: H80 – Harata, 1980; H82a – 1982a; HNI96 – Harata, Nagano, Ikela et al., 1996; HUO81 – Harata, Uekama, Otagiri, Hirayama and Ogino, 1981; MMKO99 – Muraoka et al., 1999; S85 – Saenger 1985; ShSe92 – Shibakami and Sekiya, 1992; StSa94 – Steiner and Saenger, 1994.

For most tables in this chapter, we have listed the variety of guests found in a particular host framework; a converse approach in used in Table 4.6, where we list the variety of frameworks found for hosts of the same chemical type, here ionic polyiodides of various compositions. The variety is quite surprising. Detailed crystal structures have been reported for ZZZANG10 (Cd pentaiodide) and for CYDXLI (Li pentaiodide), which has been inserted in Table 4.7 rather than in Table 4.6 in order to emphasize structural (unit cell) resemblances. A square arrangement of head-to-head dimers stacked in linear fashion along [001] is found in the tetragonal crystals of composition {2(-CD) 0.5(Cdþþ) I3 I2 27 H2O} ˚ 3; ˚ ; space group P41212; Z ¼ 8; volume per formula unit ¼ 1533 A (a ¼ 19.93, c ¼ 30.88 A Noltemeyer and Saenger, 1980; ZZZANG10). The guest anion is [I5 ] and other examples are found with the cations Kþ, NH4þ, Hþ and some divalent species; this is the stable form for Kþ and NH4þ cations. Isostructural crystals are formed with the neutral guest 4,4 0 -biphenyldicarboxylic acid [{2(-CD) C14H10O4 14H2O} (a ¼ 19.609, ˚ ; space group P41212; Z ¼ 8; volume per formula unit ¼ 1550 A ˚ 3; Kamitori c ¼ 32.257 A 0 et al., 1998; CAQPAL). The 4,4 -biphenyldicarboxylic acid guest is entirely enclosed

-CYCLODEXTRIN AS HOST

b

87

0

b a

c

1/4

1/4

1/4

1/4

1/4

1/4

a

c a

b

0

Fig. 4.6. (Left) General arrangement of -CD molecules in the tunnel inclusion complexes of Table 4.4, illustrated for the [1-propane sulphonate]. Naþ9.7H2O complex. Stack axis [001]. (Right) General arrangement of -CD molecules in the tunnel inclusion complexes of Table 4.5. illustrated for the [benzaldehyde] 6H2O complex. Stack axis [100]. (Adapted from Harata (1977a) and Harata, Uekama, Otagiri, Hirayama and Ogino, 1981.)

Fig. 4.7. A stereoview showing the head-to-tail stacking of –CD molecules in {-CD [benzaldehyde]6.0H2O}, illustrating the arrangement in the tunnel inclusion complexes of Table 4.5. Here water molecules also participate in the intracolumn stacking but in other examples the ˚ interactions are only between -CD molecules. Intermolecular O . . . O contacts of less than 3.1 A are shown by thin lines. The benzaldehyde guests can be seen inside the columns. (Reproduced from Harata, Uekama, Otagiri, Hirayama and Ogino, 1981.)

88

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.6. Various crystals with polyiodide anions showing the variety of crystal types obtained. The approximately linear anions are held within the -CD torus, with counterions and water molecules between the stacks of -CD head-to-head dimers. The formulae are based on {2(-CD) – note the change from the standard formulation used elsewhere Overall composition

Refcode/ reference

2(-CD NaI3.I2.)8H2O

CYDXTF; NS80 CYDXTE

2(-CD)[I2]8H2O 2(-CD)CsI3I212H2O Alternatively, hexagonal

CYDXTC; NS80

Other cations

a/

b/

c/

Space group

19.590

NH4þ, Kþ, Rbþ

24.440 15.750 space group 109.30 not given 12.970 12.970 7.910 120 15.8 27.37 40.2 C222 15.8

2(-CD)Ba2(I)I212H2O ZZZAND10; 13.71 NS80 2(-CD)Cd0.5 I3I227H2O ZZZANG10; H3Oþ, NH4þ, 19.90 NS80; Kþ, Rbþ, Mg2 þ , Ca2þ, Sr2 þ , Ba2þ, Zn2 þ , Cd2 þ 2(-CD) CAQPAL; 19.609 KMKO98 [4,4 0 -biphenyldicarboxylic acid]14H2O

15.8 13.71 19.90

40.2 120 17.04 120 30.80 90

P62, P6222, P31 P622 P42212

19.609 32.257 P42212

References: KMKO98 – Kamitori et al., 1998; MSFM73a – McMullan, Saenger, Fayos and Mootz, 1973a; NS80 – Noltemeyer and Saenger, 1980.

within the head-to-head dimer, with carboxyls of succeeding guest molecules linked through a pair of water molecules. When -CD was crystallized from a solution containing 4,4 0 -biphenyldicarboxylic acid and CaCl2, then orthorhombic crystals [{2(-CD) ˚ ; space group P21212; Z ¼ 8; C14H10O414H2O} (a ¼ 35.397, b ¼ 24.577, c ¼ 27.969 A ˚ 3; Kamitori et al., 1998; CAQPEP) were obtained. volume per formula unit ¼ 1550 A Structure analysis showed that there were short columns composed of two head-to-head dimers instead of the continuous one-dimensional stacks; however, the guest molecules were enclosed in much the same pattern in both forms. Are these polymorphs? The word was not mentioned by Kamitori et al. The isomorphous structures of the ﬁrst group in Table 4.7 (the organometallic guests) have been succinctly described by Klingert and Rihs (1991a) as follows: ‘‘ . . . the -CD molecules are arranged head-to-head to form a dimer, with all secondary hydroxy groups of one macrocycle linked to the adjacent one by direct hydrogen bonds. The dimers are stacked along the crystallographic c axis forming parallel channels in which the guest cations and anions are lined up alternately. The cations are encapsulated within the cavity of the dimers while the PF6 anions . . . are centred between the primary hydroxyl faces of adjacent dimers.’’ This description applies well to the complex with neutral Fe(cp)2 as guest (where the PF6 anion is absent), and also to the crystals with neutral molecular guests. The lithium

-CYCLODEXTRIN AS HOST

89

Table 4.7. Isomorphous triclinic crystals (the unit cells are reduced) with guests of various kinds. The space group is P1, Z ¼ 2 unless stated otherwise. In the first group of complexes there are organometallic cations held within the torus of the -CD head-to-head dimers, the PF6 counterions between the tail ends of adjacent dimers and water molecules between the stacks. The general formula is {2(-CD) [Mþ][PF 6 ]8H2O} (note the change from the standard formulation used elsewhere); (-CD) and PF6 are omitted for brevity, while Mþ represents the organometallic cation. The next group has two molecules and one salt as guest. The 1-octanol and valeric acid complexes have head-to-head dimers and hexagonal packing of stacks. The last two examples are presumably isostructural to the first group Organometallic guest cation

Refcode; reference

a/

b/

c/

Unit cell volume

Rh(cp)2þ8H2O

KIWZEV; KR91a,b KIWZAR; KR91a,b KIWYUK; KR91a,b JEMGUD; OH90 PEPBUH; MS-ES-F93 JEHYIE; KR90 KOGKEW; KR91b XIGBOE; S-RPLB01 ZASYOH; NVCdR94 CYDXLI10; NS80 S85

13.756 91.33 13.810 91.06 13.806 91.43 13.836 92.22 13.768 90.98 13.815 91.41 13.845 91.94 13.83 93.01 13.852 93.01 13.830 91.91 13.86

13.833 93.08 13.833 92.94 13.839 92.77 13.864 92.13 13.911 93.46 13.891 92.85 13.861 91.98 13.88 91.72 13.878 91.98 13.855 92.20 13.86

2565

S85

13.85

13.85

MSFM73a; S85 KR91a

11.911 91.3 13.892 89.63

13.870 93.75 13.926 89.20

15.561 119.67 15.560 119.76 15.520 119.80 15.694 119.76 15.601 119.47 15.639 119.64 15.641 119.85 15.72 119.58 15.719 119.32 15.690 119.82 15.63 120 15.62 120 15.669 115.01 16.585 60.26

Co(cp)2þ8H2O Fe(cp)2þ8H2O Fe(cp)29H2O CpRu(C6H6)þ8H2O Fe(cp)(C6H6)þ8H2O Fe(cp)(C7H8)þ8H2O {2(-CD) [n-butylisothiocyanate]9H2O} {2(-CD) [acetone]9H2O} 2(-CD)LiI3 I28H2O 1-octanol (Laue symmetry 6/mm) Valeric acid (Laue symmetry 6/mm) [Diethyl ether]4.1H2O Fe(cp)(C8H8)þnH2O

2574 2566 2606 2593 2601 2597 2615 2625 2602 1300 1298 2606 2786

Notes: ˚ , 90.02 1. KOGKEW gives a metrically-C-centered monoclinic cell with dimensions 13.884 23.977 15.641 A 93.91 90.08 (Z ¼ 4). Coordinates are available for checking. ˚ , 89.96 2. Fe(cp)(C8H8) gives a metrically-C-centered monoclinic cell with dimensions 13.892 24.183 16.585 A 90.80 90.18 (Z ¼ 4). Coordinates are not available for checking. ˚ , 89.95 94.30 3. JEMGUD gives a metrically C-centered monoclinic cell with dimensions 13.900 23.960 15.694 A 90.13 (Z ¼ 4). Coordinates are available for checking (Odakagi et al., 1990). 4. Na and Tl give crystals isomorphous with 2(-CD)LiI3I28H2O. References: KR90 – Klingert and Rihs, 1990; KR91a – Klingert and Rihs, 1991a; KR91b – Klingert and Rihs, 1991b; MSFM73a – McMullan, Saenger, Fayos and Mootz, 1973a; MS-FS-E93 – Meister, Stoeckli-Evans and Su¨ssFink, 1993; NS80 – Noltemeyer and Saenger, 1980; NVCdR94 – Nicolis, Villain et al., 1995; OH90 – Odagaki et al., 1990; S85 – Saenger 1985; S-RPLB01 – Sicard-Roselli et al., 2001.

90

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.8. Trigonal crystals with organometallic cations held within the -CD head-to-head dimers and PF6.counterions held between the dimers; the water molecules lie between the stacks of dimers. The general formula is {2(-CD) [Mþ] PF6nH2O, with n 13} (note the change from the standard formulation used elsewhere). In this table only the organometallic guest cation is listed. The original data come from Klingert and Rihs (1991b; T ¼ 180K) except where noted otherwise Organometallic guest cation

Refcode

a

c

Unit cell volume

Fe(cp)(indan)þ Fe(cp)(cumene)þ Fe-bis(cp)propaneþ Fe(cp)(o-xylene)þ Fe(cp)(anisole)þ Ru(cp)(acetophenone)þ (water content not given)

KOGKIA KOGKOG KOGKUM KOGLAT KOGLEX PEPCAO; MS-ES-F93

13.836 13.846 13.812 13.867 13.907 13.918

50.464 50.272 50.356 50.468 49.700 49.77

8366 8347 8319 8404 8324 8349

pentaiodide complex has the anti-isomorphous structure,2 with the charged species interchanged. The complexes of Table 4.7 provide an excellent illustration of how a particular framework can accommodate a variety of chemically different guests, and this generalization applies not only to cyclodextrin complexes. We have some understanding of the principles governing the construction of the framework but little knowledge of what determines which guests will be accepted. The examples in Table 4.8 (another group of isomorphous crystals) show that small changes in the nature of the organometallic cations can lead to a different type of crystal structure, albeit still based on dimers enclosing cations and anions between stacks. About two-thirds of the -CD structures listed in the CSD can be accommodated in isomorphous or isostructural groups (Tables 4.2 to 4.8, excluding Table 4.7). The others are found in space groups P212121,3 P214 and P21212,5 with a few exceptions. Judging from the cell dimensions, these crystals are all different but we have not made a detailed structural comparison. A ‘‘one-of-a-kind’’ structure that warrants special mention is {-CD(cyclopentanone)4.6 H2O}. This was ﬁrst studied by XRD at room temperature by Le Bas (see Tsoucaris et al., 1987; FERCIO) and then by neutron dif˚ , space group P6, Z ¼ 6; Le Bas and Mason, 1994; fraction at 20K (a ¼ 23.725, c ¼ 7.935 A KIRJOK10). Diffuse scattering at 300K has also been studied (Le Bas and Doucet, 1997). Although there is static disorder even at 20K, the high symmetry and low temperature reveal features not yet found in other -CD structures. 4.2.3

Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes

It has been found that chemical modiﬁcation of cyclodextrins, primarily by methylation or acetylation of hydroxyl groups, leads to hosts with properties different from those of the 2 ‘‘Two substances are said to be anti-isomorphous when their crystal structure[s] are geometrically identical but with the positions of corresponding atoms or ions interchanged.’’ (Evans, 1966, p. 194). 3 HOGCIP, KOBLOC, MEWFUP, QOYLEV, RAXPOV, ROQVUO, TEVCEC, VEHQAA, ZIBWIQ, ZIBWOW. 4 BOLVUT, CDXNEH, OBUMED, RIQDIE, RIQDOK. 5 HEHQAM, MESYAK.

-CYCLODEXTRIN AS HOST

91

native cyclodextrins. The compounds are shown in the schematic formula, with their trivial names (R00 ¼ CH3 for all formulae). R⬙O6C6H3C O3R⬘ 5 O4

4

1

O5 3

2 O2R

n 6 6 7 7

R R0 CH3 H CH3 CH3 CH3 H CH3 CH3 Scheme 4.1

n

name per-dimethyl--CD per-trimethyl--CD per-dimethyl--CD per-trimethyl--CD

The crystal structure of 6A,6C,6E-tri-O-methyl--CD6.7H2O (i.e. three alternate CH2OH groups methylated) has been reported (Durier, Buisson, Due´e, Driguez and Taravel, 1992; PEZKAG), but not (as yet) of any of its inclusion complexes. Crystal data ˚ , V(asymmetric unit) ¼ 1321.0(2) A ˚ 3, are a ¼ 13.975(1), b ¼ 29.162(2), c ¼ 12.965(1) A space group P212121, Z ¼ 4. The molecules are packed in herringbone fashion and there is some resemblance to -CD7.6H2O (form III). Two water molecules are ordered inside the torus, and one ordered, and 3.7 disordered, outside it. The chemically modiﬁed -cyclodextrins whose inclusion complexes have been studied crystallographically are hexakis(2,6-di-O-methyl)--CD (C48H84O30, called per-dimethyl-CD) and hexakis(2,3,6-tri-O-methyl)--CD (C54H96O30, per-trimethyl--CD). In per-dimethyl--CD the O(3) hydroxyl groups form O(3)-H . . . O(2) intramolecular ˚ . The crystal structures of the hydrogen bonds which vary in length from 2.87 to 3.16 A per-dimethyl--CD 1 : 1 complexes with I2, acetone (ROQVOI) and 1–propanol (KAF˚, GAZ10) are isomorphous (for the I2 complex: a ¼ 14.124, b ¼ 10.667, c ¼ 21.443 A ˚ 3; KAFFUS10) ¼ 106.3 , space group P21, Z ¼ 2, volume of the asymmetric unit 1552 A and have been shown to be clathrates, with the guests enclosed within the tori of the host molecules (Harata, 1990b). The 1 : 1 complex of per-dimethyl--CD with 3-iodopropionic ˚ , volume of acid is orthorhombic (VERVET; a ¼ 10,707, b ¼ 14.504, c ¼ 41.448 A ˚ 3, space group P212121) and also has a clathrate structure (Harata, asymmetric unit 1616 A 1989). It is striking that these three complexes are anhydrous although crystallized from water, in contrast to the hydrated complexes generally formed. Per-dimethyl-CDacetonitrile dihydrate (Aree, Hoier, Schulz, Reck and Saenger, 2000a; WEXKIT) is also orthorhombic P212121 but not isomorphous with VERVET. Among the interesting properties of the permethylated cyclodextrins is their solubility behavior, summarized as follows by Aree, Uson et al. (1999): ‘‘ . . . the solubility coefﬁcients in water become negative, i.e. they are better soluble in cold than in hot water, where they precipitate or crystallize (Uekama and Irie, 1987) . . . methylated CDs have been crystallized from hot and cold water at 60–89 C and at 4–18 C . . . The crystals that could be obtained from hot water are anhydrous hexakis(2,6-di-O-methyl)-–CD

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

92

(Harata, 1995; Steiner, Hirayama and Saenger, 1996), anhydrous hexakis(2, 3, 6-tri-Omethyl)-–CD and anhydrous heptakis(2, 6-di-O-methyl)-–CD (Steiner and Saenger, 1995a), heptakis(2, 3, 6-tri-O-methyl)-–CDH2O (Caira, Grifﬁth et al., 1994b) and octakis(2, 3, 6-tri-O-methyl)-–CD 2 H2O (Steiner and Saenger, 1998b),’’ Many of these structures (and others) are noted in the following pages. In per-trimethyl--CD all hydroxyl groups have been methylated and the methoxy oxygens can act only as hydrogen bond acceptors. The methoxy groups extend above and below the mean plane of the macrocyclic ring, thus increasing the height of the ˚ (instead of 8 A ˚ for -CD) and decreasing the cross-section truncated cone to 11 A at the 6-methoxy end (Fig. 4.8); this leads to a vase shape (cf. Section 3.4 on cavitands and caviplexes). There is no intramolecular hydrogen bonding and thus the macrocyclic rings are more ﬂexible than those of -CD, with consequent enhancement of the possibilities for chiral discrimination, as has been demonstrated for the diastereoisomeric complexes of R- and S-mandelic acid [PhCH(OH)COOH] (Harata, Uekama, Otagiri and Hirayama, 1987). The four complexes whose structures have been determined fall into three groups (Table 4.9). The limited number of water molecules present is a striking feature of the compositions compared to those of the -CD complexes. The packing of pertrimethyl--CD molecules in the tunnel complexes is compared in Fig. 4.9. The principal

z y x

Fig. 4.8. Stereoview of hexakis(2,3,6-tri-O-methyl)--CD as found in its per-trimethyl--CD. [ p-iodoaniline]H2O complex (Table 4.9). The bracketed moieties are shown included in the torus. The 2,3-methoxy groups are at the bottom of the diagram (‘head’ of the molecule) and the 6-methoxy groups at the top (‘tail’). (Data from Harata, Uekama, Otagiri and Hirayama, 1984.)

sinb

I

II

III

Fig. 4.9. Schematic diagrams of the stacking arrangements in the tunnel inclusion complexes of pertrimethyl--CD: (I) p-iodoaniline; (II) benzaldehyde; (III) p-nitrophenol. (Reproduced from Harata, Uekama, Otagiri, Hirayama and Sugiyama, 1982.)

-CYCLODEXTRIN AS HOST

93

Table 4.9. Structural classification of the inclusion complexes of hexakis(2,3,6-tri-O-methyl)-˚ , deg. V/FU ¼ volume CD (per-trimethyl--CD); compositions as in Table 4.2; cell dimensions in A ˚ 3) per formula unit. These are all tunnel structures, with head-to-tail packing along [001] and (A reported in space group P21; Z ¼ 2. However, note that CECMAY has been reinterpreted as C2221 (Marsh et al., 2002), and that the space group of the last complex is P212121; Z ¼ 4 Guest and water content

Refcode/reference

a

b

c

V/FU

Class IA:[C6H6NI] H2O [p-iodoaniline] [R-mandelic acid]2H2O

BEYLOG; HUO82a CECMEC10; HUO87 BOHWUQ; HUOHS82 BUPDIZ, JEJWOK; H90a JEJXAX; H90a BUPDIZ; HUOH83a BUDKEQ; HUOH82b CECMAY10; HUO82a CECMAY11; MHKH02 MYM01

11.440

23.674

13.531

91.90

1831

11.624

23.739

13.786

106.56

1823

11.604

23.832

13.593

106.11

1799

11.604

23.669

13.824

106.72

1818

11.586

23.641

13.762

106.45

1808

11.59

23.285

13.901

106.98

1794

11.307

14.578

22.118

96.36

1812

13.123

23.187

13.113

107.19

1906

15.571

21.116

23.187

14.636

21.637

23.45

[benzaldehyde]

[(R)-phenylethanol] [(S)-phenylethanol]H2O Iodoacetic acidH2O Class IB: [p-nitrophenol]H2O Class II: [S-mandelic acid]3H2O Reinterpretation with space group C2221 (R)-1,7-dioxaspiro [5.5]-undecane5.1 H2O

1857

References: H90a – Harata 1990a; HUO82a – Harata, Uekama, Otagiri and Hirayama, 1982a; HUOH82b – Harata, Uekama, Otagiri and Hirayama, 1982b, 1984; HUOH83a – Harata, Uekama, Otagiri and Hirayama, 1983a; HUO87 – Harata, Uekama, Otagiri and Hirayama, 1987; HUOHS82 – Harata, Uekama, Otagiri, Hirayama and Sugiyama, 1982; MHKH02 – Marsh et al., 2002; MYM01 – Makedonopoulou, Yannakopoulou et al., 2001.

interactions between host molecules are of the van der Waals type, in contrast to the other cyclodextrin complexes where the hosts are blanketed by large numbers of water molecules. Here, if present, the few water molecules are hydrogen bonded to guest and host within the host tunnel and do not link host molecules. Despite the overall similarities in molecular arrangement, there are subtle differences of detail which are ﬁrst revealed by small differences in cell dimensions. There is a considerable measure of adaptability in the per-trimethyl--CD tunnel inclusion complexes. A remarkable enantiospeciﬁc separation of the enantiomers of the racemic olive ﬂy pheromone 1,7-dioxaspiro[5.5]undecane [] by complexation of the (R)-enantiomer with hexakis(pertrimethyl)--CD and of the [S]-enantiomer with heptakis(pertrimethyl)-CD has been reported by Mentzafos, Mavridis and Yannakopoulou (1999) and Makedonopoulou, Yannakopoulou et al. (2001). The binding constants of the two complexes determined by NMR in aqueous solution are respectively 6600 M1 for the

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

94

[R]-enantiomer – hexakis(per-trimethyl)--CD complex and 935 M1 for the [S]enantiomer – heptakis(per-trimethyl)--CD complex. These differences can be explained by the details of the interactions between enantiomer and cyclodextrin in the respective pairs. In the complex of the (R)-enantiomer with hexakis(pertrimethyl)--CD the guest interacts not only with the enclosing host but also with other hosts in the crystal lattice; C–H . . . O interactions appear to be particularly important. On the other hand, the diastereomers of hexakis(pertrimethyl)--CD with R-and S-phenylethanol are isomorphous (JEJWOK and JEJXAX in Table 4.9) and enantiomeric separation does not appear feasible. O

O O

O

[S] enantiomer

[R]-enantiomer

Scheme 4.2

The mode of insertion of the same guest molecules in the tunnel inclusion complexes of -CD and per-trimethyl--CD is compared in Fig. 4.10. There are similarities for p-iodoaniline but not for the other two guests; however, it would be premature to generalize on the basis of the meagre available evidence. The conformations of per-trimethyl--CD and per-trimethyl--CD have been discussed in detail together with the host–guest inclusion geometry (Harata, Uekama, Otagiri and Hirayama, 1982b, 1984). W I H H H

C

C

C C

C C O

O

H H

H

C H

H

Benzaldehyde

C

C C

C C

C

H C C C H

H

C

H

H

C H

H

C

C N

H

H

H

p-Iodoaniline

H

I H

C

C

C C

C C H

N

H H

H

W O H H

C

N C

O C C

C C

H H

H C

H

O C C

H C C

O H

H

C H

O N O

A p-Nitrophenol

B

Fig. 4.10. Schematic diagrams of the modes of inclusion of the same guest molecules in -CD tunnel inclusion complexes (on the left) and per-trimethyl--CD tunnel inclusion complexes (on the right). The O(2,3) hydroxyls are at the lower ends of the truncated cones. Note the water molecules included in two of the right hand diagrams. (Reproduced from Harata, Uekama, Otagiri and Hirayama, 1982b.)

-CYCLODEXTRIN AS HOST

95

4.3 b-Cyclodextrin as host The -cyclodextrin molecule (C42H70O35) consists of seven 1,4--linked D-glucose residues in the 4C1 chair conformation (Fig. 4.11). The secondary hydroxyls are hydrogen bonded around the macrocyclic ring, increasing its stability and reducing its ﬂexibility. The primary hydroxyls have conformations which depend on the host–guest relationship; in general these hydroxyls have a gauche–gauche conformation and point away from the centre of the macrocycle. However, in some instances the C(6) hydroxyls of glucose residues G3 and G4 have the gauche–trans conformation and point towards the centre of the macrocycle; {-CD[1,4-diazabicyclo[2.2.2]octane]13H2O} (Table 4.10) is an example. This conformation is maintained by hydrogen bonding linking the hydroxyls through a water molecule.

Fig. 4.11.(a) Stereoview of -CD looking downwards from the tail (O(6) end) of the -CD molecule in its complex with [2,5-diiodobenzoic acid]7H2O. All the primary hydroxyls are shown with gauche–gauche conformations pointing away from the centre of the macrocycle; the intramolecular hydrogen bonding between adjacent secondary hydroxyls is clearly seen at the head of the molecule at the bottom of the diagram. Complex is listed in Table 4.14. (Reproduced from Hamilton, Sabesan and Steinrauf, 1981.)

Fig. 4.11.(b) Side-view of the -CD conformation in -CD[1,4-diazabicyclo[2.2.2]octane]13H2O complex, showing the C(6) hydroxyls of G3 and G4 with gauche–trans conformation, on the right hand side of the molecule, pointing towards the centre of the macrocycle. The 6-hydroxyls (the narrower tail of the molecule) are at the top of the diagram. Complex is listed in Table 4.10; oxygens cross-hatched. (Data from Harata, 1982b.)

96

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

˚ , deg.) Table 4.10. Crystal data for isomorphous -CD clathrate inclusion complexes. Unit cells (A have been reoriented where required to maintain a common pattern. All crystals have space group P21 with Z ¼ 2, except where stated otherwise. Compositions are expressed as {-CD[m(guest)] nH2O} with -CD being omitted for brevity. Measurements by XRD at room temperature (nominal 298K) except where stated otherwise; ND ¼ neutron diffraction. V/FU ¼ volume per formula unit ˚3 in A Guest Group I (a) (clathrates) 11H2O (ND at 298K)* 11H2O (ND at 120K) 1.8 HCl8H2O 2HI8H2O CH3OH6.5H2O C2H5OH8H2O (ND – 298K; deuterated crystal) C2H5OH8H2O (ND – 15K; deuterated crystal) KOH9H2O 0.5(DMSO)7.35 H2O Benzyl alcohol [C6H6N2O]6H2O (nicotinamide) [diethanolamine]6.4H2O [but-2-yne-1,4-diol]6.2H2O [propane-1,3-diol]7H2O [C4H10O2]6H2O (1,4-butanediol) (1,5-pentanediol)6.2H2O [diethylene glycol]6H2O [glycerol]7.2H2O [ethylene glycol]8 H2O (squaric acid)6.65 H2O

Refcode; reference

a

b/

c

V/FU

BUVSEQ02; BSHB84 BUVSEQ03; ZSM86 ZZZBVD; SB77 BOBPEN; LS82b BOBPIR; LS82b SIGHOF01; SMS91 SIGHOF02; SMS91 KOBRIC; CNV91 VACZIJ; AC02 DEBGOG; HUOHO85 CACCOY; HKFO83 YIYSII; SKGS95 ZIGZIY; SKGS95 YIYTAB; SKGS95 KUTKOZ; SKS92 YIYSOO; SKGS95 YIYSUU; SKGS95 PIJGOE; GSKS93 PIJGIY; GSK93 MIFHAK; CFM01

21.26

10.31 112.3 10.03 112.5 10.27 109.0 10.28 113.3 10.11 111.0 10.21 111.472 10.00 109.0 10.58 108.4 10.285 109.86 10.101 112.81 10.37 110.5 9.987 111.85 10.092 111.30 9.976 110.88 9.973 110.87 10.014 111.25 9.969 111.62 9.954 111.20 10.021 111.47 10.068 110.16

15.30

1533

14.89

1491

15.04

1515

15.30

1538

15.33

1521

15.215

1527

15.23

1473

15.22

1544

15.155

1532

15.356

1522

15.37

1525

15.247

1506

15.223

1544

15.274

1503

15.271

1508

15.240

1526

15.276

1507

15.251

1509

15.208

1504

15.231

1520

21.62 20.75 21.25 21.03 21.125 20.46 20.20 20.906 21.287 20.43 21.310 20.988 21.116 21.199 21.451 21.288 21.322 21.212 21.117

-CYCLODEXTRIN AS HOST

97

Table 4.10. (Continued ) 0.3(formic acid)7.7 H2O

ASR03

20.986

0.4(acetic acid)7.7 H2O

ASR03

21.044

DIRVOP; H84 POVSIC; StSa98c

20.12

Group I (b) (clathrates) [C6H12N4]6H2O (hexamethylene-tetramine) Trans-cyclohexane-1,4-diol5.4 H2O Group II (brickwork or slipped-tunnel) [C6H12N2]13H2O (diazabicyclo[2.2.2]octane) [C11H11N3SO2]8.3H2O (sulfathiazole) Miscellaneous: space group P212121, Z ¼ 4 2{(Mg(H2O)6 Cl2}3.5H2O (CaCl2)211H2O

20.042

10.169 110.92 10.157 110.67

15.171

1512

15.263

1526

15.29

1557

15.123

1572

16.60 117.4 16.50 117.3

15.44

1752

15.56

1741

10.35 102.1 10.378 102.30

BISTAY; H82b LILLUN; CGN94c

15.40

ZEZTED; NCCR95 HIDZAV; NCCR96

15.95

18.61

23.36

1734

15.88

17.58

24.27

1694

15.26

* A 12-hydrate has been reported (Lindner and Saenger, 1982b; Hamilton, Steinrauf and Van Etten, 1968 (BCDEXD, 01–05, 10; QQQAEV)) with approximately the same cell dimensions as the 11-hydratePerhaps this is an example of concomitant small compositional and structural variationsThe reversible dehydration has been studied (Steiner and Koellner, 1994)The XRD structure at 300K has been reported (Steiner and Koellner, 1994; BUVSEQ01). References: AC02 – Aree and Chaichit, 2002; ASR03 – Aree, Schulz and Reck, 2003; BSHB84 – Betzel, Saenger, Hingerty and Brown, 1984; CFM01 – Crisma et al., 2001; CGN94c – Caira, Grifﬁth, Nassimbeni and van Oudtshoorn, 1994c; CNV91 – Charpin, Nicolis, Villian, Rango and Coleman, 1991; GSKS93 – Gessler, Steiner, Koellner and Saenger, 1993; H82b – Harata, 1982b; H84 – Harata, 1984; HKFO83 – Harata, Kawano, Fukunaga and Ohtani, 1983; HUOHO85 – Harata, Uekama, Otagiri, Hirayama and Ohtani, 1985; LS82b – Lindner and Saenger, 1982b; NCCR95 – Nicolis, Coleman, Charpin and de Rango, 1995; NCCR96 – Nicolis, Coleman, Charpin and de Rango, 1996; SB77 – Szjetli and Budai, 1977; SKGS95 – Steiner, Koellner, Gessler and Saenger, 1995; SKS92 – Steiner, Koellner and Saenger, 1992; SMS91 – Steiner, Mason and Saenger, 1991; StSa95 – Steiner and Saenger,1995; StSa98c – Steiner and Saenger,1998c; ZSM86 – Zabel, Saenger and Mason, 1986;

4.3.1 -Cyclodextrin as host in clathrate inclusion complexes The crystal data are given in Table 4.10; there are some twenty isomorphous (or nearly so) cage complexes (Class I) and one slipped-tunnel (brickwork) structure (Class II), which are illustrated in Figs. 4.12 and 4.13. The -CD clathrates resemble those of -CD in that both can be divided into similar structural types. The arrangement in Class II is head-totail but the slippage between adjacent planes is such that there is very little overlap between successive -CD molecules and hence only minimal hydrogen bonding between them. The two C(6) hydroxyls, which have gauche–trans conformations, point in towards the centre of the macrocycle in the undecahydrate and in the diazabicyclo[2.2.2]octane complex but without disrupting any of the intramolecular hydrogen bonds made by the secondary hydroxyls and without disturbing the round shape of the

98

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

macrocycle. Gessler, Steiner, Koellner and Saenger (1993) have concluded that ‘‘the general behaviour of the guest molecules is similar for all inclusion complexes of -CD with small hydrophilic molecules studied so far. If the complexed molecule is too small to ﬁll the cavity, several water molecules are also included, thereby forming a cluster of hydrogen-bonded guest molecules. This cluster is dynamically disordered: the molecules are mobile, and perform jumps between different alternative (but discrete) sites. In solution, such rearrangements certainly occur in an even more pronounced way than in the crystalline solid state.’’ One structure that does not ﬁt into any of the tabulated groups is {-CD2,7˚ , ¼ 109.28 , dihydroxynaphthalene4.6 H2O} (a ¼ 14.082. b ¼ 19.079, c ¼ 12.417 A space group P21, Z ¼ 2; Anibarro et al., 2001; CACQED); nevertheless, the packing principles are similar. The 2,7-dihydroxynaphthalene molecule is completely included in the -CD cavity with its long axis along the -CD molecular axis, leading to marked elliptical distortion. These moieties are arranged in herring-bone fashion with the 4.6 water molecules distributed at the narrow (tail) end of the -CD cavity. Another exceptional structure is that of {-CDmefenamic acidxH2O} (a ¼ 15.480. b ¼ 25.589, ˚ , ¼ 98.976 , space group P21, Z ¼ 2; Pop et al., 2001; MUPNEQ) where c ¼ 9.297 A mefenamic acid is 2-[2,3-dimethylphenyl-amino]benzoic acid; the moieties are arranged in herring-bone fashion. This structure is noteworthy because it was solved using highresolution room-temperature synchrotron data from polycrystalline samples; this is the ﬁrst such structure determination and carries important implications for study of CD complexes unobtainable as single crystals. There is a glass transition at about 150 K and a ﬁrst-order transition in {-CD11H2O} at 226K, with H ¼ 10.2 kJ/mol and S ¼ 451 J K1 mol1 (Hanabata, Matsuo and Suga, 1987); the ﬁrst-order nature of the transition is hinted at by the appreciably different cell dimensions at 298 and 120K (Table 4.10). Neutron diffraction (Betzel, Saenger, Hingerty and Brown, 1984; Zabel, Saenger and Mason, 1986) shows that the phase change is due to a cooperative ordering of hydrogen bonds, which are dynamically disordered above 226K; the glass transition is ascribed to freezing of the conﬁguration of protons participating in a four-membered ring of water molecules found only in the low temperature phase. Partially deuterated {-CD[C2H5OH3H2O]5H2O} has also been studied at 15K by neutron diffraction (Steiner, Mason and Saenger, 1989); at room temperature most hydroxyl groups and water molecules, especially those in the cavity region containing [C2H5OH3H2O], are extensively disordered. However, a well ordered network of hydrogen bonds is found at 15K. Later work (Steiner, Mason and Saenger, 1991) used fully deuterated crystals. There are two structures with divalent metal cations which have -CD packings related to the herringbone structure type. These are {-CD2{(Mg(H2O)6Cl2}3.5H2O} (Nicolis, Coleman, Charpin and Rango, 1995; ZEZTED) and {-CD(CaCl2)211H2O} (Nicolis, Coleman, Charpin and Rango, 1996; HIDZAV) (Table 4.10, Miscellaneous). The presence of metal cations (also in the KOH complex) involves new structural considerations. Kþ can be included without much disturbance of the overall structure, as is shown by the resemblance of the cell dimensions and symmetry of the KOH complex to those parameters of the large group of -CD complexes with organic guests. However, divalent cations require more drastic changes for their accommodation. Indeed, Nicolis, Coleman et al. (1995) comment: ‘‘The structure [of the Mg complex] may be considered

-CYCLODEXTRIN AS HOST

99

z y

Fig. 4.12. Diagram of the crystal structure of hexamethylenetetramine (HMT) complex of -CD (DIRVOP) viewed down the [100] axis. This is a representative of the clathrate structures (Table 4.10, Group Ib). The HMT guests (emphasized) are enclosed within the -CD tori, which have a herringbone arrangement. The water molecules have been omitted for clarity and the intermolecular hydrogen bonding is not shown. (Data from Harata, 1984.)

b

b

a

c a

c sin b

Fig. 4.13. The slipped-tunnel or brickwork structure of {-CD[diazabicyclo[2.2.2]-octane] 13H2O}, illustrating structures listed in Table 4.10 (Group II) (cf. Fig. 4.2(c)). (Reproduced from Harata, 1982b.)

in two ways: ﬁrst, a novel arrangement of –CD monomers into which an inorganic motif is inserted or second, a space-ﬁlling arrangement of a –CD assembly within an inorganic matrix . . . The nature of the structure is such that it is difﬁcult to say which substructure, organic or inorganic, determines the overall packing.’’ We add a second quotation about HIDVAZ (Nicolis, Coleman et al. (1996): ‘‘Suitable crystals . . . were obtained after 1 year, by slow evaporation of a highly concentrated CaCl2/–CD aqueous solution.’’ A novel complex of composition {-CD8(pyridine)3H2O}, crystallized from a CD–pyridine–water gel system is noted here because the -CD molecules are present as monomers (Rango, Charpin, Navaza, Keller, Nicolis, Villain and Coleman, 1992;

100

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

˚ , ¼ 101.87 , P21, KUFHOI). The cell dimensions are a ¼ 14.70, b ¼ 14.74, c ¼ 21.78 A Z ¼ 2. One pyridine is enclosed within the -CD cavity, one is at the primary hydroxyl level and six, together with the water molecules, are in tunnels between the host molecules; thus the composition is better expressed as {-CD[2(C5H5N)]6(C5H5N)3H2O}. The crystals contain 40% pyridine by weight in a low density packing of -CD molecules. This has been described as a ‘‘brickwork’’ structure by Dodds (1999). 4.3.2 4.3.2.1

-Cyclodextrin as host in tunnel inclusion complexes Structural data

The tunnel inclusion complexes of -CD are isostructural and can be divided (with perhaps one known exception) into the ﬁve isomorphous groups given in Tables 4.11 to 4.15. This classiﬁcation is due to Mentzafos, Mavridis, Le Bas and Tsoucaris (1991), who have made other important contributions, discussed below, to the systematization of the crystal chemistry of this family of complexes. Perhaps the most striking feature of the tunnel inclusion complexes is the appearance of head-to-head -CD dimers, with direct hydrogen bonding between the O(2,3) ends of the truncated cones (Fig. 4.14). These dimers are the structural units in the -CD tunnel inclusion complexes and are linked to one another in stacks by hydrogen bonds via water molecules. The driving force for dimer formation appears to be the creation of a large apolar environment for enclosing hydrophobic guests. The various complexes are then distinguished by different modes of stacking of the dimers. We shall ﬁrst give the facts – crystal data and packing arrangements for the ﬁve isomorphous groups, and then show how Mentzafos et al. (1991) have accounted for these arrangements in terms of different packings of essentially similar layers. In the ﬁrst group of tunnel (CH) structures (Table 4.11) adjacent dimers in a stack are slightly laterally displaced but their axes remain parallell. The reduced triclinic unit cells in Table 4.12 fall into two groups when the standard ˚ , 113, 99, 103 ordering a < b < c is used. The ﬁrst group has 15.2, 15.5, 18 A ˚ , 99, 113, 103 . This presumably and the second group has 15.2, 15.5, 18 A implies that the structural roles of a and b are interchanged between the two groups. The ternary complexes of pyrene with octanol and cyclohexanol (Table 4.14) have particularly interesting structures, illustrated for the octanol complex in Fig. 4.15 (p. 110). The pyrene molecules are enclosed not within the internal tunnels of the -CD molecules but within the hydrogen bonded portion of the dimer, and without appreciably perturbing the structure of the dimer. A tentative generalization was made that, in analogous complexes, other aromatic molecules could occupy the same site as pyrene and that the third component need not be an alcohol. The second group (IM; Table 4.12) has been listed separately because these structures are of the slipped-tunnel (brickwork) type), the two barbital complexes differing in having one-dimer and two-dimer lengths of chain respectively. In the screw tunnel (SC) structures (Table 4.13; Fig. 4.16) the integrity of the dimers is maintained but these are now both mutually displaced and tilted. Further evidence for the importance of the dimers is given by the ternary {-CD[acetylsalicylic acid0.5(salicylic acid)]11.7H2O} complex where the three guest molecules are enclosed within a -CD dimer (DIFHOP, Table 4.12, Group II, Nishioka, Nakanishi, Fujiwara and Tomita, 1984).

-CYCLODEXTRIN AS HOST

101

Fig. 4.14.(a) Stereoview of the stacking of -CD head-to-head dimers in the tunnel inclusion structure of -CD[2,5-diiodobenzoic acid]7H2O; the disordered guest molecule and the water molecules are not shown. This is an example of the second group of isomorphous -CD tunnel inclusion complexes with a tunnel (CH) structure, listed in Table 4.14. The space group for this group is C2, with four formula units in the unit cell. (Reproduced from Hamilton, Sabesan and Steinrauf, 1981.)

Fig. 4.14.(b) Two stereoviews of a space-ﬁlling model of the -CD dimer with enclosed guest molecules in the {-CD[1-adamantanecarboxylic acid]16H2O} structure. The upper view is looking down from the tail of the molecule (i.e. the primary hydroxyl end) and the lower view is normal to the sevenfold axis of -CD; water molecules are not shown. The two -CD moieties and the two 1-adamantanecarboxylic acid moieties (almost entirely enclosed in the -CD cavity, with one carboxyl group protruding more than the other) are both crystallographically independent. The interlocking of secondary hydroxyl oxygen atoms which link the -CDs to form hydrogen bonded head-to-head dimers is clearly shown in the lower diagram. This example comes from the group of isomorphous -CD tunnel inclusion complexes with an intermediate (IM) structure listed in Table 4.12. The space group is P1, Z ¼ 2. These are also called slipped tunnel or brickwork structures. (Reproduced from Hamilton and Sabesan, 1982b.)

102

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.11. Crystal data for some -CD tunnel inclusion complexes with a tunnel (CH) structure; compositions as in Table 4.5. The space group is P1, Z ¼ 2. The reduced cells are given, with standard orientation (a < b < c); these show that the Group I and Group II structures are isostructural Guest

Refcode/ reference

Group I. [C8H8N2O3]7H2O; ( p-nitro-acetanilide)* [C8H8NOBr]13.5H2O; p-bromoacetanilide (benzoic acid)0.35(ethanol)10.3 H2O Group II. [(n-C3H7OH)]9H2O; n-propanol (metastable phase, at 120K; polymorph II). 1,7-dioxaspiro-5,5-undecane# 0.7(Z-tetradecane-7-en-1-al)11.6 H2Ox

a/

b/

c/

CHANAO; HMP78; XADHIT; CD99 AC03a

15.13 88.65 15.20 87.16 15.210 89.13

15.54 81.84 15.61 81.71 15.678 74.64

15.69 76.86 15.74 76.61 15.687 76.40

BCYDPR; JS79 FERCOU; TLRV87 YRM02 XUBXUN

15.316 104.23 15.60 101.4 15.475 101.856

15.461 103.98 15.72 101.7 15.466 101.909

15.575 100.92 15.93 103.2 15.720 103.769

V/FU

1778 1798 1751

1673 1800 1722

Notes: * Pseudo-monoclinic C2 symmetry; # 1,7-dioxaspiro-5, 5-undecane is the pheromone of the olive ﬂy. x (Z-tetradecane-7-en-1-al) is the sex pheromone of the olive pest Prays olea; one molecule is within the dimer and the other between the dimers. References: AC03a – Aree and Chaichit, 2003; CD99 – Caira and Dodds, 1999; HMP78 – Harding, Mclennan and Paton, 1978; JS79 – Jogun and Stezowski, 1979; TLRV87 – Tsoucaris, Le Bas, Rysanek and Villain, 1987; YRM02 – Yannakopoulou et al., 2002.

Tunnels are no longer evident in the chessboard group (CB; Table 4.14). In flurbiprofen A is:

CH3 A

C

In fenoprofen A is :

H

COOH S-(+) enantiomer

F O

Scheme 4.3

Some indication of the inﬂuence of guest on overall structure can be obtained from the -CD complexes with ﬂurbiprofen (2-(2-ﬂuoro-4-biphenylyl)propionic acid) and fenoprofen (2-(3-phenoxyphenyl)propionic acid), where structures have been reported with most of the possible combinations of racemic and enantiomeric guests.

Table 4.12. Crystal data for the second isomorphous group of -CD tunnel inclusion complexes with an intermediate (IM) structure (also called slipped tunnel or brickwork structures); compositions as in Table 4.10. The space group is P1, Z ¼ 2The reduced cells are given, with standard orientation (a < b < c); these show that the Group I structures are isomorphous, as are the Group II structures, but Groups I and II are not isomorphous Guest; water content Group I [C11H16O2]15H2O; 1-adamantanecarboxylic acid at 108K. (Note (a)) [C7H8O].xH2O m-cresol (120K); [()-[C15H13O2F]10H2O; ()-(2-(2-ﬂuoro-4-biphenylyl)-propionic acid; ﬂurbiprofen) [(S)-( þ )-[C15H13O2F]10.5H2O; (S)-( þ )-(2-(2-ﬂuoro-4-biphenylyl)propionic acid) [1.5(p-HOC6H4I)]12H2O; p-iodophenol; 153K

Refcode; reference

a/

b/

c/

V/FU

BOGCAB; HS82

15.255 113.54 15.327 113.07 15.420 113.63

15.491 98.87 15.366 99.68 15.490 99.36

17.747 102.54 17.887 102.64 18.633 103.05

1807

15.446 113.52 15.352 113.10 15.440 113.02 15.389 113.43 15.31 112.66 15.40 112.86 15.446 112.99 15.45 113.1

15.513 99.32 15.363 99.40 15.530 98.99 15.519 99.07 15.50 99.47 15.519 99.07 15.452 99.35 15.47 99.4

18.107 102.89 17.985 102.80 18.060 103.44 17.896 103.01 18.30 103.32 17.896 103.01 18.056 103.16 18.08 103.1

1861

15.45 113.6

15.55 99.4

18.09 103.5

1854

BCDMPH; JMS79 CEDMUT; UHI83

CIGXOF; UIH84 BCDPIH10; SJEB78

N-acetyl-L-phenylalanine]12H2O

AGAZIR; ACBS02

[C12H15NO3]13H2O (110K); N-acetylphenylalanine methyl ester N-acety-p-methoxy-L-phenylalanine11.5 H2O

DOCVUM03; S85 CBS01

N-acetyl-L-phenylalanine amide 13H2O

CS01

0.8(nonanoic acid)12 H2O

TEJHAR; RM96b

[0.5(C20H32O4)]10.3H2O; Iloprost is a 1:1 mixture of 16R and S diastereoisomers 4-biphenylacetic acid.xH2O

SHSH89

HHA92

1814 1843

1827 1863 1836 1879 1836 1854 1860

Table 4.12. (Continued ) Guest; water content

Refcode; reference

Group II 0.5[C11H10O2]9H2O; (ethyl cinnamate

BIDMOQ; HST-PU85

[1.5(n-C3H7OH]12H2O; n-propanol at 153K (note (b)) [(C9H8O4)0.5(C7H6O3)]11.7H2O; (acetylsalicylic acid0.5 (salicylic acid)) (3,4-xylidine complex stated to be isomorphous); note (c). 0.5{[C13H24O2]2(C2H6O]24.5 [H2O]}; 1,13-tridecanedioic acid; 173K 0.5{[C14H26O4]0.2(C2H6O]10.93 [H2O]}; 1,14-tetradecanedioic acid 0.5{[C12H22O4]1.16(C2H6O]13.7 [H2O]}; 1,12-dodecanoic acid; 100K. 0.5{[C12H22O4]0.5 (C2H6O]11.1[H2O]}; 1,12-dodecanedioic acid [1.5(R,S)()-(C8H10OS)]17H2O; (R, S)()-methyl-p-tolylsulphoxide [(C8H12N2O3)15.5H2O; (5,5-diethylbarbituric acid (barbital)), Form I N-acetyl-L-phenylalanine]12H2O

CDEXPR, BCDNPR10; JS79, SJEB78 DIFHOP; NNFT84

LONGIE; MTM99; CACPOM; MM01 WISREV; MM00; WISRIZ; MM00 GESVUV; FTMV88; DEVVAB; NAFT84; AGAZOX; ACBS02

N-acetyl-R-phenylalanine]12H2O

AGAZUD; ACBS02

Tert-butyl benzoic acid

HEGXUM; RMHD94

a/

b/

c/

V/FU

15.392 99.74 15.299 99.40 15.247 99.99

15.486 113.61 15.424 113.50 15.475 112.71

18.186 102.78 17.980 103.00 18.310 102.63

1854

15.280 99.79 15.436 99.78 15.251 99.90 15.409 99.71 15.432 99.25 15.497 99.70 15.390 99.27 15.410 98.74 15.417 99.69

15.510 113.13 15.492 113.01 15.456 113.13 15.488 113.12 15.476 113.29 15.549 112.30 15.390 113.39 15.470 113.72 15.476 113.08

18.207 103.02 18.242 102.75 18.153 102.81 18.220 102.90 17.984 102.96 18.123 103.63 17.890 102.75 18.150 103.53 18.244 102.94

1818 1865

1851 1877 1837 1868 1846 1881 1823 1851 1870

7-hydroxy-4-methylcoumarinxH2O

BAS00

7-hydroxyoumarinxH2O

BAS00

2( p-hydroxybenzaldehyde)4.72 H2O; note (d)

BAI02

[(C8H12N2O3)12.5H2O; (5,5-diethylbarbituric acid (barbital)), Form II (4 formula units per cell); note (d)

DEVVEF; NAFT84

15.37 99.47 15.46 99.22 15.262 92.67 15.529 99.89

18.01 113.21 15.55 113.21 15.728 96.97 15.568 93.47

18.01 103.35 18.16 103.23 16.350 103.31 32.327 103.82

1858

Notes: (a) Two other cells have been given for this complex but their relation to the structure solved is not clear (see QQQAEY). (b) 15.229 is also given. (c) In the (acetylsalicylic acid)2(salicylic acid)) complex, the salicylic acid molecule is in the centre of the -CD dimer. (d) The last two complexes have structure combining features of the tunnel and slipped-tunnel arrangements, and are placed here for convenience. They are not isomorphous with the other entries. References: ACBS02 – Alexander et al., 2002; BAI02 – Braga, Aree, Imamura et al., 2002; BAS00 – Brett, Alexander and Stezowski, 2000; CBS01 – Clark, Booth and Stezowski, 2001; CS01 – Clark and Stezowski, 2001; FTMV88 – Fujiwara, Tomita, Marseigne and Vicens, 1988; Vicens, Fujiwara and Tomita, 1988; HHA92 – Harata, unpublished, noted in Harata, Hirayama, Arima, Uekama and Miyayi, 1992; HS82 – Hamilton and Sabesan, 1982; HST-PU82 – Hursthouse, Smith, Thornton-Petit and Utley, 1982; JMS79 – Jogun, McLennan and Stezowski, 1979; MM00 – Makedonopoulou and Mavridis, 2000; MM01 – Makedonopoulou and Mavridis, 2001; MTM99 – Makedonopoulou, Tulinsky and Mavridis, 1999; NAFT84 – Nakanishi, Arai, Fujiwara and Tomita, 1984; NNFT84 – Nishioka, Nakanishi, Fujiwara and Tomita, 1984; RMHD94 – Rontoyianni, Mavridis, Hadjoudis and Duisenberg, 1994; RM96b – Rontoyianni and Mavridis, 1996; S79 – Stezowski, 1985; SHSH89 – Steiner, Hingrichs, Saenger and Hoyer, 1989; SJEB78 – Stezowski, Jogun, Eckles and Bartels, 1978; UHI83 – Uekama, Hirayama, Imai, Otogiri and Harata, 1983; UIH84 – Uekama, Imai, Hirayama, Otogiri and Harata, 1984.

106

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.13. Crystal data for the isomorphous group of -CD tunnel inclusion complexes with a screw tunnel (SC) structure; compositions as in Table 4.5. The space group for this group is P21, with four formula units in the unit cell Guest; water content;

Refcode; reference

a

b/

c

V/FU

[C8H11N]16H2O (p -ethyl-aniline);

CDETAN; TFT81 TFT81

15.30

15.58

1881

15.53

1883

NIZGUY; CGNO96 DUTLIN10; HC88b GETPEA; HC88a GETPAW; HC88a CIVBUE; NFT84 KIFPAQ; S-R99 SAJPIC; HHUT88

15.342

32.31 102.4 32.49 102.6 32.54 102.44 32.23 101.2 32.12 100.8 32.76 101.5 33.189 104.85 32.545 103.56 35.31 102.7

15.324

1868

15.32

1850

15.28

1845

15.35

1880

15.562

1900

15.437

1884

15.50

2069

15.255

1821

15.621

1868

15.47

1902

15.609

1890

[C6H6NI]16H2O (p-iodo-aniline); (L-menthol)14.5H2O [R,S-()-C15H14O3]15H2O; (R,S-()-fenoprofen); at 123K [S-( þ )-C15H14O3]12H2O; (S-( þ )-fenoprofen); at 138K [R-( )-C15H14O3]13H2O; (R-( )-fenoprofen) [phenobarbital]13.5 H2O Adamantone [C11H15O3N3F]9.7H2O; (1-hexylcarbamoyl-5-ﬂuorouracil) (carmofur) C12H10N2O212.7H2O; p-amino-p 0 -nitrophenyl 4,4 0 -diaminobiphenyl9.7H2O [S-( )-(C8H10OS)]17H2O; (S-( )-methyl-p-tolyl-sulphoxide) (Z ¼ 8) [1.5(cyclizine)]12.5H2O; (Z ¼ 8).

QACXEX; BLCS99; GYM03 GESWAC10; VFT88 CDN01

15.29

15.28 15.31 15.26 15.229 15.428 15.51

15.454 15.394 15.495 15.246

31.693 102.92 31.995 103.74 65.04 102.6 65.075 102.6

Note: fenoprofen is (3-phenoxyphenyl)propionic acid. References: BLCS99 – Brett, Liu, Coppens and Stezowski, 1999; CDN01 – Caira, Dodds and Nassimbeni, 2001; CGNO96 – Caira, Grifﬁth, Nassimbeni and Oudtshoorn, 1996; GYM03 – Giastas et al., 2003; HC88a – Hamilton and Chen, 1988a; HC88b – Hamilton and Chen, 1988b; HHUT88 – Harata, Hirayama, Uekama and Tsoucaris, 1988; NFT84 – Nakanishi, Fujiwara and Tomita, 1984; S-R99 – Sanchez-Ruiz et al., 1999; the chemical composition was not given; TFT81 – Tokuoka, Fujiwara and Tomita, 1981; VFT88 – Vicens, Fujiwara and Tomita, 1988.

{-CD[()-ﬂurbiprofen]10H2O} (Uekama, Hirayama, Imai, Otogiri and Harata, 1983) and {-CD[(S)-( þ )-ﬂurbiprofen]10.5H2O} (Uekama, Imai, Hirayama, Otogiri and Harata, 1984) have very similar structures (Table 4.12); in the ﬁrst of these the R-( ) enantiomer is found in one half of the -CD dimer and the S-( þ ) enantiomer in the other half, with a head-to-head arrangement of the guests in which the carboxyls are hydrogen bonded to a primary hydroxyl of the -CD and to a water molecule. A very similar

Table 4.14. Crystal data for the isomorphous group of -CD tunnel inclusion complexes with a tunnel (CH) structure; compositions as in Table 4.10. The space group for this group is C2, with four formula units in the unit cell Guest and water content

Refcode; reference

a

b/

c

V/FU

0.5(KI79H2O) (actually P21 but pseudo C2)

COCMIQ; BHN83

19.61

15.80

1790

NaI38H2O (details not given)

CYDXTF; NS80

19.58

15.75

1778

0.5{[Fe(cp)(mesitylene)]þPF66H2O}

KOGLIB; KR91

19.241

15.768

1745

0.5{[Fe(cp)(biphenyl)]þP F68H2O}; (actually P21 but pseudo C2) [ethyl p-aminobenzoate]7.5H2O

KOGLOH; KR91

19.206

15.674

1733

BIHJEH; HS82

18.75

15.66

1690

[C8H8O2]11H2O (m-toluic acid)

QQQAFA; HSV68

18.86

15.76

1728

[C7H5O2I]11H2O (m-iodobenzoic acid)

QQQAFG; HSV68

18.88

15.69

1724

[(C7H3I2O2]9H2O (2,5-diiodobenzoic acid)

QQQAFJ; HSS81, HSV68

19.19

15.74

1761

[C8H9NO2]13H2O (acetaminophen)¤

CD00

19.207

15.700

1740

[0.5(cimetidine)]11H2O

D99

19.22

15.75

1757

[C10H13BrO]9H2O (2-bromo-5-t-butylphenol)

QQQAFS; HSS81, HSV68

19.24

16.02

1798

[C10H13BrO]9H2O (2-bromo-4-t-butylphenol);

HSV68, HSS81

19.19

15.97

1779

[C7H5O2Br]13H2O (m-bromobenzoic acid)

QQQAFP; HSV68

19.23

15.80

1760

[3,3-dimethylbutylamine]11H2O

VIJXAN; MHT91

19.19

15.89

1773

[0.94(3,5-dimethylbenzoic acid)]9.1H2O

YOVVIO; RM94

19.37

16.00

1811

[4-t-butyltoluene]8.5H2O

KUTJUE; MH92

19.24

24.51 109.5 24.44 109.3 24.415 109.55 24.334 108.88 24.53 110.2 24.67 109.5 24.77 110.0 24.76 109.6 24.48 109.52 24.57 109.1 24.66 108.9 24.58 109.17 24.58 109.5 24.56 108.8 24.71 108.9 24.47 109.9

15.84

1753

Table 4.14. (Continued ) Guest and water content

Refcode; reference

a

b/

c

V/FU

[0.5(cyclopentadienyl mesitylene iron PF6)] H2O

KOGLIB; KR91

19.24

15.77

1745

[0.5(cyclopentadienyl biphenyl iron PF6)] H2O

KOGLOH; KR91

19.21

15.67

1732

[benzophenone] (water content not given)

DEVTED; LBdE84

19.24

15.94

1775

[biphenyl] (water content not given)

DEVTIH; LBdE84

19.34

15.80

1760

spiroacetal

TEMCIX; RLVT96

19.368

15.940

1787

[0.75(octanol)0.5(pyrene)].7.25H2O;

PUKPIU; UR98

19.326

15.922

1778

[1.5(cyclohexanol)0.5(pyrene)].5.25H2O;

PUKPOA; UR98

19.254

15.914

1767

[0.5 ((Z)-9-dodecen-1-ol)]9.6H2O0.5C2H5OH

ZUZXOH; MMH96

19.238

15.790

1752

0.5[C13H26O2].9.8H2O Tridecanoic acid

SOBHUM, 01, 02; MPAM00

19.363

15.937

1799

0.5[C14H26O2].97.5H2O (Z)-Tetradec-7-enoic acid

SOBJEY, 01, 02; MPAM00

19.316

15.936

1788

0.5(-naphthyloxyacetic acid)

ODEJOW; KYMM01

19.341

15.975

1801

Poly(tris(ethylene glycol))8H2O

BEZLAT; REFER; 173K

18.726

15.398

1653

C42H70O351.625(C3H6O)13H2O Poly(trimethylene oxide)13H2O C42H70O351.625(C3H6O)13H2O Poly(propylene glycol)13H2O 0.3(ethanol)12 H2O

KMK00 110K

19.369

15.983

1796

KMK00 110K

19.332

15.961

1880

AC03b

19.292

15.884

1785

1.5(C9H6O2)12 H2O; coumarin

GOSQOU; BAC99

19.322

24.42 109.6 24.33 108.9 24.56 109.5 24.49 109.8 24.450 108.72 24.441 109.00 24.467 109.47 24.477 109.52 24.597 108.55 24.564 108.98 24.632 108.77 24.475 110.48 24.540 108.92 24.572 109.00 24.691 109.35 24.641 106.76

16.050

1829

6-methylcoumarin

BAS00

19.210

7-methylcoumarin

BAS00

19.348

7-methoxycoumarin

BAS00

20.058

Butyrophenone11.5H2O

DGPOO; BS00

19.352

Valerophenone11H2O

DOGPUU; BS00

19.339

Cloﬁbric acid Trans-cinnamic acid

CBM01 (not seen) XERTET; KMM00

19.422

4,7-dimethylcoumarin. 17H2O#

MASBAJ; BAS00

19.513

1,2-bis(4-aminophenyl)ethane12.35H2O

GYM03

19.319

[C10H11NO3]14.2H2O (diacetamate) (Z ¼ 8)

D99

19.275

[C8H15N7O2S3]10.5H2O (famotidine) (Z ¼ 8)

D99

37.72

¤ #

24.600 109.46 24.582 109.84 24.441 109.84 24.599 109.38 25.581 109.08 24.461 108.65 24.024 104.49 24.19 103.92 24.187 109.12 15.50 102.2

15.726

1752

15.784

1765

15.662

1806

15.916

1787

16.010

1871

15.941

1794

18.414

1862

33.315

1889

34.289

1888

26.91

1922*

The ibuprofen complex is isomorphous (Brown, 1997). Structure not yet determined. cf. MASBIR, MASBOX for other substituted coumarins.

References: BAC99 – Brett, Alexander, Ckark, Ross, Harbison and Stezowski, 1999; BAS00 – Brett, Alexander and Stezowski, 2000; BHN83 – Betzel, Hingerty, Noltemeyer, Weber, Saenger and Hamilton, 1983; BS00 – Brett and Stezowski, 2000; CBM01 – Caira, Bourne and Mvula, 2001 (not seen); CD00 – Caira and Dodds, 2000; D99 – Dodds, 1999; GYM03 – Giastas, Yannakopoulou and Mavridis, 2003; HS82 – Hamilton and Sabesan, 1982; HSS81 – Hamilton, Sabesan and Steinrauf, 1981; HSV68 – Hamilton, Steinrauf and Van Etten, 1968; KR91 – Klingert and Rihs, 1991b; KMM00 – Kokkinou et al., 2000; KYMM01 – Kokkinou, Yannakopoulou, Mavridis and Mentzafo, 2001 LdR84 – Le Bas, de Rango, Ryanek and Tsoucaris, 1984; MPAM00 – Reported as triclinic by Makedenopoulou et al (2000) and corrected to monoclinic by Marsh et al. (2002); MHT91 – Mavridis, Hadjoudis and Tsoucaris, 1991; MMH96 – Mentzafos, Mavridis and Hursthouse, 1996; NS80 – Noltemeyer and Saenger, 1980; RLVT96 – Rysanek et al., 1996; RM94 – originally given as triclinic by Rontoyianni and Mavridis (1994) and corrected to monoclinic by Herbstein and Marsh (1998); UR98 – Udachin and Ripmeester, 1998; UWR00 – Udachin, Wilson and Ripmeester, 2000.

110

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Octanol

Pyrene

Octanol

Fig. 4.15. The tunnel (CH) structure of {-CD[0.75octanol0.5pyrene]7.25H2O} viewed approximately along [010]. The hydrogen-bonded -CD head-to-head dimers are clearly visible, the pyrene is in a hydrophobic site between the molecules of the dimer, and the octanol molecule, whose OH and methyl ends could not be distinguished, extends between dimers. Note that here, and in Fig. 4.16, the tunnel axis runs horizontally and not, as is more usual in such diagrams, vertically. (Reproduced from Udachin and Ripmeester, 1998.)

w

c sin b

A– b

B A⬘

Fig. 4.16. A schematic representation of the molecular packing of the head-to-head dimers in {-CD[ p-ethylaniline]16H2O} (CDETAN) seen along [100]. A and B represent the crystallographically independent -CD molecules and the solid circles the water molecules. The guest molecules, enclosed within the macrocyclic rings, are not shown explicitly. This is an example of the screw tunnel (SC) structures listed in Table 4.13. (Reproduced from Tokuoka, Fujiwara and Tomita, 1981.)

arrangement is found when the guest is the S-( þ ) enantiomer. The -CD complexes with (R,S)- (Hamilton and Chen, 1988b), R-( )-(Hamilton and Chen, 1988a) or S-( þ )fenoprofen (Hamilton and Chen, 1988a) present a somewhat different picture; although isomorphous (Table 4.13) there are differences in cell dimensions and water content. This is in accord with the fact that these complexes are diastereoisomers. In the R-( ) complex the guests are in a head-to-head arrangement while in the S-( þ ) complex there is a head-to-tail arrangement. The complex with (R,S) guests actually has a S : R ratio of 3 : 1, showing that there has been a pair of S guests in head-to-tail arrangement, or a pair of

-CYCLODEXTRIN AS HOST

111

Table 4.15. Crystal data for the isomorphous group of -CD tunnel inclusion complexes with a chessboard (CB) structure; compositions as in Table 4.10. The space group for this group is C2221, with eight formula units in the unit cell Guest and water content

Refcode/reference

a

b

c

V/FU

[benzil] (water content not speciﬁed [phenylethylmalonic acid] (water content not speciﬁed) [1-hydroxymethyl-adamantane] 11H2O trans-{Pt(PMe3)Cl2(NH3)] 5.5H2O [C11H16O]10H2O (4-tert-butylbenzyl alcohol) 2-aza-5-hydroxy-adamantane 10.5 H2O [2-methyl-2,4-pentanediol] 11.5H2O [C10H14O]13H2O (m-t-butylphenol), Z ¼ 16; probably a superstructural version. [C8H8O2Hg]12H2O phenylmercuric acetate, space group P22121, Z ¼ 4

DEVTON; MM91

19.58

24.00

32.84

1929

DEVTUT; LBdR84

19.09

24.27

32.58

1887

FASXUS; H85

19.16

24.27

32.58

1894

GIPFEQ; ASS88

19.43

24.08

32.50

1901

KOFJEU; MM91

19.196 24.393 32.808 1920

MECQUK; BGKB00 19.144 23.950 32.670 1872 TECYIJ; ZTK96

19.69

24.13

36.61

2174

QQQAFM; HSV68

19.15

24.33

62.78

1828

QQQAFD; HSV68

17.66

11.45

32.74

1655

References: ASS88 – Alston, Slawin, Stoddart, Williams and Zarycki, 1988; BGKB00 – Bobek et al., 2000; H85 – Hamilton, 1985; HSV68 – Hamilton, Steinrauf and Van Etten, 1968; placed here because of possible relationships with cell dimensions of other complexes in this table. LBdR84 – Le Bas, de Rango, Ryanek and Tsoucaris, 1984; MM91 – Mentzafos, Mavridis, Le Bas and Tsoucaris, 1991; ZTK96 – Zhukhlistova, Tischenko, Kuranova, Vainshtein, Mattson and Korpella, 1996;

R guests in head-to-head arrangement. Thus structural features of the diastereoisomers are copied to the pseudo-racemate. 4.3.2.2 An overall structural description Mentzafos et al. (1991) have shown that it is possible to transform the unit cells of the various groups of isomorphous complexes to a partially common measure. Thus the unit cells of the intermediate group (IM, Table 4.12) transform to a (non-standard) cell ˚ , ¼ 98.7, ¼ 116.3, ¼ 89.8 . The screw tunnel (SC; with a ¼ 19.2, b ¼ 24.2, c ¼ 18.1 A Table 4.13) structures can also be transformed to cells with dimensions approximately ˚ , ¼ 90.6 , space group P21 (here the unique monoclinic a ¼ 19.3, b ¼ 23.9, c ¼ 32.5 A axis is [001]). Similar results can be obtained for the ﬁrst (triclinic) group of tunnel structures (Table 4.11), and it will immediately be noticed that the orthogonal a and b axes in the C2 (CH; Table 4.14) and C2221 (CB; Table 4.15) groups have similar values. Thus ˚ 2; the invariant packing unit in all these structures is a C-centred layer with an area of 460 A there is a pseudo-close-packed (or hexagonal) arrangement of -CD dimers, with each dimer ˚ and four others at 15.4 A ˚ ( ¼ 0.5 [(192 þ 242)1/2]). surrounded by two others at 19.3 A

112

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

CH mode

SC mode

CB mode IM mode

Fig. 4.17. Schematic view of the packing of -CD dimers. In the upper part of each of the various modes each -CD monomer is represented by a heptagon of O4 atoms. In the lower part the lateral displacement between two consecutive -CD dimers is shown with each heptagon representing a -CD dimer. (Reproduced from Giastas et al. (2003)).

The four packing modes shown in Fig. 4.17 have been clearly described by Giastas et al., (2003; p. 296): ‘‘ . . . All have the common feature that they consist of close-packed layers of -CD dimers and are generated by the two-dimensional invariable layers’ different relative positioning. In the CH mode the dimer’s sevenfold axis forms an angle of approximately 10 with the stacking axis. The two-dimensional layers stack in parallel so that the dimers align almost on top of each other to form channels, slightly deformed in the interface between dimers (interdimer interface). The channels are hydrophobic and the guests inside them are shielded from the water environment. The lateral displacement ˚ . On the contrary, in CB of two consecutive -CD dimers along the channel is 2.7 A ˚ , every dimer mode the lateral distance between two dimers of successive layers is 8.9 A being surrounded by solvent molecules. The primary faces and therefore the guest are exposed to the polar environment of water molecules and neighbouring hydroxy groups. The dimer’s sevenfold axis forms an angle of approximately 10 with the stacking axis, but the two-dimensional layers are related by a twofold screw axis and

-CYCLODEXTRIN AS HOST

113

they are not parallel (dihedral angle of 20 ). In the IM mode, a case between the CH and CB modes, adjacent layers are parallel but the dimer’s sevenfold axis forms an angle of approximately 20 with the stacking axis. Consequently, dimers are far from ˚ (the inner diameter of the primary exactly aligned, their lateral displacement being 6 A face of -CD). Thus, a breaking of the channel is observed that leaves parts of the guests free to interact with hydroxy groups of adjacent hosts, as well as with water molecules. Finally, in the SC mode, although the lateral displacement between two ˚ as in the CH mode, the dimer’s consecutive -CD dimers along a channel is only 2.7 A sevenfold axis forms an approximate angle of 10 with the stacking axis but the two-dimensional layers are related by a twofold screw axis and they are not parallel, therefore the guests interact with water molecules and hydroxy groups of adjacent host channels. The guest(s) emerging from the two primary faces of the dimer, is (are) situated between the previously mentioned practically invariant layers and therefore plays a crucial role in the packing. . . . ’’ The important role of the guests in determining the arrangement of the layers was illustrated (Makedonopoulou and Mavridis, 2000) by comparing the structures of -CD dimer complexes containing long aliphatic monocarboxylic and ,!-dicarboxylic acids with host : guest ratio 2 : 1; one dimer is threaded by one molecule of a long guest. Aliphatic monoacids with 12–16 C atoms induce tunnel packing (CH; Table 4.14) while aliphatic diacids with 10–16 C atoms have an intermediate packing mode (IM; Table 4.12). Their suggestion is that ‘‘ in the case of the aliphatic monoacids the hydrophobic end of the amphiphilic guests inﬂuences the packing towards the channel [CH] mode in order to protect that part of the guest from the polar aqueous environment that surrounds the dimers. The carboxyl groups, found entrapped in the hydrophobic channel, self-associate forming carboxylic dimers and thus stabilizing the whole system. In contrast, in the case of the diacids the two polar ends of the guest are free to interact with the solvent environment.’’ The number of water molecules per -CD ranges from 7.5 (biphenyl) to 13.4 (1-adamantanecarboxylic acid), spread over 12–16 sites. Although the water molecules have high displacement factors, indicating disorder and appreciable thermal motion, Tsoucaris and coworkers (Mentzafos et al., 1991) deduced that there does exist a quasiinvariant water network organized in layers. There are two separate subnetworks, in one there is hydrogen bonding of water to primary hydroxyls and in the other to secondary hydroxyls. These networks make an important contribution to the overall cohesion of the crystal because there are few direct hydrogen bonds between dimers. Between one and three waters are linked only to other waters (the so-called secondary hydration sphere). There is evidence from the displacement factors that the waters are more tightly linked than the guest molecules. The disposition of the guest molecules depends on their nature – on their size and where the hydrophobic and hydrophilic groups are located and how these interact with the -CD hosts and water molecules. The overall resemblances between the different structures in this family have been demonstrated; the differences, small and not-so-small, derive from the detailed nature of the host–guest interactions, and those involving water molecules. In contrast to the -CD complexes, where only about two-thirds of the structures fall into isostructural or isomophous groups, most of the -CD complexes ﬁt into one of the categories given in the above Tables.

114

4.3.3

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Exceptional -cyclodextrin structures

There are, at the time of writing, three other -CD structures that do not ﬁt into the classiﬁcation scheme described above. The ﬁrst is {-CD[C14H10Cl2NO2]Naþ 11H2O}, where [C14H10Cl2NO2]Na þ is the sodium salt of the anti-inﬂammatory agent diclofenac, 2-[(2,6-dichlorophenyl)amino]benzeneacetic acid (Caira, Grifﬁth, Nassimbeni and van Oudtshoorn, 1994a (HEHJEJ); Caira, Grifﬁth and Nassimbeni, 1998; ˚ (this is MANNOE). The space group is P61, with Z ¼ 6, a ¼ 15.956(8) and c ¼ 50.95(1) A the ﬁrst -CD complex found with a hexagonal space group although there are a number of -CD complexes with hexagonal space groups (Table 4.3)). The units of the complex are arranged in a regular head-to-tail fashion about the 61 axis, which is approximately normal to the mean plane of the -CD ring. The guest molecules are inserted between the hosts; Caira et al. describe this as the formation of ‘‘an endless helical host channel with a ˚ .’’ Formation of -CD dimers is presumably inhibited because the 2,6pitch of 51 A dichlorophenyl groups are too bulky to enter the tori of the -CD molecules. The second is {-CD[C14H10Cl2NO2]Naþ16H2O}, where [C14H10Cl2NO2]Naþ .is the sodium salt of the anti-inﬂammatory agent meclofenamate, 2-[(3-methyl-2,6dichlorophenyl)amino]benzoic acid; the crystals are orthorhombic, space group P212121, ˚ (Caira, Grifﬁth and Nassimbeni, with Z ¼ 4, a ¼ 15.087(2), b ¼ 17.967(2), c ¼ 20.634(4) A 1998; MANNOE). The crystal structure has some resemblances to those of the complexes of per-trimethyl--CD (next paragraph). The third is {-CD[0.5(C13H22N4O3S)] 12.5H2O}, where the guest is ranitidine; the crystals are orthorhombic, space group P212121, with Z ¼ 4, ˚ (Dodds, 1999). The structure is not known. a ¼ 15.10, b ¼ 15.37, c ¼ 37.03 A

4.3.4

Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes

-Cyclodextrins chemically modiﬁed by methylation have advantages as pharmaceutical carrier molecules over the parent compound because of higher aqueous solubility and greater protection against hydrolysis both in solution and the solid state. The chemically modiﬁed -cyclodextrins whose inclusion complexes have been studied crystallographically are heptakis(2,6-di-O-methyl)--CD (C56H98O35, abbreviated as per-dimethyl--CD) and heptakis(2,3,6-tri-O-methyl)--CD (C63H112O35, abbreviated as per-trimethyl--CD). In per-dimethyl--CD the O(3) hydroxyl groups form O(3)˚ and the H . . . O(2) intramolecular hydrogen bonds with an average length of 2.85(3) A macrocycle has a round and nearly symmetrical structure rather like that of the parent -CD. Five crystal structures have been reported for complexes with per-dimethyl-CD as host; the cell dimensions (Table 4.16) show that there are three different structural arrangements. The conformation of the host molecule in the adamantol complex is reported to be similar to that of -CD in its complexes but the nature of the packing was not described. The isomorphous pair of p-iodophenol and p-nitrophenol complexes have clathrate structures in which, remarkably, the organic guests are located between the host molecules and only the water molecules are included within the tori (Fig. 4.18). The carmofur (1-hexylcarbamoyl-5-ﬂuorouracil) complex has the guest disordered between two sites, with the hexyl group of one guest inserted into the torus from the secondary hydroxyl side, while the other guest is located between host molecules. The only other example of intercalation of a guest between CD hosts is

-CYCLODEXTRIN AS HOST

115

Table 4.16. Crystal data for clathrate inclusion complexes with per-dimethyl--CD as host Guest and water content

Refcode/reference

a

b/

c

V/FU

13.821 13.976 14.163 14.797 14.779 15.463 14.163 24.21 11.080

17.424 20.763 20.828 18.853 18.965 18.922 23.096 19.33 14.932

29.610 28.807 29.261 28.989 28.741 27.852 27.641 18.27 44.906

1783 2090 2158 2022 2014 2037 2260 2138

14.278

15.731

31.149

1749

Group II. Space group P21; Z ¼ 2 [C11H15O3N3F]3H2O; carmofur SAJPOI; HHUET88

15.70

15.95

2014

2H2O

CEQCUW; ASLH99

15.241

23.324

1851

0.5 (acetic acid)1.5 H2O

NITSIS; SN97

15.165

18.53 106.6 10.639 101.80 10.613 102.02

23.188

1825

Group I. Space group P212121 (Z ¼ 4) Anhydride ZULQAY; StSa95a 14.7H2O (at 100K). BOYFOK03; SPHG01. 14.7H2O (at 300K). BOYFOK04; AHSRS00 DEZMOK10; H88 6H5O[IC]2H2O; p-iodophenol DEZMIE10; H88 [ p-nitrophenol]2H2O [C11H8O2]3H2O; 2-naphthoic acid WAGHAN; H93, 99 Prostaglandin PGF2 BOYCAX; SCE81 BEFJOL; CES81 [adamantol]12H2O (at 120K) m-cresol acetate COFLOY; PG84 Cloﬁbric acid CBM01 (not seen) CH3CN2H2O AHSRS00a

References: AHSRS00a – Aree, Hoier, Schultz, Reck and Saenger, 2000a; ASLH99 – Aree, Saenger, Leibnitz and Hoier, 1999; CBM01 – Caira, Bourne and Mvula, 2001 (not seen); CES81 – Czugler, Eckle and Stezowski, 1981; H88 – Harata, 1988; H93 – Harata, 1993; thermal motion of the guest has been analyzed (H99 Harata, 1999); HHUET88 – Harata, Hirayama, Uekama and Tsoucaris, 1988; PG84 – Pohlmann, Gdaniec, Eckle, Geiger and Stezowski, 1984; SCE81 – Stezowski, Czugler and Eckle, 1981; SN77 – Selkti et al., 1997; SPHG01 – Stezowski, Parker, Hilgenkamp and Gdenic, 2001; StSa95a – Steiner and Saenger, 1995a.

o

b

a

Fig. 4.18. A schematic diagram of the crystal structure of the isomorphous complexes of the perdimethylated--CD and p-iodophenol or p-nitrophenol, showing the water molecules included in the tori and the guest molecules located between the hosts. (Reproduced from Harata, 1988.)

{-CD[m-nitrophenol]m-nitrophenol6H2O} (see Table 4.4). No explanation has yet been advanced for these exceptional arrangements. An interesting serendipitous result was obtained when postulated per-dimethyl -CD was complexed with synthetic (hence racemic) 1,7-dioxaspiro-[5.5]undecane, which is the

116

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

Table 4.17. Crystal data for the tunnel inclusion complexes with per-trimethyl--CD as host; space groups P212121 with Z ¼ 4 Guest and water content

Refcode; reference

a

b

c

V/FU

Uncomplexed monohydrate

HEZWAK; CGN94b, SS98 GELKEN10; HHA92 RONWOG; BCNO96 CAMPIP; HUOH83 PAFSOE; HHA92 ZIFQOU; CGN94/5 COYXET20; HUI88 COYXAP10; HUI88 PINMAA; MMS94 QOYLIZ; MYM01 XAQJII; RMIB98, CP01 NIZHAF; CGNO96 MODHUI; CP01 CBM01 (not seen) BEYLOG; HUOH82a

14.823

19.382

26.534

1902

15.67

20.80

25.49

2077

15.232

21.327

27.597

2241

15.00

21.37

28.21

2261

14.890

21.407

28.540

2275

15.18

21.41

27.67

2248

15.271

21.451

27.895

2284

15.092

21.714

28.269

2316

14.796

22.444

27.720

2301

10.936

25.530

29.640

2069

11.149

25.664

29.427

2105

11.060

26.138

29.669

2144

11.190

26.080

29.185

2129

11.440

23.674

13.531

1831

[C6H5IO] m-iodophenol [C13H18O2] (S)-ibuprofen [C6H5OI]4H2O p-iodophenol [C14H12O2]H2O 4-biphenylacetic acid [C14H14O3](S)-naproxen* [C15H13O2F] (S)-( þ )-Flurbiprofen [C15H13O2F]H2O (R)-( )-Flurbiprofen [C14H28O2]2H2O ethyl laurate [S]-1,7-dioxaspiro-[5.5] undecane0.57 H2O methylcyclohexane (L-menthol]2H2O (248K) (R)-5-ethyl-1,3,5-trimethylhydrantoin Cloﬁbric acid p-iodoanilineH2O

* (S)-6-methoxy--methyl-2-naphthaleneacetic acid. References: BCNO96 – Brown, Caira, Nassimbeni and Oudtshoorn, 1996 CBM01 – Caira, Bourne and Mvula, 2001 (not seen); CGN94/5 – Caira, Grifﬁth, Nassimbeni and van Oudtshoorn, 1994/5; CGN94b – Caira, Grifﬁth, Nassimbeni and van Oudtshoorn, 1994b; CP01 – Cardinael et al., 2001; HHA92 – Harata, Hirayama, Arima, Uekama and Miyaji, 1992; HUI88 – Harata, Uekama, Imai, Hirayama and Otagiri, 1988; HUOH82a Harata, Uekama, Otagiri and Hirayama, 1982a; HUOH83 Harata, Uekama, Otagiri and Hirayama, 198a, b; MMS94 – Mentzafos, Mavridis and Schenk, 1994; MYM01 – Makedonopoulou, Yannakopoulou et al., 2001; RMIB98 – Rontoyianni, Mavridis, Israel and Beurskens, 1998; SS98 – Steiner and Saenger, 1998.

major component of the pheromone of the olive fruit ﬂy; the guest is a volatile liquid at room temperature (cf. Table 4.11). Structure analysis of the triclinic crystals (P1, Z ¼ 1; Rysanek, Le Bas, Villain and Tsoucaris, 1992; JOSWOD), which contained also a methanol molecule, showed that the host was in fact 2a,2b,2c,2d,2e,2f,3a,3g,6a,6b,6c,6d,6e,6f,6g-pentadeca-O-methyl--cyclodextrin. Thus

ROTAXANES AND CATENANES OF CYCLODEXTRINS

117

ﬁve rings had been 2,6-dimethylated, ring A trimethylated and ring G 3,6-dimethylated; the overall formula of the complex was {C57H100O35[C9H16O2]CH3OH}. The guest was totally enclosed within the macrocycle and resolution had occurred on crystallization, as only the S-enantiomer was found. The uncomplexed per-trimethyl--CD monohydrate and the anhydrous m-iodophenol complex (ﬁrst two in Table 4.17) have cell dimensions which are related to those of the following six, but nevertheless are signiﬁcantly different. In the monohydrate, the pertrimethyl--CD macrocycle has six rings in the 4C1 conformation, while G2 is in the unusual 1C4 conformation; in the m-iodophenol complex one trimethylglucose unit adopts the uncommon 0S2 high-energy skew-boat conformation, intermediate between 4C1 and 1 C4. These conformational differences must be taken into account in any assessment of the energetics of complexation. The other fully methylated complexes shown in Table 4.17 are essentially isostructural despite differences in water content, and have a tunnel structure with stacking of head-to-tail host molecules along [010]; however, adjacent molecules in the stack are shifted laterally so that the stack axis is zigzag rather than straight. In all these complexes the host molecule is considerably distorted from the regular, round shape of -CD itself towards an elliptical cross section because intramolecular hydrogen bonds cannot be formed and because of the steric hindrance of the methyl groups; the phenyl ring of the guest is within the cavity, with the phenolic OH protruding and hydrogen bonded to two water molecules. The fully methylated host does not form a complex with racemic ﬂurbiprofen but instead separate complexes are formed with R- and S-ﬂurbiprofen. The ﬂurbiprofen guests in the fully methylated complexes have a head-to-tail arrangement in contrast to the head-to-head arrangement found in their -CD complexes (Section 4.3.2). The enantiospeciﬁc separation of the enantiomers of the racemic olive ﬂy pheromone 1,7-dioxaspiro[5.5]undecane [] by complexation of the (R)-enantiomer with hexakis(pertrimethyl)--CD and of the [S]-enantiomer with heptakis(pertrimethyl)--CD has already been noted. The binding constants of the two complexes determined by NMR in aqueous solution are respectively 6600 M-1 for the (R)-enantiomer – hexakis (pertrimethyl)--CD complex and 935 M-1 for the [S]-enantiomer – heptakis (pertrimethyl)--CD complex. These differences can be explained by the details of the interactions between enantiomer and cyclodextrin in the respective pairs.

4.4 Rotaxanes and catenanes of cyclodextrins As noted earlier, these compounds, reviewed by Nepogodiev and Stoddart (1998), straddle the borders of present relevance; we consider only those compounds where crystal structures have been reported. Pseudorotaxanes of composition {2(-CD)[1,12diaminododecane]14 H2O)} (Rontoyianni and Mavridis, 1999; BOLVUT) and {2(CD)[12-diaminododecanoic acid]0.6(ethanol)14.4H2O} (Eliadou et al., 1999; VEHQAA) have the long-chain molecules threaded through the torus of head-to-head -CD dimers; the complexes are not isomorphous. These are true complexes in our present sense. Some other examples are probably out-of-bounds. It has been contended that cyclodextrins require chemical modiﬁcation by replacement of hydroxyl by bulky substituents

118

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

in order to behave as useful models for enzymes. This has been done for -CD by monosubstitution of an hydroxyl by a bulky hydrophobic group; speciﬁcally, among the substituents used have been t-butyl-thio (Hirotsu, Higuchi, Fujita, Ueda, Shinoda, Imoto and Tabushi, 1982), phenylthio (Kamitori, Hirotsu, Higuchi, Fujita, Yamamura, Imoto and Tabushi, 1987) and –CH2NH(CH2)6NH2 (Dimitrius, Terzis, Coleman and de Rango, 1996). Unsymmetrical disubstitution has also been used to give 6A,6D-deoxy-6A-(tbutylthio)--CD (Fujita, Matsunaga, Imoto, Hirotsu, Kamitori and Higuchi, 1987). Crystal structure analysis shows that these are all self complexes, in which the -CD portion of the molecule acts as host and the substituent as guest, the substituent on one host being enclosed within the macrocycle of an adjacent molecule. O

O

O

O

NH O

per-dimethyl-b-CD O O

O

O

O

NH

bislactam

Scheme 4.4

The 2-catenane of heptakis(2,6-di-O-methyl)--CD and a macrocyclic bislactam (Armspach, Ashton, Moore, Spencer, Stoddart, Wear and Williams, 1993; YAPSEN) resembles more the 2-catenane shown in Fig. 3.9 than it does the -CD clathrate and tunnel inclusion complexes described above; thus Fig. 3.9 gives a better impression of the molecular shape than the schematic diagram shown above. Again we have crossed the border.

4.5 4.5.1

-Cyclodextrin as host

-Cyclodextrin as host in clathrate inclusion complexes

The structure of {-cyclodextrin[nH2O]} (-CD is C48H80O40) has been determined in three separate studies and a comparison is illuminating. The reports agree in regard to the overall structure, which is of the cage type and resembles the -CD cage structures; the -CD molecules are stacked along [010]. However, small differences in water content and cell dimensions were reported (Table 4.18), as well as differences in the distribution of water molecules in the unit cell. Another difference is that CYOCAM has one of the glucose residues disordered (even though the measurements were made at 120 K) while the macrocycle is completely ordered in CIWMIE10. Similar minor differences in crystals from different batches have been encountered with -CD complexes (Fujiwara, Yamazaki, Tomizu, Tokuoka, Tomita, Matsuo, Suga and Saenger, 1983; Steiner, 1990) and in

-CYCLODEXTRIN AS HOST

119

Table 4.18. Comparison of crystal data reported in determinations of the crystal structure of hydrated -CD. The complexes crystallize in space group P21 with Z ¼ 2 Water content, and temperature

Refcode; reference

a

b/

c

V/FU

[17 H2O] (at 120K)

CYOCAM; MS80

20.253(8)

16.892(6)

1731

[14 H2O] (at 300K)

CIWMIE10; H87

20.271(2)

16.847(2)

1831

[11 H2O] (at 300K) ND

CIMSAS; HBS84

20.287(10)

10.494(5) 105.32(1) 11.098(2) 104.97(1) 22.079(7) 105.07(4)

16.858(12)

1823

References: HBS84 – Hingerty, Betzel and Saenger, 1984; MS80 – Mclennan and Stezowski, 1980; H87 – Harata, 1987.

{-CD[n-propanol]17H2O} (see below). These differences presumably reﬂect real differences between the samples used (often in the detailed nature of low-occupancy water sites) and point up the need for caution in discussing the ﬁne details of complicated chemical and crystal structures. 4.5.2 -Cyclodextrin as host in tunnel inclusion complexes In addition to the cage structures (only one example to date) there is a group of almost isomorphous tunnel structures (Table 4.19). The crystal structure of these tetragonal crystals deserves special comment, as has been emphasized by Steiner and Saenger (1998a) who discuss the overall packing and the rarity of space group P4212 especially among organic structures (0.006% of those listed in the Spring 1997 update of the Cambridge Structural Database). The crystal structure of {-CDn-propanol17H2O} (this is the ‘‘formula unit’’) has been described in detail by Ding, Steiner and Saenger (1991), who also compare results obtained for two different crystals of the n-propanol complex (SIBJAO, SIBJES). We describe the family of structures in overall terms, starting with the ﬁrst four entries in Table 4.19. There are 6 formula units in the unit cell, with three crystallographically-independent -CD molecules stacked one above the other along [001] in Wyckoff positions (c) at 0, 1/2, z etc. (three different values of z). The asymmetric unit consists of three groups of two adjacent (linked) glucose rings, with each -CD molecule being obtained by the operation of the fourfold axis on the appropriate pair of glucose rings. Successive -CD molecules in a stack are hydrogen bonded in a sequence of head-to-head (A–B), tail-to-tail (B–C) and head-to-tail (C–A) interactions (A, B, C refer to succeeding molecules up the [001] axis in Fig. 4.19; this ABC notation is not standardized and we follow Steiner and Saenger (1998) in their Fig. 3, but not in their usage of ‘‘head’’ and ‘‘tail;’’ for our usage see Fig. 4.2 and footnote on p. 79)). The headto-head pair corresponds to the dimer found in some -CD and, particularly, in -CD tunnel inclusion complexes (see, for example, Fig. 4.16). The water and alcohol molecules are contained, in a disordered fashion which varies from crystal to crystal, both within the -CD tori, and in the columnar interstitial spaces between the -CD molecules (Fig. 4.19). Now consider what happens when -CD is crystallized from a solution of 12-crown-4, as

120

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

was ﬁrst done by Vo¨gtle and Mu¨ller (1979). Crown ether complexes are obtained which are essentially isomorphous with the ﬁrst group of four (Kamitori, Hirotsu and Higuchi, 1986). The 12-crown-4 (CREt) molecules are enclosed within the heads of the -CD molecules; thus the sequence along [001], shown in the left hand column of Fig. 4.20, has no enclosed CREt when the -CDs are juxtaposed tail-to-tail, single CREt molecules when the contact is tail-to-head, and a pair of CREts when the contact is head-to-head. The crown ether molecules are not disordered because they have intrinsic fourfold symmetry. Successive crown ether molecules in a stack are mutually rotated, with the angles between the pairs A/B, B/C and C/A 9.8, 11.2 and 21.0 (the zero sum is required to maintain translational symmetry). When crystallization is carried out in the presence of the salts LiSCN or KCl (Kamitori, Hirotsu and Higuchi, 1987), the pair of CREts contains the cation as {(CREt)Mþ(CREt)]} and this arrangement is also found with NaCl (Kamitori, Hirotsu and Higuchi, 1988); thus the crown ethers are present as neutral molecules and in (12-crown-4)2Mþ complexes. Rb does not form an analogous complex; NH4þ does not appear to have been tried. The anions are located, together with the waters, in the interstitial tunnels between the columns of -CD molecules. All these complexes, with their wide tunnels, lose solvent very easily.

Table 4.19. Crystal data (at room temperature) for some nearly isomorphous tetragonal tunnel inclusion complexes of -CD; space group P4212; Z ¼ 6. The compositions are given as {-CD[x(guest)nH2O} Guest and water content

Refcode; reference

a

c

V/FU

CH3OH C2H5OH n-C3H7OH17H2O

NUNRIX; SS98

23.808(4) 23.823(9) 23.840(5)

23.140(3) 23.227(5) 23.227(6)

2170(1) 2193(1) 2200(1)

23.805(2) 23.808(2) 23.75(2) 23.842(2) 23.816(4) 23.824(1) 23.77 23.80 23.82 23.37

23.196(7) 23.175(2) 22.92(2) 23.132(2) 23.072(3) 23.083(1) 23.15 23.22 23.21 23.91

2182(1) 2189 2155 2192 2181 2184 2181 2192 2195 2176

C6H5CH2OH C8H16O4*9H2O C8H16O4*1/3(LiSCN)7.7H2O C8H16O4*1/3(KCl)9H2O C8H16O4*1/3(NaCl)7.7H2O [1/3(C18H22N2)16.4H2O (cyclizine)# [2/3(C10H16N6S)14.7H2O (cimetidine) [2/3(C8H15N7O2S3)18.7H2O (famotidine) [2/3(C13H22N4O2S)16.3H2O (ranitidine) Polyethylene glycol Cloﬁbric acid

CYDXPL, LS80; SIBJAO, SIBJES, DSS91 DOCYID; KHH86 FEJFIJ; KHH87 FEJFOP; KHH87 SAJNAS; KHH88 D99 D99 D99 D99 UWR00 CBM01 (not seen)

* 12-crown-4 (CREt) References: CBM01 – Caira, Bourne and Mvula, 2001 (not seen); D99 – Dodds, 1999DSS91 – Ding, Steiner and Saenger, 1991; KHH86 – Kamitori, Hirotsu and Higuchi, 1986; KHH87 – Kamitori, Hirotsu and Higuchi, 1987; KHH88 – Kamitori, Hirotsu and Higuchi, 1988; LS80 – Lindner and Saenger, 1980; SS98 – Steiner and Saenger, 1998; water content not given speciﬁcally, but it must be close to 17 H2O; UWR00 – Udachin, Wilson and Ripmeester, 2000.

-CYCLODEXTRIN AS HOST

N

N

121

CH3

Cyclizine

Scheme 4.5

Now consider the tetragonal 3 : 1 -CD cyclizine structure. The guest is incorporated into the space between the molecules of the head-to-head dimer, with one guest molecule for each repeat of three -CD molecules up the [001 axis. The cyclizine is disordered in a number of ways – ﬁrstly, the piperazine ring can point either up or down, secondly, the cyclizine molecule as a whole can take up one of the four rotationally equivalent positions. There is not enough room within a stack for incorporation of a second cyclizine. However, the tetragonal complexes of -CD with the smaller cimetidine, famotidine and ranitidine guests have 3 : 2 compositions (Table 4.19). Full structure analyses were not carried out for these complexes but we may surmise that two cimetidines, etc. replace one cyclizine within the head-to-head dimer, with appropriate disorder. The crystal structures of the cimetidine, famotidine, ranitidine and cyclizine complexes are of particular interest – their isomorphism with the other -CD complexes strongly

a b

Fig. 4.19. View of part of the crystal structure of the propanol tunnel inclusion complex of -CD, seen down [001]. The symmetry elements of the space group are shown. For simplicity only the A -CD molecules (deﬁned in Fig. 4.20) are shown but this is adequate to show the arrangement of the stacks. The small circles show the water molecules within the internal tunnels of the -CD molecules, while the larger circles show the water molecules in the interstitial tunnels between the -CD molecules. (Reproduced from Ding, Steiner and Saenger, 1991.)

122

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

HEAD

CREt C

TAIL TAIL HEAD HEAD

B

B CREt C

CREt

C

A

TAIL HEAD

CREt C

TAIL TAIL

A

B

B CREt

HEAD HEAD TAIL

A

CREt 0

A

C

ab

Fig. 4.20. Schematic diagram of the arrangement of the -CD molecules in the stacks in the tunnel inclusion complexes; a slice parallel to the ð110Þ plane is shown. The heads and tails of the -CD molecules in the left-hand column are indicated. The designation ‘CREt’ shows that the 12-crown-4 molecules are included in the heads of the -CD molecule; an isolated ‘CREt’ indicates a neutral crown ether molecule, while a juxtaposed pair shows either a pair of neutral molecules or, when crystallization is carried out in the presence of LiSCN, NaCl or KCl, the cationic species {(CREt)2Mþ}. (Modiﬁed from Steiner and Saenger, 1998a.)

suggests that in fact there is only one packing mode for all -CD complexes. This could be tested by checking cell dimensions and symmetry for other -CD complexes already reported. Among these are the 15 different complexes, reported by Vo¨gtle and Mu¨ller (1979); a variety of crown ethers, cryptands, cryptates and coronates were guests, and compositions included 1 : 1, 2 : 1, 1 : 1 : 1, 1 : 1 : 2, 2 : 1 : 1 ratios. Also, crystalline 1 : 1 complexes of -CD with ferrocene, acetylferrocene and 1,1 0 -diacetylferrocene have been reported by Harada, Hu, Yamamoto and Takahashi (1988). Crystal data or structures, apart from those noted above, do not appear to have been reported. Steiner and Saenger (1998) have pointed out that the disorder in the tetragonal -CD complexes makes it difﬁcult to determine the molecular dimensions of -CD with the same precision that has been achieved for - and -CD, nor could the interactions among the moieties be deﬁned in detail. Thus caution is needed before drawing far-reaching conclusions from the limited information currently available. 4.5.3

Chemically modiﬁed -cyclodextrins as hosts in inclusion complexes

Following the trend set earlier with chemically-modiﬁed - and -cyclodextrins, a number of permethylated -cyclodextrins have been prepared, and three different hydrates studied crystallographically (Table 4.20). Octakis(2,3,6-tri-O-methyl) -cyclodextrin is C72H128O40.

CYCLIC OLIGOSACCHARIDES AS CYCLODEXTRIN ANALOGS

123

Table 4.20. Crystal data for three permethylated -cyclodextrin hydrates. The compositions are given as {(C72H128O40).nH2O}. The last host is (C48H64O32) Composition

Refcode; reference

a

2.5H2O

GIWMAA; StSa98b XERSIW; AHSRS00 BEBJAT; AU99 ZUSYOB; YM96

17.730

4.5H2O 4.8H2O Octakis(3,6-anhydro)-CD14H2O

c

V/FU

Space group; Z

16.875

32.172

2271

P212121; 4

10.788

29.058

32.291

2531

P212121; 4

28.872

18.018 98.15 10.305 123.08

33.170

2209

P21; 8

15.406

1477

C2; 2

22.200

b/

References: AHSRS00b – Aree et al., 2000b AU99 – Aree, Uson et al., 1999; StSa98b – Steiner and Saenger, 1998b; YM96 – Yamamura et al., 1996.

4.6 Larger cyclodextrins Larger cyclodextrins ( for n ¼ 9 glucose units, " for n ¼ 10 and for n ¼ 11), were ﬁrst isolated by French in 1957 (French, Pulley, Effendberger, Rougvie and Abdullah, 1965) and crystal structures have been reported for the (Fujiwara, Tanaka and Kobayashi, 1990; SIYKOA, 13.75 hydrate), " (Jacob, Gessler, Hoffmann, Sanbe, Koizumi, Smith, Takaha and Saenger, 1998; NOBBOV, 20.7 hydrate), (14; Jacob et al., 1998; NOBBUB, 27.3 hydrate) oligomers and for that with 26 glucose units (Gessler, Uson, Takaha, Krauss, Smith, Okada, Sheldrick and Saenger, 1998). Even larger cyclodextrins with 100 or more glucose units in the ring have been prepared (Takaha, Yanase, Takata, Okada and Smith, 1996). Whether inclusion complexes are formed by the larger cyclodextrins remains an open question at the time of writing (2003). The larger cyclodextrins do not have regular truncated-cone structures but are folded back upon themselves; thus guest inclusion seems unlikely. However, measurement of inclusion complexing capacity by capillary electrophoresis (Larsen, Ueda and Zimmerman, 1997) suggests that complexes may be formed by some guests. For example, the formation constant for the -CD–ibuprofen complex is 2600 M1, while corresponding values for the - and -CD ibuprofen complexes are 1013 and 225 M1 respectively.

4.7 Cyclic oligosaccharides as cyclodextrin analogs A series of novel CD analogs composed of alternating D- and L- rhamnopyranose (R) and mannopyranose (M) residues has been synthesized (Ashton, Cantrill, Gattuso, Menzer, Nepogodiev, Shipway, Stoddart and Williams, 1997), and we give some information about crystal structures that have been published (Table 4.21). 1-MM has a clathrate type structure while the other three molecules have tunnel arrangements. Although it has been mentioned that inclusion complexes are formed by

C Y C L O D E X T R I NS , A ND S OM E AN A L O G S , A S H O S T S

124

Table 4.21. Crystallographic information about cyclic oligosaccharides that may be cyclodextrin analogs n; CD analog

1R

2R

Crystal data

1-MM

3; -CD

CH2OH

CH2OH

2-RM

4; -CD

CH3

CH2OH

2-RR

4; -CD

CH3

CH3

3-RR

5; "-CD

CH3

CH3

C36H42 D18O309D2O; C2/c, Z ¼ 4 (molecules are centrosymmetric); ˚, a ¼ 28.005(2), b ¼ 9.807(2), c ¼ 20.853(2) A ˚ 3. NOHKEA ¼ 117.09(1) , V ¼ 5098.8(9) A (Ashton, Cantrill et al., 1997). 2{(C12H20O9)4}67H2O; P4, Z ¼ 1 (two independent molecules with four fold symmetry in the asymmetric unit); ˚, a ¼ b ¼ 24.200(5), c ¼ 7.918(3) A ˚ 3. TAHREZ V ¼ 4637(2) A (Ashton, Brown et al., 1996). C48H80O326Me2CO13H2O; C2/c, Z ¼ 4 (molecules have two fold axes); a ¼ 34.432(5), ˚ , ¼ 116.981) , b ¼ 7.986(2), c ¼ 31.910(3 A 3 ˚ V ¼ 7820(2) A . NOHKAW (Ashton, Cantrillet al., 1997). C60H100O406Me2CO10H2O; P1, Z ¼ 2 (two independent centrosymmetric molecules); ˚, a ¼ 15.130(6), b ¼ 19.077(5), c ¼ 20.017(5) A ¼ 72.74(2), ¼ 87.60(3), ¼ 88.60(3) , ˚ 3 NIHDIR V ¼ 5513(3) A (Gattuso, Menzer et al., 1997),

these hosts6, details have not yet been published. It does not seem too hazardous to predict that the crystallography of these inclusion complexes will prove as interesting as that of the cyclodextrins. References Alexander, J. M., Clark, J. L., Brett, T. J. and Stegowski, J. J. (2001). Proc. Nat. Acad, Sci., 99, 5115–5120. Alston, D. R., Slawin, A. M. Z., Stoddart, J. F. and Williams, D. J. (1985a). Angew. Chem. Int. Ed. Engl., 24, 786–788. Alston, D. R., Slawin, A. M. Z., Stoddart, J. F. and Williams, D. J. (1985b). J. Chem. Soc., Chem. Commun., pp. 1602–1604. Alston, D. R., Slawin, A. M. Z., Stoddart, J. F., Williams, D. J. and Zarycki, R. (1988). Angew. Chem. Int. Ed. Engl., 27, 1184–1185. Anibarro, M., Gessler, K., Uson, I., Sheldrick, G. M. and Saenger, W. (2001). Carbohydr. Res., 333, 251–256. 6 ‘‘Given the fact that these compounds share with the naturally-occurring CDs an ability to form inclusion complexes with other molecules, they could ﬁnd themselves enjoying many biomedically-directed and materialsoriented applications in the future’’ (Gattuso, Menzer, Nepogodiev, Stoddart and Williams, 1997).

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Saenger, W. (1980). Angew. Chem. Int. Ed. Engl., 19, 344–362. Saenger, W. (1984). ‘‘Structural aspects of cyclodextrins and their inclusion complexes’’ in Inclusion Compounds, edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Vol. 2, pp. 231–259, Academic Press, London etc. Saenger, W. (1985). Isr. J. Chem., 25, 43–50. Saenger, W., Beyer, K. and Manor, P. C. (1976). Acta Cryst., B32, 120–128. Saenger, W., Jacob, J., Gessler, K., Steiner, T., Hoffmann, D., Sanbe, H., Koizumi, K., Smith, S. M. and Takaha, T. (1998). Chem. Rev., 98, 1787–1802. Saenger, W., McMullan, R. K., Fayos, J. and Mootz, D. (1974). Acta Cryst., B30, 2019–2028. Saenger, W. and Noltemeyer, M. (1976). Chem. Ber., 109, 503–517. Saenger, W., Noltemeyer, M., Manor, P. C., Hingerty, B. and Klar, B. (1976). Bioorg. Chem., 5, 187–195. Saenger, W. and Steiner, T. (1998). Acta Cryst., A54, 798–805. Sanchez-Ruiz, X., Alvarez-Larena, A., Jaime, C., Piniella, J. F. Redondo, J., Virgili, A., SanchezFerrando, F., Germain, G. and Baert, F. (1999).Supramol. Chem., 10, 219–223. Schardinger, F. (1904). Wien Klin. Wochenschi, 17, 207. Selkti, M., Navazza, A., Villain, F., Charpin, P. and De Rango, C. (1997). J. Incl. Phenom. Molec. Recogn. Chem., 27, 1–12. Senti, F. R. and Erlander, S. R. (1964). ‘‘Carbohydrates’’ (Chapter 9) in Non-Stoichiometric Compounds, edited by L. Mandelcorn, Academic Press, London and New York. Shibakami, M. and Sekiya, A. (1992). J. Chem. Soc., Chem. Comm., pp. 1742–1743. Shibakami, M. and Sekiya, A. (1994). Carbohydr. Res., 260, 169–179. Sicard-Roselli, C., Perly, B. and Le Bas, G. (2001). J. Incl. Phenom. Molec. Recogn. Chem., 39, 333–337. Steiner, T. (1990). Ph. D. Thesis, Freie Univ. Berlin, Germany. Steiner, T., Hinrichs, W., Saenger, W. and Hoyer, G-A. (1989). Carbohydr. Res., 192, 43–49. Steiner, T., Hirayama, K. and Saenger, W. (1996). Carbohydr. Res., 296, 69–82. Steiner, T. and Gessler, K. (1994). Carbohydr. Res., 260, 27–38. Steiner, T. and Koellner, G. (1994). J. Am. Chem. Soc., 116, 5122–5128. Steiner, T., Koellner, G. and Saenger, W. (1992). Carbohydr. Res., 228, 321–332. Steiner, T., Koellner, G., Ali, S., Zakim, D. and Saenger, W. (1992). Biochem. Biophys. Res. Comm., 188, 1060–1066. Steiner, T., Koellner, G., Gessler, K. and Saenger, W. (1995). J. Chem. Soc., Chem. Comm., pp. 511–512. Steiner, T., Mason, S. A. and Saenger, W. (1989). Z. Krist., 186, 281–282. Steiner, T., Mason, S. A. and Saenger, W. (1991). J. Am. Chem. Soc., 113, 5676–5687. Steiner, T. and Saenger, W. (1994b). Carbohydr. Lett., 1, 143–150. Steiner, T. and Saenger, W. (1995a). Carbohydr. Res., 275, 73–82. Steiner, T. and Saenger, W. (1995b). Chem. Commun., pp. 2087–2088. Steiner, T. and Saenger, W. (1998a). Acta Cryst., B54, 450–455. Steiner, T. and Saenger, W. (1998b). Angew. Chem. Int. Ed. Engl., 37, 3404–3407. Steiner, T. and Saenger, W. (1998c). J. Chem. Soc., Perkin 2, pp. 371–377. Stezowski, J. J. (1985). Trans. Am. Cryst. AsSoc., 20, 73–82. Stezowski, J. J., Czugler, M. and Eckle, E. (1981). Proc. I. S. Cyclodextrins, p. 151. Stezowski, J. J., Jogun, K. H., Eckle, E. and Bartels, K. (1978). Nature, Lond., 274, 617–619. Stezowski, J. J., Parker, W., Hilgenkamp, S. and Gdenic, M. (2001). J. Am. Chem. Soc., 123, 3919–3926. Stoddart, J. F. and Zarycki, R. (1989). Cyclodextrins – Monographs in Supramolecular Chemistry. Royal Society of Chemistry, London. Storsberg, J., Ritter, H., Pielartzik, H. and Groenendaal, L. (2000). Adv. Mater, 12, 567–569.

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Szejtli, J. 1982). Cyclodextrins and Their Inclusion Compounds. Akade´miai Kiado´, Budapest. Szejtli, J. (1988). Cyclodextrin Technology, pp. 450. Kluwer Academic Publishers, Dordrecht. Szetjli, J. (1998). Chem. Rev., 98, 1743–1753. Szetjli, J. and Budai, Zs. (1977). Acta Chim. Acad. Sci. Hung., 94, 383–390. Szetjli, J. and Osa, T. (1996). Editors, Cyclodextrins, Volume 3 of Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Pergamon, Oxford. Tabushi, I. (1982). Accts. Chem. Res., 15, 66–72. Takaha, T., Yanase, M., Takata, S., Okada, S. and Smith, S. M. (1996). J. Biol. Chem., 271, 2902–2908. Tanaka, Y., Sakuraba, H. and Nakanishi, H. (1990). J. Org. Chem., 55, 564–567. Tokuoka, R., Fujiwara, T. and Tomita, K. (1981). Acta Cryst., B37, 1158–1160. Tokuoka, R., Abe, M. Fujiwara, T., Tomita, K. and Saenger, W. (1980). Chem. Letts., pp. 491–494. Tsoucaris, G., Le Bas, G., Rysanek, N. and Villain, F. (1987). J. Incl. Phenom., 5, 77–84. Udachin, K. A. and Ripmeester, J. A. (1998). J. Am. Chem. Soc., 120, 1080–1081. Udachin, K. A., Wilson, L. D. and Ripmeester, J. A. (2000). J. Am. Chem. Soc., 122, 12375–12376. Uekama, K. and Irie, T. (1987). In Cyclodextrins and their Industrial Uses, Duchene, D., Ed.; Editions de Sante, Paris, pp. 395–439. Uekama, K., Hirayama, F., Imai, T., Otogiri, M. and Harata, K. (1983). Chem. Pharm. Bull., 31, 3363–3365. Uekama, K., Imai, T., Hirayama, F., Otogiri, M. and Harata, K. (1984). Chem. Pharm. Bull., 32, 1662–1664. Vicens, J., Fujiwara, T. and Tomita, K. (1988). J. Incl. Phenom., 6, 577–581. Villiers, A. (1891). Compt. Rend. Acad. Sci. Paris, 112, 536–538. Vo¨gtle, F. and Mu¨ller, W. M. (1979). Angew. Chem. Int. Ed. Engl., 18, 623–624. Yamamura, H., Masuda, H., Kawase, Y., Kawai, m., Butsugan, Y. and Einaga, H. (1996). Chem. Commun., pp. 1069–1070. Yannakopoulou, K., Ripmeester, J. A. and Mavridis, I. M. (2002). J. Chem. Soc., Perkin 2, pp. 1639–1644. Zabel, V., Saenger, W. and Mason, S. A. (1986). J. Am. Chem. Soc., 108, 3664–3673. Zhukhlistova, N. E., Tischenko, G. N., Kuranova, I. P., Vainshtein, B. K., Mattson, P. and Korpella, T. (1996). Kristallograﬁya, 41, 97–108.

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Chapter 5 Crystal chemistry of some DNA oligonucleotides and their complexes

The interaction between DNA and drugs is of great importance in molecular biology and medicinal chemistry. Drugs that target nucleic acids have wide application in nucleic acid recognition, regulation of biological processes and the development of therapeutic agents against cancers and virus-related diseases. Deng, Pan and Sundaralingam, 2003 . . . and, to crown all, Kinnaird and I had to conduct Sheridan down a damned corkscrew staircase, which had certainly been constructed before the discovery of fermented liquors, and to which no legs, however crooked, could possibly accommodate themselves. Lord Byron 31 October, 1815

Summary: We start with brief introductions to the fundamentals of oligonucleotide structure and to some current aspects of crystal chemistry common to cyclodextrin complexes, tetraphenylporphyrin-metal complexes and oligonucleotides and their complexes. This is followed by an outline of the special features of X-ray crystal structure analysis as applied to oligonucleotides, including the limitations on the resolution attainable. The implicit assumption usually made that native oligonucleotides are unary (single component) phases while their complexes (intercalation and minor groove binders are the two principal types) are binary can be a useful working hypothesis but neglects the important effects of solvent and ion content. In contrast to most of the published work, where priority has been given to features of biological importance, here we stress the crystal chemical aspects of hexamer, octamer, decamer and dodecamer oligonucleotide crystals, covering both native and complexed modiﬁcations. Many of the crystal structures are, group wise, isomorphous (same crystal structures despite differences in chemical nature). Differences in base-pair sequence sometimes break the isomorphism but usually not. Other different crystal types are often found in addition to the major isomorphous families. An important problem is that the chemical compositions (solvent content, presence and number of ions) are often not known so it can be difﬁcult to decide whether particular clusters of related crystals are polymorphs (different crystal structures although the chemical compositions are the same) or have different compositions. Comparison of unit cell volumes is a useful but limited tool in making such decisions. Attempts are made to classify particular crystalline complexes in phase rule terms as primary solid solutions or phase rule compounds. There are resemblances in behavior and structural features to the cyclodextrins.

5.1 Introduction 5.2 Fundamentals of oligonucleotide structure 5.2.1 General aspects 5.2.2 Single crystal x-ray diffraction studies of oligonucleotides

134 136 136 140

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5.3

Crystal chemistry of oligonucleotides and oligonucleotide-guest structures 5.3.1 Polymorphism, isomorphism, and heteromorphism 5.3.2 Phase rule relationships 5.3.3 Applications of these concepts 5.4 Intercalated hexanucleotide-drug complexes with B-DNA structures 5.4.1 The anthracycline drugs 5.4.2 Nogalamycin and derivatives 5.4.3 The 9-aminoacridine drugs 5.4.4 Native hexanucleotides and comparison of crystal structures 5.5 Isomorphism and polymorphism of A-DNA octanucleotides and the binding of spermine 5.6 Minor groove binders 5.6.1 Drug molecules that enter the minor groove 5.6.2 Decameric oligonucleotides 5.6.3 Polymorphs or intermediate phases? An example from the decanucleotides 5.6.4 Dodecameric oligonucleotides 5.7 General survey of the crystal chemistry of oligonucleotide and oligonucleotide-guest structures References

5.1

142 142 143 144 145 145 151 154 156 158 167 167 171 178 183 187 189

Introduction

The double-helix structure of deoxyribose nucleic acid (DNA), ﬁrst reported by Watson and Crick in 1952, has attracted more attention and had more inﬂuence on the development of modern molecular biology than any other structure determination. The genetic material is composed of DNA, and the complementary nature of the two sets of base pairs in the two strands of the double helix provide a natural way of transmitting genetic information. DNA itself has only been obtained in the form of well oriented ﬁbres up to some microns in length and so the amount of detail that can be extracted from structure analyses is severely limited. Thus a great advance was made when short sequences of DNA bases (synthetic oligonucleotides, also referred to as ‘‘DNA oligomers’’) were ﬁrst synthesized in the 1970s and crystallized, thus allowing the execution of crystal structure analyses on fragments of relatively small size. This has shown that the original model of DNA derived from ﬁber diffraction is, not unexpectedly, somewhat oversimpliﬁed and has allowed the acquisition of much more structural detail (Neidle, Schneider and Berman, 2003). Our interest here is in the structures of the molecular complexes formed between drug molecules of various kinds and various DNA oligomers (hexamers, octamers, decamers and dodecamers) and speciﬁcally in their crystal chemistry. Thus we ﬁrst review apposite fundamentals of DNA structure and then introduce those aspects of phase diagrams, isomorphism and polymorphism relevant here. The complexes can be classiﬁed in two main groups – the

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ﬁrst has the drug molecules intercalated between two successive base pairs and the second has the drug molecule nestling in the minor groove of the DNA oligomer; we treat these separately, In these complexes the DNA fragment is the ‘‘host’’ and the drug molecule the ‘‘guest;’’ some attention is given to the structures of the native hosts (i.e. without guests) because the variety that is found impinges on the structures of the complexes. There are a number of excellent reviews that give more detail than is possible here. The Oxford Handbook of Nucleic Acid Structures (Neidle, 1999) is one recent compendium; another, edited by Demeunynck, Bailly and Wilson (2003), has 25 chapters by 27 authors; besides its broad coverage of topics relevant to this chapter, and far beyond, it includes an illuminating introductory chapter by Waring and Wakelin (2003) and a very useful collection of some thousands of references with titles. The principal data resource is the Nucleic Acid Database (Berman, Westbrook et al., (2002); there were some 2500 entries by late 2004, not all relevant here. Bloomﬁeld et al. (2000) give an overall survey in their Nucleic Acids. Structures, Properties and Functions. Yang and Wang (1999) give an overview of DNA-drug interactions. A Google search for ‘‘nucleic acid databases’’ gave 240 000 hits. Our coverage is selective rather than comprehensive – we omit many important topics outside the mainstream of past and current activity. Most authors emphasize the effects of base sequence on the detailed structure of the oligonucleotides and how the details of the binding of drug molecules differ from one group of oligonucleotides to the next; thus most structural papers include exhaustive analyses of oligonucleotide structure. Their goal has been to account for the large differences found in drug behavior despite small differences in chemical structure. Packing effects on oligonucleotide structure were once considered to be minimal with only passing attention paid to crystal structures as such. Accumulation of information has led to a change in attitude and most structures show appreciable environmental inﬂuence. Readers are directed to the original studies for detailed analyses of the geometries and binding interactions in the native oligonucleotides and their drug complexes, including discussions of water structure and the role of metal ions. This material must eventually ﬁnd application also in discussions of crystal structure, but that stage of development has not yet been reached. Here we draw attention to an approximation that pervades this whole chapter. It is convenient to refer to the complexes as oligonucleotide-drug complexes, with the subliminal implication that the systems are binary. However, about half (by weight) of the crystals consists of solvent (mainly water, more or less organized) and there are also metal cations and spermine. It is surely correct to assign the major structural signiﬁcance to the oligonucleotide-drug portion but the residue may not be neglected, as has been pointed out by many authors (e.g. Guerri, Simpson and Neidle, 1998). Also, one should not forget that an extrapolation is involved when making inferences about DNA structure and behavior based on results obtained for DNA oligomers. However, there seem to be good reasons to believe that such extrapolations are generally permissible. There is an important area that impinges on the subject matter of this chapter – the formation of complexes between proteins and DNA. However, this would require a book on its own and we give only a leading reference (Goldman, 1996).

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5.2

Fundamentals of oligonucleotide structure

5.2.1

General aspects

The gross structure of DNA is well known, and the DNA oligomers have structures based on the same general principles. The description is conveniently given in terms of a spiral staircase, where the helical outer frame is composed of deoxyribose phosphate groups, and the treads (steps) of hydrogen-bonded pyrimidine–purine pairs. The sugar phosphate groups are negatively charged and so counterions, generally sodium and/or magnesium (calcium and barium are also possibilities, as is spermine (Scheme 5.4)), must accompany the double helix, and are usually embedded in an (often ill-deﬁned) envelope of water molecules; DNA is usually about 50% water by mass. Thus, in formal terms, the oligonucleotides are salts or salt-molecule complexes, depending on the ionization state of the drug molecules. DNA has been found to occur in three stereochemical forms – in A and B the helices are right-handed while left-handed helices are found in the Z form. In earlier work counterions were only positively identiﬁed in the Z-DNA hexamers, the B-DNA decamers and some of the DNA-drug complexes,1 but this situation is changing with the increased resolution being attained in crystal structure analyses. We shall ﬁrst discuss the individual components of the whole association, and then consider how they are combined into an oligomer of particular conformation. The base pairing has received most attention in the past. Watson and Crick showed that treads of the required dimensions to bridge between the two sugar phosphate spirals were obtained by hydrogen bonding guanine–cytosine (GC) and thymine–adenine (TA) pyrimidine–purine base pairs (Fig. 5.1). These are the complementary Watson–Crick base pairs and the implication is that each C in one strand can only be hydrogen bonded to G in the other strand, and similarly for the TA pair. Thus the two strands of the double helix are antiparallel (Fig. 5.2). Although Watson–Crick base pairing is by far the most common, work during the last forty years has shown that other base pairings do occur and are relevant to the structures of the DNA oligomers. The ﬁrst of these alternative pairings was encountered by Hoogsteen (1959) in the crystal structure of the 1:1 complex of 1-methylthymine and 9-methyladenine. Among other examples of mismatched pairs (‘‘wobble’’ base pairs) are the pyrimidine–purine pairs CHþG (CHþ symbolizes protonated cytosine), TG (with three bridging water molecules included in the hydrogen bonding scheme), CA (one bridging water) and the purine–purine pair GA, which is found in three variations G(anti)A(syn), G(syn)A(anti) and G(anti)A(anti). The oligonucleotides discussed below are mostly self-complementary and based on Watson–Crick base pairing. However, the strands are not required to be identical – a complementary example with nonidentical strands is (5 0 -CGCAAAAAAGCG-3 0 ) (5 0 -CGCTTTTTTGCG-3 0 ) (Nelson, Finch et al., 1987; Table 5.13) while a noncomplementary example (also with non-identical strands) is {(5 0 -CG[5BrC]ATATTTCGC-3 0 ) þ (5 0 -CGCAAATATGCG-3 0 )}, which has GT and CA non-Watson–Crick base pairs (Aymami, Nunn and Neidle, 1999; Table 5.13).

1

The conformations denoted by Z, A and B will be deﬁned below.

FUNDAMENTALS OF OLIGONUCLEOTIDE STRUCTURE H

H

H

H C C

O

C N 50°

To chain

0.2

8n

C

m

H

T

Thymine

137

N

0n

H

C

H

N

0.3

Adenine

m

C

N

N

C

A

O C

1.1

C C

1 nm H

N

H

N 51° To chain

52 ° H

H

H

C

N

C

C

Cytosine To chain

N 52°

0.2

H

C 0n

N

H 0.2

m

m

N 8n

m

Guanine C

N

9n

H 1.0

m

O

0.3

C O

9n

G C

C C

N

N

C

H

N 54° To chain

H

Fig. 5.1. The complementary T-A and CG hydrogen bonded Watson–Crick pyrimidine-purine base pairs. Line drawings with dimensions are on the left and space-ﬁlling models on the right. (Adapted from Fig. 31.3 of Lehninger, 1977.)

3⬘

5⬘

Strand I

Strand II

C

G

G

C

A

T

T

A

C

G

G

C

5⬘

3⬘

Fig. 5.2. A model of the base pairing in a hexameric oligonucleotide; base sequence is listed from 5 0 to 3 0 . The dashed lines joining the base pairs represent the hydrogen bonding schemes shown in more detail in Fig. 5.1. In this example, and in most of the other oligonucleotides discussed here, the two strands are antiparallel and identical, but identity is not required. The hexameric oligomer is designated d(5 0 -GCTAGC-3 0 )2. (Adapted from Fig. 31.4 of Lehninger, 1977.)

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

138

The sugar–phosphate arrangement in a single strand is shown schematically in Fig. 5.3. The bases are linked by 3 0 ,5 0 -phosphodiester bonds; the particular fragment illustrated can be written as d(5 0 -ApGpCpT-3 0 ), where d represents deoxy (RNA fragments, with an hydroxyl on the 2 0 ring carbon, are shown as ‘r’ or by lower case letters (‘c’ instead of ‘C’)), ‘p’ represents phosphate and A etc are abbreviations for the bases; a more usual notation is d(AGCT), with the duplex nature of the oligonucleotides discussed here emphasized by using the notation d(AGCT)2. The chain has a certain amount of conformational ﬂexibility. We quote the concise descriptions of the conformations of A, B and Z forms given by Kennard and Hunter (1991; see also Kennard and Salisbury, 1993): ‘‘The A form has 11

H N

O O

P

n–1

O

X

C H C H H C

O n

C

A

N

H C

H O

C

H

N

C

N

C

N

H

O H C C H

O

H

P

O

O6 N 8 5⬘

H

6

9

4 3

N

N

4⬘

1⬘

H

N

2⬘

3⬘

G

1N 2

O 4⬘

O

5

7

N2 H H

H

C

N

O 1

O

P

n+1

O

N

O

O

O O4 CH3 O

5 4 6 1

O

P

n+ 2

O

N

O

N

H

T

3 2

O2

O

Y

O O

P

O

O

Fig. 5.3. Schematic arrangement of the four Watson–Crick bases and sugar-phosphate groups in a single strand of a fragment of DNA. Y shows the direction of the chain that runs from the 5 0 carbon to the 3 0 carbon. X indicates a nucleotide residue. A full notation for the duplex would be d(5 0 -ApGpCpT-3 0 )2. (Reproduced from Fig. 26 of Kennard and Hunter (1991)).

FUNDAMENTALS OF OLIGONUCLEOTIDE STRUCTURE

139

base pairs per turn of helix with 32.7 twist between adjacent base pairs. The rise per ˚ . The bases are oriented anti about the glycoside bond and the furanose base pair is 2.7 A ring adopts the C3 0 endo conformation. The global helix axis lies in the major groove with the bases displaced some distance away . . . . The B form has 10 base pairs per turn, ˚ . The glycoside orientation is anti a helix twist of 36.0 and a rise per base pair of 3.4 A 0 and the sugar conformation tends to C2 endo. The global helix axis is through the base pairs . . . . The Z form is a left-handed helix with a zigzag sugar–phosphate backbone, hence the name. The Z form is mostly adopted by alternating cytosine/guanine sequences and can be considered as a repeat of d(CpG) steps. There are 12 base pairs per ˚ . The helix twist, glycoside orientation and sugar conformation turn and a rise of 3.7 A depend on whether the pyrimidine or purine is being considered or whether it is the ﬁrst or second base pair of the dinucleotide step.’’ In ﬁbers, whether the A or B form is obtained depends on environmental conditions and this led to the notion that these conformations represent discontinuous states, only stable in very different environments. This point of view has been revised and it is now accepted that A and B forms have similar energies, and stabilization of one or other depends on sequence as well as on oligomer arrangements in the crystals; thus a continuum of right-handed DNA conformations, spanning the range from A to B, could be expected. An example is given in Fig. 5.9. A rough ﬁrst approximation to the shape of oligonucleotides describes them as right cylinders; this is shown in some packing diagrams such as Fig. 5.7. A better approximation has the surface of the molecules molded into helical minor and major grooves (Fig. 5.4). The larger oligonucleotides (e.g the dodecanucleotides) are often kinked in the sense that

Minor groove

Major Groove

Fig. 5.4. Schematic representation of the major and minor grooves of a B-oligonucleotide. The helical laths represent the sugar-phosphate periphery and the cross-bars the base pairs. (Diagram kindly supplied by Prof. Noam Adir (Technion, 2004)).

140

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

they can be divided into two quasi-cylindrical units with axes inclined to one another; the d(CGCCCGCGGGCG) dodecamer (Table 5.5; Malinina, Fernandez, Hyunh-Dinh and Subirana, 1999) is an example. We quote from Tidwell and Boykin (2003): ‘‘In principle, molecules can bind to either the major or minor grooves of DNA. Due to the great difference . . . in the dimensions of the two grooves, targeting them requires vastly different shaped molecules. The major groove . . . is much wider than the minor groove; the groove width values for ˚ , respectively . . . the major groove is averaged-sequence B-form DNA are 11.6 and 6.0 A the site of binding of many DNA interacting proteins . . . [with only] limited reports of non-protein molecules that bind to the DNA major groove . . . Minor groove binding usually involves greater binding afﬁnity and higher sequence speciﬁcity than that of intercalator binding.’’ 5.2.2

Single crystal x-ray diffraction studies of oligonucleotides

The detail obtainable from the results of crystal structure analyses depends ultimately on the nature of the samples, assuming that instrumentation and computing facilities are ‘‘state of the art.’’ The crystals considered in this book cover a wide spectrum of ‘‘diffraction quality’’ ranging from ‘‘exceptional’’ ({benzeneAgClO4} Section 11.11.1) through ‘‘standard’’ (most of the structures) to ‘‘poor’’ (some of the intercalation complexes of Chapter 9). The crystalline oligonucleotides are usually somewhere between ‘‘standard’’ and ‘‘poor.’’ The unit cells are relatively large (volumes of ˚ 3), the number of reﬂections some thousands and the R factors around 50 000 A obtained around 15–20%. Some improvement can be obtained by structure determination at low temperatures (typically 100K) but this is still the exception rather than the rule. We also note that the small (or minute) quantities of material available do not facilitate crystallochemical studies. There are indications from cell dimension measurements that not all crystals of some complexes are identical. For example, independently prepared crystals of {d(CGCGAATTCGCG)2-Hoechst 33258} measured ˚ 3 whereas two other at 173, 248 and 273K all have cell volumes close to 61 000 A ˚ 3 (see Table 5.13). A crystals (measured at 288 and 298K) had volumes of 67 000 A difference of 10% is surely to be ascribed to compositional or structural differences rather than experimental error. Similar examples are to be found below in the tables of crystallographic data (e.g. d(CCCGCGGG) in Table 5.7 (Fernandez, Subirana et al., 1997)). In small-molecule crystal structure analysis the usual procedure is to deﬁne the unit cell contents by a chemical formula (obtained by chemical analysis) or, at least, a mass content obtained through the measured density. Neither chemical analysis nor measured density is generally reported for biomolecular crystals and we use the cell volume as a designator of content. This is a measurable and useful entity despite its incomplete information tally. The assumption is usually made that equality of cell volumes (or their relationship by a small integer) implies similarity of chemical composition. A landmark review by Dickerson (1992), written when about 100 crystal structures of DNA oligonucleotides and complexes had been reported, contains a treatment of

FUNDAMENTALS OF OLIGONUCLEOTIDE STRUCTURE

141

the structure analysis process and much structural information that is still relevant. Some we shall extract here; that part omitted will repay study. Dickerson’s main classiﬁcation was in terms of helical conﬁguration (A, B, Z2 and irregular) with a secondary division in terms of space group. As our main interest is in the complexes our ﬁrst division is between the two main groups of complexes – intercalation complexes and minor groove complexes;3 fortunately there is little overlap. Our next criterion is oligonucleotide length (hexamers, octamers, decamers and dodecamers), with a further subdivision in terms of sequence. We have grouped together isomorphous crystals and attempted to identify polymorphism. Native crystals and complexes are treated together because there is considerable overlap between some of these groups. Other problems of deﬁnition stem from the limited resolution of many data sets. This may be a result of inadequate crystal (diffraction) quality or of real disorder effects. One criterion of ‘‘resolution’’ is how far out (in reciprocal space) the measured reﬂections ˚; 1A ˚ atomic resolution extend. This is usually expressed as the direct space value X A corresponds to a Bragg angle of 60 for Cu K radiation. Other ‘‘diffraction quality’’ criteria are discussed by Dickerson (1992). One consequence of disorder is found among minor groove complexes (see below) that have been divided into two types of model – in Class I models the drug molecule takes up a single position in the minor groove while in Class II models there is apparent end-to-end disorder of the (almost symmetrical) drug molecule that may result from incorrect analysis because of the limited resolution of the data set (Goodsell, Kopka and Dickerson, 1995). Thus reports of Class II structures should be treated with some reserve. An authenticated example is the monoimidazole lexitropsin complex of the dodecamer d(CGCGAATTCGCG) (Goodsell, Ng et al., 1995). The next landmark is surely the establishment of the Nucleic Acid Database (NDB; Berman, Olson et al., 1992) and its subsequent development. The NDB contains detailed experimental and structural information (from crystal growth through diffraction techniques through geometrical results) for more than 2 000 structures (NMR studies are included although not considered here), as well as tools for analyzing this treasure trove. In our Table 5.1 we reproduce the description given in Table 1 of Berman, Westbrook et al. (2002). We have used the NDB to provide data for the limited number of topics covered in this chapter. The NDB does not give information about solvent content of reported structures (perhaps because this may change as analyses improve). The limitations of earlier and current results have been stressed in the paragraphs ˚ are above but the face of the future can also be seen. Resolutions of 0.7 A now being achieved both in protein and nucleic acid crystallography. For example, the B-DNA double helix structure of 5 0 -CCAGTACTGG-3 0 has been ˚ using a combination of liquid nitrogen temdetermined to a resolution of 0.74 A ˚ ) (Kielkopf, Ding, Kuhn and perature and synchrotron radiation (wavelength 0.78 A Rees, 2000). 2 3

We do not discuss Z-DNA because of limitations of space. Sometimes called ‘‘parallel’’ (to the planes of the base pairs) and ‘‘perpendicular’’.

142

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.1. The information content of the NDB (reproduced from Berman, Westbrook et al. 2002) with some additions Primary experimental information stored in the NDB Structure summary – descriptor NDB, PDB and CSD names; coordinate availability; modiﬁcations, mismatch and drug binding. Stuctural description – sequence; structure type; descriptions about modiﬁcations, mismatches and drugs; description of asymmetric and biological units. Citations – authors, title, journal, volume, pages, year. Crystal data – cell dimensions, space group. Data collection description – radiation source and wavelength; data-collection device; temperature; resolution range; total and unique number of reﬂections. Crystallization description – method; temperature; pH value; solution composition. Reﬁnement information – method; program; number of reﬂections used for reﬁnement; data cutoff; resolution range; R factor; reﬁnement of temperature factors and occupancies. Coordinate information – atomic coordinates, occupancies and temperature factors for asymmetric unit; coordinates for symmetry-related strands; coordinates for unit cell; symmetry-related coordinates; orthogonal or fractional coordinates. Derivative information stored in the NDB Distances – chemical bond lengths; virtual bonds (involving P atoms) Torsions – backbone and side-chain torion angles; pseudo-rotational parameters. Angles – valence bond angles, virtual angles (involving P atoms) Base morphology – parameters calculated by different algorithms Non-bonded contacts Hydrogen bonding classiﬁcation Valence geometry RMS deviations from small molecule standards Sequence pattern statistics CIF information – coordinates, structure factors.

5.3 5.3.1

Crystal chemistry of oligonucleotide and oligonucleotide-guest structures Polymorphism, isomorphism, and heteromorphism

There are many striking resemblances, and also some differences, in the crystal chemistries of cyclodextrin inclusion complexes (Chapter 4), tetraphenylporphyrin-MII inclusion complexes (Chapter 8) and oligonucleotide native crystals and complexes. The established concepts of polymorphism and isomorphism are basic to the discussion and we ﬁnd it convenient to introduce a new term ‘‘heteromorphism.’’ We deﬁne these terms immediately below, and then illustrate and compare them for particular examples from the three groups of cyclodextrins, tetraphenylporphyrin-MII moieties and oligonucleotides. Our approach is that terms and deﬁnitions currently accepted in small-moiety crystallography should be applied to inclusion complexes and biomolecules with minimal change. 1. Polymorphism. Experience and calculation show that many different packing arrangements have similar lattice energies4 (Lommerse et al., 2000) and this gives rise 4 Free energies rather than enthalpies should be considered but entropy is more difﬁcult to calculate and is often explicitly or implicitly ignored.

OLIGONUCLEOTIDE AND OLIGONUCLEOTIDE-GUEST STRUCTURES

143

to the phenomenon of polymorphism. A formal deﬁnition of polymorphism is: when the same chemical compound occurs in two different crystalline forms these are called polymorphs; we use ‘two’ for simplicity but polymorph clusters can be larger than pairs. When a ﬁrst order phase transformation occurs from one phase to the other between low temperature and the melting point, then the two phases are said to be enantiotropically related. If such a phase transformation does not occur then the two phases are monotropically related. A particular chemical substance can show both enantiotropic and monotropic behavior; quartz is one of many examples. The implication of the word ‘same’ is that there is no difference in chemical formula between the two phases. Should a difference in chemical nature (e.g. diamond Sn and metallic Sn) be allowed? These deﬁnitions were developed for small-moiety crystallography (including here inorganic crystals and metals) and not much attention has been given to assessing their applicability to biomolecular crystallography. The matter becomes much more complicated when dealing with biological molecules because of the presence of such large quantities of solvent (generally water) in the crystals, as well as ions. Analogous problems can occur with minerals. Polymorphism seen in the context of classical physical chemistry has been reviewed recently (Herbstein, 2004). 2. Isomorphism. Two crystals are deﬁned as isomorphous5 when they crystallize in the same space group, in very similar unit cells and with very similar atomic coordinates. The term ‘‘very similar’’ has not been deﬁned in quantitative terms, although progress, summarized by Dziubek and Katrusiak (2003), has been made in this direction. When the two structures are similar (without deﬁning ‘‘how similar’’) then the two materials are said to be isostructural. Are Cu, Ni and Au isomorphous or isostructural? This question is discussed in Section 10.6.1. Perhaps the best answer is that latitude and ﬂexibility in applying the deﬁnitions are preferable to rigidity. 3. Heteromorphism. This term is introduced to cover the situation where different crystals have formula units of the same volume and but different chemical compositions. These are not polymorphs because the different crystals have different compositions. This concept is found to be useful in the three categories of substance discussed here. ‘‘Hetero’’ refers to the different crystal structures and, for oligonucleotides, to different base pair sequences. In a sentence, polymorphism occurs when different crystal structures are found for the same composition, isomorphism when the same crystal structure is found despite differences in composition, heteromorphism when analogous formula units (of the same volume but different chemical compositions) occur in different crystal structures. The keywords ‘‘same’’ and ‘‘different’’ are open to interpretation. 5.3.2 Phase rule relationships In host–guest inclusion complexes, if the host crystal structure (no guest, native) is isomorphous with that of the inclusion complex then the complex is a primary solid solution phase. It is generally not known whether the host:guest ratio is ﬁxed or variable. One example where the host–guest ratio has been shown to cover a wide range is bromine 5

Our distinction between ‘‘isomorphous’’ and ‘‘isostructural’’ is not used by all authors.

144

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

hydrate (Section 7.2.7.4); this is an intermediate phase rather than a primary solid solution. An example of a true primary solid solution is trimesic acid/bromine (Section 8.3.4), but here the composition range has not been established. If the complex and native host are not isomorphous then the host–guest complex is an intermediate phase in the ‘‘binary’’ phase diagram. For understandable reasons, no one seems as yet to have tried to determine a binary oligonucleotide-second component phase diagram, where ‘‘second component’’ is, for example, a drug molecule. 5.3.3

Applications of these concepts

1. Cyclodextrin complexes. A large amount of information is embedded in the tables of Chapter 4. We take the clathrate inclusion complexes of -cyclodextrin as our illustrative example. A herringbone arrangement is found in 15 complexes of Table 4.2. ˚ , space group These complexes are isomorphous with a 9.5, b 14.3 and c 37.5 A P212121, Z ¼ 4; the guests cover a range of chemical types. There is a second group of ˚ , space 10 isomorphous complexes in Table 4.3, with a 13.6, b 15.3 and c 24.5 A group P212121, Z ¼ 4; the guests cover a range of chemical types. That the two groups have the same space group is coincidental. The two groups are heteromorphic, both unit ˚ 3. There are no polymorphs. Both groups are cell volumes being around 51 000 A different intermediate phases in the hypothetical -cyclodextrin/guest/water phase diagram. In the cyclodextrins the host molecule is invariant while the nature (perhaps number) of guest molecules differs from complex to complex, as does the water content, which is sometimes not well established. 2. {Tetraphenylporphyrin-MII(guest)2} complexes. A large amount of information is embedded in the tables of Chapter 8. In the {tetraphenylporphyrin-MII(guest)2} inclusion complexes, the host molecules differ to a small extent because of differing metal ions while the different guest molecules appear to have a greater inﬂuence on crystal structure. The chemical compositions of the tetraphenylporphyrin-MII complexes are generally well established. We take the four-coordinate inclusion complexes listed in Table 8.17 as speciﬁc examples. The second to the tenth entry in ˚ , 106, 112, Table 8.17 are all isomorphous (a 10.5, b 11.2, c 12.0 A 103 ; Type II triclinic cell (all angles 90 , space group P1, Z ¼ 1). This group is followed by a group of 20, isostructural rather than isomorphous with the ﬁrst group. These two groups are followed by a third, smaller, group with a Type I triclinic cell (all angles <90 ). This group is heteromorphic to the ﬁrst two groups, all the unit cell volumes being in the range 1100–1200 A3. Apart from a few exceptions, the metal ions are all ZnII but the guests cover a wide chemical range. There are no polymorphs. 3. Oligonucleotides. A large amount of information is embedded in the tables of this chapter. We treat hexameric, octameric, decameric and dodecameric complexes separately, using as our speciﬁc example the dodecameric complexes and native structures listed in Table 5.13, where some forty native dodecamers with different base pair sequences (except for two pairs discussed immediately after Table 5.13) and dodecamers complexed with different guests all crystallize in space group P212121 ˚ 3; these all have (Z ¼ 4), with cell volumes ranging from 60 000 to 70 000 A

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

145

sequences that can be formulated as d(CGCXGCG)2 as discussed later; X represents various different sequences of six base pairs. These dodecamers are all isomorphous. There are also eight native dodecamers (with sequences different from d(CGCXGCG)2 that crystallize in different unit cells, space groups being P1 (2 examples), R3 (3 examples) and one example each for C2, P212121 and P43 (Table 5.14). The triclinic (56761 A3) and rhombohedral (158819 A3) phases of d(ACCGACGTCGGT)2 may be the one true polymorphic pair among the examples of Table 5.14; the ratio of cell volumes is 2.80, which may, or may not, be a small integer. Structural differences among hexameric, octameric, decameric and dodecameric complexes will be demonstrated in the detailed discussion of each group. Among oligonucleotides of a given number of base pairs it is necessary to assess whether the unit cell volumes of different crystal types are the same (modulo a small integer) because this will show, in the absence of better evidence, similarities or differences of chemical composition. However, it is undesirable to label as ‘polymorphs’ those clusters without signiﬁcant differences in composition but with different base pair sequences. Such clusters are heteromorphic. For a particular oligonucleotide to show true polymorphism both phases must have the same chemical composition, including the same base pair sequence; cell volumes provide a measure of chemical composition in the absence of more deﬁnite information. True polymorphism of oligonucleotides appears to be quite rare. One possible example has been given above; another is native d(CCCGCGGG)2. The two polymorphs crystallize in ˚ 3 (Table 5.5)) and P212121 (Z ¼ 4, cell space group P43212 (Z ¼ 8, cell volume 43 880 A 3 ˚ volume 42 479 A (Table 5.7). The similar cell volumes suggest that the chemical compositions may well be the same. Identiﬁcation of true polymorphism among the cyclodextrin complexes, the tetraphenylporphyrin-MII complexes and the oligonucleotides (native and complexes) should be based on obtaining different phases of the same composition. No one seems as yet to have searched for phase transformations on heating or cooling (but see the intriguing results shown in Fig. 5.21), or tried to establish whether two (apparent) polymorphs are enantiotropically or monotropically related.

5.4 Intercalated hexanucleotide-drug complexes with B-DNA structure An early suggestion that drug molecules could be accommodated between base pairs came from various physico-chemical measurements on the acrdidine proﬂavine (Lerman, 1961). Denny (2003) writes ‘‘Intercalation is now understood to be the preferred binding mode of virtually any ﬂat polyaromatic ligand of sufﬁciently large surface area and suitable steric properties.’’ Currently three broad groups of parallel intercalators – the anthracycline derivatives, the nogalamycin derivatives and the 9-aminoacridine derivatives – are known. 5.4.1 The anthracycline drugs The anthracycline (Scheme 5.1) situation has been summarized by Neidle (1997): ‘‘The anthracyclines, of clinical importance as anticancer agents, have a daunosamine-type

146

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

sugar group appended [to the tetracyclic aglycone chromophore], frequently with a charged amine substituent. . . . Almost all [crystallographic studies . . . on exclusively hexanucleotide duplexes] show two drug molecules bound, one at each terminal base-pair site . . . The sugar group is always positioned in the minor groove, with hydrogen bonding, frequently involving water molecules, to atoms on base-pair edges.’’ O

R3

O C R1

D

C

R2

O

B

A

O

O

OH

H H3C

1⬘

O 4⬘ O

NH+3

R5

Daunomycin (¼ daunorubicin) (C27H30NO10); R1¼CH3; R2¼OCH3; R3¼OH; R4¼NH2 (or NH3þ); R5¼H. Adriamycin (¼ doxorubicin); R1¼CH2OH; R2¼OCH3; R3¼OH; R4¼NH2; R5¼H. 4’-Epiadriamycin has inversion of the stereochemistry at the 4 0 (hydroxyl) position of the amino sugar). Idarubicin (¼4-demethoxy-daunorubicin); R1¼CH3; R2¼H; R3¼OH; R4¼NH2; R5¼H. 4-O-demethyl-11-deoxydoxorubicin R1¼R2¼OH; R3¼H; R4¼NH2; R5¼H. MAR70 R1¼CH3; R5¼4 0 -epi-2 0 -deoxyfucose.

H3C HO

NC

N

O 4⬘

1⬘

HO

R4 for various morpholino derivatives of doxorubicin, and acronyms

O

CN-MDox

N

O

MDox

N

O

OCH3 (R)- or (S)-MMDox; methoxy (R)- or (S)

Scheme 5.1

I N T E RC AL AT E D HE XANUC L E OT IDE - D R UG COMPLEXES

147

Table 5.2. Intercalation of anthracycline derivatives in hexameric oligonucleotides with oligonucleotide : drug ratio ¼ 1 : 2. All crystals have distorted right-handed B-DNA-like duplex structures with Watson–Crick base pairs; the common space group is P41212, Z ¼ 8. Dimensions in ˚, A ˚ 3. NDB entries to October, 2004. Structures at RT unless stated otherwise A Hexanucleotide

Intercalated drug

a

c

Cell Volume

NDB ID and Reference

d(CGTACG)283W

Daunomycin

27.86

52.72

40 920

d(CGTACG)2 d(CGTACG)2

adriamycin M-Dox

28.21 28.12

53.19 53.03

42 329 41 873

d(CGTACG)2 d(CGTACG)2 d(CGTACG)2 d(CGTACG)2 d(CGTACG)2

CN-M-Dox (R)-MM-Dox (S)-MM-Dox 4 0 -epiadriamycin MAR70

28.19 28.21 28.11 28.04 28.01

53.32 53.50 53.47 53.15 53.11

42 372 42 576 42 251 41 789 41 668

d(CGTACG)2

28.04

53.36

41 954

d(CGTACG)2

2 0 -bromo-4 0 epidaunorubicin NH2-CH-daunomycin

28.02

52.47

41 195

d(5 0 -CpGpT(NH2) ApCpG-3 0 )2 d(CGATCG)240W

MAR70 HCHO covalent adduct Daunomycin

28.12

52.98

41 893

27.98

52.87

41 391

d(CGATCG)243W at 113K d(CGATCG)243W

Daunomycin

27.85

52.33

40 588

Daunomycin þ spermine

28.11

53.08

41 942

d(CGATCG)2

28.16

53.40

42 165

d(CGATCG)2 at 113K

N-cyanomethyl-N(methoxyethyl)-daunomycin Adriamycin

27.92

52.39

40 839

d(CGATCG)249W

Adriamycin þ spermine

28.21

53.19

42 329

d(CGATCG)235W

idarubicin

28.13

53.68

42 199

d(CGATCG)238W

28.04

53.15

41 789

d(CGATCG)2

4 0 -epiadriamycin (spermine found in major groove) (R)- MM-Dox

DDF001; WUQR87 GLRW90 DDF053; GW95 GW95 GW95 GW95 WFUR90 DDF026; GLL91 DDF065; GPW96 DDFB24; WGLL91 DDFB25; GLL91 DDF018; MHLK89 DDF045; LPZ94 DDF020; FWU90 DD0017; SDM00 DDF044; LPZ94 DDF019; FWU90 DDF029; GW91 DDF022; WFUR90

28.21

53.50

42 576

d(CGATCG)2

(S)- MM-Dox

28.21

53.65

42 695

d(CGATCG)2

4-O-demethyl-11deoxydoxorubicin CN-M-Dox

28.18

53.14

42 079

28.19

53.35

42 396

4 0 -deoxy-4 0 iododoxorubicin

27.73

52.49

40 362

d(CGATCG)250W

d(CGATCG)2

DDF055; GW95 DDF054; GW95 DDF028; GW91 DDF056; GW95; SDM00 DDF062; BSS95

148

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.2. (Continued) Hexanucleotide

Intercalated drug

a

c

Cell Volume

NDB ID and Reference

d(CGATCG)2

2 0 -bromo-4 0 epidaunorubicin N-(2-hydroxyethyl)doxorubicin Daunomycin daunomycin

28.09

53.38

42 119

28.13

53.56

42 382

28.05 27.94

53.16 52.24

41 826 40 781

daunomycin

28.07

53.35

42 036

2 0 -bromo-4 0 epidaunorubicin Adriamycin

28.25

53.67

42 832

28.01

52.99

41 574

daunomycin

28.02

52.71

41 384

d(TGTACA)2

4 0 -epiadriamycin

28.02

52.93

41 556

d(TGTACA)2

27.96

52.57

41 097

d(TGATCA)234W

4-O-demethyl-11deoxydoxorubicin 4 0 -epiadriamycin

28.01

52.95

41 542

d(TGATCA)2

Idarubicin

28.19(3)

52.77(4)

41 935

d(TGATCA)2

daunomycin

28.11

52.88

41 784

DDF066; GPW96 DDF078; ECU98 SPS03 DDF023; WGLL91 DDF039; LHM93 DDF068; GPW96 DDF040; LHM93 DDF031; NvM91 DDF035; LBH92 DDF061; BSS95 DDF036; LGBH92 DDF038; GLBH93 DDF032; NvM91

d(CGATCG)2 (dC)(rG)d(ATCG)240W d(CGCGCG)2 d(CGGCCG)2 C84H100N25O44P549W d(CGGCCG)2 d(TGGCCA)2 C85H101N25O44P549W d(TGTACA)2

Notes: Some idea of the progress in this area can be obtained by comparing Dickerson’s ﬁve different structures in his Table IV with the 35 entries here. nW is the number of water molecules identiﬁed in the structure analysis; this is not necessarily the total water (solvent) content. Comparison of independent duplicate measurements suggests that precision of cell dimensions is a few hun˚. dredths of an A (nA) is 2-aminoadenine; MAR70 is shown in Scheme 5.1; when MAR70 was crystallized with the DNA hexamer d(CGT(nA)CG)2 a covalent methylene bridge was formed between N(3 0 ) of daunosamine and the N(2) of 2-aminoadenine; this spontaneous reaction occurred through the cross linking action of trace amounts of formaldehyde. x Two other d(CGATCG)-dd-MOX crystals were reported (Gao and Wang, 1991). One was orthorhombic, 37.90 ˚ , ¼ 108.1 , ˚ , V ¼ 87 086 A ˚ 3, space group P212121, and the other monoclinic, 26.56 52.81 36.17 A 63.30 36.30 A ˚ 3, space group P2. Structures were not determined. V ¼ 48 223 A References: BSS95 – Berger, Su, Spitzner et al., 1995; ECU98 – Ettore, Cirilli and Ughetto, 1998; FWU90 – Frederick et al., 1990; GLBH93 – Gallois et al., 1993; GLL91 – Gao, Liaw, Li et al., 1991; GLRW90 – Gao, Liaw, Robinson and Wang, 1990; GPW96 – Gao, Priebe and Wang, 1996; GW91 – Gao and Wang, 1991; GW95 – Gao and Wang, 1995; LBH92 – Leonard, Brown and Hunter, 1992; LGBH92 – Langlois d’Estantoin et al., 1992; LHM93 – Leonard, Hambley et al., 1993; LPZ94 – Lipscomb, Peek, Zhou et al., 1994; MHLK89 – Moore et al., 1989; NvM91 Nunn, van Meervelt et al., 1991; SDM00 – Saminadin, Dautant, Mondon et al. 2000; SPS03 – Shi et al., 2003; SS92 – Schuerman, Smith et al., 1996; WFUR90 – Williams, Frederick et al., 1990; WGLL91 – Wang, Gao, Liaw and Li, 1991; WUQR87 – Wang, Ughetto et al., 1987.

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

5⬘

C1 G12

149

3⬘

14

G2 C11 T3 A10 A4 T9 C5 G8 13 3⬘

G6 C7

5⬘

Fig. 5.5. Schematic side view of the d(CGTACG) complex with intercalated anthracycline drug molecules marked as 13 and 14. The drug molecule is seen down its long axis. The increase in spacing of the upper and lower two base pairs is shown schematically, as are the different hydrogen bonding schemes within the base pairs. The amino sugar portion of the drug is located in the minor groove. This diagram can be considered to be a more detailed version of Fig. 5.2. (Adapted from Wang, Ughetto et al., 1987).

The ﬁrst structure to be determined was that of the {d(CGTACG)-daunomycin} complex (Quigley, Wang et al., 1980; Wang et al., 1987). 83 water molecules were located and a hydrated sodium ion was found to coordinate with daunomycin and guanine; subsequent structure determinations (Moore, Hunter, Langlois d’Estantoin and Kennard, 1989; Frederick, Williams et al., 1990) were in good agreement. Although spermine is essential for crystallization, no spermine molecule could be located and it is possible that it is disordered in the large solvent channels along [001]; the crystals contain about 40% solvent. Other hexameric oligonucleotides complexed with anthracycline drugs (Scheme 5.1) are isomorphous (Table 5.2). Despite the overall resemblances, there are differences among the various complexes that have been illustrated and discussed in considerable detail (e.g. Moore, Hunter et al., 1989; Frederick, Williams et al., 1990); the reader is referred to the original papers. The asymmetric unit is composed of one hexameric oligonucleotide strand and one drug molecule, together with associated water molecules and metal ions. The helical rise ˚ , compared to 3.5 A ˚ at normal sites. The amino sugar lies at the intercalation sites is 5 A in the minor groove, forming hydrogen bonds to the solvent molecules (Fig. 5.5). Structurally one ﬁnds two anthracycline drug molecules bound to each hexameric oligonucleotide duplex, with the three-ring planar chromophore intercalated at the CpG steps at both ends of the duplex; one could call this the structural unit, with a volume of about ˚ 3. Irrespective of the base-pair sequence and the nature of the anthracycline,6 the 10 500 A ˚ 3; the isocomplexes all have unit cell volumes between about 40 000 and 43 000 A morphism holds despite differences in base pair sequence and guest identity. Almost forty tetragonal complexes are listed in Table 5.2; as yet there are few examples of analogous complexes crystallizing in other space groups. One example is {d(CGTACG)– 2[3 0 -desamino-3 0 -(2-methoxy-4-morpholinyl)-doxorubicin]}, which is triclinic (P1, Z ¼ 1, ˚ 3; NDB-ID DDF041; Cirilli, Bachechi et al., 1993). Two other unit cell volume 8878 A examples are given in the Notes to Table 5.2. The differences in structural-unit volumes 6

Within the limits of Table 5.2.

150

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Fig. 5.6. Stereodiagram of the d(CGATCG)-daunomycin complex viewed along the twofold axis into the minor groove. Open and ﬁlled bonds are used for DNA and daunomycin respectively. The atoms are shown as spheres of decreasing radius in the order P > O > N > C. (Reproduced from Moore, Hunter et al., 1989.)

3/8

3/8 1/4

1/4

1/4

1/4 1/8

1/8

1/4

1/4 1/8

1/8 1/4

1/4

1/4 3/8

1/4 3/8

Fig. 5.7. Schematic view down [001] shows the packing arrangement of the DNA-drug complexes in the unit cell with space group P41212. The molecular twofold axis coincides with the crystallographic twofold axis at z ¼ 0, which runs diagonally across the square. The two complexes, stacked end-toend along the two fold screw axis in the [001] direction, are related by the twofold axis at z ¼ 1/4. The solvent channels are in the areas near the 41 axes. The dashed circles represent end views of the elongated hexamer-drug complexes. (Reproduced from Wang, Ughetto et al., 1987.)

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

151

are about 10% and may suggest that the various crystals have different (solvent) compositions rather than being heteromorphs. The {(hexamer duplex)2(daunomycin)} complex is shown as a ball-and-stick stereopair in Fig. 5.6 and as a schematic packing diagram in Fig. 5.7. The molecules ˚ and height 26.5 A ˚. can be roughly represented as cylinders of diameter 20 A These cylinders, whose axes lie along [001], are approximately close packed in two dimensions. 5.4.2 Nogalamycin and derivatives Nogalamycin and derivatives (Scheme 5.2) also belong to the anthracycline family of antibiotics and are active against a number of tumor lines. However, difﬁculties in administering the drugs have discouraged clinical trials. Nevertheless, interaction of nogalamycins with DNA has remained of interest. Crystal structures of a number of hexanucleotide-nogalamycin complexes have been described (Table 5.3).

R1

R2

Nogalamycin

COOCH3

CH3

Disnogalamycin

H

CH3

U-58872

COOCH3

CHO

H

R2

OH

N+ H3C aminoglucose (positively HO charged) H3C

O

O

O

R1 OH

D

C

R2

O

B

A

O

O

CH3

H H3C

O

H3CO OCH3

Scheme 5.2

nogalose (neutral) OCH3

152

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.3. Intercalation of nogalamycin or derivatives in hexameric oligonucleotides (some modified); duplex:nogalamycin ratio is 1 : 2. All crystals have distorted right-handed B-DNA-like ˚, A ˚ 3. Chemical formulae in duplex structures with Watson-Crick base pairs. Dimensions in A Scheme 5.3. (pS) indicates that the phosphate group at the TpA step. has been replaced by phosphorothioate. [m5C] is 5-methylcytosine (5-MeC is also used). Structures at RT unless stated otherwise Hexameric oligonucleotide

Intercalated drug

a

b

c

V

NDB ID; Reference

Tetragonal P41212, Z ¼ 8 d(TGATCA)2 at 150K

nogalamycin 37.29 37.29 71.12

98 895 DDF049, 052, 063; SST96

Orthorhombic P212121; Z ¼ 4 d(TGTACA)2 at 150K

nogalamycin 26.30 51.98 67.08

91 703 DDF064; SBM96

Orthorhombic C2221; Z ¼ 8 d(CGT(pS)ACG)2

nogalamycin 22.98 47.27 64.44

69 999 LGR89

Hexagonal; P61 Z ¼ 6 d([m5C]GT(pS)A[m5C]G)2 d([m5C]GT(pS)A[m5C]G)2

nogalamycin 26.31 26.31 100.26 60 104 GLRW90 U-58872 26.27 26.27 100.23 59 903 GLRW90

Hexagonal; P6122; Z ¼ 6 d([m5C]GT(pS)A[m5C]G)239W nogalamycin 26.30 26.30 100.01 59 908 WEG90 References: GLRW90 – Gao, Liaw, Robinson and Wang, 1990; LGR89 – Liaw, Gao, Robinson, van der Marel, van Boom and Wang, 1989; SBM96 – Smith, Brannigan and Moore, 1996; SST96 – Schuerman, Smith, Turkenburg, Dettmar, Van Meervelt and Moore, 1996; WEG90 – Williams, Egli, Gao, Bash, van der Marel, van Boom, Rich and Frederick, 1990.

The hexamer-duplex/drug ratio is 1 : 2 in all the crystals. The asymmetric units of the orthorhombic and P61 hexagonal modiﬁcations contain two hexanucleotides, two nogalamycins, two hydrated magnesium ions and 113 water molecules. The P61 hexagonal modiﬁcation approximates to P6122 symmetry and, under different crystallization conditions, a higher symmetry modiﬁcation with this space group is obtained, where one strand of the DNA duplex and one drug molecule form the asymmetric unit. 39 water molecules were located. The DNA-drug interaction in both hexagonal and orthorhombic modiﬁcations has been described as follows by Liaw, Gao et al. (1989): ‘‘two nogalamycins bind to the DNA double helix in a 2 : 1 ratio with aglycon chromophore intercalated between the CpG steps at both ends of the helix. The nogalose and aminoglucose sugars lie in the minor and major grooves, respectively, of the distorted B-DNA double helix.’’ The hexagonal structures suggest that the volume per formula unit is about ˚ 3, which does not ﬁt the unit cell volumes obtained for the tetragonal and 10 000 A orthorhombic structures. The packing in the tetragonal [d(TGATCA)–nogalamycin} complex has been shown by Smith, Davies, Dodson and Moore (1995) (Fig. 5.8; a somewhat different view is given by Schuerman et al. (1996); their Fig. 4). In overall terms Fig. 5.8 is remarkably similar to the analogous ﬁgure for the d([m5C]GT(pS)A[m5C]G)2 hexagonal P61 modiﬁcation (Fig. 5.9).

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

153

a

Fig. 5.8. Partial view of the packing diagram of the P41212 crystal form of the nogalamycin/ ˚ ), d(TGATCA) complex, seen approximately along [101]. There are four layers along [001] (¼ 71 A which is horizontal in the diagram. (Reproduced from Smith, Davies, Dodson and Moore (1995).)

A

B

c/6

Fig. 5.9. Packing diagram of the P61 crystal form of the nogalamycin/d([m5C]GT(pS)A[m5C]CG) complex. The complexes are stacked end-over-end along a (and b) axes to form a sheet. One of these ˚ ). The packing of the sheets along the c direction sheets is shown in A, viewed down the c axis (100 A is shown in B; the thiophospho group abuts adjacent complexes. There are six sheets along the c axis. (Reproduced from Gao, Liaw, Robinson and Wang, 1990.)

154

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

In both structures there are layers of hexamer-drug complex moieties in (001) planes, with four layers along [001] in the tetragonal complex and six in the hexagonal complex. However, the hexagonal and orthorhombic phases are not accepted as heteromorphs because they do not have the same chemical composition as inferred from the unit cell volumes. The relation between the P61 and P6122 phases is not entirely clear; perhaps a small composition difference accompanies the small symmetry difference. The distortion of the hexamer duplex consequent on the intercalation is greater than that found in the anthracycline drug complexes – hence, a fortiori, the hexamer-nogalamycin phases are separate phases in the DNA-drug system.

5.4.3

The 9-aminoacridine drugs

The 9-aminoacridine-4-carboxamide class of compounds were originally explored as part of a broad attempt to develop acridune derivatives as anticancer drugs. Because these compounds exist as dications under physiological conditions, they are tight binding DNA intercalating agents. They are also potent cytoxins. This general background comes from Denny (2003). NH2

5

N H2

H

R O

N H

R=

H CH3 N+ CH3

R = HN +

H2

9-amino-[N-(2-methylamino)ethyl]acridine4-carboxamide

Morpholino-9-amino-[N-(2-methylamino)ethyl] acridine-4-carboxamide

Scheme 5.3

The structures listed in Table 5.4 are isomorphous. The asymmetric unit (using the 9-amino-DACA complex as example) consists of a single strand of the hexanucleotide, one intercalated 9-amino-DACA molecule, 27 ordered water molecules and, on a crystallographic two fold axis, an additional ‘end-stacked’ 9-amino-DACA molecule (necessarily disordered) and two water molecules. No metal atoms or spermine appeared. Thus the composition is {(hexamer duplex)3(9-amino-DACA)}. The two strands of DNA

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

155

Table 5.4. Intercalation of 9-aminoacridine derivatives in hexameric oligonucleotides. All crystals have distorted right-handed B-DNA-like duplex structures with Watson-Crick base pairs; the ˚, A ˚3 common space group is P64, Z ¼ 6. Dimensions in A Hexanucleotide

Intercalated drug

a

c

Cell Volume NDB ID; Reference

d(CGTACG)2 at 110K d(CGTACG)2 at 110K d(CGTACG)221W at 110K d(CGTACG)221W at 110K d(CG5-BrUACG)2 at 110K d(CCTAGG)2 at RT

9-amino-DACA

30.16

39.69

34 336

morpholinyl

30.239 39.340 34 214

5-ﬂuoro-9-amino-DACA* 30.14

39.40

34 040

5-bromo-9-amino-DACA* 30.19

39.44

34 188

DD0015; AGCDW99 DD0048; AGDW02 DD0023; AGCDPW00 DD0051; TTT

6-bromo-9-amino-DACA

30.087 39.316 33 848

TATDWC99

cryptolepine

29.96

DD0047; LCP02

39.65

33 848

Notes: 9-amino-DACA is 9-amino[N-(2-dimethylamino)ethyl]acridine-4-carboxamide morpholinyl is 9-amino-N-(2-(4-morpholinyl)ethyl)acridine-4-carboxamide cryptolepine is 5-methyl indolo[2.3b]-quinoline * occupancies of drug molecules appear to be appreciably less than 1. References: AGCDW99 – Adams, Guss, Collyer, Denny and Wakelin, 1999; AGCDPW00 – Adams, Guss, Collyer, Denny, Prakash and Wakelin, 2000; AGDW02 – Adams, Guss, Denny and Wakelin, 2002; LCP02 – Lisgarten, Coll, Portugal et al., 2002; TATDWC99 – Todd, Adams, Thorpe, Denny, Wakelin and Cardin, 1999; TTT – Teixera, Thorpe, Todd et al., to be published (DD0051).

are related by a dyad axis and form a right-handed DNA duplex with Watson–Crick base pairing. The intercalated 9-amino-DACA molecule is located between each of the CpG base pair steps with its side chain in the major groove. The additional 9-aminoDACA molecules on the two fold axis stack at the ends of each DNA helix and link one duplex to the next by hydrogen bonds to form a continuous column of duplexes in the ab plane (Fig. 5.10). Because the 9-aminoacridine complexes have both drug molecules intercalated in the hexameric duplexes and additional drug-molecules between the duplexes, these complexes are separate phases in the hexamer-drug system. ˚ 3, somewhat The volume of the asymmetric unit in these complexes is about 5 700 A larger than the value obtained for the P6122 nogalamycin complex of Table 5.2; in both examples the asymmetric unit contains a single strand of the hexamer – whether these are heteromorphs remains moot. A partial view of the packing arrangement is shown in Fig. 5.10. Layers of molecules are formed, one layer being shown in Fig. 5.10 together with the space group symmetry elements which enable one to complete the packing diagram. Successive layers along [001] are obtained by operation of the 31 screw axis.

156

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

B A

A B

Fig. 5.10. One layer of {d(CG5-BrUACG)2(6-bromo-9-amino-DACA)} projected down the [001] axis, looking directly into the major groove. The space group is P64 and the symmetry elements are shown. The helix axis of the duplex is along [100] and is intersected by a two fold axis along [001]. A and B are the intercalated and ‘‘end stacked’’ DACA molecules respectively. (Adapted from Todd, Adams, Thorpe, Denny, Wakelin and Cardin, 1999.)

5.4.4

Native hexanucleotides and comparison of crystal structures

The B-DNA structure of the native hexanucleotide d(CTCGAC)2 has been reported ˚, (Wahl, Rao and Sundaralingam, 1996; BDF068). The hexagonal crystals (40.14, 44.47 A ˚ 3, P6222, Z ¼ 6) show an A-DNA like conformation at the termini of V ¼ 62052 A the duplex. The volume per asymmetric unit is much the same as for the crystals of the various sequences complexed with a variety of drug molecules (Table 5.2) but the two types of hexanucleotide are not isostructural. A native hexanucleotide derivative Rp-d(Gp(S)CpGp(S)CpGp(S)C), where ‘‘p’’ represents a phosphate group and ‘‘p(S)’’ a phosphorothioate group, crystallizes in a modiﬁcation not yet encountered ˚ , V ¼ 23201 A ˚ 3, Z ¼ 4, P212121) elsewhere (orthorhombic, 34.90, 39.15, 20.64 A (Cruse, Salisbury et al., 1988). This is more densely packed than d(CTCGAC)2, as is shown in Fig. 5.11. The helical duplexes, considered as quasi-cylinders, are approximately close packed. The principal interactions are between cations and phosphate and phosphorothioate groups. Strand 1 of the duplex interacts mostly with symmetry-related strand 1* and similarly for strand 2. A number of possible hydrogen bonds were located.

I N T E RC AL AT E D HE XANUC L E OT IDE - DR UG COMPLEXES

157

Fig. 5.11. Stereodiagram of the packing arrangement in Rp-d(Gp(S)CpGp(S)CpGp(S)C), viewed down the [001] axis, which coincides with the helix axis. The solvent molecules are shown as open circles. 72 solvent molecules, of the approximately 143 in the asymmetric unit, have been located; some of these may be sodium or magnesium ions. (Reproduced from Cruse, Salisbury et al., 1988.)

Another native hexanucleotide has a Z-conﬁguration – indeed it was the prototype of the Z conﬁguration (Wang, Quigley, et al., 1979); this is not relevant for comparison with the B-DNA hexamers considered here. Would a hypothetical native B-DNA hexamer be expected to be isomorphous with the complexes listed in Table 5.2? Probably not, in view of the large perturbation of the hexameric duplex by the two intercalated drug molecules. If so, then the complexes are not to be classiﬁed as solid solutions but rather as separate phases in the binary hexamer– drug phase diagram. The packing arrangements in the anthracycline drug complexes differ from those in the nogalamycin and 9-aminoacridine complexes. In the anthracycline drug complexes the quasi-cylindrical molecules have their long axes along the [001] axis of the space group, leading to approximate close packing of parallel cylinders. In the hexagonal nogalamycin and acridine complexes the quasi-cylindrical molecules are arranged in the basal plane, and the layers of cylinders are arranged along the [001] axis by the operation of 31 and 64 screw axes respectively. The packing in the tetragonal and orthorhombic crystals does not appear to have been described in detail. The versatility of the d(CGATCG)2 base pair sequence should be noted. This forms some 15 isomorphous tetragonal complexes with different daunomycin-type guests (Table 5.2), monoclinic and orthorhombic crystals with dd-MOX as guest (Notes to Table 5.2), a triclinic 1 : 2 complex with 3 0 -desamino-2 0 -(2-methoxy-4-morpholinyl)daunomycin, (NDB-ID DDF041; Cirilli et al., 1993) and isomorphous hexagonal complexes with various 9-amino-DACA derivatives (Table 5.4). It is not known whether other base pair sequences behave similarly.

158

5.5

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Isomorphism and polymorphism of A-DNA octanucleotides and the binding of spermine

The self-complementary octanucleotide d(ACGTACCG)2, where the asymmetric unit is a single strand of octamer, together with about 20 water molecules, crystallizes in space group P43212 (Table 5.5). The two octamer strands are related by a crystallographic twofold axis to form a right handed duplex. Among other differently sequenced octanucleotide duplexes crystallizing in the same space group are d(GCCCGGGC)2 (Heinemann et al., 1987), d(ATGCGCAT)2 (Clark et al., 1990), d(GTCTAGAC)2 (Cervi et al., 1992) and d(GTGCGCAT)2 (Bingham et al., 1992). The brominated analog d(ACGTACC[5 BrU])2 is isomorphous, as is the spermine complex of the differentlysequenced d(GTGTACAC)2. spermine di[!-aminopropyl]-tetramethylene diamine C10H26N4 H2N–(CH2)3–NH–(CH2)4–NH–(CH2)3NH2 spermidine

!-aminobutyl-!-aminopropylamine C7H19N3 H2N–(CH2)3–NH–(CH2)4–NH2

Scheme 5.4 Formulae of spermine and spermidine

Table 5.5. The group (space group P43212, Z ¼ 8) of isomorphous tetragonal octanucleotides, mostly native but with two examples of spermine complexation. The crystals have distorted right˚, A ˚ 3. Struchanded A-DNA-like duplex structures with Watson-Crick base pairs. Dimensions in A tures at RT unless stated otherwise Octanucleotide

Intercalated molecule

a

c

Cell Volume

NDB ID; Reference

d(CCCCGGGG)2

native

43.36

24.83

46683

d(CCCGCGGG)2 d(GCCCGGGC)2 d(GGCCGGCC)2 d(GGCCGGCC)2 d(GGCCGGCC)2 d(GGGCGCCC)2

265K 288K 255K 293K

native native native native native native

41.77 43.25 42.06 42.04 40.51 43.28

25.15 24.61 25.17 25.09 24.67 24.66

43880 46035 44527 44343 40485 46192

d(GGGCGCCC)2 at 115K

native

42.74

24.57

44882

d(GTGCGTAC)2 d(GTCTAGAC)2 d(GTGTACAC)243W d(CCCTAGGG)2 d(CTCTAGAG)2 d(GTACGTAC)2

native native spermine native native native

42.22 42.56 42.43 42.22 42.52 42.50

25.07 24.41 24.75 24.90 24.33 24.79

44688 44215 44558 44382 43892 44777

ADH012; HSWR87 ADH056; ES90 ADH0106; FSV97 ADH008; HLFB87 ADH013; WFBR82 ADH058; ES95 ADH098; WFBR82 ADH026; RHES88; SGGEFR89 ADH027; ADH057; EHHFSR88; SGGEFR89 ADH047; BLZS92 ADH041; CLH92 ADH014; JZS89 ADH078; TS96 ADH020; HLK89 ADH023; CDH90

at at at at

ISOMORPHISM AND POLYMORPHISM OF A-DNA OCTANUCLEOTIDES

159

Table 5.5. (Continued ) Octanucleotide

Intercalated molecule

a

c

Cell Volume

NDB ID; Reference

d(GTACGTAC)2 at RT d(ACGTACC[5-BrU])283W at 100K; C72H81BrN30O32P7 d(ACGTACGT)2 d(ATGCGCAT)243W d(ATGCGCAT)243W

native native

42.32 43.597

25.04 26.268

44 846 49 927.5

ADH024; T90 TAP99

native native spermine

42.84 42.41 42.53

24.80 24.90 24.92

45 515 44 785 45 075

ADH070; WACW96 ADH033; CBS90 ADH032; CBS90

References: BLZS92 – Bingham, Li, Zon and Sundaralingam, 1992; CBS90 – Clark, Brown, Sanderson, Chwalinski, Neidle, Veal, Jones, Wilson, Garman and Stuart, 1990; CDH90 – Courseille, Dautant, Hospital, Langlois d’Estaintot, Precigoux, Molko and Teoule, 1990; CLH92 – Cervi, Langlois d’Estaintot and Hunter, 1992; EHHFSR88 – Eisenstein, Hope, Haran, Frolow, Shakked and Rabinovich, 1988; ES95 – Eisenstein and Shakked, 1995; FSV97 – Fernandez, Subirana, Verdaguer et al. 1997; HLFB87 – Heinemann, Lauble, Frank and Blo¨cker, 1987; HLK89 – Hunter, Langlois d’Estaintot and Kennard, 1989; HSWR87 – Haran, Shakked, Wang and Rich, 1987; JZS89 – Jain, Zon and Sundarlingam, 1989; RHES88 – Rabinovich, Haran, Eisenstein and Shakked, 1988; SGGEFR89 – Shakked, Guerstein-Guzikevich, Eisenstein, Frolow and Rabinovich,1989; T90 – Tagusagawa, 1990; TAP99 – Todd, Adams, Powell, Wilcock, Thorpe, Lausi, Zanini, Wakelin and Cardin, 1999; WACW96 – Wilcocks, Adams, Cardin and Wakelin, 1996; WFBR82 – Wang, Fujii, van Boom and Rich, 1982.

Both phases of true polymorphs of oligonucleotides must have the same chemical composition, including base pair sequence (known from the method of preparation). True polymorphism of oligonucleotides appears to be quite rare; native d(CCCGCGGG)2 is one of the few examples encountered among the oligonucleotides considered here. The two polymorphs crystallize in space group P43212 (Z ¼ 8, cell volume ˚ 3 (Table 5.7; ˚ 3 (Table 5.5; ADH0106)) and P21212 (Z ¼ 4, cell volume 42 479 A 43 880 A ADH103–5). The similar cell volumes suggest that the chemical compositions may well be the same. The octamer d(CGCTAGCG) crystallizes in two forms – orthorhombic (P212121, 24.77 ˚ , cell volume 119 187 A ˚ 3, 3 duplexes and 34 waters in the asymmetric unit) 41.52 115.89 A ˚ ˚ 3, four duplexes in the asymand hexagonal (P61, 48.7 115.9 A, cell volume 238 052 A metric unit) (Tereshko, Urpi et al., 1996). The structure of the ﬁrst of these has been reported but not (yet) that of the second, although the comment was made that the packing in the two forms was very similar. As the ratio of the cell volumes is 1 : 2, the two forms could well be polymorphs. We ﬁrst consider the behaviour of the octanucleotides as a group and then discuss the sub-groups in more detail. Six different groups of isomorphous crystals have been reported: ˚ 3; tetragonal, P43212, 18 examples; unit cell volume 44 000 A 3 ˚ ; hexagonal A, P61, 7 examples, unit cell volume 80 000 A ˚ 3; hexagonal B, P6122, 3 examples, unit cell volume 72 000 A ˚ 3; trigonal, R3, 1 example, unit cell volume (hexagonal cell) 230 000 A orthorhombic A, 4 examples (all with the same base pair sequence) P212121, unit cell ˚3 volume 41 000 A ˚ 3). 6. orthorhombic B, P21212, 1 example, unit cell volume 42 000 A 1. 2. 3. 4. 5.

160

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.6. Two different groups of isomorphous hexagonal octanucleotides (space groups P61 and P6122, both Z ¼ 6) and one trigonal group (space group R3), all native. The crystals have distorted right-handed A-DNA-like duplex structures with Watson-Crick base pairs. All of the known P61 structures are of sequence d(GGX4CC) with the four central bases comprising C, G, A, T, U and I. ˚, A ˚ 3. Structures at RT unless stated otherwise. Note that, in contrast to Table 5.3, Dimensions in A the P61 and P6122 structures here are quite different Octanucleotide Hexagonal A P61, Z ¼ 6 d(GGGGCCCC)2 d(GGGATCCC)2 d(GGGTACCC)2 d(GGGTACCC)2 at 100K d(GGGTGCCC)2 d(GGTATACC)2 d(GGCATGCC)2 d(GG[BrU]A[BrU]ACC)2

Intercalated molecule

a

c

Cell Volume

NDB ID; Reference

Native (1) native native native

45.32 46.83 46.80 46.06

42.25 44.49 44.52 44.09

82 530 84 494 84 446 81 006

ADH006; ADH007; ADH030; ADH031;

native native native native

45.62 44.97 46.29 45.05

40.99 41.76 42.97 41.72

81 133 80 056 79 739 73 425

RHES88 ADH010; SRK85 ADH076; NN97 SRC81; SRK85; DB89

32.40 32.18 32.34

79.25 78.51 78.49

72 048 70 409 71 093

ADH078; JS89 ADH038; TLBS93 ADH039; TLBS93

Hexagonal B P6122 Z ¼ 6 d(GTGTACAC)2 Native (2) d(GTGTACAC)2 From spermine (2) d(GTGTACAC)2 From spermidine (2)

MBK85 LFBH88 EFSR90 EFSR90

Notes: 1. 106 ordered solvent molecules were found around each double helix; if a density of 1.5 g cm3 is assumed, then there should be another 260 disordered solvent molecules per asymmetric unit. See Fig. 5.14 for the d(GTGCGCAC)2 packing diagram. 2. These three crystals are essentially identical; neither spermine nor spermidine was detected in the structure analysis. The best results were for the crystal grown in the presence of spermine. References: CLH92 – Cervi, Langlois d’Estantoit and Hunter, 1992; DB89 – Doucet, Benoit, Cruse, Prange and Kennard, 1989; EFSR90 – Eisenstein, Frolow, Shakked and Rabinovich, 1990; JS89 – Jain and Sundaralingam, 1989; LFBH88 – Lauble, Frank, Blo¨cker and Heinemann, 1988; MBK85 – McCall, Brown and Kennard, 1985; NN97 – Nunn and Neidle, 1997; RHES88 – Rabinovich, Haran, Eisenstein and Shakked, 1988; SRC81 – Shakked, Rabinovich, Cruse, Egert, Kennard, Sala, Salisbury and Viswamitra, 1981; SRK85 – Shakked, Rabinovich, Kennard, Cruse, Salisbury and Viswamitra, 1985; TLBS93 – Thota, Li, Bingham and Sundaralingam, 1993; TS96 – Tippin and Sundarlingam, 1996.

The tetragonal, hexagonal A, orthorhombic A and orthorhombic B unit cell volumes ˚ 3; the hexagonal B and trigonal unit cell volumes are are all around 43 000 or 80 000 A related by a factor of 3, but do not ﬁt with the ﬁrst group. It seems reasonable to infer that there are two separate groups of nominally heteromorphic structures – one comprising tetragonal, hexagonal A, orthorhombic A and orthorhombic B, and the second hexagonal B and trigonal. The orthorhombic A group has been noted by its investigators (Fernandez et al., 1997) as showing an unusual spread in cell dimensions. Also, the same sequence (d(CCCGCGGG)2) crystallizes in tetragonal (ADH0106;

ISOMORPHISM AND POLYMORPHISM OF A-DNA OCTANUCLEOTIDES

161

Table 5.7. Two different groups of isomorphous orthorhombic octanucleotides; the space groups are P212121 and P21212; both Z ¼ 4. All crystals have distorted right-handed A-DNA-like duplex ˚, A ˚ 3. Structures at RT unless stated structures with Watson-Crick base pairs. Dimensions in A otherwise Octanucleotide

Intercalated drug

a

b

c

V

NDB code and Reference

Orthorhombic A P212121; Z ¼ 4 d(CCCGCGGG)2 native d(CCCGCGGG)2 native d(CCCGCGGG)2 native d(CCCGCGGG)2 native

21.84 23.13 23.14 24.63

35.40 40.82 40.12 40.59

41.17 42.52 41.90 42.49

31 830 40 146 38 899 42 479

ADH0102; ADH0103; ADH0104; ADH0105;

Orthorhombic B P21212; Z ¼ 4 native d(GTACGTAC)2

38.60

50.82

21.74

42 227

ADH059; LDCP93

FSV97 FSV97 FSV97 FSV97

References: FSV97 – Fernandez, Subirana, Verdaguer, Pyshnyi, Campos and Malinina, 1997; LDCP93 – Langlois d’Estantoit, Dautant, Courseille and Precigoux, 1993.

A13

A13

T12

T12 T4 A5

T4 A5

Fig. 5.12. Stereopair of the d(GTGTACAC)2spermine complex, viewed into the major groove down the dyad axis. The bonds of the spermine are emphasized. This is hexagonal B structure ADH039 (Table 5.6). (Reproduced from Jain, Zon and Sundaralingam, 1989.)

Table 5.5) and orthorhombic A (ADH0105; Table 5.7) structures with cell volumes of ˚ 3 and 42 479 A ˚ 3 respectively. Here the difference ﬁts the usual behavior of 43 800 A polymorphic phases. Another same-sequence pair (GTACGTAC) crystallizes as tetragonal and orthorhombic B forms; these could also be a pair of polymorphs. The two structures have been compared in detail by Langlois d’Estantoit, Dautant, Courseille and Precigoux (1993). One marked difference is in the bend angle of the duplexes in

162

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

the different environments – this is 69 in the tetragonal form and 39 in the orthorhombic B form. The sequence d(ATGCGCAT)2 forms isomorphous tetragonal native (ADH033) and spermine-complex (ADH032) crystals; tetragonal d(GTGTACAC)2 forms only a spermine complex (ADH014; Table 5.5). The hexagonal B d(GTGTACAC)2 sequence forms isomorphous native, spermine and spermidine complexes (Table 5.6; Fig. 5.12). In all these examples, there is no obvious effect of complexation on cell dimensions; the guests were found by structure analysis. The spermine (spermidine) complexes are isomorphous with the native duplexes and thus should be considered as primary solid solution phases. It is not known whether the (relative) spermine content can range from zero (native duplex) to one (maximum spermine content of isomorphous complex). Some interesting features appeared in the ﬁrst structure determination in this area – that of tetragonal d(GGCCGGCC)2 by Wang, Fujii et al., 1982; Table 5.5. The detailed conformation of the duplex was temperature dependent, approximating more closely to B-DNA at 265K and to A-DNA at 255K (Fig. 5.13). This is a theme that has resonated since the early papers, and composition (base pairs and formation of complexes), sequence, hydration state and environment are now recognized as important factors in determining the details of oligonucleotide structures (Shakked, 1991). Our discussion uses primarily information from cell dimensions and space groups but much more detailed studies based on information gleaned from crystal structures

Minor groove

Minor groove A–DNA

a

–8°C

–18°C

b

c

8–DNA

d

Fig. 5.13. (upper row) Space ﬁlling diagrams of four DNA models, all with the sequence GGCCGGCC; the P and O atoms are emphasized. The helix axis is vertical, and a horizontal twofold axis is located in the plane of the paper; (lower row) skeletal views down the helix axis. The complexes are tetragonal, space group P43212, details in Table 5.5. (Reproduced from Wang, Fujii et al., 1982.)

ISOMORPHISM AND POLYMORPHISM OF A-DNA OCTANUCLEOTIDES

163

is becoming available. An example is the study of hydration patterns and intermolecular interactions in the isomorphous tetragonal octameric A-DNA complexes with sequences GGGCGCCC (at 293 and 115K), GGCCGGCC, CCCCGGGG and GCCCGGGC (Eisenstein and Shakked, 1995). We quote from the Abstract: ‘‘The A-DNA major groove is extensively hydrated and together with the hydration shells of the sugar–phosphate backbone can form an ordered network of fused polygons. The water structure of the phosphate backbone is less conserved than that of the grooves. Characteristic hydration patterns are associated with speciﬁc base sequences. The A-DNA minor groove provides sites for intermolecular contacts through hydrophobic and polar interactions. Well-ordered water molecules mediate interduplex interactions that involve either the grooves or the backbone, or both. The direct and water-mediated intermolecular interactions observed in the A-DNA crystal structures are relevant to various recognition motifs between DNA and other molecules.’’

Fig. 5.14. The arrangement of d(GTGCGCAC) duplexes in the tetragonal crystal (space group no. 96, P43212) projected down the [001] axis. The elliptical solvent channels run along the vertical ˚ in cross-section; these are ﬁlled with solvent molecules 21 axes and are approximately 20 10 A that are not shown. The only direct interaction between neighboring duplexes involves the abutment of the terminal base pairs of one molecule against the sugar phosphate backbone of symmetry related molecules. Note that ‘‘fourfold axis’’ in the original caption should be replaced by ‘‘twofold axis’’. (Reproduced from Wang, Fujii et al., (1982)).

164

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

c

b

a

Fig. 5.15. Projection of the structure of d(GG(BrU)A(BrU)CC)2 down [001] axis (hexagonal A, Table 5.6). The octamer crystallizes in space group P61 with one double helix in the asymmetric unit. The octamers have the A-DNA conformation with 10.9 base pairs per turn, a mean tilt ˚ . Consideration of the angle of 18 and an average separation between base pairs of 3.4 A diffuse scattering shows that the channels contain a me´lange of water molecules and B-DNA. A companion diagram of the isomorphous d(GGGGCCCC)2 given by McCall, Brown and Kennard (1985) (not reproduced here) shows six octameric molecules in an inﬁnite spiral viewed in projection down the 61 screw axis. (Reproduced from Doucet, Benoit, Cvruse, Prange and Kennard (1989).)

Table 5.8. Two different crystal types of 1:2 octamer–distamycin complexes. All crystals have distorted right-handed B-DNA-like duplex structures with modified Watson-Crick base pairs. Structures at RT unless stated otherwise Octameric oligonucleotide

Intercalated drug

a

c

V

Tetragonal P4122, Z ¼ 8; asymmetric unit contains one DNA strand, one distamycin molecule and one Mg cation d(ICICICIC)2 distamycin 27.93 58.62 45 729 d(ICATATIC)2 distamycin 27.86 58.62 45 500 d(ICITACIC)2 distamycin 28.03 58.04 45 601 d(IcICICIC)2 distamycin 27.92 57.70 44 979 d(IcIcICIC)2 distamycin 27.93 57.47 44 799

NDB code / Reference

GDHB25; CRRS94 GDLB50; CRS97 GDLB51; CRS97 CRS95 CRS95

ISOMORPHISM AND POLYMORPHISM OF A-DNA OCTANUCLEOTIDES

165

Table 5.8. (Continued ) Octameric oligonucleotide

Intercalated drug

a

b/

c

V

Monoclinic I2; Z ¼ 2; asymmetric unit contains one DNA strand and one distamycin molecule d(ITITACAC)236W distamycin 28.30 25.05 29.14 19 509 109.2 distamycin 28.11 25.33 30.88 20 491 d(ICATATIC)2 111.26

NDB code / Reference

DD0043; DPS03 GDLB49; CRS97

Notes: Lower case letters represent RNA residues. The unit cells are given for the two I2 structures; these are isomorphous. The space group used in the original publication was C2.

OH N

N

N

N

CH2OH

O H

H HO

OH

I is inosine (hypoxanthine riboside) References: CRRS94 – Chen, Ramakrishnan, Rao and Sundaralingam, 1997; CRS95 – Chen, Ramakrishnan and Sundaralingam, 1995; CRS97 – Chen, Ramakrishnan and Sundaralingam, 1997; DPS03 – Deng, Pan and Sundaralingam, 2003.

Exceptionally, the packing arrangement has been discussed in some detail for this group of isomorphous tetragonal complexes (Table 5.5). Analogous packing diagrams have been given by Bingham, Li, Zon and Sundaralingam. (1992) and Wang, Fujii et al. (1982; their Fig. 3 reproduced in Fig. 5.14). The packing in the hexagonal A family (Table 5.6) is shown in Fig. 5.15; the arrangement of spirals of octameric duplexes should be compared with the left hand diagram in Fig. 5.20 showing a spiral arrangement of decanucleotides. The synchrotron diffraction patterns from d(GG[BrU]A[BrU]ACC)2 have both a (sharp) Bragg and a diffuse component (Doucet, Benoit, Cruse, Prange and Kennard, 1989); the Bragg pattern gives an arrangement of A-DNA helices isomorphous with the other structures in Table 5.6 while the diffuse pattern was only compatible with a disordered array of B-DNA helices contained in the A-DNA framework These replace about 10%

166

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

of the water molecules found in the other structures. These unusual results were interpreted to show that ‘‘under certain conditions of crystallization the A and B conformations of the same DNA fragments can co-exist in the highly hydrated environment of the crystal lattice.’’ Indeed the arrangement described could be classiﬁed as a tunnel inclusion complex (Chapter 6), with some resemblance to neat selenourea. Some octanucleotides form minor-groove binding complexes with the natural antibiotic distamycin (Scheme 5.5). Two different crystal types (tetragonal, and monoclinic) have been found (Table 5.8). The molecular structure of the complex is shown in Fig. 5.16; both phases have essentially the same host-guest structure. The asymmetric unit in the monoclinic crystals consists of one octamer strand and one distamycin molecule; in the tetragonal crystals one double helix and two distamycin molecules. The distamycin complex of d(ICATATIC)2 crystallizes in the two space ˚3 groups P4122 and C2 (Fig. 5.17 a and b), with cell volumes of 45 500 and 20 747 A respectively; the ratio is 2.2 and it is possible (but not certain) that the two phases are heteromorphs.

Fig. 5.16. Stereodiagram of the 1 : 2 d(ITITACAC)2 complex with distamycin, showing the antiparallel side-by-side arrangement of the two distamycin molecules in the minor groove (monoclinic, Table 5.8). Complexed hairpin dimers have been shown by Kielkopf et al. (1998) (see Fig. 5.19). An example of a single propamidine molecule in the minor groove of the dodecameric d(CGCGAATTCGCG)2 duplex is shown in Fig. 5.21. (Reproduced from Deng, Pan and Sundaralingam, 2003.)

MI NOR GR OOVE BI NDE RS

167

(a)

(b)

Fig. 5.17. Stereo diagrams for (a) the tetragonal d(ICITACIC)2 structure (GDLB51) and (b) the monoclinic B d(ICATATIC)2 structure (GDLB49). The tetragonal crystals, viewed down [010] contain Mgþþ(H2O)6 cations, appearing in the form of asterisks. These ions are absent from the monoclinic crystals. This supports the conclusion from comparison of cell volumes that these two modiﬁcations are not heteromorphs (see text). The tetragonal crystals have sheets of quasi-cylindrical complex molecules in (004) planes with residual channels containing disordered solvent molecules. In the monoclinic B crystals the molecules are arranged in sheets on (011) planes. (Reproduced from Chen, Ramakrishnan and Sundaralingam, 1997.)

5.6 Minor groove binders 5.6.1 Drug molecules that enter the minor groove The general background has been given by Tidwell and Boykin (2003) and Moravek, Neidle and Schneider (2002); as noted earlier, in principle molecules can bind to either the major or minor grooves of DNA, the major groove being the binding site for many DNA interacting proteins while the minor groove is suited to small molecule binding. The oligonucleotides that complex with minor groove binders are decamers and dodecamers. These are considered separately – the decamers present a rather complex and diffuse

168

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

pattern of structures, while the pattern for dodecamers – native species and complexes alike – is much more compact. We ﬁrst group together in Scheme 5.5 the minor groove binders that have been reported. The curved proﬁle of these molecules, adapted to the general shape of the Scheme 5.5. Drug molecules that enter the minor groove N N R

N

2O

N

H

OR1

H H3C

N+

R2 =

R1 = H Hoechst 33 258

H

R1 = ethyl

Hoechst 33 342

N R1 = H Compound 16 N H NH2

H

+ H2N

NH2

N 6

4⬘

+ NH2

DAPI 4⬘,6-diamidino-2-phenylindole

CH3

O

N Guanidinium O

amide 2 N

N

CH3

H N H amide 1

N

H

Netropsin

O H

N

Amidinium NH2

H2N

+

+

amide 3 NH2

NH2

MI NOR GR OOVE BI NDE RS

CH3

169

O

N N N

O

CH3

N

H

N O

H N

N NH2 +

+

H2N

H

H Imidazole-Pyrrole Lexitropsin

NH2

NH2 CH3

O

N

amide 3 N

O

CH3

N

H N

amide 2

H H

N

Distamycin O

amide 4 +

amide 1 N

O

NH2

NH2

H H

Naturally occurring netropsin has two pyrrole rings; the guanidinium head at the left and the amidinium tail at the right are both positively charged. Imidazole-pyrrole lexitropsin is identical to netropsin except that the left pyrrole ring has been replaced by imidazole. Distamycin has an uncharged –CHO head on the left and charged amidinium tail on the right. (after Goodsell, Ng et al., 1995).

O

O R

NH2

H2N +

+ NH2

R = trimethylene; propamidine R = pentamethylene; pentamidine H2 C

R = gamma-oxa-pentamidine C H2

H2 C O

C H2

NH2

170

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

H N

N N H2N

NH2

berenil +

+

NH2

NH2

O NH2

H2N +

+ NH R

R = H; furamidine R = ethyl; BEF R = isopropyl; BIPF R = cyclopropyl; BCPF

HN R

N N N H3N+

N H

N H N

TRIBIZ N H

O H3C

minor groove, is quite striking. Aromatic diamidines have broad spectrum effectiveness against a range of microbial species. However, so far only pentamidine, despite some negative features, has found clinical use. For reasons of space we hardly consider situations where the drug is covalently linked to the oligonucleotide (e.g. Kopka, Goodsell, Baikalov et al., 1994).

MI NOR GR OOVE BI NDE RS

imidazole Im1 H N

hydroxy-pyrrole Hp2 pyrrole Py3

O H N

N

171

N H

O

H N

N H

amide Am1

OH

amide Am2

pyrrole Py4 O

H N R

N H amide Am3

O R= N H

O

HN + N H

CH3 CH3

ImHpPyPy Dp The polyamide sequence shown is ImHpPyPy Dp where is -alanine and Dp is dimethylaminopropylamide. The other guest is ImPyPy Dp (i.e. hydroxyl of Hp2 replaced by H).

5.6.2 Decameric oligonucleotides The decameric oligonucleotides present a rather complicated structural picture, summarized some years ago by Dickerson, Goodsell and Kopka (1996) for fourteen examples. At the time of writing (October, 2004) some twenty-odd decameric structures have been reported (including one complex) and they are found in six different groups (Table 5.9). ˚, 1. Nine are in a monoclinic cell, space group C2, Z ¼ 2, a 32.3, b 25.5, c 34.4 A 3 ˚ ¼ 113 , V ¼ 26 000 A , with one strand per asymmetric unit. This has been termed the CG family by Quintana, Grzeskowiak et al. (1992); decamers with the sequence type CCARxxYTGG tend to belong to this group. ˚ , V 54 000 A ˚ 3, 2. Two are in space group P212121, Z ¼ 4, a 36.6, b 42.5, c 34.7 A with one helix per asymmetric unit. The native and drug complex pair are isomorphous so the drug complex is a primary solid solution phase. There are two di-imidazole lexitropsin drug molecules side-by-side in the minor groove. 3. Four are in another orthorhombic cell, space group P212121, Z ¼ 4, a 38.9, b 39.4, ˚ , V ¼ 51 000 A ˚ 3, with one helix per asymmetric unit. This has been termed c 33.3 A the KK family by Quintana, Grzeskowiak et al. (1992); decamers with the sequence type CGAxxxxTCG tend to belong to this group.

˚,A ˚3 Table 5.9. Decameric oligonucleotides; all crystals are distorted right-handed B-DNA-like duplexes with Watson-Crick base pairs. Dimensions in A Decameric Oligonucleotide

Drug in the minor groove

Group I: monoclinic, C2, Z ¼ 2; CQ family Native d(CCAGGCCTGG)2, Native, from d(CCAACITTGG)2, 248K Ca2þ solution native d(CCAAGATTGG)2, d(CCAACGTTGG)2, native native d(CCAACGTTGG)2, native d(CCAGTACTGG)2, d(CCAGCGCTGG)2, native native d(CCAAIATTGG)2, d(CCAGGCCTGG)2, native Group II: orthorhombic, P212121, Z ¼ 4 d(CATGGCCATG)2, native d(CATGGCCATG)2, di-imidazole lexitropsin Group III: orthorhombic, P212121, Z ¼ 4; KK family native d(CGATCGATCG)2, d(CGATTAATCG)2, native

a

b/

c

Cell Volume

NDB ID/Reference

31.25 31.87

25.49 116.7 25.69 114.1

34.82 34.21

24 779 25 833

HA89 LKK93

32.52 32.25 32.00 31.73 32.24 32.21 32.15

26.17 25.53 25.37 25.79 25.35 25.14 25.49

34.30 34.38 33.63 34.22 34.19 34.14 34.82

25 556 25 978 26 737 27 022 26 933 25 116 25 490

PHC87; PYD91 PYD91; YPD91 BD0033; CD00 BD0023; KDKR00 BD0035; CD00 BD0055; LLKKD BDJ017; HA89

36.60 36.65

42.49 42.64

34.69 34.68

53 948 54 196

BDJ051; CKCD93 GDJ054; KGH97

38.93 38.60

39.36 39.10

33.30 33.07

51 025 49 911

BDJ025; GYPD91 BDJ031; QGYD92

118.9 113.4 112.98 116.9 117.17 114.70 116.71

d(CGATATATCG)2, d(CGATATATCG)2,

Native (Ca) Native (Mg)

38.76 38.69

40.06 39.56

33.73 33.64

52 373 51 489

YQD92; BDJ036 BDJ037; YQD92

Group IV: hexagonal, P6, Z ¼ 6 d(CCAGGC[5-MeC]TGG)2 d(CCAAGCTTGG)2

native Native (Ca)

53.77 53.08

53.77 53.08

39.35 34.32

98 527 83 741

HA91, HH92 BDJ052; GGK93

Group V: hexagonal, P61, Z ¼ 6 d(CCAAGCTTGG)2

native

45.32

45.32

42.25

75 151

MBK85

Group VI: trigonal, P3221, Z ¼ 6 d(CGATCG(5-MeA)TCG)2 d(CCATTAATGG)2 d(CCACTAGTGG)2 d(CCAACITTGG)2

native native native Native (Mg)

33.38 33.20 32.90 33.23

33.38 33.20 32.90 33.23

98.3 96.04 95.10 94.77

94 001 91 677 89 146 90 628

BGY93 BDJ055; GKD94 BDJ061; SG-G94 LKK93

References: BGY93 – Baikalov, Grzeskowiak, Yanagi, Quintana and Dickerson, 1993; CD00 – Chiu and Dickerson, 2000; CKCD93 – Goodsell, Kopka, Cascio and Dickerson, 1993; GKD94 – Goodsell, Kaczor-Grzeskowiak and Dickerson, 1994; GYPD91 – Grzeskowiak, Yanagi, Prive´ and Dickerson, 1991; GGK93 – Grzeskowiak, Goodsell, KaczorGrzeskowiak, Cascio and Dickerson, 1993; HA89 – Heinemann and Alings, 1989; HA91 – Heinemann and Alings, 1991; HH92 – Heinemann and Hahn, 1992; KDKR00 – Kielkopf, Ding et al., 2000; KGH97 – Kopka, Goodsell, Han, Chiu, Lown and Dickerson, 1997; LKK93 – Lipanov, Kopka, Kaczor-Grzeskowiak, Quintana and Dickerson, 1993; LLKDD – Lisgarten, Lipanov, Kopka et al., to be published; NDB BD0055; MBK85 – McCall, Brown and Kennard, 1985; PHC87 – Prive´, Heinemann, Chandrasegaran, Kan, Kopka and Dickerson, 1987; PYD91 – Prive´, Yanagi and Dickerson, 1991; QGYD92 – Quintana, Grzeskowiak, Yanagi and Dickerson, 1992; SG-G94 – Shakked, Guzikevich-Guerstein et al., 1994; YPD91 – Yanagi, Prive´ and Dickerson, 1991; YQD92 – Yuan, Quintana and Dickerson, 1992.

174

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

˚ , V 84 000 A ˚ 3, 4. Two are hexagonal, space group P6, Z ¼ 6, a 53.1, c 34.3 A with one duplex per asymmetric unit. 5. One (d(CCAAGCTTGG) 2) is in a P61 hexagonal cell, Z ¼ 6, a 45.32, c ˚ , V 75 000 A ˚ 3, This same sequence is found in P6 but the difference in cell 42.25 A volumes suggests that these are not polymorphs. ˚ , V 95 000 A ˚ 3, 6. Four are trigonal, space group P3221, Z ¼ 6, a 33.4, c 98.3 A with one helix per asymmetric unit. None of these cells match those given in Tables 5.10 and 5.11 for different groups of decamer-drug complexes. Using volume per asymmetric unit as a criterion, one may surmise that Groups I, II, III and V are heteromorphic; all have volumes per asymmetric ˚ 3. There is no evidence allowing a distinction between enantiotropes unit around 13000 A and monotropes. When molecules are ﬂexible, different conformers are often found in different polymorphs. For DNA oligomers, base pair sequence can affect conformation; additionally, solvent and ion arrangement play an important role in determining crystal structures, which consequently are not easily accounted for. One path towards unscrambling the various factors is to examine ‘‘different sequences in the same environment and the same sequence in different environments’’ (Lipanov, Kopka et al., 1993). In terms of our deﬁnitions, ‘‘the same sequence in different environments’’ implies the possibility of true polymorphism, while ‘‘different sequences in the same environment’’ implies the possibility of heteromorphism. In both situations, the two phases should have the same overall composition. The data in Table 5.9 provide some leads. Baikalov et al. (1993) have noted that the two orthorhombic phases and the monoclinic phase have similar packing densities while the ˚ 3 in the trigonal phase is more loosely packed; the ‘‘molecular’’ volumes are about 6250 A ﬁrst two groups and about 10% larger in the third, presumably due to differences in composition. In orthorhombic group III of Table 5.9, the d(CGATATATCG)2 phase has only slightly different cell dimensions when grown from solutions containing Mg2þ or Ca2þ. However, d(CCAACITTGG)2 gives a monoclinic phase from a Ca2þ solution and a trigonal phase from a Mg2þ solution. Because of the composition differences, these are not polymorphs, nor even heteromorphs – the monoclinic phase has ﬁve base pairs, one cacodylate ion7, 72 waters and one hepta-coordinated Ca2þ in the asymmetric unit, while the trigonal phase has ten base pairs, 36 water molecuiles and one octahedral Mg2þ in its asymmetric unit. Perhaps surprisingly, the trigonal phase has the simpler chemical composition. Clearly care is needed when making generalizations based on comparison of unit cell volumes and inferring structural arrangements about metal ions. The packing in the KK (d(CGAxxxxTCG)2) family is shown in Fig. 5.18. The decamers stack one on top of the other along the c axis to form pseudo-continuous helices arranged in square array, with extensive lateral contacts along the a and b directions. Besides extensive van der Waals interactions and hydrogen bonding, the octahedral Mg2þ(H2O)6 cations play a role in the cohesion; details are given by Quintana, Grzeskowiak, Yanagi and Dickerson (1992). Polyamide hairpin dimers containing the aromatic groups imidazole, hydroxypyrrole and pyrrole provide a means, through analysis of hydrogen bonding, for discriminating 7

Cacodylic acid is tetrahedral (CH3)2As¼O(OH).

MI NOR GR OOVE BI NDE RS

175

Fig. 5.18. Stereodiagram of four columns of stacked KK-type decamer helices viewed along b, with a from left to right and c from bottom to top. A skeletal representation is given above and a spaceﬁlling representation below. This diagram illustrates how the minor grooves join to build continuous diagonal channels through the crystal. (Reproduced from Quintana, Grzeskowiak, Yanagi and Dickerson (1992).)

among the four Watson–Crick base pairs. An imidazole/pyrrole (Im/Py) pair (the abbreviations are shown above in Scheme 5.5) distinguishes G-C from C-G and both of these from A-T and T-A, as has been demonstrated through the structure of decameric {d(5 0 -CCAGGCCTGG-3 0 ) (ImImPyPy--Dp)} (Kielkopf, Baird, Dervan and Rees, 1998). The distinction between A-T and T-A has been made through a detailed comparison of hydrogen bonding and other interactions in the ImHpPyPy--Dp Hp/Py and ImPyPyPy--Dp decameric oligonucleotides (i.e Hp/Py compared to Py/Py) (Kielkopf, White, Szewczyk et al., 1998) (crystal data in Table 5.10). The particular relevance here is that a second type of side-by-side packing of the polyamide in the minor groove has been

176

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.10. Binding in the minor groove – the decameric oligonucleotides are all distorted right˚ and A ˚ 3. The cells handed B-DNA-like duplexes with Watson-Crick base pairs. Dimensions are in A are all reduced and the crystallography is discussed in the text Decameric Oligonucleotide

Drug in the minor groove/spce group

a

b/

c

Cell Vol.

Reference

25.7 116.9 26.90 98.91 30.51 103.09 30.20 101.09

34.2

24848

KDKR00

53.62

61987

KBDR98

53.48

67961

51.49

66418

BDD002; KW98 BDD003; KW98

d(5 0 -CCAGGCCTGG-3 0 )2

Native; C2

31.7

d(5 0 -CCAGGCCTGG-3 0 )2

ImImPyPy--Dp;I2

43.50

d(5 0 -CCAGTACTGG-3 0 )2

ImHpPyPy--Dp;I2

42.76

d(5 0 -CCAGTACTGG-3 0 )2

ImPyPyPy--Dp; I2

43.46

Notes: The 5-bromouridine substituted crystal was isomorphous and crystallized in space group C2 (explicit cell dimensions were not given). 5-Bromocytosine substitution leads to crystallization in space group P212121 ˚ , cell volume ¼ 59 567 A ˚ 3 (KBDR98); this could be isostructural with with a ¼ 34.4, b ¼ 39.0 and c ¼ 44.4 A orthorhombic Group II of Table 5.9. The ﬁrst entry is a member of the CQ family (Table 5.9). References: KBDR98 – Kielkopf, Baird, Dervan and Rees, 1998; KDKR00 – Kielkopf, Ding, Kuhn and Rees, 2000; KW98 – Kielkopf, White et al., 1998.

demonstrated (Fig. 5.19). The structure of the d(5 0 -CCAGGCCTGG-3 0 ) (native) oligo˚ nucleotide was determined, at liquid nitrogen temperature, to the high resolution of 0.74 A ˚ . This made it possible to identify alternative using synchrotron radiation with ¼ 0.78 A conformations for phosphates, calcium ions and networks of water molecules; also some hydrogen atoms of base pairs could be identiﬁed. The oligonucleotide sequence d(5 0 -CCAGGCCTGG-3 0 )2 has already been met in ˚ 3), Table 5.9, the native form crystallizing in space group C2 (unit cell volume 24 779 A and with dimensions only slightly different from those of the ﬁrst entry in Table 5.10; presumably these are essentially the same material, The following three entries can be classiﬁed as isostructural. Reduction of the cells gives changes in cell dimensions, bringing the values closer to 90 , and a change of space group from C2 to I2. The complexes are separate phases in the phase diagram. End-to-end binding of netropsin is found (Chen, Mitra et al., 1998; GDJ059) in the minor groove of decameric d(CCCCCIIIII)2 which crystallizes in a triclinic cell (P1, Z ¼ 1, ˚ 3,). The structural unit is ˚ , 86.30, 84.50, 68.58 , V ¼ 36 992 A 32.56, 32.59, 37.64 A one decameric duplex plus two netropsin molecules; There are two such duplexes in the asymmetric unit. We have limited our coverage to duplexes with complete Watson–Crick base pairing but some exceptions are brieﬂy mentioned. There is a group of decanucleotides (Table 5.11) that actually have an octameric duplex arrangement with the ﬁrst and last bases of the sequence interacting with similar moieties in other octanucleotides. For example the decamer d(5 0 -GGCCAATTGG-3 0 )2 has a Watson–Crick base-paired B-DNA octamer duplex with the two terminal 5 0 -G and G-3 0 bases of each single strand lying within the minor groove of a symmetry-related duplex. This structure has similarities to

MI NOR GR OOVE BI NDE RS

177

Fig. 5.19. Structure of the decanucleotide d(5 0 -CCAGGCCTGG-3 0 )2 complexed with polyamide, showing the antiparallel, side-by-side arrangement of the guests in the minor groove. This diagram appeared on the cover of Helvetica Chimica Acta in illustration of a paper by Marques et al. (2002); more details are given by Kielkopf, White et al. (1998).

that of the native sequence d(5 0 -CGCAATTGCG-3 0 ) (Spink, Nunn et al., 1995) that has a two fold symmetry axis through the centre of the duplex and one DNA strand in the asymmetric unit. Despite similarities in the unit cell dimensions of the native and complexed CGCCAATTCG species (entries 2 and 3 of Table 5.11), the crystals are not isomorphous because of the difference in symmetry and the complex is a separate phase in the phase diagram. There is primary solid solubility of DAPI in the decameric oligonucleotide GGCCAATTGG (entries 4 and 5 of Table 5.11); here the asymmetric unit consists of one duplex decameric oligonucleotide and two crystallographically independent (but geometrically similar) polyamide molecules. Another example just over our borderline is d(CGACGATCGT)2; the crystals are ˚ , ¼ 113.45 (Qiu, monoclinic, space group P21, a ¼ 26.45, b ¼ 34.66, c ¼ 32.17 A Dewan and Seeman, 1997), The crystallographic asymmetric unit contains one B-DNA

178

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

Table 5.11. Unit cells of a group of isomorphous decameric oligonucleotides with octameric Watson-Crick duplex structure. The drug molecules are located in the minor groove. The first pair ˚ and A ˚ 3. has space group I212121 and the others have space group P212121 Dimensions are in A Structures at room temperature unless stated otherwise Decanucleotide Space group I212121 d(5 0 -CG(5-IC)AATTGCG-3 0 )2 d(5 0 -CGCAATTGCG-3 0 )2 Space group P212121 d(5 0 -CGCAATTGCG-3 0 )2 d(5 0 -GGCCAATTGG-3 0 )2 116W2Mg2þ, at 120K d(5 0 -GGCCAATTGG-3 0 )2

Drug in the minor groove

a

b

c

Cell Vol.

NDB ID; Reference

Native Native (1)

27.52 27.01

38.64 39.26

53.49 54.01

57 273 57 273

SNVBN95 SNVBN95

Netropsin (2) Native

24.84 26.11

39.80 36.46

54.08 52.56

53 465 49 606

DAPI (2)

25.616

36.565

52.961

49 606

NGN97 BD0006; VTM99 VSM99

Notes: 1. Berenil was present in the crystallizing medium but was not found in the electron density maps whereas netropsin did appear. 2. For formulae of berenil, DAPI and netropsin see Scheme 5.5. References: NGN97 – Nunn, Garman and Neidle, 1997; SNVBN95 – Spink, Nunn, Vojtechovsky, Berman and Neidle, 1995; VSM99 – Vlieghe, Sponer and Van Meervelt, 1999; VTM99 – Vlieghe, Turkenburg and Van Meervelt, 1999.

double helix. The nucleotide has eight Watson–Crick base pairs and a two nucleotide 5 0 -sticky end at each end of the duplex. The sequence GGCCAATTGG crystallizes as a fully base-paired Watson–Crick duplex ˚ , 105.2 ; Wood, in a monoclinic cell (space group C2, reduced cell 38.29 24.70 61.84 A Nunn, Trent and Neidle, 1997) that is not isomorphous with the monoclinic cell of ˚ , 93.91 ; Goodsell, CTCTCGAGAG (space group C2, reduced cell 40.83 24.32 49.83 A Grzeskowiak and Dickerson, 1995), These, and other examples, have crossed helix structures that we shall not explore further. 5.6.3

Polymorphs or intermediate phases? An example from the decanucleotides

We have noted previously that it is often difﬁcult to deﬁne the relationships among different crystal modiﬁcations because their compositions are not known. This has been illustrated above (Fig. 5.17) for the tetragonal d(ICITACIC)2 and monoclinic B d(ICATATIC)2 octanucleotide structures. A rather complete example of what is required is provided by Tippin and Sundaralingam (1997) for the crystals of the A-DNA decamers d(CCGGGCCCGG), d(CCGGCC[m5C]GG), d(C[m5C]GGGCC[m5C]GG) and d(CCGGGCC[m(Br)5C]GG). The crystal data are given in Table 5.12; there are three isomorphous groups–hexagonal, orthorhombic A and orthorhombic B. Packing diagrams are given in Fig. 5.20 from which it is clear that the packing density increases from hexagonal through orthorhombic A to orthorhombic B. The spermine content, determined from the structure analyses, also increases in the same order from zero molecules per double helix through 1 to 2. Although Tippin and Sundaralingam

MI NOR GR OOVE BI NDE RS

179

Table 5.12. Crystal data for various modifications of decameric oligonucleotides, some complexed with spermine. All crystals have distorted right-handed A-DNA-like duplex structures with modified ˚, A ˚ 3. All data from Tippin and Sundaralingam (1997) Watson-Crick base pairs. Dimensions in A Decameric oligonucleotide

a

b

Hexagonal P61, Z ¼ 6; double helix to spermine ratio d(CCGGGCC[m5C]GG)2 55.03 55.03 54.71 54.71 d(C[m5C]GGGCC[m5C]GG)2 55.68 55.68 d(CCGGGCC[(Br)5C]GG)2 Orthorhombic A P212121; Z ¼ 4; d(CCGGGCCCGC)2 d(CCGGGCC[m5C]GG)2 d(CCGGGCC[(Br)5C]GG)2 d(C[m5C]GGGCC[m5C]GG)2

c

V

NDB code

1:0; solvent content 67% 45.88 120 317 45.82 118 770 46.24 124 147

double helix to spermine ratio 24.91 44.87 48.14 24.78 44.57 48.00 24.36 44.29 48.05 24.83 44.72 47.91

1:1; solvent content 40% 53 816 53 015 51 849 53 199

Orthorhombic B P212121; Z ¼ 4; double helix to spermine ratio 1:2; solvent content 24% 23.74 40.89 43.60 42 316 d(CCGGGCCCGC)2 d(CCGGGCC[m5C]GG)2 23.64 40.82 43.44 41 929

P61

Ortho 1

Ortho 2

Fig. 5.20. Unit cell views of the hexagonal and orthorhombic A and B modiﬁcations of d(CCGGGCC[m5C]GG)2. The hexagonal cell is seen down the c axis, with the 61 screw axis at the origin; both orthorhombic cells are seen down their a axes. The view of the hexagonal cell down the c axis should be compared with the arrangement of the d(GGGGCCCC)2 octamers given by McCall, Brown and Kennard (1985) (see caption to Fig. 5.15). The space group is P61 in both examples. (Reproduced from Tippin and Sundaralingam, 1997.)

(1997) use the term ‘‘polymorphic’’ in their title and list of keywords, it is clear that the three types are ‘‘native’’, ‘‘monospermine’’ and ‘‘dispermine’’ phase rule compounds, no different in principle from ‘‘anhydrate’’, ‘‘monohydrate’’ and ‘‘dihydrate’’. A more exact formulation would require knowledge of the degree of hydration. Note that the base pair sequence d(C[m5C]GGGCC[m5C]GG)2 occurs in hexagonal and orthorhombic A phases, as does the sequence d(CCGGGCC[(Br)5C]GG)2, The base pair sequence d(CCGGGCCCGC)2 occurs in the two orthorhombic phases while the sequence d(CCGGGCC[m5C]GG)2 occurs in all three phases.

Table 5.13. Native dodecameric oligonucleotides and the isomorphous complexes binding drugs in the minor groove. All crystals have space group ˚,A ˚ 3. We use ‘native’ while NDB uses P212121, Z ¼ 4 and are distorted right-handed B-DNA-like duplexes with Watson-Crick base pairs. Dimensions in A ‘plain’ Dodecameric Oligonucleotide

Drug in the minor groove

a

b

c

Cell Vol.

NDB ID; Reference

d(5 0 -CGCGAATTCGCG-3 0 )2 d(5 0 -CGCGAATTCGCG-3 0 )2 at 16K (see text) d(5 0 -CGCGAATTCGCG-3 0 )2 d(5 0 -CGCGAATTCGCG-3 0 )2 d(5 0 -CGCGAATTCGCG-3 0 )2 d(5 0 -CGCGAATTCGCG-3 0 )2 160W at 137K d(5 0 -CGCGAATTCGCG-3 0 )2 at 248K d(CGCGAATTCGCG)2220 W, at 100K d(CGCGAATTCGCG)2 54W d(CGCGAATTCGCG)2 73W d(CGCGAATTCGCG)279W d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)272W d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)2 at 300K; also at 273, 248 and 173K* d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)236W

native native

24.87 23.44

40.39 39.31

66.20 65.26

66 498 60 132

BDL001; DrDi81 BDL002; DSD82; HDK85

native native native Spermine, Mg, Na

25.30 25.59 25.94 25.186

40.24 40.82 40.74 40.208

65.94 66.67 66.20 65.656

67 132 69 642 69 960 66 488

BD0005; BD0029; DrDi81 BD0041; SHMVW00 BD0054; HSVW01 BDL084; SMHW98

Monoimidiazole lexitropsin furamidine

24.03

39.26

66.30

62 549

GNKLD95

24.24

39.94

65.88

63 781

GSN98

furamidine propamidine pentamidine BIPF BCPF -oxapentamidine# 16 Hoechst-33258

25.28 25.00 24.37 24.60 25.43 24.69 24.59 25.04

40.69 40.88 40.00 40.07 40.66 40.33 40.44 40.33

66.73 67.28 66.07 65.45 66.13 66.20 65.76 65.85

68 641 68 760 64 405 64 516 68 377 65 918 65 393 66 500.

LTNB96 NJN934b EJN92 TCKW96 TCKW96 GDL027; NJN94a CB95 GDL006; QLD91

cisplatin cisplatin netropsin

24.36 24.33 24.27

40.05 40.08 39.62

66.13 66.26 63.57

64 518 64 613 61 127

d(CGCGAATTCGCG)2 d(CGCGAATTCGCG)2

berenil DAPI

24.51 25.25

39.98 40.71

66.23 66.53

64 899 68 659

#WPDD84 #WPDD84 KYG85a; SMR92b, GKD95 BSSJ90 TGC89

d(CGCGAATTCGCG)2

Cells with slightly different dimensions are given in DD0005 (SBC00), 6, 8, 9, 13 for ‘benzimidazole derivative’ see also WNTN95 d(CGCGAATTCGCG)2 Bis-(piperidino-ethyl)furamidine 25.70 40.73 66.38 69484 DD0025; NS d(CGCGAATTCGCG)2 Cells with slightly different dimensions are given in DD0034, 35 for ‘Bis-phenylfuran derivative’ d(CGCGAATT[5BrC]GCG)2 Native 24.71 40.56 65.62 65767 BDLB03; FKKDD82 d(CGCGAATT[5BrC]GCG)2 netropsin 24.27 39.62 63.57 61127 KYG85a; GKD95 d(5 0 -CGCATATAGCG-3 0 )2 native 23.54 38.86 66.57 60896 BDL007; YPGD88 d(5 0 -CGCAAAAATGCG-3 0 )2 native 24.54 40.32 65.86 65165 BDL015; DSS89 d(CGCAAATTTGCG)2 native 24.87 40.90 65.64 66768 BDL038; EBSSN92 native 25.20 41.65 65.81 69073 CFWR87 d(CGCAAATTTGCG)2, propamidine 24.78 41.16 65.51 66817 GDL032; NN95; d(CGCAAATTTGCG)2, d(CGCAAATTTGCG)2, 65W berenil 24.64 40.61 65.07 65111 BDL016; BSGN92 distamycin 25.20 41.07 64.65 66910 CFWR87 d(CGCAAATTTGCG2) d(CGCAAATTTGCG)2 II netropsin 26.48 41.26 66.88 73071 CAM89 d(CGCAAATTTGCG)2 netropsin 25.65 42.03 65.33 70430 QLD91 TRIBIZ 24.70 40.82 64.90 65436 GDL039; CGNLL96 d(CGCAAATTTGCG)2 25.27 41.32 65.11 67985 SBSN94; VGA94 d(5 0 -CGCAAATTTGCG-3 0 )2x61W I Hoechst-33258 native 24.28 39.35 66.37 63411 BDL078; S-SA97 d(CGCGATATCGCG)2 netropsin 25.48 41.26 66.88 70311 GDL001; CAM89 d(CGCGATATCGCG)2 d(CGCGATATCGCG)2 Hoechst-33258 25.59 40.56 67.10 69645 CCAW89 d(5 0 -CGC[iG]AATTTGCG-3 0 )2 Hoechst-33342 25.77 41.10 64.30 68103 RGB98 d(CGC[et6G]AATTCGCG)289W Hoechst-33342 25.686 41.065 66.416 70055 GDL021; SMR92a d(CGC[et6G]AATTCGCG)289W Hoechst-33258 25.32 40.58 66.08 67896 GDL022; SMR92a d(CGCAAGCTGGCG)2 native 25.29 41.78 64.76 68426 BDL022; WSS90 d(CGCGTTAAGCGC)2 native 25.7 40.5 67.0 69737 BDL059; BRZS95 d(CGCGTTAAGCGC)2 netropsin 26.49 40.87 67.02 69820 BRZS95 d(CGTGAATTCACG)2 native 24.78 40.85 65.67 66475 BDL028; LKD90; NGRB91 native 25.08 39.91 66.47 66533 BD0057; TN (5 0 -CGCTTATATGCG-3 0 ) þ (5 0 -CGCATATAAGCG-3 0 ) native 25.40 40.70 65.80 68023 BDL006; NFLK87 (5 0 -CGCAAAAAAGCG-3 0 ) þ (5 0 -CGCTTTTTTGCG-3 0 )

Table 5.13. (Continued ) Dodecameric Oligonucleotide

Drug in the minor groove

a

b

c

Cell Vol.

NDB ID; Reference

Non-self-complementary {(5 0 -CG[5BrC]ATATTTCGC-3 0 ) þ (5 0 -CGCAAATATGCG-3 0 )} at 110 K Non-self-complementary {(5 0 -CG[5BrC]ATATTTCGC-3 0 ) þ (5 0 -CGCAAATATGCG-3 0 )} at 110 K d(5 0 -CGCGAAUUCGCG-3 0 )2

Native þ 78 W

25.19

40.58

66.01

67476

ANN99

TRIBIZ þ 90 W

25.50

40.42

65.55

67563

DD0014; ANN99

native

25.43

39.74

65.25

65941

BDL075; PS96

Notes: * see x5.2.2 # 5-bis(4-aminophenoxy)pentane (NSC 620107) [iG] is isoguanine (2-hydroxyadenine) furamidine is 2,5-bis(4-guanylphenyl)furan TRIBIZ see Scheme 5.5 References: ANN99 – Aymami, Nunn and Neidle, 1999; BRSZS95 – Balendiran, Rao et al., 1995; BSGN92 – Brown, Sanderson, Garman and Neidle, 1992; BSSJ90 – Brown, Sanderson, Skelly et al., 1990; CCAW89 – Carrondo et al., 1989; CAM89 – Coll, Aymami, van der Marel, van Boom, Rich and Wang, 1989; CB95 – Czarny, Boykin et al., 1995; CFWR87 – Coll, Frederick, Wang and Rich, 1987; CGNLL96 – Clark, Gray et al., 1996; DSD82 – Drew, Samson and Dickerson, 1982; DSS89 – DiGabriele, Sanderson and Steitz, 1989; DrDi81 – Drew and Dickerson, 1981; EBSSN92 – Edwards, Brown, Spink, Skelly and Neidle, 1992; EJN92 – Edwards, Jenkins and Neidle, 1992; FKKDD82 – Fratini, Kopka, Drew et al., 1982; GKD95 – Goodsell, Kopka and Dickerson, 1995; GNKLD95 – Goodsell, Ng, Kopka et al., 1995; GSN98 – Guerri, Simpson and Neidle, 1998; HDK85 – Holbrook, Dickerson and Kim, 1985; HSVW01 – Howerton, Sines, VanDerveer and Williams, 2001; KYG85a – Kopka, Yoon, Goodsell, Pjura and Dickerson, 1985a; KYG85b – Kopka, Yoon, Goodsell, Pjura and Dickerson, 1985b; LGC89 – Larsen, Goodsell, Cascio et al., 1989; LKD90 – Larsen, Kopka and Dickerson, 1990; LTNB96 – Laughton, Tanious, Nunn, Boykin, Wilson and Neidle, 1996; NFLK87 – Nelson, Finch, Luisi and Klug, 1987; NGRB91 – Narayana, Ginnell, Russu and Berman, 1991; NJN94a – Nunn, Jenkins and Neidle, 1994a; NJN94b – Nunn, Jenkins and Neidle, 1994b; NN95 – Nunn and Neidle, 1995; NS – Neidle and Simpsom, to be published; QLD91 – Quintana, Lipanov and Dickerson, 1991; PS96 – Partridge and Salisbury, 1996 (to be published); RGB98 – Robinson, Gao et al., 1998; SBSN94 – Spink, Brown, Skelly and Neidle, 1994; SBC00 – Squire, Baker, Clark et al., 2000; SMHVW00 – Sines et al., 2000; SMHW98 – Shui, McFail-Imon, Hu and Williams, 1998; SMR92a, b – Sriram, van der Marel, Roelen, van Boom and Wang, 1992a, b; S-SA97 Shatzky-Schwartz, Arbuckle et al., 1997; TCKW96 – Trent, Clark, Kumar, Wilson, Boykin, Hall, Tidwell, Blagburn and Neidle, 1996; TN – Todd and Neidle, to be published; TVC93 – Tabernero, Verdaguer, Coll, Fita, van der Marel, van Boom, Rich and Wang, 1993; VGA94 – Vega, Garcia Saez, Aymami et al., 1994; WPDD84 – Wing, Pijura, Drew and Dickerson, 1984; WNTN95 – Wood, Nunn, Czarny, Boykin and Neidle, 1995; WSS90 – Webster, Sanderson, Skelly, Neidle, Swann, Li and Tickle, 1990; YPGD88 – Yoon, Prive, Goodsell and Dickerson, 1988.

MI NOR GR OOVE BI NDE RS

183

5.6.4 Dodecameric oligonucleotides Most dodecameric oligonucleotides are found in the B-DNA form and these are listed in the ﬁrst part of this section (Table 5.13) and also in Table 5.14. The relatively few examples crystallizing in the A-form are listed towards the end of the section (Table 5.15). Especially interesting are those few examples where both A and B forms are found in the same oligonucleotide, reinforcing earlier examples of an intermediate range of structures between classic A and B forms. The formulae of most of the dodecamer duplexes can be written as {d(CGCXGCG)2} where X is severally A3T3 Tabernero et al., 1993; GT2A2C Balendiran, Rao et al., 1995; GATATC Coll, Aymami et al., 1989; GA2T2C Sriram et al., 1992b; [e6G]A2T2C Sriram et al., 1992a; GA2T2 [BrC] Kopka et al., 1985b. In all of these host structures the accessible minor groove is six base pairs in length, and in all the examples the four base pairs at the centre of the duplex are AT base pairs. The unit ˚ 3. cell volumes span the range from about 64 000 to 73 000 A

Fig. 5.21. Propamidine (with its bonds emphasized) in the minor groove of the dodecameric duplex d(CGCGAATTCGCG)2. The mode of complexation should be contrasted with the side-by-side arrangement noted earlier (Figs. 5.16 and 5.18). (Reproduced from Nunn and Neidle, 1995.)

184

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

The structure of the native dodecamer (d(CGCGAATTCGCG)2) was ﬁrst determined by Drew and Dickerson (1981). The asymmetric unit consists of one double stranded helix; in addition, one spermine and 72 water molecules were identiﬁed. The density of the crystals could not be measured because ‘‘the crystals fell apart;’’ however, that the crystals were 50% water was used as a working hypothesis. Redetermination of this structure at atomic resolution (Tereshko, Minasov and Egli, 1999) and 120K has shown the important structural role of ordered Mg2þions (two hexahydrates and one pentahydrate per asymmetric unit). Dickerson, Goodsell and Kopka (1996) have summarized the crystal chemistry of ﬁfteen differently sequenced native B-DNA dodecamers; all crystallize (from a variety of conditions) in space group P212121, Z ¼ 4, a 24.9, b 40.4, c ˚ , This is the cell given in Table 5.13 for the dodecamer-drug complexes. Thus the 66.2 A dodecamer-drug complexes should be considered to be primary solid solutions of drug molecules in the native B-DNA dodecamer. The structure determination of d(5 0 -GGCCAATTCGCG-3 0 )2 at 16K is, so far, the only example of a structure determination at such a low temperature, and the only one that has been followed at intervals of a few degrees both in the cooling and heating regimens (Fig. 5.22). The curve of cell volume against temperature shown in Fig. 5.22 is quite different from analogous measurements such as those given in Chapter 16 (Figs. 16.9, 16.15 and 16.24). Here the crystal appears to have been frozen into a static condition at about 200K, below which the volume does not change despite cooling to 16K; this is remarkable indeed. Drew et al. comment ‘‘This break [in the V–T ] curve at 200K marks what we shall term the solvent solidiﬁcation point, leaving open the question of whether this represents a true phase change.’’ Another surprise occurred on heating – at about ˚ 3, accompanied by a change 210K the volume decreased sharply from 61 000 to 55 000 A to monoclinic symmetry, which appears to have persisted to room temperature. These curious phenomena do not appear to have been studied in detail, nor do other workers carrying out structure determinations at, say, 100K appear to have searched for similar

Cell volume, Å3

75 000 a = 25.3 b =40.8 c = 66.5

70 000 a=23.4 b=39.3 c=65.3

65 000 60 000

a = 22.7 b = 38.5 c = 62.6 β = 86.4°

55 000 50 000

0

100

200

300

Temperature, K

Fig. 5.22. Cell volume versus temperature for the dodecamer d(CGCGAATTCGCG). Lattice ˚ ) for the P212121 cell are shown at both ends of the cooling curve. The crystal adopts parameters (A monoclinic symmetry on warming to 220K. Filled circles for cooling, open circles for heating. (Reproduced from Drew, Samson and Dickerson, 1982.)

Table 5.14. Crystal data for various dodecameric oligonucleotides. All crystals have right-handed B-DNA-like duplexes with Watson-Crick base pairs. ˚ , degrees, A ˚ 3. We use ‘native’ while NDB uses ‘plain’ Triclinic cells have been reduced. Dimensions in A Dodecanucleotide

Space group

a/

b/

c/

Cell Volume

NDB ID; Reference

d(ACCGAATTCGGT)2

P1; 3 independent duplexes in unit cell P1; 3 independent duplexes in unit cell C2, Z ¼ 8

39.46 119.54 40.11 116.20 64.83

39.93 103.56 40.54 97.38 25.35

52 197

BD0052; HR01

56 761

BD0002; HR01

58 068

LH93

P212121, Z ¼ 8 R3 R3

44.8 64.067 65.89

39.82 92.08 40.47 99.32 35.36 92.24 66.1 64.067 65.89

42.9 44.679 47.09

127 039 158 819 177 051

DGS93 BD0001; HR01 BDL035; TVM91

R3 P43, Z ¼ 8 P41212, Z ¼ 8

41.96 40.207 40.197

41.96 40.207 40.197

101.4 57.575 77.336

154 611 93 076 124 959

BD0004; LM98 BD0003; RR98 BD0026; NKD00

d(ACCGACGTCGGT)2 d(CGTAGATCTACG)2 d(CGCGAAAAAA/CGa)2, d(ACCGACGTCGGT)2 (ACCGCCGGCGCT)/ (GGCGCCGGCGGT) d(CGCGAATTCGCG)2 d(ACCGGTACCGGT)2 d(CATGGGCCCATG)2

References: DGS93 – DiGabriele and Steitz, 1993; HR01 – Hizver, Rozenberg, Frolow, Rabinovich and Shakked, 2001; LH93 – Leonard and Hunter, 1993; LM98 – Liu, Malinina, Hyunh-Dinh and Subirana, 1998; NKD00 – Ng, Kopka and Dickerson, 2000; RR98 – Rozenberg, Rabinovich, Frolow, Hegde and Shakked, 2001; TVM91 – Timsit, Vilbois and Moras, 1991.

186

CRYSTAL CHE MISTRY OF SOME DNA OLIGONUCLEOTIDES

effects, perhaps because ﬂash cooling has become the method of choice. The 16K, 300K and brominated cytosine structures have been compared by Kopka, Fratini, Drew and Dickerson (1983) particularly with respect to water structure. Crystal packing of the native oligonucleotide dodecamer has been described by Dickerson and Drew (1981) – the two terminal CG base pairs at each end of the duplex interact with those of a neigboring duplex by interlocking of their minor grooves through interduplex N–H . . . N hydrogen bonds between the guanine bases across the minor groove. This packing arrangement serves to stabilize the DNA and provides an A þ T rich region in the centres of the oligonucleotides that is free of packing effects and to which ligands can bind. In overall terms this description holds for all the isomorphous structures listed in Table 5.14, with details differing from example to example. The native dodecamers crystallize in a number of other structures, mostly one-of-a-kind and these are summarized in Table 5.14, with crystal symmetries running from triclinic through to rhombohedral. The Drew–Dickerson d(CGCGAATTCGCG)2 duplex, the prototype for so many orthorhombic crystals of different sequence but similar crystal structure, has been crys˚ , cell volume ¼ 154 611 A ˚ 3; tallized in the rhombohedral system (R3, 41.96, 101.40 A Liu, Malinina et al., 1998). The provenance of the new modiﬁcation is ascribed to the presence of Ca2þ in the crystallizing solution instead of the more usual Mg2þ. The rhombohedral crystal structure has a quasi-hexagonal arrangement of the duplexes

Fig. 5.23. The pseudo-hexagonal arrangement of molecules at the same layer of columns shown in projection down the c axis. There are three different sets of molecules about the threefold axes. ˚ between phosphate groups. The calcium ion is on the Dotted lines show contacts of less than 7 A threefold axis. (Reproduced from Liu et al. 1998.)

GENERAL SURVEY OF THE CRYSTAL CHEMISTRY OF OLIGONUCLEOTIDE 187

Table 5.15. Crystal data for various dodecameric oligonucleotides. The crystals have right-handed ˚, A-DNA-like duplexes with Watson-Crick base pairs or mixed A and B forms. Dimensions in A ˚3 degrees, A Dodecanucleotide

Space group

a

b

c

Cell Volume

NDB ID; Reference

d(CCCCCGCGGGGG)2 d(CCGTACGTACGG)2 d(GCGTACGTACGC)2, d(CGCCCGCGGGCG)2

P3221 P6122 P6122 P212121, Z¼4 P41212, Z¼8

45.2 46.2 46.2 31.29

45.2 46.2 46.2 42.60

65.0 71.5 71.5 46.00

115 006 132 166 132 166 61 316

ADL025; VAF91 ADL045; BZS92 ADL046; BJZS92 MFHS99

40.197

40.197

77.336

124 959

BD0026; NKD00

d(CATGGGCCCATG)2

References: BJZS92 – Bingham, Jain, Zon and Sundaralingam, 1992; BZS92 – Bingham, Zon and Sundaralingam, 1992; MFHS99 – Malinina, Fernandez et al., 1999. VAF91 – Verdaguer, Aymami, Fernandez-Forner et al., 1991.

(Fig. 5.23). In the dodecamer molecule only the central decamer is in the B-form, the terminal cytosines being highly disordered. This reminds one of similar behaviour described earlier for some decamers (see Table 5.11). Dodecamers in the A-form are much less frequent than those in the B-form; some examples are given in Table 5.15. The ﬁrst three entries have more or less the standard A conformation. The d(CGCCCGCGGGCG)2 sequence ‘‘shows a unique conformation, quite different from all previously studied oligonucleotide duplexes; the central octamer has an A conformation but with a sharp 65 kink in the centre; the terminal base steps have a B-like conformation; the major groove is completely closed in the centre, a hollow molecule is thus found. The results obtained conﬁrm the high degree of variability of DNA structure.’’ (Malinina et al., 1999). The tetragonal d(CATGGGCCCATG)2 duplex (Ng, Kopka and Dickerson, 2000) has interesting crystallochemical features. The crystals have an unusually high solvent content – some 60% by weight. The structure shows archetypical features of both A- and B-DNA. The authors comment ‘‘ . . . crystals of G3C3 are not isomorphous with any previous oligonucleotide structure, whether A, B or Z . . . trapping of a stable intermediate [structure] suggests that the A- and B-DNA are not discrete, as previously believed’’ (cf. Section 5.2.1).

5.7 General survey of the crystal chemistry of oligonucleotide and oligonucleotide-guest structures It is simplest to start with the dodecameric oligonucleotides and work backwards. The entries in Table 5.13 show that a large group of native dodecamers are all isomorphous ˚ , space group P212121, Z ¼ 4) despite a wide variability in (a 26, b 41, c 66 A composition and sequence. This applies even to the noncomplementary example {(CG[5BrC]GAATTCGCG) þ (CGCAAATTTGCG)}. This isomorphism extends to all the minor groove drug complexes, again with a wide range of variation in composition and sequence of the base pairs and the chemical nature of the drugs. A conclusion is that the

188

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overall crystal structure is determined by the general shape and interactions of the duplexes and that differences of composition and sequence, and presence or absence of a second component, provide only minor perturbations not sufﬁcient to disturb the overall structure. These complexes are primary solid solution phases. However, one caveat is needed. There are a few examples of other phases (of the native duplexes) that do not ﬁt with the thirty-odd entries of Table 5.13; they may be heteromorphs. These dodecamers all have the B-DNA conformation. There are a few dodecamers that have the A-DNA conformation, and two that have mixed conformations. The decamers present a more complicated picture. The twenty-odd differently sequenced decamers (14 were discussed by Dickerson, Goodsell and Kopka, 1996) crystallize in six different space groups (Table 5.9). In terms of cell volume the two orthorhombic and one monoclinic modiﬁcation may well be heteromorphs (54 000, ˚ 3 (in round ﬁgures)) but the hexagonal and trigonal modiﬁcations 25 500 and 26 000 A ˚ 3). A decision must be based on the detailed crystal differ somewhat (84 000 and 95 000 A structures. Interestingly, there are two groups of natı¨ve structures and one native plus two complexes (DAPI and netropsin) that crystallize in space group P212121, (Z ¼ 4, one helix per asymmetric unit), but these groups all have different detailed structures. The three polyamide complexes of Table 5.10 are isostructural and crystallize in space group I2, but their structure differs in detail from the C2 structures (Group III) of Table 5.9. The polyamide minor groove binder is apparently large enough to make a considerable contribution to the cell volume. Both B-DNA (Tables 5.9 to 5.11) and A-DNA (Table 5.12) conformations are found. The octanucleotides resemble the dodecanucleotides in that there are many native structures, almost all isomorphous despite differences of composition and sequence (Table 5.5); the one spermine complex in Table 5.5 is a primary solid solution phase. However, there is also a resemblance to the decamers, with their non-isomorphous hexagonal and trigonal phases (Groups V and VI of Table 5.9). A difference between dodecamers and octamers is that there do not seem to be any octamer complexes (either intercalation or minor groove), the spermine and distamycin complexes excepted. The octanucleotides have A-DNA conformations (Tables 5.5, 5.6 and 5.7) but the octamerdistamycin complexes of Table 5.8 have the B-DNA conformation. The hexamer intercalation complexes fall into three groups according to the nature of the intercalated molecules. The native structures that have been reported are not directly comparable with the complexes but it seems unlikely that appreciably distorted intercalates will be isomorphous with (as yet hypothetical) undistorted native structures. Thus these are three different types of intermediate phase. The hexanucleotide – intercalation complexes have B-DNA conformations (Tables 5.2, 5.3 and 5.4). Some wider comparisons can be made. There is a resemblance to the ‘moiety within molecule’ structures described in Chapter 3 in that host and guest in the oligonucleotide complexes probably remain associated in solution, although NMR results suggest that there may be compositional and structural differences. There is a resemblance to the cyclodextrin complexes of Chapter 4 for similar reasons, and also in the occurrence of large groups of isomorphous structures within each of the separate -, - and cyclodextrin families. It is perhaps not too far-fetched to see an analogy between the structural roles of the host cyclodextrins and DNA duplexes, on the one hand, and the guests (drug molecules) on the other. However, cyclodextrins are invariably found in

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Sriram, M., van der Marel, G. A., Roelen, H. L. P. F., van Boom, J. H. and Wang, A. H-J. (1992b). Biochemistry, 31, 11823–11834. Tabernero, I., Verdaguer, N., Coll, M., Fita, I., van der Marel, G. A., van Boom, J. H., Rich, A. and Wang, A. H-J. (1993). Biochemistry, 32, 8403–8410. Takusagawa, F. (1990). J. Biomol. Struct. Dyn., 7, 795–809. Tereshko, V., Urpi, L., Malinina, L., Hyunh-Dinh, T. and Subirana, J. A. (1996). Biochemistry, 35, 11589–11595. Teixeira, S. C. M., Thorpe, J. H., Todd, A. K. and Cardin, C. J. ‘‘Heavy Going: the Atomic Resolution Structure of a Topoisomerase II Poison Intercalating into DNA in Multiple Orientations also Reveals a Multiple-Adenine-Thymine Hydrogen Bonding Pattern.’’ To be Published. Thota, N., Li, X. H., Bingman, C. and Sundaralingam, M. (1993). Acta Cryst., D49, 282–291. Tidwell, R. R. and Boykin, D. W. (2003). ‘‘Dicationic DNA minor groove binders as antimicrobial agents’’ in DNA and RNA Binders – from small molecules to drugs. Edited by Demeunynck, M., Bailly, C. and Wilson, W. D. (2003). Wiley VCH, Weinheim, Vol. 2, pp. 414–460. Timsit, Y., Vilbois, E. and Moras, D. (1991). Nature, 354, 167–170. Tippin, D. B. and Sundarlingam, M. (1996). Acta Cryst., D52, 997–1003. Tippin, D. B. and Sundaralingam, M. (1997). J. Mol. Biol, 267, 1171–1185. Todd, A. K. and Neidle, S. ‘‘Crystal Structure of a Non-Self Complementary DNA Dodecamer Containing an A/T Tract: Analysis of the Effect of Crystal Environment on Local Helical Parameters.’’ To be Published. Todd, A. K., Adams, A., Thorpe, J. H., Denny, W. A., Wakelin, L. P. G. and Cardin, C. J. (1999). J. Med. Chem., 42, 536–540. Todd, A. K., Adams, A., Powell, H. R., Wilcock, D. J., Thorpe, J. H., Lausi, A., Zanini, F., L. P. G. and Cardin, C. J. (1999). Acta Cryst, D55, 729–735. Trent, J. O., Clark, G. R., Kumar. A., Wilson, W. D., Boykin, D. W., Hall, J. E., Tidwell, R. R., Blagburn, B. L. and Neidle, S. (1996). J. Med. Chem., 39, 4554–4562. Vega, M. C., Garcia Saez, I., Aymami, J., Eritia, R., van der Marel, G. A., van Boom, J. H., Rich, A. and Coll, M. (1994). Eur. J. Biochem., 222, 721–726. Verdaguer, N., Aymamı´, J., Ferna´ndez-Forner, D., Fita, I., Coll, M., Huynh-Dinh, T., Igolen, J. and Subirana, J. A. (1991). J. Mol. Biol., 221, 623–635. Vlieghe, D., Sponer, S. and Van Meervelt, L. V. (1999). Biochemistry, 38, 16443–16451. Vlieghe, D., Turkenburg, J. P. and Van Meervelt, L. V. (1999). Acta Cryst., D55, 1495–1502. Wahl, M. C., Rao, S. T. and Sundaralingam, M. (1996). Biophys. J., 70, 2857–2866. Wang, A. H-J., Ughetto, G., van der Marel, G. A., van Boom, J. H. and Rich, A. (1987). Biochemistry, 26, 1152–1163. Wang, A. H-J., Fujii. S, van Boom, J. H. and Rich, A. (1982). Proc. Natl. Acad. Sci., USA 79, 3968–3972. Wang, A.H.-J., Gao, Y.-G., Liaw, Y.-C. and Li, Y.-K. (1991). Biochemistry, 30, 3812–3815, Waring, M. J. and Wakelin, L. P. G. ‘‘Forty years on.’’(2003). in DNA and RNA Binders – from small molecules to drugs. Edited by Demeunynck, M., Bailly, C. and Wilson, W. D. (2003). VCH, Weinheim, Vol. 1, pp. 1–17. Watson, J. D. and Crick, F. H. C. (1953). Nature, (Lond.), 171, 737–738. Webster, G. D., Sanderson, M. R., Skelly, J. V., Neidle, S., Swann, P. F., Li, B. F. and Tickle, I. J. (1990). Proc. Natl. Acad. Sci., USA, 87, 6693–6697. Wilcocks, D. J., Adams, A., Cardin, C. J. and Wakelin, L. P. G. (1996). Acta Cryst., D52, 481–485. Williams, L. D., Egli, M., Gao, Q., Bash, P., van der Marel, G. A., van Boom, J. H., Rich, A. and Frederick, C. A. (1990). Proc. Natl. Acad. Sci., USA, 87, 2225–2229. Williams, L. D., Frederick, C. A., Ughetto, G. and Rich, A. (1990). Nucl. Acids Res., 18, 5533–5541. Wing, R. M., Pjura, P., Drew, H. R. and Dickerson, R. E. (1984). EMBO J., 3, 1201–1206.

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Part III Host–guest inclusion complexes

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Introduction to Part III Host–guest inclusion complexes

I came home today – and this guy was sitting there and I said ‘‘Hey, pal! What’s going on here?’’ – and when he smiled he had these big white teeth like luxury hotels on the Florida coastline. And when he closed his mouth it looked like a big scar. And I said to myself ‘‘Holy smokes – looks like some kind of guest-host relationship to me!’’ Laurie Anderson quoted in TIME Magazine (Music) February 21, 1983

The molecular complexes to be discussed in Part III are crystalline and their inclusion properties derive from the arrangement of host and guest moieties in the solid state. In this sense they differ from the complexes considered in Part II, which are considered to exist (to greater or lesser extent) in solution as well as in the solid state. A necessary requirement for classiﬁcation as a host–guest inclusion complex is that host and guest can be distinguished; generally the much larger host component forms an array that includes the guest. As we have noted earlier (our deﬁnition of ‘complex’ in Chapter 1), the overall crystal structure is determined by host–host interactions, although host–guest interactions may make an essential contribution to the stability of the complex. Thus our emphasis is placed on the nature of the host and its arrangement, with the guests ﬁlling a secondary role. However, a more general view requires that this approach be modiﬁed when there is strong host–guest interaction, and we return to this point below. Two principal types of host arrangement can be discerned – the tunnel inclusion complexes (Fetterly, 1964) and the clathrates (Powell, 1964). In the ﬁrst type the guests are included in tunnels between the host molecules and can be in mutual contact (head-tohead or head-to-tail) while in the second the guests are in cages separated one from the other by intervening host molecules. Guest–guest interactions can generally be ignored in the clathrates but may make a small contribution to overall enthalpy in tunnel complexes. The distinction between the groups is often not clearcut – for example tunnels tending towards hourglass shape may behave effectively as cages towards larger guest molecules but not towards smaller ones. Two principal types of host interaction can be discerned, and these distinctions cut across the tunnel/clathrate boundary. The host can interact through directional bonding of various kinds, of which hydrogen bonding is undoubtedly the most important in terms of current knowledge, or through nondirectional forces, such as the ubiquitous dispersion forces (often referred to, also here, as van der Waals’ forces). Host–guest interactions can be similarly divided, with van der Waals interactions being encountered more often than host–guest hydrogen bonding. Much recent work has shown that particular hosts can form complexes of different types, not necessarily all inclusion complexes, with different sorts of guests, and we shall use the term polyfunctionality to encompass this ability; usually only one of these

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functionalities is relevant to the formation of inclusion complexes. For example, thiourea forms S-linked coordination complexes with main group and transition metals, hydrogenbonded complexes with small molecules such as parabanic acid (also other sulphurcontaining molecules can form donor-acceptor compounds with acceptors such as iodine) and NH . . . S hydrogen bonds to itself to give inclusion complexes. Only the mutual hydrogen-bonding functionality is important in the context of inclusion complexes. Two questions arise at this point. Firstly, what are the parameters inducing a particular component (here called a host) to form an inclusion complex with a second component of one type (here called a guest) but, say, a hydrogen-bonded pair with another type of component, this being a molecular compound with the host–guest nomenclature no longer appropriate? The short answer is that we really do not have an adequate explanation, and this holds also for the presumably simpler one-component systems (Gavezzotti, 1994, 1998). Secondly, how important are the host–guest interactions in inclusion complexes? Remember that initially, in the days of Powell’s great contributions, the emphasis was on inclusion and enclosure, and host–guest interactions, although never forgotten, were recognized only sotto voce. This imbalance was redressed by the schools of Cram and Lehn, with their stress on the supramolecular nature of molecular complexes and compounds. We shall see that in inclusion complexes the host–guest interactions can range from minimal to sufﬁciently important to distort the host framework. We describe such frameworks as being ‘‘interrupted’’ by the intervention of the guest. We use the more restricted term versatility to refer to the ability of a particular host molecule to form inclusion complexes of various structural types. Thus thiourea is a nonversatile molecule because it forms only rhombohedral tunnel inclusion complexes while urea is more versatile because it forms hexagonal, rhombohedral and orthorhombic tunnel inclusion complexes. Urea shows even more versatility with the homologous ,!dinitriles (NC(CH2)nNC) as guests; at least eight different types of structure were found for n ¼ 1–8, 10, 12 and there is a clear change between n ¼ 5 and 6 from layered hydrogenbonded 1 : 1 molecular compounds (where the host/guest distinction does not apply) to tunnel inclusion complexes (Hollingsworth, Santarsiero and Harris, 1994). Trimesic acid, whose functionality as an acid is not important in the present context even though it does form salt-molecule complexes with amino and other acids, is even more versatile because, as neat host, it forms interstitial clathrates and also tunnel complexes of two different kinds; the monohydrate forms another kind of tunnel complex. Versatility stems from the mutual adaptation of host to guest, leading to the possibility of forming inclusion complexes of different structural types; it is intended for use in a broad rather than narrow sense. Within the framework of a group of isomorphous or isostructural inclusion complexes we use the term adaptability to refer to the adjustment of a particular type of host structure to various guests; this word has been borrowed from Powell (1964, see p. 469) who writes ‘‘A greater adaptability [of the dimensions of the unit cell] to the shape of the enclosed molecule is to be expected.’’ Thus we shall apply this term to the variation of cell dimensions with guest type for a group of isomorphous structures, well illustrated for the inclusion complexes of tri-o-thymotide (Lawton and Powell, 1958; Powell, 1964; Chapter 8.2) and extend its use to isostructural situations where there is similarity of structural arrangement without the identity of space group and near identity of cell dimensions demanded of isomorphous structures; many illustrations can be found among the cyclodextrin inclusion complexes (Chapter 4) and elsewhere.

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It is useful to consider what we would ideally wish to know about a particular host that has been shown to form inclusion complexes; these considerations have also guided our choice of subjects for inclusion in the chapters of Part III. One of the ﬁrst questions to be answered is the capability of the host to form inclusion complexes – what guests are compatible with the host and are there any chemical limitations on the types of guests. It would be best if this information, usually obtained from preparative experiments, was reinforced by determination of phase diagrams, both for the binary host–guest systems and for ternary host–guest–solvent systems (for some systems it would desirable to have pressure included as a variable). Crystal structures of appropriate complexes should be determined at room temperature and at low temperatures chosen after measurement of speciﬁc heat–temperature curves (or of other physical properties dependent on temperature). Low temperature structures would give information about guests that are often disordered at room temperature. The Cp–T curves would also show the occurrence of phase transformations below room temperature. Suitable neutron diffraction measurements would give information about the mechanisms of phase transformations. Solid state NMR measurements (1H, 2H, 13C and other nuclei) give information about dynamics of host and guest not generally obtainable by XRD. Thermodynamic measurements of free energies, enthalpies and entropies of formation (in the solid state) are required for an understanding of the interactions between the components governing formation and stability of the complexes. Again it would desirable to have these parameters measured over a range of temperatures. This is quite a tall order and the only systems that come close to meeting all these requirements are the tunnel inclusion complexes of urea and the polyhedral clathrate hydrates (more speciﬁcally the gas hydrates). A thermodynamic distinction between two types of inclusion complex is noted here. An inclusion complex may be either a primary solid solution of guest in host, or it may be a separate phase in the host–guest phase diagram. The crystal structure of the solid solution will be that of the pristine host but the presence of the guest introduces distortions and irregularities that may well require application of sophisticated nonstandard diffraction techniques for their elucidation. If the inclusion complex is a separate phase then the thermodynamics of the transformation from the (empty) pristine host arrangement to the (empty) host arrangement in the new phase is an important factor to be taken into account together with contributions of the host–guest interactions to the overall stability. Primary solid solution is relatively rare among inclusion complexes; examples are the inclusion of hydrogen and helium in some high pressure ice phases (Section 7.2.3), and complexes of Dianin’s compound (4-p-hydroxyphenyl-2,2,4-trimethylchroman; Section 7.4.2). Most host–guest inclusion complexes have crystal structures different from those of the pristine hosts; thermodynamic and structural studies have been coordinated particularly for urea and thiourea tunnel inclusion complexes (Chapter 6), the complexes of quinol (Section 7.2.1) and the gas hydrates and related clathrate hydrates (Section 7.3). The preparation of a large number of individual inclusion complexes, often referred to as solvates, has been reported and the crystal structures of some of these have been determined (Davies, Finochiarro and Herbstein, 1984). However, most of these occurrences have not yet been the subjects of systematic chemical or crystallographic study and thus have not been included. We have preferred to restrict our choice of examples to those families of inclusion complexes where the chemical and structural foundations have been reasonably well established, or where interesting new chemical or structural principles are

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being revealed. For each group – the tunnel inclusion complexes and the clathrates – we have distinguished between less versatile and more versatile hosts. These are essentially qualitative and time dependent concepts, particularly as a less versatile host may well become more versatile as investigation is pursued. Although the distinction has proved useful in organising the large amount of available material, its limitations should not be forgotten. The ﬁrst chapters in Part III deal with tunnel inclusion (Chapter 6) and clathrate complexes (Chapter 7) of less versatile hosts; it follows from our deﬁnition of ‘versatility’ that the distinction between these two types of complex can be made. This is followed by Chapter 8 dealing with inclusion complexes formed by more versatile hosts; here the distinctions made above – between tunnel and clathrate complexes, and between directionally bonded and nondirectionally bonded hosts – largely fall away. The concept of topology of inclusion complexes has already been introduced in Chapter 1 (particularly see Fig. 1.2). Thus Chapter 6 deals with zero-dimensional and Chapter 7 with onedimensional guest sites. The trio of possibilities is completed in Chapter 9, where twodimensional arrays of guests are sandwiched between lamellae of host molecules.

References Davies, J. E. D., Finochiarro, P. and Herbstein, F. H. ‘‘Inclusion compounds formed by other host lattices’’, in Inclusion Compounds, Vol. 2, pp. 407–453, edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Academic Press, London. (1984). Fetterly, L. C. (1964). ‘‘Organic adducts’’, in Non-Stoichiometric Compounds, edited by L. Mandelcorn, pp. 491–567, Academic Press, New York etc. Gavezzotti, A. (1994). Accts. Chem. Res., 27, 309–314. Gavezzotti, A. (1998). Cryst. Revs., 7, 5–121. Hollingsworth, M. D., Santarsiero, B. D. and Harris, K. D. M. (1994). Angew. Chem. Int. Ed. Engl., 33, 649–652. Lawton, D. and Powell, H. M. (1958). J. Chem. Soc., pp. 2339–2357. Powell, H. M. (1964). ‘‘Clathrates’’, in Non-Stoichiometric Compounds, edited by L. Mandelcorn, pp. 438–490, Academic Press, New York. Powell, H. M. (1984). ‘‘Introduction’’, in Inclusion Compounds, Vol. 1, pp. 1–28, edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Academic Press, London.

Chapter 6 Tunnel inclusion complexes formed by hosts of lesser versatility

and shades Of trellis-work in long arcades, and cirque and crescent framed by wall William Wordsworth

Summary: Crystalline tunnel inclusion complexes have one-dimensional tunnels in their structures; the host molecules, which constitute the matrix, may be bonded together by directional bonds (generally hydrogen bonds) or van der Waals forces while the guest molecules in the tunnels generally interact with the host molecules by van der Waals forces, although some examples are known of host–guest hydrogen bonding. The nature of the guest appears to be limited only by the size and shape of the tunnel available to it, although there are some examples of speciﬁc host–guest interactions. The arrangements of the host molecules in the matrix are generally different from those in the neat hosts and in this situation the tunnel inclusion complexes are separate phases. The Bishop–Dance complexes – which are primary solid solution of guest in host – are exceptions to this rule. Most of the examples quoted show effects of interaction between host and guest which manifest themselves as minor changes in cell dimensions of isomorphous crystals or as distortions of a basic crystal structure type. Guest molecules are generally disordered in the tunnels at room temperature but order on cooling, often in a number of stages, accompanied by interaction with and distortion of the framework, usually manifested as phase transformations. Diffraction patterns from many complexes are composed of separate contributions from the host framework and the guest arrangement, both being modiﬁed by mutual interaction of host and guest. The complicated effects that can ensue are illustrated by studies of {3urea[1/4(n-hexadecane)]} over the temperature range 30–400K.

6.1 Introduction 6.2 Tunnel inclusion complexes with directionally bonded hosts 6.2.1 Urea, thiourea and selenourea as hosts 6.2.1.1 Introduction 6.2.1.2 Types of guest in hexagonal urea inclusion complexes 6.2.1.3 Guests which give rhombohedral urea inclusion complexes 6.2.1.4 Guests which give rhombohedral thiourea inclusion complexes 6.2.1.5 Hermann’s comprehensive structural model 6.2.1.6 Diffraction patterns from tunnel inclusion complexes 6.2.1.7 Hexagonal urea tunnel inclusion complexes 6.2.1.8 Determination of guest molecule conformation from diffuse x-ray scattering

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6.2.1.9 Variation of structure with temperature, with particular reference to {3(urea)[1/4(n-hexadecane)]} 6.2.1.10 Interruption of urea framework by host–guest hydrogen bonding 6.2.1.11 Rhombohedral urea, thiourea and selenourea tunnel inclusion complexes 6.2.1.12 Monoclinic complexes derived from the rhombohedral complexes 6.2.1.13 Behavior of some rhombohedral inclusion complexes on cooling 6.2.1.14 The orthorhombic Type 4 urea tunnel inclusion complexes 6.2.1.15 The hypothetical Type 5 orthorhombic tunnel inclusion complexes 6.2.1.16 The crystal structure of selenourea and its relation to the structures of the tunnel inclusion complexes 6.2.1.17 Thermodynamics of the formation of the tunnel inclusion complexes 6.2.2 The Bishop–Dance hosts – exo-2,exo-6-dihydroxy2,6-dimethylbicyclo[3.3.1]nonane and analogs 6.2.2.1 Introduction 6.2.2.2 The helical tubuland structures 6.2.2.3 The ellipsoidal tetragonal clathrate complexes of some Bishop–Dance hosts 6.2.2.4 Derived structures 6.2.3 Ta4P4S29 – an inorganic framework containing sulphur chains 6.2.4 The tunnel hydrates 6.2.4.1 Tunnel hydrates with several water molecules per tunnel cross-section 6.2.4.2 Tunnel hydrates with one water molecule per tunnel cross-section 6.3 Tunnel inclusion complexes with van der Waals bonded hosts 6.3.1 Tunnel inclusion and other complexes of deoxycholic acid and related compounds 6.3.1.1 The complexes of deoxycholic acid 6.3.1.2 The complexes of cholic acid 6.3.2 Substituted spirocyclophosphazenes as hosts 6.3.3 Tritriptycene – a C62H38 hydrocarbon of D3h symmetry with three U-shaped bays 6.3.4 Trans-anti-trans-anti-trans-Perhydrotriphenylene as host 6.3.5 N-(p-tolyl)tetrachloro-phthalimide as host 6.4 Comparison of the various tunnel inclusion complexes References

6.1

219 227 231 235 236 245 245 247 247 251 251 251 264 267 268 269 269 271 272 272 273 281 291 297 298 307 310 311

Introduction

Perhaps the ﬁrst crystalline tunnel inclusion complex to be studied by modern diffraction methods was the dioxane complex of {(CH3)3AsPdBr2}2 (Wells, 1938); however, this ﬁeld did not attract widespread attention until after the Second World War, when Bengen’s (1951) work became known. We quote from Fetterly’s (1964) description: ‘‘The discovery that urea forms crystalline adducts with long, straight-chain organic compounds was made accidentally by Bengen in 1940 (German Patent Application OZ123438,

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18 March, 1940) while conducting tests with urea in a study of its action on proteins in pasteurized milk. He noted under certain conditions the fat separates out in such a form as to justify the use of urea in a method for determining the fat content in milk. When he was bothered by what appeared to be frothing and an emulsion, he added a small amount of n-octyl alcohol and set aside his samples. Later he observed long crystals at the interface of the liquid layers. On attempting to reproduce these unexpected crystals, he made the classic discovery that they also form when saturated aqueous urea solution is mixed with n-octanol. From this point, investigation soon extended the adduct formation to include higher alcohols, acids and ﬁnally n-parafﬁns and other straight-chain compounds.’’ These observations led to the opening of a whole new area of investigation and applications (Farina, 1984), including the discovery of analogous complexes formed by thiourea and selenourea. We are not able to resist one other quotation: in these complexes ‘‘The urea and thiourea molecules form [a] honeycomb arrangement . . . and the hydrocarbon molecules form the honey.’’(Rutherford and Calvo, 1969). The tunnel inclusion complexes of urea, thiourea (ﬁrst reported by Angla, 1947a) and selenourea (ﬁrst reported by Bekkum, Remijnse and Wepster, 1967) form the ﬁrst group where the hosts are directionally bonded and are discussed together because of their strong chemical and structural resemblances. However, there is a basic structural distinction between the hexagonal tunnel inclusion complexes of urea on the one hand and the rhombohedral tunnel inclusion complexes of urea, thiourea and selenourea on the other. The tunnel dimensions in these two types of crystal are similar but there are important differences in the arrangements of the host molecules in the tunnel walls, the hexagonal complexes having a helical, chiral arrangement of host molecules while there is a layered, non-chiral arrangement of host molecules in the rhombohedral complexes. The vital difference is that in the ﬁrst group the force ﬁeld is rather uniform both along the direction of the tunnel axis and normal to it. Thus guest molecules with quasi-cylindrical symmetry do not have preferred locations along the tunnel axis or azimuthal orientations about it when kT is greater than the host–guest interaction energy. In contrast, the force ﬁeld along ˚ in the rhombohedral complexes and guests the tunnel axis has a periodicity of 5.5 A with similar periodicities will lock in to the host structure and favour formation of rhombohedral rather than hexagonal complexes (see Table 6.1 below; Lenne´, Mez and Schlenk, 1968). We consider the hexagonal inclusion complexes to be helical tubulates, other examples of which are exo-2,exo-6-dihydroxy-2,6-dimethylbicyclo-[3.3.1]nonane and its analogs (see Section 6.2.2) and Ta4P4S29. The term ‘tubulate’ was ﬁrst introduced by Weber and Jossel (1983) to describe an one-dimensional open-tunnel structure. We deﬁne a helical tubulate as a structure in which the host moieties are arranged in a helical framework leaving tunnels in which guest molecules are accommodated. Although the three examples discussed here are all chiral, racemic arrangements are also possible. In similar vein one can describe the rhombohedral inclusion complexes as having cylindrical tubulate structures. The urea and thiourea tunnel inclusion complexes have been quite thoroughly investigated from both chemical and structural points of view. A rational overall structural picture has been proposed and the available chemical information ﬁts into this framework. However, there is a vast amount of detail to be added, particularly in regard to crystallographic changes that occur on cooling, when most complexes seem to behave in ways that are speciﬁc to the guest involved. The other systems have not been studied to the same

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extent, either chemically or structurally. One can rationalize the directional interactions of the hosts of Section 6.2 but it seems difﬁcult to predict the behavior of the rather disparate compounds of Section 6.3; for example, it remains a mystery (to me) why only one of the ten stereoisomers of perhydrotriphenylene should form inclusion complexes. The following general considerations (adapted from Yeo, Harris and Guillaume, 1997) are important for determining the structures of tunnel inclusion complexes – (1) host–host interactions, (2) host–guest interactions, (3) intratunnel guest–guest interactions, (4) intertunnel guest–guest interactions, (5) host conformations, (6) guest conformations. Their relative importance depends on the nature of host and guest, and the temperature (and pressure). The urea inclusion complexes probably constitute the best studied family. At one extreme, when host–guest interactions are weak (as for parafﬁn guests) and the temperature high (say 300K), then host–host interactions dominate. Cooling leads to phase changes due to perturbation of host structure by increasingly important (compared to thermal ﬂuctuations) host–guest interactions. At the other extreme, host–guest interactions can be strong enough to produce appreciable modiﬁcation of the basic host framework. And there is a vast, and little explored, area between these two extremes.

6.2

Tunnel inclusion complexes with directionally bonded hosts

6.2.1 6.2.1.1

Urea, thiourea and selenourea as hosts Introduction

The historical background to the formation of related tunnel inclusion complexes by the homologous molecules urea, thiourea and selenourea has been sketched above; the guests cover a wide range of different chemical types. The crystal structures of the inclusion complexes differ from those of the pure hosts (apart from selenourea, where this statement needs some qualiﬁcation) and thus the complexes form separate phases in the phase diagrams. Urea forms hexagonal complexes with n-parafﬁns (Smith, 1950, 1952) and rhombohedral complexes with bulkier guests (Lenne´, Mez and Schlenk, 1968). For some guests both hexagonal and rhombohedral complexes can be obtained, depending on the details of the crystallization process. Thiourea (Lenne´, 1954) and selenourea (Bekkum, Remijnse and Wepster, 1967) form rhombohedral complexes isostructural with the rhombohedral urea complexes. Some guests can form rhombohedral complexes with both urea and thiourea and some others show similar behaviour vis-a-vis thiourea and selenourea. The differences in the shapes of the tunnels in the urea and thiourea complexes are somewhat larger than those between thiourea and selenourea complexes. Preparation of the complexes is generally by simple mixing of components, with or without a solvent, and crystallization by slow cooling. Much of our knowledge of the preparative and structural chemistry of the urea and thiourea complexes, and their thermodynamics, comes from the work, similar in scope and carried out more or less simultaneously, of groups at two industrial research laboratories, Shell Development Co. in the United States and BASF in Germany. The contributions of W. Schlenk, Jr. and coworkers are especially noteworthy. There have been a number of reviews (Fetterly, 1964; Schlenk, 1965; Bhatnagar, 1967; Takemoto and Sonoda, 1984; Hollingsworth and Harris, 1996).

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Fig. 6.1. Stereodiagram of the crystal structure of urea viewed approximately along the c axis. (Reproduced from Swaminathan, Craven and McMullan, 1984.)

˚ at 12K; space The crystal structure of tetragonal urea (a ¼ 5.565(1), c ¼ 4.684(1) A group P4 21 m, Z ¼ 2) is shown in Fig. 6.1 (Swaminathan, Craven and McMullan, 1984; UREAXX). The molecules and hydrogen bonds are conﬁned to the (110) and (110) planes of the unit cell which intersect and leave tunnels having a square cross-section of overall ˚ ; urea, in its neat crystals and in its tunnel inclusion complexes, is the size 3.94 3.94 A only molecule known where a carbonyl O atom accepts four hydrogen bonds. The two ˚ at 12K. The independent N . . . O hydrogen bond distances are 2.985(1) and 2.955(1) A diameter of the tunnel available to a potential guest molecule in neat urea would be, at ˚ after van der Waals radii have been taken into account. Thus tetragonal urea most, 1.5 A does not form tunnel inclusion complexes – the topology is right but not the dimensions. Thiourea is a ferroelectric which has many higher-order incommensurate phases between the room-temperature paraelectric and the low-temperature (Tc ¼ 202K) ferroelectric phase. At 295K it crystallizes in an orthorhombic cell (a ¼ 5.488(3), b ¼ 7.663(3), ˚ , Z ¼ 4, space group Pbnm, molecular symmetry Cs-m) in a closely packed c ¼ 8.564 A hydrogen-bonded structure without any tunnel-like features (Takahashi, Onodera and Shiozaki, 1990; THIOUR). The structure of selenourea is discussed brieﬂy below. 6.2.1.2 Types of guest in hexagonal urea inclusion complexes The formation of hexagonal urea tunnel inclusion complexes with over three hundred different guests has been described (Lenne´, Mez and Schlenk, 1970). The potential guests studied included homologous series of the following structural types: n-parafﬁns, cyclohexylalkenes, secondary alkyl alcohols and chlorides, ketones, ethers, thioethers, carboxylic and dicarboxylic acids and their esters, 1,3-diglycerides. Unbranched parafﬁns from n-hexane onwards form crystalline complexes with urea. If the n-alkyl chain is sufﬁciently long, the presence of terminal ring groups does not prevent formation of complexes (e.g. 1-cyclohexyl- and 1-phenyleicosane, H11C6– (CH2)18–CH3 and H5C6-(CH2)18-CH3, form complexes) whereas a methyl group centered on a C13 chain inhibits complex formation (Schiessler and Flitter, 1952).

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208

1-Iodopentane and 1-bromoheptane are the lowest n-alkyl halides to form complexes (Radell, Bradman and Bergmann, 1964), n-butyric acid is the smallest carboxylic acid and acetone the smallest ketone (Radell and Hunt, 1958). Diacyl peroxides (R–C(¼O)–O–O–C(¼O)–R; e.g. R ¼ C7H15, C10H21, C11H23) form complexes (Harris and Hollingsworth, 1990). The alkyl silanes RsiH3 (R¼n–C6H11 and above) and the di-n-alkyl silanes R2SiH2 (R ¼ C2H5 and above) form tunnel inclusion complexes (Muller and Meier, 1964a), as do linear di-n-alkoxy silanes (RO)2SiH2 (R ¼ C2H5 and above) (Muller and Meier, 1964b), the latter being generally more stable than the former. Crystalline urea inclusion complexes are formed from alcoholic solutions of urea and HgR2 (where R ¼ C2H5 and above) but not from RHgBr or compounds such as C4H9(CH2)5HgC4H9 (Bahr and Meier, 1958) n-Parafﬁn and di-n-alkyl silane guests are accommodated in the tunnels in head-to-tail fashion while alkyl carboxylic acids and n-alkyl silanes pack in head-to-head, tail-totail fashion.

6.2.1.3 Guests which give rhombohedral urea inclusion complexes These are much less common than the hexagonal variety, with perhaps 20–30 examples having been recorded, compared to the hundreds of hexagonal complexes known. There are two types of guest which appear to favour the rhombohedral structure. The ﬁrst type comprises small molecules such as trioxane, which does give a rhombohedral complex (Cle´ment, Mazieres and Guibe´, 1972; QQQEVP) and acetone and dioxane, where the situation has to be clariﬁed (‘‘Auswertung noch nicht abgeschlossen’’ (see p. 2439 in Lenne´, Mez and Schlenk, 1968). The second type comprises molecules whose length is ˚ , the half-periodicity of the tunnel in the rhomclose to some integral multiple of 5.5 A bohedral complexes; sometimes both hexagonal and rhombohedral complexes are formed. Some illustrations are given in Table 6.1; about a dozen other examples are known where both crystal types have been obtained (Lenne´, Mez and Schlenk, 1968; Hadicke and Schlenk, 1972). ˚ ) of guest molecule and the type of urea inclusion complex Table 6.1. Relation between length (A formed Guest

Nominal length of guest molecule

Nearest integral ˚ multiple of 5.5 A needed to favor rhombohedral structure

Structure type (H ¼ hexagonal, R ¼ rhombohedral)

2,13-dimethyltetradecane 2,14-dimethylpentadecane 2,15-dimethylhexadecane 2,16-dimethylheptadecane 2,17-dimethyloctadecane 2,18-dimethylnonadecane 2,19-dimethyleicosane

20.0 21.3 22.6 23.9 25.2 26.5 27.8

– 4 5.5 ¼ 22.0 4 5.5 ¼ 22.0 – – 5 5.5 ¼ 27.5 5 5.5 ¼ 27.5

H H and R R H H R R

DIRECTIONALLY BONDED HOSTS

209

6.2.1.4 Guests which give rhombohedral thiourea inclusion complexes Thiourea forms tunnel inclusion complexes with a much wider variety of guests than does urea, whose guests are essentially n-parafﬁns and their derivatives. The most stable thiourea complexes are formed with guests which have a branched chain or otherwise non linear structure, or are globular in shape or are substituted with fairly bulky groups. Schlenk (1951) has listed 108 guests divided into a number of categories, to which we add some further examples (with separate references) without pretending to present a complete list: Parafﬁns and oleﬁns: e.g. 2,3-dimethylbutane through 2,2,4-trimethylbutane to 2,6,9,12,15-pentamethylheptadecane Alkyl halides, alcohols, ketones, acids, esters: e.g. isopropyl iodide, isobutyl chloride, 2-bromooctane Cycloparafﬁns and related ring systems: e.g. cyclopentane, cyclohexane, cyclooctane, cyclo-hexene, cyclohexa-1,4-diene, cyclooctatetraene Aromatic derivatives: e.g. isobutylbenzene, 2,3-dimethylnaphthalene, 1,6-dimethylnaphthalene, perhydroﬂuorene, perhydroanthracene. n-alkycyclohexanes (with the number of carbon atoms in the alkyl chain varying from 0 to 14) (Schlenk, 1951) dicyclohexyl-!,! 0 -polymethylenes (with the number of carbon atoms in the polymethylene chain varying from 0 to 9) (Lenne´, Mez and Schlenk, 1968) chlorocyclohexane (Harris and Thomas, 1990a); various trans-1,4-disubstituted cyclohexanes; cis-and trans–decalin; adamantane (van Bekkum, Palm, Verkade and Wepster, 1970); durene (Teter and Hettinger, 1955); ferrocene (Cle´ment, Claude and Mazieres, 1974; Hough and Nicolson, 1978); CHCl3 (Angla, 1947a); CCl4 (Angla, 1947a); alicyclic alcohols and ketones (Angla, 1947b). Schiessler and Flitter (1952) tested some 50 hydrocarbons of varying types for formation of inclusion complexes with thiourea: some 25 such complexes were obtained, leading to the conclusion that the cross-section of the guest should be within the limits ˚ , as measured on Fisher–Hirschfelder models. Complexes were (6.8 0.3) (5.8 0.5) A not formed readily if the dimensions were near the tolerance limits and, if formed, tended to be unstable. Phenyl groups tended to interfere with the formation of thiourea (and urea) complexes; n-parafﬁn chains attached to otherwise suitable molecules had similar deleterious effects on the formation of thiourea complexes. Although it has often been stated that n-parafﬁns do not form inclusion complexes with thiourea, it has been reported (McLaughlin and McClenahan, 1952) that such complexes can be obtained when n 12; a possible explanation is coiling of the parafﬁn chain within the tunnel. Tunnel inclusion complexes of selenourea have been prepared (Bekkum, Remijnse and Wepster, 1967) with 11 different guests (e.g. 4-t-butyl-1-neopentylbenzene, trans-1,4isopropylcyclohexane, adamantane, camphor), all of which also form complexes with thiourea. The cell dimensions of the selenourea complexes vary more with different guests than do those of the urea and thiourea complexes, perhaps because the weaker Se . . . H-N hydrogen bonds allow easier adaptation of the host matrix to the steric requirements of the guests. However, selenourea appears to be more selective in its choice of guest compounds than thiourea; for example, thiourea forms complexes with both cis and trans

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isomers of 1-t -butyl-4-neopentylcyclohexane, whereas selenourea forms complexes only with the latter, thus enabling separation of isomers. 6.2.1.5 Hermann’s comprehensive structural model The structural chemistry of the urea and thiourea tunnel inclusion complexes can be summarised in terms of a structural model put forward by C. Hermann and described by Otto (1972). All these complexes are based on tunnels of hexagonal cross-section with the guest molecules disposed about the axes of the tunnels, and the walls of the tunnels containing the host molecules. The host molecules are arranged in spirals whose axes lie along the line of intersection of each group of three adjacent tunnels; these spirals are the basic structural motifs. A typical spiral, that of urea, is shown in Fig. 6.2, where one notes that there is hydrogen bonding of adjacent molecules within a spiral and also between different spirals; all possible hydrogen bonds are formed, oxygen acting as acceptor to four N–H bonds. The host molecules in the spirals are arranged about threefold screw axes; these are chiral, with a right-handed screw (31 axis) designated as R and a lefthanded screw (32 axis) as L. Hermann pointed out that there were only ﬁve ways (Fig. 6.3) of arranging such spirals to give the required structures, assuming left and right handed spirals to be equally probable. Types 1 and 2 are the two enantiomorphic forms of hexagonal urea complexes; Type 3 occurs in the rhombohedral urea, thiourea and selenourea tunnel inclusion complexes; Type 4 occurs in the orthorhombic crystals of urea with 1,4-dichlorobutane URDCLB), 1,5-dichloropentane or 1,6-dibromohexane as guest (Otto, 1972);Type 5 has not yet been reported. Trigonal selenourea has the Type 1 structure but the position of the

N C O L

L

N

Fig. 6.2. The L (32) screw axis illustrated for the hexagonal urea tunnel inclusion complexes, the dashed lines showing hydrogen bonds between O (large circles) and NH2 groups. The heavy vertical lines show the direction of the c axis. This diagram corresponds to Diagram 1 of Fig. 6.3. (Reproduced from Bhatnagar, 1967.)

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211

R

L L

L

R

R

1

2 R

L

L

R

L

R

L R

R 3 L

L R

L

R R

R 4

5 L

L L

R

R

R

L L

Fig. 6.3. The ﬁve ways of arranging spirals of 31(R) and/or 32(L) symmetry to give the structures found for urea, thiourea and selenourea tunnel inclusion complexes. One is looking down the spiral shown in Fig. 6.2; hydrogen atoms of NH2 groups have been omitted. (Diagram adapted from Otto (1972) and Harris and Thomas (1990a).) Projection diagrams such as those shown above can be misleading as they do not show the three-dimensional arrangement of the hydrogen bonds, which is different in each structure type. This is illustrated by the stereodiagram of the left-handed helical arrangement (coordinates from Harris and Thomas, 1990). The chiral ribbons, which are deﬁned by the anti N–H . . . O hydrogen bonds, run antiparallel to each other along the vertical c axis. The hexagonal channels are linked by their edges to form the solid-state honeycomb structure. At each z coordinate, the two urea molecules from separate helices are related by a two fold axis perpendicular to the channel axis. (Reproduced from Brown, Chaney, Santasiero and Hollingsworth, 1996.)

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Fig 6.3 (Continued )

guest is occupied by a selenourea spiral similar to that at the corners of the hexagon (Rutherford and Calvo, 1969) so that no distinction can be made between host and guest. The ﬁve structural types described above are not interconvertible without breaking of hydrogen bonds and interchange of 31 and 32 spirals, the occurrence of a particular structure type depending on the nature of the guest. However, both hexagonal and rhombohedral urea complexes of a few guests have been found. The crystallographic and thermodynamic relations between such pairs do not appear to have been investigated; presumably they are polymorphs (if the compositions are identical) but relative stabilities have not been determined nor whether they transform enantiotropically or monotropically. Each structure type can itself undergo deformation to a derived structure of different symmetry, as a consequence of ordering of the guest arrangement on cooling, and concomitant changes in the host matrix. However, drastic changes in the positions of the spirals do not occur in such transformations, which are generally single crystal to single crystal, possibly accompanied by twinning. 6.2.1.6 Diffraction patterns from tunnel inclusion complexes We consider the diffraction patterns to be expected, in general terms, from structures of the tunnel inclusion complexes before describing, in more detail, each of the structure types, and some of the phase transformations that have been encountered. The general principles of such diffraction patterns have been understood implicitly since the ﬁrst

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213

structure determinations were carried out in the early 1950s; in particular, Laves and coworkers extracted much information from the diffuse scattering, as described below. A general discussion has been given by Frey (1997). We follow here the explicit and detailed description given by Harris and Thomas (1990b) but with some emendations. In one limit, the guest molecules are ordered with respect to those of the host and the X-ray diffraction patterns are those of a single crystal containing the two components in ordered array; an approximation to this situation is provided by {3(thiourea)[adamantane]} and {3(selenourea)[adamantane]} described below. In the other limit, the guest arrangement is disordered while that of the host is ordered, under the constraints imposed by the overall structure of the complexes. Thus X-ray diffraction photographs from crystals of tunnel inclusion complexes usually show two different types of scattering in reciprocal space, one being a regular lattice consisting of sharp (Bragg) reﬂections while the second component, incommensurate with the ﬁrst, is much more diffuse. The Bragg diffraction pattern (the H diffraction pattern) derives, in ﬁrst approximation, from the host matrix while the diffuse pattern (the G diffraction pattern) comes from the guest arrangement. A large variety of beautiful photographs has been presented by Nicolaides and Laves (1963), and by Harris and Thomas (1990b); we show one example (Fig. 6.4). Measurement of geometry and intensities from the H pattern will give the structure of the host matrix by application of the standard methods of crystal structure analysis, while analysis of the G pattern will give information, of a more or less limited kind, about the guest arrangement. A linear periodic array of scatterers in a tunnel will give a diffraction pattern consisting of an array of sheets in reciprocal space (Fig. 6.5). The average molecular length Lc can be calculated from the (reciprocal space) periodicity m of the sheets as Lc ¼ m/ m, where is the wavelength used. In fact, the scatterers are not points (as in Fig. 6.5) but have structure, which can be derived from the intensities of the sheets in reciprocal space through calculation of one-dimensional structure factors as F(00m) ¼ fn[cos 2mzn þ i sin 2mzn], where zn are the atomic coordinates projected onto the direction of the tunnel axis, and fn are the atomic scattering factors; the summation runs from n ¼ 1 to n ¼ N where N is the number of atoms in the repeat unit along the tunnel axis. Applications are discussed below. Up to this point we have assumed that host and guest arrangements do not interact and, hence, that H and G diffraction patterns will each give information only about their source

(hk 3)h (hk 2)h (hk 1)h (hk 0) – (hk 1)h – (hk 2)h – (hk 3)h

(hk 5)g (hk 3)g (hk 1)g – (hk 1)g – (hk 3)g – (hk 5)g

Fig. 6.4. X-ray diffraction photograph (Ni-ﬁltered Cu K radiation) of {urea[x(dioctanoyl peroxide)]} oscillated about the c axis. Indexing of layer lines of the H pattern is shown on the left and of the G pattern on the right; the resolution of the latter into fairly sharp reﬂections is more pronounced than is usual. (Reproduced from Harris and Thomas 1990b.)

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214

C

C*

Fig. 6.5. A one-dimensional array of point scatterers in direct space (representing the guest) is shown on the left, and the corresponding diffraction pattern of sheets in reciprocal space, on the right. Any perturbation in the periodicity of the one-dimensional array will lead to broadening of the sheets in the c* direction. The relationship between host and guest periodicities along c can be expressed as njcgj ¼ mjchj; when m and n are small integers then the two periodicities are commensurate; if n/m is irrational then the periodicities are incommensurate. (Reproduced from Harris and Thomas (1990b).)

C*

C

l=3 l=2 l=1 (hk 0) – l=1 – l=2 – l=3

these two-dimensional lattices are reciprocal to each other

b a

Fig. 6.6. The left hand portion of the diagram shows an arrangement of one-dimensional scatterers in real space without longitudinal correlation between adjacent tunnels (the host framework is omitted for clarity). The right hand portion of the diagram shows that, for m 6¼ 0, there are sheets of scattering in reciprocal space, as before. In projection (i.e. when m ¼ 0), the guest sublattice has the same periodicity as the host sublattice and we are in the single-crystal limit where both host and guest sublattices contribute to the hk0 reﬂections of the diffraction pattern. When there is correlation between the arrangement of the guests in the tunnels, then the sheets of scattering will show structure; this is illustrated in Fig. 6.4. (Reproduced from Harris and Thomas 1990b.)

structures (apart from the hk0 reﬂections, as noted in the caption to Fig. 6.6). Experience shows that this approximation holds reasonably well at room temperature, but it begins to fail when the crystals are cooled. In principle, the host arrangement will be modulated by the guests, and conversely. An excellent, but complicated, example is provided by the behaviour of {3(urea)[1/4(hexadecane)]}, which is discussed below.

DIRECTIONALLY BONDED HOSTS

6.2.1.7

215

Hexagonal urea tunnel inclusion complexes

(i) Chemical compositions: The chemical formula is generally expressed as {3(urea)[x(guest)]}, where x is not necessarily integral and the square brackets denote here, as elsewhere, inclusion of the guest in the host matrix. The non-stoichiometric compositions of the tunnel inclusion complexes of urea and a variety of guests have been summarised for different guests by Fetterly (1964). The molar ratios are given by the following equations: n-parafﬁns m ¼ 0.65n þ 1.51; n-acids m ¼ 0.71n þ 1.08; n-alcohols m ¼ 0.66n þ 1.55. where m ¼ urea/guest and n is number of carbon atoms in the guest molecule. We consider the n-parafﬁns as an example; m will have nearly integral values only for n ¼ 10 (8.01), 13 (9.96) and 16 (11.91) (larger values of n not considered here). Thus the structures will in general be ‘incommensurate,’ a term deﬁned in the caption to Fig. 6.5 and discussed below. This will be expressed experimentally by the presence of diffuse scattering in the diffraction patterns. We have not found information in the literature to test this somewhat simple-minded prediction except for hexadecane, where the description below shows that it is not entirely conﬁrmed. A more sophisticated approach due to Rennie and Harris (1990) applies to an idealized one-dimensional structural model with inﬁnite, rigid and periodic host framework (repeat distance ch) and equally spaced rigid, identical guest molecules (repeat distance cg) lined up along the tunnel axis (Fig. 6.7). A practical deﬁnition of ‘commensurate’ is that sufﬁciently small integers p and q can be found such pch qcg, all othersituations leading to ‘incommensurability.’ Broadly speaking, the inclusion complex is incommensurate if the energy of interaction between host and guest substructures does not depend upon the position of the guest along the tunnel while commensurability will be found if there are preferred positions for the guests (i.e. the guest can ‘lock in’ to the host). Another important parameter is the guest–guest offset, Dg. This will be Dg in 2/3 of all pairs of adjacent tunnels, and 2Dg for the remaining pairs. In principle, the offset concept can be extended to a third dimension and this would provide a complete description of the host–guest structure; in practice, there is invariably too little experimental information for reliable conclusions to be drawn. If the guest host periodicity ch

guest–guest offset ∆g

host guest host guest host cg guest periodicity

Fig. 6.7. Two dimensional representation of a tunnel inclusion complex showing host and guest repeat distances, and the guest–guest offset. (Adapted from Rennie and Harris, 1990.)

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symmetry is lower than that of the host framework, then, for the urea inclusion complexes, there are six different arrangements of these two kinds of offset, and this leads to formation of domains in the crystal. Rennie and Harris (1990, 1992) have applied their mathematical analysis to a calculation of the guest periodicity in the urea–n-hexadecane complex, using Lennard-Jones equations for the host–guest and guest-guest interactions. ˚ obtained is in excellent agreement with recent experimental The value of 22.6 0.1 A ˚ less than that calculated taking only end-to-end guest results. This periodicity is 0.5 A interactions into account: in other words, the guest–guest interaction is repulsive. The overall structure is incommensurate and there is no lock-in. As we shall see below, this model breaks down when the temperature is reduced and the interaction energies become larger than kT. (ii) Cell dimensions and crystal structure at room temperature. The cell dimensions of ˚ , space group the hexagonal urea tunnel inclusion complexes are a 8.2, c 11.0 A P6122 (Type 2 of Fig. 6.3) or P6522 (Type 1); Z ¼ 2. The six urea molecules in the unit cell are located on twofold axes; thus the two nitrogens are crystallographically equivalent, a point important in interpreting some of the spectroscopic results, especially the 14 N pure NQR spectra of the complexes (see below). p The hexagonal tunnel has a height of ˚ (¼ c) and an edge of 4.8 A ˚ (¼ a / 3), leaving an internal cross-section 11.0 A ˚ (i.e. after taking the van der Waals radii of the urea available to the guest of 5.3 6.0 A molecules into account (Schlenk, 1955)). Full room-temperature structure determinations, based on the H (Bragg) diffraction patterns, have been reported for the urea inclusion complexes of n-hexadecane (Smith, 1952; Harris and Thomas, 1990b; Forst, Jagodzinski, Boysen and Frey, 1990; ZZZAKG 03 (XRD), 04 (ND)), 1,10-dichloro-n-decane (and the 1,10-dibromo analog (Harris, Smart and Hollingsworth, 1991)), dioctanoyl peroxide, diundecanoyl peroxide, lauroyl peroxide and bis-(6-bromohexanoyl) peroxide (Harris and Thomas, 1990b). The same host matrix structure appears in all these crystals at room temperature but there are differences at low temperatures, which are discussed below. The crystal structure of {3(urea)[1/4(n-hexadecane)]} has been studied more extensively than that of any other tunnel inclusion complex. The ﬁrst determination of the room temperature structure of the urea framework, by Smith (1952), using photographically measured intensities, has been followed by an X-ray diffractometric study (Harris and Thomas, 1990b), and, most sophisticated of all, a combined X-ray and neutron diffractometric study (Forst, Jagodzinski, Boysen and Frey, 1990). There is no doubt about the overall arrangement of the urea molecules in the framework but various points of detail remain to be settled, the problems arising from the fact that H and G diffraction patterns are not completely independent, as was assumed in the earlier studies. We shall ﬁrst be satisﬁed with an overall description, essentially following Smith (Fig. 6.8); the changes that occur on cooling are described below. Two-thirds of the urea molecules lie in the walls of a particular tunnel and one-third point away from it (but, of course, lie in the walls of other tunnels). As noted earlier, an important consequence of the spiral arrangement of the urea molecules in the tunnel walls is that the force ﬁeld in the tunnel is rather uniform both along the direction of the tunnel axis and, to a lesser extent, normal to it; n-parafﬁn guest molecules with extended planar conformation do not have preferred locations along the tunnel axis at temperatures where kT is greater than the host-guest interaction energy but there are six lower-energy azimuthal orientations with molecular planes at multiples of 60 to the a axis; these energies depend on the position of guest

DIRECTIONALLY BONDED HOSTS

c

217

(b)

b

c

a

(a)

(c)

Fig. 6.8. Crystal structure of {3(urea)[1/4(n-hexadecane)]}: (a) View down tunnel axis [0001]. Hydrogen bonds are indicated by dashed lines. The hexagonal and orthohexagonal cells are shown by broken and dotted lines respectively. (b) Projection along the orthohexagonal a axis, showing hydrogen bonding. (c) View along the orthohexagonal b axis. The hydrogen bonds are shown by heavy broken lines, while the light double lines show hydrogen bonds connecting atoms directly below those shown in the ﬁgure; the disordered positions of the n-hexadecane chains are suggested by the zigzag lines. Although the hexagonal structure is drawn in space group P6122 (61 and 31 axes; Type 2 of Fig. 6.3), the absolute conﬁguration of the crystal used was not determined. The spirals along c (cf. Fig. 6.2) run horizontally in (c). The oxygens are shown as the large open or stippled circles and nitrogens as circles of intermediate size. The atomic numbering, given in the original ﬁgure, has been removed to enhance the clarity of the diagrams. (Reproduced from Smith, 1952.)

along the tunnel axis (Parsonage and Pemberton, 1967). Each oxygen atom is hydrogen ˚ and the longer bonds bonded to four nitrogens, the shorter bonds each being about 2.93 A ˚ ; for comparison, we note that in (neat) urea each oxygen is hydrogen each about 3.04 A ˚ and the longer bonds bonded to four nitrogens, the shorter bonds being each 2.955(1) A ˚ (at 12K). Thus the hydrogen bonding of the urea molecules is only each 2.985(1) A slightly different in the two different crystalline environments. The diffraction patterns show sharp Bragg reﬂections with half-l values, indicating that ˚ , the host and guest arrangements originally being the true repeat along c is 22.02 A considered as commensurate. Later work (see Table 6.2 below) suggests that some modiﬁcation may be necessary. The n-hexadecane molecule is slightly shorter in the ˚ ); this was accounted for by complex than in its fully extended conformation (22.84 A rotation of the end methyl groups or small deviations from full extension of the hydrocarbon chain. The volume occupied by an urea molecule in tetragonal urea at 298K is ˚ 3, and that of n-hexadecane in triclinic n-hexadecane (Norman and Mathisen, 1972; 75.6 A ˚ 3; thus the volume occupied by six urea molecules and 1/2 of an QQQFBP) is 406 A

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˚ 3, which should be compared n-hexadecane molecule in their respective crystals is 656.6 A 3 ˚ with 645.5 A , the unit cell volume of the inclusion complex. There is a small contraction ( 1.7%) on formation of the complex at room temperature. (iii) Absolute conﬁguration: The absolute conﬁguration of the urea sublattice of the hexagonal urea inclusion complexes (which is another way of expressing the choice between the two enantiomorphic space groups, or of deﬁning the sense of rotation of the spirals of urea molecules in the intersections of the tunnel walls) has been determined by the following, rather intricate, method (Schlenk, 1968, 1973a, b, c). Inclusion complexes with various long chain ketones (e.g. undecan-1-one) as guests were found to have the plate-like habit needed for measurement of the speciﬁc rotation of the crystals about the c axis (for theory see Nye (1957), Chapter 14). The speciﬁc rotation measured over the wavelength range 230–578 nm was found to be independent of the nature of the guest (chosen to be achiral). About half of the crystals measured were found to be laevorotatory; these all had Type A structures, which had earlier been deﬁned (Schlenk, 1968) as those which, when seeding a racemic solution of urea and -methylbutyric acid decyl ester, gave a preponderant amount of inclusion complex containing the dextrorotatory (þ) ester. Such deﬁnition is essential as not all crystals of urea inclusion complexes have habits that permit measurement of the speciﬁc rotation of the crystal. The next step was to decide whether the Type A crystals had left or right handed urea spirals. This was done by studying, with the aid of models and diagrams, whether 1,2- and 1,3-dimethylalkanes of known optical conﬁguration (e.g.(þ)(9R,10R)-9,10-dimethyloctadecane) which formed Type A crystals, ﬁtted best into left or right handed urea spirals. The study was carried out for six 1,2- and three 1,3-dimethylalkanes and for various groups of methylalkanones, and it was shown that Type A crystals contained right handed spirals, i.e. they crystallized in space group P6122 (Type 2 of Fig. 6.3). These crystals, although containing right handed spirals, are laevorotatory i.e. they rotate the plane of polarized light counterclockwise. It would be useful (perhaps essential) to conﬁrm these conclusions by carrying out a full crystal structure analysis of an ordered hexagonal urea inclusion complex containing a guest of known optical conﬁguration. Alternatively the Bijvoet method could be applied, using the anomalous scattering of oxygen (Engel, 1972); this could be a rather taxing experiment (Rabinovich and Hope, 1980). 6.2.1.8 Determination of guest molecule conformation from diffuse x-ray scattering The theoretical background has been outlined above. Most studies have been made with oscillation or stationary crystal photographic methods, using ﬁltered or (preferably) monochromatic radiation. The length of a guest molecule in a tunnel depends (Laves, Nicolaides and Peng, 1965) on (a) the number of atoms in the chain, (b) the amount of overlapping of the ends of the molecules in the tunnel, (c) whether the guest is locked into structural features of the host framework, (d) details of the guest conformation such as the degree of coiling, and (e) details of the guest conﬁguration such as presence of cis (Z) or trans (E) isomers (Nicolaides and Laves, 1958). The reference state is usually taken as the extended form of the corresponding n-alkane. Molecular lengths are obtained from measurements of spacings while structures, projected one-dimensionally, are derived from the intensities of the reﬂections; the model is varied to obtain best agreement between observed and calculated structure factors. The method was ﬁrst applied, for urea and

DIRECTIONALLY BONDED HOSTS

219

thiourea tunnel inclusion complexes, to the spacings of diffuse lines (Nicolaides and Laves, 1954) and then extended to comparisons of intensities (Nicolaides and Laves, 1956); it can of course be used for any system where host and guest sublattices are incommensurable and a one-dimensional approximation is applicable (e.g. the pentaiodide ion in trimesic acid pentaiodide (see Section 10.3)). Applications include demonstration of the all trans conﬁguration of squalene in its thiourea complex (Nicolaides and Laves, 1965), location of substituents in long-chain compounds using intensity calculations (Nicolaides and Laves, 1954), determinations of molecular lengths in a wide variety of complexes (Nicolaides and Laves, 1963) and comparison of the lengths of particular guests in their urea and thiourea complexes (Laves, Nicolaides and Peng, 1965). The lengths of about 400 guest molecules in 35 different categories (e.g. n-alkanes, symmetrical monomethylalkanes, secondary alcohols, dialkylketones, chloroalkanes) were measured in one application (Lenne´, Mez and Schlenk, 1970) and later extended to other types of guest (Hadicke and Schlenk, 1972). Detailed investigations of the G (diffuse) diffraction patterns from urea inclusion complexes of diacyl peroxides (Harris and Hollingsworth, 1990) and n–C24H50 (Fukao, 1994a,b) have been reported. 6.2.1.9

Variation of structure with temperature, with particular reference to {3(urea)[1/4(n-hexadecane)]}

Interrelated static and dynamic changes take place in urea tunnel inclusion complexes (and, of course, in many other types of complex) on cooling, and these have been studied by a variety of techniques. In general terms there are clear behavioral resemblances among the various hexagonal urea inclusion complexes but the details depend on the nature of the guest. For example, many investigations have shown that urea-n-parafﬁn systems all appear to show the common feature of a ﬁrst order transition on cooling. The temperatures of the major transition as measured by DTA (Chatani, Anraku and Taki, 1978; ZZZAKG02) are shown in Fig. 6.9, and this provides additional evidence for inﬂuence of the guest. Only two values are available for odd-numbered parafﬁns (n ¼ 11, 15), and this is not sufﬁcient to decide whether odd and even parafﬁns behave differently, especially in view of the spread of values for the even parafﬁns. We brieﬂy recall some of the salient features of the physical methods that have been used; these remarks, adapted from some of the papers to be quoted later, will also apply to analogous studies of many other types of molecular complex and compound. Diffraction measurements will be most successful in providing information about the ordered parts of the structure; here, speciﬁcally, about the urea or thiourea framework over the whole temperature range and about the guest molecules at temperatures low enough for the guests to be ordered. Analyses based on measurements of (X-ray or neutron) Bragg reﬂections alone give information about the average structure, while studies of diffuse scattering give information about the disorder in the crystal. It is not possible to distinguish between static and dynamic disorder using X-ray diffraction but this can be done by neutron diffraction, measurements of elastic scattering (i.e. without change of wavelength (energy)) giving information about static disorder while measurements of inelasticscattering give information about dynamic disorder. Calorimetric measurements will provide information about thermal processes occurring in both host and guest sublattices; inferences about changes in molecular arrangement occurring in a transition are often

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220 200 180 Ttr(K) 160 140 120 100 9

14

24 29 19 ‘n’ in Cn H2n + 2

34

Fig. 6.9. Temperatures of the (apparently) ﬁrst order phase transition (hexagonal to orthorhombic) in {urea[n-parafﬁn]} tunnel inclusion complexes plotted against number of carbons in the guest. Additional values (up to n ¼ 45), that do not change the overall picture, are given by Fukao, Horiuchi, Taki and Matsushige, 1990. (Adapted from Chatani, Anraku and Taki, 1978.)

checked by comparing measured and calculated entropy changes. Calorimetric and diffraction studies refer to the system as a whole. NMR measurements provide a very powerful technique for studying molecular dynamics in the solid state. Proton NMR spectroscopy has been extensively used in the past but has the disadvantage that line width, second moment and relaxation data reﬂect average properties over the whole spin system. The 2H NMR spectrum reﬂects, because of the quadrupole interaction involved, the behaviour of isolated nuclei and is essentially not affected by magnetic interactions with other nuclei. For systems like the urea and thiourea tunnel inclusion complexes there is a particular advantage in being able to deuterate either host or guest and hence study one or other by 2H NMR spectroscopy. Motion in the range 103 to 108 Hz may be described as of ‘‘intermediate’’ rate on the 2H NMR quadrupolar time scale and such motion affects the 2H NMR line shape in a manner dependent upon its 3 angular extent and also its rate. Motion of rate < 10 Hz8 has no effect on the line shape and is said to be in the ‘‘slow’’ regime. Motion of rate > 10 Hz is said to be in the ‘‘fast’’ limit, and the line shape becomes insensitive to further increase in the rate of motion, though still characteristic of the angular extent of the motion. In most studies a particular technique is applied to a number of complexes but there is more to be learned when the results obtained by a variety of techniques are compared for a particular complex; we shall do this for {3(urea)[1/4(n-hexadecane)]} (referred to as {urea[n-C16H34]}), which has been studied more comprehensively than other complexes. The molar ratio of urea to n-C16H34 has been given as 11.91, and the complex could therefore be expected to be dimensionally commensurate, but the mismatch, although small, is important, as is shown by the diffraction studies discussed below. We start with the results of physical measurements, which have been gathered together in Fig. 6.10, using the same temperature scale to facilitate comparison among the results. The Cp–T values (Pemberton and Parsonage, 1965) show deviations from a smooth curve only in the 130–160K region, with an apparently ﬁrst-order transition appearing at 152K, and some

DIRECTIONALLY BONDED HOSTS

221

T(K) 100

200

300 (a)

a (Å)

8.24 8.19 8.14

14.0

XRD

13.8

1295

(c)

1255

(e)

203 J/mol K

16 130

8

140

80 75 70

Cp

12

85

150

Cp(J/mol deg)

1275

160 T(K)

(d) 1H

4 0

12

NMR

(d)

8

6 4

4 2 0 100

200 T(K)

LINE WIDTH (gauss)

SECOND MOMENT (gauss2)

Vol (Å3)

14.2 b(Å)

(b)

0 300

Fig. 6.10. Comparison of the results of various types of physical measurements on {urea [n-C16H34]}. (a, b, c) The XRD measurements of cell dimensions are from Chatani, Anraku and Taki (1978). The high temperature form is p given as an orthohexagonal cell with twice the volume of the ˚ conventional hexagonal cell (bO ¼ 3(aH). The c-axis varies smoothly with temperature (11.015 A ˚ at 153K and 10.988 A ˚ at 98K) and does not show a discontinuity at 150K. (d) The at 298K, 11.007 A 1 H wide line NMR measurements (left: Second moment; right: line width) come from Umemoto and Danyluk (1967) and refer only to the behavior of the guest as d4-urea was used. (e) The speciﬁc heat measurements, from Pemberton and Parsonage (1965), refer to one mol of urea. Comparison with the Cp–T and 2H NMR (Fig. 6.11) measurements shows that ﬁner temperature intervals are needed for the XRD and 1H NMR measurements. The curves are guides to the eye.

anomalous behaviour around 135K; these results are shown on an expanded temperature scale. NMR 1H line widths and second moments for {urea-d4[n-C16H34]} increase rapidly below 140K (Gilson and McDowell, 1961; Umemoto and Danyluk, 1967). The rigid lattice approximation appears to apply (by extrapolation) below about 100K but observed values are appreciably smaller than calculated values above 140K; this will be

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considered below. The temperature dependence of the bands in the C–H stretching region of {urea[n-C16H34]} has been studied by Raman spectroscopy (Snyder, Scherer and Gaber, 1980). All bands become signiﬁcantly narrower on cooling but the intensity of the intense methylene antisymmetric stretching fundamental at 2885 cm1 shows, anomalously, a sharp change of slope at 148K when plotted against 1/T; presumably this corresponds to the major peak in the Cp–T curve. 2 H NMR spectra of polycrystalline {urea[n-C16D34]} have been measured over the temperature range 295–115K (Harris and Jonsen, 1989) (Fig. 6.11).

ω-reorientations 60° jumps

D3C

At 115K, the CD3 group is rotating rapidly about its symmetry axis, but there is also evidence for a combination of 60 jumps and !-reorientations (not simultaneous) below 146K, where there is a striking change in the appearance of the spectra, associated with the major peak in the Cp–T curve. The motions remain essentially unchanged up to 295K, where they include 60 jumps about the long axis of the molecule, torsional libration (of approximately 25 ) about the penultimate C–C bond and rotation of the CD3 group. The most comprehensive diffraction studies yet made of any urea inclusion complex by a particular group are of {urea[n-C16H34]}, using Bragg and diffuse scattering of both X-rays and neutrons (Forst, Jagodzinski, Boysen and Frey, 1990; Forst, Boysen, Frey, Jagodzinski and Zeyen, 1986; Forst, Jagodzinski, Boysen and Frey, 1987). Even so, as a b, b⬘

b, b⬘ 295 K

b a

b

a

b 147 K

b

146 K

b

115 K

b a

100

0 –100 kHz

Fig. 6.11. 2H NMR patterns of polycrystalline {urea[n-C16D34]}. Three superimposed powder patterns can be identiﬁed, labeled 0 a 0 (CD3 group), 0 b 0 (CD2 adjacent to CD3) and 0 b 0 (all other CD2); 0 b 0 and 0 b 0 become resolved only at higher temperatures. (Reproduced from Harris and Jonsen, 1989.)

DIRECTIONALLY BONDED HOSTS

223

Table 6.2. Summary of structural data for {urea[n-C16H34]} (reproduced from Forst, Boysen, Frey, Jagodzinski and Zeyen, 1986) T (K)

Phase

>380 380

I

365

II

148

III

120

IV

Average structure Decomposition to tetragonal urea þ n-C16H34 Hexagonal P6122, a0 8.2, ˚ c0 11 A Trigonal P312, ˚ ¼ 2c0 c 22 A Orthorhombic P 212121; a 8.2, ˚ b 14.2, c 11 A Triclinic (two lattices?)

Order/disorder

Longitudinal disorder in adjacent tunnels; orientational disorder in each tunnel. Longitudinal disorder in adjacent tunnels; orientational disorder in each tunnel. Mutual longitudinal deformation of end groups; (microdomains in ab plane). Lateral orientational order of guests in adjacent tunnels. ˚ k c. Domain structure (host) 200 A

these authors note, complete clariﬁcation was not obtained and there is scope for further work. There are also studies by other groups, using both single crystal (Harris, Smart and Hollingsworth, 1991; Chatani, Taki and Todokoro, 1977; ZZZAKG) and polycrystalline samples (Harris, Gameson and Thomas, 1990). We summarize the major conclusions here and refer the reader to the original papers for additional detail. The phase relations found in the system are given in Table 6.2. The hexagonal structure stable from 380 to 365K is that characteristic of most urea tunnel inclusion complexes at room temperature, and is the structure analyzed for {urea[n-C16H34]} at room temperature (Section 6.2.1.7(ii)). The I , II transition is found only for the n-hexadecane guest and is perhaps due to similarity between the length ˚ , including allowance for Van der Waals radii of of a hexadecane molecule ( 22.6 A ˚ ); it is outside the temperature terminal methyl groups) and twice the c-axis repeat (22.0 A range covered in Fig. 6.10. As the terminal methyl groups cannot exactly match the positions of the potential wells in the urea matrix there is a mutual interaction between framework and guest molecules leading to a doubling of the c-axis repeat and more ﬂexibility for lock-in. One should also note that there is evidence from 2H NMR spectroscopy for 14% gauche content in the C2–C3 bond and 9% in the C3–C4 bond of n-hexadecane (in {urea[n-C16H34]}) at room temperature (Cannarozzi, Meresi, Vold and Vold, 1991). The additional degrees of motional freedom of the guest may account for the lower values of the second moment of the hexadecane 1H NMR lines (1.5 G2 at 240K), compared both to calculation (6.0 G2, with free rotation of the hydrocarbon chains) and to the experimental values obtained for the dodecane (2.2 G2), tetradecane (2.5 G2) and octadecane (2.9 G2) complexes. Domain boundaries may occur when the mismatch is such that methyl groups are close to potential maxima. The II , III transition at 148K, analogs to which occur in the other urea[n-parafﬁn] complexes, corresponds to the peak in the Cp–T curve at 152K, to the break in the plot of I(2885 cm1) against 1/T, to striking changes in the 2H NMR spectra, and in the Debye–Scherrer X-ray powder patterns obtained by Harris, Gameson and Thomas (1990). Major changes in the 1H NMR spectra also occur in this temperature region. This major

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transition occurs when the thermal energy (RT 1.25 kJ/mol) becomes comparable with the potential barrier to the free rotation of the guest molecules; the values for n-CnH2nþ2 guests (n ¼ 10 to 36) vary from 111 to 218K (Fig. 6.9). According to Chatani et al. (1977), the orthorhombic crystals obtained after transformation from the hexagonal (or trigonal) phase have space group P212121 (Z ¼ 12), and are triply twinned; however, Forst et al. (1990) show that there are six orientations, characterized by a small angular deviation ( 1 at 78K) of the orthorhombic a, b axes from the corresponding orthohexagonal axes. The twinning implies that a full structure determination of the orthorhombic form would be difﬁcult, as both Harris et al. (1991) and Forst et al. (1990) have noted. The structure of the isomorphous orthorhombic {urea[1,3-butadiene]} has been reported (Chatani and Kuwata, 1975). The temperature dependence of the cell dimensions is shown in Fig. 6.10. There are no signs of discontinuities at 135K, where there is a minor peak in the Cp–T curve or at 120K, where Forst et al. (1990) have reported a ﬁrst order transformation (see below). However, there are abrupt changes (in opposite directions) in a and b at 145K, which correlate well with the change in the 2H NMR spectrum at 146K (Fig. 6.11). The c axis and the volume appear to be continuous (although more detailed measurements would be desirable) and this accords with the remark (Chatani et al., 1977) that the transformation does not show any hysteresis. The II , III transformation at 150K is sometimes referred to as an order-disorder transformation, presumably because ordering of the guests occurs. The entropy of transition at 152K is 3 J/mol K for the formula unit {3(urea)[1/4 (n-hexadecane)]}; testing this value against R ln m gives 1.43 for m. The transformation appears, from a thermodynamic point of view, to have both ﬁrst and second order features. The II , III transition is associated with lateral ordering of the guests in neighbouring tunnels. Below the transition temperature only ﬂuxional oscillations are possible about the mean guest molecule orientation in the tunnels, and the urea framework distorts to conform to this orientation (Fig. 6.12). At 120K there is a further ordering process III , IV, shown by a sharpening of the diffuse scattering and splitting of Bragg reﬂections. Neutron diffraction shows that this is a ﬁrst order transition involving mainly static processes (i.e. there is essentially no inelastic neutron scattering). There is additional longitudinal ordering of the guest molecules in adjacent tunnels which induces higher-order modulations into the urea framework leading to formation of a domain structure. The domains ˚ in length along c, thus containing chains of about nine n-hexadecane are about 200 A molecules. Curiously, there is no evidence for this transition in the speciﬁc heat or spectroscopic measurements, although it does occur in a region of rapid change in the NMR spectra; conversely, the activity in the Cp–T curve around 135K does not appear to be reﬂected in structural changes. Clearly there is room for further study of the Cp–T behaviour. The complexity of the structure of phase IV at 32K is illustrated by the remarkable oscillation photograph shown in Fig. 6.13, and this also shows the wealth of information potentially available from appropriate diffraction photographs. There are four layer lines (l ¼ 1 4, marked by L) due to the periodicity in the c direction of the host urea ˚ c-axis repeat). There matrix (note that the various l indices are deﬁned in terms of the 11 A are nine layer lines (l 0 ¼ 1 9, marked by L 0 ) due to the periodicity in the c direction of the hexadecane guest; at lower diffraction angles the L and L 0 patterns cannot be resolved. The L 0 pattern corresponds to the diffuse s layer pattern appearing at higher temperatures

DIRECTIONALLY BONDED HOSTS

225

bh

b0 a0

6

9.7

9.1

0

4.7

7

9.26

4.71

Fig. 6.12. Schematic structures of {urea[n-C16H34]}. Upper diagram: The hexagonal structure viewed down the tunnel axis; the parafﬁn chain is shown in various orientations in order to emphasise its disorder. The orthohexagonal cell is also outlined. Lower diagram: The orthorhombic structure viewed down the tunnel axis, showing the distortion introduced by ordering of the orientations of the parafﬁn chains (schematic representation). No attempt has been made to represent the multiple orientations of the orthorhombic cell with respect to the orthohexagonal cell. (Reproduced from Chatani, Anraku and Taki, 1978.)

and identiﬁed as due to the guest (Forst, Jagodzinski, Boysen and Frey, 1990). There is one layer line (l00 ¼ 1, marked by L00 ) which corresponds to the d diffuse layer system perpendicular to c* and considerably broadened in the c* direction, which is found at ˚ C–C–C repeat period of the higher temperatures. This has been ascribed to the 2.56 A almost-periodic alkane molecule. The ﬁne splitting of some of the L reﬂections is ascribed ˚ domain structure) induced by to higher-order modulations of the host lattice (the 200 A longitudinal ordering of C–C–C portions of the guest in neighbouring tunnels. The various ordering processes that occur as the temperature is reduced can be understood in overall terms as a progressive reduction in the motional freedom of the guest molecules leading towards their crystallization as a separate sublattice. However, the residual diffuse scattering on Fig. 6.13 shows that a completely ordered superstructure of host and guest is not achieved even at the lowest temperatures. Although the guest

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sublattice remains incommensurate with the host framework, there is a mutual interaction which gives rise to the complicated domain structure. Forst et al. (1987) conclude that it would ‘‘be more adequate to term this class of substance as parafﬁn enclosure compounds instead of urea inclusion compounds.’’ Our emphasis has been, of course, in quite the opposite direction. The details of the diffraction patterns from urea inclusion compounds containing n-alkane guests depends on the nature of the guest, and a wealth of information is emerging from such studies. An excellent summary comes from Weber, Boysen and Frey (2000), which we quote in abbreviated form: ‘‘Urea inclusion compounds (UICs) . . . consist of a honeycomb-like urea host structure with a quasi-hexagonal lattice, forming open tunnels parallel to c in which various [guests, here n-alkanes] are embedded. UICs belong to the class of composite crystals, where host and guest substructures have different translational and/or point symmetry. In particular, they show complex disorder phenomena for various reasons: (i) both substructures have a different ‘‘dimensionality,’’ viz. in the ‘‘tubes’’ of the three-dimensional ordered urea–host framework, a predominantly one-dimensional guest structure, the alkane chains, are embedded; (ii) the orthorhombic or monoclinic eigen symmetry of the alkane molecules is in competition with the hexagonal symmetry of the urea host structure; (iii) both substructures have – along the unique axis – non-matching, in general incommensurate, translational periods . . . [The] interactions [between both substructures] are responsible for frustrations which become evident from mutual (incommensurate) modulations and disordering, [which is] highly temperature dependent, including possible structural phase transformations. The basic structural features of the host and guest structures are reﬂected by typical diffraction patterns: sharp Bragg reﬂections of the three dimensional urea host and narrow diffuse layers (‘s-layers’) perpendicular to the c axis corresponding to the onedimensional guest structure. As the s-layers show some intensity modulations and are superimposed by weak Bragg-like reﬂections, however, this rough division is not fully adequate, and lateral correlations between the guest molecules cannot be neglected. In addition, mutual modulations of host and guest lattices give rise to three-dimensional and one-dimensional satellite scattering accompanying the Bragg reﬂections and the s-layers respectively . . . .Another characteristic diffuse diffraction feature of UICs is the set of so-called [diffuse] ‘d-bands’ . . . explained by a longitudinal and lateral disorder of the guest molecules.’’ The structures of the low-temperature orthorhombic phases of the urea inclusion complexes of 1,10-dibromo-n-decane (ROPQOC) and 1,12-dibromo-n-dodecane (ROPQUI) have been determined (Yeo and Harris, 1997)), and of that with 1,10decanedicarboxylic acid (Yeo, Harris and Guillaume, 1997; NATNIF). The same host matrix structure appears in all these crystals at room temperature but there are differences at low temperatures due to different manners of ordering of the guests. The ﬁrst two ˚ ) discomplexes are isomorphous and have the P212121 structure (cell 8 14 11 A ˚ ); the cussed above, but the third transforms to space group C2221 (cell 16 28 11 A ˚ for all three crystals. These more complete structure analyses were tunnel axis is 11 A made possible because the phase transitions were ‘‘single crystal’’ to ‘‘single crystal,’’ complications due to the multiple twinning found in other systems being absent. In all three low-temperature structures the lateral ordering is fairly complete but longitudinal ordering (the location of the guest molecules along the tunnel axes) is still lacking, i.e. the

DIRECTIONALLY BONDED HOSTS

227

Table 6.3. Crystal data for urea inclusion complexes showing deformation of the room-temperature hexagonal urea framework to orthorhombic or monoclinic at lower temperatures. The tunnel axes are shown in bold. N ¼ number of formula units in the unit cell Formula {(urea)3[0.21(1,10-dibromodecane)]} at 108K {(urea)30.27[(1,12-dibromododecane)]} at 108K {(urea)6[(1,10-decanedicarboxylic acid)]} (at 173K) {(urea)3x[1,6-dibromohexane]}

a/

b/

c/

N Space group

Reference

8.080 13.945* 11.007

4

P212121 (1)

8.186 14.133* 10.930

4

P212121 (1)

16.305 28.321* 11.000

8

C2221

(2)

13.381* 4

P21/n

(3)

8.560 10.889 92.82

p ˚ 14 A ˚ , or multiple thereof, thus pointing up the relationship between orthorhombic and ortho* 38A hexagonal cells. Notes: (1) Yeo and Harris, 1997; the axes have been reoriented from those in the original paper in order to emphasize the relationship between RT and LT structures. (2) Yeo, Harris and Guillaume, 1997; this entry should be compared with that for 1,10-undecanedione guest in Table 6.4, showing that the ordering in the a, b, c directions differs in the two crystals although both have the same C2221 space group. (3) see Hollingsworth and Harris, 1996, Table 4.

structure remains incommensurate. The coordinates given for the atoms of the guests in these structure determinations are unlikely to be reliable, and coordinates are not even given for the bromines of the ﬁrst two structures! Many lessons can be learned from these results. One is not surprising – the experiments of twenty and thirty years ago bear repeating in order to take advantage of the much greater power now available from new technologies. For example, the cell dimensions determined laboriously from diffraction photographs of single crystals at rather wide temperature intervals could be measured at much closer intervals and with greater accuracy by using neutron diffraction or synchrotron radiation on polycrystalline samples (Finney, 1995). A second is the wealth of detail obtainable from single crystal XRD photographs using monochromatic radiation and stationary and/or oscillating samples; surely area detector techniques have much to offer here. A third is the synergistic effect of investigating the same set of phenomena by as many different methods as possible, and comparing the results in detail, as we have tried to illustrate in Figs. 6.10 and 6.24. A fourth is that study of commensurate structures yields much more, and more ﬁrmly based, information than does that of incommensurate structures, but for most guests of a homologous series only the latter are available. 6.2.1.10 Interruption of urea framework by host–guest hydrogen bonding In the previous section we have reviewed deformation of the hexagonal urea framework normally found at room temperature to lower-symmetry arrangements. However, we emphasize that the urea framework remains intact despite the deformation; urea–urea

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L

4.5

L⬘

9

4.25 4

L⬙

1

8 7

3

6 5

2

4 3

1

2

0.5 0.25 0

1

Fig. 6.13. Section of a normal beam oscillation photograph (Cu K1 radiation) of {urea[n-C16H34]} at 32K taken with c vertical showing the complicated structure of phase IV. Indices L mark the Bragg layers of the host, L 0 those of the guest (corresponding to the diffuse s sheets) and L00 the position of the d–band; s and d are deﬁned by Forst, Boysen, Frey, Jagodzinski and Zeyen (1986) and Forst, Jagodzinski, Boysen and Frey (1987) and in the text. (Reproduced from Forst, Boysen, Frey, Jagodzinski and Zeyen (1986).) (I am greatful to Dr Hans Boysen for an original print.)

hydrogen bonds are not broken. The deformation results from the increased host–guest interaction that occurs on cooling. More drastic effects can also occur. These are of two kinds. In the ﬁrst, inclusion complexes are not formed but instead mixtures of urea and a second component crystallize to give binary arrangements of many different sorts. This often, but not only, occurs with lower members of a homologous series (see Table 7 of Hollingsworth and Harris, 1996); for example, 1,3-dicyanopropane, 1,4-dicyanobutane and 1,5-dicyanopentane form 1 : 1 hydrogen bonded compounds with urea (not of the tunnel variety), while tunnel inclusion complexes are formed by some of the higher ,!-dicyanoalkanes (that with 1,6dicyanohexane is monoclinically distorted). We do not discuss here the structures of binary adducts that are not tunnel inclusion complexes. We now consider the second kind of effect – formation of interrupted structures in which some framework urea–urea hydrogen bonds are replaced by urea–guest hydrogen bonding. These are examples of the general phenomenon found in tunnel inclusion complexes where the host-to-guest interactions are sufﬁciently important to interrupt, but

DIRECTIONALLY BONDED HOSTS

229

Table 6.4. Crystal data for urea inclusion complexes showing interruption of the urea framework. The tunnel axes are shown in bold. N ¼ number of formula units in the unit cell Formula unit

a/

b/

c/

N

Space group

Reference

{(urea)7[2,7-octanedione]} {(urea)8[2,9-decanedione]} {(urea)9[2,10-undecanedione]} {(urea)6[1,8-dicyanoo¨ctane#]}

8.211 8.229 8.345 15.125

8.211* 8.229* 13.939 7.487/ 104.10

76.91 44.16 32.982 25.815

6 3 4 4

P6122 P3112 C2221 C2/c

(1) (2) (3) (4)

p ˚ (or some * To obtain the orthohexagonal cell these values must be multiplied by 3, and approximate to 14 A multiple thereof ). # sebaconitrile; structure determined at 98K; there is no tunnel axis in simple terms (see below). Notes: (1) Brown, Chaney, Santarsiero and Hollingsworth, 1996; structure determined at 291K. (2) Hollingsworth, Brown, Hillier, Santasiero and Chaney, 1996. (3) Brown and Hollingsworth, 1995. (4) Hollingsworth, Santarsiero and Harris, 1994.

not destroy, the host framework by formation of hydrogen bonds between host and guest (cf. some of the tunnel inclusion complexes of trimesic acid). Hollingsworth and Harris (1996) have discussed the urea inclusion complexes of alkanediones, ,!-dicyanoalkanes and ,!-dihaloalkanes by comparing the structures of the inclusion complexes found within each homologous series (for a particular family of guests) and showing how the very interesting physical properties of the crystals can be explained in terms of their structures. We shall not repeat this material but rather emphasize the host–guest interactions in particular commensurate crystals of these groups as illustrations of the wider topic of inclusion complexes where the usual structures are distorted or deformed because of appreciable host–guest interactions. We ﬁrst discuss the complexes with host-guest hydrogen bonding. Detailed results have been given for {(urea)7[2,7-octanedione], for which atomic coordinates are available (TOZHOF; Brown, Chaney, Santarsiero and Hollingsworth, 1996). There are 3 1/2 urea molecules and 1/2 2,7-octanedione molecules in the asymmetric unit, and thus 42 ureas and six guests in the unit cell. The 1/2 urea molecule is located at Wyckoff positions (b) (2x, x, 1/12, etc), with two fold symmetry, while the other ureas are in general positions. The guest molecules are located about Wyckoff positions (b) (x, 0, 0 etc.) and also ˚ have two fold symmetry. The hydrogen bonds between ureas range from 2.94 to 3.08 A ˚ in length. A limited view down while that between carbonyl oxygen and urea N is 3.08 A the tunnel axis is shown in Fig. 6.14. The usual structure is modiﬁed, but not drastically so. Packing diagrams have been given for the {(urea)8[2,9-decanedione]} and {(urea)9[2,10undecanedione]} structures and these show host–guest hydrogen bonding similar to that described for the octanedione complex. However, atomic coordinates have not been deposited and a detailed description is not possible. The departures from the usual structural arrangement are greater in {(urea)6 [1,8-dicyanoo¨ctane]} (LEMHIU, coordinates available; Hollingsworth, Santarsiero and Harris, 1994), and this makes the structure rather difﬁcult to depict. There are three ureas in the asymmetric unit, and 1/2 of a guest molecule, which has two fold symmetry and is

T UN N E L I N C L US I O N C O M P L E XE S

230

Fig. 6.14. View down the tunnel axis of {(urea)7[2,7-octanedione]}, showing a single guest molecule hydrogen bonded to two urea molecules of different helices (in the sense of the lower part of Fig. 6.3). These two urea molecules are turned away from the tunnel axis by 38.5 . The O¼C . . . C¼O torsion angle of the guest molecule is 160 . (Reproduced from Brown, Chaney, Santarsiero and Hollingsworth, 1996.) C

C

z y x

A

A

Fig. 6.15. Stereoview down the tunnel axis of two unit cells of {(urea)6 [1,8-dicyanoo¨ctane]} (LEMHIU). Many atoms have been removed for clarity. The urea atoms are shown by smaller circles and the atoms of the guest by larger circles. N . . . O hydrogen bonds between molecules of the urea framework and N . . . N hydrogen bonds linking urea to guest are shown. Mutual displacement of parts of the urea framework are shown. (Data from Hollingsworth, Santarsiero and Harris, 1994.)

DIRECTIONALLY BONDED HOSTS

231

urea-urea O...N H-bonds C

G-urea N...N H-bonds

B

1,8-dicyanooctane guest (G)

z A y

x

Fig. 6.16. Part of the {(urea)6 [1,8-dicyanoo¨ctane]} structure viewed down [010]. Many atoms have been removed for clarity. Hydrogen bonding of the guest molecules (larger circles) to the urea framework (smaller circles) is shown. (Data from Hollingsworth, Santarsiero and Harris, 1994.).

located about Wyckoff position (e). The stereoview of Fig. 6.15 shows that the hexagonal framework is not complete, and the projection of Fig. 6.16 shows that the guest molecules are offset from one another, i.e. there are zigzag tunnels instead of the linear tunnels of the usual structural arrangement. The three independent oxygens are hydrogen bonded to ˚ ; the cyano nitrogen is linked to nitrogens of ureas with lengths ranging from 2.88 to 3.01 A ˚ ; as before, the host . . . two different urea nitrogens with N . . . H–N distances of 3.19 A guest interaction does not seem to be particularly strong. We shall not describe this rather complicated pattern of hydrogen bonds in more detail. 6.2.1.11 Rhombohedral urea, thiourea and selenourea tunnel inclusion complexes (i) Cell dimensions and structure: These complexes all have the structure shown as Type 3 in Fig. 6.3. The chemical formula is expressed as before as {3(host)[x(guest)]}; ˚ , 104.5 ; thiourea the rhombohedral cell dimensions are: urea complexes, a 9.0 A ˚ , 104.3 ; space ˚ , 104.0 ; selenourea complexes, a 10.4 A complexes, a 10.0 A group R 3 c, Z ¼ 2. The host molecules are located on two fold axes. The structures of these complexes are usually described in terms of the triply primitive hexagonal unit cell containing 18 host molecules (i.e. Z ¼ 6), with dimensions (in the same order as above) of ˚ . The hexagonal tunnel has height 11.0 a 14.2 (15.8; 16.5); c 11.0 (12.5; 12.9) A ˚ and edge 4.8 (5.37; 5.5) A ˚ . The relationship between the rhombohedral (12.5; 12.9) A unit cell and the hexagonal tunnel is shown in Fig. 6.17. Despite the resemblance to the (primitive) hexagonal urea structure, the rhombohedral structure differs in that the arrangement in the tunnel walls is not spiral but layered; the rhombohedral crystals are centrosymmetric, not chiral. There is a layer of sulphur atoms (using a thiourea complex as an example; see Fig. 6.19) pointing into the tunnel at z ¼ 0, followed by two

232

T UN N E L I N C L US I O N C O M P L E XE S

C

O

b

a Z

Y X

a

Fig. 6.17. Relationship between the rhombohedral and (low-temperature) monoclinic unit cells and the outline of the hexagonal tunnel, illustrated for thiourea complexes. The axes of the rhombohedral cell are shown by the full lines x, y and z while c ¼ x þ y þ z is the threefold axis of the corresponding triply-primitive hexagonal cell. Only a few of the thiourea molecules are shown. The axes of the monoclinic cell are a ¼ x, b ¼ y þ z, c. (Reproduced from Cle´ment, Mazieres, Gourdji and Guibe´, 1977.)

layers of thiourea molecules in the walls of this tunnel at z ¼ 1/6 and 2/6. Thus the potential ﬁeld experienced by a guest molecule within the tunnel varies with z and this gives rise to a tendency to localize guest molecules in particular regions along the tunnel axis, and to favor inclusion of molecules whose dimensions along the tunnel axis are multiples of c/2; for example in the {3(thiourea)[cyclohexane]} complex (Lenne´, 1954) the cyclohexane molecules are localised in the vicinity of the sulphur atoms at z ¼ 0 and 1/2. We mention here that there is more variability in the cell dimensions of the isostructural rhombohedral tunnel inclusion complexes than in the analogous hexagonal complexes; also there do not appear to be any examples of host-guest interactions which interrupt the host framework. Full X-ray diffraction structure analyses have been made of the isomorphous {3(thiourea)[adamantane]} (VADWUS) and {3(selenourea)[adamantane]} (VADXAZ) complexes (Gopal, Robertson and Rutherford, 1989) and a stereodiagram of the ﬁrst is shown in Fig. 6.18. The adamantane guest is two fold disordered in the tunnels. Each S (Se) atom forms four (two pairs of ) hydrogen bonds, with lengths 3.462(7) and ˚ (3.51(2) and 3.65(2) A ˚ ). The NH . . . Se hydrogen bonds are weaker than their 3.496(5) A oxygen and sulphur counterparts, and this leads to greater variability in cell dimensions of selenourea inclusion complexes. 2H NMR studies show that there are no phase transitions between 333 and 119K (MacIntosh, Frazer, Gruwel, Wasylishen and Cameron, 1992).

DIRECTIONALLY BONDED HOSTS

233

Fig. 6.18. Stereoview of a tunnel in {3(thiourea)[adamantane]}. Only one orientation of the twofold disordered adamantane is shown in each site. (Reproduced from Gopal, Robertson and Rutherford, 1989.)

The structure of {3(tu)[CCl4]} at 170K has been determined (a ¼ 15.539, ˚ ; Fait, Fitzgerald, Caughlan and McCandless, 1991; FABTAD10); this is c ¼ 12.529 A phase III (although the space group was reported as R 3 rather than the usual R3c, this has been reinterpreted by Marsh et al., 2002 (FABTAD11)). The guest molecule is disordered. Speciﬁc heat measurements (Sekii, Matsuo and Suga, 1990) show a ﬁrst order transition (from phase I to II) at 41.3K (DHtrans ¼ 149 J/mol; DStrans ¼ 3.7 J/mol K) and a second order transition (from phase II to III) at 67.2K (DHtrans ¼ 241 J/mol; DStrans ¼ 3.9 J/mol K). The 35Cl NQR spectrum shows two lines at 7.4K, i.e in the phase stable in the lowesttemperature region (Adolphi, Conradi and Matsuo, 1994). This has been interpreted in terms of the ordered structure shown in Fig. 6.19, the CCl4 molecule being located at a site of two fold symmetry. At 170K, the CCl4 molecule is disordered over three sites, and this is compatible with the total entropy change between phases I and III (R ln 2.6). There is as yet no information about the structures of phases I and II from diffraction. A14N NQR study of the II to III transition does not seem to have given easily-interpretible results (El Ghallali, Gourdji, Guibe´ and Pe´neau, 1994). A new structural feature appears in the isomorphous 3 : 1 complexes of thiourea with (6-benzene)CrCO3 (GARTIC10), (4-trimethylenemethane)-FeCO3 (SESLUX) and (5-cyclohexadienyl)MnCO3 (GARTUO10); these have essentially the same structure as, say, {3(thiourea)[adamantane]} but the guest molecules are ordered in a polar array and the space group is R3c (Fig. 6.20). These complexes were designed to be noncentrosymmetric in order to be capable of second harmonic generation (Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989). The {3(thiourea)[(6-benzene) CrCO3]} complex has about twice the SHG efﬁciency of urea (which provides a widely used reference standard).

234

T UN N E L I N C L US I O N C O M P L E XE S

Layer 1

Layer 4

S C In-plane CI Out-of-plane CI

Layer 1 Tunnel axis

Fig. 6.19. Postulated structure of {3(tu)[CCl4]} in its lowest-temperaturephase I, based on 35Cl NQR measurements. The twofold axis of the guest molecule is normal to the tunnel axis. (Reproduced from Adolphi, Conradi and Matsuo, 1994.)

b

a

b c

Fig. 6.20. Crystal structure of {3(thiourea)[(6-benzene)Cr(CO)3]} at 203K; a ¼ 16.130, ˚ , space group R3c, Z ¼ 6. The upper diagram shows the view down the tunnel c ¼ 12.569 A axis, with two guest molecules in each tunnel; the lower diagram is the view normal to the tunnel axis, showing only the polar arrangement of guest molecules, thioureas being omitted for clarity. (Reproduced from Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989.)

DIRECTIONALLY BONDED HOSTS

235

6.2.1.12 Monoclinic complexes derived from the rhombohedral complexes Either cooling or the particular shape of the guest can lead to distortion of the rhombohedral lattice to monoclinic; a number of examples are known and it is convenient to summarize the structural results before discussing the behavior of the complexes on cooling. We give ﬁve examples in Table 6.5; the tunnel axis is [001] in all the examples and the disordered guests are all located about crystallographic centers. The ﬁrst four structures are isomorphous, and the ﬁfth isostructural. The structure of {3(thiourea)[H2C¼C(CH3)–C(CH3)¼CH2]} has been determined at 143K (the complex is unstable at room temperature, while the guest polymerizes rapidly under X-radiation at 193K). The relationship between triply primitive hexagonal axes and the monoclinic axes are: am ¼ 2=3ah þ 1=3bh 1=3ch ;

bm bh ;

cm ch :

The appreciable deformation (Fig. 6.21) of the previously hexagonal tunnels was ascribed to the ordered longitudinal packing of the guest molecules in the tunnels. The 2,3-dichloro-1,3-butadiene complex is isomorphous with that of dimethyl-butadiene, as are the complexes with polymerized guests (Chatani and Nakatani, 1972). Although the cell dimensions of the 2,3-dimethyl-1,3-butadiene and 1,5-cyclooctadiene complexes are similar, the symmetry elements of the space group are differently oriented and the tunnel axis is along [001] for the ﬁrst of these complexes and along [101] for the second (structure at 173K).

˚ , deg, A ˚ 3) for monoclinic {3(thiourea)[guest]} complexes; the space Table 6.5. Crystal data (A group is P21/a for the five examples, and all have Z ¼ 4 Guest/T

Refcode; reference

a

b/

c

Cell volume

2,3-dimethyl-1,3-butadiene; 143K Chlorocyclohexane; 85K

CN76

9.52(3)

12.55(4)

1683

JSH96

9.651

12.478

1753

1,5-cyclooctadiene; 173K

9.630(4)

12.615(5)

1770(1)

x(Squalene); 298K

WINZUO; GRB95 NL65

12.72

1837

0.5[2,6-diethyl-naphthalene)]; 298K

PIDRID; SSOK93

14.643(3)

15.42(3) 114.0(4) 15.964 114.22 16.05(5) 114.83(3) 15.72 115 9.282(2) 92.14(2)

12.571(3)

1707

10.14

References: GRB95 – Garneau, Raymond and Brisse, 1995; a and c have been interchanged to increase the similarity to the other structures; JSH96 – Jones, Shannon and Harris, 1996; Rietveld reﬁnement at 85K; rhombohedral to monoclinic transition at 190–194K; NL65 – Nicolaides and Laves, 1965; composition must take into account the extension of the long squalene molecule through several thiourea unit cells; NL76 – Chatani and Nakatani, 1976; SSOK93 – Shindo, Shindo, Ohnuma and Kabuto, 1993 (reoriented).

T UN N E L I N C L US I O N C O M P L E XE S

236

b N

sin

(a)

N C

5.24

S

5.15

5.77 5.28

q 4.30 p r

(b)

Fig. 6.21. (a) The structure of {3(thiourea)[H2C ¼ C(CH3)––C(CH3) ¼ CH2]} shown in projection down [001]. The distortion of the original hexagonal structure is shown by the values of the angles p, q, r which are respectively 141, 115.5 and 103.5 , and by the dimensions inserted. (b) Relationship of the unit cell in projection down [001] (outlined) to the overall arrangement of the distorted tunnels. (Reproduced from Chatani and Nakatani, 1976.)

6.2.1.13

Behavior of some rhombohedral inclusion complexes on cooling

As examples we shall use the isostructural {3(thiourea)[ferrocene]} (abbreviated {3tu[(C5H5)2Fe]} (FERTUR01), {3(thiourea)[cyclohexane]} ({3tu[C6H12]}) and {3(urea)[trioxane]} ({3u[C3H6O3]}) complexes. The information is comparable with that given for (hexagonal){3(urea)[1/4 n-hexadecane]} although gaps remain in some of the crystallographic details. The crystal structure of {3tu[(C5H5)2Fe]} at room temperature is isomorphous with ˚ instead of the more those of other rhombohedral thiourea complexes, but with a ¼ 16.36 A ˚ . The Fe atom is at 0, 0, 1/4, a site with 32 symmetry; the ﬁve-membered rings usual 15.8 A are three-dimensionally disordered (Hough and Nicolson, 1978). The crystals are orange at room temperature, and become yellow on cooling, as does ferrocene itself. The diffraction pattern at 100K showed broadened peaks, suggesting the occurrence of phase transformations to lower symmetry phases. Nothing substantial is yet known about the crystallography of any processes occurring on cooling, but there are calorimetric

DIRECTIONALLY BONDED HOSTS

237

(Sorai, Ogasahara and Suga, 1981; Sorai and Shiomi, 1986), Mo¨ssbauer (Gibb, 1976; Lowery, Wittebort, Sorai and Hendrickson, 1990) and NMR (1H (Cle´ment, Gourdji and Guibe´, 1980), 2H (Lowery, Wittebort, Sorai and Hendrickson, 1990; Heyes, Clayden and Dobson, 1991) and 13C (Nakai, Terao, Imashiro and Saika, 1986)) studies, which we shall now describe; the calorimetric, Mo¨ssbauer and 2H NMR studies are remarkably detailed. The excess heat capacities (i.e. with respect to an interpolated smooth curve) arising from the phase transitions are shown in Fig. 6.22; the enthalpies and entropies of the ﬁve transitions were measured and are included in the diagram (Sorai, Ogasahara and Suga, 1981). The corresponding measurement for the (C5D5)2Fe complex has also been reported (Sorai and Shiomi, 1986), the two diagrams being very similar. The phase transition V , IV showed hysteresis and hence was classiﬁed as ﬁrst order, while the order of the VI , V transition, despite indications of hysteresis, remained ambiguous; the other three transitions were second order. The transitions are associated with motions of the ferrocene molecules in the tunnels among a set of four orientations, which are shown schematically in Fig. 6.23. It should be noted that there is no indication, from any of the available physical measurements, which extend down to 87K, of freezing-in of the intramolecular rotations of the cyclopentadienyl rings. We shall now attempt to integrate the results of all these physical measurements, working upwards from the lowest temperatures. The information is about the reorientational motion of the ferrocenes, as very little is known about changes in the thiourea matrix. Comparison with other thiourea and urea systems suggests that there will be concomitant (and coupled) changes in the details of host and guest arrangements. A contrary view is that of Lowery et al. (1990) who,

60

1474 9.23

∆CP /JK–1 mol–1

50

263 1.79 14 0.08

40

30

Phase VI

V

IV

35 0.19 III

77 0.36 II

I

20 TC3 10

TC4

TC5

TC1 TC2

0 120

140

160

180 T/K

200

220

240

Fig. 6.22. The excess heat capacities arising from the phase transitions of {3tu[(C5H5)2Fe]}. The critical temperatures are (from TC1 to TC5) 147.2, 159.8, 171.4, 185.5 and 220K. The enthalpies (J/mol) and entropies (J/mol K) of the transitions are shown next to the peaks in the DCP/T curve. (Reproduced from Sorai, Ogasahara and Suga, 1981.)

T UN N E L I N C L US I O N C O M P L E XE S

238

basing themselves on the 2H NMR spectra of {3tu[(C5D5)2Fe]}, have concluded that ‘‘aside from rapid small amplitude reorientations at the higher temperatures, the thiourea molecules forming the hexagonal tunnels are stationary from 140 to 298K.’’ It is generally assumed that below 120K the parallel and perpendicular orientations (of the ferrocenes) are approximately equally populated, without there being any reorientation among them (Fig. 6.24); diffraction evidence is needed for more detailed deﬁnition of the low temperature crystal structure(s). The major reorientation takes place in the two associated phase changes in the region 120–163K. Sorai, Ogasahara and Suga (1981) consider in detail how the measured entropy changes shown on Fig. 6.22 should be allocated among the various reorientational processes; for example, 1.79 J/mol K was assigned to the VI)V transition.

(A) View down channel axis Perpendicular, or equatorial orientations

Parallel, or axial orientation

z

View normal to channel axis

(B)

z

(C)

Fig. 6.23. Schematic diagram showing the inclusion of the ferrocene molecules in the tunnels of the thiourea matrix. There is evidence from a single crystal 2H NMR study (Lowery, Wittebort, Sorai and Hendrickson, 1990) that the parallel orientation shown in the diagram is an approximation and that there are actually three orientations (related by a threefold axis) inclined at 17 to the tunnel axis. At high temperatures the ferrocenes are randomly oriented among the , , and z orientations. (Reproduced from Sorai, Ogasahara and Suga, 1981.)

DIRECTIONALLY BONDED HOSTS

239

This entropy change can be accounted for by a model (Fig. 6.23) in which reorientation between the three perpendicular sites (, , ) takes place within a group of three ferrocene molecules, which are perhaps located one above the other within a tunnel, giving a calculated entropy change of 1/3 R ln 3 (¼ 3.04 J/mol K); this is the ‘‘fast jump’’ process identiﬁed by Gibb (1976) from Mo¨ssbauer measurements. The ﬁrst order change V , IV involves the disordering of such groups as well as interchange between perpendicular and parallel orientations (this is Gibb’s ‘‘slow jump’’ process, the rate being <105 s1), with the corresponding entropy change calculated as R ln 4 1/3 R ln 3 (¼ 8.5 J/mol K). This should be compared with the assigned value of 9.23 J/mol K. Arrhenius parameters for the exchange between the three perpendicular orientations have been determined from the 2H NMR line shapes as Ea ¼ 6.4 0.5 kJ/mol and A ¼ (2.15 0.5) 107 s1; corresponding values for the less-facile perpendicular–parallel interchange are Ea ¼ 10.1 1.0 kJ/mol and A ¼ (1.5 0.6) 108 s1. Above 220K NMR spectra cannot distinguish between these two processes; a splitting of 1.5 kHz in the room temperature spectrum indicates that all reorientation is in the fast limit (>108 Hz), with 65% of the molecules in the three perpendicular orientations and 35% in the parallel orientation. By 340K, the ferrocenes are equally distributed among the four orientations and tumbling rapidly. Descriptions at a molecular level have not yet been proposed for the other three phase transitions, which occur in a region of rapid change in the NMR and Mo¨ssbauer spectra and probably reﬂect the highly correlated nature of the interchanges between parallel and perpendicular orientations (Lowery, Wittebort, Sorai and Hendrickson, 1990). The results available about the thermal behavior of {3tu[C6H12]} are even more complete than those for {3tu[(C5H5)2Fe]}. When comparing these results (Fig. 6.24), one should note that cell dimensions and 14N pure quadrupole resonance frequencies will be most sensitive to changes in the thiourea framework, 1H NMR and Cp–T curves to both host and guest, and 2H NMR to the motions of the deuterated compound(s), which can be host and/or guest; of course, the host–guest interaction somewhat blurs these distinctions. The speciﬁc heat measurements (Cope, Gannon and Parsonage, 1972a) show one major thermal event at 130K and two much smaller events at 148K and 170K, and otherwise a smooth variation of Cp with T; only the anomalous region is shown in Fig. 6.24. The peak at 130K is surely to be identiﬁed with the ﬁrst order phase change shown in the graph of lattice parameters against T (Fig. 6.24; Clement, Mazieres, Gourdji and Guibe´, 1977). The values of DHtr (1577 J/mol) and DStr (12.1 J/mol K) obtained from a DSC measurement (Poupko, Furman, Mu¨ller and Luz, 1991) are not very different from those given above for the ﬁrst order transition in {3tu[ferrocene]}(1474 J/mol and 9.23 J/mol K). The minor peak at 148K appears to correspond with the splitting of the NQR line at 150K and to the (not very well established) change in slope of the lattice parameter curves at 145K. The temperature dependence of the þ 14N pure quadrupole resonance frequencies1 (Cle´ment, Mazieres and Guibe´, 1971; Cle´ment, Gourdji and Guibe´, 1975) is in agreement with these assignments; from room temperature down to 150K there is only one line which then splits into six components and this number remains unchanged below 130K, where sharp changes in frequencies indicate a ﬁrst order phase change; there are no changes at 1 14 N (I ¼ 1) gives three NQR lines at ¼ (3 )e2Qq/4 and 0 ¼ þ ; however, the latter line occurs at very low frequencies and intensities and is generally not observed.

T UN N E L I N C L US I O N C O M P L E XE S

9.20

(a)

9.10 III

b(Å)

9.00 15.8 15.4 15.0 14.6

II

(b)

I

(e) 2540

XRD 128 K

150 K

1770 V(Å3)

(c) 1730

2530

NQR

V+ (kHz)

d(100)(Å)

240

1690 120

2520

(d) CP(J/mol K)

110

800 J/mol K

100

110

140

170 T (K)

90 80 70 110

CP 130 150 T (K)

170

Fig. 6.24. (a, b, c) Cell dimensions of {3tu[C6H12]} as a function of temperature; the c dimension ˚ ) does not vary with temperature. (Adapted from Cle´ment, Mazieres, Gourdji and Guibe´, (12.5 A 1977.) (d) Calorimetric measurements for {3tu[C6H12]}. (Reproduced from Cope, Gannon and Parsonage, 1972a.) (e) The temperature dependence of the 14N þ spectrum. Only ﬁve lines of the spectrum of Phase III are shown, the absent line being at slightly higher frequencies – 2550 kHz at 128K to 2570 kHz at 77K. (Reproduced from Cle´ment, Gourdji and Guibe´, 1975.)

170K (Fig. 6.24). There are three thiourea molecules in the rhombohedral unit cell at room temperature with the six nitrogens related by crystallographic symmetry elements, thus leading to only one NQR line. Below 150K the unit cell doubles in volume giving six thioureas or twelve nitrogens per cell; as there are six independent lines the nitrogens must be equivalent in pairs. The determination of the space group is incomplete; it was stated (Cle´ment, Mazieres, Gourdji and Guibe´, 1977) that the space group corresponding to the thiourea sublattice was P2/c while that of the crystal as a whole was given as P1, P1 or P2. Phase III appears to have the same symmetry as Phase II which does not lead to a change in the number of NQR lines; the cell volume in Phase III is 2.5% less than in Phase II. As an overall explanation for all these results it has been suggested (Cle´ment, Mazieres, Gourdji and Guibe´, 1977) that there are just three phases in the temperature region between 130 and 300K, thus withdrawing an earlier proposal (Cle´ment, Gourdji and Guibe´, 1975) of an additional phase change at 241K.

DIRECTIONALLY BONDED HOSTS

(a)

(b)

168 K 100 T1 sec 10

123 K

S2 (gauss2)

241

Thiourea 130 K

3 149 K

1 2

134 K 0.1

Cyclohexane 127 K

1 150 K .01 73

93

113

133

153

173

4

193

T (K)

6 8 103/T

10

Fig. 6.25. (a) The temperature dependence of the second moment S2 of the proton NMR absorption line in {3tu[C6H12]} (dots). The squares are for a sample containing 50% C6H12 and 50% C6D12. (Reproduced from Cle´ment, Mazieres, Gourdji and Guibe´, (1977).) (b) The temperature dependence of the relaxation time T1 for protons of the thiourea and cyclohexane molecules in {3tu[C6H12]}. The temperatures of the abrupt changes in T1 are indicated. (Reproduced from Cle´ment, Gourdji and Guibe´, 1975.)

Phase III

133K

! Phase II

148K

! Phase I

NMR studies provide additional information about the behaviour of the cyclohexane guests. 1H NMR line widths show a change at 130K for the thiourea protons and at 230–300K for the cyclohexane protons; although line widths are good indicators of the onset of molecular motions, experience suggests that they are not always sensitive to the occurrence of phase changes. The experimental value of the second moment for {3tu[C6H12]} at 77K is 3.9 G2 (Fig. 6.25(a)) whereas that calculated for a rigid lattice is 18.4 1 G2. Reorientation of C6H12 about its triad axis would give S2intra ¼ 3.6 G2, even if the triad axis were tilted by up to 30 to the tunnel axis. Thus the cyclohexane molecules are reorienting even at the lowest temperature reached in the NMR measurements. The relaxation times T1 (Fig. 6.25(b)) for the thiourea sublattice show abrupt changes at 130 and 168K, corresponding to peaks in the speciﬁc heat curves; the T1 changes in the cyclohexane sublattice at 127 (sharp) and around 149K also match features of the Cp–T curves. Thus the different physical techniques give compatible and complementary indications of changes in structure, although descriptions at the molecular level are still lacking. The further reductions in S2 above 133K and again above 150K are due to additional motions, which have been elucidated in a detailed study by deuterium NMR spectroscopy covering the temperature range 116–333K (Poupko, Furman, Mu¨ller and Luz, 1991); 2 H NMR curves for the lower temperature range are shown in Fig. 6.26. The 2H NMR spectrum at 127K shows a superposition of two equally intense, axially symmetric powder patterns, which are interpreted in terms of cyclohexane molecules

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242

Species B

Species C

141 K

213 K

135 K A+B

163 K C

133 K A+B

151 K B+C

131 K A+B

147 K B+C 145 K

127 K A 100

B+C 0

–100 50 Frequency (kHz)

0

–50

Fig. 6.26. 2H NMR spectra from 3tu[C6D12] samples at various temperatures, recorded by the quadrupole echo sequence method. The spectrum at 127K corresponds to Phase III, those between 131 and 151K are from Phase II, and those from 163 and 213K are from Phase I. The species A, B and C are identiﬁed in the text. (Reproduced from Poupko, Furman, Mu¨ller and Luz, 1991.)

rigidly ﬁxed with their triad axes along the tunnel axes but rapidly reorienting about these axes i.e. there is axial rotation of the cyclohexanes below the ﬁrst order phase transition. This motion leads to relaxation of the equatorial deuterons by a threefold jump process, while the axial deuterons do not change; this is referred to as Species A in Figs. 6.27 and 6.28. The parameters of the Arrhenius rate equation for a jump to one of the adjacent sites are A ¼ 1.83 1013 s1 and Ea ¼ 10.5 kJ/mol. Both the diffraction patterns and the 1H T1 relaxation time vs. T 1 curve show that there is a concomitant change in the thiourea matrix at the phase transition but the details have not been worked out. The motion of the cyclohexanes in the tunnels changes in the temperature region of stability of Phase II. From below the III ) II phase transition to immediately above it, only Species A is present, but its uniaxial reorientational motion is changed by gradual addition of a fast wobbling component in the biaxial potential of the channnel; this is Species B, which is the only species present at 143K. Above this temperature rapid chair–chair interconversion takes place (Species C) and this continues up to the highest temperature reached. The varying proportions of Species A, B and C are shown in Fig. 6.28. The order parameter can be calculated from the average quadrupolar splitting (Fig. 6.29). The NMR studies show that ordering of the cyclohexane molecules takes place on cooling over the range 300–220K, without appreciable crystallographic changes. The anomalous region in the speciﬁc heat starts at about 170K, where there is a change in T1 for the thiourea protons, but the nature of the corresponding physical change is not known. There is a crystallographic disorder ) order transition at 150K, due to changes in

DIRECTIONALLY BONDED HOSTS

243

1 0.9 Relative intensity

0.8 0.7

B A

C

0.6 0.5 0.4 0.3 0.2 0.1 0 125 130 135 140 145 150 155 160 T (K)

Fig. 6.27. Relative abundances of species A, B and C in phase II, as a function of temperature. The curves are guides to the eye. (Reproduced from Poupko, Furman, Mu¨ller and Luz, 1991.)

orientations or motions of the cyclohexane molecules. At about 130K there is a ﬁrst order crystallographic transformation, with appreciable changes in the details of the arrangement and librations of the thiourea molecules. The cyclohexane molecules continue to reorient down to at least 77K. The curve of heat capacity vs. T has been calculated (Cope, Gannon and Parsonage, 1972b) on the basis of an order , disorder model in which the cyclohexane molecules can occupy any of six positions, interacting both with the host framework and neighbouring guest molecules in the same and adjacent tunnels. The predicted curve was much broader than the experimental curve and peaked at a lower temperature. The disagreement is not surprising as this transition is one in which the principal changes are due to the thiourea framework. The behaviour of {3(urea)[trioxane]} on cooling (Cle´ment, Mazieres and Guibe´, 1972; Claude, Cle´ment and Dworkin, 1977) is similar, but not identical, to that of the isostructural {3(thiourea)[C6H12]} (Fig. 6.28). The speciﬁc heat curves show three apparently ﬁrst order peaks at 190, 203 and 244K, in good agreement with DTA and DSC studies. From the latter (Gelerinter, Luz, Poupko and Zimmerman, 1990) the following enthalpies and entropies of transition for {3(urea)[C3D6O3]} were obtained for the three transitions IV ! III (276 J/mol, 1.46 J/mol K), III ! II (276 J/mol, 1.39 J/mol K) and II ! I (1187 J/mol, 4.95 J/mol K). The 14N NQR spectrum has been measured over the temperature region 130 to 300K (Cle´ment, Mazieres and Guibe´, 1972) and shows only a smooth variation of frequency with T for two þ and one lines. It was suggested in explanation that the trioxane guest molecules are distributed over sites of 3 and 32 symmetry in different parts of the crystal and this subjects otherwise equivalent nitrogen atoms to different electric ﬁeld gradients. This behaviour of the NQR spectrum is quite different from the results of the analogous measurements for the isostructural {3(thiourea)[C6H12]} complex (Fig. 6.23(a)) where only one þ line was found for the rhombohedral structure, which then split further on cooling through both second order and ﬁrst order transitions. The NMR line width of the

T UN N E L I N C L US I O N C O M P L E XE S

244

140 120

A

(kHz)

100

Phase III

Phase II

Phase I

80 60 B

40

C

20 0 90

110

130 150 T (K)

170

190

Fig. 6.28. A plot of the average quadrupole splitting < Q> ¼ < Qax>, (left hand ordinate) of the axial deuterons of C6D12 in the various solid phases of 3tu[C6D12]. The value of < Q> at 333K is 11 kHz. The order parameter of the molecular C3 axis can be calculated from the relation S ¼ < Q>/(125 kHz). The asymmetry parameters for the spectra in the various phases are III ¼ 0; II ¼ 0.17–0.25; I ¼ 0. (Adapted from Poupko, Furman, Mu¨ller and Luz, 1991.)

800 2785

CP(J/mol K)

700 600 500

IV

III

II

I

400 300 200 160

180

200 220 T (K)

240

260

Fig. 6.29. Cp vs. T for {3(urea)[C3H6O3]}. The experimental points lie on smooth curves in the rest of the 0–300K range. The lines are guides to the eye. (Adapted from Claude, Cle´ment and Dworkin, 1977.)

trioxane protons shows changes at 120, 190 and 240K, the latter two changes corresponding to the ﬁrst order transitions at 189 and 243K. However, the speciﬁc heat curve does not show anomalously high values in the region about 120K. The diffraction patterns were reported to show a rhombohedral ) monoclinic transformation at 244K but no changes at 201 and 189K. However, there is a further change at (unspeciﬁed) lower temperatures in which a contracts, b expands and c remains unchanged (cf. Fig. 6.23). There are thus four phases in {3(urea)[C3H6O3]}, and much is now known about the behaviour of the guest molecules as a result of 2H NMR studies on {3(urea)[C3D6O3]} and

DIRECTIONALLY BONDED HOSTS

245

{3(deutero-urea)[C3H6O3]} (Gelerinter, Luz, Poupko and Zimmerman, 1990). We start with phase IV, where the spectra show that, below 130K, the trioxane molecules are essentially static on the NMR time scale. As the temperature increases towards the IV ) III transition, the trioxane molecules start reorienting by a three-site jump mechanism for which the Arrhenius parameters for one-directional jumps are Ea ¼ 20.1 kJ/mol and A ¼ 1.1 1013 s 1; fast wobbling of the trioxanes about their C3 axes sets in above 170K Although there are distinct changes in NMR line shape going through the IV ) III transition, the line shape remains the same in phases III and II, indicating similar behaviour of the trioxane molecules. Actually two inequivalent species, A and B, of trioxane were found, with a relative abundance of about 2 : 1, A being ordered more or less as in phase IV while B is much less ordered (can these be the trioxane guest molecules distributed over sites of 3 and 32 symmetry?). In phase I the trioxane molecule is similar to species B referred to above; fast ring inversion sets in on further heating, with kinetic parameters similar to those found for trioxane in liquid-crystalline and solution environments, while in crystalline neat trioxane there is no ring inversion below the melting point (338K). 6.2.1.14 The orthorhombic Type 4 urea tunnel inclusion complexes The complexes with 1,4-dichlorobutane, 1,5-dichloropentane and 1,6-dichlorohexane are Type 4, with orthorhombic symmetry and space group Pbcn (Otto, 1972). The ideal unit cell dimensions for {3(urea)[1,4-dichlorobutane]} calculated from the dimensions of the hexagonal urea tunnel are as follows, with measured values in square brackets: p ˚ , b ¼ 3 4.75 ¼ 14.25 [14.15] A ˚ , c ¼ 11.00 [10.96] A ˚. a ¼ 3 4.75 ¼ 8.23 [8.34] A There are additional weak reﬂections in the 1,4-dichlorobutane diffraction patterns which indicate an ordering of the guest molecules but this was not explored in detail. The crystals with 1,6-dibromohexane as guest are monoclinic with a slightly distorted variant of the Type 4 structure. The complex {3(thiourea)[ 0.5(2,6-diethylnaphthalene]} crystallizes in a monoclinic ˚ , ¼ 92.14(2) , Z ¼ 4, space unit cell with a ¼ 14.643(3), b ¼ 9.282(2), c ¼ 12.571(3) A group P21/a (Shindo, Shindo, Ohnuma and Kabuto, 1993). Professor J. S. Rutherford (Bulawayo) has suggested that this is a distorted variant of the Type 4 structure. 2,6Diethylnaphthalene is important as a feedstock of speciality high-performance polymers such as poly(ethylene 2,6-naphthalenedicarboxylate). The isomers of diethylnaphthalene have similar physical properties and so are difﬁcult to separate by distillation or crystallization but the 2,6-isomer selectively forms a thiourea complex – hence the interest in the structure. A noncentrosymmetric variant of this structure type is taken up by {3(thiourea) ˚ , Z ¼ 4, [(4-1,3-cyclohexadiene)Fe(CO)3]} (a ¼ 12.562(1), b ¼ 16.128(1), c ¼ 9.536(1) A space group Pna21) (Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989; GARTOI10) (Fig. 6.30). This complex has a second harmonic generation (SHG) efﬁciency of about 40% of that of urea. 6.2.1.15 The hypothetical Type 5 orthorhombic tunnel inclusion complexes No example of this type has yet been encountered; it would be expected to have space group Pbca (Fig. 6.31).

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246

1/4

R

L a down b

R

L R

c

L

Fig. 6.30. Projection of {3(thiourea)[(4-1,3-cyclohexadiene)Fe(CO)3]} structure down [100]. The symmetry elements of space group Pna21 are shown. The handedness of the thiourea spirals is marked by L and R. (Adapted from Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989.)

1/4

R

L L

R

L

R

L

R

R

L R

1/4

L 1/4

1/4

Fig. 6.31. Hypothetical Type 5 tunnel inclusion complex, space group Pbca. The handedness of the spirals is marked by L and R. The cell dimensions predicted for a urea complex are: p ˚ , b ¼ 3 4.75 ¼ 14.25 A ˚ , c ¼ 11.00 A ˚ . (Reproduced from Otto, 1972.) a ¼ 2 3 4.75 ¼ 16.46 A

DIRECTIONALLY BONDED HOSTS

247

6.2.1.16

The crystal structure of selenourea and its relation to the structures of the tunnel inclusion complexes There is no relation between the crystal structures of tetragonal urea and orthorhombic thiourea, on the one hand, and those of their hexagonal or rhombohedral inclusion complexes on the other. Not so for selenourea which crystallizes in the trigonal system ˚ (both at 173K), space group P31 (or P32), Z ¼ 27). The (a ¼ 15.201(5), c ¼ 12.950(5) A crystal structure (Rutherford and Calvo, 1969; SEUREA) shows that there are nine selenourea spirals in the unit cell. If we consider, for the moment, only the spirals at the corners of the hexagons in Fig. 6.3, then the structure is of Type 1 (or 2, depending on absolute conﬁguration of the crystal studied). However, there are also spirals (of the same handedness as those at the corners of the hexagons), which are located on crystallographic threefold screw axes along the central axes of the hexagons. The two sets of spirals are essentially structurally equivalent although this is not required by the symmetry of the space group. Thus selenourea could be described as a self-inclusion complex. The two interlocking, but nonbonded, sets of spirals constitute a one-dimensional analog of the nonbonded but interlocking three-dimensional networks found in the quinol clathrates. 6.2.1.17 Thermodynamics of the formation of the tunnel inclusion complexes This subject, much studied soon after the discovery of these complexes (Schlenk, 1949; Redlich, Gable, Dunlop and Millar, 1950; Redlich, Gable, Beason and Millar, 1950; Zimmerscheid, Dinerstein, Weitkamp and Marschner, 1950), has attracted only little recent attention (Parsonage and Staveley, 1984). As Schlenk (1949) noted, an inclusion complex is, from a thermodynamic point of view, a true chemical compound (‘‘so wie etwa die Substanz CuSO45H2O’’) and not an absorbate. Put differently, this means that these complexes form separate phases in the binary host–guest phase diagram with crystal structure different from those of host and guest, and are not solid solutions of the guest in the neat crystals of the host. We consider the thermodynamics of the following reaction, which has, for convenience, been written in terms of urea (c ¼ crystal) although it is easily generalized to other types of inclusion complex. UreaðcÞ þ x(Guest (liq)) ) Inclusion complex(c)

ð6:1Þ

Although most of the published results are expressed in terms of one mole of guest, it is often convenient to use one mole of host as reference, especially when it is necessary to emphasize the crystallographic similarity of the complexes. A number of methods have been used to measure the various thermodynamic quantities; vapor pressure (p) of guest in equilibrium with the complex has been measured by a dew point method and compared with that of the pure guest (p0), both over a range of temperatures. Then DHf, the enthalpy of formation of the inclusion complex, is obtained from the van’t Hoff equation, d(ln K)/ d(1/T) ¼ DHf/R, where K ¼ p/p0; we use the approximation that DHf is independent of temperature. Values of K can also be obtained from measurements on the solution equilibrium urea(solid or solution) þ guest(solution) , inclusion complex

ð6:2Þ

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248

where an aqueous or non-aqueous solvent can be used. Values of log K for urea complexes of n-alkanes and for the thiourea complexes of cyclohexane and CCl4, are plotted against 1000/T in Fig. 6.32. We limit our discussion to these complexes, but measurements for many other types of guest have been reported (see Fetterly (1964) for summary). Values of DHf can also be obtained by direct calorimetry, a method used by Schlenk (1949) and Zimmerschied et al. (1950). Values of DSf can be obtained by combining DGf (¼RT ln K) and DHf values, and also (sometimes, when there are not too many intervening phase transitions) from measurements of the speciﬁc heats of complex and components. Using the values from Fig. 6.32 at 1000/T ¼ 3.36 (i.e. T ¼ 298K), we ﬁnd that DGf (kJ per mol guest, 298K) ¼ 10.46 1.66n, where n is the number of carbons in the n-alkane; thus, in agreement with experiment, only complexes with n-heptane and above will be stable. We summarize DHf and DSf values from various sources in Table 6.6. The DTA measurements were carried out at temperatures of 50–120 C; nevertheless, from the semiquantitative (numerical) agreement of his DHdec values with DHf values from calorimetry and vapour pressures at lower temperatures, McAdie (1962) concluded that the complexes decomposed to tetragonal urea and liquid guest on heating. The formation of the inclusion complexes from ureaþliquid guest (equation 6.1 above) is an exothermic process and the complexes are enthalpy stabilized at 298K. If we consider the hexadecane complex, then we can estimate its enthalpy of formation from crystalline hexadecane by adding the enthalpy of fusion of hexadecane (DHfus ¼ 47.3 kJ/mol; m.pt. ¼ 291K); the enthalpy of formation of the complex is 44.4 kJ/mol guest, and the complex is still enthalpy stabilized. The entropies of formation of the complexes (from liquid guests) are all negative, and this implies, in a rough way, that the parafﬁns are more

3

log K (formation)

2.5

C(16)

2 C(10)

1.5

C(9)

C(12)

1 0.5

C(8)R

TU C(7)

0 –0.5 2.8

2.9

3

3.1

3.2 3.3 1000 /T

C(8)S

3.4

3.5

3.6

3.7

Fig. 6.32. Log K versus 103/T for formation of urea and thiourea complexes (equation 6.1); the equilibrium constants were obtained from vapor pressure measurements. The urea complexes are all of n-parafﬁns, denoted as Cn etc; C8(S) values are from Schlenk (1949) and all the other values from Redlich, Gable, Dunlop and Millar (1950) including C8(R). The thiourea complexes (TU) are of CCl4 (to the right) and cyclohexane (to the left) (Redlich, Gable, Beason and Millar, 1950), the experimental points lying along the same line. The temperature range is from 273 to 353K.

DIRECTIONALLY BONDED HOSTS

249

Table 6.6. Values of Hf and Sf from various sources for {urea[n-paraffin]} inclusion complexes, and two thiourea complexes. The preferred values for Hf are averages of ‘‘vapour pressure’’ and ‘‘calorimetry’’ values, and for Sf ‘‘specific heat’’ values, taken from Pemberton and Parsonage (1966), who estimate their error to be 4 J/mol K. The ‘‘vapour pressure’’ values, which seem to be systematically high, are bracketed in the Table Guest

Host/ Guest Ratio

C7H16 C8H18 C9H20 C10H22 C11H24 C12H26 C15H32 C16H34 tu–CCl4 tu-cyclohexane

6.1 6.73 7.4 8.1 10.0 9.3 11.75 12.0 3.0 3.0

Hf (kJ/mol)

Vapour pressure

Calorimetry

25.4 44.0 49.4 52.7

31.8

Sf (J/mol K)

DTA (Mc-Adie, 1962)

41.4 61.1

67.4 87.9 13.7 10.7

56.1 95.4

95.8

Hf/ mole guest

Hf/ mole host

Vapour pressure/ mole guest

28.2 44.0 49.4 52.7 61.1 67.4

4.55 6.53 6.67 6.51 6.11 7.25

(90.1) (138) (151) (158)

91.7 13.7 10.7

7.64 4.57 3.56

(200) (234*) (244) (40.6) (30.5)

Speciﬁc heats/ mole guest

148 151 185 207

Sf / mole host

(14.8) (20.5) (20.4) 18.3 16.2 15.7 17.3 (13.5) (10.2)

* interpolated value.

ordered in the tunnels than in the pure liquids. Referring again to the hexadecane complex, we obtain the entropy of formation of the complex from crystalline hexadecane (ignoring the effects of small differences in temperature) by adding the entropy of fusion of hexadecane, which is 159 J/mol K, giving a value of 48 J/mol (guest) K. This implies that hexadecane is more ordered in the tunnels of the complex than in its neat crystals, which seems surprising. The two thiourea complexes included here are both enthalpy stabilized, but to a lesser degree than the urea complexes; however, the differences are not that striking when considered on a ‘moles host’ rather than on a ‘moles guest’ basis. The formation of an inclusion complex, at a particular temperature and pressure, from its components can be envisaged to take place through the following steps (the calculation is formulated for a composition {Host[x(Guest)]}, and thus the thermodynamic parameters of the inclusion complex are given as J/mol host (or J/K mol host): (1)

The crystalline host is converted from its stable (neat compound) structure to the empty matrix (this implies that the complex is a different phase from the neat host and that formation of a primary solid solution is not considered here) Stable hostðcÞ ) Empty matrix(c) DXtrans ¼ Xmatrix Xstable , where X is free energy, enthalpy or entropy. This process is endothermic.

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(2)

The guest is converted from its stable structure to the vapour phase DXvap

Guest (liq or cryst) ) Guest(vapor) or DXsubl , according as guest is liquid or crystalline:

This process is endothermic. (3)

The vapour of the guest enters the empty matrix to form the inclusion complex Empty matrix(c) þ x[Guest(vapor)] ) Inclusion complex(c) DXincl ðDXdec ¼ DXincl for the inverse process of decomposition): This process is exothermic, unless the complex is entropy-stabilized.

The overall process for formation of the crystalline inclusion complex is Stable host(c) þ x[Guest (liq or cryst)] ) Inclusion complex(c) DXform ¼ DXtrans þ x½DXvap ðor DXsubl Þ þ DX incl : This conceptualization is quite general and has been applied to a number of inclusion complexes, as will be noted at appropriate points. Of the quantities on the right hand side of the equation, DXincl and DXtrans are not known. Now, following Schlenk (1949), we show how DHincl and DHtrans can be estimated for urea inclusion complexes formed from tetragonal urea and liquid n-parafﬁn guests. This is ˚ ) be the length of urea tunnel most easily formulated in terms of moles of guest. Let lP(A ˚ between interacting with the included guest, and Qincl be the enthalpy of interaction per A ˚ ) be the corresponding overall length of urea tunnel tunnel and guest. Let (lPþ2.4) (A ˚ between parafﬁn chains, taken lengthwise) (i.e. there is a noninteracting distance of 2.4 A and Qtrans be the enthalpy of transformation from tetragonal to (hypothetical) hexagonal ˚ . Then urea per A DHf (per mole of guest) ¼ ðlP Qincl Þ þ ððlP þ 2:4Þ Qtrans Þ þ DHvap : ˚ , and DHvap can be obtained from standard tables; Qtrans and For n-octane, lP ¼ 10.4 A DHvap are endothermic, and DHf (values from Table 6.6) and Qincl exothermic. Similar equations were set up for n-heptane, n-decane and n-hexadecane; values of Qtrans ˚ ) and Qincl (¼14.4 kJ/A ˚ ) were obtained by linear regression. As one mole(¼5.45 kJ/A ˚ , DHtrans ¼ 10.2 kJ/mol urea; DHincl depends cule of urea occupies a tunnel length of 1.87 A on the nature of the guest but the interaction enthalpy per CH2 group of gaseous guest is 19 kJ/mol. These values are somewhat different from those given by Schlenk (DHtrans ¼ 3.7 kJ/mol urea, DHincl 15 kJ/mol per CH2 group) because of different DHf and DHvap values used in the two calculations. These DHtrans values are considerably larger than those for, say, - and -quinol (see Section 7.3.1). The p–T and T–composition projections of the phase diagram of urea–n-heptane calculated (Farina, Di Silvestro and Colombo, 1986) from Schlenk’s vapour pressure measurements are shown in Fig. 6.32. These diagrams will be discussed later together with those of perhydrotriphenylene inclusion complexes.

DIRECTIONALLY BONDED HOSTS 160

150

251

LH + LU

140

p (heptane) mm

120

t °C

Liquid

100

100

LH + U

Existence region of inclusion complex

80 60

50

40

Solid LH + C

20 0 0

10

20

30

40

t (°C)

50

0 H

0.5 mol fraction urea

C+U 1.0 U

Fig. 6.33. Urea–n-heptane phase diagrams; left, p–T projection and right, T–X projection. LH is liquid heptane (f.pt. –91 C; b.pt. 98 C). Note that n-heptane and urea are not miscible in the liquid phase. (Adapted from Farina, Di Silvestro and Colombo, 1986.)

6.2.2 The Bishop–Dance Hosts – exo-2,exo-6-dihydroxy2,6-dimethylbicyclo[3.3.1]nonane and analogs 6.2.2.1

Introduction

In 1979 Bishop and Dance reported that 2,6-dimethylbicyclo[3.3.1]nonane-exo-2,exo-6diol (6.1; we use the same numbering of hosts as used by Bishop et al. in their series of papers, but with the preﬁx 6 indicating our chapter number, details being given in the next section) formed a series of trigonal tunnel inclusion complexes with a chiral helical tubuland structure. Since then much effort has been invested in generalizing the chemical basis of this discovery and it has been found that ten related molecules form similar crystal structures, some of which are inclusion complexes, and some not. The general composition of the group of tunnel inclusion complexes is {3(host)[(guest)x]} (x 1) (Bishop, Dance, Hawkins and Lipari, 1984; Bishop, Dance, Hawkins and Scudder, 1987; Bishop and Dance, 1988, 1991). Two of the hosts (6.2 and 6.4) also form a different series of racemic tetragonal ellipsoidal clathrate complexes, the general composition being {4(host)[guest]}. Usually a particular guest forms only one of these structural types, but there are examples (1,2-dichlorobenzene, CHCl3, C6H5Br) where both types (trigonal and tetragonal) have been obtained, the type depending on crystallization conditions. For these examples, there are (at least) two complexes, of 4 : 1 and 3 : 1 compositions, in the 6.2 (or 6.4)–guest phase diagram. Thus two of the Bishop–Dance hosts, and in potential others, form two distinct structural families of inclusion complexes, and we shall treat each of these families separately. We shall refer to the overall group of hosts as Bishop–Dance hosts. A particularly comprehensive account has been given by Bishop (1996). 6.2.2.2

The helical tubuland structures

The molecules 6.1–6.6 (Fig. 6.34) form a group of related hosts, all of which crystallize in closely similar structures, and some of which form tunnel inclusion complexes. Two

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252

C4 O

C3 C2

C5

C6 C1

C7 O

C8

O C3

C3 O O C3*

C3* O

Type A

Type B

Fig. 6.34. The Bishop–Dance hosts – a perspective view of 6.1 down its twofold axis is shown in the top part of the ﬁgure. In the lower part schematic views (also from above the central methylene group) are given of Type A (6.1, 6.3, 6.5, 6.6) and Type B (6.2, 6.4) molecules; some hydrogens have been removed for clarity. The Type A hosts have C3–C3* not bridged in 6.1, and bridged by –CH2–CH2– (ethano) in 6.3 and by –CH2–CH2–CH2– (propano) in 6.5. In 6.6 there is no bridging between C3–C3* but the central –CH2– (methano) is replaced by –CH2–CH2– (ethano). A diagram of 6.7 is given later and other representations of some of the molecules are shown in Fig. 6.40. The Type B hosts have C3–C3* bridged by –CH2–CH2– in 6.2 and by –CH2–CH2–CH2– in 6.4.

strategies were employed in the attempt to develop a family of chemically related hosts. The ﬁrst was to replace the methyls in 6.1 by hydrogens or ethyls (Bishop, Choudhury and Dance, 1982); these compounds were found not to form inclusion complexes. The second strategy was to connect between C3 and C7 (C3*) by ethano and propano bridges, as shown in the formulae (Fig. 6.34); it was found that there was retention of stereochemistry at C2 and C6 in 6.3 and 6.5 and inversion in 6.2 and 6.4 (numbering as in 6.1). From a chemical point of view hosts 6.1, 6.3, 6.5 and 6.6 form one group (called Type A) and 6.2 and 6.4 another (called Type B). Remarkably, all six compounds gave isostructural chiral trigonal crystals (i.e. spontaneous resolution had taken place on crystallization) based on the formation of tight spirals of hydroxyl . . . hydroxyl hydrogen bonds. These were called helical tubulands and, as noted earlier (Section 6.1), we have appropriated this useful name for application to analogous structures with a wider variety of hosts. However, many chemically-related compounds crystallize in quite different arrangements (e.g. layer structures; Hawkins, Scudder, Craig, Rae, Raof, Bishop and Dance, 1990) and some progress has been made towards understanding the factors involved in the formation, or

DIRECTIONALLY BONDED HOSTS

253

not, of helical tubuland inclusion complexes (Dance, Bishop and Scudder, 1986; Bishop, Craig, Dance, Kim, Mallick, Pich and Scudder, 1993; Bishop, Craig, Dance, Scudder and Ung, 1993). We have alluded to the overall problem in the Introduction to Part III, and avoided discussing the speciﬁc problem concerning urea adducts (see Section 6.1.2.10). The essential features required for a molecule to form helical tubuland structures of the P3121 type have been summarized as follows (Bishop, Dance, Hawkins and Scudder, 1987; Bishop, Craig, Dance, Scudder, Marchand and Wang, 1993), to which we have added two extra requirements (#5 and #6): 1. The diol molecules must have two fold symmetry, as shown in Fig. 6.34; this symmetry can be exact or obtained by averaging of equivalent conformations. 2. Some variability is permitted in the alicyclic bridging skeletons, which are also required to have some ﬂexibility. 3. Substituent groups around the periphery appear to be deleterious. 4. The tertiary alcohol groups must have a methyl substituent, which seems to have the correct properties to support the tunnel wall structure. ˚ and the O–C . . . 5. The intramolecular O . . . O distance must be approximately 5.7 A C–O torsion angle must be 75 for Type A molecules or 95 for Type B structures (see Table 6.7). 6.7, 6.8 and 6.9 do not meet these requirements and we make some comments about this later. 6. In order that Type A and B hosts can form the same structure types, they must have the same disposition of hydroxyls and methyls. This happens when a Type A molecule is viewed down the two fold axis through the central methylene group from above, or up from below (as shown in the equivalent views of ball and stick models in Fig. 6.35). TYPE A

TYPE B

6.1

6.2

6.3

6.4

Fig. 6.35. Ball-and stick models of some examples of Type A and B molecules viewed down their two fold axes. The molecules have been oriented so that the hydroxyl and methyl groups are similarly disposed in both types of molecule. This requires that the alicyclic skeletons be differently disposed in the two types, as explained in the text. Some hydrogens have been omitted for clarity. The oxygens are lightly shaded and the carbons dark shaded. The H–O–C–CH3 torsion angles are in the range 51–67 .

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254

Table 6.7. Nomenclature of the Bishop-Dance hosts, and some geometrical features Number

Chemical composition

Type A host molecules 6.1 C11H20O2

6.3

C13H22O2

6.5

C14H24O2

6.6

C12H22O2

6.7

C13H18O2

6.8

C14H20O2

6.9

C14H20O2

6.10

C12H20O2S

Type B host molecules 6.2 C13H22O2

6.4

Neat 6.2 in SODVUC

C14H24O2

Systematic name

˚ d(O . . . .O 0 ) A

2,6-dimethylbicyclo [3.3.1]nonane-exo-2, exo-6-diol 2,7-dimethyltricyclo [4.3.1.13,8]-undecane-anti-, 2,anti-7-diol 2,8-dimethyltricyclo [5.3.1.13,9]-dodecane-anti-2, anti-8-diol 2,6-dimethylbicyclo [3.3.1]decane-exo-2, exo-6-diol 4,7-dimethylpentacyclo [6.3.0.02,6.03,10.05,9] undecane-anti-4,anti-7-diol 4,7-dimethylpentacyclo[6.4.0.02,6.03,10.05,9] dodecane-anti-4,anti-7-diol 4,7,11-trimethylpentacyclo [6.3.0.02,6.03,10.05,9] undecane-anti-4,anti-7-diol 2,7-dimethyl-9-thiatricyclo[4.3.1.13,8]-undecane-anti-, 2,anti-7-diol

5.59

73.4

5.53

79.2

5.51

71.3

5.98

163.6

6.01

174.1

5.98

163.6

5.43

88.3

5.55

94.3

5.68

97.4

5.38 5.29 5.36

81.7 84.5 90.1

2,7-dimethyltricyclo [4.3.1.13,8]-undec-ane-syn-2, syn-7-diol 2,8-dimethyltricyclo [5.3.1.13,9]-dodecane-syn-2, syn-8-diol

(O–C . . . .C 0 O 0 ) (deg.)

The descriptions syn and anti refer to the OH functions relative to the larger of the bridges across the molecular twofold axis.

Crystal data for the trigonal tunnel inclusion complexes of the Type A hosts 6.1 and 6.7, and of neat 6.3 and 6.5 are given in Table 6.8, and also of the trigonal tunnel inclusion complexes of the Type B hosts 6.2 and 6.4. The hosts 6.1 and 6.7 form isostructural crystalline tunnel inclusion complexes while the crystals of 6.3 and 6.5 (which belong to the same isostructural family) do not contain guest molecules; the hosts 6.2 and 6.4 form a second, closely related, isostructural group of complexes. The a axes of crystals of the

DIRECTIONALLY BONDED HOSTS

255

˚ and those of Type B hosts in the range Type A hosts lie in the range 11.9–12.5 A ˚ 13.2–13.8 A. The cell dimensions are unusual for the constancy of c (but with some exceptions) and the variation of a with the nature of both hosts and guests; similar behavior is found with some cyclophosphazene tunnel inclusion complexes (see Section 6.3.2). 6.1 has been shown to form isostructural inclusion complexes of formula {3(6.1)[(guest)x]} (0.75 x 1.2) with iodineþethanol* (x ¼ 0.5), acetonitrile*, 1,2dimethoxyethane*, 1,2-dichloroethane*, ethyl acetate*, chloroacetic acid*, propanoic acid*, trichloroethene, thiophene*, chlorobenzene*, toluene*, dioxane*, acetic acid, formamide, N-methylformamide, ethylbenzene, p-xylene, m-xylene, cyclohexene, diethylamine, mesityl oxide, acetoneþwater, dimethyl sulphoxide, bromobenzene, m-dichlorobenzene, 1,3-dibromopropane, chloroform, ethyl 2-bromopropanoate and 2,5dibromothiophene (Ung, Gizachew, Bishop, Scudder, Dance and Craig, 1995). Complexes of 6.1 with o-dichlorobenzene, o-xylene, cyclohexanone and trans-1,2-dibromocyclohexane were not obtained. Results of extended X-ray reﬁnements which take the contributions of the (asterisked) guest molecules into account were given in Ung, Gizachew et al., 1995. 6.2 has been reported (Ung, Bishop, Craig, Dance and Scudder, 1992a) to form trigonal inclusion complexes with the following guests – ethyl acetate, CCl4, CBr4, 1,1,1trichloroethane, 1,2-dibromoethane, 1,3-dibromopropane, 1,4-dibromo-butane, o-xylene, m-xylene, p-xylene, o-dichlorobenzene, m-dichlorobenzene, ethylbenzene, n-butylbenzene, chlorocyclohexane, 1,2-dibromocyclohexane, diethyl ether, di-n-butyl ether, 1,2-dimethoxyethane, n-hexane. We have arranged the crystal data of Table 6.8 by host and then in order of ascending cell volume, which also provides a natural division between the Type A and B hosts; it is remarkable that the same overall structure type is retained over a (unit cell) volume range ˚ 3. How should these crystals be classiﬁed in terms of host-guest phase from 880 to 1151 A diagrams? In the Type A group, neat 6.1 (recrystallized from the non-complex forming solvent mesitylene) is reported (Ung, Gizachew et al., 1995) to have the same crystal structure as the trigonal inclusion complexes with various guests; thus the inclusion complexes of 6.1 are primary solid solutions of guest in host and so differ from most other tunnel inclusion complexes such as those of urea and thiourea (see Section 6.2.1.15). The question is not relevant for 6.3, 6.5, 6.8 and 6.9 (all Type A) as their tunnels are too small for them to form inclusion complexes (Fig. 6.39) (Hawkins, Bishop, Craig, Dance, Rae and Scudder, 1993). Crystal data do not appear to have been reported for neat 6.6 and 6.7. The behaviour of 6.2 as host is particularly interesting. Neat 6.2 has a hydrogen-bonded layer structure with three independent diol molecules in the asymmetric unit ˚ , ¼ 109.42(1) , Z ¼ 12, space group P21/c; (a ¼ 7.398(2), b ¼ 25.166(3), c ¼ 20.076(4) A Ung, Bishop, Craig, Dance and Scudder, 1991; SODVUC); some geometrical features (Table 6.7) differ for 6.2 molecules in the neat crystals and in the complexes. Although the guest molecules in the trigonal tunnel complexes are generally highly disordered at room temperature, those of 6.2 with Br(CH2)3Br, CCl4 and o-xylene are well ordered (Ung, Bishop, Craig, Dance and Scudder, 1992a). 6.2 shows a further complication – recrystallized from benzene it gives tetragonal crystals of composition {4(C13H22O2)[C6H6]}, which have a clathrate structure; o-dichlorobenzene gives trigonal (host:guest ratio 3 : x where x 1) or tetragonal (host : guest ratio 4 : x where x 1) crystals, depending on crystallization conditions. Thus the 6.2–o-dichlorobenzene phase diagram includes the neat 6.2 crystals and the trigonal and tetragonal inclusion complexes, all three as separate

256

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Table 6.8. Crystal data (294K) for some isostructural neat crystals and/or inclusion complexes of 6.1–6.7. The space group is P3121 (no. 152, or enantiomorph P3221, no. 154) except for neat 6.3, for which it has not been finally established. There are three host molecules in the unit cell, which have symmetry C2–2 in the crystals, and are located at Wyckoff positions x, 0, 1/3 etc. Additional crystal data for 6.1 with acetonitrile, chloroacetic acid, propanoic acid, trichloroethene, chlorobenzene, toluene and dioxane are given by Ung, Gizachew et al., (1995) Formula Type A host molecule {3(6.1)[(C4H10O2)0.75]} 1,2-dimethoxyethane {3(6.1)[(I2.–C2H5OH)0.5]} {3(6.1)[(ClCH2.–CH2Cl)0.75]} {3(6.1)[C4H8O2]} ethyl acetate {3(6.1)[C4H4S]} thiophene Neat 6.3 Neat 6.5 (Note 1) {3(6.6)[(CHCl3)1.5]} chloroform {3(6.7)[(C3D6O)1.2]} deutero-acetone Neat 6.8 Neat 6.9 Type B host molecule {3(6.2)[C4H8O2]} ethyl acetate {3(6.2)[Br(CH2)3Br]} {3(6.2)[(CCl4)1.2]} {3(6.2)[C6H4Cl2]} o-dichlorobenzene {3(6.2)[(C8H10)1.2]} o-xylene {3(6.4)[(C30H50)0.23) squalene {3(6.4)[C6H6]} benzene {3(6.4)[(ferrocene)0.75]}

Refcode / reference

˚) a(A

˚) c(A

˚ 3) V(A

KUBYUB; UBC92b

12.0416(3)

7.0110(2)

880.39(4)

KUBZEM; UBC92b ZACSEY; UGB95 EXHNEA20; UGB95 KUBZAI10; UCB95 FALRIT; DBH86 PICHAK; HBC93 BCD93

12.068(2) 12.075(1) 12.165(1) 12.4083(5) 11.906(1) 12.3430(4) 13.383(1)

6.984(3) 6.987(1) 7.001(1) 6.9702(4) 6.990(1) 6.8288(3) 7.026(1)

880.8(4) 882 897.3(2) 929.39(4) 858.1(1) 900.99(4) 1089.8(1)

WALDOC; BCD93

12.4957(6)

7.3076(3)

988.1(1)

POHYEQ; ABC97 ZEHFIB; BCS95

12.329(1) 12.609(2)

7.508(1) 7.209(2)

988.4(1) 992.6(3)

BUXRER10; DBH86 PAPSOO; UBC92a PAPSII; UBC92a VUSYIR; UBC93

13.192 13.206(2) 13.2812(2) 13.3717(6)

6.914 6.915(2) 6.904(1) 6.9045(4)

1042.0 1044.4 1054.6 1069.14

PAPSUU; UBC92a PIKJEY; UBCDRS93 FALROZ; DBH86 PIKJAU; UBCDRS93

13.380(2) 13.677(1) 13.740 13.7480(6)

6.905(1) 7.0533(9) 7.030 7.0312(5)

1070.5 1142.6 1149.5 1150.9

Notes: ˚ , ¼ 92.13 , (1) 6.5 has a stereoisomer (syn-2,anti-8) SEWYEY with a ¼ 12.473, b ¼ 13.056, c ¼ 15.449 A P21/c, Z ¼ 8. References: ABC97 – Ahn, Bishop, Craig, Downing and Scudder, 1997; BCD93 – Bishop, Craig, Dance, Scudder, Marchand and Wang, 1993; BCS95 – Bishop, Craig, Scudder, Marchand and Liu, 1995; BDH86 – Bishop, Dance and Hawkins, 1983; DBC92b – Ung, Bishop, Craig, Dance and Scudder, 1992b; DBH86 – Dance, Bishop, Hawkins, Lipari, Scudder and Craig, 1986; HBC93 – Hawkins, Bishop, Craig, Dance, Rae and Scudder, 1993; UBC92a – Ung, Bishop, Craig, Dance and Scudder, 1992a; UBC93b – Ung, Bishop, Craig, Dance and Scudder, 1993b; UBCDRS93 – Ung, Bishop, Craig, Dance, Rae and Scudder, 1993.

phases (cf. Ung, Gizachew et al., 1995). This is discussed below (Section 6.2.2.3). The well-resolved powder patterns (Fig. 6.36) show that it will be possible to study changes occurring on heating/cooling of the separate phases, including phase changes and chemical transformation.

DIRECTIONALLY BONDED HOSTS

257

tetragonal clathrate inclusion complex

trigonal tunnel inclusion complex

0

10

20 degrees 2

30

40

Fig. 6.36. Powder diffraction patterns (Cu K radiation) of the trigonal and tetragonal complexes of 6.2 with o-dichlorobenzene. (Adapted from Ung, Bishop, Craig, Dance and Scudder, (1993b).)

Single crystals of neat 6.4 have not yet been obtained but powder X-ray diffraction and IR spectroscopy indicate that its structure differs from those of the trigonal inclusion complexes; trigonal and neat crystals are thus separate phases. No information is available about the reported tetragonal clathrates. The relationships between the structures with 6.1–6.4 as hosts have been discussed in considerable depth (Bishop and Dance, 1988; Dance, Bishop and Scudder, 1986). 6.1 is ‘‘a potent host molecule. Helical tubulates are formed with a wide variety of small guests including alkenes, aromatic hydrocarbons, haloaromatics, ketones, ethers, esters, sulﬁdes, amines and nitriles’’ (Ung, Bishop, Craig, Dance and Scudder, 1992b); the other diols show similar behaviour and it is clear that spatial rather than chemical properties of the guests are dominant. We shall describe the structure of 6.2 as representative and only brieﬂy consider the other structures. The projection down [001] is shown in Fig. 6.37. The wall of a particular tunnel is made up of three host molecules in one orientation (>CH2 pointing inwards) and three in the opposite orientation (–CH2–CH2– pointing inwards); adjacent tunnels have converse arrangements. Parenthetically, it is this ordered combination of opposite orientations, together with the small range of intramolecular d(O . . . O) distances, that allows hosts of both types to form such similar arrangements in the solid state. The diol molecules are hydrogen bonded together along spirals in which each diol functions, within the spiral, as a double hydrogen bond donor or as a double hydrogen bond acceptor in alternating sequence. Part of a spiral is shown schematically as a linear diagram (the ring system of 6.2 is shown as a heavy line):

donor ....HOC(2)

acceptor donor acceptor C(6)OH....OC CO....HOC COH....OC CO.... H

H

H

H

258

T UN N E L I N C L US I O N C O M P L E XE S

Fig. 6.37. Projection of the trigonal complex of 6.2 with o-dichlorobenzene viewed down a threefold screw axis axis. For clarity, only hydroxyl hydrogens have been inserted (the smallest circles) and the guest molecules have been omitted. The limits of the diagram are 0 a 2, 0 b 2, 0.25 c 1.25; a single unit cell is emphasized.

˚ and that in 6.2 is 5.43 A ˚ ; thus inversion of The O . . . O distance2 within 6.1 is 5.60 A conﬁguration at the substituted carbons (C(2) and C(6)) between 6.1 (representative of Type A host) and 6.2 (Type B host) does not change a fundamental geometrical parameter of these molecules. It is important to note that the triangle shown in projection in Fig. 6.37 is not planar, and is actually the projection of the spirals shown in Fig. 6.38. Now let us return to Fig. 6.37; if one starts with the molecule at the top left corner of the unit cell, the apex CH2 group is located at z ¼ 3/6. Moving clockwise around the tunnel wall the next molecule, which is hydrogen bonded to the ﬁrst, has its apex CH2 group at z ¼ 5/6, i.e. a shift along z by 2/6. This is the requirement that two adjacent molecules in the tunnel wall should be hydrogen bonded. If one moves around the six molecules of the tunnel wall, and upwards along z, one returns to the top left hand corner (equivalent) molecule at z ¼ 15/6, i.e. a shift of 2c. This implies that the tunnel wall is made up of a spiral of hydrogen bonded molecules, with a pitch of 2c. However, the crystallographic periodicity is c, implying that there is a second spiral displaced along c by one period. The two coaxial spirals are internally but not mutually hydrogen bonded. The double spiral is shown in Fig. 6.39. One spiral is shown in space-ﬁlling form in Fig. 6.40, where the 2

These distances vary somewhat from complex to complex because of packing effects.

DIRECTIONALLY BONDED HOSTS

259

3c

2c

c

Representation of host molecule

b

Origin

Spiral about a three-fold screw axis

Fig. 6.38. Schematic diagram of the hydrogen-bonded spirals in the trigonal 6.2 tunnel inclusion complexes. For clarity, the molecule is represented as a V, with a CH2 group at the apex and the hydroxyls at the ends of the two arms. Complete representations are in the center of the diagram and ˚, half representations on the sides. The hydrogen bonds are shown as broken lines; d(O . . . O) ¼ 2.99 A < O . . . O . . . O ¼ 112.8 , (O . . . O . . . O . . . O) ¼ 106.2 .

Fig. 6.39. Stereodiagram of the double spiral of hydrogen bonded diol molecules forming the walls of one helical tunnel in the trigonal crystal structure of 6.1. [x(guest)]. The view is along the c axis and the spirals are left handed; one spiral starts at the top of the diagram and the other at the bottom. The spirals ˚ (¼ c) and are not hydrogen bonded to one another. The are separated in the z direction by 7.00 A generality of this arrangement among the trigonal Bishop-Dance complexes is demonstrated by using 6.1 as host in this diagram, and P3221 space group. (Reproduced from Andreetti, 1984.)

central tubular tunnel which contains the guests is also apparent. The traveled reader, en route to the Cistine Chapel, will no doubt have noticed that the double staircase leading to the Vatican Museum has just this structure; another architectural example is ‘Le Grand Escalier’ in the sixteenth century Chateau Chambord in the Loire Valley. Each of the donor hydroxyls in a spiral can act as an acceptor and conversely, and this available hydrogen bonding capability is used to link the spirals together laterally to form

260

T UN N E L I N C L US I O N C O M P L E XE S

the three dimensional crystal. This is shown in Fig. 6.41 where the ‘spines’ of the structure are enclosed in circles, with 32 axes (not shown) running normal to the page through their centres; it is important to remember that the three hydrogen bonds shown within any circle are at different heights along z and that diol molecules related by the 32 axes

Fig. 6.40. Stereodiagram of a space ﬁlling representation of one of the spirals shown in Fig. 6.35, from the same viewpoint. (Reproduced from Dance, Bishop and Scudder, (1986).)

a

b

Fig. 6.41. Projection view, parallel to the threefold screw axes, of the diol network in the crystals of 6.1 (and its inclusion complexes); the ﬁlled circles and dotted lines represent OH hydrogen atoms and hydrogen bonds respectively; other hydrogen atoms were omitted for clarity. The hydrogen bonded spines are circled and the tunnels are outlined as triangles. This ﬁgure should be compared with Fig. 6.37; despite the difference in the hosts (6.1 and 6.2) the overall structures are the same. (Reproduced from Bishop and Dance, 1988.)

DIRECTIONALLY BONDED HOSTS

261

running along the c edges of the unit cell are in different spirals of the double spiral (Figs. 6.39 and 6.40). Six structures of Table 6.8 are compared in Fig. 6.42; the outlined inner regions show the projected tunnel boundaries giving the ‘‘unobstructed cross-sectional areas’’ (UCA, previously designated Aun) that are available to guest species of any length for movement along the tunnel without steric impediment. Recent values (Bishop, 1996, Table 1) for the ˚2 nine helical structures 6.1–6.9 are 19.8, 29.2, 2.8#, 32.3, 1.2#, 34.0, 22.7, 9.9# and 8.9# A # (the values marked by are for the guest-free material). The common feature of the structures is the hydrogen bonding in the ‘spine’ regions; it is perhaps surprising that these hydrogen bonds are of appreciably different strengths, with d(O . . . O) ¼ 2.81, 2.98, 2.81 ˚ respectively. It is clear from the values of UCA that 6.3, 6.5, 6.8 and 6.9, and 3.05 A although isostructural with the other complexes, have constrictions in their tunnels which prevent the formation of tunnel inclusion complexes. 6.7 has a suitable UCA and does form complexes despite some shape differences (Table 6.7). The structures of complexes of ferrocene ((C5H5)2Fe) and squalene (2,6,10,15,19, 23-hexamethyl-2,6,10,14,18,22-tetracosahexaene, C30H50) with 6.4 have also been reported (Ung, Bishop, Craig, Dance, Rae and Scudder, 1993). These complexes, which have compositions (by NMR) of {3(6.4)(ferrocene)0.75} and {3(6.4)(squalene)0.21} respectively, are isomorphous with {3(6.4)(benzene)}; the anomalous scattering from the

OH

HO H3C

CH3

CH3

H3C

OH

HO

6.1 6.2

HO

OH

H 3C

CH3

OH

HO

6.3

6.4

OH

HO

CH3

H3C

HO

OH

H3C

CH3

CH3

H3C

6.5

6.6

Fig. 6.42. Comparative projections down [001] of one tunnel only for the inclusion complexes of 6.1, 6.2, 6.4 and 6.6, and of the neat crystals of 6.3 and 6.5. All six diagrams are on the same scale. Key hydrogen atoms deﬁning the van der Waals surface of the host tunnels are shown as black dots. For other details see the caption to Fig. 6.41. (Reproduced from Bishop, Craig, Dance, Scudder, Marchand and Wang, 1993.)

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262

Fig. 6.43. Side view of one tunnel in the {(6.4)3[(squalene)0.21]} complex showing the included squalene molecule. The oxygens of the diol molecules are emphasized. One column of diol molecules has been removed for clarity. The double spiral of diol molecules is seen edge-on. (Reproduced from Ung, Bishop, Craig, Dance, Rae and Scudder, 1993.)

Fe of ferrocene allowed the space group of the crystal used to be established as P3121 (such a determination of absolute conﬁguration has limited value unless related to other chiral physical properties of the crystal, for example the face development). The guest molecules are disordered in both these complexes and special techniques were used for their reﬁnement. It was found that three ferrocene molecules were disordered over four unit cell repeats in the [001] direction, that its ﬁve fold axis was inclined at 66 to [001], and that it was also disordered orientationally. The arrangement found for the squalene complex is shown in Fig. 6.43. That the disposition of the hydroxyls is vital to the ability to form trigonal helical tubuland complexes while the nature of the atomic arrangement bridging them is secondary is neatly shown by the fact that 6.7 (Fig. 6.44) forms such complexes with ethyl acetate and deutero-acetone (Table 6.8). The distance between oxygen atoms in 6.7 ˚ (compared to 5.6 A ˚ in 6.1). 6.8 and 6.9 form isostructural helical complexes is 5.98 A (Table 6.8) but the values of the unobstructed cross-sectional areas (UCA) are so small (9.9 ˚ 2 respectively) that only very small guests will perhaps form complexes. and 8.9 A H

OH

HO CH3 6.7

OH HO

CH3

CH3

CH3 6.8

OH

HO

CH3 6.9

CH3

DIRECTIONALLY BONDED HOSTS

263

Fig. 6.44. Formulae 6.7–6.9 shown above as conventional line diagrams (some hydrogens omitted for clarity), with 6.7 below viewed down the molecular twofold axis (all hydrogens are shown). This twofold axis is not immediately obvious in the line diagram.

In the composition formulae {3(host)[guest]x}) of the tunnel inclusion complexes, ‘x’ takes on only a limited set of values – these are 0.75, 0.86, 1, 1.2 and 1.5 (squalene is an understandable exception at 0.21). The structural explanation is as follows. A single unit cell, with three host molecules, has a single tunnel (see Figs. 6.36 and 6.40); thus ‘x’ gives the ‘number’ of guest molecules in a single period of the tunnel along z. When x ¼ 0.75 (6.1 with monoglyme, 1,2-dichloroethane; 6.2 with ferrocene), there are three guest molecules in four unit cells; for 0.86 (6.1 with trichloroethylene, toluene), there are six guests in seven unit cells; for 1 (6.1 with acetonitrile, ethyl acetate, thiophene, chlorobenzene, dioxane; 6.2 with ethyl acetate, 1,3-dibromopropane, CBr2F2, o-dichlorobenzene; 6.4 with benzene), there is one guest per unit cell; for 1.2 (6.1 with 1,2-dichloroethane, propanoic acid; 6.2 with CCl4, o-xylene; 6.7 with acetone-d6), six guests in ﬁve unit cells; for 1.5 (6.6 with CHCl3), three guests in two unit cells. The guest molecules are necessarily orientationally disordered within the tunnels and also longitudinally, except for the x ¼ 1 situation. However, the compositions are commensurate in the sense used for urea inclusion complexes; thus one wonders whether analogous diffuse scattering occurs at room temperature, and phase transitions on cooling. We have not encountered such reports. A comparison of the hexagonal (not rhombohedral) urea and the trigonal Bishop–Dance tunnel inclusion complexes (respectively, UTIC and BDTIC) is rewarding: 1. Both are chiral, UTIC because of the chiral arrangement of the achiral urea host molecules, and BDTIC because of spontaneous resolution of chiral host molecules and their arrangement in a chiral space group.

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264

2.

3.

4.

5.

Some BDTIC are primary solid solutions of guest in host, others are separate phases in the host-guest phase diagram. All UTIC are separate phases in the host-guest phase diagram. The UTIC often show spectacular diffuse (X-ray) scattering, the details of which vary with the nature of the guest. There are also phase changes at low temperatures. Neither of these features has been reported for the BDTIC, perhaps because they have not been sought. The UTIC can be commensurate or incommensurate, depending on the nature of the guest. The BDTIC appear to be commensurate and only a limited number of speciﬁc host:guest ratios have been reported, as described above. Examples are 3 : 0.75, 3 : 0.86, 3 : 1, 3 : 1.2 and 3 : 1.5. Strong hydrogen bonding between host and guest can lead to partial deformation of the host framework in both types of complex (for BDTIC see 6.2.2.4 ‘‘Derived structures’’ below).

6.2.2.3 The ellipsoidal tetragonal clathrate complexes of some Bishop–Dance hosts These structures should logically be discussed in Chapter 7 but it is convenient to place them here because the hosts belong to the same chemical family. We have noted above that 6.2 recrystallized from benzene gives the prototype ellipsoidal clathrate {4(6.2)[C6H6]}, which is tetragonal, space group I41/acd, a ¼ 23.021, ˚ , V ¼ 10011 A ˚ 3, Z ¼ 8(BUXRIV10; Hawkins, Bishop, Dance, Lipari, Craig c ¼ 18.889 A and Scudder, 1993). Other guests giving the ellipsoidal clathrate structure with 6.2 include acetone, acetonitrile, dichloromethane (LORQOY; Bishop, Craig, Dance, Scudder and Ung, 1999), toluene, nitrobenzene, benzylcyanide, chlorobenzene, bromobenzene, o-dichlorobenzene, p-dichloro- and p-dibromobenzene, p-bromo- and p-nitrotoluene (Ung, Bishop, Craig, Dance and Scudder, 1992a). Chloroform and bromobenzene form both types (trigonal and tetragonal) of inclusion complex with 6.2 ((Ung, 1993). 6.10 is another host which comes into this group, forming an isomorphous clathrate with CHCl3 as guest. Note that 6.10 is a Type A host and (according to available reports) forms only a tetragonal ellipsoidal clathrate (with chloroform) but not trigonal helical tunnel inclusion complexes, in contrast to the other Type A hosts. Crystal data and references are summarized in Table 6.9.

HO

OH

CH3

CH3

6.10

S

In contrast to the trigonal complexes of ethyl acetate and other guests with 6.1, 6.2 and 6.4, spontaneous resolution does not occur on crystallization of 6.2 with benzene but a

DIRECTIONALLY BONDED HOSTS

265

Table 6.9. Crystal data for the tetragonal ellipsoidal clathrates of two Bishop–Dance hosts (cf. Table 4 of Bishop, 1996) Formula

Refcode / reference

˚) a(A

˚) c(A

˚ 3) V(A

{4(6.2)[CS2]} {4(6.2)[CH3CN]} {4(6.2)[CH2Cl2]} {4(6.2)[C6H6]} {4(6.2)[o-C6H4Cl2]} {4(6.10)[CHCl3]}

POLFIF; BCMS94 LORQUE; BCDSU99 LORQOY; BCDSU99 BUXRIV10; HBDLCS93 VUSYEN; UBCDS93b QULLAK; BCDKMPS93

23.031(2) 22.979(1) 23.007(1) 23.021(1) 23.442(4) 23.042(3)

18.773(1) 18.864(1) 18.869(2) 18.889(2) 18.928(4) 19.022(3)

9958(2) 9961(1) 9988(1) 10010(1) 10401(3) 10099(2)

References: BCDKMPS93 – Bishop, Craig, Dance, Kim, Mallick, Pich and Scudder, 1993; BCDSU99 – Bishop, Craig, Danc, Scudder and Ung, 1999; BCMS94 – Bishop, Craig, Marougkas and Scudder, 1994; HBDLCS93 – Hawkins, Bishop, Dance, Lipari, Craig and Scudder, 1993; UBCDS93b – Ung, Bishop, Craig, Dance and Scudder, 1993b.

racemic structure is obtained. It would be interesting to see whether a complex is obtained by crystallization of resolved 6.2 from benzene. The resolved 6.2 could, at least in principle, be obtained by hand separation of enantiomorphic crystals of {6.2[1/3(ethyl acetate)]}; presumably neat 6.2 would appear instead of a complex. It is interesting to note that 2,6-dimethylideneadamantane-1,3,5,7-tetracarboxylic acid forms 1 : 2 inclusion compounds with mesitylene, with space group I41/acd and structural similarity to the ellipsoidal clathrates (Ermer and Lindenberg, 1991; VOBFUN; cf. VOBFOH, VOBGAU). Using 1,2-dichlorobenzene as guest allows preparation of either the helical tubuland type or the ellipsoidal clathrate type of crystal, depending on crystallization conditions (Ung, Bishop, Craig, Dance and Scudder, 1993b). It has been reported that 6.2 can also form both types of inclusion complex with CHCl3 and C6H5Br as guests (Ung, Bishop, Craig, Dance and Scudder, 1992b). These authors studied the relative stability of the 6.2– 1,2-dichlorobenzene polymorphs (sic) by heating samples in sealed tubes at 60–65 for 20 hours, and found that the tetragonal form was stable under these conditions but that the trigonal form had almost completely transformed to the tetragonal form. They inferred that the ‘‘ellipsoidal clathrate structure is of lower energy and the one preferred when allowed by constraints of guest size and shape.’’ We note that the two forms are not polymorphs3 but phases of different composition (4 : 1 and 3 : 1 respectively) in the binary 6.2–1,2-dichlorobenzene phase diagram. Furthermore the ellipsoidal form is racemic while the helical tubuland form is enantiomorphic; racemization of 6.2 during transformation seems extremely unlikely as this would require breaking covalent bonds. A possible explanation is that the sample of 6.2 used was a conglomerate (mixture of both enantiomorphs). The matter is both complicated and interesting, and requires further investigation. Although these phenomena remind one of the urea channel inclusion complexes which, for some guests, can be obtained as either hexagonal (enantiomorphic) or rhombohedral (racemic) (Table 6.1), the resemblance is superﬁcial. The behavior of the urea complexes appears to be true polymorphism, and the change from enantiomorphic to 3

Polymorphism is deﬁned as ‘‘the appearance of different crystal structures for the same chemical entity.’’

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266

c

origin

a

Fig. 6.45. Schematic representation of the tetragonal ellipsoidal clathrate structure viewed down [100]. The projected material lies within the limits 0 x 0.50; 0.25 y 0.75; 0.25 z 1.00. The guests are shown for convenience as spheres, but it should be noted that this hides their mutual orientation as shown for the benzene complex below (Fig. 6.47). The hosts are represented as (H)O–C—C–O(H); in the double spiral on the left (O–C–C–O) is 88 , and –88 in the double spiral in the center. Hydrogen bonds are shown by dashed lines. Left and centre spirals are linked by slightly non-planar quadrilaterals (torsion angles about the bonds 9 ).

c

a

b

Fig. 6.46. A ball and stick representation of the tetragonal ellipsoidal clathrate structure viewed down [100]; only hydroxyl hydrogens have been included. The projected material lies within the limits 0 x 0.50; 0.25 y 0.75; 0.25 z 1.00. The guests are shown for convenience as spheres, but it should be noted that this hides their mutual orientation as shown for the benzene complex below (Fig. 6.47). This diagram is to be compared with Fig. 6.45.

racemic involves a change of arrangement, only hydrogen bonds being broken and reformed; however, here too further investigation seems desirable. The crystal structure of the tetragonal clathrates is complicated; detailed descriptions have been given by Bishop (1996) and in earlier papers by this group. Host diol molecules occupy the 32 general positions of the centrosymmetric space group I41/acd, with the

DIRECTIONALLY BONDED HOSTS

267

Fig. 6.47. Cross-sectional representation of the cavities in {4(6.2)[C6H6]}, linked along the twofold axes parallel to [001], showing the van der Waals surface due to the hydrogen atoms of the host molecules, and the major (80%) orientation of the benzene guest molecules (the minor orientation is rotated 30 about the benzene sixfold axis). The benzenes are at 222 (D2) sites and contiguous sites along [001] are related by the 4 (S4) operation. (Reproduced from Bishop, Dance and Hawkins, 1983.)

guest molecules (possibly disordered) at the eight positions with D2-222 symmetry. The host molecules are segregated by enantiomer around 41 and 43 axes where they form double spirals (Ung, Bishop, Craig, Dance and Scudder, 1993b). This is illustrated schematically in Figs. 6.45 and 6.46 for the isomorphous complexes of 6.2 listed in Table 6.9. The structure of {4(6.10)[CHCl3]} is similar. The tunnels in these complexes are so constricted that they are better described as having clathrate rather than tunnel structures; this is shown in Fig. 6.47 for the benzene complex of 6.2, where the benzene guests are 80% ordered in one orientation. 6.2.2.4 Derived structures When 6.1 is crystallized together with p-chlorophenol or hydroquinone, or 6.2 with p-methoxyphenol, structural arrangements related to those of the helical tubuland family are obtained. Because of this relationship it is more convenient to discuss them here rather than in Chapter 12 (Hydrogen Bonded Molecular Complexes and Compounds), where they strictly belong. {6.1p-chlorophenol} (SUFFOO10) and {6.10.5(hydroquinone)} (SUFFUU10) are ˚, isostructural (a ¼ 6.927(1) [6.864(1)], b ¼ 12.696(1) [12.829(1)], c ¼ 19.286(4) [15.974(1)] A ˚ 3, both P21/c, Z ¼ 4) (Ung, ¼ 94.83(1) [103.099(3)] , U ¼ 1690.1(4) [1370.0(2)] A Bishop, Craig, Dance and Scudder, 1994); {6.2p-methoxyphenol} is also isostructural (Bishop, Craig, Dance, Scudder and Ung, 1994). In {6.1p-chlorophenol} the hydroxyl of the p-chlorophenol molecule occupies one of the positions of the hydrogen bonded spine, forming two dimensional sheets instead of tunnels (Fig. 6.48). This is a mixed framework structure in the nomenclature of Chapter 12. {6.2p-methoxyphenol} has a very similar structure, while in {6.10.5(hydroquinone)} the bifunctional hydroquinone bridges

268

(a)

T UN N E L I N C L US I O N C O M P L E XE S

(b)

p-chlorophenol

Fig. 6.48. Derived structures: (a) the trigonal hydrogen bonded spine . . . OH . . . OH . . . OH.. constitutes the structural core of the helical tubuland lattice of 6.1 and its tunnel inclusion complexes; (b) the similar spine found in {6.1p-chlorophenol} and {6.2p-methoxyphenol} where one of the sites is taken up by the X–C6H4–OH molecule. (Reproduced from Ung, Bishop, Craig, Dance and Scudder, 1993a.)

between two hydrogen bonded spines. These derivative structures are racemic, in contrast to the usual run of trigonal helical tubuland structures. 6.2.3

Ta4P4S29 – an inorganic framework containing sulphur chains

Metal-grey single crystals of tantalum disulphide thiophosphate were synthesized from the elements and found (Fiechter, Kuhs and Nitsche, 1980) to crystallize in the tetragonal ˚. system in the centrosymmetric space group I41/acd with a ¼ 15.849(3), c ¼ 13.143(4) A The TaPS6 compound was formulated as Ta[PS4jS2], the notation being intended to emphasize the presence of two kinds of sulphur atoms. The structure, shown in Fig. 6.49, led the authors to comment ‘‘Another interesting feature of the Ta[PS4jS2] structure is the existence of tunnels extending along the fourfold screw axes. It appears probable that foreign atoms or small molecules can be inserted into and move in these tunnels, the free ˚ .’’ diameter of which is about 4.65 A This prophecy was realized by preparation of a compound of composition Ta4P4S29 by heating stoichiometric quantities of the elements in an evacuated tube for 10 days at 500 C (Evain, Queignec, Brec and Rouxel, 1985). The black crystals were tetragonal with ˚ , V ¼ 3309.9 A ˚ 3, Z ¼ 4. The space group of the crystal used for a ¼ 15.571, c ¼ 13.652 A the analysis was shown to be P43212, which is chiral. The basic framework of the structure has composition TaPS6 and is made up of bicapped biprismatic Ta2S12 units, including sulphur pairs, bonded to each other through tetrahedral PS4 groups which share sulphurs. Thus the two structures are made up of the same [Ta2S12] and [PS4} units linked in the same way, but the [Ta2S12] biprisms are differently tilted. The large tunnels running through the framework in the [001] direction contained S10 chains (average ˚ , <S–S–S ¼ 105.8 ) in the form of right-handed helices; there were only d(S–S) ¼ 2.052 A

DIRECTIONALLY BONDED HOSTS

269

x y

Fig. 6.49. View of the contents of the unit cell of Ta[PS4jS2], looking down [001]. Ta ﬁlled, S hatched, P quartered. (Data from Fiechter, Kuhs and Nitsche, 1980.)

van der Waals interactions between framework and chains. Fibrous sulphur contains similar ˚ , <S–S–S ¼ 106 ) but of both senses. The semiconducting and helices (d(S–S) ¼ 2.07 A diamagnetic inclusion complex was formulated as {TaV4PV4(SII)16-(S2II)4[1/2S010]}. There are other analogous structures. Cycloo¨ctasulphur has been shown to be encapsulated in an open metal-sulphide framework grown from molten cesium polysulphide ﬂuxes (Marking and Kanatzidis, 1995). The complex has the formula {Cs2Sn3S7[1/2S8]} and is monoclinic (space group C2/c, Z ¼ 8); neat Cs2Sn3S7 has not yet been prepared. The structure of the complex is based on Sn3S4 defect cubane units connected by (-S)2 bridges forming large open rings in Sn3S72 anionic layers. These layers are stacked along [001] and mutually aligned so that tunnels are formed. The Csþ cations are located between the layers, while the S8 molecules are in the tunnels in a disordered arrangement of two conformations. A Te8 ring has been reported in Cs3Te22 (Sheldrick and Wachtold, 1995), and Se and Te chains have been injected into the zeolite mordenite (Bogomolov, Poborchoy, Romanov and Shagin, 1985; Terasaki, Shiokawa, Ito, Watanabe and Thomas, 1989). 6.2.4 The tunnel hydrates Most families of tunnel inclusion complexes are characterized by a particular host which forms a structure in which many different kinds of guest can be accommodated. The tunnel hydrates are characterized by a variety of hosts which all crystallize in sheets pierced by tunnels in which water molecules, the common guest, are accommodated. The group of tunnel hydrates to be discussed here constitute a different phase from the anhydrous crystals of the host, with further subdivisions depending on the degree of host– water hydrogen bonding and on the number of water molecules per tunnel. There are also crystals in which the water is absorbed zeolitically but these will not be considered here. 6.2.4.1

Tunnel hydrates with several water molecules per tunnel cross-section

In this group of complexes the tunnels have lateral dimensions large enough to accommodate several water molecules which are bonded both to one another (across and along

270

T UN N E L I N C L US I O N C O M P L E XE S

the tunnel) and also to the host framework. One example is N,N 0 -ethylenediaminesuccinic acid pentahydrate (EDDS; 6.11). EDDS is a hexadentate chelating agent which is isomeric with ethylenediamine tetraacetic acid (EDTA) and chemically quite similar to it. However, a major difference between EDDS and EDTA is that the former has two asymmetric carbon atoms; if EDDS is synthesized from, say, l-aspartic acid then both these carbons (asterisked in the formula, where all except the hydroxyl hydrogens have been omitted) will have the same chirality. The pentahydrate of EDDS synthesised in this way crystallizes in space group P21212 with Z ¼ 2 (Scarbrough and Voet, 1976; ENSUCP); thus the EDDS molecule has two fold symmetry in the crystal. The EDDS molecules are hydrogen bonded together to form networks with tunnels (along [001]) large enough to contain ﬁve water molecules (Fig. 6.50). Although the water molecules are not part of the network, they are hydrogen bonded both to EDDS molecules and to one another. The pentahydrate loses water to the atmosphere rather easily. O –O O

+ * N

+ N *

OH O

HO O – O

Rather similar networks of host molecules which leave central tunnels containing water molecules are found in {(þ)-isoo¨livil[acetoneH2O]}, where the acetone is also located in the tunnels (Wong, Manners and Palmer, 1977; ISOVIL10), and in tetracycline hexahydrate (Caira, Nassimbeni and Russell, 1977; TETCYH01). The water molecules are

Fig. 6.50. Stereoview of the unit cell of EDDS pentahydrate, looking down [001], with [100] horizontal and [010] vertical. Water oxygen atoms are represented as 50% probability ellipsoids. Intermolecular hydrogen bonds between EDDS molecules are shown as broken lines; hydrogen atoms have been omitted for clarity. (Reproduced from Scarbrough and Voet, 1976.)

DIRECTIONALLY BONDED HOSTS

271

bonded both to one another and to the surrounding network, of which they do not, however, form a part. 6.2.4.2 Tunnel hydrates with one water molecule per tunnel cross-section ˚ ), {caffeine[0.8 H2O]} Theophylline monohydrate (Sutor, 1958b; THEOPH4) (c ¼ 4.50 A 5 ˚ (Sutor, 1958a (CAFINE ); Gerdil and Marsh, 1960) (c ¼ 3.97 A), {thymine[0.8 H2O]} ˚ )), and {biuret[0.8 H2O]} (Hughes, Yakel and (Gerdil, 1961; THYMMH) (c ¼ 3.65 A ˚ ) all have rather Freeman, 1961 (BIUHYD); Craven, 1973 (BIUHYD10)) (c ¼ 3.82 A similar structures in which the host molecules lie in pleated sheets pierced by tunnels whose cross-sections are such as to permit accommodation of zigzag chains of water molecules. O H3C

O

N

N N

O

R

N

CH3 R=H thophyline = CH3 caffeine

H

O

O CH3

N N

H

O

N

NH2 NH2

H thymine

biuret

The common feature in their cell dimensions is the shortness of the c axes, which are about equal to the thickness of the pleated sheets. The water molecules are hydrogen bonded both to the host molecules and to one another, as illustrated in Fig. 6.51 for {thymine[0.8H2O]}. In theophylline monohydrate successive water molecules in a chain hydrogen bond to successive theophylline molecules and are thus ordered, but in {caffeine[0.8H2O]} one out of every ﬁve water molecules in a chain, on the average, appears to be missing. {Deutero-biuret[0.8H2O]} was also studied by neutron diffraction (Craven, 1973) but the nature of the chains could not be deﬁned more clearly. It would seem that these structures are incommensurate at room temperature, presumably because of differences between the thickness of the pleated sheets of host molecules and the periodicity of the chains of water molecules; however, the water molecules are essential for maintaining the pleated sheets. Other possible examples are trimesic acid trihydrate ˚ ) (Herbstein and Marsh, 1977), the isomorphous pair 2,4,6which has a short c axis (3.68 A trinitro-1,3-benzenediol2/3H2O (BOCNEM) and the corresponding triol (BOCNIQ) (Pierce-Butler, 1982), and salazopyrine1/2(N,N-dimethylformamide)2.25H2O (van der Sluis and Spek, 1990; SENCIX), which differ in detail from the previous examples. The basic chromium acetate compound {(OCr3(CH3COO)63H2O)þ[Cl .6H2O]} has its anions and (crystal) water molecules in tunnels (Chang and Jeffrey, 1970; CRACOP11). The related tris(5-acetyl-3thienyl)methane dihydrate {(TATM)2H2O} is noted in Section 8.6.

4 THEOPH10 is an independent re-determination of the structure by Sun et al. (2002), with change of the space group from P21 to P21/n. 5 Update: CAFINE01 (Edwards et al., 1997).

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272

b z

x

y

M4 M3

H2O M5

H2O

M2 1 2

1 4

N2 O M1

O2 N1

–1 4

–1 2

O1

Fig. 6.51. A clinographic projection of the crystal structure of thymine[0.8H2O], with the chains of water molecules emphasized. Molecules M1, M2, M3 and M4 are successively related by centers of symmetry at 0,0,0; 1/2,0,1/2 and 101 respectively. M5 is related to M2 by the glide plane (dotted parallelogram) at y ¼ 1/4, and to M3 by a twofold screw axis at 1/2, y, 3/4. (Reproduced from Gerdil, 1961.)

6.3 6.3.1

Tunnel inclusion complexes with van der Waals bonded hosts Tunnel inclusion and other complexes of deoxycholic acid and related compounds

The term ‘‘choleic acid,’’ coined by Demarc¸ay (1838), was used by Lachinov (1885) (Latschinoff ) for the crystalline compound isolated from ox bile, which was later shown to be an inclusion complex of deoxycholic acid containing a mixture of palmitic and stearic acids. Thereafter this term was applied in a more restricted sense to describe the molecular complexes of deoxycholic acid and apocholic acid; however, sufﬁcient information is now available to make the use of such overall terms unsatisfactory and we shall avoid ‘‘choleic acid’’ where possible. The formulae of the steroids DCA (deoxycholic acid), CA (cholic acid), ACA (apocholic acid) and CDCA (chenodeoxycholic acid) are shown below, as well as a perspective, side-on view of the DCA molecule which emphasizes that it is far from planar (Scheme I). All these hosts form tunnel inclusion complexes of related structural types, and also other complexes which are not inclusion complexes. We discuss them together here because of the chemical relationships among the hosts, in a hopefully pardonable retreat from our strict constructionist structural principles! There are a number of general reviews with a stress on the historical background (Sobotka, 1934; Fieser and Fieser, 1959; Herndon, 1967) while the structural chemistry has also been discussed (Giglio, 1984); there is a comprehensive chemical and structural review by Miyata and Sada, 1996). The preparation of inclusion complexes of DCA was ﬁrst reported in 1916 (Wieland and Sorge, 1916). The crystal structures of many DCA and cholic acid inclusion complexes are now known (84 hits for DCA and 100 for cholic acid in November, 2002 version of CSD), and structures have also been reported for some examples of cholanamide, ACA and CDCA complexes.

VAN DER WAALS BONDED HOSTS

H3C 21

R1

20

CH3

22 23

17 1

C

CH3

273

D HO

O

HO

O

2

HO

A

B

4

6

R2

6.12 OH

H3C CH3

C

CH3

A

D

B

HO 6.13

There are a number of variations on the formula 6.12: 1. R1 ¼ OH, R2 ¼ H deoxycholic acid (DCA); 3,12-dihydroxy-5ß-cholan-24-oic acid; C24H40O4. 2. R1 ¼ H, R2 ¼ OH chenodeoxycholic acid (CDCA ); 3,7-dihydroxy-5ß-cholan-24-oic acid; C24H40O4. 3. R1 ¼ OH, R2 ¼ OH cholic acid (CA); 3,7,12-trihydroxy-5ß-cholan-24-oic acid; C24H40O5. 4. In cholanamide (3,7,12-trihydroxy-5ß-cholan-24-amide; C24H41NO4) the hydroxyl of the carboxyl group of cholic acid is replaced by amide NH2. 6.13 is apocholic acid (ACA), C24H38O4.

6.3.1.1 The complexes of deoxycholic acid There is some confusion about the crystal structure of neat DCA, suitable single crystals being difﬁcult to prepare. Go and Kratky (1934; ZZZRES) reported an orthorhombic cell ˚ , without space group or structure. However, Ferro, with a ¼ 31.37, b ¼ 49.90, c ¼ 14.12 A Quagliata, Giglio and Piacente (1981) reported that microcrystals give powder patterns closely similar to those of orthorhombic {(DCA)2[phenanthrene]}. This possibly implies that the orthorhombic DCA complexes are primary solid solutions of guest in host, contrary to evidence from the phase diagrams noted below. A 13C cross polarization/ magic angle spinning NMR spectrum has been reported for a polycrystalline sample of neat DCA (Heyes and Dobson, 1990), from which it is possible to infer that there is one molecule in the asymmetric unit. This crystallographic information is compatible with the known structures of the orthorhombic Group 1A and 1B complexes (Table 6.10), but does not exclude other possibilities.

T UN N E L I N C L US I O N C O M P L E XE S

274

Hydrophobic side C18 C19 Head

Ring D

Ring B

C7

Tail Ring C

C12

C21 =O

Ring A

OH C24 Hydrophilic side

OH

C3

OH

The DCA molecule is viewed approximately in the mean plane of Rings B, C and D. The DCA molecule has an hydrophobic side with three protruding methyl groups and an hydrophilic (polar) side with two hydroxyls and one carboxyl. The standard numbering of the atoms is shown in part, as well as the distinction between hydrophobic and hydrophilic sides of the molecule. The torsion angle ¼ (C17–C20–C22–C23) as shown in the uppermost diagram of the Scheme; this is chemical numbering for DCA and may differ for other situations.

DCA forms orthorhombic, tetragonal and hexagonal inclusion complexes (and sodium deoxycholate forms helical macromolecular associations in solution (Blow and Rich, 1960)); there are also a few monoclinic DCA complexes. The inclusion nature of the tetragonal and hexagonal complexes is not as marked as that of the orthorhombic complexes. The guests in these molecular complexes include such varied substances as organic acids (mono and dibasic), aliphatic and aromatic hydrocarbons, alkaloids, alcohols, azo dyes, esters, ethers, phenols, -carotene, methyl orange. In the group of orthorhombic complexes the hydrophobic sides of the DCA molecule make up the tunnel walls (and also in the tetragonal crystals, but in a somewhat different sense as described below), while the converse occurs in the hexagonal crystals. The crystal structure of CDCA (Lindley, Mahmoud, Watson and Jones, 1980; CHNOCH) has been reported; all the hydroxyl and carboxyl groups are involved in the network of hydrogen bonds between the molecules. The crystal structures of a number of inclusion complexes of cholic acid (Section 6.3.1.3 below) and of some non-inclusion type complexes have been reported; the structure of cholic acid itself is based on an extensive network of hydrogen bonds (Miki, Kasai, Shibakami, Chirachanchai, Takemoto and Miyata, 1990; JEWDEY). Phase diagrams (melting and thaw points) have been determined for the following systems: ACA with montanic acid (CH3(CH2)25CH2COOH) and stearic acid (CH3(CH2)15CH2COOH) (Rheinboldt, Pieper and Zervas, 1927), ACA with palmitic acid (CH3(CH2)13CH2-COOH) and cetyl alcohol (CH3(CH2)14CH2OH) (Rheinboldt, Flume and Ko¨nig, 1929), ACA with camphor (Rheinboldt, Ko¨nig and Flume, 1929) and DCA with stearic acid, palmitic acid and cetyl alcohol (Rheinboldt, Flume and Ko¨nig, 1929), DCA with camphor (Rheinboldt, Ko¨nig and Flume, 1929). All the diagrams have very

VAN DER WAALS BONDED HOSTS

275

200 180 Melting points

t (°C)

160

Eutectic

140

Thaw points

120

Inclusion complex

100 80 Eutectic

60 0

0.2

0.4 0.6 0.8 Mol. Fraction ACA

1

Fig. 6.52. Phase diagram of ACA (C24H40O4) with montanic acid, redrawn from Rheinboldt, Pieper and Zervas (1927). There are eutectic points at 1 and 99 mol.% ACA. The 8 : 1 compound of ACA and montanic acid is at 88.9 mol.% ACA, in the region of the maximum melting point. The lines are guides to the eye.

similar appearances, which rather resemble the phase diagram of perhydrotriphenylene with n-heptane (Fig. 6.65; Farina and Di Silvestro, 1980, 1982). We have recalculated the phase diagram of ACA with montanic acid, plotting temperature against mole fraction of ACA (instead of weight fraction) (Fig. 6.54); the complex is a phase different from neat ACA. The guests in the orthorhombic group of DCA complexes include the following types: 1. alkanes (branched and unbranched pentanes to decanes) (Huntress and Philips, 1949); hexadecane and dodecane; 2. fatty acids (acetic through stearic, including branched chains) (Herndon, 1967); 3. aromatic hydrocarbons (toluene, the xylenes, naphthalene, acenaphthene, phenanthrene, 1,2-benzanthracene, 1,2,5,6-dibenzanthracene, methylcholanthrene, hexahydromethylcholanthrene (Fieser and Newman, 1935); complexes were not formed with chrysene, pyrene, triphenylene, perylene and 1,2-benzpyrene. Although any explanation of negative results is necessarily inconclusive, it seems probable that only aromatic molecules with relatively small cross-sections can form complexes while larger aromatics do not – the criterion is geometric rather than chemical, the shapes of the tunnels in the structures described below being such that only smaller molecules can enter. A similar situation is encountered with the tunnel inclusion complexes of N-(p-tolyl)tetrachlorophthalimide (Section 6.3.5). The orthorhombic inclusion complexes all contain the same structural motif, which is a pleated bilayer sheet composed of hydrogen-bonded DCA molecules lying about the (200) planes (Fig. 6.53). Hydrogen bonds between hydroxyls O(3), O(12) and the carboxyl oxygens link DCA molecules both in the [010] and [001] directions; if one uses the O(3)– H . . . O(24) ¼ C hydrogen bond along [010] as designator, then this can be called a ‘headto-tail’ complex, but the real situation is more complicated. The hydrophilic portions of

276

T UN N E L I N C L US I O N C O M P L E XE S

O

b

S D G

H V

V

C

B

T

a

Fig. 6.53. Schematic structure of orthorhombic DCA molecular complexes, using the following symbols: B bilayer of DCA molecules (shown stippled); G guest molecule; H helical hydrogen bonding scheme holding hydrophilic sides of DCA in bilayer; V van der Waals contacts between hydrophobic sides of DCA bilayer; C tunnel along [001] with hydrophobic walls, containing guest molecules; O origin of unit cell; S 21 axis at z ¼ 0 in P21212 or at z ¼ 1/4 in P212121; T twofold axis in P21212 or 21 axis in P212121, including both exact 21 and approximate 2 axes in those examples with true space group P212121 but which approximate to P21212. (Reproduced from Jones, Schwarzbaum, Lessinger and Low, 1982.)

the molecules face into the interiors of the bilayers and thus hydrogen bonding of guest to host is not possible. Adjacent bilayer sheets are juxtaposed so as to leave tunnels in the [001] direction, with only van der Waals interactions between adjacent bilayers. To quote Jones, Schwarzbaum, Lessinger and Low (1982): ‘‘The remarkable capacity of DCA for accommodating such a wide variety of guest molecules in the channels of these orthorhombic crystals does not result from any conformational changes in the individual DCA molecules, but is possible because the same basic DCA bilayers can be shifted in major and subtle ways relative to each other along a and/or b and/or c such that the combined host-guest crystal complex achieves a stable conﬁguration. Since the guest molecules are packed into hydrophobic channels, the accommodations seem to be those which maximise van der Waals attraction, that is, those which result in the closest packing in the crystal as a whole.’’ The torsion angle shown in Scheme I is (þ)-gauche, i.e. around 60 . The only exception encountered is for COXDEY (Table 6.10), which is ()-gauche. To a ﬁrst approximation all the orthorhombic DCA tunnel inclusion complexes form ˚ , with one isostructural group with a 25.5–27.35, b 13.35–13.81 and c 7.1–7.2 A ˚ 3. Further 4 {DCA-x[guest]} units in a unit cell whose volume ranges from 1250 to 1350 A subdivisions can be made in terms of space group (Craven and de Titta, 1972). Complexes ˚ are Group IA, those with space group P212121 and with space group P21212 and c 7.2 A ˚ are Group IB (both Z ¼ 4, one DCA molecule in the asymmetric unit) and those c 7.2 A ˚ are Group IC (Z ¼ 8, two DCA molecules in the with space group P212121 and c 14.4 A asymmetric unit). Some of the orthorhombic complexes whose structures have been reported are classiﬁed in Table 6.10. Although this sample may well not be representative of the total population, we note that the numbers of reported structures are 6, 18 and 7 in Groups IA, B and C respectively, suggesting that Group IB structures are most widespread; however, this does not take into account the many DCA-fatty acid complexes, most of which belong, at least to a ﬁrst approximation, in Group IA.

VAN DER WAALS BONDED HOSTS

277

In the Group IA complexes, exempliﬁed by 2 : 1 DCA-[(þ)camphor], the adjacent bilayer sheets are at the same height along z because they are related by the twofold axis parallel to [001]. The guest (þ)camphor molecule is twofold disordered and ﬁts into one translation along [001]. The 2 : 1 DCA-[()camphor] complex has a very similar structure, with three to six sites for the disordered camphor molecule; it seems unlikely that these enantiomers could be separated by formation of DCA complexes. Go and Kratky (1934) have reported that many fatty acid complexes crystallize in Group IA (palmitic (ZZZQCS), stearic (ZZZQHO), lauric (ZZZQIC), caprylic (ZZZQIM), heptanoic (ZZZQIO) and propionic (ZZZQIU) acids; the DCA:guest ratios are 4 : x with x depending on the nature of the guest. ˚ (c/2) in the In the Group IB complexes adjacent bilayers are mutually shifted by 3.6 A [001] direction. An example is the 1 : 1 {DCA-[acetic acid]} complex where the acetic acid molecules form hydrogen bonded chains along the tunnels. The p-diiodobenzene, phenanthrene and palmitic acid-ethanol complexes have closely similar structures; the trebling of the c axis in the phenanthrene complex is due to the disposition of the guest, not of the host, molecules. In Group IC (exempliﬁed by {2DCA[cyclohexanone]}), opposing walls of the DCA tunnel are related by a crystallographic twofold screw axis and also by an approximate two fold axis (because the two crystallographically independent DCA ˚ (c/2) translation along c, and because c is molecules are related approximately by a 7.07 A now double the length found in Groups IA and IB). Thus the space group is strictly ˚ , and approximately P21212 with c ¼ 7.07 A ˚ . A similar P212121 with c ¼ 14.14 A arrangement is found in {2DCA-[norbornadiene]}. Continuity of the tunnels along [001] was demonstrated (Suheiro, 1988) by preparation of DCA complexes of polyethers (of composition [–(CH2)m–1–CHR–O–]n, where R ¼ H, m ¼ 2, 3, 4, 6 and R ¼ CH3, m ¼ 2); the polyethers had molecular weights of 3000. X-ray powder diffraction patterns indicated that the complexes had the usual type of orthorhombic structure, although ﬁner distinctions could not, of course, be made. One striking feature of the orthorhombic deoxycholic acid inclusion complexes, especially those with long-chain fatty acids as guests, is that the DCA:guest ratio is always one of small integers; for example 4 : 1 for C3 to C7 fatty acids, 6 : 1 for C8 to C15 and 8 : 1 for C16 and higher. Thus the situation is quite different from that in the urea tunnel inclusion complexes where the ratio is, in general, incommensurate. Earlier workers subjected this point to much experimental testing by analysis of samples prepared from solution and the consistency of the result was puzzling, especially at a time when the structures were not known. Even today the implication is that there must be empty spaces in the tunnels whenever the ratio of the [001] translation period to the length of the guest molecule cannot be expressed as a ratio of small integers; for example, palmitic acid would be expected to occupy three unit cells and a small part of a fourth along [001]. On the basis of their determination of the structure of the palmitic acid complex, Coiro, Giglio, Mazza, Pavel and Pochetti (1982; CHOPAL) suggested that an ethanol molecule is present between the palmitic acid molecules and thus the complex is ternary with composition {8DCA[palmitic acidethanol]}. Although the two types of guest were not found directly by structure analysis because of disorder, some generalisation of the proposal appears permissible because of the reported presence of ethanol in many such complexes (Giacomello and Bianchi, 1943). However, the phase diagrams noted above also indicate (but perhaps not with the necessary precision) compositions such as {8DCA[palmitic

T UN N E L I N C L US I O N C O M P L E XE S

278

Table 6.10. Classification of orthorhombic DCA inclusion complexes in terms of periodicity along c and space group. The composition is given as {xDCA[y(guest)]} Guest ˚) Group IA (P21212, c 7.2 A DCA/guest (x : y) 2:1 (þ)-camphor ()-camphor ferrocene di-t-butylthioketone thiocamphenilone Dibromoethane ˚) Group IB (P212121, c 7.2 A DCA/guest (x : y) 1:1 Acetic acid 2:1 ethylmethylketone diethylketone m-chloroacetophenone (103K) p-diiodobenzene Ethyl acetate(163K) pinacolone phenylacetylene styrene naphthalene 5:3 Acetone (103K) 5:2 acetophenone 8:3 3:1

4:1 8:1:1

p-ﬂuoroacetophenone methylpentylketone phenanthrene 1,2-benzanthracene Propiophenone (103K) p-ﬂuoropropiophenone (103K) p-dimethylamino-azobenezene Palmitic acidethanol

˚) Group IC (P21212, c 14.4 A DCA/guest (x : y) 2:1 cyclohexanone (R)-3-methylcyclohexanone (S)-3-methylcyclohexanone norbornadiene

Torsion Refcode angle

Reference

63.8 63.4 63.4

JSLL82 CCMP95 MEPSH00

CHOLCM HICHIK FEHYAS01 (360K) COXDEY

65.1 (Note 2) 62.0 FIYGAV

62.2 58.5 62.3

DECHAC# DANSOA DANSIU DAJLEF

61.8 61.0 61.7

DCPBID# JIFSOG COFNEQ DOSKEB

PVR84 PVR87 BG62

CdT72 CCMP95 CCMP95 TCP-B85

62.6 62.2

CGPQ72 NNSZ86 CMPGP85 GMS85 FQGP81 FQGP81 DXCHAC P-BCTSLL80 DAJLAB, TCP-B85; BARJOT10 CP-BLL87 BEGHOK10 W-LV87; CP-BLL87 DANSUG P-BTCLL85 DCPHEN CGPQ72 FIQ83 FEHMEK W-LVP-BCMFLL87 FEHMIO W-LVP-BCMFLL87

63.2 62.8

BIVKAS CHOPAL

CGM82 CDG80

65.0 58.3

DANSEQ

P-BTCLL85

DCANBD

T79 T79 DFGMP81

61.6 62.8 63.0 62.8 61.0 62.1

66.2, 66.7

VAN DER WAALS BONDED HOSTS

279

Table 6.10. (Continued ) Guest di-t-butyldiperoxycarbonate quadricyclane ferrocene Cis-N-nitroso-2, 6-dimethylpiperidine (130K) N-nitrosopiperidine (130K)

Torsion angle 63.4, 66.1 62.7, 67.2 66.4, 66.8 66.9 61.5

Refcode

Reference

DXCHBC# DANFUT

FLLP-BTZ75 CGMP84

RAZGII (100–294K) JOQJAA

MEPSH00 GMP99

JOQHUS

GMP99

Notes: (1) Limited crystal data have been reported for a number of complexes without full structure determinations; see, for example, Giacomello and Bianchi (1943) and Go and Kratky (1934). (2) This is the only example encountered of a ( )-I conformation for DCA. # no coordinates References: BG62 – Bonamico and Giacomello, 1962; CCMP95 – Candeloro de Sanctis, Coiro, Mazza and Pochetti, 1995; CDG80 – Coiro, D’Andrea and Giglio, 1980; CdT72 – Craven and de Titta, 1972; CGMP84 – Coiro, Giglio, Mazza and Pavel, 1984; CGMPP82 – Coiro, Giglio, Mazza, Pavel and Pochetti, 1982; CGPQ72 – Candeloro de Sanctis, Giglio, Pavel and Quagliata, 1972; CMPGP85 – Coiro, Mazza, Pochetti, Giglio and Pavel, 1985; CPBLL87 – Chang, Popobvitz-Biro, Lahav and Leiserowitz, 1987; DFGMP81 – D’Andrea, Fedeli, Giglio, Mazza and Pavel, 1981; FIQ83 – Ferro, Imperatori and Quagliata, 1983; FLLP-BTZ75 – Friedman, Lahav, Leiserowitz, Popovitz-Biro, Tang and Zaretzkii, 1975. FQGP81 – Ferro, Quagliata, Giglio and Piacente, 1981; GMS85 – Giglio, Mazza and Scaramuzza, 1985; GMP99 – Gdaniec, Milewska and Polonski, 1999; JSLL82 – Jones, Schwarzbaum, Lessinger and Low, 1982; MEPSH00 – Mu¨ller, Edwards, Prout, Simpson and Heyes, 2000; NNSZ86 – Nassimbeni, Niven, Stuart and Zemke, 1986; P-BCTSLL80 – Popovitz-Biro, Chang, Tang, Shochet, Lahav and Leiserowitz, 1980; PRV87 – Padmanabhan, Ramamurthy and Venkatesan, 1987; PVR84 – Padmanabhan, Venkatesan and Ramamurthy, 1984; T79 – Tang, 1979; TCP-B85 – Tang, Chang et al., 1985; W-LVP-BCMFLL87 – Weissinger-Levin, Vaida et al., 1987.

acid]} and here the presence of ethanol cannot be supposed because of the high temperatures involved. It would be worthwhile to carefully compare (preferably at low temperature) the structures of solution-grown and melt-grown single crystals of one of these inclusion complexes. An exception to the orthorhombic structures described above is the monoclinic struc˚, ture found for {2DCA[o-xylene]} (a ¼ 7.238(7), b ¼ 26.171(12), c ¼ 13.510(9) A ˚ 3, Z ¼ 2, P21; WALHUM; ¼ 60.1, 60.3 ). Inspection of ¼ 90.91(9) , V ¼ 2559(3) A the cell dimensions shows at once the resemblance to the orthorhombic structures and this has been conﬁrmed by determination of the crystal structure (Candeloro de Sanctis and Giglio, 1979; Cerrini, Pochetti, Gallese and Possagno, 1993). The 13C CP/MAS NMR spectroscopy of {2DCA[ferrocene]} has been studied over the temperature range 160–350K (Heyes and Dobson, 1990), and extended by additional XRD and NMR studies (Mu¨ller et al., 2000), the results of which are now brieﬂy described.

T UN N E L I N C L US I O N C O M P L E XE S

19.4

2680

19.2

2660

19

Cell volume (cub. A)

Chemical shift (ppm) for C21

280

18.8 18.6 18.4 18.2

2640 2620 2600 2580 2560

18

2540

17.8 90

140

190

240 T (K)

290

340

90

140

190

240 T (K)

290

340

Fig. 6.54. {2DCAferrocene): (a) Plot of chemical shift for the two peaks of C21 versus T. It was not possible to distinguish between one and two peak models in the temperature range from 330 to 360K and so this region has been left blank. (b) Plot of V vs. T; V has been normalized to the hightemperature P22121 cell but volume should be doubled below 305K. There is a change of slope around 305K but no clear volume discontinuity, hence Mu¨ller et al. categorize the phase transformation as second order. (Data from Mu¨ller et al. (2000); Dr C. K. Prout (Oxford) is thanked for helpful correspondence.)

The 13C NMR resonance from C21 (of a methyl group, see Scheme 1) is split into two lines which coalesce at 360K (Fig. 6.54(a)); this is in keeping with there being two ˚ ) and one crystallographically independent DCA molecules at low temperature (a 14 A ˚ at high temperature (a 7 A). Cell dimension–temperature plots show essentially identical behaviour for all three axes (perhaps surprisingly for such an anisotropic structure) and so can be summarized by a volume–T plot (Fig. 6.54(b)). The onset of the change is at ˚ structure) 305K, above which temperature the intensities of h odd reﬂections (in the 14 A gradually decrease, and then disappear at 360K. Differential scanning calorimetry shows no distinct endo- or exothermic event in the range 293–360K. Thus both these techniques suggest that the phase change is second order in the Ehrenfest (1933) sense, with a gradual progression from an ordered low-temperature phase to a disordered hightemperature phase, with Tc 305K. Much detail has been omitted but two points can be made. Firstly, the order–disorder transition occurs when a degree of motion of one of the components increases signiﬁcantly; this also occurs in the order–disorder transitions discussed in Chapter 16. Secondly, there are many indications that behavior similar to that of {2DCAferrocene} occurs in many other DCA–guest complexes, the temperaturedependent behaviour of which surely warrant study at a similar level of detail. The results of van der Waals energy calculations on the orthorhombic DCA complexes have been summarised by Giglio (1984); many subtleties of the bilayer shifts can be reproduced despite neglect of host-guest interactions, while disordered guest molecules can be located in the tunnels when these are taken into account. Similar calculations have been made for the hexagonal complexes (see below). The DCA complexes are rather stable against loss of guest – for example, the xylene complex loses xylene in air only at the melting point of the complex (423K).

VAN DER WAALS BONDED HOSTS

281

Fig. 6.55. Stereoscopic views of the 2 : 1 DCA-[acetone] (left) and 1 : 1 ACA-[acetone] (right) complexes, looking down [001]. The cell parameters are, respectively, a ¼ 25.809(5), b ¼ ˚ , space group P212121, four molecules of DCA and two molecules of 13.610(2), c ¼ 7.233(1) A ˚ , space group P212121, acetone (disordered) per cell, and a ¼ 24.47, b ¼ 14.26, c ¼ 7.50 A 4 molecules of ACA and of acetone (disordered) per cell. Note that this ﬁgure is rotated by 90 compared to Fig. 6.53, and only half of the bilayers are shown above. (Reproduced from Lahav, Leiserowitz, Popovitz-Biro and Tang, 1979.)

Dissolution of a carboxylic acid complex in ethanol and recrystallization will lead to replacement of the acid by ethanol, although a number of recrystallizations may be needed for complete replacement. In similar fashion xylene will replace ethanol and acetic acid xylene; however, these processes do not appear to have been studied quantitatively. Vapor pressure measurements have been made for the complexes of DCA with styrene and naphthalene (Ferro, Quagliata, Giglio and Piacente, 1981) and also with phenanthrene, 1,2-benzanthracene (Ferro, Imperatori and Quagliata, 1983) and 11,12benzoﬂuoranthene (Ferro, Quagliata and Conte, 1983); only the guest vaporizes in the temperature ranges investigated. The enthalpies of formation of the crystalline complexes are given as 15 5, 24 5, 49 8, 22 10 and 5 5 kJ/mol; thus these complexes are enthalpy-stabilized. The enhanced stability of the phenanthrene complex is in accord with the ordering of the guest molecules in its crystal structure. The structure of only one complex of ACA appears to have been reported, that with acetone (composition nominally 1 : 1) (Popovitz-Biro, Tang et al., 1985; APCHAC10; ¼ 62.2 ). The similarity to the Group IB structures is shown in Fig. 6.55.

6.3.1.2

The complexes of cholic acid

Many guests form complexes with cholic acid (but not fatty acids, according to Rheinboldt and Lauber (1929)). A short list has been given by Nakano, Sada and Miyata (1994) and a more extensive list by Nakano, Sada, Kurozumi and Miyata, (2001). Among the guests are: 1:1. benzene, toluene, ethylbenzene, 1,5-hexadiene, 2,5-norbornadiene, chlorobenzene;

282

T UN N E L I N C L US I O N C O M P L E XE S

2 : 1. 1-methylnaphthalene, myrcene, ethylcyclohexane, dibutyl ether, -ionone, methyl decanoate. 3 : 2. tetralin, cyclohexane. The crystal structures of many of these complexes have been reported (Table 6.11). Neat cholic acid has a structure different from those of the complexes so that these represent separate phases in the cholic acid–guest phase diagrams (which do not appear to have been reported). The overall situation, based on 23 new crystal structures and 28 from the literature, has been neatly summarized by Nakano et al. (2001): ‘‘The facially amphiphilic molecular structure of cholic acid gives rise to the bilayer structure by means of van der Waals association of lipophilic faces and hydrogen bonding between hydrophilic faces.’’ Although there are considerable resemblance to the DCA complexes, there are also marked differences. Nakano et al. (2001) distinguish four groups that result from different conformations of the cholic acid side chain (values for ranging around ( )180 (trans), and (þ)60 ((þ)-gauche)6 and different interdigitations of the methyl groups ( and ) in ˚ gives the the lipophilic faces; sliding of the upper layer of the -type stacking by 4.5 A -type stacking). Four types, (-trans, -(þ)-gauche, -trans and -(þ)-gauche) result from the combination of the two factors, and these are shown by subtle differences among the cell dimensions of the types of complex despite their overall resemblances (Table 6.11). All these crystals have the same basic arrangement of cholic acid bilayers but the stacking modes, and the details of the inclusion of the guests, are somewhat different; examples of each type are shown in Fig. 6.56 and more detail is given for 1 : 1 {cholic acid-[acetophenone]} (Miki, Masui et al., 1988; VABSOG) in Fig. 6.57. The cholic acid molecules are hydrogen bonded to give hydrophilic bilayers (interacting by dispersion forces) in the (100) planes; these layers are mutually arranged so as to provide tunnels along [010] in which the acetophenone molecules are accommodated. The headto-tail bilayers have a parallel arrangement in the DCA complexes, but are antiparallel in the cholic acid complexes. Some 120 inclusion complexes of cholanamide with various guests have been reported, while some 50 compounds did not form inclusion complexes (Sada, Kondo, Uchioda et al., 1998). For reasons of space we do not discuss these in detail but some useful comparisons can be made with those of cholic acid. Notice, ﬁrst, that the three cholanamide complexes in Table 6.11 have cell dimensions very close to those of the monoclinic -trans group, particularly for {cholic acid[-(S)-valerolactone]}. Thus the ‘‘assembly mode of the hosts’’ (a phrase of Sada et al. (1993)) is the same in these two groups of complexes. But there is an important difference – the additional hydrogen of cholanamide (–NH2 compared to –OH) allows for hydrogen bonding of guests to the host framework. We note here a number of other complexes of DCA and analogs, which can hardly be called inclusion complexes; however, it is more convenient to place them here than ˚ , c 49 A ˚, elsewhere. The structures of two isomorphous tetragonal complexes (a 14 A space group P41212, Z ¼ 8) have been reported; the compositions are 2 : 3 DCA:H2O (DOCHHY; Coiro, D’Andrea and Giglio, 1979; Tang et al., 1979) and 2 : 1 : 1 DCA : ethanol : H2O (DCAETO; Candeloro de Sanctis, Coiro, Giglio, Pagliucca, Pavel 6

The ( )-gauche conformation is found but is rare.

VAN DER WAALS BONDED HOSTS

283

(a)

(b)

(c)

(d)

Fig. 6.56. The four structural patterns found for the inclusion complexes of cholic acid: (a) -(þ)gauche (the diagram is speciﬁcally for benzene as the guest); (b) -trans (phenetol); (c) -gauche (ethynylbenzene); (d) -trans(benzyl alcohol). Compare Table 6.11. (Adapted from Nakano et al., 2001.)

T UN N E L I N C L US I O N C O M P L E XE S

284

CA hydroxyl head

CA carboxyl tail

hydrophobic layer guest tunnel hydrophilic layer

guest tunnel

z

x

Fig. 6.57. Crystal structure of 1 : 1 {cholic acid-[acetophenone]} in projection down [010]. Unit cell parameters are in Table 6.11. The hydrogen bonding network between the oxygen atoms is shown by broken lines. The acetophenone oxygens are not hydrogen bonded. The head-to-tail directions of cholic acid molecules run in opposite directions in the two partners of the bilayer; this is the converse of the situation in the DCA inclusion complexes (cf. Fig. 6.55). The torsion angle about the bond marked as is 58.4 (full deﬁnition in Scheme 6.1). (Adapted from Miki, Masui, et al., 1988.)

and Quagliata, 1978) and the DCA arrangements are essentially identical, with only small differences in the dispositions of the guest molecules. As Giglio (1984) points out, there are relations between unit cell dimensions of orthorhombic and tetragonal crystals: atetr borth 2 corth ;

ctetr 2 aorth :

These stem mainly from the size of the DCA molecules and do not reﬂect resemblances in ˚ ) lies parallel to borth, atetr (and crystal structure. Thus the DCA molecule (length 14 A btetr) and determines the lengths of these axes; the separation between two rows of the ˚ , accounting for the lengths of corth and of 1/2(atetr); ctetr is same monolayer is about 7 A about four times the approximate distance between two bilayers in both the tetragonal and orthorhombic crystals. The conformation of the DCA molecules is similar to that in the orthorhombic crystals. However, in the tetragonal crystals hydrophilic sides of the DCA molecules face one another and are hydrogen bonded to form tunnel walls enclosing water and/or ethanol molecules, which also participate in the hydrogen bonding.

VAN DER WAALS BONDED HOSTS

285

Table 6.11. Classification of CA inclusion complexes (composition {CA. [guest]}) on the basis of ˚ , deg.) and unit cell volume (A ˚ 3). The CA : guest ratio is 1 : 1 except where unit cell dimensions (A noted otherwise. The 1 : 1 complexes are generally monoclinic, space group P21, Z ¼ 2, except for a few triclinic complexes, triclinic and monoclinic structures being related. The 2 : 3 complex has space group P21, Z ¼ 4. There are also a few related orthorhombic complexes. Three cholanamide complexes have been included in the Table for comparison Composition -trans; 180 Orthorhombic No guest Acrylonitrile Polymorph I Triclinic Methyl acetate

Refcode / reference

a/

b/

c/

Space group

V

Torsion angle

JEYDEW; MKSCTM90 PEMZAI01; NSM96

16.477(4)

8.394(3)

16.993(3)

2350

167.3

16.882

8.497

17.019

P212121, Z¼4 P212121, Z¼4

2528

171.3

12.223(2) 90.18(1) 12.279 90.41 12.53 90.69 12.655 91.93 12.289 90.39 12.474 91.09

8.189(1) 105.72(2) 8.245 105.69 8.28 107.2 8.354 106.02 8.238 105.83 8.252 106.31

14.204(2) 94.03(1) 14.157 94.23 14.16 94.9 14.125 94.68 14.246 94.97 14.214 94.43

P1, Z¼2 P1, Z¼2 P1, Z¼2 P1, Z¼2 P1, Z¼2 P1, Z¼2

1364

159.3 166.6 167.9 158.4 157.9 165.8 174.3 155.8 157.9 165.8 155.6 171.8

12.183

7.878 104.16 8.003(2) 104.76(2) 8.117 103.81 7.909 106.03 8.609 105.18 8.610(5) 105.21(2)

14.300

P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2

1331

162.3

1414

169.5

1407

166.2

1394

175.0

1459

159.7

1449

154.6

ethyl acetate (polymorph I) methylacrylonitrile

PIWKIP; CNS94a PIWKOV02; NKSM01 NSKM01

Acetone (CA : acetone 1 : 1.5) 0.5(Methyl acetate) 0.5(isopropyl acetate) 0.5(acetone) þ 0.5 (1,2-dichloro-benzene)

ZEJDUN; CNS94b NOJPIL; S96 NOJPOR; S96

Monoclinic 105 Acrylonitrile Polymorph II -(S)-valerolactone; diethyl ketone N-nitroso-piperidine (100K) benzyl alcohol 4-ﬂuorobenzyl alcohol

PEMZAI02; NSM96 JOLFIZ; MKSTM91 ZEJFEY; CNS94b JOQHEC; GMP99 GUNPIO; NSKM01 YUNZAI; STS95

-(þ)-gauche; 60 ; monoclinic, Ethyl acetate PIWKOV; Polymorph II CNS94a PIWKOV01; NKSM01 Benzene WEYNUJ; NSM94 Fluorobenzene GUNLOQ; NSKM01

13.010(3) 12.787 13.258 12.636 12.632(5) 115 13.668(3)

13.627(4) 13.57

14.049(4) 13.960 13.818 13.900 13.806(3)

1375 1396 1428 1382 1399

7.824(4) 113.53(1)

14.095(2)

P21, Z¼2

1385

65.2

8.038(9) 114.25(2) 8.06 114.4

14.076(4)

P21, Z¼2 P21, Z¼2

1406

62.7

1405

62

14.10

T UN N E L I N C L US I O N C O M P L E XE S

286

Table 6.11. (Continued ) Composition

Refcode / reference

a/

b/

c/

Space group

V

Torsion angle

Chlorobenzene

GUNLUW; NSKM01 GUNKOP; NSKM01 GUNMAD; NSKM01 GUNMEH; NSKM01 GUNLAC; NSKM01 LAFCAW; CNS93 LAFCEA; CNS93; SS94b VABSOG; MMK88 GUNMUX; KSKM01 BIFQAI; S97; NSKMOI BIFQEM; S97

13.66

14.01

60

1421

61

1413

65

1423

61

1431

60

1411

60.3

1418

60.0

1447

58.4

1416

59.0

1423

58.2

1460

62.6

13.709

P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2

1411

ECARAB; BBFFP01 MIWTIV; PSGNH01 RABKEG; STS95c TEMWOX; S96b ZUZDON; STS95c ZUZDUI; STS95a ZUZFAB; STS95c YUNYOV; STS95b YUNYOV01; STS95 PIWKUB; CNS94a GUNNIM; NSKM01

8.10 114.6 8.083 114.05 8.10 114.6 8.10 114.2 8.15 114.6 8.049(1) 115.20(2) 8.106(3) 113.52(1) 8.093(1) 113.69(1) 8.111(1) 113.65(1) 8.133 114.12 8.266 114.61 8.150 114.10 8.019 112.81 8.154 113.27 8.078 114.42 8.147 113.71 8.109 115.54 8.135 115.94 8.549 113.02 8.510(4) 113.15(2) 7.969(1) 113.53(1) 8.085 114.75

1430

61.8

1386

62.2

1456

59.9

1416

61.2

1425

57.8

1416

61.8

1429

62.5

1466

62.6

1467

58.3

1411

65.7

1417

59.2

P21, Z¼2 P21, Z¼2

1455

164

1441

167

toluene bromobenzene iodobenzene styrene Aniline Nitrobenzene Acetophenone Benzaldehyde benzonitrile p-nitrotoluene Bicyclo(3.2.0)hept2-en-6-one 0.5(benzil) 4-ﬂuoro-acetophenone p-toluidine 2-ﬂuoroaniline 4-ﬂuoroaniline 3,4-diﬂuoroaniline 2-ﬂuorobenzyl alcohol (note 1) 2-ﬂuorobenzyl alcohol (note 1) Ethyl propionate anisole

13.740 13.69 13.68 13.57 13.742(2) 13.579(2) 13.719(2) 13.565(2) 13.642 13.495

13.392 13.540 13.577 13.613 13.834 13.928 13.351 13.421(5) 13.571(1) 13.566

˚ -trans; 180 ; monoclinic, c 16 A phenol GUNPEP; 12.07 NSKM01 N-methylaniline GUNPOU; 12.00 NSKM01

7.92 111.9 7.96 111.6

14.01 14.01 14.09 14.24 14.095(2) 14.048(1) 14.229(2) 14.055(6) 14.055 14.398 14.024 14.002 14.353 14.182 14.034 13.993 14.029 13.966 13.978(3) 14.237(1) 14.225

16.39 16.22

VAN DER WAALS BONDED HOSTS

287

Table 6.11. (Continued ) Composition

Refcode / reference

a/

b/

c/

Space group

V

Torsion angle

Benzyl chloride

GUNMIL; NSKM01 GUNMOR; NSKM01 GUNKUV; NSKM01 GUNNUY; NSKM01 GUNLIK; NSKM01 POZPUP; GP98 POZPUP01; S97a POZPUP02; NSKM01 GUNNEI; NSKM01 GUNNAE; NSKM01 GUNNOS; NSKM01 GUNPUA; NSKM01 RABJUV; STS95 RABKAC; STS95 JOQHIG; GMP99

12.34

7.82 111.7 7.83 111.5 7.83 111.8 7.94 109.9 7.881 112.06 7.940 109.20

16.24

P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2

1456

174

1459

173.0

1469

174.8

1468

170

1483

173.4

1498

170

P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2

1498

170.0

1478

179.5

1475

171

1481

171

1492

167.6

1487

175.6

1447

167.8

Benzyl bromide ethylbenzene Benzylmethyl ether Allyl benzene n-propiophenone

Benzyl formate Phenyl acetate phenetol N-ethylaniline 3-chloroaceto-phenone 3-ﬂuoroaceto-phenone N-nitroso-4methylpiperidine (100K) cis-N-nitroso-2, 6-dimethylpiperidine (300K)

JOQHOM; GMP99

12.29 12.41 12.11 12.434 12.300

12.085 12.256 12.11 12.14 12.580 12.794 12.353

12.754

16.30 16.28 16.24 16.328 16.240

7.961 109.70 7.897 109.67 7.97 108.5 7.95 108.2 7.984 112.23 7.813 113.13 7.675 111.09

16.208

7.881 111.97

11.355

P21, Z¼2

1525

166.8

16.798(4)

P21, Z¼2 P21, Z¼2

1414

65.2

1423

62.8

15.46

P21, Z¼2

1417

69.8

8.056

P212121 Z¼4 P21, Z¼4 P21, Z¼2

2934

59.7

2661

52.5 60.3 177.3

˚ ; 118 . -gauche-A; 60 ; monoclinic, c 16 A n-Propyl acetate PIWLAI; 12.101(2) 7.884(3) CNS94a 118.04(2) i-Propyl acetate PIWLEM; 12.141(2) 7.979(3) CNS94a 117.76(2) ˚ ; 106 . -gauche-B; 60 ; monoclinic, c 15.5 A ethynylbenzene GUNLEG; 12.264 7.803 NSKM01 106.80 Miscellaneous, some with related unit cells m-chloroaniline QOQFAD; 14.624 24.903 YC01 0.5(o-xylene) YOYFIB; 13.827 25.612 NSM95 90.99 Acetone3H2O LEVTAH; 13.111 7.759 CNS94c 105.70

16.212 16.12 16.14 16.045 16.172 16.359

16.604(3)

7.515 14.893

1459

T UN N E L I N C L US I O N C O M P L E XE S

288

Table 6.11. (Continued ) Composition

Refcode / reference

a/

b/

c/

Space group

V

Torsion angle

Bis(acetic acid)

ZUPKIE; NSM96 ZZZKJE; NH65 ZUPKEA; NSM96 YUNYUB; STS95 ZEJFAV; CNS94b LISYUH; D00 YAZTIC; SS94b

13.353

8.189 112.17 7.849 113.53 15.363

13.993

1417

176.9 166.1 No coordinates 176.9

8.485(4) 101.30(2) 8.171 105.40 7.620 97.53 7.847 106.58

28.512(5)

P21, Z¼2 P21, Z¼2 P212121 Z¼4 P21, Z¼4 P21, Z¼4 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2 P21, Z¼2

4H2O Acetic acid 1 : 1.5 3-ﬂuorobenzyl alcohol (note 2) methyl ethyl ketone 4-aminopyridine 3.18H2O 2(3-ﬂuoroaniline)

1 : 1 {Cholanamideguest} complexes; Propan-2-ol LILGES01; SKU98 Rac-butan-2-ol TEHPUR; BKSMM96 (R)-butan-2-ol TEHPOL; BKSMM96 (S)-butan-2-ol TEHPIF; BKSMM96 1,4-dioxane LAHGAC01; SKU98

13.696 13.831 13.459(5) 12.597 10.975 14.326

monoclinic; trans 13.103 7.799 104.66 13.251(2) 7.869(1) 104.82(1) 13.286(1) 7.853(1) 105.12(1) 13.226(1) 7.871(1) 104.7(1) 13.170 7.868 104.97

14.043 12.400

27.954 19.749 16.125

14.092 14.045(1) 14.075(1) 14.028(1) 14.098

1384 2634 3193

1637

64.0 167.3 156.3 165.3 156.9

1737

176.3

1393

156.6

1416

159.1

1418

162.4

1412

159.8

1405

162.9

2780

Notes: (1) Crystals of YUNYOV01 were grown by standard crystallization from solvent whereas those of YUNYOV were prepared by an absorption method. The cell dimensions are very similar but the CA conformations differ. (2) YUNYUB differs from all the other CA inclusion complexes in having different conformations for the two crystallographically independent CA molecules. References: BBFFP01 – Bertolasi et al., 2001; BKSMM96 – Briozzo, Kondo, Sada, Miyata and Miki, 1996; CNS93 – Caira, Nassimbeni and Scott, 1993; CNS94b – Caira, Nassimbeni and Scott, 1994b; CNS94b – Caira, Nassimbeni and Scott, 1994b; CNS94b – Caira, Nassimbeni and Scott, 1994c; D00 – Dastidar, 2000; GMP99 – Gdaniec, Milewska and Polonski, 1999; GP98 – Gdaniec and Polonski, 1998; MKSCTM90 – Miki, Kasai, Shibakami, Chirachanchai, Takemoto and Miyata, 1990; MKSTM91 – Miki, Kasai, Shibakami, Takemoto and Miyata, 1991; this is a rare example of enantiomer discrimination; MMK88 – Miki, Matsui et al., 1988; NKSM01 – Nakano, Katsuta, Sada and Miyata, 2001; NSKM01 – Nakano, Sada, Kurozumi and Miyata, 2001; NSM94 – Nakano, Sada and Miyata (1994); NSM96 – Nakano, Sada and Miyata (1996); PSGNH01 – Polonski et al., 2001; S95 – Scott, 1995; S96a, b – Scott, 1996a, b; S97a, b – Scott, 1997a, b; SKMTM93 – Sada, Kondo, Miyata, Tamada and Miki, 1993 SKU98 – Sada, Kondo, Miyata and Miki, 1994; SS94b – Shibakami and Sekiya, 1994b; STS95c – Shibakami, Tamura and Sekiya, 1995; TP-BLL79 – Tang, Popovitz-Biro, Lahav and Leiserowitz, 1979; YC01 – Yoswathananont et al., 2001.

VAN DER WAALS BONDED HOSTS

289

˚ , space The structures of two isomorphous hexagonal complexes (a 15.1, c 18.7 A group P65, Z ¼ 6) have been reported; the compositions are DCA: [ethanol:H2O] ¼ 3 : 2 : 1 (H2O (Candeloro de Sanctis, Giglio, Petri and Quagliata, 1979) and DCA:[dimethyl sulphoxide:H2O] ¼ 2 : 1 : 1 (Giglio and Quagliata, 1975). In these two complexes the DCA ˚ around the 65 axis of molecules are hydrogen bonded to form a spiral of diameter 4 A the crystal; the hydrogen bonding is quite different from that in the orthorhombic crystals and O(12) is not involved in the bonding between host molecules. The guest ethanol and water molecules are contained within the interior tunnels of the spirals and are hydrogen bonded to the host molecules. The spirals themselves are arranged in hexagonally closepacked fashion in the crystal, with the hydrophobic regions of the molecules in contact; there are only van der Waals forces between the spirals. One consequence of the differences between the hydrogen bonding schemes in the orthorhombic and hexagonal crystals is that the DCA molecules take up somewhat different conformations in these two types of complex. Calculations (Giglio and Quagliata, 1975) suggest that it is the energy gains from the various possible hydrogen bonding schemes which provide the driving force for the various arrangements and that these offset the energy losses expended in altering the DCA conformations. The interior of the tunnels in the hexagonal crystals is hydrophilic; in the {2DCA[ethanolH2O]} complex there appear to be short ethanol–water–ethanol chains which give additional stabilization to the complex by forming hydrogen bonds to O(12). The dimensions of the tunnels are more strictly deﬁned in the hexagonal than in the orthorhombic complexes. The range of guests accommodated in the hexagonal is much more limited than that found in the orthorhombic complexes because hydrogen bonding is both stronger than van der Waals bonding and has more stringent directional requirements. Helical arrangements of hydrogen bonds rather similar to those in the hexagonal DCA complexes are found in the so-called ‘‘low temperature polymorph’’ of CDCA (see

Fig. 6.58. CDCA-solvent complex, viewed down the c axis; the isolated circles indicate the guest ˚ , Z ¼ 6, space group P65. There are region. The crystals are hexagonal, a ¼ 22.25, c ¼ 10.26 A twofold screw axes at the centers of the cell edges and of the long diagonal. (Reproduced from Rizkallah, Harding, Lindley, Aigner and Bauer, 1991.)

290

T UN N E L I N C L US I O N C O M P L E XE S

formula 6.12, note 2), which is actually a tunnel inclusion complex with a variable guest content (Fig. 6.56; Rizkallah, Harding, Lindley, Aigner and Bauer, 1990; the bromobenzene ‘clathrate’ is listed as VEFYAG). The structure determination is noteworthy because it was carried out on a crystal of dimensions 500 40 60 , using synchrotron ˚ ). The tunnels, which have hydrophobic internal surfaces, are wide radiation ( ¼ 0.895 A ˚. enough to accommodate molecules with van der Waals diameters up to 8 A The physiological role of DCA-fatty acid complexes is not certain but they may have a part in excretory processes (Smith, 1973). Certain human intestinal stones have been found to consist chieﬂy of DCA-fatty acid complexes (8 : 1 ratio) (Fowweather, 1949); DCA also plays an important role in the formation and solubilization of gallstones (Dirscherl and Gerhards, 1961). There is spectroscopic evidence for interaction between DCA and organic molecules also in solution; solubilization of hydrocarbons in alkaline aqueous solutions by addition of DCA may be due to micelle formation in which the hydrogen bonded bilayers found in the inclusion complexes could play some role. A detailed picture has not yet been given. The 1 : 1 complexes of cholic acid with methanol, ethanol, 1-propanol and three ﬂuoroethanols are isostructural (Table 6.12). There are no bilayers and the guest molecules are contained within cavities interconnected by narrow tunnels; there is an intricate arrangement of ﬁve hydrogen bonds between three cholic acid molecules and the guest molecules. These complexes are not inclusion complexes in the present sense. Jones and Nassimbeni mention that 1-butanol and 2-propanol form complexes with cholic acid (space group P6522) but details were not given; Nakano, Sada and Miyata (1994) consider 1-butanol and 2-propanol to be non-complexing solvents, and the contradiction remains to be resolved. There are hydrates of cholic acid, a monohydrate in space group P21 (Z ¼ 2; Lessinger, 1982; Shibakami, Tamura and Sekiya, 1995; BUGJES), a hydrate in P6522 (Z ¼ 12; Lessinger and Low, 1993; Shibakami, Tamura and Sekiya, 1995b; DIPFAJ10; Lessinger gives this as a hemihydrate and Shibakami as a monohydrate) and a tetrahydrate (ZZZKIE) included in Table 6.12. There is also a methanol monohydrate (NUMVEW) and an acetic acid complex (ZUPKEA). Compositions similar to those found among the orthorhombic DCA inclusion complexes of long chain guests are indicated by the melting point diagrams reported for some Table 6.12. Crystal data for 1 : 1 Cholic acid complexes with some alcohols and fluoroethanols. The crystals are isomorphous with spce group P212121 and Z ¼ 4. The CA molecules all have the trans conformation Composition

Refcode/Reference

a

b

c

V

Torsion angle

Methanol Ethanol 1-propanol 2-ﬂuoroethanol 2,2-diﬂuoro-ethanol 2,2,2-triﬂuoro-ethanol

JEGMIR; JS72, JN90 CHOLET; JN90, JS72 JEGMUD; JN90 ZIPYUS; SS94a ZIPZED; SS94a ZIPZIH; SS94a

14.560 14.653 14.951 14.585 14.461 14.562

15.198 15.045 15.026 15.319 15.314 15.41

11.625 11.739 11.864 11.792 11.848 11.72

2572 2588 1665 2603 2623 2645

166.2 169.9 167.8 170.5 170.2 171.5

References: JN90 – Jones and Nassimbeni, 1990; JS72 – Johnson and Schaefer, 1972; SS94a – Shibakami and Sekiya, 1994a.

VAN DER WAALS BONDED HOSTS

291

Table 6.13. Compositions (from phase diagrams) of some steroid complexes of unknown structure Host dehydro-epi-androsterone dehydro-epi-androsterone dehydro-epi-androsterone dehydro-epi-androsterone dehydro-epi-androsterone androsterone cholesterin

acetate acetate acetate acetate

Guest

Host : guest molecular ratio

stearic acid stearic acid lauric acid benzoic acid phenylurethane stearic acid stearic acid

8:1 16 : 1 and 8 : 1 6:1 4:1 6:1 4:1 4:1

steroid systems (Dirscherl and Gerhards, 1961). Some typical compositions are given in Table 6.13. Structural evidence is lacking and analogies should be drawn with caution because the forms of the phase diagrams are quite different from those found for DCAand ACA-fatty acid systems. There are tunnels of rectangular cross-section in the 5 : 1 tunnel inclusion complex of zeyloxanthonone (C28H34O5) with palmitic acid (Dean, Herbstein, Kapon and Reisner, 1991; KIFWUR). The crystals are orthorhombic with a ¼ 29.095(4), b ¼ 9.508(2), ˚ , space group Pbca, Z ¼ 8. The molecules are linked by intermolecular c ¼ 20.718(2) A ˚ ) in one dircarbonyl . . . hydroxyl hydrogen bonds (d(O(5)–H . . . O(3) ¼ C) ¼ 2.70(2) A ection, and dispersion forces in the other two. Thus these complexes are classiﬁed as intermediate between the urea and thiourea complexes (all hydrogen bonded) and those of DCA and perhydrotriphenylene.

OH

O O

A HO

B

C

O

Zeyloxanthonone: hydroxyl O(5) is at the left of the diagram and carbonyl O(3) at the right

6.3.2 Substituted spirocyclophosphazenes as hosts The substituted spirocyclophosphazenes 6.14–6.16 (but not 6.17) form tunnel inclusion complexes with a variety of guests (Allcock, Allen, Bissell, Smeltz and Teeter, 1976), as does 6.18 (Alcock et al., 2000). The subject has been reviewed (Allcock, 1978, 1984; Kobayashi, Isoda and Kubono, 1996). The crystal structures of neat 6.14–6.16 have been reported (Table 6.14); because of the spiro nature of the arrangements about the P atoms of the central ring, the substituent rings are approximately perpendicular to the planes of the phosphazene rings and there is considerable ﬂexibility about the linkages

T UN N E L I N C L US I O N C O M P L E XE S

292

120°

140° 120°

60°

110°

Benzene tunnel inclusion complex

Guest free

p-Xylene clathrate

Fig. 6.59. The host molecule 6.15 in different environments viewed normal to the plane of the phosphazene ring. The large differences in molecular shape are quite remarkable. (Reproduced from Kobayashi, Isoda and Kubono, 1996.)

through oxygen. An example of this structural feature is shown in Fig. 6.59, where the host 6.15 in its neat crystals and in two complexes is viewed normal to the plane of the phosphazene ring. Host 6.14 forms hexagonal inclusion complexes with tetralin, cumene, norbornadiene, iso-octene, trans-decalin, cyclohexane, n-heptane, CS2, styrene, ethyl acetate, CCl4, ethanol and various substituted benzenes (Allcock and Siegel, 1964). The neat crystals of 6.14 are monoclinic (Allcock, Levin and Whittle, 1986); thus the inclusion complexes are separate phases in the host-guest phase diagrams. An early report of polymorphism does not appear to have been substantiated. The amount of guest retained at room temperature depends on its nature, e.g. the ideal molar ratio 6.14/guest is 0.5 (based on the crystal structure noted below) while values of 0.59 and 0.11 were obtained for o-xylene and ethanol respectively. The guests are disordered in the tunnels. More recent results show that 6.14 forms the same sort of hexagonal inclusion complexes with substituted ethylenes (eight examples ranging from trans-stilbene to trans-trans-trans-1,6-diphenyl-1,3,5-hexatriene) and two quasi-linear tetrathiophenes (Sozzani et al., 2004a) and also with polyethylene, polyethylene oxide and polytetrahydrofuran (Sozzani et al., 2004b). The molecular complexes have melting points some 150–200K higher than those of the guests themselves. Advanced NMR methods were used to show that the enhanced stability of the complexes was due to the cooperative effect of multiple (although weak) CH . . . interactions.

O

O P

N O

P O

N N

P

O

O

6.14: tris(o-phenylenedioxy)cyclotriphosphazene

VAN DER WAALS BONDED HOSTS

293

Host 6.15 forms 1 : 3 inclusion complexes with benzene and 1 : 1 complexes with p-xylene and p-chlorotoluene, while 6.16 gives inclusion complexes when recrystallized from toluene, p-xylene, cycloalkenes, alkenes or alcohols (Allcock and Walsh, 1971; Allcock, Stein and Bissell, 1974); only the structure of the p-xylene complex appears to have been reported. 6.18 forms inclusion complexes with o-xylene, 1,2-dichlorobenzene, p-xylene, benzene, tetrahydrofuran and cyclohexane; the ﬁrst two are isomorphous but the other structures all differ (Alcock et al., 2000). The inclusion complexes can be prepared by recrystallization from appropriate organic solvents or by a spontaneous process which occurs when the neat solid is brought into contact with the liquid or vapour of many organic compounds (Allcock and Siegel, 1964). More recently, amorphous thin ﬁlms of host exposed to vapours of guest have been employed, followed by examination by electron microscopy (Kobayashi, Isoda and Kubono, 1996). A somewhat similar process of complex formation appears to occur with potassium benzene sulphonate and organic guests (Barrer, Drake and Whittam, 1953).

O O

O P

N O

P

O

N O

N

N

P

P

O

N

P

O P O

O

N

O

O

6.15: tris(2,3-naphthalenedioxy)cyclotriphosphazene

6.16: tris(1,8-naphthalenedioxy)cyclotriphosphazene

Crystal data are summarized in Table 6.14; one notes a wide range of structural possibilities. The known tunnel inclusion complexes of 6.14 are all isomorphous, with the same space group (P63/m) and similar cell dimensions. A portion of a representative crystal structure, that of {6.14[0.5C 6H6]}, is shown in Fig. 6.60 (a). Although water has very different chemical properties from those of the organic guests, it nevertheless ﬁts (perhaps surprisingly) into the same structural pattern. 6.15 forms a hexagonal complex with benzene, with a different composition (1 : 3) from the hexagonal 6.14 complexes, a similar value of [001] but a different value of [100]. These are all tunnel inclusion complexes, as is triclinic {6.16[p-xylene]}. The general disposition of the three host molecules along the tunnel axes is rather similar in the three types of complex but the host molecules are differently interleaved and the tunnel cross-sections are appreciably different. In particular, the tunnels in the complexes of 6.14 and 6.15 have similar shapes but ˚ respectively) while those in the complexes different sizes (diameters of 5 and 9 to 10 A ˚ ). of 6.16 have both different sizes and shapes (the cross-section varies from 5.2 to 7.0 A Many of the physical properties can be understood in terms of these structural features.

T UN N E L I N C L US I O N C O M P L E XE S

294

˚ , deg. A ˚ 3) for the tunnel inclusion complexes of some Table 6.14. Room temperature crystal data (A spirocyclophosphazenes. Ideal compositions observed so far are {6.14[0.5(guest)]}, {6.15[3(guest)]} and {6.15[guest]}, and {6.16[0.5(guest)]} Host

Guest

Refcode; reference

6.14

Monoclinic, guest-free Water

p-chlorotoluene C6F6

DOFSUM; ALW86 DOFTAT; ALW86 PXZBEN; AABST76 PHOPNB; AABST76 PXZOXY; AABST76 ZZZADM; AABST76 ZZZADJ; AABST76 AFL82 AFL82 HAVHAN; KAIK94 NDXPZB10; AS74 JULJAB; KAIKT93 LEPSAA; KATIK94 KKIK93

6.16

p-xylene

ASB74

1 : 0.5

6.18

1,2-dichlorobenzene p-xylene

AP00

1:2

AP00

1:1

Benzene Bromobenzene o-xylenex p-xylene Mesitylene

6.15

Styrene 4-bromostyrene Guest-free Benzene# p-xylene

Host/ guest ratio

T(K)*

1:2

a/

b/

c/

Unit cell volume

Space group; Z

25.086

25.913

3821

P21/n; 8

11.606

5.911 95.97 –

10.087

1177

P63/m; 2

1:x

<210

11.804

–

10.054

1213

P63/m; 2

1 : 0.5

–

11.66

–

10.09

1188

P63; 2

1 : 0.59

250

11.915

–

10.046

1235

P63/m; 2

1:x

210

11.68

–

10.12

1196

P63/m; 2

1:x

273

11.65

–

10.20

1199

P63/m; 2

1 : 0.25 1 : 0.48

<210 218

11.680 11.605 32.265

10.093 10.112 27.518

1191 1179 5150

P63/m; 2 P63/m; 2 C2/c; 8

1:3

233

15.726

– – 5.825 95.25 —

10.076

2158

P63/m; 2

1:1

353

10.609

13.705

23.535

3422

Pbcn, 4

23.653

20.826

13.622

6705

Pbca, 8

18.818

14.496

5837

C2/m, 8

8.206 102.0 14.880

22.057 104.1 14.747, 90.8 23.277

13.318 109.1 13.429

1484

P1, 2.

4651

P212121; 4.

12.724 97.55

19.347 106.13

9.124 72.46

2054

P1, 2

1:1

* Temperature of onset of guest molecular motion (from 1H NMR spectra) # At room temperature, thiophene and ﬂuorobenzene form complexes isomorphous to those of benzene; at lower temperatures chlorobenzene, furan, bromobenzene and o-, m- amd p-diﬂuorobenzene form such complexes. A monoclinic complex with ferrocene has also been reported but without details (KAIK94). x CSD diagram shows m-xylene. References: AABST76 – Allcock, Allen, Bissell, Smeltz and Teeter, 1976; AFL82 – Allcock, Ferrar and Levin, 1982; ALW86 – Allcock, Levin and Whittle, 1986; AS74 – Allcock and Stein, 1974; ASB74 – Allcock, Stein and Bissell, 1974; KAIK94 – Kubono, Asaka, Isoda and Kobayashi, 1994; KAIKT93 – Kubono, Asaka, Isoda, Kobayashi and Taga, 1993; KATIK94 – Kubono, Asaka, Taga, Isoda and Kobayashi, 1994; KKIK93 – Kubono, Kurata, Isoda and Kobayashi, 1993; crystal structure not yet reported; AP00 – Allcock et al., 2000.

VAN DER WAALS BONDED HOSTS

295

The hexagonal complex{6.15[3C6H6]} loses benzene at 65 C/25 mm Hg or at 105 C/1 atm, while triclinic {6.16[p-xylene]} is much more stable, releasing p-xylene only at 200 C. Variable-temperature 1H NMR studies give the temperatures at which different guest molecules start to undergo extensive molecular motion in the tunnels. For a particular guest (e.g. benzene) the onset of guest thermal motion occurs at progressively higher temperatures along the series of complexes with different hosts. The order of the size of the channels is 6.15 > 6.14 > 6.16 but it is thought that guest-guest interactions probably lower the mobility in the 6.15 complex. The high stability of {6.16[0.5 (p-xylene)]} was attributed to the conﬁning effects of constrictions in the channels, which convert the tunnels almost into cavities. For a particular host the motion of the guest becomes more restricted as the guest molecule increases in size. It seems probable that there will be phase changes on cooling, but this issue does not seem to have been explored. 6.15 also forms clathrate (cage) complexes with p-xylene and p-chlorotoluene; these are noted here for convenience. Despite the geometrical similarity of the guests (and the well-known structural interchangeability of chlorine and methyl), the complexes are not isomorphous, although there are obvious crystallographic resemblances. In the crystal structure of 6.17 the biphenylenedioxy ring systems are inclined at angles of 50 to the mean plane of the cyclophosphazene ring system (Allcock, Stein and Stanko, 1971), while in the other hosts the substituent ring systems are perpendicular, or nearly so, to the mean cyclophosphazene ring plane. It has been suggested that 6.17 cannot

I

II

0

5

III

Fig. 6.60. (a) Stereodiagram of the tunnel formed by the host molecules in the benzene tunnel inclusion complex of 6.14, viewed down [0001]. (b) Comparison of the tunnel cross-sections in the inclusion complexes of 6.14 (I), 6.15 (II) and 6.16 (III). (Both diagrams reproduced from Allcock, Allen, Bissell, Smeltz and Teeter, 1976.)

296

T UN N E L I N C L US I O N C O M P L E XE S

form tunnel inclusion complexes because it lacks the ‘‘paddle wheel’’ structure required for the formation of tunnel walls.

O

O P

N O

N

P O

P N

O

O

6.17: tris(2,2'-biphenylenedioxy)cyclotriphosphazene

Thermodynamic parameters for formation of inclusion complexes of a number of cyclophosphazenes have been determined (Table 6.15) from measurements of vapor pressures according to the following decomposition reaction: fH ½nG gs , Hs þ nGg where H is the host, G is guest and the s, g subscripts refer to solid and vapor states. If one takes into account the enthalpy of sublimation of benzene (44.0 kJ/mol), then the enthalpy of formation of {6.15[2(benzene)]} according to the hypothetical reaction Hs þ nGs , fH ½nG gs is 30.8 (4.2) kJ/mol (at an unspeciﬁed temperature). However, there is a problem here because the 6.15 to benzene ratio is given as 1 : 3 by Allcock and Stein (1974) and 1 : 2 by Whitaker, Simon and Victor (1971), and the measurements cannot be properly interpreted until the composition is established. The structure of the 1 : 3 complex of hexaphenylcyclotriphosphazene (Ph2PN)3 with 1,1,2,2-tetrachloroethane is not known. Table 6.15. Values of thermodynamic parameters (kJ/mol; J/mol K) at 298K for the decomposition reaction given above Complex

G

H

S

{6.15[2(benzene)]} (WSV71) {(Ph2PN)3[3(1,1,2,2-tetrachloroethane)]} (WBFGS68) {2,2 0 -dichloro-4,4,-6,6-tetraphenylcyclo-triphosphazene CH3CN} (WG69)

36(4) 46.9(0.8) 7.1(0.2)

119(4) 109(8) 49(2)

279(11) 209(21) 139(6)

References: WBFGS68 – Whitaker, Barreiro, Furman, Guida and Stallings, 1968; WG69 – Whitaker and Guida, 1969; WSV7 – Whitaker, Simon and Victor, 1971.

VAN DER WAALS BONDED HOSTS

O

297

O P N

N O

P

N

O

P

O

O

6.18

6.3.3 Tritriptycene – a C62H38 hydrocarbon of D3h symmetry with three U-shaped bays Tritriptycene (6.19) has been synthesized and the crystal structure of the 1 : 1 acetone tunnel inclusion complex determined (Bashir-Hashemi, Hart and Ward, 1986; FATSOI). The molecule has a paddle-wheel shape (Fig. 6.61) not too different from those of the cyclophosphazene derivatives discussed in the preceding section, but is much more rigid. The net distance (i.e. allowing for the van der Waals diameters) across the U-shaped bays ˚ . The tunnel structure is shown clearly in Fig. 6.62, the acetone guests are is 5.5 A orientationally disordered and each guest site is only 1/3 occupied. It was suggested that tritriptycene forms a 1 : 3 complex with water, but details were not given. The occurrence of a family of isostructural complexes seems not unlikely.

Fig. 6.61. Stereoview of tritriptycene, with 30% probability ellipsoids. (Reproduced from BashirHashemi, Hart and Ward, 1986.)

T UN N E L I N C L US I O N C O M P L E XE S

298

A

O

B

A O C

B

B

Fig. 6.62. Stereoview of four unit cells of {tritriptycene[acetone]}, with 20% probability ellipsoids, ˚ , Z ¼ 2, P63/m. viewed down [0001]. The crystal data are a ¼ 16.646(3), c ¼ 11.553(4) A (Reproduced from Bashir-Hashemi, Hart and Ward, 1986.)

6.3.4

Trans-anti-trans-anti-trans-perhydrotriphenylene as host

Perhydrotriphenylene (C18H30) has ten stereoisomers, of which six are from three enantiomeric pairs and four are meso forms (Farina and Audisio, 1970a). The most stable of these is the enantiomeric trans-anti-trans-anti-trans stereoisomer 6.20, which we designate as PHTP, following general practice; only one of the two enantiomers is shown. PHTP constitutes about 60% of the product yield in the synthesis and is also the most easily isolated as it is the least soluble of the isomers. The enantiomers have been separated (Farina and Audisio, 1970b). Both racemic and enantiomeric PHTP form tunnel inclusion complexes with a large variety of guest molecules (Farina and Audisio, 1970b; Farina, Allegra and Natta, 1964); most of the published work (Farina,1984) concerns the complexes of racemic PHTP and it is to these that we shall refer in general, as it appears, from many hints in the literature, that diffraction quality crystals of complexes of enantiomeric PHTP have not yet been obtained. Aspects of the physical and structural chemistry of the complexes, including the polymerization of monomers in the tunnels, have been reviewed (Farina, Di Silvestro and Sozzani, 1996). Some 400 potential guests have been checked for formation of tunnel inclusion complexes with PHTP and some 80 were found to form such complexes (Fro¨mming and Oppermann, 1974). The following list, which is certainly not complete, is taken from a number of sources: 1. 2. 3. 4. 5. 6. 7.

n-alkanes, from C5 through C36; aliphatic dienes, including butadiene, cis- and trans-pentadiene, trans,trans -hexa2,4-diene, 2,5-dimethylhexa-2,4-diene; saturated monocarboxylic acids, from hexanoic (C6) to hexacosanoic (C26); saturated dicarboxylic acids from hexanedicarboxylic (C6) through to hexadecanedicarboxylic (C16); unsaturated carboxylic acids, including sorbic (C6) and four C18 acids; alcohols and diols, from heptanol (C7), octanol, dl-octanol-2, and others up to octadecan-9-diol-8,11 (C18); aliphatic and aromatic aldehydes, including heptanal, octanal, 2-methylundecanal, 4-methoxybenzaldehyde;

VAN DER WAALS BONDED HOSTS

H H

H

299

H

H H

Fig. 6.63. Different views of PHTP (6.20). Most hydrogens of methylene groups have been omitted for clarity. The central ring, with its hydrogens, is emphasized.

8. 9. 10. 11.

12. 13. 14.

halogenated compounds, including CHCl3, CCl4, heptyl and octyl bromide, 11-bromo- undecanoic acid; aliphatic ketones, including 2-, 4-, 5-, 6- and 7-tridecanone (C13), 1-octan-5-one (C8), 1-decan-3-one(C10); aromatic carboxylic acids, including benzoic and 4-methylbenzoic acid, cinnamic acid and its hydroxy and 4-methoxy derivatives; aromatics, including benzene, toluene, 1-phenyl-2-methylpropane, 1-methyl7 and 1-ethylnaphthalene, 1,6-diphenyl-1,3,5-hexatriene, trans-stilbene, 2,2,11,11tetramethyl-3,5,7,9-dodecatetraene; cyclic compounds, including dioxan, cyclohexane, decalin and tetralin; linear macromolecules such as polyethylene, cis- and trans-1,4-polybutadiene, polyoxyethyleneglycol; twenty molecules of varying kinds, all with non-linear optical (NLO) properties, form tunnel inclusion complexes with PHTP (Hoss, Ko¨nig, Kramer-Hoss, Berger, Rogin and Hulliger, 1996);

The number and variety of the guests remind one of the tunnel inclusion complexes of urea and thiourea; both urea and PHTP show a certain selectivity towards linear longchain guests, but urea does not form complexes with CHCl3 or CCl4, although {3(thiourea)[CCl4]} is well known. PHTP has two polymorphic phases (Table 6.16); the P21/n phase (crystal structure at 173K by Harlow and Desiraju, 1990) is stable up to the melting point (398K) while the C2/c phase (m.pt. 390K) is monotropic with respect to it (Farina, Di Silvestro, Grassi and Sozzani, quoted in Farina (1984)). Neither of these phases has a structure similar to those of the inclusion complexes, so the latter constitute separate phases in the host–guest phase diagrams. This is illustrated by the melting point diagram for the PHTP-transstilbene system given by Fro¨mming and Oppermann (1974) and that for the PHTP-nheptane system given by Farina (1984) (Figs. 6.64 and 6.65)). As Farina (1984) points out, the inclusion complexes of PHTP are low-stability binary adducts and will be expected to behave, from the standpoint of the phase rule, similarly to hydrates and other binary systems where the stability of the phase rule compound formed is limited to the solid state and melting or dissolution leads to decomposition of the compound (Farina and 7 Note that Harlow and Desiraju (1990) crystallized neat PHTP from this solvent, and an inclusion complex was not formed.

T UN N E L I N C L US I O N C O M P L E XE S

300

130 125

temperature (°C)

120

liquid (L)

115 stilbene + L

C+ PHTP

L+C

110 105 100

stilbene + C

95 0 stilbene

20

40

60

80

100 PHTP

mol % PHTP

Fig. 6.64. T–x phase diagrams for the binary PHTP system with trans-stilbene as guest. (Adapted from Fro¨mming and Oppermann (1974).)

L

C

100

L+C

C+ PHTP

50

0

0 n-heptane

50 mole% PHTP

100 PHTP

Fig. 6.65. T–x phase diagrams for the binary PHTP system with n-heptane as guest. (Reproduced from Farina, 1984).

Di Silvestro, 1980, 1982). The phase diagrams each show the formation of only one inclusion complex; similar results were obtained for systems with n-alkanes and polyethylene as guests, and there is some resemblance to the phase diagram of apocholic acid and montanic acid (Fig. 6.52). The form of the phase diagrams for the PHTP inclusion

VAN DER WAALS BONDED HOSTS

301

165

M.Pt. (°C)

155 Complex with polyethylene as guest melts at 178 °C

145

135

125

115 5

10

15

20 25 30 n of CnH2n+2

35

40

Fig. 6.66. Melting points of the n-alkane tunnel inclusion complexes of PHTP plotted against the number of carbon atoms in the guest molecule; complexes with n even are shown by ﬁlled squares and with n odd by open circles. As the melting points appear to lie on two separate curves, there may be a structural change between n ¼ 20 and 30. Data taken from Table 5 of Farina, 1984.

complexes is quite different from those of the urea inclusion complexes (Fig. 6.29), where incongruent decomposition is found below the melting point of urea (132 C). The melting points of PHTP–n-alkane inclusion complexes have been determined (Farina, Di Silvestro, Grassi and Sozzani, 1984) and are shown in Fig. 6.66; there is no distinction between the melting points of odd and even alkanes as is found, for example, for the melting points of the analogous urea inclusion complexes. The tunnel inclusion complexes have structures based on a common pattern of hexagonally arranged stacks of superimposed PHTP molecules, with tunnels containing the guest molecules running between the stacks. Details of unit cell size and space group depend on the nature of the guest molecule. It is clear from the cell dimensions given in Table 6.16 that the fundamental structure is based on the stacking of PHTP molecules one ˚ . This is the structure implied for above the other to give a stack axis periodicity of 4.8 A ˚ in space {PHTP-n-heptane]} by the hexagonal cell dimensions of a ¼ 14.40, c ¼ 4.78 A group P63/m. Furthermore Zhost ¼ 2 requires that the PHTP molecules have symmetry Cs-m incompatible with their structure. Thus the PHTP molecules are probably stacked in short sequences of (þ) and () enantiomers, with an average site occupancy of 50% for each. When the separated (þ) or () enantiomer is used as host the space group is P63 and such averaging is no longer necessary (Farina and Audisio, 1970b). The n-heptane ˚ channel-axis periodicity and must therefore be disordered guest is longer than the 4.78 A both azimuthally and longitudinally. Photographs of crystals rotated or oscillated about the tunnel-axis direction show continuous diffuse layer lines corresponding to a period˚ , about 0.5 A ˚ less than that expected for the planar extended conformation of icity of 10.7 A n-heptane. Possible conformational models for the included molecules have been investigated from the diffuse scattering and by testing various ways of ﬁtting the guests into the channels (Allegra, Farina, Immirzi, Colombo, Rossi, Broggi and Natta, 1967). The resemblances to the diffraction patterns obtained from the {urea–[n-alkane]} tunnel

T UN N E L I N C L US I O N C O M P L E XE S

302

˚ , deg.) for the two polymorphs and some tunnel inclusion complexes of Table 6.16. Crystal data (A racemic PHTP. In this table the cells of monoclinic crystals have c unique to facilitate comparison with the hexagonal and rhombohedral cells. Z gives the number of molecules of each component in the unit cell b

c

Guest

a

Polymorph I PHTRPL03 HD90 Polymorph II PHTRPL01 AFI67 n-C7H16 PHTPHP AFI67 CHCl3 PHTPCF AFI67 dioxane QQQCQG AFI67 cyclohexane TPTRPC AFI67 benzene AFI67 butadiene CA71 1-(4-nitrophenyl)-piperazine (NPP)NOVWOK; KBA96

18.315 15.319 5.298 95.53 P21/n

4

–

16.94

10.41

9.73

113.5 C2/c

4

–

14.40 25.08 25.11 25.55

14.40 25.08 25.11 25.55

4.78 4.78 28.68 43.02

120 120 120 120

2 6 36 54

0.45 3 15 21

2. 3.

0.76 1 0.8

4.

15.70 13.9 4.78 121 13.35 14.72 4.78 115 15.023 23.198 4.730 90

Space group

P63/m P63/m R 3 R 3

Zhost Zguest Notes

2 P21/m 2 Cmc21 4

1.

5; at 100K, see text.

Notes: 1. At 173K. The polymorph was crystallized from 1-methylnaphthalene, which is noted above as forming an inclusion complex with PHTP. The contradiction needs resolution. PHTRPL02 (Luca et al., 1983) appears identical to PHTRPL03 but a space group was not given. 2. This structure type is also found for complexes with other n-hydrocarbons, n-ethers, n-carboxylic acids, n-esters, iso-octane and CCl4 as guests. There is no coherence between host and guest sub-lattices. 3. Room temperature form. 4. Cell dimensions are average values for the three guests, benzene, toluene, bromoform. The crystals were described as monoclinic without details of space group. 5. The twenty guests with NLO properties referred to above give analogous crystals with monoclinic or orthorhombic symmetry (Hoss, Ko¨nig, Kramer-Hoss, Berger, Rogin and Hulliger, 1996). References: AFI67 – Allegra, Farina, Immirzi, Colombo, Rossi, Broggi and Natta, 1967; CA71 – Colombo and Allegra, 1971; HD90 – Harlow and Desiraju, 1990; KBA97 – Ko¨nig, Bu¨rgi, Armbruster, Hulliger and Weber, 1997.

inclusion complexes are obvious, and one would expect analogous behaviour, involving ordering of the guests and consequent phase changes, on cooling PHTP complexes. Such studies have not yet been reported8 nor have speciﬁc heats (or other physical properties) been measured at low temperatures. The chloroform complex is an ordered version of the fundamental structure (see Fig. 6.67); the two channels have different symmetries with the guest molecules ordered in one set and disordered about centres of symmetry in the other. There is a ﬁrst order transition at 58 C in which this distinction may be removed and both channels include ˚ axis periodicity means that the pseudo-mirror symmetry of disordered guests. The 4.78 A the PHTP molecules remains. This restriction falls away in the rhombohedral dioxane and cyclohexane complexes where the c-axis has to be multiplied by factors of 6 and 9 8

The structure of PHTP-NPP, described below, did not show changes between 55–300K.

VAN DER WAALS BONDED HOSTS

303

(a)

b⬘

a⬘

=a

⬘

b= b⬘/ √3

y x

y x a = a⬘/ √3

(b)

b=

0

0

2 1

Y

x

4Å

Fig. 6.67. Schematic comparison of the molecular packing in the tunnel inclusion complexes of PHTP with (top) n-heptane and (below) CHCl3. n-Heptane is represented by circles and chloroform by three short segments at 120 . The geometrical relationship between the two unit cells in projection is shown in the upper diagram. The small arrows show the shifts of the PHTP molecules of the CHCl3 complex from their positions in the heptane complex; this leads to an increase in cell volume by a factor of 3.035 (25.08/14.4 ¼ 1.742). Reproduced from Allegra, Farina, Immirzi, Colombo, Rossi, Broggi and Natta, 1967.

304

T UN N E L I N C L US I O N C O M P L E XE S

3.7 3.7

4.02

4.1

3.92

3.7

1

0 3.9 4.28

3.5

3.8 3.4 3.3 3.3 Z Y 2Å

Fig. 6.68. The modulated structure of PHTP-cyclohexane viewed in projection down the [010] axis. Only part of the unit cell is shown. (Reproduced from Allegra, Farina, Immirzi, Colombo, Rossi, Broggi and Natta, 1967.)

respectively. The PHTP positions along the tunnel axis in the cyclohexane complex have ˚ ; the cyclohexane molecules been shown to be helically modulated with a radius of 0.4 A are orientationally disordered but interlocked with the displaced PHTP molecules (Fig. 6.68). The disorder in projection has been modeled by a very computer-intensive method developed by Welberry and coworkers (Mayo, Proffen, Bown and Welberry, 1999), which has also been applied to modeling of the diffuse scattering from urea-nalkane channel inclusion complexes. The model takes into account both disorder of the cyclohexane guest molecules and distortion of the host matrix. The latter is an important feature because the rhombohedral crystals transform reversibly into a micro-twinned monoclinic structure at 273K. The benzene and butadiene complexes appear to be isostructural; crystal quality was adequate for structure determination only for the butadiene complex (Colombo and Allegra, 1971). The principal difference from the structures described earlier is that the butadiene molecules are here ordered in the channels; their propinquity allows for facile polymerization under the inﬂuence of X- or -rays. The inclusion complex of 1,4-transpolybutadiene with PHTP has two polymorphic forms, with a transition at 70 C (Iwayanagi, Sakurai, Sakurai and Seto, 1968). Among other macromolecules that form inclusion complexes with PHTP are polyethylene and polyoxyethylene. All these crystals are isomorphous with {PHTP[n-heptane]}, but those with isotactic 1,4-trans-polypentadiene and 1,4-trans-poly-2,3-dimethylbutadiene as guests appear to have different structures not yet reported. PHTP is an especially interesting host for the formation of crystals with nonlinear optical properties as co-crystallization experiments show that it includes many of the most efﬁcient NLO molecules currently available (Hoss, Ko¨nig, Kramer-Hoss, Berger, Rogin and Hulliger, 1997; Ko¨nig and Hulliger, 1996). The complex {PHTP[NPP]0.2} (NPP ¼ 1-(4-nitrophenyl)-piperazine (6.21)) has been studied in some detail (Ko¨nig,

VAN DER WAALS BONDED HOSTS

305

Bu¨rgi, Armbruster, Hulliger and Weber, 1997), and some of their principal results are given here as a paradigm for the study of polar tunnel inclusion complexes.

NO2

N N NPP; 6.21

The crystals form as yellowish needles, up to several millimeters in length; they melt at 429K whereas ( )PHTP melts at 403K and NPP at 410K (cf. Fig. 6.64). They show second harmonic generation (SHG), pyroelectric and electro-optic (EO) properties. Oscillation and precession X-ray photographs (essentially unchanged over a temperature range from 55 to 300K) show a repeating pattern of equally spaced planes in reciprocal space (along c*) with diffuse and sharp scattering features. Every ﬁfth plane (cor˚ ) shows only Bragg-like, sharp diffraction spots, while the responding to d(001) ¼ 4.73 A scattering associated with the four planes in between is essentially continuous within the planes and sharp normal to them. A set of relatively distinct but weak reﬂections is superimposed on the diffuse planes. The structure was determined at 100K. There are stacks of disordered (þ)- and ( )PHTP molecules along [001], analogous to those shown in Fig. 6.69; the PHTP molecules conform to space group Cmcm. However, homochiral PHTP molecules ﬁt together better in a stack than heterochiral molecules, and so each particular stack is homochiral and the averaging is done over stacks as a whole. Further analysis, based principally on the weak Bragg reﬂections, showed that the polar NPP molecules were lined up in a head-to-tail arrangement, and that the chains in adjacent tunnels were parallel (Fig. 6.69); the NPP molecules in a tunnel are located so that the ˚ with the mean plane of a neighcentres of the phenyl rings coincide to within 0.05 A bouring PHTP molecule. Additional experiments showed that crystals containing 1.4 mol% of the tailor-made growth additive 1-(p-tolyl)piperazine (TP) entirely lost polar physical properties. The conclusions from the experimental study can be summarized as follows: 1. Occurrence of SHG, EO and pyroelectricity conﬁrm polarity along [001], and show that the space group of the crystal as a whole is Cmc21. 2. Reversal of the pyroelectric effect along [001] and the lack of polar growth properties indicate twinning across (001). ˚ (i.e. about 10 NPP 3. The polar domains along [001] have a length of at least 100 A molecules). 4. Consistency of the physical properties of crystals grown under different conditions showed that these properties are not due to chance but must be attributed to special features of the nucleation and growth process. Consider the growth process in a particular tunnel. If a nitro group of NPP is exposed, then the (increasing) relative strengths of nitro . . . nitro, NH . . . NH and NH . . . nitro interactions indicate that the next NPP molecule will be linked, tail-to-head, by nitro . . . H–N hydrogen bonding, and so on, giving a polar chain. If a N–H group is exposed then the chain will be of opposite polarity, but the feasibility of N–H . . . N–H

T UN N E L I N C L US I O N C O M P L E XE S

306

c9/5

P H T P

Fig. 6.69. Schematic diagram of {PHTP[(NPP) 0.2]} showing NPP molecules in the tunnels. The ˚ and the repeat distance along [001] (vertical) is 5 4.73 ¼ arrow at upper left represents 4.73 A ˚ , the length of two NPP molecules. The NPP molecules are hydrogen bonded between nitro 23.65 A groups (at the top of each molecule) and H–N groups (at lower end). The chains of NPP molecules in the different tunnels are parallel. (Reproduced from Ko¨nig, Bu¨rgi, Armbruster, Hulliger and Weber, 1997.)

hydrogen bonding makes it possible to reverse the chain sequence. Thus nitro groups will be exposed at both ends of a growing tunnel, with the macroscopic crystal being a twin of two antiparallel polar domains. As growth in all the tunnels will be governed by the same mechanism, the polar chains in adjacent tunnels will be parallel (and not randomly ˚ . Application of Markov statistics has allowed oriented) despite their separation by 15 A these qualitative considerations to be given a quantitative hue. A rather similar treatment has been developed independently for polar urea inclusion complexes by Harris and Jupp (1997a, b). Vapour pressure measurements as a function of temperature have given values (Table 6.17) for the enthalpies of the following reactions: ðInclusion complexÞcryst: ) ðPHTPÞc þ ðguestÞvapor

DHv

VAN DER WAALS BONDED HOSTS

307

Table 6.17. Enthalpies of reaction (kJ/mol) for some PHTP inclusion complexes. Guest

Hv

Hdec

(Hv – Hdec)

Hvap of guest

n-heptane cyclohexane dioxan chloroforma chloroformb

45.2 31.8 34.7 38.9 28.9

11.7 0.8 0.8 8.4 0.4

33.5 31.0 35.5 30.5 29.3

31.9 32.8

a b

31.4

polymorph stable at room temperature; polymorph stable above 58 C.

ðInclusion complexÞcryst: ) ðPHTPÞc þ ðguestÞliquid

DHdec

The measured values of (DHv–DHdec) should be equal to the enthalpy of vaporization of the various guests, and this is tested with satisfactory results in the ﬁnal column of Table 6.17. The tunnel inclusion complexes of urea and thiourea follow a single structural pattern and individual structures are marked by great crystallographic similarity. Thus urea and thiourea show little versatility or adaptability in the structures of their complexes. In contrast, the tunnel inclusion complexes of perhydrotriphenylene show both versatility and considerable adaptability. 6.3.5 N-(p-tolyl)tetrachloro-phthalimide as host Pratt and Perkins (1918) reported that N-(p-tolyl)tetrachlorophthalimide (TTP; 6.22) crystallized from ethanol and glacial acetic acid as white plates of the neat compound but from aromatic solvents, or from solutions containing aromatic molecules of various kinds, as yellow needles of composition {4(TTP)[guest]}; they recognized that these were molecular complexes. Cl

O

Cl CH3

6.22

Cl Cl

O

The ﬁndings of Pratt and Perkins about the chemical nature of the TTP complexes have been conﬁrmed, a number of structures have been determined (Herbstein and Kaftory, 1981) and the results have been put into a broader context (Herbstein, 1987). The guests must have some aromatic character (e.g. tetralin forms a complex but decalin and cyclohexane do not) but the size of permitted aromatics is limited (pyrene is the aromatic molecule with the largest cross section to form a complex). Heteroaromatics (e.g. pyridine and -picoline are permissible guests but not aromatic quinones (e.g. p-benzoquinone and 2-methyl-p-benzoquinone do not form complexes). TTP has a possible functionality as an acceptor in –* charge transfer compounds (by analogy to the well-known acceptor tetrachlorophthalic anhydride) and the complexes with perylene and ﬂuoranthene

308

T UN N E L I N C L US I O N C O M P L E XE S

appeared to be of the charge transfer type (structures were not determined); tetrabenzonaphthalene did not form an adduct with TTP while phenothiazine was the only compound tested (out of 28) which formed adducts of both types. These results are explicable in terms of the crystal structure of the complexes. All the tunnel inclusion complexes were found to be isomorphous with cell dimensions which ˚ from one guest to another – there is minimal varied only by a few hundredths of an A ˚ , ¼ 106.4 , with adaptability. The cell dimensions are a ¼ 22.27, b ¼ 3.91, c ¼ 19.91 A 4 TTP molecules in the unit cell; the space group of the overall structure (i.e. without taking the effects of the guest into account, see below) is C2, which is a Sohnke group (o-dichlorobenzene guest BAVVAV; o-xylene guest BAVVEZ). The TTP molecules are arranged so as to leave a tunnel of elliptical cross section with dimensions close to those of a benzene ring viewed edge-on. The walls of the tunnel are lined with Cl and O atoms of the host molecules. The reason for the limitation in size of the guest molecules is immediately apparent – they must be able to ﬁt into the tunnels. However, it is not at all clear why the guests must be aromatic; unfortunately the guests could not be located along the tunnel axis in the room-temperature structure determinations and thus there are no clues about their mode of interaction with the atoms of the tunnel walls. The chirality appears to be a solid state conformational effect – the p-tolyl groups are rotated by about 55 about the C–N bonds and the TTP molecules are thus chiral; spontaneous resolution of the TTP conformational enantiomers has taken place on crystallization. The yellow color of the complexes was ascribed to intramolecular charge transfer, there being limited resonance interaction between the donor and acceptor portions of the nonplanar TTP molecule. There is no intermolecular charge transfer interaction between host and guest. The crystallography is in fact more complicated than as described above. This is ˚ , most complexes because the true tunnel-axis periodicity of the unit cell is 7.8 A showing sets of weak layer lines corresponding to the doubled periodicity. In some complexes the reﬂections on these weak layer lines conform to the monoclinic subcell of the TTP molecules but in others their symmetry is lowered to triclinic, and an example of such a complex is shown in Fig. 6.70. The weak reﬂections due to the guest molecules provide, in potential, information about their disposition but it has not yet been found possible to exploit this to determine the full crystal structures. As in so many other examples of molecular compounds and complexes, low temperature studies would also be of value here. TTP has an interesting polymorphism with some relation to the structures of the inclusion complexes. The -polymorph (stable up to 173 C; space group Cmca, Z ¼ 8) has a structure (Kaftory, 1978; TOCPIM) very different from that of the complexes; there are intermolecular localized C ¼ O . . . Cl charge transfer interactions while the two ring systems of which the molecules are composed are mutually perpendicular, the lack of colour being ascribed to the consequent lack of intramolecular charge transfer interaction between donor and acceptor portions. However, the -phase (stable from 173 C to the melting point at 214 C, quenchable to room temperature; space group P21/c, Z ¼ 8; ˚ , very TOCPIM11) has a structure composed of stacks of TTP molecules, with b ¼ 3.97 A similar to those in the tunnel inclusion complexes; however, there are two kinds of stacks, composed of two differently linked sets of molecules (Fig. 6.71). The structure consists of sheets of molecular stacks in the (100) planes; in one set of sheets there are intermolecular C ¼ O . . . Cl charge transfer interactions as in the -phase, while in the interleaved set of sheets there is van der Waals bonding between molecules disposed approximately as in

VAN DER WAALS BONDED HOSTS

309

(a) b† = 2bm

Q2

Q⬘2 P2

P⬘2

Q⬘1

Q1

P1

P⬘1

1 a sin b m 2 m 1 a sin b † 2 † 1 1 C = c sin 2 m 2 †

(b) P(xyz)

a†

CL1 C1 CL2

C6 C7

C2 C3 1 a = 2 m 1 a sin 2 †

CL3

origin

g†

bm = 12

Q( 12 + x, 12 + y, z)

C13

C15 C12 C9 C11 C10

C14

O1

N

Q( – 12 + x, 12 + y, z)

C5 O2 C4 CL4

b†up

P⬘(x,y,z)

0

5Å

Fig. 6.70. Projections of the structure of the {4(TTP)[o-xylene]} tunnel inclusion complex: Above View down the monoclinic c axis (which is the same as the triclinic c axis), showing two monoclinic cells (lightly outlined) and one triclinic cell (heavily outlined). The eight crystallographically independent TTP molecules in the triclinic cell are shown schematically, labelled so as to show their relationship to the four TTP molecules of the monoclinic subcell shown in the lower part of the diagram. Below Projection down the [010] axis of the overall unit cell of monoclinic symmetry; the monoclinic am and cm axes are in the plane of the page, as is ct (because t ¼ 90 ), but at runs down to the left below the plane of the page. The coordinates shown with the labels of the molecules refer to the monoclinic subcell. The van der Waals envelopes of the atoms lining the tunnels of elliptical cross-section are shown schematically; the actual cross-section of the tunnel depends on the y coordinate. The molecules at y are emphasised. (Reproduced from Herbstein and Kaftory, 1981.)

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310

A molecules

B molecules

4

O(2) 4

A molecules

3.47 3 2.91

3 4 3.60

3.74 3.73

c

b down

a

Fig. 6.71. -TTP, projection of the unit cell contents onto (010). The structure consists of interleaved sheets of stacks of A and B molecules, which are conformationally identical but interact differently, as noted in the text. The short O . . . Cl contacts in the A strips are indicated by the ˚ . (Reproduced from Herbstein and Kaftory, 1981.) distance 2.91 A

the molecular complex, adjacent molecules being related by centres of symmetry rather than two fold axes. The two sets of sheets are linked by van der Waals interactions. The conformation of the TTP molecules in the -phase is essentially identical to that in the complexes, and the yellow colour of both is attributed to the same intramolecular charge transfer interactions. A difference is that the complexes are chiral while the -phase is achiral. Thus one can see that structural elements are carried over, in part, from one polymorph to the next as well as to the molecular complexes.

6.4

Comparison of the various tunnel inclusion complexes

Tunnel inclusion complexes consist of a host framework, with guests included in essentially linear tunnels. In all our examples the empty host framework is unstable with respect to the pristine host; thus the tunnel inclusion complexes are separate phases in the

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host–guest phase diagram. No example is known where the guest is in solid solution in a pristine host structure; this contrasts with the situation in the clathrates, where a few examples of primary solid solutions are known. Other behavior depends on the strength of the host–guest interaction, and on the possibility that host–guest interaction is sometimes stronger than host–host interaction. This latter effect shows itself most vividly in the urea complexes, where, for certain guests, the host framework is interrupted by formation of host–guest hydrogen bonds. Such interruption has not yet been encountered in the thiourea inclusion complexes. Host–guest interaction also manifests itself in the form of phase changes that occur on cooling. These have been widely studied in the urea and thiourea complexes, with their hydrogen bonded frameworks. {2(DCA)ferrocene} is the only example so far encountered in complexes with van der Waals bonded frameworks. However, there seems no reason to doubt wide occurrence also in complexes with van der Waals bonded frameworks, and variable-temperature studies of these complexes should provide interesting results.

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Chapter 7 Clathrate inclusion complexes formed by hosts of lesser versatility

So from the beginning man was conscious of shell, peel and skin. Also he had a highly developed hand directly usable as an enclosing device and basic to much achievement since then. Successor man has used this hand to make enclosures for himself and his family . . . some of these things are today repeated for the individual who is so familiar with the idea that he uses it in myth and metaphor, claiming, sometimes, to be cribbed, cabined and conﬁned, bound in (but by his own fears) or, maybe, seeing himself or another as a prisoner (but of system, doctrine, conscience and the like). In one way or another everyone understands what it is like to be hemmed in. H. M. Powell, 1984

Summary : Cavities in frameworks constructed from linked host molecules can be ﬁlled (all or in part) by guest molecules of appropriate size and shape, thus forming clathrate inclusion complexes. In general (but there are some exceptions), there are no covalent or hydrogen bonds between host and guest and the host-guest interactions are due to dispersion and polar forces. Guest-guest interactions (often, but not always justiﬁably, neglected) are through dipolar and dispersion forces. In one group of clathrates the interaction among the host molecules is strongly directional, aiding in the formation of periodic arrays of cavities. One prevalent motif is the four-connected tetrahedral node found in the polyhedral clathrates, a group which includes the metalloid clathrates (with covalent bonding between pairs of framework atoms (Si, Ge, . . . )), the clathrasils (with ionic-polar bonding between SiO2 groups) and the gas hydrates (of different kinds), where there is hydrogen bonding between adjacent framework water molecules and, sometimes, additional linkaging. A remarkable concatenation of geometrical and chemical factors governs the formation of the frameworks of these clathrates. A second prevalent motif is the ring of six hydrogen-bonded hydroxyl groups found in the quinol and phenol clathrates, and those of Dianin’s compound. The statistical mechanics of the formation of solid solutions of guests in the host frameworks has been worked out and applied particularly to the -quinol clathrates and, in lesser detail, to the gas hydrates; a substantial number of phase diagrams have been determined for these systems. Most of these clathrates have crystal structures different from those of the pristine hosts and hence are intermediate phases in the binary phase diagrams; Dianin’s compound provides a fairly rare example of formation of a primary solid solution. Clathrates can also be formed when there are only nondirectional dispersion forces between host molecules, and the inclusion complexes of tetraphenylene are used as an example. Finally, the hydrogen-bonded motifs found in the quinol etc. clathrates have inspired the synthesis of covalently bonded analogs, and these hexahosts also form clathrates.

7.1 Introduction 7.2 Directionally bonded hosts

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7.2.1

Quinol 7.2.1.1 7.2.1.2 7.2.1.3

(hydroquinone; 1,4-dihydroxybenzene) as host Crystal structures of quinol polymorphs and -quinol clathrates Low temperature phase transitions in -quinol clathrates Introduction to statistical thermodynamics of clathrate structures and application to the quinol clathrates 7.2.2 Crystal structure of {(6H2O) [hexamethylene tetramine]} 7.2.3 Clathrates derived from existing structures 7.2.3.1 Helium hexahydrate 7.2.3.2 Cadmium cyanide clathrates 7.2.4 Overview of the polyhedral clathrates (including metalloid structures, clathrasils, gas hydrates, clathrate and semiclathrate hydrates) 7.2.4.1 Historical and general introduction 7.2.4.2 Restrictions on the shapes of the polyhedra 7.2.4.3 Packing of pentagonal dodecahedra 7.2.5 Metalloid structures 7.2.6 Clathrasils 7.2.7 Gas hydrates (structures with pentagonal dodecahedra) 7.2.7.1 Relation between guest type and structure type in the gas hydrates 7.2.7.2 Stoichiometry and thermodynamics of the gas hydrates 7.2.7.3 Prototype CS-I and CS-II crystal structures at low temperatures 7.2.7.4 Br2 86H2O is the only bromine hydrate, and the implications of this result 7.2.7.5 Gas hydrates with charged frameworks (ionic clathrate hydrates) 7.2.8 Peralkylonium hydrates and related structures 7.2.8.1 Introduction 7.2.8.2 Structures based on the CS-I structure 7.2.8.3 Structures based on the CS-II structure 7.2.8.4 Structures based on the HS-II structure 7.2.8.5 Structures based on the HS-I structure and its superstructure SHS-I 7.2.8.6 Structures based on the OS-I structure 7.2.8.7 Structures based on the TS-I structure 7.2.8.8 The effectiveness of the alkyl substituents in forming hydrates 7.2.9 Varieties of structures formed by a particular guest 7.2.10 The alkylamine hydrates 7.2.11 Structures without pentagonal dodecahedra (some with charged frameworks) 7.3 Hosts with a combination of directional bonds and van der Waals interactions 7.3.1 Phenol (and related compounds) as hosts 7.3.1.1 Phenol 7.3.1.2 Guayacanin as host 7.3.2 Dianin’s compound (4-p-hydroxyphenyl-2,2,4-trimethylchroman) and related compounds as hosts 7.4 Van der Waals linked hosts 7.4.1 Tetraphenylene as host 7.5 Hexahosts and related compounds 7.6 Conclusions and a perspective view References

323 323 331 333 345 346 346 347 348 348 353 355 360 363 370 370 372 379 381 383 383 383 384 385 385 385 387 387 389 389 389 392 396 396 396 398 399 406 406 408 410 411

DIRECTIONALLY BONDED HOSTS

323

7.1 Introduction Molecules of complex shape often pack together in crystals such that cavities remain between them; similar situations occur for molecules of simpler shapes joined by directed (often hydrogen) bonding. If the cavities remain empty then these arrangements are usually thermodynamically unstable with respect to a denser, cavity-free packing, but ﬁlling the cavities, even partially, leads to stabilization. In such clathrate structures the guest component is entirely enclosed in a framework formed by the host. It is geometrical rather than chemical factors which determine whether a given molecular species can be enclathrated in a particular host framework. The ‘‘clathrate’’ nomenclature was introduced by H. M. Powell in 1948 (see Chapter 2 and Davies (1999)). One type of clathrate complex – the gas hydrates – was ﬁrst encountered almost two hundred years ago and a second – the quinol clathrates – almost a century and a half ago, although they were only characterized as such some ﬁfty-odd years ago. The intermolecular bonding in both the water and quinol frameworks is via hydrogen bonds, but van der Waals interactions are often sufﬁcient for the formation of frameworks stabilized by the presence of guests, e.g. in the tri-o-thymotide (Section 8.2) and tetraphenylene clathrates. Both types of interaction occur in the complexes of phenol while there are directed covalent interactions in the metalloid structures and clathrasils. The literature is very extensive; we note here only one of the earlier books (Hagan, 1962) and some general reviews (Parsonage and Staveley, 1984; Davidson and Ripmeester, 1984; Sixou and Dansas, 1976; Ripmeester and Ratcliffe, 1991) while more speciﬁc references are given in the body of the text. This chapter has been arranged so that a substantial part of the experimental information is summarized before the statistical thermodynamical treatment of the stability of the clathrates is discussed in detail. Relatively little attention is paid here to the motions of guests (and hosts) and the reader is referred to the more extensive coverage by Sixou and Dansas (1976) and Ripmeester and Ratcliffe (1991). As noted earlier, the integration of structural results (from diffraction) with thermodynamical and statistical thermodynamical principles has been developed more substantially in the ﬁeld of the clathrates than for any other group of inclusion structures. The pioneering work of van der Waals and Platteeuw has been very substantially advanced by the Canadian (Davidson, Ripmeester) and Siberian (Dyadin) schools. After some trepidation, we have decided that the most transparent means of introducing this material is to provide a general introduction immediately after discussing the structural results for the quinol clathrates, and then to use the theory and associated experimental measurements to discuss the stability of these materials. Later applications to the clathrate hydrates will be made after having described the structural background for these materials. 7.2 Directionally bonded hosts 7.2.1 Quinol (hydroquinone; 1,4-dihydroxybenzene) as host 7.2.1.1 Crystal structures of quinol polymorphs and -quinol clathrates Although the ﬁrst quinol clathrate was prepared by Wo¨hler (1849) some 150 years ago, the principles underlying the structures in this family of complexes were clariﬁed only after

324

CL AT HRATE INCLUS ION COMP LEXES

the end of the Second World War by crystallographic (Palin and Powell, 1947, 1948) and thermodynamic studies (van der Waals and Platteeuw, 1959); there are excellent introductions to the subject (Powell, 1964, 1984; MacNicol, 1984a) and a more recent comprehensive account (Mak and Bracke, 1996). The quinol system appears to be monotropic with -quinol stable up to the melting point, but there are two additional polymorphs, both metastable under ambient conditions. The ﬁrst of these is -quinol, which can be crystallized from n-octane as an empty clathrate structure (Lindemann, Shklover and Struchkov, 1981); another method is by recrystallization from air-free propanol in the presence of a seed of the argon clathrate, giving almost pure -quinol (99.8%) (Evans and Richards, 1952). In general the -quinol structure requires stabilization by addition of suitable guest molecules. The second is -quinol, which does not have any clathrating properties. We ﬁrst consider the structures of the polymorphs and their inter-relations and then pass on to the structures and thermodynamics of the clathrates. The crystal data for the three polymorphs are given in Table 7.1; the - and -polymorphs have much the same density of packing but this is considerably less in (empty) -quinol. The relationships among the structures of the three polymorphs of quinol are quite remarkable. The -polymorph (Wallwork and Powell, 1980) has a structure consisting of two parts, linked together (Fig. 7.1). One part is a double helix of chains of hydrogen bonded molecules around threefold screw (31) axes, and the other is an interpenetrating cage structure of hydrogen bonded molecules around centres of symmetry on threefold inversion ( 3) axes. The interpenetrating cage structure is very similar to that of the -quinol clathrates described below and provides an explanation for the fact that -quinol has been shown to take up small amounts of gaseous guests; the structure is such that the maximum stoichiometry is one guest per 18 quinol molecules. Such ‘‘structural parsimony’’ – the use of structural elements in more than one context – is found in other systems, for example trimesic acid and its polymorphs and complexes (Section 8.4).

Fig. 7.1. Stereodiagram of part of the crystal structure of -quinol – the interpenetrating cage structure so similar to that in -quinol is shown on the right hand side of the diagram and the double helix of quinol molecules on the left, the line indicating the 31 axis. (Reproduced from MacNicol (1984a).)

DIRECTIONALLY BONDED HOSTS

325

Fig. 7.2. ORTEP sterodiagram of the -quinol clathrate of HCl. Hydrogen bonds are stippled. The whole unit cell is shown (but not the H atom of HCl), the direction of view being approximately perpendicular to that in Fig. 7.3. (Reproduced from Boeyens and Pretorius (1977).)

Fig. 7.3. Schematic diagram of parts of the two interpenetrating frameworks of the -quinol structure. The larger circles represent OH groups, linked together in hexagons by hydrogen bonds shown as horizontal lines. The benzene rings bridging the hydrogen bonded hexagons are shown. An acetonitrile molecule is shown enclosed in the cage formed by the interpenetration of the two frameworks. (Reproduced from Mak (1982).)

The structure of the empty -polymorph is analogous to that of the HCl clathrate shown in Fig. 7.2; the -quinol framework is centrosymmetric but the crystal as a whole will be polar if the guest is in a polar arrangement, as for HCl and CH3OH, or centrosymmetric if the guest arrangement is also centrosymmetric (either because of inherent symmetry or disorder). The ﬁrst structure of this series to be determined was that of the methanol clathrate. The structure is based on the formation of two interpenetrating frameworks (Fig. 7.3) which are not bonded to each other – in other words they are catenated

326

CL AT HRATE INCLUS ION COMP LEXES

(cf. Section 8.3). The hydroxyl groups of six quinol molecules form a planar hexagon with alternate quinol molecules pointing diagonally above and below the hexagon. Interpenetration of two such frameworks gives an overall structure with cavities occupied by guest molecules. Details of the cage structure are shown by the relationship of the two partial networks (Fig. 7.3). We use our usual nomenclature for inclusion complexes – {n(host) [m(guest)]}. The third quinol polymorph, the -form, has a rather different structure with spirals of hydrogen bonded quinol molecules formed about two fold screw axes, the resulting sheets being weakly linked by van der Waals forces to give an easily cleaved layer structure. It is not included as it is not relevant in the present context. The crystallization diagram (not a phase diagram as equilibrium was not attained) of the system quinol–SO2–H2O at about room temperature has been reported (Chekhova, Polyanskaya, Dyadin and Alekseev, 1975) and shows a primary solid solution of -quinol containing up to 2 mol% SO2 and a range of -quinol solid solutions containing from 13.5–31.5 mol% SO2. The -phase can contain He, Ne, Ar, Xe, CH4, N2, O2 or SO2 in solid solution (for references see Chekhova et al. (1975)), although in much more restricted amount than in -quinol; a crystal of composition {0.021SO2 p-C6H4(OH)2} has about the limiting amount and its cell dimensions are very close to ˚ less in a and 0.01 A ˚ larger in c) although the volume per those of -quinol itself (0.02 A formula unit is, surprisingly, a little less; however, these differences may well not be signiﬁcant. Quinol–guest appears to be the only system encountered so far that shows both primary solid solution of guest in pristine host and formation of a separate clathrate phase (cf. introduction to Part III). The -quinol clathrates have been found to crystallize in three groups of isomorphous structures, which form an isostructural family (Table 7.1). Among the guests are Ar, Kr, Xe, HCOOH, CO2, HBr, C2H2, CH4, S2O (Kutty, Sharma and Murthy, 1971), N2O, C3H8 (Peyronel and Barbieri, 1958), as well as mixtures such as CH3OH þ SO2 and SO2 þ HCl. The composition given above for the -phase clathrate of SO2 does not take into account the possible presence of water – for example, a crystal of the -phase with cell parameters ˚ , dm ¼ 1.458 g cm3, Z ¼ 3 can be calculated to have the a ¼ 16.308(5), c ¼ 5.810(10) A composition {3(quinol) [0.2H2O 0.9SO2]}; analysis gave 0.6H2O, the discrepancy presumably being due to occluded water (Lindemann, Shklover and Struchkov, 1981). When the guest molecules are themselves either quasi-spherical or disordered then the cavities remain quasi-spherical, giving Type I complexes (space group R3). Distortion occurs when the guest interacts with the framework, as do HCl and methanol, giving Type II complexes (space group R3). The cavities are all of the same kind and size in complexes of Types I and II but this no longer holds for Type III complexes (space group P3). In the CH3CN clathrate the ordered anisotropic guest leads to signiﬁcant changes in cell dimensions and reduction in lattice symmetry giving rise to three crystallographically independent cavities, with one guest molecule pointing in the opposite direction to the other two. -{3(quinol) [CH3NC]} presents a problem in classiﬁcation – in terms of space group it belongs in Type II but unit cell shape would place it in Type III. Palin and Powell (1948) have commented ‘‘The slight variation in the unit cell dimensions for the different compounds are related to the dimensions of the enclosed molecule . . . a ¼ 16.58, c ¼ 5.47 . . . represent the natural dimensions determined by the equilibrium of the parts of the -quinol framework alone . . . Simultaneously with increase in c there is in nearly

Table 7.1. Crystal data for the polymorphs of quinol and the - and -quinol clathrates. The classification of the -quinol clathrates as Types I, II, III follows MacNicol (1984a) and is based on space group Compound/Reference/ REFCODE Quinol Polymorphs -quinol WP80; HYQUIN02 -quinol (Type I) LSS81; HYQUIN05 -quinol M-M66

Crystal class

˚) a (A

˚) c (A

Vol./formula ˚ 3)# unit (A

Z

dm g cm3

Space group

R*

38.46

5.65

134.0

54

1.35

R 3

R

16.613

5.475

145.4

9

1.26

R 3

4

1.33

P21/c

1.366

R 3

˚ 3; ˚ , ¼ 107 , V ¼ 132.5 A monoclinic, a ¼ 8.07, b ¼ 5.20, c ¼ 13.20 A pairs of molecules at independent centers of symmetry.

- and -Quinol Clathrate Inclusion Complexes -{quinol [0.016SO2]} R 38.26 Type I -{3(quinol) [0.62C2H2]} PP48; ZZZVKY -{3(quinol) [0.74CO2]} PP47; ZZZVLW -{3(quinol) [0.9SO2]} PP48 -{3(quinol) [HCOOH]} PP47; ZZZVLO -{3(quinol) [0.87Xe]} BFSV89; JAMKEN -{3(quinol) [0.87H2S]} HM83; ZZZVLG11 Type II -{3(quinol) [0.89 CH3OH]} M82; ZZZVLI01

5.605

132.3

54

R

16.63

5.46

145.3

3

R 3

R

16.17

5.82

146.4

3

R 3

R

16.29

5.81

148.4

3

R 3

R

16.42

5.65

146.6

3

R 3

R

16.610

5.524

146.6

3

R 3

R

16.67

5.518

147.6

3

R 3

R

16.62

5.562

147.9

3

R3

Table 7.1. (Continued ) dm g cm3

Compound/Reference/ REFCODE

Crystal class

˚) a (A

˚) c (A

Vol./formula ˚ 3)# unit (A

Z

-{3(quinol) [0.87 HCl]} BP77; HYQHCL (XRD); HYQHCL01(ND) -{3(quinol) [0.884 SO2]} GPDA75, PA82; QUOLSO01 x -{3(quinol) [0.9 SO2 0.6 H2O]}; PA82; ZZZAPG x -{3(quinol) [CH3NC]} CM83; BUSPAG

R

16.65

5.453

148.3

3

R

16.311

5.821

149.0

3

1.46

R3

R

16.31

5.810

155.3

3

1.46

R3

R

15.95

6.348

155.4

3

trigonal

16.003

6.245

153.9

3

1.34

P3

R

16.215

13.846

350.3

3

1.65

R 3m

trigonal

17.102 (5)

23.904 (9)

336.4

4

1.54

P 3m1

Type III -{3(quinol) [CH3CN]} CM83; HQUACN01 Miscellaneous 3{(quinol) [C60]} E91,; SOMGIK {4.5 (quinol) [C70] [C6H6]} ER93; HASWIH

Space group R3

R3

Notes: x The SO2 clathrate analyzed by Palin and Powell (1948) was reported to be Type I. The original 300K study of SOMGIK had R ¼ 0.196; this has been superceded by SOMGIK01 to 04 (BRS00) at 100, 200, 300 and 373K, with R 0.04. * R ¼ rhombohedral. References: BFSV89 – Birchall, Frampton, Schrobilgen and Valsdo´ttir (1989); BP77 – Boeyens and Pretorius (1977); BRS00 – Blanc, Restori, Schwartzenbach et al., 2000; CM83 – Chan and Mak (1983); E91 – Ermer (1991); ER93 – Ermer and Ro¨bke (1993); GPDA75 – Chekhova et al., 1975; HM83 – Ho and Mak (1983) (7); LSS81 – Lindemann, Shklover and Struchkov (1981); M82 – Mak (1982); M-M66 – Maartman-Moe (1966); PA82 – Polyanskaya, Alekseev, Bakakin and Chekhova (1982); PA82 – Polyanskaya, Andrianov, Alekseev, Bakakin, Dyadin, and Chekhova (1982); PP47 – Palin and Powell (1947); PP48 – Palin and Powell (1948); WP80 – Wallwork and Powell (1980).

DIRECTIONALLY BONDED HOSTS

329

every case a decrease in a . . . ’’ Inspection of comparable unit cell dimensions reported for various -quinol clathrates suggests that considerable caution must be exercised before drawing conclusions from their variations; the measurements are of various degrees of precision and the compositions are not always unequivocal. Calculation of unit cell dimensions is discussed below. The single framework shown in Fig. 7.3 has been termed a super-cube or a superpolonium network by Ermer (1991); we remind the reader that Po is the only element to crystallize in a simple cubic structure. In this nomenclature the centres of the (OH)6 rings are the corners of the cubes and the p-phenylene groups are the cube edges; there is an appreciable trigonal distortion in {3(HQ) [C60]}. The cavities in such a single network ˚ , which is just the diameter of the C60 football. Simple mixing of have a diameter of 10 A quinol and C60 in 3 : 1 ratio in benzene and slow evaporation gave large (up to 7 mm in length), shiny black (dark brownish red in transmission) crystals of the 3 : 1 complex. Their structure (Fig. 7.4) is just as anticipated, but with remarkable additional detail. The C60 molecules are contained in a single network of the same type as found in -quinol but considerably distorted – for example, the hydrogen-bonded hexagons that are planar in -quinol are here almost as puckered as in cyclohexane (both have D3d symmetry, and bond and torsion angles are respectively 112.9 , 50.5 ({3(HQ) [C60]}) and 111.4 , 54.9 (C6H12)) and the cages are considerably elongated (compared to those in -quinol) in order to accommodate the fullerene guest. The stability of the complex, and its colour, are ascribed to charge transfer interactions between quinol as -donor and C60 as -acceptor. One cannot do better than quote Ermer : ‘‘The ‘giant’ C60 molecules enforcing the single host network . . . have a molecular mass 2.2 times larger than that of the three HQ molecules, and occupy 50% of the crystal volume. (HQ)3C60 represents one of the rare inclusion compounds with more guest than host . . . One is irresistibly reminded to a tropical snake devouring a prey of disproportionately larger cross-section than that of her (sic!) normally slim body . . . the question arises whether the labels ‘host’ and ‘guest’ should be reversed . . . ’’

5Å

5Å

Fig. 7.4. Ball-and-stick stereoview of the super-polonium architecture of {3(HQ) [C60]}. Note particularly the puckered rings of oxygen atoms and contrast these with the analogous planar rings in Figs. 7.2 and 7.3. (Reproduced from Ermer (1991).)

CL AT HRATE INCLUS ION COMP LEXES

330

Ermer (1991) found that the [C60] molecule was disordered in its enclosure, the molecular site symmetry being 2/m, and the details have now been studied further by determining the crystal structure at 100, 200, 293 and 373K (Blanc et al., 2000). No phase transition was detected over this range of temperatures. The most favourable orientation (a)

(b)

(c)

Fig. 7.5. Stereoviews of the three H-bonded quinol cages found in {4.5(HQ) [C70] [C6H6]}. The diagrams are all to the same scale. The H-bonds are shown as open sticks. (a) Twin peanut enclosure of two A type C70 molecules; (b) Single enclosure of B type C70 molecule; (c) Tetrahedral enclosure containing dimeric benzene sandwich. (Reproduced from Ermer and Ro¨bke (1993).)

DIRECTIONALLY BONDED HOSTS

c

o a

331

c

o

b

b

a

Fig. 7.6. A stereoscopic schematic representation of the H-bonded superoctahedral quinol host network of {4.5(HQ) [C70] [C6H6]}. The unit cell edges (O, a, b, c) are shown by thinner lines. The small spheres symbolize the (OH)6 rings (at their midpoints) acting as octahedral centres and the thick rods represent the HQ p-phenylene bridges. A twin cage (‘‘peanut’’) is shown on the left with its two A-type C70 guests and a single cage at the top with a single C70 guest. The tetrahedral cage containing the twin benzene sandwich is shown at center front. Single orientations of the actually disordered guest molecules are shown. (Reproduced from Ermer and Ro¨bke (1993).)

of [C60] with respect to the phenyl rings of HQ has [C60] C–C bonds pointing to the centres of the phenyl rings. However, this does not match the 3m symmetry of the cage, hence the orientational disorder. The remarkable {3(HQ).[C60]} structure is outshone by the even more remarkable {4.5(HQ) [C70] [C6H6]} structure. Mixing of quinol and C70 in 6 : 1 ratio in benzene and slow evaporation gave shiny black hexagonal plates, with a clear brownish red colour in transmission; crystal data are given in Table 7.1. Two C70 molecules are enclosed in the peanut shaped cavity shown in Fig. 7.5(a). One C70 molecule is in a medium-sized single cage (Fig. 7.5(b)) and two benzene molecules are in a tetrahedral cage (Fig. 7.5(c)), although this requires conﬁrmation. The combinatory arrangement of these three enclosures to give the crystal is shown in Fig. 7.6. The enclosing frameworks are made up of quinol molecules with their hydroxyl groups linked to form six-rings which are appreciably distorted from planarity. The basic structural principles employed in the simple -quinol clathrates are carried over to the two quinol-fullerene complexes, but with dramatic extensions. 7.2.1.2 Low temperature phase transitions in -quinol clathrates There are phase transitions on cooling in some -quinol clathrates (for summary see Parsonage and Staveley (1984, pp. 33–34) and also Matsuo and Suga (1984)). Thus {3(quinol) [HCN]} has a sharp peak in the Cp–T curve at 177.8 0.1K, with S 0.69 R corresponding to a disordering of two orientations (ln 2 ¼ 0.693) (Matsuo, Suga and Seki, 1970), and the {3(quinol) [0.95(H2S)]} complex a peak at 7.6K (the only one in the range 1–300K) (Ukegawa, Matsuo and Suga, 1985). The (calorimetrically determined) transitions in {3(quinol) [x(CH3OH)]} depend on composition and are absent for x5 *0.55; the temperatures of the transition are inversely dependent on composition, Tc ¼ 65.7, 61.0,

CL AT HRATE INCLUS ION COMP LEXES

332

54.4 and 44.4K for x ¼ 0.974, 0.897, 0.837 and 0.728 (Matsuo, 1970). Framework and guest behaviour in {3(quinol) [0.98(CH3OH)]} have been studied in considerable detail (Matsui, Terao and Saika, 1982) over the range 4.2–363K by a combination of 13C high resolution solid state NMR spectroscopy and measurements of T1 proton relaxation times (the sample composition was not given explicitly but has been inferred here from the Tc value of 67K); single crystals of size 3 5 10 mm were used. Above 67K a single and axially symmetric 13C chemical shift tensor was observed for the trapped methanol, showing that the molecules reorient themselves among three potential minima in the cavity. Analysis of the T1 results gave the motional parameters for the C3 reorientation as Ea ¼ 2.9 0.8 kJ/mol, t0 ¼ 3.7 1012 s, and for inversion about the centre of the cavity as Ea ¼ 10.0 0.4 kJ/mol, t0 ¼ 2.5 1014 s. Each 13C absorption line for both quinol and methanol splits into three below 67K, indicating that the methanol molecules ordered into six orientations while the symmetry of the quinol sublattice was reduced below R3. The directions and librational frequencies of the C–O bond axes were determined from the

TP

θ (degrees)

40 C-axis θ

C–O axis

θ

30

0

100

(a)

C-axis

1

2

200 T (K)

(b) 3

θ

300

C-axis

O θ

H

δ(CO)

C–O bond

P δ(Z)

6

5

4

H

C HH

Fig. 7.7. -{3(quinol).[CH3OH]} clathrate : (a) the temperature dependence of the angle between the c axis and the C–O bond direction of the guest methanol molecule; (b) details of the positioning of the methanol guest. (Reproduced from Matsui, Terao and Saika (1982).)

DIRECTIONALLY BONDED HOSTS

333

13

C methanol chemical shift tensor; ordering of the methanol dipoles, methyl tunneling and residual C3 reorientational motion were also investigated. The temperature dependence of the angle between the C–O bond of the methanol and the c-axis of the crystal is shown in Fig. 7.7. There is good agreement between these NMR results and room temperature X-ray diffraction results (Mak, 1982) which show that the C–O bond of the methanol is tilted by 35 from the c axis giving close contact with three of the oxygen atoms of the sixmembered OH ring; angles of 40 at 300K and 32 below 100K were deduced from dielectric susceptibility measurements (Ripmeester, Hawkins and Davidson, 1979). The structure below the phase transition is ferroelectric with the spontaneous polarization along the c axis (Murakami, Komukae, Osaka and Makita, 1990). Similar structural results were obtained for the HCl clathrate where the Cl atoms interact with the hydroxyl oxygens and the HCl molecule lies on a cone with its generator inclined at 33 to the c axis (Boeyens and Pretorius, 1977). However, spectroscopic, calorimetric and dielectric susceptibility measurements show a large degree of angular freedom of the guest down to the lowest temperatures (Matsui, Terao and Saika, 1982), so there appears to be a contradiction between the diffraction and other measurements. No phase transitions have been found in the HCl quinol clathrate in the range 1.5–300K. In the isomorphous SO2 clathrate there is also threefold disorder of the guest but only weak interaction with the framework. Here one set of dielectric constant measurements indicates a phase change at 40K (on cooling, there being some hysteresis) (Schneider, Tornau, Vlasova and Gurskas, 1985), but not another (Davidson, Davies, Gough, Leaist and Ripmeester, 1990). Having studied a variety of samples, the latter authors ‘‘emphasize the need for well-characterized, uniform samples if meaningful results are to be obtained and interpreted.’’ 7.2.1.3

Introduction to statistical thermodynamics of clathrate structures and application to the quinol clathrates We begin with a very simple physical model. Consider a crystalline molecular host framework containing empty cavities of one kind, and allow this to absorb a monatomic gaseous guest, with one molecule (atom) in each occupied cavity but not all cavities necessarily occupied; the guest molecules do not interact with one another. A solid solution is formed, the stability of which will be determined by the interplay of enthalpy and entropy, G ¼ H – TS having to be negative for the solid solution to be stable. A necessary requirement for formation of the solid solution is that the interaction between the molecules of the guest and the cavity walls should be exothermic (H negative). The entropy change is determined by a number of factors; there will be a large and negative contribution from the entropy difference between freely translating gas molecules and those conﬁned within the cavities. If the cavities are not completely ﬁlled then the negative change in translational entropy will be partially offset by a positive conﬁgurational entropy resulting from the distribution of gas molecules over the cavities. The equilibrium will be temperature and pressure dependent. This model is analogous to Langmuir’s model of monolayer gas adsorption on a solid surface (Berry, Rice and Ross, 1980), as was pointed out by van der Waals and Platteeuw (1959).

334

CL AT HRATE INCLUS ION COMP LEXES

This simpliﬁed model needs to be extended in the following ways: 1. 2. 3. 4.

5. 6.

The empty framework may not be stable with respect to the normal (pristine) crystalline form of the host material. The free energy of transformation must be included. The guests may distort the host framework. The host framework may have cavities of more than one kind, with different capacities to accommodate guest molecules. The guest molecules will not in general be monatomic and their orientations and librations within the cavities must be taken into account; in some clathrates more than one molecule may enter a particular cavity (but so far this has not been incorporated into the theory). The guest molecules in different cavities may interact, possibly in anisotropic fashion. Classical statistics is used in all treatments; this means that the results do not apply at low temperatures.

Earlier studies on the statistical thermodynamics of clathrate solid solutions (one type of cavity and one guest (van der Waals, 1956; van der Waals and Platteeuw, 1956); two types of cavity and one guest (Platteeuw and van der Waals, 1959); two types of cavity and different types of guest (Barrer and Stuart, 1957)) were consolidated by van der Waals and Platteeuw (1959) into a paper which remains the fundamental reference despite the elapse of more than forty years, and is distinguished by its clear exposition of the theory and its bringing together of theory and experiment. Other useful accounts are by Powell (1964) and Davidson (1973). Many of the earlier simplifying assumptions have been eliminated in a second wave of treatments from Dyadin and colleagues in Novosibirsk; we include only those available in English. Phase diagrams of clathrate solid solutions, taking guest-guest interactions into account, were calculated by Belosludov, Dyadin and Chekhova (1984) and Belosludov, Dyadin, Chekhova, Kolesov and Fadeev (1985) for quinol-noble gas systems. A related approach was taken by Schneider, Tornau, Vlasova and Gurskas (1985). A recent review is by Belosludov, Lavrentiev and Dyadin (1991). Application of the theory to clathrate hydrates has been made by Dyadin and Belosludov (1996). We ﬁrst consider experimental results for the -quinol clathrates, and then relate these to theory, followed by discussion of how the theories lead to calculation of the phase diagrams of these clathrate systems. Application to clathrate hydrates is given later after discussion of those structures. Formation of -quinol clathrate solid solution from the empty -quinol structure by addition of guest molecules is symbolized by the overall reaction: c þ (guest)g , c (solid solution)

ð7:1Þ

This can be divided into two stages: c (empty) ) c (empty)

ð7:2Þ

c (empty) þ (guest)g ) c (solid solution):

ð7:3Þ

Reaction (7.1) is an univariant equilibrium, the vapor pressure having a deﬁnite value at any particular temperature. The equilibrium composition of the -solid solution depends on temperature and pressure of guest and on the interaction between guest and quinol. Experimental investigation of these solid solutions is greatly complicated by kinetic

DIRECTIONALLY BONDED HOSTS

335

factors; for example, the quinol-argon clathrate has a dissociation pressure of 3.4 atm. at 298K but can be kept indeﬁnitely in a stoppered vial. Clearly argon atoms have difﬁculty in escaping from their cages. This leads to very slow attainment of equilibrium, a problem overcome by van der Waals and Platteeuw (1956) by addition to the system of a third component (a liquid whose vapour pressure was too low to affect the equilibria in the -quinol–(-quinol clathrate)–gas system and whose molecules were too large to be enclathrated), and by Barrer and Ruzicka (1962) by shaking the (quinol þ guest) mixture with small glass or steel balls, giving rapid equilibration even at 77K. It is convenient to express the reactions involved in a uniform and consistent manner so that numerical values of the thermodynamic quantities are directly comparable; each phase is enclosed in parentheses and followed by a descriptor. The reactions given above can be written more explicitly as 3fðHQÞgðc; formÞ þ qðMðgÞÞ ) f3ðHQÞ ½qðMÞ gðc; formÞ

ð7:1aÞ

fXððqÞð0ÞÞg: 3fðHQÞgðc; formÞ ) f3ðHQÞ ½0 gðc, empty formÞ fXðð0Þð0ÞÞg:

ð7:2aÞ

f3ðHQÞ ½0 gðc; formÞ þ qðMðgÞÞ ) f3ðHQÞ ½qðMÞ gðc; formÞ fXððqÞð0ÞÞg:

ð7:3aÞ

Here HQ ¼ quinol, M ¼ guest, q is the fraction of cavities occupied in general, 3 is the ratio of HQ molecules to cavities in the -quinol clathrate; q ¼ qc (the critical fraction of cavities occupied) at the three-phase invariant point (-HQ, -clathrate, gas M(g)); subscripts ‘‘c’’, ‘‘g’’, . . . represent crystal, gas, . . . The thermodynamic quantities pertaining to reaction (7.1a) are written as X((q)(0)), where X ¼ G, H, S, V and the ﬁrst-mentioned phase ((q)) is product and the second () reactant, i.e. X ¼ X(product) – X(reactant). When q ¼ 0 then we have X((0)(0)) for the transformation (HQ)c ) (HQ, empty)c (equation 7.2a). To avoid misunderstandings, we shall often explicitly state the number of moles of quinol or gas involved in particular reactions. It is often convenient to express the standard reaction as having all the cavities ﬁlled (i.e. q ¼ 1); thus one mole of guest would be the gaseous product of the decomposition reaction. We ﬁrst consider the measurement of the thermodynamic quantities pertaining to the empty - and -quinol frameworks, and then the interaction of guest with -quinol. The enthalpy of the transformation c ) c has been derived from the difference in the enthalpies of solution of - and (empty) -quinol measured directly in a twin calorimeter (Evans and Richards, 1952), and also by using -quinol clathrates with a range of guest concentrations, prepared by using different pressures of the gaseous guest. H((q)(0)) was then obtained by extrapolating to zero guest concentration (Fig. 7.8). H((q)(0)) is a linear function of q when the guests are small molecules such as Ar and O2 (Evans and Richards, 1954). The direct and extrapolation methods gave H((0)(0)) ¼ 0.54(13) and 0.88 kJ/mol quinol respectively. Parsonage and Staveley (1960) give 0.80 kJ/mol quinol from extrapolation of enthalpy of solution measurements of methane clathrates of different compositions.

CL AT HRATE INCLUS ION COMP LEXES

336

30.0 25.0

–∆H (kJ)

20.0 15.0 10.0 5.0 qc = 0.34 0.0 –5.0 0

0.2

0.4 0.6 q (mol guest)

0.8

1

Fig. 7.8. Values of enthalpy of formation H((q)(0)) (equation (7.1a); i.e for 3 mols quinol) measured by Evans and Richards (1954) at 298K for -quinol clathrates of Ar (open and ﬁlled circles) and O2 (crosses). The slope gives H((1)(0)) and the intercept H((0)(0)). The equation of the best straight line through all the points is H (kJ/mol guest) ¼ 24.79q–2.65 (R2 ¼ 0.9953). We have here ignored the possibility, considered by Evans and Richards, that slope and intercept depend on the nature of the Ar or O2 guest. However, the values for the methane clathrate (small dots enclosed in ellipses) (Parsonage and Staveley, 1960) show that H((1)(0)) does vary for different guests. The value for the krypton clathrate (q ¼ 1) is 24(3) kJ/mol (differential calorimeter; Grey, Parsonage and Staveley, 1962)) and provides supporting evidence in the same direction.

The free energy G((0)(0)) (¼G – G) of the c ) c transformation can be derived (van der Waals and Platteeuw, 1959; Deming, Carlisle, Lauerman, Muckerman, Muirhead and Child, 1969) from measurements at various temperatures of the dissociation pressure and values of qc at the three-phase invariant point 3 3 fHQ ½M gðs; formÞ ¼ HQðs; formÞ þ MðgÞ; qc qc the symbols being deﬁned above. The theory of ideal solid solutions (van der Waals and Platteeuw, 1959) gives the following relationships: 1 Gðð0Þð0ÞÞ ¼ ½RT lnð1 qc Þ

3 Hðð0Þð0ÞÞ þC Gðð0Þð0ÞÞ ¼ RT

at a particular temperature; for measurements made at a number of temperatures.

Van der Waals and Platteeuw (1959) measured qc (¼0.34, irrespective of the nature of the guest) for clathrates with the small molecule guests Ar and Kr and found

DIRECTIONALLY BONDED HOSTS

337

G((0)(0)) ¼ 343 J/mol quinol. Combining this with the mean of the earlier values of H((0)(0)) (710 J/mol quinol) gives S((0)(0)) ¼ 1.23 J/K mol quinol. Neither enthalpy nor entropy values are expected to be markedly temperature dependent. -Quinol is enthalpy stabilized with respect to (empty) -quinol at 298K; all the evidence suggests that these two polymorphs are monotropically related. Deming et al. (1969) have made measurements of qc and dissociation pressures over a range of temperatures for methane (10–26 C) and methyl ﬂuoride (25–50 C) clathrates (Table 7.3). It has been suggested that the values of H((0)(0)) increase with guest size because of distortion of the -framework but cell dimensions do not support this suggestion; for example, the cell dimensions of the empty -quinol clathrate and that containing 0.87Xe ˚ , V(per quinol) ¼ 145.3 (146.6) A ˚ 3. as guest are a ¼ 16.613 (16.610), c ¼ 5.474 (5.524) A Cell dimensions (Table 7.1) hardly differ for the H2S (R3) and CH3OH and HCl (both R3) clathrates but there are more substantial changes for the SO2 (R3) and, especially, CH3CN (P3) clathrates. A measurement of H((0)(0)) for the latter by the extrapolation method would be very interesting. Comparison of speciﬁc heats for (empty) - and -quinol would give direct values for H((0)(0)) and S((0)(0)). S(298) for 1 mol of (empty) -quinol is 140 J/K (from Cp measurements on argon (Parsonage and Staveley, 1959) and methane (Parsonage and Staveley, 1960) clathrates of different concentrations and extrapolation to q ¼ 0); the two derived curves agree within 5% and the entropies at 298K agree well (139.2 and 140.0 J/K per mole of -quinol respectively; Parsonage and Staveley, 1960). Measurements for -quinol do not appear to have been made; it seems unlikely that the precision would be greater than that of the values given in Table 7.2. We have paid some attention to the thermodynamics of the - and the -quinol polymorphs because this seems to be the only example where the empty clathrate framework has been isolated and subjected to measurement. The parameters deﬁning the relative stability of the two polymorphs are fundamental to understanding the stability of the overall clathrate system. The available results for quinol do not appear to be very accurate, possibly due to difﬁculties in producing suitable samples. Evans and Richards (1954) considered the free energy of formation (G ¼ H – TS) of the -clathrates in terms of the enthalpy and entropy of the reaction {-3(quinol)} þ Mgas ¼ {-(3(quinol)) [M]}. The H values in Table 7.3 range from 20 to 55 kJ/mol. If the -quinol framework is undisturbed on formation of the

Table 7.2. Summary of reported values (for 1 mol of quinol) of thermodynamic parameters for X((0)(0)). The units of G and H are kJ/mol and for S J/K mol Clathrate Empty polymorphs (Type I) Ar and oxygen (Type I) CH4 (Type I) CH3F (Type II)

H((0)(0))

G((0)(0))

S((0)(0))

1

0.54(12) 0.71 (Ar)2; 0.77(O2)2 0.213(109)3; 0.504 0.586(180)3

0.3475 0.410(4)3 0.444(12)3

1.761 0.67(38)3 0.46(67)3

References: (1) Evans and Richards, 1952; (2) Evans and Richards, 1954; (3) Deming et al., 1969; the large errors are ascribed to the narrow temperature ranges used; (4) Parsonage and Staveley, 1960; (5) Child, 1964b.

338

CL AT HRATE INCLUS ION COMP LEXES

Table 7.3. Values of thermodynamic parameters X((1)(0)) for the formation of -quinol clathrates. The units of G and H are kJ/mol and for S J/K mol. The values for X((1)(0)) are for 3 mols quinol and 1 mol guest; this is equation 7.3a, with q ¼ 1. Only clathrates that have been classified crystallographically have been included in this table Guest Type I Ar Kr Xe CH4 oxygen nitrogen HCOOH CO2 H2S C2H2 Type II CH3F CH3OH SO2 HCl

qc (298K)

H((1)(0))

S((1)(0))

0.345 0.345

25.11 23.3(33)3 40.66 29.2(3)2 23.11 24.31 51.01 55.64 43.54 39.74

84

38.52 461 (approximate) 43.54 38.51

1012

0.392

0.422 0.475

Type III CH3CN

31.44

Others HBr

42.71

862

(1) Evans and Richards, 1954; (2) Deming et al., 1969; (3) Grey, Parsonage and Staveley, 1961; (4) McAdie, 1963, 1966; van der Waals and Platteeuw, 1959; (6) Allison and Barrer, 1968.

clathrate, then S will be equal to the difference in the entropy of the guest molecules M in the gas phase and in the clathrate. In general this will be large and negative, e.g. the translational entropy of HCl gas is 153.6 J/mol K at 298K, corresponding to TS of 45.8 kJ/mol; the actual value will be somewhat larger (less negative) because of residual entropy due to libration and disorder of HCl within the cavity and, if the cavities are not all ﬁlled, the contribution of the conﬁgurational entropy. Thus it is clear that the enthalpy and entropy contributions to G are opposed and G will be expected to be small. It has been reported that reversible vapor pressures are obtained on heating SO2 and CH3OH clathrates; the derived free energies were small (Wynne-Jones and Anderson, 1952). Values of H((1)(0)) of 59 and 38 kJ/mol were obtained from plots of ln p against 1/T; the latter agrees reasonably well with the corresponding value in Table 7.3. Measurements have been made of speciﬁc heats of the -quinol clathrates of Ar (Parsonage and Staveley, 1959), CH4 (Parsonage and Staveley, 1960), Kr (Grey, Parsonage and Staveley, 1961), and CO, N2 and O2 (Grey and Staveley, 1963–4). Subtraction of the contribution of the empty -quinol framework (Parsonage and Staveley, 1960) gave the enthalpy contributions of the guests as a function of temperature (Fig. 7.9). Cp of empty -quinol is about 420 J/3 mol quinol deg., so the contributions of one mole of

DIRECTIONALLY BONDED HOSTS

339

guest is only a few percent of the measured Cp and cannot be expected to be highly precise. The resemblance in the curves for nitrogen and CO should also be noted; this is not the ﬁrst example of similarities in behavior of these two gases. The differences among the partial speciﬁc heat curves reﬂect differences in the modes of guest motion in the cavities over the temperature range. The curves are usually interpreted in terms of the cell model, where it is assumed that the motion of the guest is entirely decoupled from that of the host framework. While this may be a reasonable assumption for the lighter guests, it does not apply to heavier guests such as Kr. Here 83Kr Mo¨ssbauer measurements by Hazony and Ruby (1968) have been interpreted in terms of rattling of the guest atoms within the cages, and modiﬁcation of the dynamics of the framework because of the coupling to the Kr guests. Measurement of the properties of the empty frameworks of clathrates and of their interaction with guests is generally not feasible as crystals cannot be obtained; as noted above, the quinol-guest system is the exception rather than the rule. Thus it is important to develop methods of calculating the required properties. As a ﬁrst step in this direction, the AMBER force ﬁeld (developed by Weiner, Kollman, Nguyen and Case, 1986) was used by Zubkus, Shamovsky and Tornau (1992) to perform empirical force ﬁeld calculations of the interaction of the -quinol clathrate framework with 27 different gases; use of the CVFF force ﬁeld was also studied but the results were less satisfactory and will not be considered here. The -quinol clathrate structure was assumed throughout to be Type I; as the results cited in Table 7.1 show, this is an oversimpliﬁcation, at least for CH3OH, HCl and CH3CN of the guests considered. The total energy of the crystal was equal to the potential energy which includes allowance for bond stretching, angle bending, torsional distortion, out of plane bending, van der 100

200

300

40 CO

CP J/mole gas K

40 N2

30 30

O2 20 Kr 0

100

200 T (K)

300

Fig. 7.9. Cp values for one mol of guest in -quinol clathrates; data from references in the text. Lines are guides to the eye; note the shifts along the ordinate. The values (not shown) for Ar are similar to those for Kr, and those for methane to those for oxygen.

CL AT HRATE INCLUS ION COMP LEXES

340

Calculated ∆H( (0)(1)) kJ/mol guest

80 SO2

70 CH3OH

60 50 N2

40 O2

30

CH4

20 10 0 0

10 20 30 40 50 60 Measured ∆H((0)(1)) kJ/mol guest

70

Fig. 7.10. Comparison of measured and calculated (Zubkus, Shamovsky and Tornau, 1992) values of H((0)(1)) for some quinol clathrates. Note that these values are endothermic and refer to the decomposition reaction.

Waals interactions (Lennard-Jones 6-12 potential), electrostatic interactions and hydrogen bonding. Comparisons of observed and calculated interaction energies (Fig. 7.10) and unit cell dimensions were made. The interaction energies agree reasonably well, although calculated values are systematically some 8 kJ/mol higher than observed values. The measured and calculated values for the cell dimensions of the empty -quinol ˚ ), structure do not agree well (a ¼ 16.61 (meas), 16.44 (calc); c ¼ 5.47 (meas), 5.73 (calc) A and there is no correlation (not shown) of the measured and calculated deviations from these separate baseline values. The value of the inclination angle between c axis and O . . . O vector of the -quinol molecule was also calculated; Palin and Powellp(1948) have shown, assuming standard molecular dimensions, that 5.5(1 þ cos ) ¼ a/ 3 and 5.5 sin ¼ (2/3)c. Thus is not independent of the cell dimensions. Orientations of the guest molecules within the cavities were also calculated but here experimental values are lacking for comparison. Child (1964a) has discussed the values of the enthalpies and entropies of dissociation of the quinol clathrates compared to those of vaporization of the liquid guests at their boiling points. We ﬁrst consider enthalpies, shown in Fig. 7.11. The relationship is H((1)(0)) ¼ 1.85H(vap) þ 11.91 (R2 ¼ 0.9591). Methanol is clearly anomalous, perhaps due to strong hydrogen bonding in the liquid phase. Child inferred that H((1)(0)) 2H(vap) and suggested that vaporization of a liquid could be envisaged as occurring in two hypothetical steps in which removal of 1 mole of liquid and simultaneous creation of 1 mole of holes is accompanied by an enthalpy increase of 2H(vap) (offset by an enthalpy decrease of –H(vap) when the holes collapse to give a normal liquid). In the clathrate the holes remain. Details of the interaction between guest and framework molecules would have to be taken into account in a quantitative explanation and this has been done in the results summarized in Fig. 7.11.

DIRECTIONALLY BONDED HOSTS

341

70

∆H( (0)(1)) kJ/mol

60 50 40 CH3OH 30 20 10 0 0

10

20 ∆H(Vap) kJ/mol

30

40

Fig. 7.11. H((0)(1)) versus H(vap), units of kJ/mol. H(vap) refers to liquid guest at boiling point. From left to right along the abscissa, the ﬁlled circles are for Ar, Kr, N2, O2, SO2, CH4, HCl, HBr, HCOOH; CH3OH was not included in determining the straight line.

The entropies of vaporization of nonassociated liquids (molecular weights 100) are 100 J/mol K; this is Trouton’s rule, ﬁrst proposed in 1884. Child (1964a) has pointed out that the values of S((1)(0)) are not very different for the quinol clathrates with small molecule guests noted in Fig. 7.11 and Table 7.3 (it does not matter much whether equation (7.1a) or (7.3a) is used as S((0)(0)) 5 J/3 mol quinol K). This leads to the important conclusion that the clathrates are not entropy-stabilized. The entropy change corresponding to the inverse of equation (7.1a) (i.e. dissociation), normalized to 1 mole of gaseous guest, has been shown (Child, 1964b) to be Sðð0ÞðqÞÞ ¼ R lnðV=Vf Þ RTð@ ln Vf =@TÞv þ R þ R ln q þ Rðð1 qÞ=qÞ lnð1 qÞ

ð7:4Þ

under the conditions that there are only dispersion and repulsion terms in the host-guest interaction; V is the molar volume of gaseous guest in the standard state, Vf is the ‘‘free’’ volume per mole in the clathrate and is a measure of the empty space in the cavities, and q is the fraction of cavities occupied. The ﬁrst term on the right hand side of equation (7.4) is the increase in entropy on expanding a gas from Vf to V; the second term is related to the departure of the host-guest potential from a square well; R derives from the communal entropy of the gas molecules which the enclathrated guest molecules do not have; the last two terms give the negative of the conﬁgurational entropy, Sc, of the clathrate. For the Ar clathrate, qc ¼ 0.34 and Sc ¼ 15.6 J/mol K. Thus we can estimate S((0)(q)) 80.8 þ 0 þ 8.3 – 15.6 73.5 J/mol K (we have used V ¼ 22.4 l and Vf ¼ 1.29 cm3). This is in reasonable agreement with the measured value (84 J/mol K (Table 7.3)) and the entropy of vaporization of Ar (S(vap) ¼ H(vap)/Tb ¼ 6530/87.3 ¼ 74.8 J/mol K). The major problem with this calculation comes from the uncertainty in estimating the appropriate value of Vf.

342

CL AT HRATE INCLUS ION COMP LEXES

We now move on to the problem of calculating the phase diagram of the quinol–guest systems. The theory is ﬁrst set out in a rather general form and will then be particularized for the quinol clathrate system; this is essentially an abbreviated version of the presentation of Belosludov, Dyadin, Chekhova and Fadeev (1984). In the i phase (i ¼ , , ) the chemical potentials of host component (Q) and guest (G) are given by 2 iQ ¼ 0i Q þ i ½kT lnð1 yi Þ 1=2yi Ui

ð7:5Þ

i þ kT ln½ yi ð1 þ Si Þ=2hi ð1 yi Þ

i ¼ yi U

ð7:6Þ

where 0i Q is the chemical potential of the (empty) host framework in the i phase; i is the number of cavities of type i per host molecule Q ( ¼ 1/18 for -quinol, 1/3 for -quinol, 1/23 and 3/23 for the two types of cavity in the Type I gas hydrate, 2/17 and 1/17 for the two type of cavity in the Type II gas hydrate); yi is the fractional degree of ﬁlling of the cavities by the guest molecules (0 yi 1); 1/2Ui is the dispersion interaction energy between guest molecules in the cavities; 1/2UiD is the dipolar interaction energy between guest molecules in the cavities, with the guest molecules all oriented (in one of two opposite directions) along some common axis; i ¼ Ui þ Si UiD ; Ui ¼ Ui þ S2i UiD ; U hi ¼ 2a3i giØi (T) exp[–Wi(0)/kT], where ai is the radius of the cavity, Wi(0) is the potential energy of the guest molecule in the cavity of the host framework (the host–guest interaction); 2a3i gi/V is the ratio of the free volume of the guest molecule in the i cavity to its molecular volume in the gas phase; Øi ðTÞ ¼ ð2m kT=h2 Þ3=2 j ðTÞ where m is the mass of the guest molecule and j(T) is its internal partition function (Øi (T) is the molecular partition function of the gaseous guest, with the volume factor removed); D S1 i ln½ð1 þ Si Þ ¼ 2yi Ui =kT½ð1 þ Si Þ=ð1 Si Þ ; Si being the order parameter in the i phase. In order to simplify the representation of the three variables (P, T, concentration (xi ¼ iyi/ (1 þ iyi)) governing the behaviour of a two component system (host plus guest1), the vapor pressure is plotted against temperature for all the possible states with three phases in equilibrium. Application of the phase rule (F ¼ C – P þ 2 ¼ 2 – 3 þ 2 ¼ 1) shows that the system will have a deﬁnite vapor pressure at every temperature and hence the data can be plotted on a two-dimensional diagram. A clear discussion is given by Glasstone (1947) for the Na2SO4–H2O system. The three-phase curves meet at a point, the quadruple point (P0, T0), where all four phases are in equilibrium, i.e. the chemical potentials of the host component in the four phases are all equal, and those of the guest component are all equal, i.e. Q ¼ Q ¼ Q ¼ G Q;

¼ ¼ ¼ G :

ð7:7Þ

The chemical potentials of the components in the gas phase (total pressure P) and their partial pressures are governed by the ideal gas laws. The equations governing these parameters together with equations (7.5) and (7.6) are inserted in (7.7) and give a group of 1

We consider only one kind of guest but generalization to many kinds has been included in some treatments.

DIRECTIONALLY BONDED HOSTS

343

six transcendental equations in y, y, y , xG, P, T, which have to be solved in order to calculate the phase diagram of the system. This is discussed in some detail by Belosludov et al. (1985) but will not be considered here. The present problem is ﬁrst to calculate P0 and T0, and then the three-phase curves for the quinol-noble gas system, where certain approximations are permissible (e.g. the guests are not dipoles so UiD ¼ 0; the phase is liquid quinol, in which the guest has negligible solubility; in the vapor phase the guest behaves as an ideal gas, while the host has zero partial pressure; the guest–host interactions in the - and -phases are the same; the guest– guest interaction is neglected here but its inﬂuence was considered later). Thus g g ¼ g; W W ¼ W and hence h ¼ h; y y ¼ y; Ø (T) ¼ Ø (T) ¼ ØG (T). Following Belosludov et al. (1984) the parameters of the quadruple point are (to a ﬁrst approximation): y0 ¼ 1 exp½0 ðÞðÞ=ð ÞkT

T0 ¼ Tm f1 þ ½ 0 ðÞðÞ=ð Þ =HmL g (subscript ‘‘m’’ refers to melting point) P0 ¼

kT0 y0 expðW=kTÞ: 3 2a g ð1 y0 Þ

The approximate expressions for y0 and T0 do not contain parameters dependent on the nature of the guest, while the changes caused by using the full equations are very small. Belosludov et al. (1984) give values for y0 varying between 0.398 and 0.401 for the guests Ar, Kr, Xe, N2, O2, CH4 (all nonpolar) and HCl (dipolar). Similarly T0 lies between 446.7 and 448.9K for the same guests (Tm ¼ 445.46K). This constancy does not hold for P0, which is dependent on the nature of the guest through a, g and W. A convenient parameter for assessing the guest dependence of P0 is the Lennard-Jones–Devonshire ", where the interaction between two atoms separated by R is given by u(R) ¼ 4"{(/R)12 – (/R)6}; the parameter is the distance for which u(R) ¼ 0 and " is the value of u(R) at its minimum (R ¼ 21/6). The P0–" relationship is shown in Fig. 7.12. There is reasonably good agreement between calculated and measured values of P0 (Kr 15.2 (calc), 13.8 atm (meas); Xe 5.57, 5.8); obviously experimental tests of theory will proceed more sensitively through P0 than through y0 and T0. Phase diagrams for quinol-xenon are shown in Figs. 7.13 and 7.14. The phase diagrams for quinol-krypton (Dyadin, Chekhova and Sokolova, 1987) and quinol-argon (van der Waals and Platteeuw, 1959) are qualitatively similar, but quantitatively different. The equilibrium concentration of methanol in -quinol/methanol at 298K is 0.49 instead of 0.34, as calculated for the noble gas clathrates, and this has been ascribed to a larger value of ((0)(0)) consequent on distortion of the cavities by the larger methanol molecules. However, this has been disputed by Belosludov, Dyadin, Chekhova and Fadeev (1984), who point out that the measured distortions of the cavities are often small (see Table 7.1). Instead they suggest that it is guest-guest interaction which causes the increase in the value of ((0)(0)); a model calculation using the Lennard-Jones–Devonshire formula for Xe completely ﬁlling the cavities gives 1/2U ¼ 1200 J mol1. The matter is somewhat controversial as this approach requires that the absolute value of H((0)(0)) is not more than 40–60 J mol1, whereas direct measurement gives 883 J (mol quinol)1.

CL AT HRATE INCLUS ION COMP LEXES

344

90 N2

80 70

P0(atm)

60 Ar

50

O2

40 30 CH4 20 Kr Xe

10

HCl

0 0

100

200 ε (K)

300

400

Fig. 7.12. The variation of the calculated quadruple point pressure P0 with the Lennard-Jones parameter ". (data from Table 1 of Belosludov et al. (1984).)

450 b – L– G

a–b–L

T (K)

a–L–G quadruple point

445

a–b–G

metastable 440 0

5

10

15

P, atm.

Fig. 7.13. P–T phase diagram for the quinol–xenon system. The continuous lines show results of calculations for the stable three-phase equilibria, and the dashed lines the metastable equilibria. The dots show the experimental results of Kazankin, Palladiev and Troﬁmov, 1972. (Reproduced from Belosludov et al. (1991).)

DIRECTIONALLY BONDED HOSTS

T = 298 K

345

P = 5 atm

P atm

TK 446.6 440.8

4 420

a

2

b

380

a

b

0.075 0

x nα 0.1

0.2 x nβ

0 x nα 0.1

0.2 x nβ

Fig. 7.14. An isobaric and an isothermal section of the P–T–x phase diagram for the quinol–xenon system. The broken vertical lines show the concentrations of xenon for the hypothetical situations where the cavities in the - and -quinol phases are completely ﬁlled. (Adapted from Belosludov, Dyadin, Chekhova and Fadeev (1984).)

7.2.2 Crystal structure of {(6H2O [hexamethylene tetramine]} The hydrogen bonded hexagon with alternate molecules pointing up and down is an important motif in many clathrate structures to be described later; it is found in the clathrates of phenol and of Dianin’s compound and has been used in the design of the hexa-host clathrate forming molecules (Section 7.5) (MacNicol, 1984b); it is also found in the ice-I (disordered protons) and ice-II (ordered protons) structures. We note here one speciﬁc example where the host molecules are water and form a framework analogous to one of the frameworks in the quinol clathrates. The guest is hexamethylene tetramine [HMT; (CH2)6N4] which is unusual in that its solubility in water increases with decreasing temperature, a property shared with some other tertiary amines and explained in terms of an increasing association with water at lower temperatures. The existence of a crystalline hexahydrate decomposing at about 13.5 C has been known for many years (Cambier and Brochet, 1895; Delepine, 1895, 1897). The crystals are ˚ , c ¼ 8.670 A ˚ R3m, Z ¼ 3; Mak, 1965; HXMTHT) and the rhombohedral (a ¼ 11.620 A structural framework is based on a slightly-puckered ring of hydrogen-bonded water molecules with the mean ring plane parallel to (0001). These rings then form hexagonal cages by being stacked one above the other, separated by the hexagonal c spacing; neighbouring columns are staggered in the [0001] direction, in accordance with the rhombohedral symmetry. The host framework is then completed by cross-linkage of neighboring columns by hydrogen bonds (Fig. 7.15), giving rise to to an arrangement equivalent to that of a single framework in the -quinol structure, each benzene ring there (Fig. 7.2) being replaced here by an hydrogen bond; one proton of each water molecule is disordered over two sites. The HMT molecules occupy cavities in the water framework, each guest molecule being suspended ‘‘bat like’’ (in Mak’s vivid phrase) from the upper walls of the cavity. This material is classiﬁed as a semi-clathrate hydrate (see Section 7.2.4 below) because the

CL AT HRATE INCLUS ION COMP LEXES

346

C

2

2

1 2

1 2

2

1

2

1 2

1 1

2

1 1

1

1 H(4)

2 2

C C N C N N

1

1

C

C 1 1

2

1 1

1

C

N

2

2

1

2 2

1

2 2

1 b

2 2

1

2

1

O(1) 1 2

2 2

O(2) 2

1

a

Fig. 7.15. Perspective drawing of the crystal structure of HMT hexahydrate. The eight (H2O)6 rings that form the immediate surroundings of a guest molecule are shown. Hydrogen atoms, except those in the H-bonds to HMT, are omitted for clarity. The axes are of the triply primitive hexagonal cell; c is along [111] of the rhombohedral cell. Note that only three of the four N atoms of HMT act as H-bond acceptors. (Reproduced from Mak (1965).)

guest molecule is hydrogen bonded to the water framework. Isostructural complexes are unlikely to be formed because of the speciﬁc geometry required in this structure. 7.2.3

Clathrates derived from existing structures

In general, existing structures are too closely packed to be able to accommodate guest molecules. However, one may envisage exceptions to this rule if the guest molecules are very small or if the host frameworks are very extended. The clathrates would then be primary solid solutions. Helium hexahydrate constitutes a true example of the ﬁrst type and Cd(CN)2 clathrates quasi-examples of the second type. 7.2.3.1

Helium hexahydrate

Helium, which is too small to form a stable Type I or II gas hydrate (see below), forms an hydrate of ideal composition {6H2O [He]} under pressure (62% occupancy at 0.29 GPa, 79% at 0.47 GPa) (Londono, Kuhs and Finney, 1988; Londono, Finney and Kuhs, 1992). The crystal structure was determined by powder neutron diffraction at 195K (and the ˚ , space pressures noted) and shown to be rhombohedral, a ¼ 12.934(1), c ¼ 6.216(1) A group R 3. This is the structure of ice II, with ordered hydrogens in the H-bonds; the He atoms are enclosed between the six-membered rings of water molecules (Fig. 7.16). It is

DIRECTIONALLY BONDED HOSTS

347

Fig. 7.16. Structure of {6H2O [xHe]} showing the He atoms occupying sites approximately halfway between the two types of six-membered ring in the ice-II structure. The two types of crystallographically independent water molecule are shown in black and white respectively. The rhombohedral [111] axis is horizontal (diagram by SCHAKAL, written by E. Keller, University of Freiburg, FRG). (Reproduced from Londono, Kuhs and Finney (1988).)

considered a true example because it is derived from an existing structure. In terms of the phase rule, this is a primary solid solution of helium in ice II. The dependence of occupancy ( He) on pressure follows ideal solution behaviour

He ¼

CHe PHe 1 þ CHe PHe

where CHe is the Langmuir constant (¼ 0.07(1) GPa1) and PHe is the helium fugacity. The Ih (ordinary ice) structure can accommodate H2, He or Ne in solid solution under pressure, and phase diagrams have been calculated (Dyadin and Belosludov, 1996). No structural work appears to have been carried out. 7.2.3.2 Cadmium cyanide clathrates Cd(CN)2 is a prototype for the formation of tetrahedral arrangements analogous to those formed by other ABn (n ¼ 0, 2) moieties in which there is a tetrahedral disposition of bonds about A and the B groups can form linear (or quasi-linear) links in both directions; examples of ABn to be encountered later are Si, Ge, OH2 and SiO2 Cd(CN)2 itself has an anticuprite structure in which there are two identical interpenetrating but not-linked diamond-type networks (more accurately -cristobalite-type networks). If one of these networks is removed then a single network with adamantane-like cavities is formed (Fig. 7.17). These cavities are occupied, in a series of isomorphous cubic crystals, by a variety of hydrocarbon and halocarbon molecules such as CHCl3, CH3CHCl2, ˚ ; SAJREA), C2H5CHClCH3, CHCl2CHCl2, CH3CCl3, CHCl2CHCl2 (a ¼ 12.691(2) A ˚ ; SAJRIE) and methylcyclohexane (Kitazawa, CClF2CCl2F, cyclohexane (a ¼ 12.685(2) A Nishikiori, Kuroda and Iwamoto, 1988). Although the crystals lose guest fairly easily at room temperature, the structure of {Cd(CN)2 [CCl4]} could be determined at ˚ , Z ¼ 8, space group Fd 300K (a ¼ 12.668(2) A 3m; SAJRAW); the CCl4 molecules are

348

CL AT HRATE INCLUS ION COMP LEXES

Fig. 7.17. Structure of {Cd(CN)2 [CCl4]}, showing only the Cd(CN)2 framework; the origin has been shifted by 1/4 along each of three cube-axis directions. The adamantane-like cage is shown by the solid lines; the large circles are Cd and the small circles C or N. (Reproduced from Kitazawa, Nishikiori, Kuroda and Iwamoto, (1988).)

disordered in the cavities. This is considered to be a quasi-example as the single-network Cd(CN)2 structure does not exist. ˚ ; the isostructural Zn(CN)2, with a Zn–CN–Zn The Cd–CN–Cd span length is 5.485 A ˚ span length of 5.12 A does not give analogous clathrates. More complicated structural frameworks based on the Cd(CN)2 network have been synthesized (Abrahams, Hoskins, Liu and Robson, 1991) but these are beyond the scope of this book. 7.2.4

Overview of the polyhedral clathrates (including metalloid structures, clathrasils, gas hydrates, clathrate and semiclathrate hydrates)

7.2.4.1 Historical and general introduction The ﬁrst gas hydrate encountered seems to have been that of SO2 – Joseph Priestley noticed in 1777–8 that the ‘‘ice’’ formed by cooling aqueous solutions of SO2 sank; this anomalous ice was analyzed as SO2 10H2O some ﬁfty years later (La Rive, 1829). The compound H2SO3 6H2O is now described as the gas hydrate SO2 7H2O in a well known textbook of inorganic chemistry (Cotton and Wilkinson, 1980). Early characterizations of chlorine hydrate as solid chlorine by Pelletier in 1785 and Carsten in 1786 were shown to be wrong by Davy (1811), who obtained the solid hydrate by bubbling chlorine gas into cold water. The hydrate was analysed as Cl2 10H2O by Faraday (1823) and more accurately later, as discussed below (historical references in Chapter 2). Bromine hydrate was reported in 1829 by Lo¨wig but without an analysis; in fact, four hydrates had

DIRECTIONALLY BONDED HOSTS

349

been thought to have been identiﬁed over the years, with 12, 10, 8.6 and 7 molecules of H2O for each Br2 (Dyadin and Belosludov, 1996), but it has now been shown that there is only one bromine hydrate (Section 7.2.7.4). Many other gas hydrates were prepared in the period between 1880 and 1925, principally by de Forcrand and Villard; for example, argon hydrate was reported within one year of the discovery of argon (Villard, 1896, 1897). The historical background up to about 1925 has been summarised by Schroeder (1926). However, the nature of the gas hydrates was clariﬁed only in the early 1950s by model building studies (Claussen, 1951) and crystal structure analyses of key compounds by von Stackelberg and coworkers, and Pauling and Marsh (1952). Many of the earlier crystallographic studies were carried out by von Stackelberg and his school (1949, 1954), following their still earlier preparative and thermodynamic studies; we do not discuss these results in detail but note that the structure of the SO2 gas hydrate was determined in 1942 by H. Fru¨hbuss (Dissertation, Bonn) and that of the double hydrate of CHCl3 and H2S by J. Pieutuchowsky in 1941 (Diplomarbeit, Bonn). Hydrates of methane and other constituents of natural gas (Makogon, 1974, 1987; Cox, 1983; Sloan, 1998) have caused occasional problems in pipelines by forming solid deposits at unexpectedly high temperatures (Fig. 7.18). More importantly, such deposits have been discovered in nature (Chersky, Makogon and Medovski, 1970), in permafrost regions of the Arctic on land and on continental slopes and rises offshore; for example, the Deep Sea Drilling Project off the Paciﬁc Coast of Guatemala found the zone from 1926 to 1955 metres to consist almost entirely of solid gas hydrate. Some twenty ﬁve sites had been identiﬁed by 1980 (Kvenvolden and McMenamin, 1980). Some estimates of the worldwide reservoir are as high as 1.5 1018m3, large enough to suggest that natural gas hydrates form a potential energy source (Chersky, Makogon and Medovski, 1970; Pearson, Halleck, McGuire, Hermes and Wright, 1983; Katz, 1971a,b; Byk, Makogon and Fomina, 1980; Kvenvolden, 1994). Interest continues, as news items entitled Fire and Ice Under the Deep Sea Floor (Appenzeller, 1991) and Fire from Ice (Adam, 2002) attest. Pressure is an important variable in gas hydrate chemistry but not considered here because of space limitations; a leading reference is Kuhs (2004). Metalloid analogs to the gas hydrates, exempliﬁed by compositions such as K8Ge46, were ﬁrst reported in 1965 (Kasper, Hagenmuller, Pouchard and Gros, 1965), when the resemblance between the structure of the rare mineral melanophlogite and those of the gas hydrates was also recognized (Kamb, 1965). This led somewhat later to the development of a structurally related group of silica-based compounds, the clathrasils (Gies, Liebau and Gerke, 1982; Gies, 1991; Gies and Marler, 1996). The analogy between H2O and SiO2 based structures is, of course, well known; for example, hexagonal ice Ih is isostructural with -tridymite and cubic ice Ic with -cristobalite. There had been parallel advances in apparently unrelated ﬁelds. Alkylamine hydrates, some of which contained surprisingly large numbers of water molecules, had been studied by Pickering (1893) by phase diagrams and reinvestigated (in part) later (Somerville, 1931), while polyhydrates of many peralkylammonium salts had been prepared (Fowler, Loebenstein, Pall and Kraus, 1940). The structural inter-relations between these two groups of compounds and the gas hydrates were only revealed by the extensive crystallographic studies of Jeffrey2 and coworkers. Much work, especially on the hydrates of 2

George A. Jeffrey 1915–2000.

350

CL AT HRATE INCLUS ION COMP LEXES

Fig. 7.18. A huge pillar of solidiﬁed (natural) gas hydrate produced in a methane pipeline rupture under below-zero (63 C) conditions; the height of the pillar can be estimated, by comparison with the hut, as about 60 m. The photograph was taken in Siberia by Novosti Press Agency and is reproduced from Makogon (1987).

peralkylammonium salts and analogs (referred to together as peralkylonium salt hydrates) and the trialkylamine oxides and analogs (referred to together as the trialkyline oxide hydrates), has been carried out by Dyadin3 and coworkers in the Soviet Union and also more recently by Nakayama and coworkers in Japan. There have been a number of excellent reviews (van der Waals and Plateeuw, 1959; Powell, 1964; Jeffrey and McMullan, 1967; Jeffrey, 1969; Davidson, 1973; Jeffrey, 1984a; Jeffrey, 1984b; Dyadin and Udachin, 1984, 1987; Dyadin and Belosludov, 1996; Jeffrey, 1996) and books (Bercez and Bala-Achs, 1983; Sloan, 1998). The polyhedral clathrates,4 a convenient phrase covering the gas hydrates and analogs (including the 3 4

Yuri A. Dyadin 1935–2002. The series of crystal structure analyses by Jeffrey and coworkers is entitled Polyhedral Clathrate Hydrates.

DIRECTIONALLY BONDED HOSTS

351

metalloids and clathrasils), the alkylamine hydrates, the peralkylonium salt hydrates and the trialkyline oxide hydrates, are one of the most widely and deeply studied families of molecular compounds and complexes, with roughly equal amounts of attention having been given to the structural and the physico-chemical aspects. Jeffrey (1996) has used the following classiﬁcation of the polyhedral clathrates: (i) The ‘‘true clathrates’’ have uninterrupted frameworks and the guest molecules or salts do not participate in the framework structure; there are van der Waals interactions between neutral framework and neutral guest. The gas hydrates and analoges are the prime examples. (ii) In the ‘‘ionic clathrates’’ the cation (or anion) participates in the framework which may undergo considerable modiﬁcation in order to accommodate the bulky anion (or cation). The framework–guest interaction is ionic. (iii) In the ‘‘semiclathrates’’ functional groups of the guest molecules enter into a speciﬁc hydrogen-bonding relationship with the water molecules of the framework, while the hydrophobic groups occupy voids in the structure as in the ‘‘true clathrates’’. The hydrates of the trialkylamine (phosphine, stibine) oxides belong formally to this category.

Polyhedral clathrates

Semiclathrates

True clathrates

Interrupted frameworks

Uninterrupted frameworks

Metalloid structures

Clathrasils

(guests not linked to framework)

Gas hydrates

Peralkylonium salt hydrates (anions part of framework; cations interrupt framework)

Alkylamine polyhydrates

Trialkyline oxide hydrates

(guests H-bonded to framework)

(guests bonded to framework through participating oxygen atoms)

Fig. 7.19. Diagram showing relationships among the various types of polyhedral clathrate structures. The classiﬁcation is based on a combination of chemical and structural considerations.

CL AT HRATE INCLUS ION COMP LEXES

352

The structures are marvellous examples of the adaptation of pure geometrical principles to the demands of real chemical molecules. Perhaps Coleridge in Kubla Khan told us more than he could have suspected: It was a miracle of rare device, A sunny pleasure-dome with caves of ice.

More prosaically, Jeffery (1996) has commented that ‘‘ . . . present knowledge is likely to be only the tip of the iceberg in hydrate structural chemistry . . . ’’ Our description of the structures of the polyhedral clathrates will be based to a large extent on the accounts of Jeffrey, Davidson, Dyadin and their coworkers. We shall ﬁrst describe the overall geometrical features of these structures, leading to deﬁnition of some of the polyhedra encountered and introduction of the distinction between those structures that contain pentagonal dodecahedra and those that do not. We then consider the structural group containing pentagonal dodecahedra and uninterrupted frameworks, starting with the metalloid and clathrasil analogs to the gas hydrates and proceeding to the cubic gas hydrates themselves. The thermodynamics and stoichiometry of the gas hydrates is considered in Section 7.2.7.2. We then broaden the treatment by including structures with interrupted frameworks, starting with those of the peralkylonium salt hydrates and trialkyline oxide hydrates and then consider the alkylamine hydrates. Finally, hydrates not based on pentagonal dodecahedra are discussed. Thus we weave together structural and chemical considerations but make no claim to complete consistency – the discerning Table 7.4. Various nomenclatures used to describe the polyhedral clathrates Symbol

Name

Space group Previous name/ example

Structures containing dodecahedral cavities CS-I (SCS-I) Cubic Structure I Pm3n (Superstructure of CS-I) CS-II Cubic Structure II Fd3m HS-I HS-II HS-III

Hexagonal Structure I Hexagonal Structure II Hexagonal Structure III

TS-I RS-I OS-I

Tetragonal Structure I P42/mnm Rhombohedral Structure I R3m Orthorhombic Structure I Pbam

Structures not containing dodecahedral OS-II Orthorhombic Structure II Tet-II Tetragonal II Cub-I Cubic I

P6/mmm P63/mmc P6/mmm

cavities Fmmm I4/mcm I43d

Cub-II

Cubic II

Im3m

Tet-III

Tetragonal III

I41/amd

Structure I or Type I gas hydrate Structure II or Type II gas hydrate No example known No example known Structure H hydrate; dodecasil 1H Bromine hydrate dodecasil 3R RS-I (Dyadin and Udachin, 1987)

Jeffrey (1984a) (Table 2) I II IV V Not considered by Jeffrey III

nonasils 16X 156H2O VI (X¼ (CH3)3CHNH2) VII HEF6 5H2O HF (E¼P, As, Sb) Sigma-2

DIRECTIONALLY BONDED HOSTS

353

reader will note, for example, that the clathrasils are all treated together ignoring distinctions due to presence or absence of pentagonal dodecahedra. The relationships among the various structural types and groups of compounds which comprise the polyhedral clathrates are set out in Fig. 7.19; there is some overlap between the structural and chemical bases of this classiﬁcation in the sense that there are some (but very few) alkylamine polyhydrates with true clathrate structures. We shall ﬁrst consider the arrangements found in the gas hydrates and their analogs, including those few structures not based on pentagonal dodecahedra, and later proceed to discussion of the polyhedra found in the peralkylonium salt hydrates and semiclathrate hydrates. We shall use a nomenclature for the polyhedral clathrates based on that used by Dyadin and Udachin (1987) to describe in general terms their crystallography, but extended here to cover the whole ﬁeld as it is currently known. The relationship of this nomenclature to those used by other authors is set out in Table 7.4. 7.2.4.2

Restrictions on the shapes of the polyhedra

The structures are all based on polyhedral frameworks of four-connected tetrahedral moieties, which we shall refer to generally as T 4; speciﬁcally T 4 can be Si or Ge, SiO2or H2O. These will give neutral frameworks but participation of some other atoms can give charged frameworks. The tetrahedral disposition of the bonds about T4 implies that each vertex of the polyhedra comprising the overall structure must have an order of exactly three (the order is the number of bonds directed (on the same side of a supporting plane) so they can be edges of the same polyhedron) (King, 1972). Furthermore, the angles between the edges of the polyhedra must be close to tetrahedral in order to minimise angle strain, leading to the following order of preference for the shapes of regular plane faces: pentagonal (most favourable) > hexagonal > quadrilateral triangular. Angle strain will not be appreciably altered by moderate deviations from regularity because decrease of some angles (further from tetrahedral) must be accompanied by increase of others (closer to tetrahedral) as the sum of the internal angles of a planar n-gon is constant at (n – 2). Appreciable bending of the faces of the polyhedra is also not to be expected. Although these considerations show that the pentagonal face will tend to be preferred in all polyhedra and that the preferred polyhedral shape will be the slightly distorted pentagonal dodecahedron, nonetheless experience shows that other types of face and polyhedron are also found. Two groups of structures can be distinguished – those based on various packings of pentagonal dodecahedra and those which do not contain any pentagonal dodecahedra (Fig. 7.20). These two groups cut across the boundaries of guest type and uninterrupted or interrrupted frameworks and will be discussed separately, starting with a consideration of the packing of pentagonal dodecahedra. The pentagonal dodecahedron is one of the platonic solids, with 12 regular pentagonal faces, 20 vertices (T 4 moieties) and 30 edges. The faces must be planar in the ideal structure and the bond angles, at 108 , are nearly tetrahedral with only small deviations from tetrahedrality encountered in real structures (for example the H–O–H angle in water is ideally 104 ). The pentagonal dodecahedron cannot by itself ﬁll space (its ﬁvefold axes are not compatible with the requirements for long range order in a crystal, that can only be

CL AT HRATE INCLUS ION COMP LEXES

354

Polyhedral clathrates

Structures based on packing of Pentagonal dodecahedra

Structures without pentagonal dodecahedra

CS-I, CS-II TS-I HS-I, HS-II, HS-III OS-I

Cub-I, Cub-II Tet-II OS-II (nonasil)

Fig. 7.20. Classiﬁcation of the polyhedral clathrates into two structural groups in terms of presence or absence of pentagonal dodecahedra. Some examples of structural types (deﬁned and described in the following sections) are given in each category.

fulﬁlled by bodies with 2, 3, 4 or 6 fold symmetry)5 and therefore must be associated, in an ordered fashion, with other polyhedra (that can and generally do have nonplanar faces and unequal edges and/or angles) in order to form an arrangement which satisfactorily ﬁlls space in the crystal. The following relationships hold for the parameters describing closed convex threedimensional polyhedra with all vertices of order 3. King (1972), who listed all convex polyhedra of order 3 with up to 18 faces, and Wells (1975) give good summaries of the relevant solid geometry. FþV¼Eþ2 Euler’s rule 3V ¼ 2E Relationship between edges and vertices i (i Fi) ¼ 2E Relationship between edges and faces Totality of faces i Fi ¼ F (Here Fi refers to the number of faces with i sides or edges; for example F4 is the number of quadrilateral faces.)

1. 2. 3. 4.

For a given set of V, E and F values there are many polyhedra corresponding to different solutions of equations (3) and (4). We shall list the polyhedra found experimentally to date in structures with uninterrupted frameworks; these are described in terms of the number of faces of a given kind, together with the numbers of vertices, edges and faces which, of course, satisfy Euler’s rule. Thus the pentagonal dodecahedron is described as 512 (i.e. it has twelve pentagonal faces), with 12F þ 20V ¼ 30E þ 2. 1. 2. 3.

8-hedra 9-hedra 12-hedra (D) 5

(4454), (5464) (4158) (512), (435663)

8F þ 12V ¼ 18E þ 2 9F þ 14V ¼ 21E þ 2 12F þ 20V ¼ 30E þ 2

This sentence was phrased in the pre-icosahedral era; time will tell how it needs to be modiﬁed.

DIRECTIONALLY BONDED HOSTS

(a)

(b)

(c)

(d)

355

Fig. 7.21. (a) pentagonal dodecahedron (D), (b) 14-hedron (T), (c) 15-hedron (P) and (d) 16-hedron (H). These are the polyhedra found, either in association with the pentagonal dodecahedron, or separately, in the gas hydrate and analogous structures. Reproduced from Jeffrey and McMullan (1967).

4. 5. 6. 7. 8. 9.

14-hedra (T) 15-hedra (P) 16-hedra (H) 17-hedra 18-hedra 20-hedra

(51262), (4668) (51263) (51264) (43596273) (51266) (58612), (51268)

14F þ 24V ¼ 36E þ 2 15F þ 26V ¼ 39E þ 2 16F þ 28V ¼ 42E þ 2 17F þ 30V ¼ 45E þ 2 18F þ 32V ¼ 48E þ 2 20F þ 36V ¼ 54E þ 2

The polyhedra 3–6 are shown in Fig. 7.21. The next problem is to consider how the dodecahedra can pack together to form closely packed ordered structures. 7.2.4.3

Packing of pentagonal dodecahedra

Jeffrey and McMullan (1967) point out that there are only two ways of joining pentagonal dodecahedra which preserve fourfold ﬁrst-neighbor coordination about T 4 moieties at the vertices. These are: (a) formation of hydrogen bonds between vertices of different dodecahedra, either directly or through additional T 4 moieties (sharing edges or corners would give ﬁve or sixfold coordination), (b) sharing common faces of adjacent dodecahedra. On this basis the possible structures can be divided into four groups (Fig. 7.22) of which the ﬁrst and third are immediately relevant to the discussion of the cubic gas hydrates and their analogs.

356

CL AT HRATE INCLUS ION COMP LEXES

Polyhedral clathrates based on pentagonal dodecahedra

Vertex linked in three dimensions

Face sharing in two dimensions with vertex linking in the third

Face sharing in three dimensions

Face sharing within limited groups of dodedahedra, with vertex linking between groups

Fig. 7.22. Possible ways of packing pentagonal dodecahedra so as to ﬁll space.

(i) Vertex linking in three dimensions. Consider eight pentagonal dodecahedra at the corners of a cube, surrounding a dodecahedron at the center. When the central dodecahedron is rotated by 90 (about a cube axis) with respect to those at the corners, then eight vertex to vertex links can be formed from central to surrounding dodecahedra. The structure (space group Pm3n – Oh3)6 is analogous to that of CsCl, but with the different ions replaced by differently-oriented dodecahedra. This is the structure of cubic 2[(nC4H9)3SF] 40H2O, to be discussed later. The Type I gas hydrate structure (CS-I; see Table 7.4 for nomenclature) is obtained by addition of six T 4 moieties at the Wyckoff (d) positions (1/4,1/2,0, etc) of the space group; these then form bonds to the remaining twelve vertices of the central dodecahedron. The unit cell contains 46 T 4 moieties, which are distributed as follows: 6 at positions (c) with symmetry 4 2m; 16 at positions (i), with symmetry 3; 24 at positions (k), with symmetry m. The T 4 moieties can be considered to be arranged in six pentagonal dodecahedra (D or M ), centred at the twofold positions (a) of symmetry mmm, and six 14-hedra (T or M14), centred at the sixfold positions (d) of symmetry 42m (Fig. 7.23). The hydrogen bond O . . . O distance in the water framework of the Type I gas hydrate ˚ , and this gives a cell edge of 12 A ˚ , with the pentagonal dodecahedron (M12) is 2.8 A ˚ ˚ 3 while the 14-hedron has an having a net diameter of 5.2 A and a net volume of 74 A ˚ ˚ 3 (van der ellipsoidal cavity of dimensions 6.2 3.2 A with a net volume of 266 A Waals radii of the framework atoms are taken into account in calculating these volumes). These values, which depend on the nature of the T 4 moiety, set limits to the sizes of guest molecules which can be accommodated in the cavities, which are not necessarily all occupied. The traditional way of expressing composition is in terms of ‘hydration 12

6 The space group number assigned by the International Union of Crystallography is No. 223; the symbol Pm3n used in International Tables for X-Ray Crystallography (First edition, 1952; Second edition 1965) has been replaced by Pm 3n in International Tables for Crystallography (First edition, 1983; Fifth revised edition 1998). Both symbols are used here interchangeably.

DIRECTIONALLY BONDED HOSTS

357

Fig. 7.23. The polyhedral T 4 moiety framework of the Type I gas hydrate structure; only a limited number of the polyhedra have been included in the diagram in order to keep matters simple. The pentagonal dodecahedra are lightly outlined and the 14-hedra emphasized. The center of the cell at 1=2,1=2,1=2 is marked by the cross. (Reproduced from Jeffrey and McMullan (1967).)

number’ Gð¼ 46=ðm þ nÞ ¼ 5:75 for a Type I gas hydrate with all cavities occupied). Alternatively the content of the unit cell is given as {46T 4 [n(M14)] [m(M12)]}, i.e. n guests in the M14 cages and m in the M12cages, where n ¼ 6 and m ¼ 2 in the ideal, fully-occupied structure; the fractional occupancies of the large (M14) and small (M12) cages are often denoted as qL and qS (sometimes L and S ). As we have done elsewhere, we place the whole formula within parentheses, with framework former ﬁrst and then the enclathrated species within square brackets. It seems more logical to express compositions in terms of unit cell contents than in other ways, but hydration numbers are so well entrenched in the gas hydrate literature that it is often convenient to use them as well. (ii) Single layer packing. Slightly distorted pentagonal dodecahedra (angle distortions 3 ) can be packed together to give a two-dimensional arrangement of hexagonal symmetry, each dodecahdron sharing faces with four other dodecahedra. The layers are stacked one on the other with sequence . . . AA . . . ; in addition to the [512] (D) dodecahedra within the layers there are two other types of cage – two [435663] (D00 ) cages and one eicosahedral [51268] (E) cage per unit cell – between the layers (Fig. 7.24). The E cage is large and D and D00 are small. This is the dodecasil 1H structure, the simplest of these polytypes. The space group is P6/mmm and the ideal composition is expressed as 0 {34 T 4 [1(M20)] [2(M12 )] [3(M12)]}.

CL AT HRATE INCLUS ION COMP LEXES

358

A third major type of gas hydrate (see Section 7.2.7 below; HS-III in addition to CS-I and CS-II), called structure H hydrate, was discovered in 1987 using NMR methods (Ripmeester, Tse, Ratcliffe and Powell, 1987). The guests include methylcyclohexane, methylcyclopentane, 2-methylbutane, 2,3-dimethylbutane, 2,2-dimethylbutane, 2,2,3-trimethylbutane, hexamethylethane, hexachloroethane, 2,2-dimethylpentane, 3,3dimethylpentane, cycloheptene, cyclooctane, cis-cyclooctene, adamantane, bicyclo[2.2.2]-oct-2-ene, 2,3-dimethyl-2-butene, 2,3-dimethyl-1-butene, 3,3-dimethyl-1-butene, 3,3-dimethyl-1-butyne, cis-1,2-dimethylcyclohexane, t-butylmethylether, 2-adamantone, tetra-methylsilane and isoamyl alcohol. Indexed X-ray and neutron powder diffraction

a c⬘ c

a⬘

S16L8·136H2O

Structure II Fd 3m 512

51264

S3S2L·34H2O

Structure H p6/mmm 512

435663

51268

Fig. 7.24. (upper) The hexagonal layer obtained by packing slightly distorted pentagonal dodecahedra as described in the text; (lower) the cages between . . . ABC . . . stacked cubic layers [(111) planes] and . . . AA . . . stacked hexagonal layers. (Reproduced from Jeffrey (1984b) and Ripmeester and Ratcliffe, 1991.)

DIRECTIONALLY BONDED HOSTS

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patterns indicate that this class of gas hydrate is isomorphous with dodecasil 1H. Conﬁrmation has come from determination of the structure of the hydrate {34H2O [2,2-dimethylpentane] [5Xe, 5H2S]} at 173K (a ¼ 12.212(2), c ¼ 10.143(2) ˚ , P6/mmm, Z ¼ 1; Udachin, Ratcliffe, Enright and Ripmeester, 1997b; PEXQIS). Why A did it take so long? ‘‘Crystals were grown in a sealed tube from the four phase mixture of 2,2-dimethylpentane, Xe, H2S and ice at approximately –20 C for 6 years. On the walls . . . there formed transparent well-edged hexagonal prisms . . . ’’ (my italics). An example of a composite structure, incorporating elements of both the CS-II and HS-III structures, has been found in {30.33 H2O [0.86 choline hydroxide]. ˚ , trigonal tetra-n-propylammonium ﬂuoride} at 243K (a ¼ 12.5335(1), c ¼ 90.525(1) A R3; Z ¼ 12; Udachin and Ripmeester, 1999a; XAWPAM). (Choline is (CH3)3N þ CH2CH2OH.) We describe the structure in somewhat oversimpliﬁed terms. The cholines are located in two types of large cages, and the cations in large supercages formed by coalescence of dodecahedral and other types of cage; choline is hydrogen bonded to a displaced water molecule in one of the supercages but not in the other. Along the (unprecedently long) c axis, there is a sequence of CS-II and HS-III domains arranged in layers with a complicated sequence. It is suggested that variants of this hydrate structure may play an important role in natural settings. (iii) Triple layer packing (face sharing in three dimensions). If additional T4 moieties are placed between the layers described in the previous section so as to give additional dodecahedra and 16-hedra, then a cubic structure is formed with an . . . ABCABC . . . sequence of layers in which there is three-dimensional face sharing between dodecahedra leaving 16-hedral voids. When T 4¼H2O then the 16-hedron, which is almost spherical in ˚ and a net volume of 151 A ˚ 3. The normal to the layer shape, has a net diameter of 6.6 A is the [111] axis of the cube; the space group is Fd3m. There are [51264] cages between the layers, centred at the eightfold positions (b) of symmetry 4 3m, while the dodecahedra are centred at the 16-fold positions (c) of symmetry 4 3m. The 136 T 4 moieties are

Fig. 7.25. Stereodiagram illustrating the characteristic packing of oxygen polyhedra in the CS-II type structure. Two 16-hedra are centred at (3/8, 3/8, 3/8) and (5/8, 5/8, 5/8) and two clusters of four 12-hedra centred at (1/8, 1/8, 1/8) and (7/8, 7/8, 7/8). The view is down the a axis. The solid circles show the centres of 12- and 16-hedra. (Reproduced from McMullan and Kvick (1990).)

360

CL AT HRATE INCLUS ION COMP LEXES

distributed with 8 in (a), with symmetry 4 3m; 32 in (e) with symmetry 3m and 96 in (g) with symmetry m. The composition is expressed as {136T 4 [8(M16) 16(M12)]}; i.e. {136D2O [8CCl4] [8Xe]}; KELKUH at 13K and KELKUH01 at 100K. This is the structure of the Type II gas hydrate (Fig. 7.25) and of the dodecasil 3C clathrasil. In analogy with cubic and hexagonal close packing, an . . . ABABAB . . . hexagonal arrangement of the layers is also possible. Such a structure would have space group P63/mmc and the same stoichiometry as the cubic modiﬁcation. The semiclathrate iso-propylamine hydrate (CH3)2CHNH2 8H2O has a distorted version of this structure. We shall now discuss the metalloid structures, the clathrasils and the gas hydrates as realizations of these geometrical principles. 7.2.5

Metalloid structures

The ﬁrst hint of these structures came from studies of the thermal decomposition of compounds formed between alkali metals and Si (or Ge), suggesting the formation of compounds reported tentatively (Hohmann, 1948) as KSi8, RbSi8 and CsSi8, and later as KSi6, RbSi6 and CsSi8 (Scha¨fer and Klemm, 1961). Deﬁnitive results were obtained by thermal degradation of alkali silicides and germanides of formula ME (M¼Na, K, Rb, Cs; E¼Si, Ge) (Kasper, Hagenmuller, Pouchard and Cros, 1965; Cros, Pouchard and Hagenmuller, 1970), or exposure of powdered Group IV metal to alkali metal vapors under argon at 600–700 (Gallmeier, Scha¨fer and Weiss, 1969) to give intermediate phases (as single crystals) of composition {Si46 [Na8]} and {Si136 [Nax]} (x < 11) in the Si–Na system, and analogous E46M8 phases in other systems. {Si46 [Na8]} is cubic ˚ , space group Pm (a ¼ 10.19(2) A 3n) and has the CS-I (Type I) gas hydrate structure with ˚ (cf. all the cavities ﬁlled by Na atoms. The Si–Si distances in the framework are 2.37 A ˚ 2.35 A in diamond-structure Si), while the Na to Si distances are too large for any bonding. The electrical and magnetic properties suggest that there is a certain localization of the 3s electron of Na. The less well deﬁned {Si136 [Nax]} (x < 11) has the CS-II gas ˚ , space group Fd3m), and the formula proposed hydrate structure (a ¼ 14.62(2) A was {136Si [6 3Na] [3 2Na]}. Both types of compound have chemical properties similar to those of silicon, the alkali metals being chemically inert; neither material reacts with strong acids, apart from HF which also attacks silicon. Phases of the type {(XY)46 [M8]} (M¼Na, K; X¼Al, Ga, In; Y¼Si, Ge) have been prepared (Westerhaus and Schuster, 1977) and are similarly chemically inert. When the framework atoms are ordered in the XY (X 6¼ Y) compounds, the space group is P43n; if X and Y cannot be distinguished then the space group is Pm 3n. In agreement with Pauling and Marsh’s (1952) results for CS-I chlorine hydrate, the polyhedra are not regular; for example, in ˚ and one of 2.43 A ˚ , with two angles {Si46 [K8]} the dodecahedron has four sides of 2.38 A at 107 and three at 110 , while the hexagonal face of the 14-hedron has four angles of 124 and two of 111 ; similar, but more accurate, results have been reported ˚ ; < Si–Si– for {Si46 [Na8]} (d(Si–Si) ¼ 2.306(2), 2.371(2), 2.373(2). 2.393(3) A Si ¼ 105.2(1), 105.8(1), 105.9(1), 124.8(1) ) (Reny, Gravereau, Cros and Pouchard, 1998). Defect structures are also known; in {Sn44 [K8]} one-third of the Sn atoms which lie across the shared hexagons of the CS-I structure are left empty (at random) and the compound should be formulated as {(3b-Sn1)8(4b-Sn0)36 [Kþ]8} (Zhao and Corbett, 1994); Corbett notes analogous but unpublished examples from von Schnering’s

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laboratory. Reports of superconductivity (Tc 6K) in CS-I type Si-based structures containing Ba and transition metals have attracted attention; there are also possible thermoelectric applications of Ge clathrates. The cell dimensions for many of this group of compounds, and for the halogen analogs (see below) are collected in Table 7.5. The data given in this table enable one to ascertain the effects on cell size of changes in both framework and enclathrated atoms. Thus ˚ and by Sn to an expansion of 1.32 A ˚; replacing Ge by Si leads to a contraction of 0.51 A ˚ replacing Na by K leads to an expansion of 0.11 A. Halogen analogs of the alkali metal–Group IV compounds have been prepared (Menke and von Schnering, 1973) by reaction of the elements in sealed tubes at 700 C, giving shiny single crystals of composition {Ge38A8 [X8]}, where X¼Cl, Br or I; A¼P, As or Sb. Single crystal X-ray diffraction studies of {Ge38P8 [Br8], {Ge38P8 [I8]} and {Ge38As8 [I8]} showed that these had CS-I gas hydrate structures, with ordered arrangements of the framework atoms in space group P43n, there being 8Ge in 8(e) positions with x 0.18 etc. and 8A atoms in 8(e) with x 0.82 etc. (in space group Pm3n these would be the 16-fold (i) positions). Presumably the ordering was demonstrated for the phosphorus compounds and inferred for the others. This ordering was not conﬁrmed in a brieﬂy described neutron diffraction study of {(Ge38As8)8þ [8I1]}, which was assigned space group Pm3n (Chu, Chu and Ray, 1982); neutron diffraction showed that eight Ge and eight As atoms were disordered over the 16-fold (i) positions, with the remaining Ge atoms in the six fold (c) and 24-fold (k) positions (Chu, Chu, Rosenstein and McMullan, 1982). This material is an n-type semiconductor, with a resistivity of 1 ohm cm at 300K. Analogous results were obtained for {Ge14(GaSb)12Sb8 [I8]} (Menke and von Schnering, 1976); the bracketed Ga and Sb atoms were disordered over the 6(c) positions at 0, 1/4,1/2 etc. In {Ge43.33I2.67 [I8]} the framework iodines are disordered over the 6(c) sites and are presumed to be present as tetrahedral I3þ (Nesper, Curda and von Schnering, 1986). This compound was formed during an unsuccessful attempt to synthesize ˚ when Br is replaced by I, by 0.11 A ˚ when As {Ge46 [Xe8]}! The cell expands by 0.09 A ˚ when Sb replaces As. replaces P and by 0.26 A The compounds K8Sn25, K6Sn23Bi2 and Ba8Ga16Sn30 are not clathrate metalloids but there are certain structural resemblances (references in Nolas et al., 1999). After a period of some dormancy, interest in these materials has revived, particularly in the CS-II type silicides and germanides. Single crystals (polyhedral in shape, bluish, with metallic lustre) have been prepared of {Si136 [Na16][Cs8]} and {Ge136 [Na16][Cs8]} (Bobev and Sevov, 1999; Ramachandran, Diefenbacher, Sankey, Sharma, Marzke, O’Keefe, Gryko and McMillan, 1999). The materials are remarkably air- and moisturestable. The smaller Na completely occupies the smaller Si(Ge)20 cage, and the larger Cs the larger Si(Ge)28 cage. These are the 16-fold dodecahedral (512) and the eightfold 16-hedral (51264) cages in the nomenclature used in the previous section (Section 7.2.4.3) and later in discussing the gas hydrates. Rb is too small for the large cages and K too large for the small cavities. The Na–Cs pair is so far the only successful combination of guests. Powder studies (Rietveld analyses) on {Si46 [Na8]} and {Si136 [Nax]} (Reny, Gravereau, Cros and Pouchard, 1998) showed that both dodecahedral and 14-hedral cages were fully occupied in the CS-I compound, but that, in the CS-II compound, the ‘‘sodium atoms are exclusively, not only preferentially, located in the eight large Si28 sites for x 8, and that, for 8 x 24, the smaller Si20 sites are progressively occupied with

Table 7.5. Cell dimensions of E46M8 (E¼Si, Ge and other combinations) (CS-I structure) and E136XxYy (CS-II structure) compounds. Standard ˚ and for the halogen analogues 0.001 A ˚ ; more precise values are indicated uncertainties of measurements for alkali metal compounds are 0.01–0.02 A specifically. Space group P4 3n is denoted by #, while the space group for the other CS-I compounds is Pm3n. The space group for the CS-II compounds is Fd3m Compound

˚) a (A

Compound

˚) a (A

Compound

˚) a (A

CS-I structure type {Si46 [Na8]} (GSW69) {Si46 [Na8]} (RGCP98)

10.19 10.1983 (2)

{Si46 [K8]} (GSW69)

10.30

{Si38Ga8 [K8]}

10.427

{Si38Ga8 [Rb8]

10.469

{Al18Ge28 [Na8]} (G70) {Ge46 [K8] (GSW69) {Al23Ge23 [K8]} (WS77) {Al23Ge23 [K8]} (WS77) {In18Ge28 [K8]} (WS77) {Ge38Al8 [Rb8]} (vS98) {Ge38Ga8 [Rb8]} (vS98) {Ge38Ga8 [Cs8]} (vS98)

10.70# 10.71# 10.80# 10.76 – 10.822 10.783 10.835

{Sn46 [Na8]} (GSW69) {Sn46 [K8]} (N99) {Sn44.6 [Rb8]} (ZC94) {Sn44 [K1.6 Cs6.4]} (ZC94) {Sn38Ga8 [K8]} (vS98) {Sn38Ga8 [Rb8]} (vS98) {Sn38Ga8 [Cs8]} (vS98)

12.03 12.030 12.054(1) 12.084(1) 11.935 11.964 12.006; 12.079 at 300K (N00)

{Ge38In8 [K8]} (vS98) {Ge38In8 [Rb8]} (vS98) {Ge38P8 [Cl8]} (MvS73) {Ge38P8 [Br8]} (MvS73) {Ge38P8 [I8]} (MvS73) {Ge38As8 [Br8]} (MvS73) {Ge38As8 [I8]} (CCR82; CCRM82) {Ge38Sb8 [Br8]} (MvS73) {Ge38Sb8 [I8]} (MvS73) {Ge14(GaSb)12Sb8 [I8]} (MvS76) {Ge43.33I2.67 [I8]} (NCvS86)

10.997 11.033 10.351# 10.407# 10.507# 10.516# 10.616 10.789 10.870 11.273# 10.814

{Sn38Al8 [Rb8]} (vS98)

12.036

{Sn42Zn4 [Cs8]} (N00)

12.093 at 11K

Ge136[Na16][Cs8] (BS99)

15.4805 (6)

Sn104Ga32[Ba16] (vS98)

17.054

CS-II structure type Si136[Na16][Cs8] (BS99) Si136[Na16][Na4] (RGCP98) (see text)

14.7560 (4) 14.7030 (5)

References: BS99 – Bobev and Sevov, 1999; single crystal measurements; CCR82 – Chu, Chu and Ray, 1982; CCRM82 – Chu, Chu, Rosenstein and McMullan, 1982; GSW69 – Gallmeier, Scha¨fer and Weiss, 1969; MvS73 – Menke and von Schnering, 1973; MvS76 – Menke and von Schnering, 1976; N99 – Nolas et al., 1999; this contains earlier references; N00 – Nolas et al., 2000; NCvS86 – Nesper, Curda and von Schnering, 1986; RGCP98 – Reny, Gravereau, Cros and Pouchard, 1998; vS98 – von Schnering and coworkers (1998); WS77 – Westerhaus and Schuster, 1977; ZC94 – Zhao and Corbett, 1994.

DIRECTIONALLY BONDED HOSTS

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increasing x.’’ These results have been conﬁrmed by 23Na NMR spectroscopy. The ˚ for x 11, and then increases to 14.72 A ˚ cell dimension is constant at a ¼ 14.642 A for x ¼ 24. Thermodynamic studies do not appear to have been reported but the same theory as used for the gas hydrates should apply here essentially unchanged. There are differences in cage occupation between the gas hydrate and metalloid structures. Using the Xe CS-I gas hydrate as example, its composition has been measured as {46H2O [5.89Xe] [1.43 Xe]} (Section 7.2.7.2), i.e. partial occupancy of both types of cage. Only full occupancy has been found in all the {E46 [M8]} structures noted above. In the CS-II gas hydrate, with ideal formula {136H2O [8M16] [16M12]}, complete occupancy of the 16-hedral cages was found for eighteen CS-II hydrates studied (Section 7.2.7.2). In {Si136 [Nax]} Reny et al. (1998) found that the Na atoms ﬁrst ﬁlled the eightfold 16-hedral (51264) cages, without changing the cell dimension, and then entered the smaller 16-fold dodecahedral (512) cages, with appreciable effect on a. The remarkable difference is that a specimen with composition {Si136 [Na1]} could be prepared, i.e that the empty {Si136 []} framework required very little stabilization from host-guest interaction, or, in other words, that the free energy difference between the ‘‘polymorphs’’, ‘‘diamond Si’’ and ‘‘empty {Si136 []} framework,’’ although positive, is rather small. A caveat is necessary; these samples have been prepared at high temperatures and examined after quenching to room temperature – but what are the relevant equilibrium conditions? 7.2.6 Clathrasils We give a brief introduction to the classiﬁcation of clathrasils for the reader unfamiliar with the overall mineralogical background (Liebau, 1985). One starts with the tectosilicates (Liebau, Gies, Gunawardane and Marler, 1986), which are phases containing threedimensional frameworks of corner linked [TO4] tetrahedra. A distinction is then made between dense and porous tectosilicates, the latter having less than 21 [TO4] tetrahedra per ˚ 3. Porosils are a subclass of the porous tectosilicates and have the general formula 1000 A SiO2 nM, indicating three-dimensional four-connected SiO2 frameworks with guest molecules M occupying voids in the framework. The clathrasils have closed pores, i.e. the windows between polyhedra are too small for passage of guest molecules without decomposition of the whole structure, while zeosils have open pores, the windows between the polyhedra being large enough for the passage of guest molecules. The very important zeolites, which will not be discussed here for reasons noted earlier (see Preface), have partial replacement of Si by Al and have the general formula Axþ y/x[Aly Si1yO2] mH2O nM. The smallest polyhedral building units from which the clathrasil framework can be generated are called fundamental polyhedra. The names are assigned as follows: Nonasils are frameworks generated from 9-hedra. Dodecasils are frameworks generated from 12-hedra. Deca-dodecasils have 10-hedra and 12-hedra as fundamental polyhedra. A polytypic symbol is then added : thus dodecasil 1H has an hexagonal one-layer structure, while dodecasil 3C has a cubic three-layer structure based on the same hexagonal layers as in 1H. The name can be followed by a list of the polyhedra in the structure (with

CL AT HRATE INCLUS ION COMP LEXES

364

fundamental polyhedra enclosed in double brackets) and by a designation of the crystallographic symmetry, as space group (e.g. Fmmm), point group (mmm) or crystal class (orthorhombic). Thus the general formula for the nonasil family is 88SiO2 8M8 8[[M9]] 4M20 (Fmmm) where Mmi is the polyhedron with mi faces and n is the number of such polyhedra in the structure. The (chemical) contents of the polyhedral cages can also be designated if required. The nomenclature, due to Liebau and coworkers, is used in full or abbreviated form as required. The framework densities of the various silica modiﬁcations and the clathrasils form a continuous series (Table 7.6) but with a ratio of almost 2 : 1 between that of coesite, the highest density silica, and silica sodalite, the lowest density porosil. The general method of synthesis of clathrasils is from aqueous solutions of silica under hydrothermal conditions using appropriate template molecules and temperature and pressure conditions in order to obtain the clathrasil desired (Table 7.7); Gies (1991) notes that ‘‘the guest species truly act as templates giving rise to pores in the host framework which reﬂect the geometry of the templates.’’ Durations as long as three months were necessary for some samples. Synthesis in the absence of air showed that ‘‘hilfsgassen’’ (small molecules such as nitrogen and oxygen which play an important role in stabilizing, especially, CS-II gas hydrates (see below)) do not play an important role in stabilising clathrasils (Gunawardane, Gies and Liebau, 1987). Dodecasil 1H has been studied by CP MAS NMR and found to give narrow 29Si lines indicating a well crystallized sample, while the 13C spectrum showed that the template molecule 1-amino-adamantane was retained intact in the structure (Groenen, Alma, Bastein, Hays, Huis and Kortbeek, 1983). The crystals are well formed morphologically and have the hardness of quartz. Structural information for the different types of clathrasils is summarized in Table 7.8. Investigation of the clathrasils has its origins in the study of the rare mineral melanophlogite, found in Sicily (ﬁrst description by Lasaulx, 1876), Italy, Bohemia, California and FSU and always associated with an appreciable amount of hydrocarbon impurity e.g. the mineral from Bohemia analyzes as C2.2H17.3O5.4S0.1 46SiO2 (Zak, 1972). Kamb (1965) suggested that the material had the CS-I gas hydrate structure and this has been conﬁrmed by later work (Gies, Gerke and Liebau, 1982; Gies, 1983b). At room temperature natural melanophlogite is tetragonal and microtwinned and there is a displacive phase transformation to the cubic phase at 65 C (exact temperature depends on ˚ , space group Pm3n; the sample used composition of sample). At 200 C a ¼ 13.436(3) A ˚ 3) of Table 7.6. Framework densities (Dfr ¼ number of tetrahedra per 1000 A different silica modifications and some porosils. (Reproduced from Gies, Liebau and Gerke, 1982) Phase

Dfr

Phase

Dfr

Coesite Quartz Keatite Cristabolite Tridymite Silica glass Silica ZSM-48

29.2 26.5 25.0 23.3 22.6 22.0 19.8

Nonasil Melanophlogite Dodecasil 3C Dodecasil 1H Decadodecasil 3R Silica sodalite

19.4 18.9 18.6 18.4 17.6 17.4

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Table 7.7. Experimental conditions for synthesis of some clathrasils (medium is H2O in absence of air; for effects of ethylenediamine and air see Groenen, Alma, Bastein, Hays, Huis and Kortbeek, 1983) t C

Name of clathrasil

Template molecules

Melanophlogite

Kr, Xe 160 60 CH3NH2 <200 tetrahydrofuran; tetrahydrothiophene 1-aminoadamantane 180–240 piperidine Kr, Xe 160 150 CH3NH2 240 trimethylamine þ NMeþ 155 4 þ NEt4 1-aminobutane <180 2-aminobutane; 2-aminopentane; 2-methylpyrrolidine; 2-methylpiperidine; 2-methylpiperazine; hexamethylimine; 2-(aminomethyl)THF; 1,2-diaminocyclohexane pyrrollidene 160–200 1-aminoadamantane 170

Dodecasil 1H Dodecasil 3C

Nonasil

Decadodecasil 3R (G86b) Silica sodalite (BD85)

ethylene glycol

150

Pressure (atm.)

Duration

330 hrs (S81) several weeks

6–8 weeks 15–20 days

propanol References: BD85 – Bibby and Dale, 1985; G86b – Gies, 1986b; S81 – Schlenker, Dwyer, Jenkins, Rohrbaugh, Kokotailo and Meier, 1981.

(from Mt Hamilton, California) had completely occupied cages with CH4 and N2 in the M14 cage and CO2 and N2 in the M12 cage (Gies, 1983b). Melanophlogite can also be prepared synthetically; for example, melanophlogite of composition {46SiO2 [6X14] [0.6X12]} was obtained with Kr and Xe (at 160 C and 60 atm.) as guests (Gies, 1983a). The crystals with spherical guests are cubic at room temperature but those with aspherical guests such as tetrahydrofuran or tetrahydrothiophene are tetragonal and microtwinned; the enthalpy of transition to the cubic phase is 100J/mol SiO2. In melanophlogite the ˚ while the Si–O–Si angles range from 148–180 , with average Si–O distance is 1.58 A similar values being found in other clathrasils. The distances are shorter and the angles larger than in the silica polymorphs and this is ascribed to disorder of the oxygen atoms. ˚ 3 (different authors give diffferent values) and that The [512] cage has a volume of 97 A 12 2 3 ˚ . The diffraction studies, which essentially reﬂect the long of the [5 6 ] cage is 136 A range order of the crystals, have been complemented by 29Si NMR (Fyfe and Gies, 1990),

Table 7.8. Summary of structural information for the clathrasils (cf. Figs. 7.15 and 7.16); the symbols CS I etc are explained in Table 7.4. The chemical compositions are given in terms of SiO2 content and maximal cage occupancy; the cages are designated by the superscripts : 12 ¼ dodecahedron etc. In ˚ 3 are too small to be occupied by the templating guest but can be (and are) occupied by O2 and/or N2 from practice cages with volumes less than about 80 A the air. (Based on Table 4 of Gies and Marler, 1996) Clathrasil family, and chemical composition

Crystal system/ structure type

Structures based on packing of pentagonal dodecahedra Melanophlogite cubic CS-I {46SiO2 [2M12] [6M14]} cubic CS-II Dodecasil 3C {132SiO2 [16M12] [8M16]} hexagonal HS-III Dodecasil 1H {34SiO2 [3M12] [3M12’] [1M20]} Decadodecasil 3R rhombohedral RS-I {120SiO2 [6M10] [9M12] [3M19]} Decadodecasil 3H trigonal {120SiO2 [6M10] [9M12] [1M15] [4M19] [1M23]} Structures without pentagonal dodecahedra tetragonal Tet-III Sigma-2 {64SiO2 [8M9] [4M20]}

Crystal data

Cage characteristics – number of cages per unit cell; cage type; ˚ 3. net cage volume in A

Pm3n a ¼ 13.436

2[512] V 80

6[51262]

V 160

Fd3 a ¼ 19.402

16[512] V 80

8[51264]

V 250

P6/mmm a ¼ 13.783 3[512] V 80 c ¼ 11.190 R 3m a ¼ 13.860 6[435661] V 35 c ¼ 40.891 P3m a ¼ 13.9 6[435663] V 35; c ¼ 40.9 4[435126183] V 350

I41/amd a ¼ 10.2387 c ¼ 34.5829 Nonasil {88SiO2 [8M8] [8M9] [4M20]} orthorhombic OS-II Fmmm a ¼ 22.323 b ¼ 15.058 c ¼ 13.627 cubic Cub-II Im3m a ¼ 8.827 Silica sodalite {12SiO2 [2M14]} Octadecasil {20SiO2 [2M6] [2M18]} Tetragonal I4/m a ¼ 9.2 c ¼ 13.4 Monoclinic C2/m a ¼ 14.0 RUB-3 {24SiO2 [2M18]} b ¼ 13.7 c ¼ 7.4 ¼ 102.5

2[435663] 1[51268] V 430 V 50 2[512] 6[435126183] V 350 V 70 9[512] V 80; 1[465683] V 230 1[5186283] V 540

8[4356] V 25

4[51264]

V 390

8[5464] V 25

8[4158] V 30 8[58612]

V 290

2[4668] V 130 2[46] V 8 2[46546682] V 300

2[46612] 2[445462]

V 280 V 35

DIRECTIONALLY BONDED HOSTS

367

which is sensitive to the short range order. The high ﬁeld values of the chemical shifts ( –120 ppm with respect to TMS) conﬁrm the relatively high Si–O–Si bond angles and short Si–O bond lengths found in the crystal structure analysis. Dodecasil 1H is the simplest of the clathrasils with an . . . AAAA . . . packing of hexagonal layers (Fig. 7.24). The compound of composition {34SiO2 [piperidine] [2N2] [3N2]} crystallizes in the hexagonal space group P63/mmm with a ¼ 13.783(4), ˚ (Gerke and Gies, 1984; COBMIP). The structure-determining piperidine c ¼ 11.190(3) A guest is partially disordered in the M20[51268] cages. The 1-aminoadamantane dodecasil ˚ , showing that a is 1H, with N2 in the smaller cages, has a ¼ 13.825(3), c ¼ 11.189(2) A more affected by the nature of the guest than c; four crystallographically different preferred orientations were found for the partially disordered guests (Gies, 1986a; DIGDOM01). There is a gas hydrate analog (Gough, Handa, Ratcliffe, Ripmeester and Tse, 1987) with methylcyclohexane or H3COC(CH3)3 as guests and H2S or Xe as ‘‘hilfsgas.’’ The ﬁrst example of a dodecasil 3C was the so-called high silica zeolite ZSM-39 þ of composition fð135:6ðSiO2 Þ:0:4ðAlO2 ÞÞ½0:4ðNaþ ; NMe4 ; NEtþ 4 Þ g crystallizing in a ˚ (Schlenker, Dwyer, Jenkins, Rohrbaugh, CS-II gas hydrate structure with a ¼ 19.36(2) A Kokotailo and Meier, 1981). The ZSM-39 methylamine clathrate is isomorphous ˚ ; FOPGOG; Long et al., 1987). A sample of composition (a ¼ 19.403 A {136SiO2 [8M16] [16M12]} (with the M12 cages occupied by N2 and small amounts of CH4 and Kr, and the M16 cages by N(CH3)3 þ CO2) crystallized in space group Fd3, a ˚ (Gies, 1984). The crystals are cubic at room subgroup of Fd3m, with a ¼ 19.402(1) A temperature when the guests are quasi-spherical molecules such as Kr, Xe, N(CH3)3 while aspherical molecules such as THF, tetrahydrothiophene or piperidine give optically anisotropic crystals at room temperature with symmetry lower than cubic. As with melanophlogite there is then a displacive transformation at higher temperature to a cubic phase; this occurs at 110 C when THF is the guest, the enthalpy of transformation being 100J/mol SiO2. The relationships between the cell dimensions of the dodecasils 1H and 3C are: p p a1H ¼ a3C = 2; c1H ¼ a3C = 3: The ratio of cell dimensions for CS-I and CS-II gas hydrates are nearly independent of the nature of the T 4 moiety (Table 7.9). Nonasil[4158] has been synthesized using a number of different template molecules (Table 7.6) (Marler, Dehnbostel, Eulert, Gies and Liebau, 1986; FIWWAJ). The crystals with 2-aminopentane as guest (overall composition {(88SiO2) [4M20] [8M9] [8M8]} are ˚ , space group Fmmm; orthorhombic with a ¼ 22.232(6), b ¼ 15.058(4), c ¼ 13.627(4) A the guest molecules are in the 20-hedra. The non-spherical shape of the guest molecules is apparently the controlling inﬂuence in the synthesis of nonasil[4158]. The guest molecules can be driven out on heating the compound to 950 C, with retention of the nonasil[4158] framework; this is unusual behaviour for a clathrasil. Decadodecasil 3R has been synthesized and characterised as the missing link between clathrasils and zeolites (Gies, 1986b). Details of preparation and crystal data are given in Tables 7.7 and 7.8. Pseudohexagonal layers of face sharing pentagonal dodecahedra [512] ˚ 3) are formed. These layers are stacked in rhombohedral ABC sequence (free volume 70 A linked through additional SiO4 tetrahedra which form six membered rings [Si6O18]. Two

CL AT HRATE INCLUS ION COMP LEXES

368

new types of cavity are formed between the layers, a decahedron [435661] (free volume 35 ˚ 3), the latter containing the structure ˚ 3) and a 19-hedron [435126183] (free volume 350 A A determining 1-aminoadamantane guest molecules while atmospheric gas molecules (mainly N2) are in the dodecahedra. As the framework can be formed by linking decahedra and dodecahedra through common faces, both of these are fundamental polyhedra. The ˚ , thus leading to eight-membered rings of the 19-hedra have a free diameter of 4.5 A formation of a two dimensional pore system parallel to (001). Ordinarily the guest molecules block access to these pores so the material is classed as a clathrasil. However, the guest molecules can be decomposed and driven off by heating to 500 C without destroying the framework, thus converting the material into a zeosil – hence the ‘‘missing link’’ description. The structure of the silica sodalite containing ethylene glycol has been determined (Richardson, Pluth, Smith, Dytrych and Bibby, 1988; FURVUJ (XRD), FURVUJ01 ˚ , space group Im3m, unit cell (ND)). At room temperature this is cubic (a ¼ 8.827 A ˚ ) of typical crystals of CS-I and CS-II gas Table 7.9. The cell dimensions (A hydrates and analogues, and the constancy of their ratio T4

Composition

aI

Si

{Si46 [Na8]} {Si136.[Nax]}

10.19(2)

melanophlogite dodecasil 3C

13.436

{46H2O [7.3Xe]} {136H2O [8Ar] [ ]}

11.84(2)

SiO2 H2O

aII

aII/aI 1.435

14.62(2) 1.444 19.402 1.442 17.07(4)

Fig. 7.26. Stereoplot of a representative orientation of the ethylene glycol molecule in the sodalite cage of silica sodalite. The framework Si and O atoms are shown by ellipsoids while the atoms ˚ and Si–O– < Si ¼ 159.7(2) . of ethylene glycol are shown as spherical. d(Si–O) ¼ 1.587(2) A (Reproduced from Richardson, Pluth, Smith, Dytrych and Bibby, 1988.)

DIRECTIONALLY BONDED HOSTS

369

contents {Si12O24 [2(C2H4(OH)2)]}) but there is a sluggish phase transformation to a lower symmetry (probably monoclinic) on cooling below 200K. The guest is disordered at room temperature; one of the orientations and the surrounding sodalite cage is shown in Fig. 7.26. The truncated octahedron [4668], which is the fundamental cage of the sodalite structure, can be packed to form a three dimensional arrangement; no ﬁve membered rings are present in this structure. Analogous minerals are the nosean-sodalite family of felspathoids, of which ultramarine {6(NaAlSiO4) Na2Sx} is one member. This structure is based on the packing of

Fig. 7.27. The structure of Sigma-2, showing stereoviews of the large (upper) and small (lower) cages which make up the framework; Si atoms are at the vertices and oxygen atoms at the centres of the bonds. The overall framework is shown below; Si atoms are at the vertices while oxygen atoms have been omitted for clarity. (Reproduced from McCusker, 1988.)

370

CL AT HRATE INCLUS ION COMP LEXES

cubo-octahedral units, where the vertices are occupied not by single atoms but by (Al, Si)O4 tetrahedra. The aluminosilicate framework is neutralized by interstitial Naþ ions, while sodium sulphides or sulphur are also present interstitially as guest molecules and help to stabilize the relatively porous framework. The holes in the six-ring faces of the cubo-octahedra are large enough to permit relatively easy base exchange, and these materials are not clathrasils. The colours of ultramarines (the semiprecious mineral lapis lazuli) depend on the oxidation state and nature of the guest molecules in the cavities (sulphur gives white, green or blue products, selenium a blood-red and tellurium a yellow colour). The structure of a hitherto-unknown clathrasil (Sigma-2, {Si64O128 [4(1-aminoadamantane)]}, has been determined (McCusker, 1988) from synchrotron powder data ˚ , space group I41/amd), using direct methods and then (a ¼ 10.2387(1), c ¼ 34.3829(1) A Rietveld reﬁnement. There are no pentagonal dodecahedra but two new cage types (Fig. 7.27), with the guest molecules accommodated in disordered fashion in the larger cage. The synthesis from aqueous solutions of an intriguing highly acid crystalline tetrabutylammonium hydrogen silicate (Gerke, Gies and Liebau, 1982) may indicate a linkup of the clathrasils with the peralkylonium salt hydrates (Section 7.2.8). The (single) crystals ˚ , Dm ¼ 1.448(5) g cm3 and the unit cell are face-centred cubic with a ¼ 28.605(6) A content is approximately [(C4H9)4N]24H144[Si168O420] 144H2O. If the synthesis was carried out in the presence of polydentate amines H2N(CH2CH2NH)nH (n ¼ 1,2,3; en, dien, trien ) then the water could be partly (n ¼ 1) or completely replaced; for example, ˚ , Dm ¼ 1.446(5) g cm3 with approximate unit the en phase is also cubic (a ¼ 28.715(3) A cell contents [(C4H9)4N]24H144[Si168O420] 84H2O 36en). The corresponding tetrabutylphosphonium hydrogen silicate was obtained if [(C4H9)4P]OH þ en were used. Crystal structures have not yet been reported. 7.2.7

Gas hydrates (structures with pentagonal dodecahedra)

We retain this name as a convenient cover-all for polyhedral clathrates with uninterrupted frameworks in which the vertex T 4 moieties are water molecules. Designation of the guest molecules as ‘‘gas’’ has historical signiﬁcance only; many guests are liquid at 0 C, which is a suitable reference temperature. The ‘‘classical’’ gas hydrates are CS-I and CS-II (Table 7.4), with about 120 different guests known (Davidson, 1973; Davidson, Handa, Ripmeester, Tse, Dahn, Lee and Calvert, 1986). The more recent discovery of Structure H hydrate (HS-III; Section 7.2.4.3) makes the duo a trio. 7.2.7.1 Relation between guest type and structure type in the gas hydrates A selection of the guest molecules forming CS-I and II gas hydrates is shown in Table 7.10; the arrangement is roughly in terms of largest overall molecular dimension, i.e. including the van der Waals envelopes of the guest molecules. It had earlier been thought that guests of up to some limiting size would form CS-I hydrates and larger guests CS-II hydrates as the guests in CS-I hydrates do not exceed ˚ in largest dimension while the guests which enter the 16-hedra of CS-II about 5.5 A ˚ . This boundary is hydrates appeared to have their largest dimension in the range 5.5–6.6 A

DIRECTIONALLY BONDED HOSTS

371

Table 7.10. Molecules which form binary CS-I (Structure I) and CS-II (Structure II) gas hydrates arranged schematically in order of their largest dimension. A table of this kind was originally presented by von Stackelberg and Mu¨ller (1954) and then in revised form by Davidson (1973). We have included some more recent results, particularly in the box at bottom right, but no claims are made for completeness

6.5 “Largest van der Waals diameter ” Å

CBr2F2 (CH3)3CH, (CH3)3CF, C2H5Br, propylene oxide, cyclobutanone CH3CH = CH2,CHCl3, CCl3F C3H8, cyclopentene, C2F4, CH2 = CHCl, CH3CHCl2, furan, acetone C2H5Cl, CCl2F2, CH3CF2Cl, CBrClF2 cyclopentane, CH2Cl2, CHCl2F, (CH3)2O, dihydrofuran

6.0

5.5

5.0

Structure II tetrahydrofuran SF6, CBrF3 CH3I, CHBrF2 1,3-dioxolane COS, C2H2, CH2 = CHF, CH3CHF2, CH3SH, (CH3)2O BrCl, C2H4, (CH2)3, C2H5F, CHClF2 ClO2, C2H6, CH3Br Cl2, SbH3, CH2ClF, (CH2)2O CHF3, CF4, CH3Cl N2O, SO2 AsH3, CH2F2

Structures I and II

Structure I

CO2 4.5

4.0

CH3F Xe, H2Se, PH3

H2S, CH4 CO

N2 Kr, O2

Structure II

Ar

somewhat ill-deﬁned; for example trimethylene oxide forms hydrates of both types, while COS and CH3Br form CS-I hydrates on their own but CS-II hydrates in the presence of H2S (Davidson, 1973). However, more recent experimental work has demonstrated that smaller molecules such as Ar, Kr (Davidson, Handa, Ratcliffe, Tse and Powell, 1984), O2 and N2 (Tse, Ratcliffe, Handa and Powell, 1986) form CS-II hydrates in which both dodecahedral and 16-hedral cages are partially ﬁlled; a single crystal of an air hydrate (N2 : O2 ratio 1.6–1.9) found in an ice core at a depth of 1500 m at Dye-3, Greenland has been shown to have the CS-II structure (Hondoh, Anzai, Goto, Mae, Aigashi and Langway, 1990). This lower border area of stability between the two structure types is rather diffuse as CH4 and CO (Davidson, Desando, Gough, Handa, Ratcliffe, Ripmeester and Tse, 1987a), which are hardly appreciably larger than Ar, etc., form CS-I hydrates; some guests show phase diagrams in which both structure types appear. The gas hydrates of the low-boiling gases are stable only under considerable pressures; some

372

CL AT HRATE INCLUS ION COMP LEXES

dissociation pressures (in bars) at 0 C are Ar (96), Kr (15), O2 (120), N2 (161), CH4 (26) and CO (128); of course, there is an appreciable kinetic barrier to decomposition at atmospheric pressure, where they are metastable. Filling of the dodecahedral cages by molecules of a third component leads to appreciable stabilization of the CS-II hydrate structure; the historical background was summarized by Davidson (1973, see pp. 115–119). The stabilizing effects of atmospheric N2 and O2 were demonstrated during the nineteenth century, as well as those of a variety of other gases, including especially H2S (von Stackelberg and Meinhold, 1954); the ﬁrst double hydrate, of CHCl3 and H2S, was reported by Loir in 1852. These ternary components were called ‘‘hilfsgassen’’ (helping gases) by von Stackelberg. Use of ‘‘hilfsgassen’’ makes it possible to prepare CS-II hydrates of many larger molecules (e.g. CCl4) that do not form hydrates by themselves. A neat experiment (following Jeffrey (1996)) is to bubble H2S into cold chlorine water and produce a white precipitate of the double hydrate. Udachin and Ripmeester (1999a) have noted that any hydrophobic molecule with van ˚ should be able to ﬁt into the large E cage of the HS-III der Waals diameter of 7.0–8.5 A type of hydrate, and that it should possible to substitute at least one methyl group per molecule of a hydrocarbon guest by OH, SH, Br or I, from one to all methyls by F or Cl, and at least one CH2 group by O, S or C¼O. This gives a large number of possible guests. 7.2.7.2 Stoichiometry and thermodynamics of the gas hydrates Current theory (van der Waals and Plateeuw, 1959) treats the gas hydrates as solid solutions of guest molecules in the cages formed by the frameworks7 of host molecules. Thus the concentration of the guest would be expected to depend on the concentration of the guest in the solution (or the pressure of the gas) from which the crystals were grown. These expectations were conﬁrmed by equilibrium studies of the ethylene oxide–water system (Glew and Rath, 1966) which showed that the compositions (determined via precise density measurements) of the crystals obtained depended on the temperature of crystallization and on the concentration of the solution; crystals richer in ethylene oxide were obtained at lower temperatures and/or higher solution concentrations. The process of hydrate formation requires provision of energy to convert the most stable host structure (for water at 0 C, 1 atm. this would be hexagonal ice) into the framework found in the gas hydrate considered, which would be offset by the gain in interaction energy between host and guest molecules (more correctly, the free energies should be considered). Thus there will be a limiting composition below which the hydrate is unstable; furthermore there will be an optimal (lowest free energy) distribution of guests among the available sites. The minimum condition of stability for the CS-I gas hydrate is given by ideal solution theory as: w ¼ kT½lnð1 qS Þ þ 3 lnð1 qL Þ=23

ð7:8Þ

where is the chemical potential of the water molecules in the empty hydrate framework relative to ice (or liquid water) at 0 C and qS and qL are the degrees of occupancy of 7 The term ‘‘empty lattice’’ is common in the literature. However, as Henry Lipson often pointed out, ‘‘lattice’’ has a speciﬁc mathematical meaning and should be avoided in this context. We prefer to use ‘‘framework.’’

DIRECTIONALLY BONDED HOSTS

373

the small (dodecahedral) and large (14-hedral) cages which just stabilize the hydrate. We quote from an unidentiﬁed source8 ‘‘The empty lattice of either clathrate hydrate structure is unstable and has never been synthesized in the laboratory. The empty lattice serves as a reference state (though a hypothetical one) for the hydrate and a knowledge of its thermophysical properties is important in understanding the lattice dynamics, testing water-water interaction potentials, prediction of the phase equilibria in water (or ice)–hydrate-former systems and analysis of the motions of the encaged molecule.’’ Accurate measurement of composition for gas hydrates is rather difﬁcult and we refer the reader to Cady’s (1983a) discussion for details; it is only fairly recently that most of the problems seem to have been overcome. One would wish to know not only the overall composition but also the distribution of guest molecules among the available cages. A number of methods have been used. In one a physical signal which differs for guests in the different cages is measured; this has been done successfully by using 129Xe NMR spectroscopy for Xe hydrates (Davidson, Handa and Ripmeester, 1986), and use of other NMR methods allows extension to other types of guest (Collins, Ratcliffe and Ripmeester, 1990). In another method a guest is used which will not enter one type of cage, e.g. cyclopropane enters only the larger cages in CS-I gas hydrates. A variation uses hydrates in which the larger cages are fully occupied and occupation of the smaller cages by another guest is measured. An attractive method in principle is measurement of cage occupation factors from X-ray or neutron diffraction structure analyses but disorder of the guests causes problems. Care must be taken that any quantitative analyses intended to be on binary systems are not in fact made on systems which are inadvertently ternary due to the presence of ‘‘hilfsgassen.’’ The most suitable CS-I and II gas hydrates for fundamental thermodynamic studies are respectively those of xenon and krypton, where the guests ﬁt into the cavities without distortion and the requirements for ideal solution behaviour are most nearly met. The hydration number of Xe gas hydrate has been determined as 6.286 0.030 at 0 C and 1.55 bar (Davidson, Desando, Gough, Handa, Ratcliffe, Ripmeester and Tse, 1987b), and the value of qS/qL measured by 129Xe NMR spectroscopy as 0.73 0.02 (qS/qL ¼ 3IS/IL (IS and IL are signal intensities), which takes into account that there are three times as many large cages as small). Combining these values and using Equation 7.8 gives w ¼ 1297 110 J/mol and the composition of the hydrate as {46H2O [5.89Xe] [1.43Xe]}. Thus both types of cage are incompletely occupied (but not to the same extent, as shown by qS ¼ 0.716 0.016, qL ¼ 0.98 0.007), instead of the more simplistic picture in which the 14-hedral cages are completely ﬁlled before guest molecules enter the dodecahedral cages. A similar value for w was obtained from measurements on cyclopropane gas hydrate (Dharmawanda, Parrish and Sloan, 1980) where the guest molecules are too large to enter the dodecahedral cages. These values of w correspond to a limiting hydration number of 7.764 0.037 for CS-I hydrates where the guests are so large that they cannot enter the dodecahedral cages; the corresponding unit cell composition is {46H2O [(5.925 0.028)G] []}, not quite all of the 14-hedral cages being ﬁlled. Compositions and cage occupancies are summarized in Table 7.11 for a number of CS-I hydrates. The experimental results (mostly from NMR) have been

8

Assistance in identifying this quotation will be appreciated.

CL AT HRATE INCLUS ION COMP LEXES

374

translated into compositions expressed as {46H2O [nG]S [mG]L}, the fully-occupied formula being {46H2O [2G]S [6G]L}. It is striking that, except for CO, the large cavities are almost (but not quite) fully occupied and to a ﬁrst approximation, to the same extent, whereas there is appreciable variability in the occupancy of the small cavities, inversely proportional to the size of the guests with the exception of C2D2 (Fig. 7.28). Thermophysical parameters for some CS-I and II gas hydrates are summarized in Table 7.12. We note that an early estimate (Child, 1964b) of (I)w (1255 J/mol) for CS-I hydrates at 273K is very close to the measured values. The value usually taken for (II)w Table 7.11. Hydration numbers, ratio of cage occupancies, compositions and cage occupancies for a number of CS-I hydrates. Data from Davidson, Handa and Ripmeester (1986) except for CO from Desando, Handa, Hawkins, Ratcliffe and Ripmeester, 1990. The asterisks denote that D2O was used instead of H2O qS/qL

Hydration number

nS

nL

CD3F* CD3Cl D2S* H2Se D2Se* C2D2 C2D4 CH4 CO Xe

0.61 0.15 0.27 0.06 0.85 0.04 0.73 0.05 0.75 0.08 0.42 0.01 0.21 0.04 0.92 0.01 1.11 0.06 0.73 0.02

6.48 0.32 7.13 0.18 6.11 0.11 6.29 0.11 6.21 0.18 6.83 0.07 7.26 0.13 6.03 0.08 6.22 0.24 6.29 0.09

1.20 0.53 1.66 1.43 1.48 0.83 0.42 1.79 2.00 1.43

5.90 5.92 5.87 5.88 5.93 5.91 5.92 5.84 5.40 5.88

Occupancy of dodecahedral cages

Guest

2.000

1.500

1.000 C2D2 0.500

0.000 3.9

4.4 4.9 5.4 Largest van der Waals diameter (Å)

Fig. 7.28. The occupancy of the dodecahedral [512] cages in CS-I gas hydrates as a function of guest size; maximum possible occupancy is 2. Occupancy data taken from Table 7.11.

DIRECTIONALLY BONDED HOSTS

375

Table 7.12. Thermophysical parameters for some CS-I and II gas hydrates. KL ¼ Langmuir constant (bar)1. The numbers of guest molecules for CS-I hydrates are with reference to a framework content of 46 H2O (ideal values nL ¼ 6, nS ¼ 2) Gas hydrate

CS-I Xe 6 29H2O1 Xe 5 90H2O cyclopropane. 5 93H2O (CS-II) Kr 6 10H2O2a

w J/mol

Hw J/mol

Large cage

Small cage

qL

No. of guest mols.

KL

qS

No. of guest mols.

KL

35 13

0.716 0.8996

1.43 1.80

1.70 0.14

0.9233

14.77

1.752b

1297 110 1287 1297

931

0.981 0.9996

5.89 5.998 5.925

1068

764

0.9425

7.54

Notes: 1 the values for Xe 6.29H2O are for the equilibrium conditions 0 C, 1.55 bar. (Davidson, Handa and Ripmeester, 1986.) 2 (a) the composition of the Kr hydrate is {136H2O [7.54Kr16] [14.77Kr12]}. The ideal values are nL ¼ 8, nS ¼ 16) (Handa and Tse, 1986); (b) Barrer and Edge, 1967.

for CS-II hydrates at 273K is 808 J/mol (Parrish and Prausnitz, 1972). The corresponding value for the quinol and polymorphs (Ar and Kr guests) is 343 J/mol quinol (Section 7.2.1.3). Composition measurements have been made for a number of other CS-I hydrates (including those with Xe, H2S, SO2, CH3Cl as guests) at 0 C and various guest pressures (precautions were taken to ensure that only water and guest were present in the experimental vessel); the hydration numbers were shown to decrease with increasing pressure in accordance with the predictions of ideal solution theory (Cady, 1981, 1983b). This was also probably true for CH3Br and CHClF2 while for Cl2 qualitative but not quantitative agreement was obtained (Fig. 7.29). With increasing molecular size in the order Xe, SO2, Cl2, CH3Cl, CH3Br, CHClF2 the tendency to occupy the smaller cage becomes less in comparison with the tendency to occupy the larger cage. However, the smaller cages are partially occupied by even the largest of these molecules (Fig. 7.28). We have already noted that the immediate environment of the water molecules is very similar in hexagonal ice and in the CS-I and CS-II gas hydrates (similar hydrogen bond distances and tetrahedral arrangements of ﬁrst neighbours). Calorimetric measurements suggest that speciﬁc heats are essentially the same for hexagonal ice and the CS-I and CS-II gas hydrates with guests such as Xe and Kr (Handa, 1986), but that with larger guests (e.g. propylene oxide, 1,3-dioxolane, 2,5-dihydrofuran, 1,3-dioxane) (Handa, 1985) the heat capacity of the empty framework is greater than that of ice and its temperature dependence is different from that of ice. The thermal expansion of the CS-I ethylene oxide hydrate has been measured over the range 18–260K; the results can be ﬁtted by the polynomial ˚ ¼ 11:835 þ 2:2173 105 TðK1 Þ þ 2:2415 106 T2 ðK2 Þ: aðTÞA

CL AT HRATE INCLUS ION COMP LEXES

376

Pressure, atmospheres

4

CHCIF2

3

CH3CI

CI2

Xe

2

CH3Br

1

H2S

SO2

0 7.8

7.4

7.0 6.6 Hydration number

6.2

5.8

Fig. 7.29. Pressure vs. composition relationships for CS–I gas hydrates at 0 C. The dots represent experimental results while the lines are derived in part from ideal solution theory. (Reproduced from Cady, 1983a.)

˚ ) over the temperature range 20–250K The cell parameter increased by 1.1% (0.13 A whereas for ice in the same range a increases by 0.4% and c by 0.6%. Thus the force ﬁeld governing the dynamics of the water molecules is more anharmonic in the hydrates than in ice (Tse, McKinnon and Marchi, 1987). Analogous information comes from comparison of cell parameters for various CS-I gas hydrates (Table 7.13) and from far IR spectra (Bertie and Jacobs, 1982). The former results show that substitution of smaller guests by larger increases the lengths of the hydrogen bonds by 0.5–1% while the IR spectra show that the vibrational frequencies of the water molecules are lowered by 2.5–3%. Similar but smaller effects of guest size are found in the metalloid structures. It would be useful to compare (extrapolated) cell dimensions at 0K with some parameter representing molecular size, but the measurements are lacking. For the CS-I ˚ (s.u.’s 0.01 A ˚ ) while for some forty hydrates at 273K, a lies in the range 11.75–12.15 A ˚ . The effects of varying occupancy would have to CS-II hydrates the range is 17.0–17.6 A be taken into account for the CS-I but not for the CS-II hydrates. A plot of lattice parameter versus van der Waals diameter and molecular volume at 173K has been presented for a number of CS-II hydrates (Udachin, Ratcliffe and Ripmeester, 2002). There is a general trend of lattice parameter with size of guest but it is not completely regular. The enthalpies of dissociation of a number of CS-I hydrates have been measured calorimetrically (Table 7.14). The CS-II gas hydrate has the ideal formula {136H2O [8M16] [16M12]}. Statistical analysis of the results of composition determinations for 18 different CS-II hydrates

DIRECTIONALLY BONDED HOSTS

377

Table 7.13. Cell dimensions for a number of Types I and II binary gas hydrates. The temperatures of measurement are given CS-I Hydrate

˚) a (A

T (K)

CS-II Hydrate

˚) a (A

T (K)

CH4 Xe Ethylene oxide

11.77(1) 11.84(2) 11.89

100 110 110

Ar Kr O2

17.07(4) 17.08(8) 17.07(1)

100 100 5(ND of deuteriohydrate)

Ethanol(CS69) Trimethylene oxide Cyclopropane (HM69a,b)2

11.88 11.95 11.97

108 110 110

N2 air

17.11(6) 17.24(6)

100 100

(CH3)2O 17.27(11) 123 For comparison, the following values for the metalloid structures have been copied from Table 7.5. {Si46 [Na8]} 10.1983 300 {Si136[Na16] [Na4]} 14.7030 300 Notes: CS69 – Calvert and Srivastava, 1969; HM69a,b – Cyclopropane forms a CS-I hydrate below 257.2 and above 274.7K, and a CS-II hydrate between 257 and 274.7K (Hafemann and Miller, 1969a,b).

Table 7.14. Calorimetrically determined enthalpies of dissociation Hm (in kJ/mol) for some CS-I and II gas hydrates at 0 C, i.e. for the reaction fnH2 O ½G g ¼ nH2 OðiceÞ þ Gð1barÞ The hydration numbers are given for the various hydrates Composition

Hm

Composition

Hm

CS-I gas hydrates Xe 6.29H2O Xe 5.90H2O

25.4(2) 26.5(2)

CH4 6.00H2O C2H6 7.67H2O

18.1(3) 25.7(4)

CS-II gas hydrates 2.79Kr 17H2O

19.5(2)

C3H8 17H2O i-C4H10 17H2O

27.0(3) 31.1(2)

showed that these all had complete ﬁlling of the 16-hedral cages, i.e. the M16 : H2O ratio was 1 : 17 (Gough and Davidson, 1971). Similar results were obtained by Cady (1981, 1983b), who found hydration numbers of 17 at 0 C for SF6 (2–3 atm.), CCl2F2 (0.4–3 atm.) and C3H8 (3.5–4.2 atm.), independent of pressure over the ranges shown. These values agree with the more detailed results obtained later, especially by NMR methods, and discussed above. There are reports that 1,3- and 1,4-dioxane, and some other guests, give hydrates with half-ﬁlling of the 16-hedral cages (Carbonnel and Rosso, 1973) but this has been disproved (Davidson, Gough, Lee and Ripmeester, 1976). Small molecules (Ar, Kr, O2, N2) can occupy both cages; only limited information about cage occupancy is available.

CL AT HRATE INCLUS ION COMP LEXES

378

The Hm values in Table 7.14 can be compared with those determined (Parrish and Prausnitz, 1972) by measuring enthalpies for the process fCS-II hydrate ½CHCl3 g þ 1 mole rare gas ) fCS-II hydrate ½CHCl3 ½rare gas g i.e. where the large cavities in the CS-II hydrate are completely ﬁlled and the rare gas atoms enter the smaller dodecahedral cavities. The values of Hc for Ar, Kr and Xe were 26, 28 and 31 kJ/mol respectively. Application of these methods to the phase diagrams of the gas hydrates has been discussed by van der Waals and Plateeuw (1959) and Davidson (1973). When the critical temperature of the gaseous guest is below room temperature, then the binary phase diagram is similar to that of quinol–noble gas. When the critical temperature of the gaseous guest is above room temperature, then the liquid phases participate in the equilibria; the SO2–H2O phase diagram, shown in P–T projection in Fig. 7.30 is typical of this situation. ˚ ), ﬁrst reported in 1778 by Priestley and identiﬁed SO2 forms a Type I hydrate (a ¼ 11.97 A as an hydrate by de la Rive in 1829 (see Section 7.2.4.1). 100 Roozeboom Tammann and Krige

50

h–I–

20

h – 1–

1

2

10 P(atm)

h+

5

1+ 2 2 1 – 2–

h – 2– g

2

Q2

h+g

1.0

h – 1– g

0.5

1+g

h–I–g

Q1

0.2

I – 1– g

I+g 0.1 –12

g

–8

–4

0

4

8

12

16

°C

Fig. 7.30. P–T projection of the SO2–H2O phase diagram. The experimental points are from Roozeboom (1884, 1885) and Tamman and Krige (1925). ‘1 is the liquid phase rich in water and ‘2 that rich in SO2; h is hydrate, I ice and g gas. The critical constants of SO2 are Tc ¼ 157 C and Pc ¼ 78.6 atm. The region of stability of the hydrate is bounded by the h-I-g, h-‘1-g and h-‘1-‘2 equilibrium lines. (Reproduced from Davidson, 1973.)

DIRECTIONALLY BONDED HOSTS

379

An alternative approach to the study of the stability of the CS-I gas hydrates has been proposed by Rodger (1990) on the basis of molecular dynamics computer simulations. These contradict the assumption made in the standard theory of van der Waals and Plateeuw (1959) that the free energy of the (metastable) host framework (lattice) is independent of which molecules, if any, are occupying the cavities. It was concluded that ‘‘although the properties of the host lattice are remarkably insensitive to the nature of the guest molecule, they do depend appreciably on the number of guest molecules present.’’ The simulations show that ‘‘the water lattice is unstable rather than metastable, and as such, the guest molecules must serve to damp out those critical lattice vibrations that lead to rearrangement of the host matrix . . . the excluded volume of the guest molecules seems to mechanically alter the behaviour of the host lattice, and this perturbation plays an important part in stabilizing gas hydrates in the bulk.’’ It would seem best to continue to use the standard theory, at least until quantitative predictions (not yet available) demonstrate the superiority of the alternative approach. 7.2.7.3 Prototype CS-I and CS-II crystal structures at low temperatures The structure of CS-I ethylene oxide gas hydrate (see also Glew and Rath, 1966) has been determined by X-ray diffraction at 248K ({7.2H2O C2H4O}; McMullan and Jeffrey, 1965; ETHYLO) and by neutron diffraction at 80K, using a deuterated sample ({7.66D2O C2H4O}; Hollander and Jeffrey, 1977; ETXDHY). Essentially the same results were obtained, neutron diffraction conﬁrming the disorder of the deuterons in the hydrogen bonds (and hence that the space group was indeed Pm3n but suggesting a more complex disorder of the ethylene oxide molecules than had been inferred by X-ray dif˚, fraction). The hydrogen-bonded O . . . O distances are 2.766, 2.776, 2.811 and 2.844 A ˚ which are similar to those found in hexagonal ice (2.75 A at 193K). The O–O–O angles in the pentagonal faces range from 104.9(1) to 110.1(1) and in the hexagonal faces are 110.6(1) and 124.7(1) , in good agreement with earlier results; the D–O–D angles are closer to tetrahedral values (or 108 ) but still differ signiﬁcantly from them. Both determinations indicated that the crystals used had 0.4 molecules of air in the dodecahedral cages. The structures of three CS-II hydrates have been determined with high precision : {136H2O [8C4H2O] [7.4H2S]}(Mak and McMullan, 1965; m. pt. 294.45K; XRD, 255K; THFHSH); {136H2O [8CS2] [16H2S]}(Henkel, unpublished); {136D2O [3.5Xe] [8CCl4]} (ND at 13K (KELKUH) and 100K (KELKUH01) (McMullan and Kvick, 1990). In the ﬁrst of these structures it was found that the tetrahydrofuran molecules in the 16-hedra were disordered and freely rotating, in agreement with dielectric absorption measurements (Davidson, Davies and Williams, 1964). There was residual electron density in the dodecahedra corresponding to about 46% occupation by the H2S molecules. The independent angles in the planar pentagonal faces of the dodecahedra range from ˚ ) hexagonal faces are 119.9 ; the 105.7 to 111.5 and in the slightly puckered ( 0.05 A ˚ H-bond distances range from 2.767 to 2.812 A, very similar to those in the CS-I gas hydrates. In the third structure the guests ﬁt very snugly into the dodecahedral and 14-hedral cavities respectively (Fig. 7.31). The independent deuterium-bonded O . . . O ˚ at 13K. Although the molecular distances are 2.731(1), 2.759(1), 2.781(2) and 2.785(1) A

CL AT HRATE INCLUS ION COMP LEXES

380

(a)

(b)

Fig. 7.31. Van der Waals surfaces representing enclosure of Xe in 12-hedron (a) and CCl4 in 16-hedron (b). The views are normal to the pentagonal and hexagonal faces respectively. Atoms of the upper and lower faces of the two cages are omitted for clarity. The CCl4 molecule is shown in one of its three ‘equilibrium’ orientations. (Reproduced from McMullan and Kvick, 1990.)

symmetry of CCl4 ( 4 3m) conforms to that of the 16-hedral cavity, nevertheless CCl4 is disordered over seven preferred orientations (with large libration amplitudes) even at 13K. The deuterium atoms are disordered in the hydrogen bonds in a manner very similar to that found in ice Ih (Kuhs and Lehman, 1987). The recent widespread introduction of area detector methodology into x-ray crystal structure determination has opened a new chapter in the determination of guest location, guest conformation and cage occupancy in the gas hydrates, exempliﬁed by a number of recent studies ((Udachin, Ratcliffe and Ripmeester, 2001, 2002; Kirchner, Boese, Billups and Norman, 2004). Detailed results have been obtained for the CO2, ethane, methane and propane CS-I hydrates, the benzene-xenon and propane-ethanol CS-II hydrates and the methylcyclohexane-methane and adamantine-methane Structure H hydrates. The following quotation from Udachin et al. (2002) gives some sense of what is now attainable. ‘‘As previously identiﬁed by 129Xe NMR spectroscopy, this guest combination gives ˚ . The degree of ﬁlling a Cubic II hydrate (Fd3m) with a unit cell parameter a ¼ 17.363 A of the large cavity is 1.0, and Xe partially occupies the small cavities [degree of ﬁlling 0.82(8)], with the Xe atom at the center of the small cavity. The composition of the hydrate is C6H6 1.63(17)Xe 17 H2O [or, as we prefer, {136 H2O [8 C6H6] [13.0(14) ˚ from the center of the large cavity and Xe]}]. The center of the benzene molecule is 0.27 A the benzene plane is tilted at 24.8 from the hexagonal face of the large cavity. We note that in previous NMR studies, signiﬁcant occupancy of the large cage by xenon was noted. This can be understood in terms of the time that it takes for crystals to take on their equilibrium compositions. The NMR studies were performed during and shortly after the conversion of structure I xenon hydrate to the double hydrate inside the sealed tube. The diffraction studies were performed after the sample annealed over a period of several years.’’

DIRECTIONALLY BONDED HOSTS

381

7.2.7.4 Br2 8.6H2O is the only bromine hydrate, and the implications of this result The bromine hydrates, their composition(s) and structure(s), provide a long-standing puzzle in the chemistry of the polyhedral hydrates, only recently clariﬁed (Udachin, Enright, Ratcliffe and Ripmeester, 1997). The ﬁrst bromine hydrate (composition given as Br2 10H2O) was reported in 1829 (Lo¨wig, 1829). Some fourteen reports followed. Dyadin and Aladko (1977) concluded that, at 0 C, Br2 forms crystalline hydrates with the following hydration numbers : 12.02(6), 10.00(1), 8.32(4), 6.98(6) (the ﬁrst comes from their own work and the others represent weighted means of all available results; ﬁgures in brackets are s.u.’s). All these hydrates were stated to be phases of constant composition despite wide variations in Br2 concentration in the equilibrium solution phase. Cady (1985) reported a hydration number of 7.9 for the only phase (apparently tetragonal) that was obtained in his experiments; however, Dyadin and Udachin (1987) have asserted that Cady actually obtained a mixture of the two lower hydrates. A structure has not yet been suggested for the 12-hydrate, but the 10-hydrate was assumed to have an hexagonal structure with 40 water molecules per unit cell (HS-I), and the 7.0 hydrate to have the CS-I structure. Allen and Jeffrey (1963) obtained tetragonal single crystals of the 8.3 hydrate in the form of clear red needles, up to 5 mm long and 1 mm in diameter, and proposed the TS-1 structure but without atomic coordinates. There is a preliminary report of a neutron ˚, diffraction study of the deuterated complex at 100K; a ¼ 22.910(4), c ¼ 12.034(3) A P42/mnm) (Brammer and McMullan, 1993), conﬁrming the Allen–Jeffrey proposal; Br2 enters the 14- and 15-hedra. However, a detailed report has not yet appeared. Conclusive clariﬁcation of the whole situation has been provided by Udachin, Enright et al. (1997), who also give an interesting historical review. These authors prepared 16 different single crystals, with compositions ranging from Br2 8.62H2O to Br2 10.68H2O, from solutions of different bromine concentrations. There were differences in colour and morphological habit. Nevertheless, diffraction showed that all the crystals were tetragonal (at 173K ˚ ). a ¼ 23.044(1), c ¼ 12.075(1) A We ﬁrst describe the crystal structure, which is consonant with the Allen–Jeffrey proposal, in overall terms in order to relate it to other structures described below (Section 7.2.8.7). Slightly distorted pentagonal dodecahedra can share faces in groups of ﬁve to form a convenient cell for description (Fig. 7.32(a)). Let these pentads be arranged in a ˚ ) such that the pentad centred at the origin is related to that tetragonal cell (a 24, c 12 A centred at 1/2,1/2,1/2 by an n glide parallel to (100) at x ¼ 1/4 (see diagram of space group P42/mnm (No.136) in International Tables for X-Ray Crystallography (1952) for more detail). This relationship is analogous to that between the dodecahedra at origin and center of the unit cell in the CS-I structure. The 10 pentagonal dodecahedra contain 148 water molecules, to which another 24 water molecules must be added to complete the fourfold coordination about each oxygen atom. Such a tetragonal cell has sixteen 14-hedra (T), four 15-hedra (P), and ten dodecahedra (D) – thus the ideal formula is {172H2O [16T 4P 10D]} and the hydration number is 8.6, if one assumes the dodecahedra to be empty. In fact, there are two distinct dodecahedra, 2DAand 8DB, and two distinct 14-hedra 8TA and 8TB. Thus the unit cell content is {172H2O 2[512 (DA)] 8[512 (DB)] 8[51262 (TA)] 8[51262(TB)] 4[51263(P)]}. The bromine molecules are lodged (in disordered fashion described in some detail) in the large 14-hedral (T) and 15-hedral (P) cages (Fig. 7.32(b)). The small dodecahedral cavities are vacant or occupied by air molecules. We quote from

382

CL AT HRATE INCLUS ION COMP LEXES

Fig. 7.32. (a) Above : Structural fragment of ﬁve face-sharing pentagonal dodecahedra, view direction slightly inclined to [001] in order to remove overlap : (b) Below : Projection down [001] of the framework arrangement of the tetragonal bromine hydrate with the disordered bromine molecules within the T and P cavities. Air molecules are shown within the dodecahedra. A distorted version of this structure is found in {164H2O [5{(n-C4H9)4NþF}]}, where some of the usual clathrate hydrate cages are fused to form larger cavities in which the cations are located. (Reproduced from Udachin, Enright, Ratcliffe and Ripmeester, 1997.)

Udachin et al. : ‘‘The locations of the bromine atoms are the same for crystals grown under different conditions. However, the site occupancies differ, resulting in different degrees of cavity ﬁlling and, therefore, different hydration numbers for the crystals.’’ The earlier investigators appear to have been misled by the colour and morphological differences between crystals grown under different conditions. Thus many earlier accounts (e.g. Dyadin and Belosludov, 1996, pp. 806–809) have historical rather than scientiﬁc value.

DIRECTIONALLY BONDED HOSTS

383

This panorama of investigations also provides a striking illustration of the power of modern diffraction techniques of chemical analysis, especially when adequate attention has been paid to the speciﬁcs of specimen preparation. 7.2.7.5

Gas hydrates with charged frameworks (ionic clathrate hydrates) (see also Section 7.2.11)

In general, gas hydrates have neutral frameworks and neutral guests but there are exceptions. Single crystal X-ray diffraction showed that HPF6 7.67H2O (nominal com˚ at 111K and had a CS-I position) crystallized in space group Pm 3n with a ¼ 11.774(5) A gas hydrate structure (Mootz, Oellers and Wiebicke, 1987), with the anions in the 14hedral cages having a twofold disorder about an F–P–F axis perpendicular to the hexagonal faces. It was inferred that there was replacement, for every acid proton, of a water of the framework by an hydrogen ﬂuoride molecule, there being a random distribution of O and F atoms. The ideal composition would then be HPF6 6.67H2O HF, (or {34H2O 6HF 6H3Oþ 2[empty] 6[PF6]} in our standard form), in agreement with conclusions drawn from 19F NMR spectroscopy (Davidson, Calvert, Lee and Ripmeester, 1981). HBF4 5.75H2O and HClO4 5.5H2O have disordered versions of this structure. Structures with peralkylammonium and related cations are discussed in the next Section (Section 7.2.8). 7.2.8 Peralkylonium hydrates and related structures 7.2.8.1

Introduction

We now describe the structures of the peralkylonium salt hydrates and other hydrates in the context of the basic gas hydrate structures, actual and hypothetical. The hydration numbers for the ideal gas hydrate structures are deﬁned as k ¼ V/Z, where V is the number of water molecules in the unit cell and Z is the number of guest molecules. Analogously, a hydration number for the peralkylonium hydrate structures is deﬁned as h ¼ [V– (cZ þ nZ)]/Z, where V is the number of water molecules in the idealized unit cell, Z is the number of guest molecules, c is the charge of the anion and n is the number of water molecules displaced from the framework by one anion. An essential feature of these structures is the formation of larger cavities by coalescence of the smaller cavities typical of the gas hydrates. Some of these larger cavities are shown in Fig. 7.33. The 44-hedron (54064) is formed from four 14-hedra; the 45-hedron (54065) from three 14-hedra and one 15-hedron; the 46-hedron (54066) from two 14-hedra and two 15-hedra; the 48-hedron from four 15-hedra and the ﬁfth polyhedron from two each of the 14-, 15- and 16-hedra. In the peralkylonium salt hydrate series it is possible to vary both cation and anion and investigate how these variations affect the stability, generally measured by melting point, of the hydrate(s) formed. More information is obtained from phase diagrams. In the cation the nature, number and distribution of the alkyl groups can be varied as well as the central atom (N, P, S); it is also possible to use bolaform salts (bis quaternary ammonium salts of formula {[R3N–(CH2)n–NR3] X2}) as hydrate formers (Nakayama, 1979). The anions cover a large range of inorganic and organic anions, the latter including both aliphatic and aromatic anions; dicarboxylates of formula OOC(CH2)nCOO have also been used.

CL AT HRATE INCLUS ION COMP LEXES

384

T4

T3P

P4

T2P2

T2P2H2

Fig. 7.33. Idealized illustrations of some of the multisection (combined) voids found in the hydrates of polyalkylonium salts. The vertices of the polyhedra are the centres of the oxygen atoms or more rarely, the atoms of the polar groups of molecules or anions, and the edges represent hydrogen bonds. (Reproduced from Dyadin and Udachin, 1987.)

Classiﬁcation of the ‘‘higher’’ inclusion hydrates is complicated by the number of intersecting criteria that can be used. The hydrates can be organized on the basis of the chemical nature of the guest, the major distinction then being made between tetra-alkyl ammonium salts (and analogs), and alkylamines. This has been our principal guiding line here. The ﬁrst of these gives ionic clathrate hydrates and the second semi-ionic clathrate hydrates (sometimes abbreviated as semiclathrates). Alternatively, or better additionally, one can consider the crystal-structural relations among the various complexes formed, relating the often-distorted actual structures to the ideal types summarized, for example, in Table 7.4. Here one meets the intersection, because both alkyl-ammonium salt and alkylamine hydrates can be referred to these basic structural types. This has been our subsidiary guiding line, and accounts for the lack of strict segregation on the basis of guest type. The reader’s attention is drawn to the large amount of physico-chemical information given by Dyadin and Udachin (1987); lack of space prevents its adequate inclusion here. 7.2.8.2

Structures based on the CS-I structure

Two crystal structures have been described in this group and a number of other complexes identiﬁed as belonging to it. The cubic {40H2O [2{(n-C4H9)3SþF}]} hydrate9 has a water framework isostructural with CS-I (Jeffrey and McMullan, 1962; TBUTSF). 9 For convenience we use the same type of formulation ({nH2O [G]}) for the peralkylonium and alkylamine hydrates as for the polyhedral clathrates, despite limitations on its applicability because of participation of the guest in the framework structure.

DIRECTIONALLY BONDED HOSTS

385

The S atoms of the cations occupy those vertices of the framework which permit the six alkyl groups to extend into the six 14-hedra of the unit cell. The ﬂuoride ions are incorporated into the water framework but cannot be distinguished (by diffraction techniques) from the water molecules. The pentagonal dodecahedra are also occupied by waters or, less probably, by ﬂuoride ions. The local symmetry of the structure is lowered by the distortions caused by the cation but these are averaged out over the structure as a whole and the crystals remain cubic. A second structure, that of {28.3H2O [Bu4NOH]}, has been described only in sources that are not generally available (Gaponenko, Polyanskaya, Alekseev and Dyadin, 1983); the structure is apparently a superstructure of ˚ , Z ¼ 12 and space group P213. Another ten Bu4Nþ salt hydrates CS-I, with a ¼ 24.426 A have been reported which belong to the fundamental structure type or its superstructure (Dyadin and Udachin, 1987; see their Table 3) but detailed structures have not been reported. The anions are F, formate, acetate, propionate C2H5COO, butyrate C3H7COO, amylate n-C4H9COO, iso-valerate i-C4H9COO (DIHLOV), tungstate, oxalate (57.3; DIHMAI), OOC(CH2)nCOO with n ¼ 2, 3, with hydration numbers ranging from 20 to 28.6 per Bu4Nþ cation; {57H2O [(Bu4P)2 oxalate]} also belongs to this group. We give hydration numbers and REFCODES for some of the anions. 7.2.8.3 Structures based on the CS-II structure This structure, which is completely deﬁned by the vertices of the dodecahedra, has residual 16-hedral voids whose centres form a diamond lattice. As Jeffrey (1984b) points out, tetrahedral voids could be formed which could accommodate much larger tetrahedral cations than have so far been investigated. However, no such structures are yet known. 7.2.8.4

Structures based on the HS-II structure

The only structure known here is that of isopropylamine octahydrate (McMullan, Jeffrey and Panke, 1970; IPRAMH10), which is a distorted variant of the HS-II structure. There are 16-hedra (51264), dodecahedra (512) and 14-hedra (4251062) formed by adding four vertices to two of the dodecahedra. This generates additional small voids that are octahedral hexagonal prisms (4662). The amine molecules are bonded within the 16-hedron, the NH2 group bridging one of the edges of the polyhedron, and also in three different ways within the 14-hedra, thus interrupting the hydrogen bonding between some pairs of water molecules. If the octahedra and dodecahedra are unoccupied then the stoichiometry is 10(CH3)2CHNH2 80H2O. 7.2.8.5 Structures based on the HS-I structure and its superstructure SHS-I The two-dimensional arrangement of pentagonal dodecahedra can be joined to similar layers through water molecules lying in the planes midway between the layers, leaving large voids between them. In its undistorted form this water framework has symmetry P6/mmm, with the 40 water molecules per cell deﬁning three dodecahedra, two 14-hedra and two 15-hedra. Thus the ideal composition of a one-guest hydrate would be {40H2O [2T] [2P] []} and of a two-guest hydrate {40H2O [2T] [2P] [3D]}. Ideal structures of this type are not known but the trimethylamine hydrate {41H2O

386

CL AT HRATE INCLUS ION COMP LEXES

Fig. 7.34. Stereodiagram of the {41H2O.[4{(CH3)3N}]} structure viewed down [0001], showing 24 dodecahedra, and 26 trimethylamine molecules in their large irregular cages. (Reproduced from Panke, 1968.)

˚ at [4{(CH3)3N}]} has a closely related structure (P6/mmm, a ¼ 12.378(6), c ¼ 12.480(4) A 243K) (Panke, 1968; QQQCIY10). Three other crystal structures belonging to this family have been determined; these are orthorhombic {76H2O [2{(i-C5H11)4Nþ F}]} ˚ , Pbmm, Z ¼ 2) (Feil and Jeffrey, 1961; TAAMFH), (a ¼ 12.08, b ¼ 21.61, c ¼ 12.82 A ˚, hexagonal {36.8H2O.[{(n-C4H9)4NþH5C2COO}]} (a ¼ 12.069(2), c ¼ 36.767(6) A 10 P6 2m, Z ¼ 3) (Dyadin, Gaponenko et al., 1984) and monoclinic {46H2O [2{(n˚ , ¼ 122.0(2) , P21/m, C4H9)3Sþ F}]} (a ¼ 12.34(5), b ¼ 32.49(5), c ¼ 12.01(5) A Z ¼ 4; m.pt. 5.6 C) (Beurskens and Jeffrey, 1964; TBUTSF10). In {76H2O [2{(i-C5H11)4Nþ F}]}, four of the eighty vertices (oxygen atoms) per unit cell are replaced by nitrogens and ﬂuorines; the nitrogens expand the framework appreciably and the ﬂuorines hardly at all. The 14- and 15-hedra are distorted but still recognizable. In contrast, in {41H2O [4{(CH3)3N}]} heteroatoms are not introduced into the water framework but the presence of two additional water molecules per cell leads to large distortions in the 14-hedra and a change of the 15-hedra into large irregular cages. Thus the hydrogen bond acceptor function of the nitrogen has in effect led to destruction of the highly symmetrical water framework (Fig. 7.34). The layers of pentagonal dodecahedra found in the two previous structures remain in monoclinic {46H2O [2{(nC4H9)3SþF}]} (Beurskens and Jeffrey, 1964) but here additional water molecules are interposed between them, leading to replacement of the 14- and 15-hedra by a large, irregular cavity which can accommodate two sulphur atoms and six n-butyl chains, arranged back-to-back so that the positively-charged sulphurs are shielded from the water framework (Fig. 7.35). The ﬂuoride ions are incorporated in the water framework and cannot be distinguished from the oxygens by diffraction techniques; they may well be disordered. There are four more examples known with (iso-Am)4Nþ as cation and chloride, iodide, chromate, tungstate as anions, the hydration numbers varying from 36 to 40 per 10 This paper includes crystal data (but not coordinates) for some 16 peralkylonium hydrates with REFCODES DIHxyz where xyz¼JIN, JOT, JUZ, KAG, KEK, KOU, KUA, LAH, LEL, LIP, LOV, LUB, MAI, MEM, MIQ, MOW. More information for some of these complexes is given later.

DIRECTIONALLY BONDED HOSTS

387

Sulfur Carbon Center

010 011/2

1/2 10 1/2 11/2

Fig. 7.35. The structure of monoclinic {46H2O.[2{(n-C4H9)3SþF}]}. Showing the back-to-back arrangement of two cations in the irregular 60-hedral (42548610) cavity. Only one half of the cavity is shown for clarity, and this is occupied by the shaded carbon chain; the second half is related by a center of symmetry at 0,1,0 and is occupied by the unshaded carbon chain. The two parts share the dotted edges. (Reproduced from Beurskens and Jeffrey, 1964.)

cation, as well as a few more miscellaneous examples. Crystal structures have not been reported. 7.2.8.6

Structures based on the OS-I structure

˚ , P212121, Z ¼ 4; The only example is Bu3PO 34.5H2O (a ¼ 23.48, b ¼ 19.50, c ¼ 12.14 A m. pt. 279.7K); the crystal structure has been reported, with coordinates given only for the oxygens of the water framework (Alekseev, Gatilov, Polyanskaya, Bakakin, Dyadin and Gaponeneko, 1982). The structure is unusual in that it is chiral. Two of the framework oxygens are half-occupied, and two 3/4 occupied by water and 1/4 by phosphoryl oxygen. The framework is made of four polyhedral structural units – 16-hedra (64512), 15-hedra (63512), 14-hedra (62512), and pentagonal dodecahedra (512), the latter being unoccupied. This is a semiclathrate hydrate. 7.2.8.7 Structures based on the TS-I structure The tetragonal bromine hydrate has essentially this structure, which is discussed above (Section 7.2.7.4) because of the broad implications of those results. The hydrates of

388

CL AT HRATE INCLUS ION COMP LEXES

(CH3)2O, C3H8 and CHClF2 with similar stoichiometries probably also have this structure. There are many isostructural peralkylonium salt hydrate structures and two have been reported in detail. These are {158H2O [4{(n-C4H9)4Nþ C6H5COO}]} (a ¼ 23.57, ˚ , P42/mnm or subgroup, Z ¼ 4) (Bonamico, Jeffrey and McMullan, 1962; c ¼ 12.45 A ˚ , P42/m, Z ¼ 4) BUABZO) and {164H2O [5{(n-C4H9)4Nþ F}]} (a ¼ 23.52, c ¼ 12.30 A (McMullan, Bonamico and Jeffrey, 1963; TBUAMF). Both are based on the ideal tetragonal bromine hydrate structure but with differing distributions of cations and anions in the water framework. The bulky hydrophobic portions of the cations and of the benzoate anion ﬁll cavities in the water framework and thereby distort and disturb it; indeed in the benzoate complex the cation and anion occupy the same kind of cavities, although not simultaneously and with different arrangements. The benzoate anion is hydrogen bonded to the water framework and resembles in this regard the trialkyline hydrates; this also holds for the iso-caprionate, propionate and iso-amylate anions. Preparative and crystal data surveys have shown that there are 29 isostructural peralkylonium salt hydrate structures with Bu4Nþ as cation, 2 with Bu4Pþ and 1 with Bu3(iso-Am)Nþ (see Table 5 of Dyadin and Udachin (1987) for many details); the anions include ﬂuoride, chloride, bromide, hydroxyl, nitrate, bicarbonate, formate, acetate, m-chlorobenzoate, chromate, tungstate, monohydrogen phosphate, propionate (DIHJIN (31.6))11, butyrate (DIHJUZ (40.4), DIHKAG (35), DIHKEK (32.6)), pentanoate C5H11CO 2 (DIHKOU (39.7), DIHKUA (31.6)), hexanoate (DIHLAH (40.4)), iso-butyrate (DIHLEL (31.8)), iso-amylate, benzoate, (O2C)(CH2)n(CO2) with n ¼ 0–8 (the most stable of these has n ¼ 3 and a melting point of 20.2 C (Nakayama and Watanabe, 1978)). ˚ (space group There are about 160 water molecules per unit cell with a 23, c 12.5 A P4/mmm) but the exact amount varies somewhat from complex to complex; there are some superstructures. Determination of melting points and hydration numbers has led to classiﬁcation of tetra(n-butyl) ammonium salt hydrates with various anions as isostructural either with {164H2O [5{(n-C4H9)4Nþ F}]} or {158H2O [4{(n-C4H9)4Nþ C6H5COO]} (Dyadin, Gaponenko, Aladko and Bogatyrova, 1984; Nakayama and Usui, 1986; Nakayama, 1987). The hydrates formed by salts of (n-C4H9)4NOOCR with short alkyl groups such as R¼H, CH3, C2H5, n-C3H7, t-C4H9, C2H3 (acrylate), C3H5 (methacrylate, crotonate or 3-butenoate) have hydration numbers of 30 and melting points of 10–18 C; they are isostructural with {164H2O [5{(n-C4H9)4Nþ F}]}, as are the hydrates formed by tetra (n-butyl) ammonium carboxylates with long n-alkyl chains ranging from C4 to C10, including unsaturated C7 and C9 chains. These latter hydrates have melting points below 5 C and hydration numbers 30. The long alkyl chains of the carboxylate anions are supposed to penetrate into two face-sharing pentagonal dodecahedra. The clathrate hydrates formed by (n-C4H9)4NO3SR, with R¼H, CH3, C2H5, n-C3H7, i-C3H7, n-C4H9, n-C5H11, also fall into this category as does {60H2O [{[(n-C4H9)4N]2SO3}]}. The hydrates formed by the carboxylates with R¼C4H9, C5H11, C4H7, C5H9 (except for t-C4H9) have hydration numbers of 39 and melting points about 12 C and are supposed to be isostructural with {158H2O [4{(n-C4H9)4Nþ C6H5COO}]}, as are those of (n-C4H9)4NO3SR with R ¼ n-C3H7, n-C4H9, i-C4H9 and C6H5.

11

Hydration numbers in brackets.

DIRECTIONALLY BONDED HOSTS

389

A remarkable hydrate is formed by tetra(n-butyl)ammonium polyacrylate (R4NOOCCHCH2)n, with n 2100; the hydration number is 30 and melting point 11.2 C. This hydrate is isostructural with {164H2O [5{(n-C4H9)4Nþ F}]}. The crystal structure of the related {40H2O [{[(n-C4H9)4Nþ]n PA}]}, where PA is polyacrylate with Mw 1000, has been reported (Udachin and Ripmeester, 1999b; QAFGEJ). At 123K ˚ , space group P42/m; m.pt. 14.3 C. The cations are this has a ¼ 23.420(3), c ¼ 12.342(3) A in the T3P supercages (Fig. 7.33) and the polyacrylate anions in channels formed by agglomeration of modiﬁed T4 cages along [001]; two water molecules are omitted for every four adjoining T4 cavities. The corresponding tetra(isopentyl)ammonium polyacrylate forms a clathrate hydrate with hydration number 42 2, m.pt 19.5 C, which is isostructural with the (i-C5H11)4NF hydrate. 7.2.8.8

The effectiveness of the alkyl substituents in forming hydrates

The quasi-tetrahedral arrangement of smaller cavities coalesced to form larger cavities in the peralkylonium salt hydrates and the trialkyline oxide hydrates gives a preference to the inclusion of symmetrical tetra-alkylonium cations in the hydrates although examples of non-symmetrical cations are also known and some have been noted above. The following order of decreasing ability to stabilize hydrate structures has been given by Dyadin and Udachin (1987). iso-Am > Bu > Am > Pr > iso-Pr; iso-Bu > Et; Me > Hex, Hep. It was concluded, on the basis of the geometry of the cavities, that the neo-hexyl radical should have the greatest stabilizing ability but no data have yet been presented in support of this contention. 7.2.9 Varieties of structures formed by a particular guest We have already noted that particular guests generally form only one type of gas hydrate because of limitations imposed by the size of the guest, but that the size boundary is diffuse rather than sharp and thus there are some guests which can form both CS-I and CS-II structures (Table 7.10). Such versatility becomes enhanced in the more complicated structure types and different framework arrangements appear at different compositions. The phase diagram between (n-C4H9)4PBr and water provides an example – compounds with hydration numbers of 37.5, 32, 26 and 24 appear (Dyadin, Zelenina, Zelenin and Yakovlev, 1973). 7.2.10 The alkylamine hydrates Preparative work and phase diagrams have been reported by Pickering (1893), Somerville (1931) and Favier, Rosso and Carbonnel (1981). Crystal structures have been determined by Jeffrey and coworkers, and Jeffrey (1969, 1984a) has emphasized the relationships between these structures and those of the gas hydrates and the peralkylonium hydrates (Fig. 7.36). Compositions and some other information about the alkylamine hydrates are summarised in Table 7.15. The gas hydrate structures are based on variations of two (or three) principal arrangements, and the peralkylonium salt hydrates are mainly derived from these, with the

390

CL AT HRATE INCLUS ION COMP LEXES

large peralkylonium cations acting as structure determining elements. The alkylamine hydrates come from a much greater variety of structural types, each of which represents a different compromise between the demands of clathration and hydrogen bonding. These complexities make it very difﬁcult to predict structure, and even precise stoichiometry, in the alkylamine hydrates. The various modes of interaction of alkylamine molecules with the surrounding water framework (Fig. 7.36) have been summarized as follows by Jeffrey (1969, 1984a) (see also Table 7 of Jeffrey, 1984a): 1.

2.

3.

True clathrate, no hydrogen bonds to the water framework, as in {156H2O [16{(CH3)3CNH2}]} (McMullan, Jeffrey and Jordan, 1967). This is discussed below, with other structures that do not contain dodecahedral cavities. Formation of one donor and one acceptor hydrogen bond which bridge the water oxygen vertices at the opposite ends of a void, as in {104H2O [12{(CH3CH2)2NH}]} (Jordan and Mak, 1967; DETHHC20). Formation of two donor hydrogen bonds across two adjacent oxygens that could form an edge of a polyhedron of the regular gas hydrate type, as in {80H2O

Table 7.15. The alkylamine hydrates and their compositions (see Notes for References S, P, etc.). Nominal compositions are taken from determinations of phase diagrams and older preparative work, and more exact values from crystal structure analyses; some of the compositions refer to idealized structures. Complexes where both nominal compositions and results from crystal structure analyses are available are bracketed together. The lower hydrates are not polyhedral clathrate hydrates but are included for completeness (a) Primary amines as guests MeNH2 EtNH2 CH3(CH2)2NH2 (CH3)2CHNH2 CH3(CH2)3NH2 (CH3)2CHCH2NH2 CH3CH2CH(CH3)NH2 (CH3)3CNH2 CH3(CH2)4NH2 CH3(CH2)5NH2

3(S); 10(P) 0.5(P); f5:5ðP; SÞ; ½5:45 *g; 0.5 (P, C); 3.5 (P, C); f6:5ðCÞ; ½6:5 *g; f8ðP; CÞ; ½7:96 *g 0.5 (C); 1.5 ( C); 3.5 (P, C); 6.5 ( C); f8ðCÞ; ½7:53 *g; 0.5 (C); 1 (C); 1.5 (C); 38(C) 1(C); 1.5(C); 6.5(C); 12(C); 36(P) 0.5 (C); 1 (C); 4 (C); 6.5(C); 21(C) 0.33(C); ).5(C); 1(C); 2.25(C); 6.5(C); f9:75ðCÞ; ½9:75 *g 0.5(C); 2(C); 5.5(P); 37(P) 0.5(C); 1(C);

(b) Secondary amines as guests Me2NH Et2NH (CH3(CH2)2)2NH

f7ðP; SÞ; ½6:9 *g f6:66ðGÞ; ½6:8 *g; f8ðP; S;Þ; 8:10ðGÞ; ½8:66 *g 0.5(P,C); 5.5(P)

(c) Tertiary amines as guests Me3N Et3N

2(P); 7(P); 10(S) 2(S?,C); 3(C); 8(P); f10ðGÞ; ½10:22 *g; 57(C)

Notes: 1 References are given in brackets and are as follows : P Pickering (1893); S Somerville (1931); C Favier, Rosso and Carbonnel (1981), G Glew (1965). 2 The complexes analyzed crystallographically have compositions inserted in square brackets and are marked with asterisks. Literature references are given in the discussion below.

DIRECTIONALLY BONDED HOSTS

391

[10{(CH3)2CHNH2}]} (McMullan, Jeffrey and Panke, 1970); the structure is related to the CS-II type. 4. Formation of two acceptor hydrogen bonds from a bridging water oxygen, as in {41H2O.[4{(CH3)3N}]} (Panke, 1968) (see Section 7.2.8.5). 5. Replacement of a water oxygen vertex and bridging across a void by a hydrogen bonded dimer of two amine molecules, as in {104H2O [16{CH3CH2CH2NH2}]} (Brickenkamp and Panke, 1973; at 173K; PROAMH) (see Fig. 7.36).

(a)

(b)

(c)

(d)

(e)

(f)

Fig. 7.36. Environments of alkylamine molecules in water clathrate cages : (a) t-Butylamine guest clathrated within a 17-hedron (43596273), in {156H2O.[16{(CH3)3CNH2}]}. This complex is a true clathrate. (b) Diethylamine hydrogen bonded within 18-hedron (51266), in {104H2O [12{(CH3CH2)2NH}]}; there are also irregular cavities (435866) but no dodecahedral cavities. The guests are hydrogen bonded within both types of cavity. (c) and (d) In {41H2O.[4{(CH3)3N}]} there are dodecahedral (512), 15-hedral (51263) and 26-hedral (52462) cavities, the latter being formed from the fusion of two 14-hedra. The hydrogen bonding of trimethylamine within a distorted 15-hedron is shown in (c); in (d) the hydrogen bonding of two trimethylamine molecules and additional water molecules within the 26-hedron is shown. Compare Fig. 7.33. (e) and (f) In {80H2O [10{(CH3)2CHNH2}]} there are 8-hedra (4662), 12-hedra (512), 14-hedra (425864) and 16-hedra (51264). An isopropylamine molecule hydrogen bonded within a 16-hedron is shown in (e) and an isopropylamine molecule hydrogen bonded within a 14-hedron in (f). This structure is related to the HS-II structure type which contains only 12-hedra and 16-hedra. The C and N atoms of the amine molecules are shaded; the water oxygens are the solid vertices and the solid edges are O . . . O hydrogen bonds. The N–H . . . O hydrogen bonds are open. Hydrogen positions are not known. (Reproduced from Jeffrey, 1969.)

392

CL AT HRATE INCLUS ION COMP LEXES

Fig. 7.37. {104H2O [16(n-propylamine)]} – ORTEP stereoview of water framework. The structure contains 11-hedra (425861) and large irregular cavities formed by fusion of 14-hedra (51262) and 16-hedra (51264). The guest molecule (not shown) is hydrogen bonded to the framework from within the large cavities. (Reproduced from Brickenkamp and Panke, 1973.)

A number of tri-n-alkylamine (phosphine, arsine, stibine) oxides form clathrate hydrates (references in Dyadin and Udachin (1987)), and the crystal structure of tri-nbutylphosphine oxide 34.5-hydrate has been reported (see Section 7.2.8.6). 7.2.11

Structures without pentagonal dodecahedra (some with charged frameworks)

The division of polyhedral clathrate structures into those derived from packing of pentagonal dodecahedra and those without these energetically-favored polyhedra has already been noted (Fig. 7.20). Having considered the ﬁrst group in some detail, we now pass on to the second, where rather less information is available. These structures are based on the packing of truncated octahedra (this term is used for the (4668) polyhedron, while the cubo-octahedron is (3846) and the truncated cube is (3866); McMullan and Jeffrey, 1965). In contrast to the many possible space-ﬁlling combinations of pentagonal dodecahedra with other polyhedra, only one space-ﬁlling arrangement of truncated octahedra is possible and thus only one structure type is to be expected. The silica sodalite containing ethylene glycol is one example of such a (neutral framework) structure which has already been mentioned (Fig. 7.26; Richardson et al., 1988). Before embarking on descriptions of the structures, it is worthwhile summarizing new features that become important when the frameworks contain other groups that replace some of the water molecules. The four-connected water molecules in ice and the true clathrates are linked by hydrogen bonds containing disordered half-hydrogens. Replacement of H2O by OH or F results in proton deﬁciency, while introduction of H3Oþ gives an extra hydrogen; thus Jeffrey (1996) entitles a section dealing with this area ‘‘Proton Disorder, Deﬁciency, or Excess in Host Lattices.’’ There are many experimental difﬁculties in determining details of these crystal structures. Hydrogen positions (especially if disordered) can seldom be identiﬁed from ambient temperature x-ray diffraction studies, nor can F and O be differentiated, while low-temperature neutron diffraction studies are entirely lacking. The distances between oxygens in weak hydrogen bonds overlap those in O . . . O van der Waals contacts; sometimes polyhedra are clearly broken (a particular hydrogen bond is replaced by a van der Waals contact), but there are

DIRECTIONALLY BONDED HOSTS

393

Fig. 7.38. Diagram of the packing of truncated octahedra in the body-centered cubic crystals of silica sodalite (where the vertices are the Si atoms of SiO2 groups, cf. Fig. 7.26) and HPF6 5H2O HF (where the vertices are the oxygen atoms of the water molecules). The twofold disordered PF6 anions are enclosed within the truncated octahedra. The signiﬁcance of the arrows is explained in the caption to Fig. 7.39. (Reproduced from Jeffrey, 1984b.)

many examples of disorder. NMR (H, F) can provide information not obtainable from diffraction. Two systems with charged frameworks – the clathrate hydrates of the strong acids HEF6 (E¼P, As, Sb), HBF4 and HClO4 and the tetramethylammonium hydrates – have been studied in detail; although we discuss them separately, we shall emphasize their interconnections. After a somewhat tortured history, the compound with the nominal composition HPF6 6H2O (structure ﬁrst determined from powder data by Bode and Teufer, 1955) has been reformulated as 2{4H2O HF H3Oþ [PF6]} per unit cell. The crystals are cubic ˚ at 107K, Z ¼ 2, space group Im (a ¼ 7.544(2) A 3m; Wiebcke and Mootz, 1986); water and HF molecules are disordered over the vertices of a truncated octahedron (4668), which contains the fourfold disordered PF6 anion (Fig. 7.38). The water framework is cationic, in contrast to gas hydrate and alkylamine hydrate frameworks that are neutral, or those of the alkylonium salt hydrates which are anionic. The isotypes, with As, Sb replacing P, have the same structure. The (nominal) HPF6 7.67H2O hydrate has the CS-I gas hydrate structure, with the anions in the 14-hedra (see also Section 7.2.7.5). There are 92 hydrogen bonds with 98 protons. It was suggested that the unit cell composition was {34H2O 6HF 6H3Oþ 6[PF6]}, giving the required 92 hydrogen-bonding protons. Somewhat similar, but less well-established, proposals have been made for (nominal) HBF4 5.75H2O and HClO4 5.75H2O. The PF6 anion is too large to ﬁt into the dodecahedral cavities, which can contain the smaller BF4 and ClO4 anions; hence the compositional differences. Finally in this section, we note the isotypic hexagonal structures of (nominal) HEF6 6H2O (E¼P, As, Sb), which are derived from the HS-I (hypothetical Type IV clathrate hydrate) structure type (see Table 7.4). The HEF6 6H2O structures were

394

CL AT HRATE INCLUS ION COMP LEXES

determined without taking the superstructure into account (Wiebcke and Mootz, 1988). ˚, The hexagonal unit cell (for HAsF6 6H2O at 148K) has a ¼ 23.428, c ¼ 13.841 A space group P6/mmm. The composition is {46H2O [7X]}, and the polyhedron formula is {46H2O [4662] 3[4258(6)4] 2[51263]}; anions occupy all except the smallest ([4662]) cages. The (6) notation indicates that pairs of vertices are not connected, i.e the 14-hedron is broken. Detailed crystal structure analyses show that there are differences in the stoichiometries of the As and Sb compounds ({33H2O 7H3Oþ 7[AsF6]} and {35H2O 7H3Oþ 7[SbF6]}); perhaps addition of HF will provide the answer but this issue is still open. The existence of pentagonal dodecahedra in the CS-I and HS-I structures points up the need for a ﬂexible attitude to classiﬁcation schemes. The Me4NOH–H2O phase diagram (Mootz and Sta¨ben, 1992) has, inter alia, clathrate hydrate phases with hydration numbers 4, 4.6 (dimorphic), 5 (dimorphic), 6.67, 7.5 (dimorphic), 8.75 and 10. The 4.6, 5, 6.67 and 7.5 phases have incomplete polyhedra, while the others (apart from 4 (structure not known) and 5, stable below 207K, triclinic, Hesse and Jansen, 1991; TMAMOH03) have complete polyhedra but are proton deﬁcient. The ﬁrst example of an incomplete polyhedron was found by McMullan, Mak and Jeffrey (1966) in the orthorhombic crystals of the form of (CH3)4NOH.5H2O (space group Cmcm, Z ¼ 4). This is a distorted version of the body-centered cubic structure found in {4H2O HF H3Oþ [PF6]} (see above); the analogous formulation is {5H2O OH [(CH3)4Nþ]}. The water framework (in which the hydroxyl is incorporated, in some as yet undeﬁned way, making it anionic) has 24 hydrogen bonds but there are only 22 hydrogens. The space-ﬁlling 14-hedra (4668) of the basic structure are changed into broken polyhedra ˚ ) in order to allow for (44(4)2 66(6)2) with certain edges are expanded (from 2.78 to 4.36 A the proton deﬁciency and to contain the twofold disordered (CH3)4Nþ cations (Fig. 7.39). The orthorhombic structure has been further reﬁned at 300K by Hesse and Jansen, 1991; TMAMOH04). The monoclinic 6.67 structure (P21/m, Z ¼ 6; SOXLEW (Mootz and Sta¨ben, 1992)) has two broken polyhedra, occupied by cations, and a third type which is vacant. The framework of the stable form of {7.5H2O.[{(CH3)4NOH}]} (m. pt. 277K; tetragonal, space group I4/mcm, Z ¼ 8; FOXLOT01) consists of eight 15-hedra, containing the cations, and four vacant decahedra, the unit cell formula being {60H2O 8OH 8[51263] 4[4258]}; the framework is proton-deﬁcient with 128 protons for 136 hydrogen bonds. The host structure is isostructural with the hypothetical clathrate hydrate called ‘‘tetragonal II’’ (Table 7.4), derived from the crystal structure of {32H2O [i-C5H11PBr]} (Solodovnikov, Polyanskaya, Alekseev, Aladko, Dyadin and Bakakin, 1982). The isomorphous ternary hydroxide, {14H2O 3(OH) [Csþ 2{(CH3)4Nþ}]} (m. pt. 330K; ˚ , Z ¼ 4, intensities measured at 223K) provides the ﬁrst a ¼ 15.242(8), c ¼ 11.819(6) A example of a metal cation in a polyhedral clathrate hydrate cage (Mootz and Sta¨ben, 1994; WEZXOO). The framework is proton deﬁcient, with 124 protons for 136 hydrogen bonds; the four Cs ions occupy the decahedra. The metastable form (triclinic; FOXLOT10) is appreciably modiﬁed from the form and not all the framework atoms are fourconnected. The decahydrate contains a 17-hedron accommodating the twofold disordered cation, and a vacant nonahedron; the unit cell formula is {40H2O 4OH 4[4151066] 4[4356)}(Pnma, Z ¼ 4; Mootz and Seidel, 1990; FOXLUZ10). Mootz and Seidel (1990) have pointed out that the anionic host framework of the ˚ at 323K, Z ¼ 2, high-temperature form of (CH3)4NOH 46H2O (cubic, a ¼ 8.146(3) A

DIRECTIONALLY BONDED HOSTS

395

b c a

Fig. 7.39. The mode of incorporation of the tetramethylammoniun cation in the water framework of {5H2O OH [{(CH3)4N}þ]}. Later work (Mootz and Seidel, 1990) suggests that the cation is twofold rather than rotationally disordered. In the previous diagram (Fig. 7.38) the arrows show the hydrogen bonds of the analogous {4H2O HF H3Oþ [PF6]} structure which are broken in order to accommodate the tetramethylammoniun cation. (Reproduced from Jeffrey, 1984b.)

m; Mootz and Seidel, 1988; TMAMOH02) is isostructural with the space group Im3 cationic host framework of HPF6 5H2O HF, and can be derived from the hypothetical gas hydrate structure Cub-II (Jeffrey’s VII) (Table 7.4) by statistical substitution of one-sixth of the H2O molecules by hydroxyl ions. The unit cell formula for the host structure is {10H2O 2OH [4668]}; reﬁnement showed that the oxygen positions were 93% occupied. This cubic structure is proton deﬁcient rather than having the incomplete polyhedra of the analogous 5 hydrate. The low-temperature 4.6 ˚ , Pa3, Z ¼ 40; SOXLAS) and has incomplete hydrate is (primitive) cubic (a ¼ 21.493 A polyhedra. ˚ (space group I43d; SOXLIA) and is The 8.75 hydrate is cubic with a ¼ 18.38(2) A isostructural with the alkylamine hydrate {156H2O.[16{(CH3)3CHNH2}]} (McMullan, Jeffrey and Jordan, 1967), which is a true clathrate without hydrogen bonding of guest to the atoms of the framework. The analogous formulation of the 8.75 hydrate is {140H2O 16OH [16{(CH3)4Nþ}]}; the cations are contained within 17-hedral (43596273) cavities, while smaller octahedral (4454) cavities are vacant. The framework is proton deﬁcient with 296 protons for 312 hydrogen-bonded edges. We close this section by noting an uncharged structure not containing pentagonal dodecahedra – the trigonal (T) hydrate structure of Udachin, Ratcliffe and Ripmeester (2001a). This is the dimethyl ether (DME) clathrate hydrate of composition DME.7H2O

396

CL AT HRATE INCLUS ION COMP LEXES

(there is also a CS-II DME hydrate of composition DME 17H2O) DME 7H2O is tri˚ , space group P321. The structure can be described as gonal with a ¼ 34.995, c ¼ 12.368 A 0 {12P 12T 24T 12U 348 H2O}, where P is the 51263 cage known from bromine hydrate, T is the 51263 cage from the CS-I structure, T 0 is a previously unobserved cage 4351063 and U is a small cage designated 425861 encountered previously in a propylamine hydrate and devoid of guest.

7.3

7.3.1

Hosts with a combination of directional bonds and van der Waals interactions Phenol (and related compounds) as hosts

7.3.1.1 Phenol ˚ , ¼ 90.36 , P21, Phenol itself is monoclinic (a ¼ 6.050(1), b ¼ 8.925(2), c ¼ 14.594(3) A Z ¼ 6, at 123K; [001] taken as unique axis) (Zavodnik, Bel’skii and Zorkii, 1988; PHENOL03). There are pseudo-31 axes along [100] and the molecules are hydrogen bonded ˚. into an helical arrangement around these axes; d(O . . . O) 2.66 A Isomorphous clathrates are formed with a range of small molecules which include Xe, HCl, HBr, HI, H2S, H2Se, SO2, CO2, COS, CS2, CH3Br, CH2Cl2, CH3CHF2 and ˚, H2C¼CHF (Nikitin, 1939). The crystals are rhombohedral, space group R3, a ¼ 12.05 A ¼ 85–86 (depending on guest) (von Stackelberg, Hoverath and Scheringer, 1958). The unit cell contains 12 phenol molecules and, normally, four guest molecules; however, more smaller (e.g. HCl, HBr) or fewer larger molecules (e.g. CS2) may be enclathrated. The molecular arrangement resembles that of the quinol clathrates in that the hydroxyls of

Fig. 7.40. Stereodiagram of the rhombohedral unit cell of the phenol clathrates, where pairs of hexameric units around the rhombohedral lattice points nearest to, and furthest from the observer, have been omitted in order to show the ellipsoidal cage more clearly. Hexagons of hydrogen-bonded hydroxyl groups are shown around the corners of the unit cell; the phenyl rings have been omitted for clarity and are indicated only by lines extending from the rings of oxygens. The cavities containing only one molecule are located about the unit cell corners while the ellipsoidal cavity containing three guest molecules is centred at the unit cell centre. The crystal data come from von Stackelberg, Hoverath and Scheringer, 1958. (Reproduced from MacNicol, 1984a.)

HOSTS WITH DIRECTIONAL INTERACTIONS AND VAN DER WAALS BONDS 397

six phenols are hydrogen bonded together to form a planar hexagon, with the phenyl rings protruding alternately above and below the plane of this hexagon. Two such hexagons are aligned parallel, with enough space between them to enclose a smaller guest molecule (Fig. 7.40); this accounts for the twelve phenols of the unit cell. The structure as a whole is formed by repetition of such groupings about the eight corners of the rhombohedral unit cell, enclosing an ellipsoidal cavity between them. Thus there are two types of cavity in the cell – a larger one, which normally contains three guest molecules, and a smaller one, which normally encloses one guest molecule sandwiched between hexagons of oxygen atoms. With larger guests only the larger cavities are occupied, perhaps with less than the full complement of three guests per cavity, while with smaller guests both cavities are occupied and the larger cavity can contain up to four molecules. The phenol clathrates are appreciably less stable than those of quinol; dissociation temperatures (i.e. the temperature at which the partial pressure of guest reaches 1 atm.) and enthalpies of formation and enclathration have been measured (Table 7.16). Clathration in -phenol is a non-stoichiometric, zeolitic process, the absorption isotherms not following Langmuir’s equation, possibly because the guests accommodated in the elongated cavity interact mutually. The values of H((0)(0)) are not constant from one clathrate to the next and this has been ascribed (Allison and Barrer, 1968) to Table 7.16. Enthalpies of reaction (kJ/mol) for phenol clathrates with different guests Guest

HD AB68

Kr Xe CH4 C2H6 C2H4 CO2 SO2 HCl H2S HBr

22.4 34.3 25.9 35.3 32.0 37.9 44.8

TD(K)

HI

C

Temp. range (K)

H((0)(0))

24.7 44.4 27.2 47.7 60.7 64.9

0.7 0.83 0.65 0.88 0.89 0.86

195–228 238–252 195–223 228–244 227–241 241–249

0.59 2.7 0.25 3.7 13 7.5

NK52

30.7

277

30.6 37.7 30.9 35.4 35.6

263 312 279 298 302

Notes: 1. HD is the enthalpy of the reaction : 1 mole gas(M) þ n/ moles -phenol ) 1 mole fðn= Þ phenol [M]g; HD is the enthalpy of dissociation of the clathrate containing one mole of gas (M) as guest. 2. HI is the enthalpy of the enclathration reaction in -phenol : 1 mole gas(M) þ n/ moles -phenol ) 1 mole fðn= Þ phenol [M]g. 3. H((0)(0)) is the enthalpy of the reaction : -phenol ) -phenol and is equal to ( /n)[HDHI]. 4. TD is the dissociation temperatures (i.e. the temperature at which the partial pressure of guest reaches 1 atm.). 5. C is the critical guest composition required for the clathrate to be stable; these values are assumed to be constant over the temperature ranges shown. References: AB68 – Allison and Barrer, 1968; NK52 – Nikitin and Kovalskaya, 1952.

398

CL AT HRATE INCLUS ION COMP LEXES

perturbation of the host structure in different ways by different guests. The larger the value of c required before the clathrate phase will form, the more endothermic is H((0)(0)). The statistical thermodynamic theory of clathration due to van der Waals and Plateeuw is only approximately applicable to the phenol clathrates because among its basic assumptions are that the host framework should not be affected by the clathration and that the cavities be occupied by single guest molecules; neither applies to the phenol clathrates. Comparison of pairs of HD values in Table 7.16 suggests that there is a systematic difference between the values from the two sources. 7.3.1.2 Guayacanin as host This compound, isolated from the heartwood of Tabebuia guayacan Hemsl., has an essentially planar molecule which crystallizes as the acetone clathrate {C30H24O4 [1/ 3 with hexagonal cell dimensions 3(C3H6O)]} in the rhombohedral space group R ˚ , Z ¼ 18 (Wong, Palmer, Manners and Jurd, 1976; GUAYAC). a ¼ 24.68, c ¼ 20.59 A ˚ ) in a chair-shaped sixThe molecules are hydrogen bonded (d(O . . . O) ¼ 2.82(1) A membered ring via their hydroxyl groups, alternate molecules pointing up and down (Fig. 7.41). The cage formed by two such groupings contains two acetone molecules in an ordered arrangement; presumably clathrates would also be formed with other suitably sized guests. The major difference from the analogous clathrates of phenol

O

HO

CH3 CH3 H3C

CH3

Fig. 7.41. Stereoview (looking down c, with a horizontal) of the molecular packing in the guayacanin-acetone clathrate. The thermal ellipsoids are drawn at the 50% probability level except ˚ 2 was for atoms of the (disordered) acetone molecules where an arbitary temperature factor of 1.0 A used. (Reproduced from Wong, Palmer, Manners and Jurd, 1976.)

HOSTS WITH DIRECTIONAL INTERACTIONS AND VAN DER WAALS BONDS 399

and Dianin’s compound is the nonplanarity of the ring of oxygens, these being displaced ˚. from the mean ring plane by 0.92 A 7.3.2 Dianin’s compound (4-p-hydroxyphenyl-2,2,4-trimethylchroman) and related compounds as hosts This compound (7.1 below) was ﬁrst prepared by Dianin (1914), who noted its remarkable ability to crystallize together with many organic solvents which were tightly retained in the crystals of the molecular complexes so formed. Complexes with some 50 different guests were reported when the subject was revived after the Second World War (Baker, Floyd, McOmie, Pope, Weaving and Wild, 1956). Among the guests were Ar, SO2, I2, NH3, ethanol, CHCl3, CCl4, n-heptanol, di-t-butylacetylene, 2,2,5-trimethylhex-3-yn-2-ol, cyclopentane, cyclooctane, decalin, glycerol, SF6 and di-t-butylnitroxide. Parallel surveytype crystallographic studies (Powell and Wetters, 1956; Powell, 1964) suggested that these complexes were true clathrates and this has been conﬁrmed by later concerted synthetic studies and crystal structure analyses, principally by MacNicol and coworkers in Glasgow (MacNicol, McKendrick and Wilson, 1978; MacNicol, 1984a). These studies Table 7.17. Definition of Dianin’s compound and its analogues. For Dianin’s compound (7.1) the configuration shown is ( )-4(S) R8 R2

X

R7

R2' R6 CH3

HY

X

Y

R2

R2 0

R6

R7

R8

Serial number

Are clathrates formed?

O S O O O S O S S O O O S S Se

O O S O O O O O O NH O O S NH O

CH3 CH3 CH3 CH3 H CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3

CH3 CH3 CH3 H CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3 CH3

H H H H H CH3 H H H H CH3 H H H H

H H H H H H H H CH3 H H CH3 H H H

H H H H H H CH3 CH3 H H H H H H H

7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 7.10 7.11 7.12 7.13 7.14 7.15

Yes Yes Yes Yes (quasi-racemate) Yes (quasi-racemate) Yes Yes Yes No No No No No No No

CL AT HRATE INCLUS ION COMP LEXES

400

have proved important for a number of reasons. Firstly, directed syntheses have shown that a number of derivatives of Dianin’s compound form clathrates isostructural with the original group, the differences being understandable in terms of the differences in the molecular structures. This is an interesting example of molecular engineering. Secondly, these complexes are structurally similar to the quinol and phenol clathrates, being based on the formation of hexagonal rings of hydrogen-bonded hydroxyl groups, and thus appreciably broaden this structural family. Thirdly, the importance of this structural type has led to suggestions for the design of complex-forming hosts in which the hydrogen bonds are replaced by covalent bonds; these are the ‘‘hexa-hosts’’ discussed below (Section 7.5). Although most of the results have been obtained for Dianin’s compound itself, we shall treat the family as a whole in order to emphasize the relationships among the various members. The molecules to be considered can all be represented by a single structural formula and the individual compounds are deﬁned as in Table 7.17. The chemical numbering starts from 1 at X¼O (S) in the pyrone (thiapyrone) ring. All the molecules have a chiral centre at C(4) (see for example Dianin’s compound; 7.1); 7.4 and 7.5 have in addition chiral centers at C(2). We ﬁrst consider the behavior of the pure compounds on crystallization from a racemic solution (both enantiomers present in 1 : 1 proportion) because this is relevant to the deﬁnition of the clathrates in terms of the phase rule. Dianin’s compound crystallizes as the racemate as do 7.11 and 7.12; all the other compounds are spontaneously resolved on crystallization. Crystal data are summarized in Table 7.18, including results for Dianin’s compound which has been resolved chemically (Brienne and Jacques, 1975; Collet and Jacques, 1976–7). Table 7.18 thus contains three compounds which are essentially isomorphous and one that is isostructural. Dianin’s compound 7.1 is not spontaneously resolved on crystallization but crystallizes in a racemic rhombohedral space group (Table 7.19). Compounds 7.11 and 7.12 are not spontaneously resolved on crystallization but crystallize in achiral monoclinic space groups, which are not isostructural. A sine qua non for complex formation is that both enantiomers are present in equal amounts. This is immediately understandable in terms of the crystal structure of the

˚ ) for Dianin’s compound and analogues. The space Table 7.18. Crystal data (dimensions in A groups are all P212121 and Z ¼ 4. These data are for the neat compounds and not for the clathrates Compound

a

b

c

Resolved?

Are clathrates formed by racemic host?

(S)-7.1 7.3

10.60 10.66

13.30 13.55

10.08 10.50

Yes Yes

7.10 7.9

10.42 11.78

13.69 16.50

10.37 8.48

Chemically Spontaneously (from C6H12) Spontaneously Spontaneously

No No

Reference / REFCODE HMM79a; MPTMCH HMM79c; HPMTCM

References: HMM79a – Hardy, McKendrick and MacNicol, 1979a; HMM79c – Hardy, McKendrick and MacNicol, 1979c.

Table 7.19. Crystal data (300K unless noted otherwise) for the isostructural clathrates of Dianin’s compound and its analogues. The space groups are all ˚ ) are given for the hexagonal cell containing 18 host molecules R3 except where noted otherwise and dimensions (A Host

Reference/REFCODE

Guest

Host/guest ratio

( )7.1

M84a FKK70; DIANET FK71; DIANHP10 FKK70; DIANCH FK71, AD90, PL90; SIHJEY; SIHJEY10 LG88; GIRBOY

None Ethanol n-Heptanol CHCl3 CCl4 (at 140K)

6 6 6 6

( )7.2

( )7.15

MMW69; HPTHCR MW71; TCHHXO HMMK79 MMKW87; FIYFAU MMKW87; FIYFEY

( )7.3 ( )(S) 7.1þ(þ)(2R,4R)7.4 (þ)(2R,4S) 7.5þ(þ)(2R,4R)7.4 ( )7.5 ( )7.6

HMMW79; MPMCHR10 M84 M84 GHMM79; PMHBZP10 HMM79; METCCP

( )7.7 ( )7.8

M84a HMM79; MSOCYO10 (cyclooctane)

Xe x Ten carboxylic acids (see below) Ethanol 2,2,5-Trimethylhex-3-yn-2-ol Di-t -butylacetylene n-Hexane Ethanol (72 host molecules in unit cell) CCl4 CCl4 CCl4 CCl4 Cyclopentane (also with guests n-pentane and cyclo-hexane, both 6 : 1) Presumably none Cyclooctane (also with guests cyclopropene, cyclopentane, cyclohexane, CCl4 (all 6 : 1); C6H6 (6 : 1.2); toluene, cycloheptane (6 : 1.33)

a

c

6 : 1.4

26.94 26.969 27.12 27.116 27.147 26.912 27.023

10.94 10.990 11.02 11.023 10.939 10.901 10.922

6 6 6 6 6

: : : : :

2 1 1 1 2

27.81 27.91 28.00 28.225 57.42

10.90 10.99 11.08 10.859 10.817

6 6 6 6 6

: : : : :

2 1 1 1 1

27.063 26.94 26.64 26.936 29.22

12.074 11.19* 11.24* 10.796 10.82

32.392 33.629

8.423 8.239

: : : :

2 1 1 1

Notes and References: * Quasiracemates; space group R3. x Structures of ten carboxylic acid complexes (formic, acetic, triﬂuoroacetic, propanoic, pentanoic, isobutanoic, hexanoic, heptanoic and octanoic) have been reported by Small (2003). The ˚ . The dispositions of the compositions (( ) 7.1) : (acid) are 6 : 2 for formic and acetic acid guests and 6 : 1 for the others, and the cell dimensions lie in the range 27.13–27.30, 10.93–11.20 A disordered guest in the cavities were investigated by difference electron density maps. AD90 – Abriel, DuBois, Zakrzewski and White, 1990; FK71 – Flippen and Karle, 1971; FKK71 – Flippen, Karle and Karle, 1971; GHMM79 – Gall, Hardy, McKendrick and MacNicol, 1979; HMM79 – Hardy, McKendrick and MacNicol, 1979; HMMW79 – Hardy, McKendrick, MacNicol and Wilson, 1979; LG88 – Lee, Gabe, Tse and Ripmeester, 1988; M84 – Hardy and MacNicol, unpublished – see MacNicol, 1984; M84a – Mills, MacNicol and Wilson, unpublished – see MacNicol, 1984a; M84a – MacNicol, 1984a; MMKW87 – MacNicol, Mallinson, Keates, and Wilson, 1987; MMW69 – MacNicol, Mills and Wilson, 1969; MW71 – MacNicol and Wilson, 1971; PL90 – Pang, Lucken and Bernardinelli, 1990.

402

CL AT HRATE INCLUS ION COMP LEXES

complexes of Dianin’s compound, and by extension, those of its analogs. These fall into a number of isomorphous groups, all of which taken together are isostructural (Table 7.19). Racemic Dianin’s compound (without guests) and its (many) clathrates are all isomorphous; thus the clathrates are primary interstitial solid solutions of guests in the host framework. This is an unusual but not unprecedented situation in the crystal chemistry of organic inclusion complexes – other examples are the clathrates of -quinol (Section 7.2.1.1) and some clathrates of -trimesic acid (Section 10.3). For all these examples addition of the guest is not necessary in order to stabilize the empty host framework, in contrast to the situation in most other inclusion complexes. The only other compound, of those listed in Table 7.19, which has been shown directly to form primary interstitial solid solutions is 7.7. The other clathrates of Table 7.19 are possibly also primary interstitial solid solutions but crystal data for the neat hosts appears to be lacking. There is spontaneous resolution on crystallization for compound 7.3 (Table 7.18) so the (empty) racemate is less stable than the conglomerate of enantiomers; addition of guest leads to stabilization of the racemate. The clathrates all have essentially the same structure, based on the linking of six molecules by hydrogen bonds to form centrosymmetric hexagonal rings of hydroxyl (or thiol) groups, with alternate molecules (of alternating chirality) pointing up and down (this description must be slightly modiﬁed for the two pseudo-racemates). The groups of six molecules are stacked one above the other, with the mean planes of the hexagonal rings normal to the c -axis direction of the hexagonal unit cell. Thus a cage is formed with one six-ring of oxygens (or sulphurs) forming the ﬂoor of the cage and the next six-ring, one unit cell away along c , forming the ceiling of this cage (and the ﬂoor of the next). The walls of the cage are formed by the remaining portions of the host molecules, three pointing up from the ﬂoor of the cage and three pointing down from the ceiling (Fig. 7.42). The cage can contain three molecules of a smaller guest (e.g. methanol), two of larger guests (e.g. Xe, ethanol or CHCl3) or one of a still larger guest, such as n-heptanol. The smaller guests are often disordered while n-heptanol was found in a gauche conformation, different from its usual extended conformation.12 The linear acetylene 2,2,5-trimethylhex3-yn-2-ol lies along the 3 axis of the unit cell, with statistical disorder of OH and CH3 to conform to this symmetry. In the Xe complex, the two Xe atoms in a cage were found at the (symmetry-related) positions z 0.3 and 0.7. As the average occupancy was 0.71 for the sample used, some cages must be singly occupied with a single location for Xe. Cell dimensions of 7.1 and {7.1.[1.8(ethanol)]}have been measured (using polycrystalline samples) over the range 10–300K (Zakrzewski, White and Abriel, 1990); extrapolation to 0K (Table 7.20) allows examination of the result of incorporation of guest without the complications of anharmonic effects present at room temperature. The effects are rather small at 0K, a small contraction in a and a small expansion in c, giving a contraction of 0.2% in volume. It seems that the pre-prepared cavity accepts the guest molecules essentially without change in its shape. The major change on heating to 300K is the increase in the size of a, and the thermal vibrations of the guest lead to an appreciable increase in overall volume (2.5% for 7.1 and 3.4% for the clathrate). The effects of 12 n-Heptane is not completely extended in its channel inclusion complexes with 1-phenylalkyl-9-anthroates (Lahav, Leiserowitz, Roitman and Tang, 1977; PPANTR, ZZZBKM).

HOSTS WITH DIRECTIONAL INTERACTIONS AND VAN DER WAALS BONDS 403

temperature are appreciably larger than those of clathration. Both these measurements, and those of speciﬁc heat (also for the CCl4 clathrate) (White and Zakrzewski, 1990) show that there are no phase changes in the 0–300K range. The molar heat capacity of the enclathrated guests can be calculated from the measurements and compared with values for the neat guests (cf. Fig. 7.9). CCl4 behaves in the clathrate much as in the bulk, but the pair of hydrogen bonded ethanol molecules in the cage shows differences from bulk (solid and liquid) ethanol. The arrangement described above resembles those found in the clathrates of phenol and guayacanin. Comparison of the dimensions of the six-membered rings (Table 7.21) shows that there are appreciable differences among them, both in regard to O . . . O distances (a measure of hydrogen bond strength) and the degree of puckering. Clearly there is more variability in the strengths of the hydrogen bonds in the clathrates of Dianin’s compound and its analogs than in the quinol clathrates. Values for the phenol complex are not given because of the (inevitable) lack of precision of an analysis carried out in 1958. In the clathrates of Dianin’s compound (7.1) a waist is formed at z c/2 by the 2-methyl group syn to the p-hydroxyphenyl moiety, and the cavity has the form of an ˚ long, with maximum and minimum net diameters (i.e. after allowing hourglass about 11 A ˚ and 4.3 A ˚ for the van der Waals envelopes of the atoms of the host molecules) of 6.1 A respectively (Figs. 7.42(a) and 7.43(a)). Very similar cavity shapes are found in the closely isomorphous clathrates of 7.2 and 7.15, with ether O replaced respectively by S and Se. When the 2-methyl group is removed to give 7.5, the new compound still acts as an host but the cavity is broadened at the waist (Figs. 7.42(b) and 7.43(b)). However, the greatest ﬂattening of the cavity is found in the clathrates of 7.7 (addition of methyl in ˚ and the cavity has position 8) (Figs. 7.42(c) and 43(c)), where the c-axis shortens to 8.2 A the shape of a ‘‘Chinese lantern.’’ MacNicol notes that ‘‘this change in cavity geometry is reﬂected in selective clathration properties.’’ Cyclopentane is selectively enclathrated in 7.7 when recrystallized from an equimolar mixture of cyclopentane, cyclohexane and cycloheptane, while 7.8, with a rounder cavity, favors cyclohexane. Although the clathrates of 7.1 and 7.2 are isomorphous and structurally very similar, their 6-methyl analogs 7.6 and 7.11 pack in quite different ways. Now, referring back to Table 7.17 and bearing in mind the descriptions given above of the various clathrates, it is of interest to see why six potential host compounds do not ˚ ) and cell volumes (A ˚ 3) of 7.1 and {7.1.[1.8(ethanol)]} extrapolated Table 7.20. Cell dimensions (A to 0K, and 300K values (from Table 7.17) Compound

a(0)

( )7.1 26.69 {( )7.1 [1.8(ethanol)]} 26.60 Effects of clathration* a(0) 0.09 Effects of temperature a(300) a(0) ( )7.1 0.25 {( )7.1 [1.8(ethanol)]} 0.37 * X(T)¼X(clathrate, T) X(neat host, T).

a(300)

c(0)

c(300)

V(0)

V(300)

26.94 26.969 a(300) 0.029 c(300) c(0) 0.07 0.07

10.87 10.92 c(0) 0.05 V(300) V(0) 170 231

10.94 10.990 c(300) 0.05

6706 6691 V(0) 15

6876 6922 V(300) 46

CL AT HRATE INCLUS ION COMP LEXES

404

˚ ) of the six-membered rings of hydroxyl (thiol) Table 7.21. Comparison of the dimensions (A ˚ ) is groups in clathrates in which these rings are important structural elements. ‘‘Puckering’’ (A defined as the mean (unsigned) displacement of oxygen (sulphur) atoms from their mean plane; representative values are given. For host/guest ratios see Table 7.19; references to quinol complexes are in Table 7.1 and to Dianin-type complexes in Table 7.19 Host

Guest

d(O . . . O)

Puckering

-quinol -quinol

none none H2S SO2 CH3OH HCl CH3NC CH3CN Xe acetone ethanol CHCl3 ethanol 2,2,5-trimethylhex-3-yn-2-ol di-t–butyl-acetylene n-hexane CCl4 CCl4 CHCl3 cyclooctane

2.677(3) 2.678(3) 2.696(1) 2.727(6), 2.733(6) 2.653(5), 2.779(5) 2.61(1), 2.77(1) 2.779(6), 2.800(6) 2.792, 2.788; 2.785, 2.782; 2.745, 2.773 2.705(2) 2.81(2) 2.85 2.877(3) 2.96(1) 3.03(1) 3.07(1) 2.975(3) 3.76(1) (d(S . . . S)) 2.767(3)

0.059 0.036

guayacanin 7.1 7.2

7.15 7.3 7.5 7.7 7.8

2.78(1)

0.049

0.035 0.92 0.21 0.22 0.24 0.01 0.26 0.38 0.35

form clathrates. The two amino compounds can be eliminated at once as this group cannot form a six-membered hydrogen bonded ring of the type required. It would appear that methyl groups in position 7 interfere with the lateral packing of the columns of cages so this may account for the failure of 7.9 and 7.12 to form clathrates. However, 7.2 and 7.13 differ only in having OH and SH groups respectively, which difference is no hindrance to formation of clathrates by both 7.2 and 7.3; similarly 7.6 and 7.11 have thioether and ether rings respectively, which difference is no hindrance to formation of clathrates by both 7.1 and 7.3. It seems that the tuning is ﬁne indeed and that quantitative calculations rather than qualitative considerations will be needed to account for these delicate distinctions. We have emphasized above that the formation of six-membered rings of hydroxyl groups (also one thiol group) is a structural feature common to the hosts discussed in this section and to the quinol clathrates. How uniform are these rings? We have listed in Table 7.21 the values of d(O–H . . . O) and the degree of puckering (the average (unsigned) deviation of the oxygens (S) from their best plane). The strength of the ˚ ) to weak (d > 3.0 A ˚ ); the rings range hydrogen bonding ranges from strong (d < 2.7 A from planar (e.g. -quinol) to appreciably puckered ({3(guayacanin) [acetone]}. Any

HOSTS WITH DIRECTIONAL INTERACTIONS AND VAN DER WAALS BONDS 405

(a)

(b)

(c)

Fig. 7.42. Comparative stereoviews of the host packing in (a) the CCl4 clathrate of 7.1, (b) the CCl4 clathrate of 7.5, and (c) the neat framework of 7.7. The guest molecules are not shown. (Reproduced from MacNicol, 1984a.)

complete discussion of the thermodynamics of these clathrates would have to take into account variations in the framework, a feature usually neglected. Molecular mechanics and thermodynamic calculations have been made for n-alkane complexes (C5H12 to C9H20) of Dianin’s compound (Iwashiro, 1993). These will be stable if Gincl þ Gvap < 0, and this was found to hold for appropriate mixtures of conformations of the C5 to C8 guests. The all-anti conformation of C5H12 and C6H14

CL AT HRATE INCLUS ION COMP LEXES

406

(a)

(b)

+C

(c) +C

1.0

1.0

7.1 Å 4.2 Å (7.1 Å) 6.1 Å

0.5

7.7 Å

0.3

6.3 Å

0.5 0.3

5.2 Å 2.6 Å

2.8 Å

2.6 Å

0.0

0.0

0 1 2 3Å

Fig. 7.43. Vertical sections through the cavities in the clathrates of (a) 7.1, (b) 7.5 and (c) 7.7. (Reproduced from MacNicol, 1984a.)

comprises 90% of all the probable conformations in the cavity but mixtures of other conformations are found for C7H16 and C8H18. The calculations indicate that the inclusion complexes are enthalpy stabilized at 298K.

7.4 7.4.1

Van der Waals linked hosts Tetraphenylene as host

The formation of complexes of tetraphenylene (tetrabenzo[a,c,e,g] cyclooctatetraene) was reported at the time of its ﬁrst synthesis (Rapson, Shuttleworth and van Niekerk, 1943); these were all of composition {2C24H16 [G]}, where G ¼ benzene, CCl4, dioxan, pyridine, CHCl3 or acetone. Crystal structures have been determined at 300K for a number of complexes (Herbstein, Mak, Reisner and Wong, 1984; Wong, Luh and Mak, 1984), and the subject has been reviewed (Mak and Wong, 1987, 1996). The crystals are isomorphous ˚ , c 18.8 A ˚ , space group P42/n, Z ¼ 2). The structure of {2C24H16.[C6H6]} is (a 9.8 A shown in Fig. 7.44, where it will be seen that the tetragonal crystals contain stacks of tetraphenylene molecules separated by channels parallel to [001] in which the disordered guest molecules (located on sites of 4 symmetry) are included. Even those guest molecules (e.g. CCl4) which could conform to this point symmetry are found to be disordered. ˚ , ¼ 100.56 , As neat tetraphenylene is monoclinic (a ¼ 15.628, b ¼ 13.126, c ¼ 16.369 A 3 ˚ , space group C2/c, Z ¼ 8; Irngartinger and Reibel, 1981; BASCIH), the V ¼ 3301 A complexes constitute separate phases in the binary tetraphenylene–guest phase diagrams. The unit cell dimensions (Table 7.22) show an interesting adaptation of host location to the spatial requirements of the guests; the isomorphous structures can be divided into three groups according to the nature of the guest. The quasi-planar molecules of Group A form a fair progression, as do the quasitetrahedral molecules of Group B; however, the unit cell of tetrahedral CCl4 is more

VAN DER WAALS LINKED HOSTS

407

Fig. 7.44. Stereodiagram of the crystal structure of {2(tetraphenylene).[C6H6]}, viewed approximately down the [001] axis of the tetragonal unit cell. Both orientations of the guest molecule are shown. (Reproduced from Herbstein, Mak, Reisner and Wong, 1984.)

˚ ) of tetraphenylene channel inclusion complexes arranged according Table 7.22. Cell dimensions (A ˚3 to nature of guest. The units of volume are A Group Guest

a

c

A

tetrahydrofuran dioxane benzene

9.906(1) 9.968(1) 10.069(1)

18.503(5) 1815.7 18.553(5) 1843.5 18.431(5) 1868.6

77 97 109

119

cyclohexane

10.073(1)

18.712(3) 1898.6

124

140

18.46(1) 18.491(6) 18.546(6) 18.593(3) 18.633(5) 18.647(4) 18.932(6)

78 81 90 91 101 108 108

82

B

C

CH2Cl2 (CH3)2CO CH2Br2 CHCl3 CH3CHBrCH3 CH2BrCH2CH3 CCl4

9.892(5) 9.902(2) 9.935(2) 9.952(2) 9.973(1) 10.004(1) 9.930(2)

Unit cell Cavity Guest volume volume volume

1806 1813.0 1830.6 1831.5 1853.3 1866.2 1866.8

95 104

117

Reference/ REFCODE

HM82; BESXEC HM82; BESXOM (138K) HM82, HMRW84; BESYIH10 (115K) HM82, HMRW84; BESYON10 (153K) HM82; BESWUR HM82, BESXAY (183K) HM82; BESXIG (185K) HM82; BESWOL HM82; BESXUS HM82; BESYUZ (10 kBar) WLM84; BESYED10

References: HM82 – Huang and Mak, 1982; HMRW84 – Herbstein, Mak, Reisner and Wong, 1984; WLM84 – Wong, Luh and Mak, 1984.

elongated along [001] than one might have expected. Low temperature structures in which the guests are (hopefully) ordered would be needed to account for these anomalies. The approximate cavity volumes (¼1/2(Vcomplex – Vtetra), where Vtetra is the molecular volume of tetraphenylene as obtained from the cell dimensions of neat

CL AT HRATE INCLUS ION COMP LEXES

408

tetraphenylene) match those of the pure guests apart from a systematic discrepancy of 8%, which could indicate that the value used for Vtetra is not quite appropriate for the complexes. Two complexes of substituted tetraphenylenes are noted here as possible springboards for further study. Tetranitrotetraphenylene (positions of nitro groups unknown) gives a complex C24H12N4O8.CCl4 of unknown structure (Rapson, Shuttleworth and van Niekerk, 1943). Perﬂuorotetraphenylene forms a 1 : 1 complex with ferrocene, the structure of which has been reported (OCUJIF) but not discussed.

7.5

Hexahosts and related compounds

On the basis of the widespread occurrence of the six-membered hydrogen ring of hydroxyl groups in clathrates (Section 7.2), it has been argued that hexa-substituted benzenes should be able to function as hosts in clathrate inclusion complexes. The analogy is illustrated in Fig. 7.45 and has been extensively tested by synthetic and structural studies. About half of some 70 potential hosts formed inclusion complexes, and about a dozen crystal structures had already been reported many years ago (MacNicol, 1984b). The hexa-host analogy and related topics have been reviewed by MacNicol and Downing (1996). We give only two illustrative examples of clathrate formation. Hexakis(phenylthio)benzene (–ZR¼–S–C6H5) forms a series of isomorphous rhombohedral complexes with host/guest ratio 1 : 2 with the similar guest molecules CCl4, CCl3Me, CCl3Br, CCl3NO2 C H

O

S

S S CH2

S

S S

Fig. 7.45. The hexahost analogy illustrated – on the left the hydrogen-bonded hexamer typical of quinol and phenol clathrates is shown, with the hexa-substituted benzene analogue on the right. The six-membered rings are planar or approximately so, and the substituents point alternately above and below these mean planes. The diagrams are approximately to scale. The CH2S groups may be represented more generally as ZR and some examples are: XAr; where X ¼ O, S, Se and Ar represents a variety of substituted phenyl rings CH2 XAr CH2 X½CH2 n Ar CH2 SO2 C*HðCH3 ÞPh, giving a chiral host.

HEXAHOSTS AND RELATED COMPOUNDS

409

and CCl3CN (Table 7.24). The crystals of the neat host are triclinic so, again, the complexes are separate phases in the host–guest phase diagram (Pang, Brisse and Lucken, 1995); two independent determinations at different temperatures are in good agreement (Table 7.23). There are clear resemblances to the Dianin family. Our second example of a hexa-host is hexakis( p-t-butylphenylthiomethyl)benzene, where –ZR ¼ –CH2S–p-C6H4–C(CH3)3. This forms clathrates with host/guest ratio of 1 : 2 with cyclohexane, cycloheptane, cyclooctane, toluene, iodobenzene, phenylacetylene, 1-methylnaphthalene, 2-methylnaphthalene and bromoform, and with host/guest ratio of 2 : 1 with hexamethyldisilane and squalene (MacNicol, 1984b). When this host was recrystallized from an equimolar mixture of o- and p-xylene, the clathrate was found to contain 95% o-xylene. The 2 : 1 squalene clathrate (Freer, Gilmore, MacNicol and Wilson, 1980; SQUBPT) is triclinic with reduced cell a ¼ 14.710, b ¼ 15.773, c ¼ 19.745 ˚ , ¼ 101.81, ¼ 109.03, ¼ 98.07 , Z ¼ 1 (2 molecules of host and 1 of guest in the A unit cell), space group P 1. The squalene molecules are accommodated in continuous channels running through the crystal; the disorder of the squalene molecules was resolved and it was found that the squalene conformation in the clathrate was different from that in neat squalene at 163K. An interesting, but perverse, example is provided by hexakis( p-hydroxyphenyloxy)benzene, which forms a rhombohedral adduct with six pyridine molecules ˚ , deg, A ˚ 3) for neat crystals of hexakis(phenylthio)benzene (space group P Table 7.23. Data (A 1, ˚, Z¼1. For comparison, the rhombohedral cell of the complexes (Table 7.24) has a 10.75 A 83.2 (Z ¼ 1) Temperature

a/

b/

c/

Molecular volume

Reference/ REFCODE

300K

9.589 68.45 9.561 68.45

10.256 76.92 10.209 76.98

10.645 65.52 10.619 65.52

883

MWB95; ZERJEL

875

PBL95; ZERJEL01

220K

˚ , deg, A ˚ 3) for some inclusion complexes of hexakis(phenylthio)benzene Table 7.24. Crystal data (A (all measurements at 220K except for the CCl4 and CBr4 complexes (300K)). The compositions are C42H30S6 2(guest). The space group is R3, and the hexagonal cell contains 3 formula units Guest

a

c

Molecular volume

Reference/ REFCODE

CCl4 CBr4 Cl3C–CH3 Cl3C–Br Cl3C–NO2 Cl3C–CN

14.263 14.327 14.203 14.184 14.207 14.321

20.715 20.666 20.571 20.623 20.606 20.474

1216 1225 1198 1198 1201 1212

HMW79; HPTBZC MWB95; ZERJIP PBL95; ZAPCUQ PBL95; ZARDAX PBL95; ZARDEB PBL95; ZARDIF

References: HMW79 – Hardy, MacNicol and Wilson, 1979; MWB95 – Michalski, White et al., 1995; PBL95 – Pang, Brisse and Lucken, 1995.

410

CL AT HRATE INCLUS ION COMP LEXES

per host, and also contains one molecule of water (MacNicol, Mallinson, Murphy and Robertson, 1987; FOPHEX). The perversity arises from the fact that the pyridines are hydrogen bonded to the hydroxy groups and thus this molecular compound really belongs in Chapter 12; however, the water molecules are enclathrated. The analogy has been pushed further by synthesis of octa-substituted naphthalenes; for example, it has been found that octakis(m-tolylthio)naphthalene forms a 1 : 1 clathrate with dioxane and octakis( p-tolylthio)naphthalene a 1 : 2 clathrate (DEFCIA). Octakis(m-tolylthio)naphthalene (DEFCAS) and its dioxane clathrate (DEFCEN) are isomorphous, both crystallizing in space group P4/ncc with Z ¼ 4 (MacNicol, Mallinson and Robertson, 1985). Thus this clathrate is another example of a primary interstitial solid solution. MacNicol (1984b, pp.125–6) has commented that ‘‘an analogy may have its interest but the central questions always are, of course, whether the analogy has any validity and particularly crucial, whether it leads anywhere useful.’’ There is no doubt about the usefulness of the analogy, as even the above very small sample of interesting new hosts and clathrates demonstrates. However, there is not much resemblance between the detailed structures of the clathrates of the hexahosts and those of, say, phenol or Dianin’s compound and its analogs. The hexahosts are bulky molecules with complicated shapes, and often these cannot be packed into a crystal without leaving interstices that can be ﬁlled by a variety of guests.

7.6

Conclusions and a perspective view

Having marshalled the facts currently known to us (and bearing in mind Jeffrey’s remark about these being only the tip of an iceberg), we summarize what is known about two fundamental, and interconnected, issues raised by Dyadin, Bondaryuk and Aladko (1996) – the stoichiometry of the clathrates and their nature as phases. These authors have suggested that three types of solid solution can be distinguished : these are (a) iskhoric of Types I and II, (b) alloxenic and (c) allokiric. In Type I iskhoric (GK. " !! penetrate) solid solutions the host framework is stable even without the presence of guests. These are usually called primary (or ) solid solutions and are well known in metallurgy as substitutional solid solutions (for example, CCP Cu can take up to 33 atomic % Zn in solid solution without change of crystal structure, forming the -brasses). In the present context these would be interstitial rather than substitutional. An example is racemic Dianin’s compound 7.1 (see Table 7.19). Although no deﬁnitive studies appear to have been made, it is quite possible that there is a range of compositions i.e there is no ﬁxed host : guest ratio and the complexes are nonstoichiometric. In Type II iskhoric solid solutions, the clathrate phase has a different crystal structure from that of the pure host, and is only stable when the interstitial cavities have been ﬁlled to a certain degree. Examples of hosts are -hydroquinone (not forgetting that -hydroquinone forms Type I iskhoric solid solutions), and H2O (at atmospheric pressure – to avoid complications caused by very small guests such as hydrogen and helium). For both these hosts, the equilibrium composition depends on the ambient conditions and the nature of the guest. The complexes are nonstoichiometric. Tetragonal bromine hydrate is an excellent example (Section 7.2.7.4).

REFERENCES

411

In ternary (or higher) systems, additional possibilities arise. Alloxenic (Greek o another and " o guest) solid solutions have substitution of one kind of guest by another. A simple example is the mixed argon–krypton hydrate (CS-II) where a complete range of solid solutions is formed. This is analogous to a system like Cu–Ni, where a complete range of solid solutions is formed. Other combinations of metals can give phase diagrams with limited solid solubility and formation of intermediate phases; analogous situations occur in the polyhedral clathrates. Dyadin et al. (1995) consider ‘‘binary hydrates,’’ where there is segregation of the two kinds of guest into cavities of different kinds (sizes), to differ from alloxenic solid solutions. Presumably the matter should be argued on the basis of the particular system being considered. In allokiric (Greek o host) solid solutions units of the host framework are substituted by units of another kind. Metalloid CS-I structures like {Si38Ga8 [K8]} (Section 7.2.5) are examples; it has not yet been established whether a range of compositions is possible. A more complicated situation occurs in (nominal) HPF6 6H2O, where HF and H3O þ replace framework water molecules (Section 7.2.11). Here the requirements of charge balance limit compositional variability. In order to place our present treatment of Polyhedral Clathrates in a wider perspective, it is useful to compare it with the recent comprehensive accounts of Jeffrey (1996; hydrate inclusion compounds) and Dyadin and Belosludov (1996; stoichiometry and thermodynamics of clathrate hydrates). Our treament is at a more introductory level than either of these, but it is broader in the sense that we have included metalloid structures and the clathrasils in addition to inclusion hydrates of various kinds; we have also attempted to weave together structural chemistry and thermodynamics. Jeffrey has written a very comprehensive account of the structural chemistry of his title theme, and who could hope to match his experience and understanding in this area? Dyadin and Belosludov have included a vast amount of material on the physical chemistry of systems ranging across the whole ﬁeld, and connected this thermodynamic approach with the structural chemistry, based on many years of theoretical and experimental studies in both areas. After obtaining an overall picture from the present chapter, a reader could not do better than progress to the deeper and more extensive accounts given by these authors.

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Chapter 8 Inclusion complexes formed by versatile hosts

. . . As clay in the hands of the potter, Who contracts and expands it at will, So are we in Thy hands, O gracious Lord . . . From the Evening Prayer on the Day of Atonement.

Summary: Versatility in a host can be achieved in a number of different ways, all leading to the capability of a single host species to form a variety of inclusion complexes. A small number of examples has been chosen for illustration. Tri-o-thymotide (TOT) interacts with its neighbors (hosts and guests) only via van der Waals forces, forming clathrates with smaller guests and tunnel inclusion complexes of a number of types with larger or elongated guests; some 70 complexes of various types have been recorded. Hydrogen-bonded trimesic acid (TMA) gives tunnel inclusion complexes, with guests ranging from long-chain hydrocarbons to polyiodides, interstitial complexes with halogens and various small molecules as guests; it also forms hydrogen-bonded compounds with suitable acceptors and salts with components having some basic functionality. The Heilbron host E,E-1-[p-dimethylaminophenyl]-5-[o-hydroxyphenyl]-penta-1,4-dien-3-one has at its disposal two possible conformations and can act both as hydrogen-bond donor and acceptor; these potentialities are all exploited in the different complexes studied, which have CHCl3, m-dinitrobenzene and p-dimethylaminobenzaldehyde as second component. Over 100 complexes of racemic gossypol have been prepared and most of these can be grouped into eight different types of hydrogen-bonded arrangement, with more types undoubtedly awaiting discovery. The tripod molecule tris(5-acetyl-3-thienyl)methane (TATM) is a so-far rare example of a ﬂexile molecule (i.e. one that can occur in many conformationally isomeric states (conformers)) which forms host–guest inclusion complexes with a large variety of guests (solvents). Some forty odd different types of guest have been reported to form inclusion complexes. Five different types of crystal structure, with nine different guests, have been reported. Analysis of this substantial but nevertheless incomplete data base shows that each group of crystallographically isomorphous structures contains a particular TATM conformer with characteristic torsion angles. Finally over 200 complexes of a wide variety of guests have been prepared with unsubstituted tetraphenylmetalloporphyrins (containing metals such as Zn, Mn, Fe, 2H) as hosts; many structural resemblances suggest that there is a common interaction in all these complexes, possibly based on charge transfer guest–core and guest–metal interactions.

8.1 Introduction 8.2 Tri-o-thymotide and analogs as hosts 8.2.1 Crystallography of tri-o-thymotide and its complexes 8.2.1.1 The trigonal clathrate inclusion complexes 8.2.1.2 The hexagonal tunnel inclusion complexes

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8.2.1.3 Tunnel inclusion complexes with organometallic guests 8.2.1.4 Crossed tunnel triclinic inclusion complexes 8.2.1.5 Miscellaneous inclusion complexes 8.2.2 Analogs of tri-o-thymotide Trimesic acid and analogs as hosts 8.3.1 Introduction 8.3.2 Host–guest tunnel inclusion complexes based on noncatenated unary hexagonal networks 8.3.2.1 TMA as host 8.3.2.2 Two coordination complexes as potential hosts. 8.3.3 Host–guest tunnel inclusion complexes based on catenated hexagonal unary networks 8.3.4 Host–guest clathrate interstitial inclusion complexes based on catenated hexagonal unary networks 8.3.5 Generalization of the concept of ‘‘interruption’’ to give binary networks 8.3.5.1 TMA.H2O networks 8.3.5.2 Catenated neutral binary networks 8.3.5.3 Ionic binary networks 8.3.6 Hydrogen-bonded TMA binary complexes The Heilbron complexes Gossypol and its inclusion complexes Tris(5-acetyl-3-thienyl)methane (TATM) as host 8.6.1 Introduction 8.6.2 Chemistry of TATM and its inclusion complexes 8.6.3 Conformations taken up by the TATM molecule in the various crystallographic structure types 8.6.4 Crystallography of the inclusion complexes of TATM 8.6.5 Formation of the inclusion complexes 8.6.6 Dynamics of guest molecules in the complexes 8.6.7 Other examples (5,10,15,20)-Tetraphenylmetalloporphyrins and complexes 8.7.1 Introduction 8.7.2 Crystallography of (5,10,15,20)-tetraphenylmetalloporphyrin coordination complexes 8.7.2.1 Introduction 8.7.2.2 The four-coordinate coordination complexes 8.7.2.3 The five-coordinate coordination complexes 8.7.2.4 The six-coordinate coordination complexes 8.7.3 Crystallography of (5,10,15,20)-tetraphenylmetalloporphyrin inclusion complexes 8.7.3.1 Crystallography of four-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.3.2 Crystallography of five-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.3.3 Crystallography of six-coordinate (5,10,15,20)tetraphenylmetalloporphyrin inclusion complexes 8.7.4 Comparative crystallography of the (5,10,15,20)tetraphenylmetalloporphyrin coordination and inclusion complexes 8.7.5 Questions of nomenclature and description

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8.7.6 Can ‘‘sponge’’ structures be inferred from the chemical nature of the second component? References

507 508

8.1 Introduction In this chapter we shall discuss hosts characterized by their ability to form inclusion complexes of a number of different crystallographic types, including the possibility that the host will form both tunnel and clathrate complexes. Usually this only occurs with different guests but there are some examples where a particular guest forms both types, as in some tri-o-thymotide complexes. Another possibility is that host–host interactions for a particular host will be based on directional forces (generally hydrogen bonding) in some complexes, on nondirectional forces (generally van der Waals bonding) in others and on a combination of the two in yet others; this occurs in the Heilbron complexes. Such versatility is in contrast to the greater degree of similarity found in the structural behavior of the hosts discussed in the two preceding chapters. Again we note that this distinction may well disappear, or at least be reduced, with the passage of time. In this chapter we treat all the complexes of a particular host together, in contrast to our practice elsewhere of giving priority to structural rather than chemical resemblances. Clearly many structures discussed in this chapter could have been placed under other headings. 8.2 Tri-o-thymotide and analogs as hosts 8.2.1 Crystallography of tri-o-thymotide and its complexes Tri-o-thymotide (TOT; C33H36O3, 8.1, see also Table 8.4; Chemical Abstracts name 6H,12H,18H-tribenzo(b,f,j))[1,5,9]trioxacyclododecin-6,12,18-trione,1,7,13-tri-methyl-4,10, 16-tris(1-methylethyl)-; CSD name ‘‘tri-o-thymotide’’), ﬁrst synthesized by Naquet in 1865, forms inclusion complexes with a large variety of guests (Baker, Gilbert and Ollis, 1952), the ﬁrst of these (with benzene) having been noted by Spallino and Provenzal in 1909. The most recent, and most comprehensive, review is by Gerdil (1996). The November 2002 version of the CSD gives 32 hits for ‘‘tri-o-thymotide.’’ CH3

O C

(H3C)2HC O

O

CH(CH3)2

O

C H 3C

O C O CH(CH3)2

CH3

424

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Fig. 8.1. Stereodiagram of the TOT molecule in the (M)-(–) propeller conformation with all three carbonyl groups pointing out above the mean molecular plane. (This diagram was made available by Professor D. J. Williams (Imperial College, London); see Williams and Lawton (1975) for acknowledgement.)

The TOT molecule has been shown by NMR to exist in solution as a mixture of a major, propeller, conformation (approximate molecular symmetry C3-3) and a minor, helical conformation (C1-1). However, in its neat crystals and in its complexes it always has the shape of a somewhat ﬂattened three-bladed propeller, with all three carbonyl oxygens on the same side of the mean ring plane (Fig. 8.1). There is some ﬂexibility in the details of its conformation (for example, the angles between the normals to the three phenyl rings are 27, 43 and 43 in the pyridine complex and 30, 37 and 48 in the neat compound) and it has been suggested that such ﬂexibility plays a role in the ability of TOT to form a range of inclusion complexes. The crystals of neat TOT are racemic, having the achiral but non-centrosymmetric space group Pna21 (Brunie and Tsoucaris, 1974; Williams and Lawton, 1975). The structures of all the complexes noted below are different from those of neat TOT, and hence constitute different phases in the binary phase diagrams. The relation between the sense of optical rotation in solution and the absolute optical conﬁguration of TOT was ﬁrst determined from the chiro-optical properties of the (þ)-isomer, which was assigned the M-conﬁguration (left handed propeller form) by Downing et al., (1968). Two independent crystallographic studies have given the opposite assignment. Thus the structure of ()TOT[0.5((R)-2-butanol)] at 123K gave the M-conﬁguration for TOT on the basis of the known absolute conﬁguration of (R)-2-butanol (Gerdil and Allemand, 1979; Allemand and Gerdil, 1981; Gerdil, 1987). The experiment was not without its complications as the guest molecule took up two orientations in the cavity, related by a crystallographic two fold axis, and it was also possible to grow single crystals of (P)(þ)-{TOT.[0.5((R)-2butanol)]}. Conﬁrmatory results were obtained for TOT clathrates grown from optically enriched (S)-(þ)-2-bromobutane and optically pure (R,R)-(þ)-trans-2,3-dimethylthiirane (Arad-Yellin, Green, Knossow and Tsoucaris, 1980). Crystallographic studies of more than 70 TOT inclusion complexes have shown that these can be divided into at least four groups on the basis of the ways in which the guests are included (Tables 8.1 to 8.5). A distinction was ﬁrst made between clathrate (Table 8.1) and tunnel (Table 8.2) complexes (Lawton and Powell, 1958; Powell, 1964; Gerdil, 1987); since then a number of other crystallographic types have been found but not enough structures have yet been analyzed to permit ﬁnality in their classiﬁcation. There is a

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

425

group of linear tunnel complexes with metallorganic guests (Table 8.3) and two group of crossed tunnel complexes where benzene, cis- and trans-stilbene and methyl-cis- and methyl-trans-cinnamate have been found as guests (Table 8.4). In addition there are isostructural groups of miscellaneous complexes of as yet unknown structure (examples in Table 8.5). It seems that any alterations of arrangement needed to obtain maximum packing efﬁciency for different included guests are obtained by a combination of minor conformational changes and adjustments of packing, which are slight within each group but major between groups. The packing efﬁciency appears to be greater in the trigonal clathrates than in the hexagonal tunnel complexes and the cell dimensions of the former vary more with guest size than do those of the latter group. Powell (1964, 1984; see below) has correlated the variations in the cell dimensions with the sizes of the guests. The volume ˚ 3 in neat, racemic TOT and about 7% less than this in the per TOT molecule is 849 A enantiomeric pyridine (trigonal) clathrate. Is this an example of closer packing of enantiomers than of pairs of racemic molecules, which would be contrary to Wallach’s ‘‘Rule’’ discussed in Chapter 10? 8.2.1.1 The trigonal clathrate inclusion complexes The ﬁrst group to be discussed is that of the trigonal clathrate complexes (Table 8.1), where a necessary, but not sufﬁcient, condition for formation is that the largest molecular ˚ . The ideal composition of the clathrates is dimension should not exceed 9.5 A {2(TOT)[guest]}, and this is usually found, although C2H4I2 as guest is an exception. The guests are often disordered at room temperature. The following are among the guests forming clathrates: 1. Primary alcohols – ethanol to pentanol; methanol forms a clathrate only in the ˚ and it also presence of acetone while the largest dimension of pentanol is 9.5 A forms tunnel complexes. 2. Alkyl halides – CH3Br to n-C4H9Br (n-C4H9I forms a tunnel complex). 3. Dihalogenoalkanes – X(CH2)nX for X ¼ Br, n ¼ 1 to 3; for X ¼ I, n ¼ 1. 4. Miscellaneous – pyridine, diethyl ether, acetone, C2H4I2 (90% of the cages are empty), I2.

˚, A ˚ 3) for neat TOT (a) and its trigonal clathrate complexes (b) (at room Table 8.1. Crystal data (A temperature, unless stated otherwise). The space groups (S. G.) of the trigonal clathrates are all P3121 (absolute configuration not implied), with Z ¼ 6. Asterisks in the table denote crystals for which full structure analyses have been reported. Angles (90 , 120 ) determined by symmetry are not included Table 8.1(a) Substance (formula unit)

Reference/Refcode

a

b

c

V/Z

TOT* Z ¼ 4 Pna21

BT74 TOTHYM WL75 TOTHYM01

16.05 16.049

13.39 13.424

13.94 13.909

749 752

References: BT74 – Brunie and Tsoucaris, 1974; WL75 – Williams and Lawton, 1975.

426

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Table 8.1(b) Substance (formula unit) Trigonal clathrate complexes TOT[0.5(ethanol)]* [0.5(acetone)]* [0.5(pyridine)]* [0.5((R)(–)-2-butanol at 123K* [0.5(C5H11OH)] [0.5(bromocyclohexane)) [0.5(chlorocyclohexane)) at 158K* [0.5(thiophene))* [0.5(2-bromobutane)] at 125K [0.5(ethylmethylsulfoxide)] [0.5(benzene)] [0.5(chloroform)] ( þ )-TOT[0.5(( þ )-2-bromobutane)] at 223K [0.5(3,4-epoxycyclopentanone)] [0.5((R)-4-hydroxycyclopent-2-enone)] [0.5( þ )-trans-2, 3-dimethylthiirane)] (racemate) [0.5(S,S)-( )-2,3-dimethylthiirane [0.5(trans-(R,R)-( þ )-2, 3-dimethyloxirane [0.5(R,R)-( þ )-2,3-dimethylthiirane TSBS [0.5((S)( þ )-butanol]* at 90K

Reference; Refcode

a

c

V/ Z

LP58; WL75; TOTETL FRHP92; PENPIH BNTDG77; TOTPYD10 AG83; OTHYMD WL75 GF85; DITRON GF85; DITRIH PB96; TOYBIS AG82; BERWIE; THYBBU is stereoisomer AG82; BIGDAW NP52; ZZZWAK NP52; ZZZWAG A-Y,GKT80; THYBBU

13.443 13.46 13.67 13.642 13.70 13.794 13.604 13.585 13.620

30.143 30.30 29.90 30.180 30.74 30.876 30.605 29.914 30.075

786 792 806 785 832 848 817 797 805

13.538 13.70 13.55 13.72

30.598 29.90 30.30 30.24

809 810 803 822

GLB99; CIDDOI GLB99; CIDFEA CABRAY; A-YGKT80

13.660 13.765 13.611

30.304 30.057 30.340

816 822 811

CABREC; A-YGKT80 CABPUG; A-YGKT80

13.603 13.484

30.440 30.440

813 799

THYMTI; A-YGKT80 GG92; PABJAD

13.600 13.556

30.280 31.705

808 841

Notes: (1) – The compositions given are nominal compositions not always realized in practice. In PB96 it is stated correctly that the unit cell contains six TOT molecules, and that the host : guest ratio is 2 : 1, but the number of thiophenes in the cell should be 3 and not 1, as stated in the Abstract. It is the cavity which contains a single thiophene. (2) – Cell dimensions have been given (Arad-Yellin, Green, Knossow and Tsoucaris, 1983) for trigonal clathrate complexes (space group P3121) with the following guests: 2-chlorobutane, 2-bromobutane* (at 225K; there is an independent structure analysis at 125K (Allemand and Gerdil, 1983)), 2-iodobutane, trans-(R,R)-2,3-dimethyloxirane* (CABPUG, structure at 223K), trans-2,3-dimethylthiirane*, trans-2,3-dimethyloxetane, trans-2,3dimethylthietane, propylene oxide, 2-methyltetrahydrofuran, methyl methanesulﬁnate, 2,3,3-trimethyloxaziridine. References: AG81 – Allemand and Gerdil, 1982; AG81 – Allemand and Gerdil, 1983; A-Y, GKT80 – Arad-Yellin, Green, Knossow and Tsoucaris, 1980; BNTDG77 – Brunie, Navaza, Tsoucaris, Declercq and Germain, 1977; FRHP92 – Facey, Ratcliffe, Hynes and Ripmeester, 1992; GF85 – Gerdil and Frew, 1985; GG92 – Gnaim, Green, AradYellin, Vyas, Frolow and Keehn, 1992; TSBS is tri-3-(2-butyl)-6-methylsalicylide; GLB99 – Gerdil, Liu and Bernardinelli, 1999; LP58 – Lawton and Powell, 1958; NP52 – Newman and Powell, 1952; PB96 – Pang and Brisse, 1996; WL75 – Williams and Lawton, 1975.

In the trigonal clathrate complexes, the cell dimensions show a marked dependence on the nature of the guest; this excellent illustration of ‘‘adaptability’’ is shown in Fig. 8.2 where the a and c dimensions are plotted for an eclectic group of guests. There is a only rough linear relation between a and c, with many exceptions. However, the linear

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

427

relationship is obeyed well for the homologous series of {TOT[0.5(n-alkanol)]} complexes (data from Lawton and Powell, 1958). Thus, (to quote Powell (1964, p. 475)), ‘‘the steady increase in the clathrate [unit cell size] is [due to] . . . an adaptation of the cage size to the increasing size of its imprisoned molecule.’’ The roughness of the overall linear relationship shows that shape of guest, in addition to size, must be taken into account. The careful measurements of cell dimensions and crystal densities by Lawton and Powell (1958) (some of the densities were reported with standard uncertainties as small as 0.0003 g cm3!) demonstrated that the unit cells of these complexes always contain 6 TOT molecules and 3 guest molecules, thus implying some empty space in the cavities when smaller molecules are guests. Other guests show similar behaviour but the data are not as complete. The apparent appearance of empty space in the tunnels reminds one of the behavior of the deoxycholic acid tunnel inclusion complexes of fatty acids (Section 6.3.1). ˚ and the guest molecule is The cage has approximate dimensions 9.0 5.8 7.9 A surrounded by eight TOT molecules (Fig. 8.3). The TOT clathrates with C3H7Br (one of two polymorphs) and C4H9Br show doubled values of the a dimension, implying a lateral ordering of the guests. A structure analysis of the 2 : 1 clathrate of TOT with 2-chlorocyclohexane showed that the guest was disordered over the axial 2-chloro chair and axial 2-chloro boat conformations in 2 : 1 ratio; both the axial and the boat 31.2

31

30.8

c (Å)

30.6

30.4

30.2

30

29.8 13.4

13.5

13.6 a (Å)

13.7

13.8

Fig. 8.2. 54 pairs of a and c cell dimensions are plotted for trigonal TOT clathrates, the values being taken from Table 8.1, literature sources and Table 1 of Gerdil (1996). The ﬁlled circles are for the homologous series of TOT[0.5(n-alkanol)] complexes, with the points in order from left to right for the guests C2H5OH, CH3OH, n-C3H7OH, n-C4H9OH, n-C5H11OH. The methanol values are anomalous because this complex also contains acetone. The open circles are for a catholic variety of guests.

428

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Fig. 8.3. Stereodiagram of the eight TOT molecules surrounding the CH2I2 guest (only iodines shown) in TOT[0.5(CH2I2)]. (For acknowledgements see Williams and Lawton, 1975.)

conformations are thermodynamically disfavoured (Allemand and Gerdil, 1982). These conclusions about the guest conformations were conﬁrmed by IR spectroscopy. The crystal structure (at 298K) of the {TOT[0.5(acetone)]} clathrate and the guest dynamics (over the temperature range 77–298K) have been studied by a combination of XRD, solid state NMR and molecular modelling (Facey, Ratcliffe, Hynes and Ripmeester, 1992). The crystals are isomorphous with the other examples of the trigonal clathrate type, the acetone carbonyl bond lying along the two fold axis of the space group. Although the displacement factors of the atoms of the acetone and of the carbonyl groups of the host are larger than those of the other atoms, there was no large scale disorder. The solid state 2 H NMR study was carried out using acetone-d6, and the 13C study using acetone with the carbonyl C enriched to 12 mol%. Their main conclusions, with particular relation to the dynamics of the acetone molecule, were summarized by Facey et al., as follows. A number of dynamic processes occurred. The methyl groups of the enclathrated acetone undergo rotation at rates 107 Hz at 77K. Above this temperature a new slow motion sets in, which is primarily a two fold ﬂip of the acetone molecule about the carbonyl bond with an activation energy of 13.6 0.8 kJ/mol. There is a secondary site, energetically less favourable by 4.4 0.5 kJ/mol, at an angle of 63 10 from the favored site. The general shape of the potential was conﬁrmed by molecular mechanics calculations on a group of 410 atoms comprising the eight TOT molecules surrounding an enclathrated acetone, but quantitative agreement was difﬁcult to obtain because of the need to take into account the dynamics of the guest molecule and of the ﬂexible host molecules. The success of the study was ascribed to the use of a combination of complementary techniques, whereas each on its own was not able to provide more than a part of the overall picture. Because of the spontaneous resolution of TOT on crystallization with guests, considerable attention has been given to the possibilities of using TOT as a resolving agent for enantiomeric mixtures of suitable guests (Arad-Yellin, Green, Knossow, Ryanek and Tsoucaris, 1985). A measure of the enantioselectivity is given by the enantiomeric excess (e.e.) of the guest in a single TOT crystal of given handedness. The clathrates give e.e.

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

429

values ranging from 2 to 83% while the tunnel inclusion complexes give small but still signiﬁcant values around 5%. Ampliﬁcation of the optical purity of the guest can be obtained by successive recrystallizations. Chiral recognition using TOT complexation has been discussed in detail by Gerdil (1987, 1996). 8.2.1.2

The hexagonal tunnel inclusion complexes

Hexagonal linear tunnel complexes (Table 8.2) are formed when the longest molecular ˚ but with the other dimensions such that the guest can ﬁt into dimension exceeds 9.5 A ˚ . The ratio TOT : guest is generally a tunnel with cross-sectional diameter of about 4.3 A not that of two small integers because the guest molecules are longer than the periodicity of the host matrix in the tunnel axis direction. The following are among the guests forming tunnel inclusion complexes: 1. 2. 3. 4. 5. 6.

RX with R ¼ C5H11 and above, X ¼ OH, Br. RI with R ¼ C4H9 and above. I(CH2)6I and higher ,!-dihalogenoalkanes. ROR’, with R ¼ CH3 or C2H5, R’ ¼ C4H9. Hg(C2H5)2. The tetraketone CH3(CH2)7COCH2CO(CH2)7COCH2CO(CH2)7CH3.

˚ , deg., A ˚ 3) for the hexagonal linear tunnel complexes of TOT (at Table 8.2. Selected crystal data (A room temperature). Asterisks in the table denote crystals for which full structure analyses have been reported. The absolute structure was determined only for the last entry Hexagonal linear tunnel inclusion complexes: (long-chain guests) Composition/Reference/Refcode a c TOT[0.5((R(–))-2-butanol)] LP58 0.2(TOT)[(n-C16H33OH)] (cetyl alcohol)* WL75; TOTCET [0.5 C4H9I] LP58 [0.5Br(CH2)10Br]* S-GH 99 [0.5I(CH2)8I]* S-GH99 [0.5I(CH2)10I]* S-GH99 [0.5(n-hexane)] NP52; ZZZWAG [0.5Br(CH2)8Br]* S-GH00 (123K) (see Note (3))

V/Z

Z

Space group

14.31 14.31

28.99 29.02

858 858

6 6

P62 P61

14.25 14.294 14.319 14.285 14.20 37.162

29.03 29.039 29.111 29.123 28.90 29.207

851 856 862 858 841 832

6 6 6 6 6 42

P31 P61 P61 P62 P62 P65

Notes: (1) The compositions given are nominal compositions not always realized in practice, e.g. the cetyl alcohol complex was 6 : 1.3. (2) Cell dimensions have been given (Arad-Yellin, Green, Knossow and Tsoucaris, 1983) for tunnel complexes (space group P61) with the following guests: 2-chloro-octane, 2-bromo-octane, 3-bromo-octane, 2-bromononane, 2-bromodecane. (3) a ¼ 3as þ bs; b ¼ as þ 2bs, c ¼ cs, where the ‘‘s’’ subscript refers to the cell used for the other complexes. p a ¼ 7as. The space group is for the crystal used in the structure analysis. No Refcode. References: (1) LP58 – Lawton and Powell, 1958; NP52 – Newman and Powell, 1952; S-GH99 – Serrano-Gonzalez and Harris, 1999; S-GH00 – Serrano-Gonzalez and Harris, 2000; WL75 – Williams and Lawton, 1975.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

430

7. 8.

n-C12H25COOCH3. CH3C(H)C6H13X, with X¼OH, Br.

In the hexagonal linear tunnel inclusion complexes the dimensions of the unit cells are ˚ . Three space groups have been encountered – all similar, with a 14.2 and c 29.2 A P31, P61 and P62 (and enantiomorphs); among a group of 28 crystals of the tunnel type with unbranched guests, 19 had P61, 5 had P31 and 4 had P62 (Lawton and Powell, 1958). The changes in arrangement due to adoption of one of the other space groups are expected to be minor. The changes in cell dimensions with the nature of the guest are appreciably smaller than those found for the trigonal TOT clathrates but periodic variations do occur which depend on the nature of the guest. These are plotted against the molecular length in Fig. 8.4 and have been discussed in detail by Powell (1964); brieﬂy stated, the periodic variations are ascribed to the better ﬁt that occurs between host matrix and guest when the guest approaches certain critical lengths. The structures consist of a spiral arrangement of the roughly disc-shaped TOT molecules around the [001] axis (Fig. 8.5), leaving a tunnel ˚ ; the unhindered nature of the tunnel (Fig. 8.6) is draof approximate diameter 4.3 A matically shown by the formation of tunnel inclusion complexes of the tetraketone CH3(CH2)7COCH2CO(CH2)7COCH2CO(CH2)7CH3. Some crystals give one dimensional diffuse X-ray scattering from the guests when the periodicities of host molecule matrix and included guest molecules along the axis of the 14.35 C7Br C3OH

C7OH

C6Br

14.30

C12OH C16OH

C5I C4I

14.25

C18I C18OH

n-c12H25Co2Me

C5Br

2C/6

14.20

C18Br

C10OH

C8I

C6OH

C16I

C8Br

C8OH

a(Å)

C16Br

C7I

4C/6

3C/6

5C/6

5150 Vol.(Å)3 5100

Molecular length(Å)

29.15

C5OH

10 C5Br

15

C5I

20 C10OH

C6Br

c(Å)

25

n-c12H25Co2Me

29.10

C18Br C16I

29.05

C7I

C7OH C4I

C7Br C8OH

29.00

C18OH

C16OH C8Br

C18I

C16Br

C8I C12OH

C5OH

Fig. 8.4. Variation of cell dimensions with the (nominal maximum) length of the included molecule in the tunnel inclusion complexes of TOT. Alcohols are shown by circles, bromides as squares and iodides as triangles. (Reproduced from Powell, 1964.)

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

431

Z X Y

Fig. 8.5. Stereodiagram of the packing of the TOT host molecules in the {TOT[0.5(cetyl alcohol)]} tunnel inclusion complex. The axis of the tunnel is along c. The disordered guest molecule is not shown. (For acknowledgements see Williams and Lawton, 1975.)

tunnels are incommensurable (Lawton and Powell, 1958). Detailed studies of these diffraction effects (at 293K) have been reported by Serrano-Gonzalez and Harris (1999), who applied methods similar to those used in the study of {urea[n-alkane]} complexes and discussed earlier (Section 6.2.1). There is evidence for ordering at lower temperatures, analogous to the phenomena found in the urea complexes. The four structures determined (Table 8.2) include that of {TOT[0.5(cetyl alcohol)]} (Fig. 8.5), where the guest molecule is disordered in the tunnel at room temperature; the more precise structures are those with ,!-dihalogenoalkanes as guests. {TOT[1,8-dibromo-octane]} differs from the previous examples in that there is a commensurate relationship between host and guest sub-systems; the 293K structure does not change essentially on cooling to 123K, apart from an increase in the degree of order of the guest. There is a superstructure involving a seven-fold increase in unit cell volume (Serrano-Gonzalez and Harris, 2000). The hexagonal linear TOT tunnel inclusion complexes can be classiﬁed as helical tubulands (Chapter 6). The methyl and isopropyl groups dominate the interior of the tunnel, providing a hydrophobic environment for the guest molecules. Less attention has been paid to the structures of the tunnel inclusion complexes than to those of the trigonal clathrates, perhaps because of the interest in the potentialities of the latter as resolving agents. 8.2.1.3

Tunnel inclusion complexes with organometallic guests

TOT tunnel inclusion complexes with organometallic compounds as guests were prepared in the course of a search for complexes showing second-harmonic generation (see Chapter 6 for analogous work on thiourea inclusion complexes); desired materials must crystallize in a noncentrosymmetric space group. Of the ﬁve materials studied crystallographically

432

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

(Table 8.3), only one ﬁlls this criterion. There is a zigzag arrangement of host molecules in the {TOT[0.5(W(CO)5-pyridine)(MeOH)]} complex which leaves tunnels along [100] containing the organometallic guests (Fig. 8.6) aligned as centrosymmetric head-to-tail pairs. ˚ , deg., A ˚ 3) for the linear tunnel inclusion complexes with Table 8.3. Selected crystal data (A organometallic guests (at room temperature). Only angles not determined by symmetry have been inserted in the Table. Asterisks in the Table denote crystals for which full structure analyses have been reported. Data are taken from Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989. Compound/Refcode

a

b/

c

V/ Z

I

Space group

TOT{0.5[W(CO)5pyridine]}{0.5MeOH}* (see Note 1); SESMIN TOT [W(CO)5-4-picoline]* (see Note 2); SESMUY TOT[6-tetralin-Cr(CO)3]; SESMEI

22.91

13.71/ 95.22 23.91/ 102.62 20.36

23.36

913.8

8

I2/a

14.26

1069

4

P21/c

13.76

1018

4

Pca21

12.85 14.53

Notes: (1) The 2 : 1 TOT W(CO)5-pyridine and W(CO)5-4-aminopyridine (SESMOS) complexes are isomorphous. (2) The 1 : 1 TOT W(CO)5-4-picoline and W(CO)5-5-ethylpyridine (SESNAF) complexes are isomorphous.

b c

Fig. 8.6. The crystal structure of {TOT[0.5(W(CO)5-pyridine)(MeOH)]} viewed down [100]. The tunnels containing the organometallic guests run normal to the plane of the page. The disordered MeOH has been omitted for clarity. (Reproduced from Tam, Eaton, Calabrese, Williams, Wang and Anderson, 1989.)

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

433

8.2.1.4 Crossed tunnel triclinic inclusion complexes The crossed tunnel inclusion complexes crystallize in two groups of isostructural structures (use of reduced cells is needed to demonstrate this unequivocally) and contain a somewhat surprising variety of guests – cis-stilbene, benzene, methyl cis- and transcinnamate in Group A, and trans-stilbene and trans-p-(dimethylamino)cinnamaldehyde) in Group B (Table 8.4). The crystal structures of the benzene and trans-stilbene tunnel inclusion complexes, which belong in Groups A and B respectively, are shown in Figs. 8.7 and 8.8. The cell edges of these two complexes are very similar and they have the same space group and

˚ , deg., A ˚ 3) for two different groups (A and B) Table 8.4. Crystal data (reduced cells) are given; A of isomorphous triclinic crossed tunnel inclusion complexes (at room temperature, unless stated otherwise). Asterisks in the table and notes denote crystals for which full structure analyses have been reported

Group A TOT[0.5(cis-stilbene)]* BNTDG77; A-YBGKT79; ZZZAVX10 TOT [1.25(C6H6)]* AG83; BOLGOY TOT [0.5(methyl-cis-cinnamate)] A-YBGKT79; TOTCCI TOT [0.5(methyl-trans-cinnamate)] A-YBGKT79; TOTTCI TOT[0.75(1,3-disilylbenzene)]; BGMPR00; OBICAD Group B TOT [0.5(trans-stilbene)] BNTDG77; A-YBGKT79; ZZZAXS10* TOT[0.5(trans-p-(dimethylamino)cinnamaldehyde) Tam et al., 1989; SESNEY TOT[0.75(phenylsilane)]; BGMPR00; OBICEH Group C TOT[0.5(isopropyl-Ndintrophenylvalinate)] BNTDG77; ZZZAXP

a/

b/

c/

V/Z

Z

Space group

11.32 93.89 11.312 94.45 11.3 94.0 11.51 96.6 11.290 94.04

13.17 102.68 13.147 102.91 13.0 102.0 13.04 101.8 13.055 102.94

24.76 93.61 24.983 93.72 25.0 92.0 24.19 91.3 24.707 93.24

895

4

P 1

900

4

P 1

895

4

P 1

882

4

P 1

885

4

P 1

11.639 83.95 11.54 81.63

13.027 76.79 13.20 79.09

24.409 84.81 23.47 85.34

893

4

P 1

867

4

P 1

11.082 84.01

13.154 77.66

24.616 87.09

871

4

P 1

11.360 89.76

13.790 89.98

23.360 89.18

915

4

P 1

Notes: The compositions given are nominal compositions not always realized in practice, e.g. the triclinic benzene complex actually had the composition {TOT[0.8(benzene)]} and the cis-stilbene complex was 1 : 0.4. The results for ZZZAXP would appear to require checking. References: AG83 – Allemand and Gerdil, 1983; A-YBGKT79 – Arad-Yellin, Brunie, Green, Knossow and Tsoucaris, 1979; BGMPR00 – Borisenko et al., 2000; BNTDG77 – Brunie, Navaza, Tsoucaris, Declercq and Germain, 1977.

434

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Fig. 8.7. Stereoview of the molecular arrangement in the TOT[1.25(benzene)] tunnel inclusion complex. The origin is at the rear upper left hand corner of the cell, the [100] axis comes out towards the viewer, [010] is down and [001] is towards the right. One set of benzenes is centered at the origin, a pair of benzenes is located about the centre of the cell at 1/2, 1/2, 1/2 and another pair about 1/2, 1/2, 0 (all with equivalent positions). (Reproduced from Allemand and Gerdil, 1983.)

Fig. 8.8. Stereoview of the molecular arrangement in the TOT[0.5trans-stilbene] tunnel inclusion complex. The origin is at the rear lower left hand corner of the cell, the [100] axis comes out towards the viewer, [010] is towards the right and [001] is upward. One stilbene is centred about 1/2, 1/2, 1/2 and another about 0, 1/2, 0 (all with equivalent positions). The ﬁrst of these is equivalent to the second pair of benzenes as given in the caption to Fig. 8.7; the second does not have a benzene counterpart. (Reproduced from Arad-Yellin, Brunie, Green, Knossow and Tsoucaris, 1979.)

similar unit cell volumes, but the cell angles are different – hence they are not isomorphous. The structures are not identical because of different distributions of the guest molecules, as noted in the captions to these two ﬁgures. In both there are two sets of tunnels that are approximately mutually orthogonal but there is a third set of benzene molecules located in

T RI - O-T HY MOTIDE AND ANALOGS AS HOSTS

435

a third tunnel. The hexagonal linear tunnel complexes and the linear tunnel complexes containing organometallic guests, on the one hand, and the triclinic tunnel inclusion complexes, on the other, are structurally quite distinct, the ﬁrst two types having one set of parallel tunnels and the third two (or three) sets of mutually perpendicular tunnels. 8.2.1.5 Miscellaneous inclusion complexes There are a number of other groups of isomorphous or isostructural inclusion complexes whose structures have not yet been reported (Table 8.5). Thus TOT exhibits considerable versatility as a host. We have noted above that neat TOT forms racemic crystals but their space groups show that spontaneous resolution takes place on formation of both the trigonal clathrate and hexagonal linear tunnel inclusion complexes; thus, in the absence of complicating factors such as twinning, domain formation or disorder, a particular crystal of one of these types of complex will contain only one of the enantiomers of TOT (Powell, 1952). This was strikingly demonstrated when Newman and Powell (1952) grew large single crystals of the clathrates of TOT with ˚ , deg., A ˚ 3) for three different groups of TOT Table 8.5. Crystal data (reduced cells are given; A inclusion complexes (at room temperature). These results have been taken from Gerdil (1996, Table 3); a few miscellaneous complexes given by Gerdil have been omitted. No structure analyses have been reported. Isomorphous trigonal P31 complexes (host : guest 1 : 1) a/ b/

c/

V

Z

TOT[norbornene] TOT[norbornadiene] TOT[2,3-dihydrofuran] TOT[3,4-epoxyoxolane] TOT[2,3-epoxycyclopentan-1-one] TOT[2,3-epoxycyclohexan-1-one] (see Note 1)

10.22 10.25 10.199 10.12 10.150 10.263/ 119.9

864 853 824 822 832 865

3 3 3 3 3 3

Pbca complexes (host : guest 1 : 1) 13.184 23.086 23.977 13.19 23.59 23.83 13.319 23.427 23.760 13.332 23.751 24.250

912 927 927 960

8 8 8 8

B group of isostructural orthorhombic Pbca complexes (host : guest 1 : 1) TOT[2-cyclohepten-1-one] 13.827 37.191 14.281 TOT[2,3-epoxycycloheptan-1-one] 13.857 36.334 14.668

918 923

8 8

A group of isostructural orthorhombic TOT.[4-chloro-2-cyclopenten-1-one] TOT[3-chloro-1-cyclohexene] TOT[3-chloro-2-methylbut-1-ene] TOT[trans-2-chlorocyclohexan-1-ol]

17.11 16.98 16.730 16.88 16.747 17.071/ 90.30

17.099/ 89.87

Notes: (1) This compound was described as pseudo-trigonal but actually triclinic. Further study of the crystal symmetry seems necessary. (2) Space groups (but not other data) have been given for TOT complexes with the following guests: dl-2,3dibromobutane (Pbcn); meso -2,3-dibromobutane (P21/c); 3-bromooctane (C2/c), ﬂuothane (Pbca), meso2,3-butanediol carbonate (P21) (Arad-Yellin, Green, Knossow and Tsoucaris, 1983). (3) The 2-chlorotetrahydropyran complex crystallizes in a pseudo-hexagonal R system with a ¼ b ¼ 17.142(3), ˚ (Gerdil and Frew, 1985; DITRUT) the Br(CH2)3Br complex crystallizes in an unspeciﬁed c ¼ 10.270(2) A orthorhombic unit cell (Lawton and Powell, 1958). The structures have not been reported.

436

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

benzene,1 CHCl3 and n-hexane and showed by polarimetry that solutions made from individual crystals were optically active, the speciﬁc rotation diminishing with time because of racemization. The optical activity results from hindered rotation about the single bonds in the twelve membered ring of the TOT molecule; the activation enthalpy for racemization is about 88 kJ/mol. The trigonal 1 : 0.5 (Table 8.1) and 1 : 1 (Table 8.5) complexes of TOT and the hexagonal complexes of Table 8.2 are chiral but the others are all racemates. The reason for this difference in behavior is not understood but the distinction resides in the nature of the guest and thus it must stem from subtle details of the host–guest recognition process (cf. Section 8.6 below). 8.2.2

Analogs of tri-o-thymotide

Many potential chemical modiﬁcations of the TOT molecule are possible and their syntheses and structural properties have been reviewed in detail (Ollis and Stoddard, 1984). Some of these are sketched in Table 8.6. No trisalicylide, apart from TOT, has yet been found to crystallize as an inclusion complex, not even tri-o-carvacrotide where only methyl and i-propyl groups are interchanged with respect to TOT. Tri-o-thiothymotide, the direct sulphur analog to TOT, could not be synthesized. Among this whole series (some sixty compounds were discussed by Ollis and Stoddard, 1984) the only complexes so far reported are the 1 : 1 inclusion complexes of N,N 0 -dimethyl-N00 -benzyltri-3methyltrianthranalide and N-methyl-N 0 -benzyltri-3-methyl-trianthranalide with toluene; crystal structure analysis (Edge et al., 1981; MANTRN) of the ﬁrst of these showed it to be an enantiomorphic tunnel inclusion complex (space group P212121; Z ¼ 4) with the host in a helical conformation. However, more recently it has been reported that tri-3(2-butyl)-6-methylsalicylide (TSBS) has complex-forming properties similar to those of TOT and that analogous types of trigonal and hexagonal complexes are formed (Gnaim, Green, Arad-Yellin, Vyas, Frolow and Keehn, 1992). Trigonal clathrates are formed with nitromethane, ethyl acetate, 2-butanol (in Table 8.1), triﬂuoroacetic acid, 2-chlorobutane and probably with CHCl3, CCl4, 1-bromobutane and CH2I2. A tunnel inclusion complex is formed with 2-octanone. 3

R X

6 R

6

Y

Y X

3

Y X R

3

6 8.2 1 This must have been the enantiomorphic trigonal clathrate reported by Gerdil (1996, Table 3) and not the racemic triclinic crossed tunnel complex noted here in Table 8.4.

TRIMESIC ACID AND ANALOGS AS HOSTS

437

Table 8.6. Variations on the substituted trisalicylide structure, some of which have been tested for formation of inclusion complexes. The asterisked compound was not synthesized X

R

Y

3

6

Name of compound

Type name

C C C

¼O ¼O ¼O

O O O

Me CHMe2 CH3

CHMe2 Me CH(CH3)CH2CH3

Trisalicylide Trisalicylide Trisalicylide

C N

¼O H

S O

Me H

CHMe2 H

Tri-o-thymotide (TOT) Tri-o-carvacrotide Tri-3-(2-butyl)-6methylsalicylide (TSBS) Tri-o-thiothymotide* Trianthranilide

Trithiosalicylide Trianthranilide

8.3 Trimesic acid and analogs as hosts 8.3.1 Introduction Neutral trimesic acid (benzene-1,3,5-tricarboxylic acid; TMA) is a rather versatile host for formation of inclusion complexes because of the ability of the carboxylic acid groups to form hydrogen bonds both with one another and also to other groups such as water. Thus unary networks, containing only TMA can be formed, and also binary networks containing TMA linked in ordered fashion to other molecules. There are some examples where unary and binary networks are combined in a single compound. Networks analogous to those of TMA but based on linked coordination complexes are also possible hosts for formation of inclusion complexes. The possibilities are further extended when anionic TMA species are incorporated together with inorganic cations and, especially, organic cations. We shall describe these complexes in a logical order rather than in the chronological sequence of their discovery; the structural chemistry has been reviewed (Davies, Finochiarro and Herbstein, 1984; Herbstein, 1987, 1996), and since then considerably expanded. The November 2002 version of the CSD gives 37 hits for ‘‘trimesic acid’’ (including anions). 8.3.2 Host–guest tunnel inclusion complexes based on noncatenated hexagonal networks 8.3.2.1

TMA as host

We start with a simple analogy – isophthalic acid (1,3-benzenedicarboxylic acid) could possibly form hexagonal rings of hydrogen bonded molecules but, in fact, forms a ribbon motif of hydrogen bonded dimers (Alcala and Martinez-Carrera, 1972; BENZCD). However, when isophthalic acid is substituted in the 5-position by a bulky group such as decanol to give 5-decyloxyisophthalic acid, then hexagonal tunnels are formed with ˚ (Yang, Marendez, Gelb and Hamilton, 1994; Fig. 8.9; PIWHAE). diameters of 14 A The isophthalic acid core is planar while the decyloxy chains take up alternating up and down positions. When the bulky substituent in position 5 is replaced by a third carboxylic acid group to give trimesic acid, and this is crystallized from acetone or other suitable solvent (not water) in the presence of appropriate guests, isostructural crystalline complexes are obtained in which the TMA molecules form hexagonal sheets (‘‘chicken wire’’)

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

438

R

O O

H

R O

H

O

R

R = OC10H21

14 Å

R

R

R

Fig. 8.9. Schematic view of a ring of six hydrogen bonded molecules in the crystal structure of 5-decyloxyisophthalic acid; only one of the dimeric carboxyl groups is shown in detail.

Fig. 8.10. The basic ‘‘chicken wire’’ motif in the uninterrupted TMA network is a two-dimensional arrangement of six-molecule rings, the hydrogen bonds between carboxyl groups being represented by dashed lines. (Reproduced from Herbstein, Kapon and Reisner, 1987.)

TRIMESIC ACID AND ANALOGS AS HOSTS

439

˚ (Fig. 8.10). These are the simplest inclusion which contain tunnels of net diameter 14 A complexes of trimesic acid from a structural point of view. They are called ‘‘hexagonal TMA tunnel inclusion complexes’’ (Herbstein, Kapon and Reisner, 1987) and can be classiﬁed in terms of the number of sheets in a crystallographic repeat in the direction of the tunnel axis, and in terms of the crystallography of the unit cell; ‘‘hexagonal’’ is used as a descriptor and exact symmetry is not implied. So far twolayer, three-layer and ﬁve-layer repeats have been found. The guest molecules are contained in the tunnels and are usually disordered at room temperature. Representative crystal data are summarized in Table 8.7. As noted in Table 8.7, there are actually two groups of complexes, Group (a) with uninterrupted TMA networks (as shown in Figs. 8.10 and 8.11) and Group (b) in which

˚ , deg., A ˚ 3) for the ‘‘hexagonal’’ TMA tunnel inclusion Table 8.7. Representative crystal data (A complexes; only complexes whose structures have been determined are included except for the fivelayer octanol complex. Values of angles fixed by cell symmetry are not given Composition

a/

b/

(a) Complexes with uninterrupted TMA TMA[isooctane]a 28.60 16.60 FOPGIA 102.6 16.50 16.50 2TMA [tetradecane]b FOPGEW 2TMA[1.33(octanol)] 18.00 18.01 106.1 100.2

c/

Volume of formula unit

networks 6.93 802

Z

Space group

Unit-cell contents

Number of layers

8

C2/c

8TMA þ 8(C8H18) 6TMA þ 3(C14H30) 12TMA þ 8(C8H17OH)

2 (X3.47)

6TMA þ 2(C18H35OH)] 8TMA 8(C10H16O) þ 16(H2O) 16TMA þ 8(pyrene) þ 16 EtOH

3 (X3.49)

10.07

791.5

3

P31

17.02 116.4

741

6

P1

789

3

P1

976

4

P21212

(b) Complexes with interrupted 16.44 2TMA 79.1 [0.67(oleylalchol)c 2TMA[2(camphor)] 32.44 4(H2O)

TMA networks 15.97 10.46 83.9 61.8 16.90 7.12

2TMA[pyrene] 2(C2H5OH) at 198K; SURYUZ; KT99 2TMA[1.5(pyrene)] 2(CH3OH); UCUKUY; HKS01

28.13

16.55 95.13

14.73

854

8

C2/c

9.533 93.88

13.540 95.02

14.644 90.14

940

2

P1

2 (X3.36) 5 (X3.40)

2 (X3.56)

4TMA þ 3(pyrene) þ 4(methanol)

Notes: a There is an isomorphous complex of composition 2TMA[0.5(squalene)]. b There are isomorphous complexes of composition 2TMA[2(isooctane)]; 2TMA[2(1-octene)]; 2TMA [epichlorohydrin]. c Cell is reduced apart from choice of origin. d The absolute conﬁgurations of the crystals with chiral space groups were not determined. References: HKS01 – Herbstein, Kapon and Shteiman, 2001; KT99 – Kolotuchin et al., 1999.

440

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

guest or water molecules are included in the TMA network, which we call ‘interrupted.’ We ﬁrst discuss Group (a). The four isomorphous three-layer complexes show nearly identical cell dimensions, indicating minimal inﬂuence of the guests on the shape of the TMA network. These crystals are chiral but the absolute conﬁguration of the {2TMA[n-tetradecane]} complex (Fig. 8.11) was not determined. The TMA network appears to be centrosymmetric but there are indications (but no more than this from a room temperature determination in which the conformation of the guest molecule could not be ascertained with certainty) that the tetradecane has a coiled conformation and is thus not centrosymmetric; if so, then this may be an example of spontaneous resolution of conformational enantiomers. In the {2TMA[0.5(squalene)]} complex the periodicity along the tunnel axis is much less than the length of the squalene molecule, which is possibly not linearly extended in the cavity, as it is in its inclusion complex with urea, but folded into some sort of curved conformation, similar to the oleyl alcohol complex discussed below. A detailed structure determination was not carried out. The {TMA[isooctane]} complex, the structure of which was determined, is isomorphous but the guest molecules could not be found. The examples with interrupted TMA networks (Herbstein, Kapon and Reisner, 1988) are particularly interesting, and more widespread than expected. In the camphor complex, which is a two layer structure, water molecules intervene in two of the six carboxyl bridges of each macrocyclic ring giving a tunnel with an elliptical rather than cylindrical cross section (Fig. 8.13); unfortunately the camphor molecules could not be located in this room temperature structure analysis so that the role of the guest in engendering this distortion is not known. The space group is chiral and the ring of TMA and water molecules is not ﬂat; the absolute conﬁguration of the crystal used was not determined. Double interruption of a carboxylic acid dimer by water molecules was encountered in 1934 in oxalic acid dihydrate (Zachariasen, 1934), much studied since then; however,

b c a

Fig. 8.11. Stereoview of the {2TMA[n-tetradecane]} structure down [001], along which there are three layers. The TMA layers are appreciably nonplanar and this eliminates the congeneric centrosymmetric space group P31/m. The n-tetradecane molecules are appreciably disordered in the tunnels and their representation is only schematic. (Reproduced from Herbstein, Kapon and Reisner, 1987.)

TRIMESIC ACID AND ANALOGS AS HOSTS

441

(COOH)22H2O forms hydrogen-bonded sheets rather than chains. In the three-layer oleyl alcohol complex the hydroxyl of the guest molecule, which has a U-shaped conformation, intervenes, from both sides, in two of the six carboxyl bridges of the central of the three layers in the [001] direction. Thus only one-third of the layers are interrupted in this structure. Despite non-planarity of the layers, this complex crystallizes in a centrosymmetric space group. Double interruption of a carboxylic acid dimer by hydroxyls was encountered in the 1 : 2 complex of 1,1 0 -binaphthyl-2,2 0 -dicarboxylic acid with methanol

A

C

A

C 0

B

0

B

Fig. 8.12. Stereoview of the {2TMA[camphor]4H2O} structure down [001], along which there are two layers. The TMA layers are appreciably nonplanar and the space group is chiral, in accord with the chirality of the camphor molecules. The disordered camphor guests are not shown. (Reproduced from Herbstein, Kapon and Reisner, 1988.)

B

B

0 C

A

0 C

A

Fig. 8.13. Stereoview of the {2TMA[0.67(oleyl alcohol)]} structure down [001], along which there are three layers. Although the TMA layers are appreciably nonplanar, the space group is centrosymmetric. The oleyl alcohol molecules are fairly well ordered in the tunnels. (Reproduced from Herbstein, Kapon and Reisner, 1988.)

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

442

interrupted dimer

carboxylic acid dimer

2C

0

A

B

A B

B

2B B

A A

B

A 2A

A B

z y x

Fig. 8.14. TMPYME. Diagram of a single layer showing the hydrogen bonding scheme. Pyrene A is at general positions and is (essentially) coplanar with the TMA and the hydroxyls of the methanol molecules; pyrene B, which extends out of the plane of the page between the layers, is located about centers of symmetry. The crystallographically independent TMA molecules are designated A and B. Adjacent layers are mutually offset, the degree depending on whether they are separated by pyrene B or methanol methyls. The methyl group of only one of the methanols in the interrupted dimer is shown. (Reproduced from Herbstein, Kapon and Shteiman, 2001.)

(Weber, Cso¨regh, Stensland and Czugler, 1984; CILLUE) (see Chapter 12, Fig. 12.15), the arrangement being very similar to that in 2TMA[0.67(oleyl alcohol)], and in sulfazecin : methanol (Kamiya, Takamoto, Wada and Asai, 1981; FULFZC). The guests forming tunnel inclusion complexes with TMA are a rather eclectic group; there are unbranched (n-tetradecane) and branched (isooctane) parafﬁns, long chain alcohols of various kinds (heptanol, octanol, decanol and oleyl alcohol), alkenes (1-octene, squalene), alicyclics (camphor) and miscellaneous (methoxy ethyl ether, propellane, epichlorhydrin). However, a comprehensive survey establishing various possible guest types has not yet been made. In this (extended) group, the most detailed structure reports are for the well ordered crystals of {2TMApyrene2(ethanol)} at 198K (SURYUZ) and {2TMA1.5(pyrene) 2(methanol)} at 300K (abbreviated as TMPYME; refcode UCUKUY) (crystal data in Table 8.7). Both complexes have layer structures, the (essentially planar) layers being

TRIMESIC ACID AND ANALOGS AS HOSTS

443

constructed from rings of six TMA molecules, hydrogen bonded through four ‘‘carboxyl dimers’’ and two ‘‘interrupted dimers’’ where ethanol (methanol) is included in the R44 (12) (graph set) ring. The packing of the layers differs in the two complexes, leading to different three-dimensional structures. In the methanol complex, one pyrene molecule is located within the layer and the other, at a center of symmetry, between the layers in one type of interlayer space, while the methyls of the methanol protrude into the other type of interlayer space (Fig. 8.14). In the ethanol complex, the superpositioning of the layers is such that two types of stack are formed; one of these is mixed, containing pyrene and one of the independent TMA molecules in alternating sequence, while the other stack contains only the second type of TMA. Spectroscopic study is needed to establish whether the partial mixed stack arrangement in the crystalline ethanol complex implies donor–acceptor interaction. 8.3.2.2

Two coordination complexes as potential hosts

This is an opportune point to draw attention to two structures, both based on copper coordination complexes, in which there are analogies to the quasi-hexagonal TMA channels described above. In both examples the channels contain water or other solvent molecules and the intriguing question arises whether these could not perhaps be replaced by guest molecules of other types. There is no doubt that the geometry is right but it is not clear whether the chemical problems can be overcome; no one seems yet to have tried to ﬁnd out. Interest in the ﬁrst of these examples was originally stimulated when it was found that a series of copper complexes of composition Cu3L3(OH)X2xH2O (where HL is pyridine-2-carbaldehyde oxime (8.3) and X ¼ 1/2SO42, NO3, ClO4, or OH) had anomalously low magnetic N

N

OH

H 8.3 Pyridine-2-carbaldehyde oxime

moments (Beckett and Hoskins, 1972; CUPRAL10). The problem of the magnetic moment was solved by determining the crystal structure of {Cu3L3(OH)SO4163H2O} ˚ , space group P (trigonal, a ¼ 18.05, c ¼ 7.25 A 3, Z ¼ 2), which was found to have trinuclear (Cu3L3(OH)X2xH2O) groups in which strong metal–metal interaction had caused pairing of two of the three formally unpaired electrons; these units are analogous to TMA. {Cu3L3(OH)SO4163H2O} has trimeric units hydrogen bonded to one another in the ˚ , where the shortening is probably an [001] direction (d(O . . . O) is as short as 2.36(2) A artifact due to systematic errors) while the lateral contacts between the trimers are due to van der Waals interactions. In contrast to the TMA networks, here the interactions normal to the network plane seem to be appreciably stronger than the in-plane interactions. The channel cross section is only approximately circular, with an internal diameter of roughly ˚ . Beckett and Hoskins concluded ‘‘ . . . that most of the water of crystallization (con9A tained in the channels) is liquid in nature, moving randomly throughout the containing volume. Even though the water molecules are not rigidly held in the lattice, they seem essential to the structure of the crystal . . . ’’

444

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

S

y z

O(H)

CuI

CuI Cu

Cu

z

O(H)

S

C N O Cu

Fig. 8.15. (left) A projection of the trimer unit of Cu3L3(OH)SO42xH2O (where HL is pyridine-2carbaldehyde oxime (8.3)) viewed down its three fold axis; the sulphato group has been omitted for clarity; (right) a schematic view perpendicular to the threefold axis showing the relationship of the Cu3 core, the hydroxy group and the sulphato group. (Reproduced from Beckett and Hoskins, 1972.)

b

y 0

0

x

a

Fig. 8.16. Simpliﬁed diagram of the crystal structure of Cu3L3(OH)SO42xH2O (where HL is pyridine-2-carbaldehyde oxime (8.3)) viewed down [001]. The sulphato groups have been omitted for clarity; the copper atoms are shown by the ﬁlled circles. The channels are occupied by disordered solvent molecules. (Reproduced from Beckett and Hoskins, 1972.)

TRIMESIC ACID AND ANALOGS AS HOSTS

445

The second example was prepared by allowing ascorbic acid to oxidize in acidic aqueous solution in the presence of Cu(II) (Norman, Rose and Stenkamp, 1987; JEDKIM). Blue trapezoidal prisms of composition [(Cu2þ)9(HCl)2(cpa3)6(H2O)3]xH2O were obtained by allowing the reaction mixture to stand for three days; the composition was inferred from the results of the crystal structure analysis described below (cpa is an acronym for the branched chain dicarboxylic acid 2-carboxypentonic acid (1,2,3,4tetrahydroxybutane-1,1-dicarboxylic acid (8.4)). In the coordination complex the asterisked hydroxyls of the two carboxylic groups and the 1-hydroxyl group lose protons and are linked to Cu atoms. The compound is insoluble in water and organic solvents, and decomposes in concentrated acids or bases. O OH OH∗

∗HO C

∗HO

CH CH

O

CH2OH

OH

8.4 cpa or 1,2,3,4-tetrahydorxy-butane-1, 1-dicarboxylic acid

O C Cu CL

Fig. 8.17. A view of the structural unit in [(Cu2þ)9(HCl)2(cpa3)6(H2O)3]xH2O, (cpa is an acronym for the branched chain dicarboxylic acid 2-carboxypentonic acid (1,2,3,4tetrahydroxybutane-1,1-dicarboxylic acid (8.4)), emphasizing the two different copper sites. The Cu3Cl(cpa)3 unit with the copper ligating atoms is shown, but the two terminal alcohol units of each cpa have been omitted. (Reproduced from Norman, Rose and Stenkamp, 1987.)

446

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Fig. 8.18. A view of one polymeric layer in the crystal structure of [(Cu2þ)9(HCl)2 (cpa3)6(H2O)3]xH2O, the channels being occupied by disordered solvent molecules. The axes ˚ ) and b axes of the trigonal cell (c ¼ 7.98 A ˚ , space group P321). shown are the a ( ¼ 21.27 A (Reproduced from Norman, Rose and Stenkamp, 1987.)

The blue trapezoidal prisms were found to be trigonal, with a ¼ 21.274(5), ˚ , space group P321. The space group is one of the Sohncke group,2 but the c ¼ 7.9766(7) A absolute conﬁguration of the crystal used was not determined. Direct methods showed that one Cu atom was in a general position and one on a twofold axis, while Cl was located on a threefold axis. The Y-shaped Cu6Cl(cpa)3 unit (Fig. 8.17) is essentially equivalent to the trimesic acid molecule from a structural point of view, and the Y-units are linked similarly to those in the quasi-hexagonal TMA network of Fig. 8.11 to form an hexagonal ˚ ﬁlled with arrangement (Fig. 8.18), with cylindrical channels of net diameter about 17 A disordered solvent molecules. The diameter of the cylindrical channels is not very dif˚ ) for the TMA analog. ferent from that found ( 14 A 8.3.3

Host–guest tunnel inclusion complexes based on catenated hexagonal unary networks

The hexagonal networks of Fig. 8.11 appear in two other types of inclusion complex in a rather special arrangement. Consider for the moment six TMA molecules hydrogen bonded together in a ring to form the hexagonal motif of the TMA network shown in Fig. 8.11. The cylindrical hole in this ring is large enough to accommodate three similar 2 A Sohncke space group has symmetry elements only of the ﬁrst kind. We here follow Flack (2003), see especially pp. 914–915.

TRIMESIC ACID AND ANALOGS AS HOSTS

447

rings threaded through roughly perpendicular to the original ring; and the hole formed by the new rings can in its turn accommodate two additional rings making three in all. This gives an interlinking arrangement of triply triply catenated rings, a catenane or linkedchain structure (latin: catena ¼ chain) being one in which macrocyclic molecules are linked together mechanically without the aid of a chemical bond (Schill, 1971). Now extend this arrangement in space using intersecting networks rather than single rings. The arrangement shown schematically in Fig. 8.19 results, where the networks are seen edgeon. The TMA matrix, if composed of planar networks, cannot ﬁll space and tunnels are left which are parallel to the axes of intersection of the networks. Furthermore the overall arrangement is chiral if the network triplets are not mutually perpendicular – a simple analogy is provided by the biphenyl molecule which is only achiral if the two rings are coplanar or mutually perpendicular. Two examples of this structure type are known. The ﬁrst is ‘‘trimesic acid pentaiodide’’ (BZHTIB) and its analog in which the I 5 ion is replaced by Br5 or IBr2 . The water molecules in this compound (see caption to Fig. 8.19 for composition) are included between the networks and are not hydrogen bonded to them; it seems that their structural role is to provide a location for the proton counterions. The anions in the tunnels are

y 1/4

1/4

x

1/4

1/4

1/4

1/4

1/4

1/4

0 2Å

Fig. 8.19. Schematic diagram of the triply triply catenated hexagonal TMA networks as described in the text. The direction of view is along the plane of the networks. This is the structure of the ‘‘trimesic acid pentaiodide’’ tunnel inclusion complex, whose composition is TMA0.7H2O [0.09HI5], and its HBr5 and HIBr2 analog (Herbstein, Kapon and Reisner, 1981). It is also the structure of the interstitial inclusion complex ‘‘-TMA’’, whose composition is TMA [0.04C6H4(COOH)20.04TMA] (Herbstein, Kapon and Reisner, 1985). These complexes all crystallize in space group I222, the symmetry elements of which are shown in projection onto (001), and are isostructural. The tunnels at the corners and centre of the diagram, represented by hatched circles, are empty in -TMA but are occupied by polyhalide chains viewed end-on in the TMA polyhalides. (Reproduced from Herbstein, Kapon and Reisner, 1981.)

448

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

incommensurable with the TMA matrix and give rise to striking diffuse scattering patterns from which it is possible to infer their structures. This is entirely analogous to the situations found in the incommensurable urea, thiourea (Section 6.2.1) and TOT tunnel inclusion complexes (Section 8.2). The second example, so-called -TMA (DAZBOV), was produced by heating TMA to about 300 C, where the compound decomposes slightly as it ﬂash-sublimes and forms an interstitial clathrate complex in which stabilization comes from inclusion of benzene1,3-dicarboxylic acid decomposition products and residual TMA molecules between the networks, while the channels occupied by the anions of the TMA pentahalides remain empty. This is one of the few examples known of a binary adduct not made by crystallization from solution. 8.3.4

Host–guest clathrate interstitial inclusion complexes based on catenated hexagonal unary networks

There is a group of interstitial clathrate complexes based on anhydrous TMA, the structure of which was determined (Duchamp and Marsh, 1969; BTCOAC) many years before the work described above. Anhydrous TMA (called -TMA), crystallized from water, has a complicated structure based on nonplanar triply–triply catenated hexagonal TMA networks (space group C2/c, 48 molecules in the unit cell); the nonplanarity of the networks allows them to be essentially space ﬁlling, as can be seen from the relatively high density of 1.46 g cm3. Nevertheless, TMA, when crystallized from water containing Br2, acetone (DAZBUB), I2 (DAZCAI), resorcinol (DAZCEM) or hydroquinone (DAZCIQ), forms interstitial complexes of composition {TMA[pX]} where p ¼ 1/6 for the ﬁrst two guests and 1/12 for the latter three; the interstitial nature is shown by their densities being greater than 1.46 g cm3. These interstitial complexes are isomorphous with -TMA, the dif˚ ; thus the degree of ferences in cell dimensions being only a few hundredths of an A adaptability is small. The structure of {-TMA[1/6Br2]} has been determined (Herbstein, Kapon and Reisner, 1985; DAZBIP), the disordered bromine molecules being located between the intersecting networks (see Section 10.8). It is not clear whether p can take up any value between 0 and 1/6 (or 1/12), giving true interstitial solid solutions, or whether it is restricted to 1/6 (or 1/12), giving a compound in the phase-rule sense. There is possibly an analogy here with the bromine hydrate structure, where it has been shown that the variable bromine content depends on the conditions under which the crystals are grown (Section 7.2.7.4). 8.3.5

Generalization of the concept of ‘‘interruption’’ to give binary networks

An ‘‘interrupted’’ TMA network has a ring size larger than that achievable with the standard carboxyl dimer linkage. Thus ‘‘interruption’’ allows greater ﬂexibility in designing networks. The simple examples given above can be extended and generalized by following a proposal made by Mele´ndez and Zaworotko (1997) that a binary network should be considered as having two components, a ‘‘director’’ and a ‘‘propagator’’, which must be bifunctional. Using {2TMA[2(camphor)]4H2O} as example, TMA is the director and water the propagator. The network need not be planar, and tetrahedral directors can be envisaged (and have been used). The concept has previously been illustrated for a

TRIMESIC ACID AND ANALOGS AS HOSTS

449

single container molecule in Fig. 3.20, where the director was called a ‘‘spacer’’ and the propagator a ‘‘connector’’. Another possible way of achieving larger ring size in TMA complexes would be to replace –COOH by –CH2COOH, but benzene-1,3,5-triacetic acid is likely to be much less rigid than TMA; perhaps –C C–COOH could be used. 8.3.5.1 TMAH2O networks The complexes described above are all based on hexagonal ‘‘chicken wire’’ unary networks of TMA molecules. However, the networks can contain a second component in addition to TMA, giving a binary network. One example is the group of tunnel inclusion complexes based on planar networks of composition TMAH2O, where the water molecules are an integral part of the network. The simplest of these complexes is TMA3H2O, which has already been noted as a possible tunnel hydrate (Section 6.2.4).

L y

A

B

a x U2

C

D

U1

K E F G

c

e

d

b

H J

I

L

A

B

K

Fig. 8.20. (a) Features of a difference density projection for {TMAH2O[2/9PA]}, with TMA molecules outlined and water molecules shown as circles. The TMAH2O layer has one carboxyl group per molecule hydrogen bonded across centres of symmetry to form the usual carboxylic acid dimer arrangement but the other two carboxyl groups are hydrogen bonded via water molecules (in the centre of the cell). The difference density which represents the included PA molecules is ˚ 3. In {TMAH2O[2/9 PA]} the molecules lie in the ( contoured at levels of 1, 2, 3 e A 1 1 1) planes and the hydrogen bonds do not lie in the plane of projection but are directed out of this plane. For TMA5/6H2O this diagram serves as a slightly distorted representation of the arrangement in the TMAH2O layers. (b) The structure of TMA5/6H2O (space group P1, Z ¼ 12), showing the zigzag chains of included molecules K and L and the stacking of the framework TMAH2O networks A–J. All twelve TMA molecules are crystallographically independent. The view is along c*, with a vertical. (Reproduced from Herbstein and Marsh, 1977.)

450

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Although this structure has not been studied in detail, it is clear from what follows that it should be written as {TMAH2O[2H2O]}, where one water molecule is an integral part of the network and the other two are contained in tunnels of rectangular cross section. The complex of composition {TMAH2O.[2/9 picric acid]} has been studied in more detail (Herbstein and Marsh, 1977) and it was found that the picric acid (PA) molecules (originally chosen in the (vain) hope that they would form a substitutional solid solution by replacing TMA molecules in the TMAH2O network) were contained in the rectangular tunnels piercing the TMAH2O network (Fig. 8.20(a)). Striking diffuse scattering on oscillation photographs attested to a partially disordered arrangement of two PA guests ˚ . The unusual composition follows from the along a tunnel, with a periodicity of 16.5 A ratio of four PA molecules to nine TMAH2O layers (each layer contains two TMAH2O ˚ , 2 16.5 ¼ 33 A ˚ . Durene and mesitylene units); 9 3.64 ([001] periodicity) ¼ 32.8 A (1,3,5-trimethylbenzene) are guests in isomorphous complexes, which have not been studied in detail. An ordered chain of hydrogen-bonded methanol molecules, one ˚ within the [CH3OH] replacing [2H2O]} with a rather short O . . . O distance of 2.43 A ˚, chain, is found in an isomorphous complex (reduced cell: 3.679(1), 8.971(1), 18.038(3) A 77.76(1), 86.86(1), 88.04(1) , P1, Z ¼ 2) (Chatterjee et al., 2000; XAVQEQ); a similar complex contains chains of acetone molecules, which cannot be hydrogen bonded. The hydrate with the unusual composition TMA5/6H2O is isostructural with {TMAH2O[2/9PA]}. Its structure is revealed by rewriting the composition as {5(TMAH2O)[TMA]}, indicating that the additional TMA molecule is present as a guest in the rectangular tunnels piercing the TMAH2O layers. However, adjacent TMA guests are hydrogen bonded through carboxyl groups in the meta positions and the chain so formed is zigzag rather than linear. This is accommodated in the crystals by offsetting the TMAH2O layers in sequence (Fig. 8.20(b)). Although both the TMAH2O layers and the zigzag TMA chains are separately centrosymmetric, their arrangement lacks a centre and the space group is the P1. Comparison of reduced cells shows that these crystals are isostructural rather than isomorphous. 8.3.5.2 Catenated neutral binary networks 4,4’-bipyridine was used as a propagator molecule by Sharma and Zaworotko (1996; RAPHAR), with possibly unexpected results. The {(C9H6O6)1.5(C10H8N2)} crystals are ˚ , ¼ 99.95(6) , space monoclinic, with a ¼ 11.105(4), b ¼ 10.132(4), c ¼ 18.889(7) A group P21/c, Z ¼ 4; one bipyridine is at a centre of symmetry and one in a general position. The carboxyl dimers of neat TMA are replaced by strong N . . . H–O and weak C–H . . . O¼C links. The non-planar macrocyclic rings have chair conformations and are doubly doubly catenated (Figs. 8.21 and 8.22) to give the overall crystal structure. The calculated density (it was apparently not measured) is relatively high at 1.41 Mg m3; the presence of void space after catenation of the networks is speciﬁcally mentioned but there is no mention of possible additional enclathration of small solvent molecules. 8.3.5.3 Ionic binary networks A number of attempts have been made to engineer porous organic solids by combining cationic propagators with anionic TMA directors. Water molecules can also participate

TRIMESIC ACID AND ANALOGS AS HOSTS

451

4,4′-bipyridine TMA

Fig. 8.21. The nonplanar binary hexagonal ring motif formed from TMA and 4,4 0 -bipyridine (BP) moieties. The N . . . H–O and C–H . . . O hydrogen bonds are shown by dashed lines. (Adapted from Sharma and Zaworotko, 1996.)

BP

BP A

B

C

TMA

Fig. 8.22. The nonplanar binary hexagonal ring motif formed from TMA and 4.4 0 -bipyridine (BP) moieties. The three independent doubly doubly catenated binary networks are denoted by A, B, C. (Adapted from Sharma and Zaworotko, 1996.)

in the networks formed. Binary honeycomb networks involving various cation–anion combinations were found in the salts tris(dicyclohexylammonium) trimesate methanol solvate {3[(H2N(cyclo-C6H11)2]þ[(C6H3(CO (TOZZUD; at 173K, 2 )3]}xCH3OH ˚ , space group P63, Z ¼ 6) and dimethylammonium trimesate a ¼ 17.609, c ¼ 17.677 A

452

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

{12[(H2N(CH3)2]þ}{[(C6H3(CO2H)3]3[(C6H3(CO2H)2(CO2)]3[(C6H3(CO2H)(CO 2 )] ˚ , space group R3, Z ¼ 6, (Mele´n[(C6H3(CO2)3]} (TUBBAT; a ¼ 33.412, c ¼ 17.465 A dez, Sharma, Zaworotko, Bauer and Rogers, 1996). The honeycomb network in the ﬁrst of these salts is neutral and is based on interactions of the type shown below; there are no carboxylate dimers. The cyclohexyl groups of the ammonium ions project above and below the plane of the honeycomb sheets and almost close the cavities, which contain disordered solvent molecules. Methanols are also hydrogen bonded to oxygens of carboxylate groups. The (remarkable) second salt contains together neutral TMA and its singly, doubly and triply deprotonated anions; there are two independent honeycomb grids, one of which has [(C6H3(CO2H)3] molecules and [(C6H3(CO2H)(CO 2 )2] in 1 : 3 ratio, while the second has [(C6H3(CO 2 )3] and [(C6H3(CO2H)2(CO2 )] anions in 1 : 3 ratio. The cations cross link adjacent sheets by N–H . . . O hydrogen bonds to the anions rather than to the neutral molecules. c

c N

C R

+

H

O

H

R O

O H

H

+

C O

N c

c

c = cyclohexyl

N,N,N 0 ,N 0 -tetraalkylethylenediammonium cations (alkyl ¼ methyl, ethyl) have also been used as propagators with TMA anions as directors, and these give binary chains which are hydrogen bonded in a series of different arrangements (Mele´ndez and Zaworotko, 1997); the salts are N,N,N 0 ,N 0 -tetramethylethylenediammonium bis(benzene3,5-dicarboxylic acid-1-carboxylate) dihydrate (PIDQOI), N,N,N 0 ,N 0 -tetraethylethylenediammonium bis(benzene-3,5-dicarboxylic acid-1-carboxylate) (PIDQUO) and N,N,N 0 ,N 0 -tetramethylethylenediammonium benzene-5-dicarboxylic acid-1,3 – dicarboxylate (PIDSUQ). M(II)acetate hydrate (M ¼ Co, Ni, Zn) also gives binary chains with TMA anions (Yaghi, Li and Groy, 1996), and analogous arrangements are found in [Co(5-C5H5)2]þ (TMA)(TMA)2H2O (PUNSEW)) and [Co(5-C5H5)2]þ [Co(H2O)6]2þ (TMA3) (PUNSIA) (Braga, Angeloni, Tagliavini and Grepioni, 1998). These structures, which can be considered as steps towards the ultimate goal, will not be described in detail here. The binary networks illustrated here could alternatively have been included under the category of ‘‘Mixed Framework Structures’’ as outlined in Chapter 12.

8.3.6

Hydrogen-bonded TMA binary complexes

The crystal structure of TMAdimethyl sulphoxide (DMSO) (Herbstein, Kapon and Wasserman, 1978; TMADMS) is unusual in that the TMA molecules are mutually linked

TRIMESIC ACID AND ANALOGS AS HOSTS

453

B 3.689 3.807

3.630 3.629

A

O(4)

O(5) C(5)

2.656

2.559

C(8) O(4)

2.635

3.739

117.9

C(3)

O(3)

C(9) O(6)

C(6)

C(2) C(1) C(7)

a cos 10°

O(2) O(1) c cos 10°

b up

Fig. 8.23. One layer of the crystal structure of {TMADMSO} projected approximately onto (010). (Reproduced from Herbstein, Kapon and Wasserman, 1977.)

through single >C–OH . . . O¼C < hydrogen bonds between TMA molecules along [100] (and thus carboxylic acid dimers are not formed), and through the oxygen of DMSO along [001] (Fig. 8.23), the remaining atoms of the DMSO molecule ﬁlling the tunnels between the TMA molecules. Thus this is a layer structure with the so-called guest DMSO playing partly the role of host and partly that of guest. Ambiguity remains about the space group which could be P21 or P21/m. {TMADMSO} is on the borderline of ‘‘inclusion complexes’’, but, for completeness, we note here some other TMA complexes with neutral components and organic salts of TMA (metal trimesate salts are excluded). In the ﬁrst two of these examples there is hydrogen bonding between TMA and the second component, and these could have been included in Chapter 12. Examples of hydrogen bonded TMA complexes with dimethylformamide (XAVPOZ), dimethylamine (XAVPUF), and N,N,N 0 ,N 0 -tetramethylethylenediamine (PIDQOI01) have been given by Chatterjee et al. (2000), where both strong and weak hydrogen bonds appear to play important roles in determining the packing arrangements, which are all different. {TMA(Ph3PO)2} (prepared by reﬂuxing TMA and triphenylphosphine in 1 : 2 ratio in toluene) is triclinic (Lynch, Smith, Byriel and Kennard, 1992; P1, Z ¼ 2; KUCCUG). The crystal structure can be described as made up of units of {TMA(Ph3PO)2}, linked in chains. The two Ph3PO molecules of the asymmetric unit are linked, as acceptors, to two different carboxyls of a particular TMA molecule by fairly strong hydrogen bonds ˚ ). The OH of the third carboxyl of this TMA molecule acts (d(O . . . O) ¼ 2.50(1), 2.54(1) A

454

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

OPPh3

O

H O

OPPh3 O

Ph3PO

H

O O

H O

O

H O

O

O O

H

O

H

Ph3PO

Fig. 8.24. Schematic view of part of the TMA(Ph3PO)2 structure showing linkage of TMA and Ph3PO molecules in chains along [100] with Ph3PO molecules appended (cf. Chapter 12). The hydrogen bonds linking the TMA molecules are emphasized while the Ph3PO molecules are boxed to show up the appendage nature of the arrangement of the two moieties in the crystal.

as donor to a carbonyl oxygen of one of the ﬁrst mentioned carboxyls ˚ ). The unionized state of all three carboxyls is conﬁrmed by the (d(O . . . O) ¼ 2.61(1) A ˚ between C–OH and C¼O bond lengths. Most hydrogen distinct differences of 0.1 A bonded binary adducts with a chain structure have the components arranged in alternating fashion . . . A . . . B . . . A . . . B . . . A . . . In TMA(Ph3PO)2 there are chains of hydrogen bonded TMA molecules to which (Ph3PO)2 units are appended; the triphenylphospines do not participate in the chains. This is shown schematically in Fig. 8.24. The chains interact mutually through van der Waals linkages and are not hydrogen bonded to one another. Appendage structures are also discussed in Chapter 12. TMA and urea form three crystalline binary adducts, with 1 : 1, 1 : 2 and 1 : 3 compositions. Structural information is available only for the 1 : 3 composition (VidenovaAdrabrinska, 1994, 1996). The crystals are monoclinic (a ¼ 6.718(5), b ¼ 20.412(8), ˚ , ¼ 92.70(6) , Z ¼ 4, space group P21/n; CEKSIU); the somewhat high c ¼ 12.730(4) A RF factor of 10.4% was ascribed to polysynthetic twinning. There are seventeen independent hydrogen bonds in the structure and we shall limit ourselves here to a brief description. The formula unit is also the structural unit, with two carboxyl groups bonded to ureas, each through a pair of C–O–H . . . O¼C hydrogen bonds (d ¼ 2.479(5), 2.493(6) ˚ ; these are shown as 1 and 2 in Fig. 8.25) and C¼O . . . (syn)H–N hydrogen bonds A ˚ ) (TMA atoms on the left in all formulae where TMA . . . urea (d ¼ 2.991(6), 2.971(6) A hydrogen bonds are concerned). The TMA and these two ureas are essentially coplanar and form a set of sinusoidal ribbons which run through the crystal, with urea . . . urea ˚ ) linking the C¼O . . . H–N hydrogen bonds (d ¼ 3.035(6), 2.837(6), 2.929(6), 3.299(6) A planar portions of the structural units; it is the anti N–H groups of the ureas which participate in the formation of these chains. One could describe the chains as consisting of hydrogen-bonded urea dimers (emphasized for clarity in Fig. 8.25) linking meta

TRIMESIC ACID AND ANALOGS AS HOSTS

455

B

2 3 1

0A

C

Fig. 8.25. The slice of the TMA(urea)3 crystal structure lying in (or about) the plane of the TMA molecules. The hydrogen bonded pair of urea molecules within this plane is emphasized, while the third urea molecule (out of the plane) is seen approximately edge-on. The hydrogen bonds referred to in the text are denoted by 1, 2, 3. One sinusoidal chain of molecules is enclosed within the hatched area, but it must be remembered that hydrogen bonds between chains cross the chain boundaries. (Adapted from Videnova-Adrabrinska, 1994.)

carboxyl groups of TMA. The third urea is nearly perpendicular to this layer and is ˚ ) to the third hydroxyl of TMA. All these C–O–H . . . O¼C hydrogen bonded (d ¼ 2.545(5) A hydrogen bonds are ordered, as is shown by the occurrence of distinct single and double C–O bonds in the three carboxyl groups. Although description in terms of sinusoidal ribbons is convenient, this is not the whole story because the ribbons are not isolated but are also mutually linked by hydrogen bonding. Furthermore, the third urea, perpendicular to the ribbon plane, links adjacent layers, above and below, by hydrogen bonds; we do not give details. The crystalline complex is thus a three-dimensional hydrogen-bonded structure. TMA forms a triclinic 1 : 1 : 1 ternary complex with dioxane and water, which has pleated sheets of (neutral) TMA and water molecules, bridged by dioxanes (Herbstein and Kapon, 1978; TMESAD). There is also a ternary complex of composition glycinetrimesic acid monohydrate (space group Pna21, Z ¼ 4; Herbstein, Kapon, Maor and Reisner, 1981; GLYTMS), where glycine is present as a zwitterion, with the cationic charge localized on the NHþ 3 group. The balancing negative charge is shared between one of the carboxyls ˚ ), almost of TMA and that of glycine, which are linked by a very short (2.464(3) A symmetrical hydrogen bond. This is also reﬂected in the C–O bond lengths of these ˚ for TMA and 1.232(2) and carboxyl groups, which are 1.223(4) and 1.284(4)* A ˚ for glycine (hydrogen between asterisked oxygens). The other two carboxyls 1.275(4)* A of TMA have regular C–O bond lengths (1.215(4) and 1.318(4), and 1.212(3) and 1.303(4)

456

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

˚ ). There are no carboxylic acid dimers but one pair of carboxyl carbonyl acceptors of A TMA is linked through the donor hydroxyls of the water molecule. TMA and glycine are acids of similar strengths (pKa ¼ 2.12 and 2.34 respectively) and it was suggested that this was the reason for the formation of an almost symmetrical hydrogen bond. Histidine forms a salt with TMA and both {L-histidinium trimesate.1/3acetone} (LHISTM) and {DL-histidinium trimesate1/3acetone} (DLHTMS) have essentially– identical cell dimensions and related space groups (P212121 and Pna21 respectively) (Herbstein and Kapon, 1979); the acetone could be replaced by water but the crystals were of poorer diffraction quality. The structures contain ribbons of cations and anions extending along [010]. Each ribbon has histidinium ions of one sense of chirality only; in the L-salt all ribbons are congruent while in the DL-salt the sense of chirality alternates in the [100] direction, normal to the ribbon axis. 8.4

The Heilbron complexes

Soon after the end of the First World War it was reported by Heilbron and Buck (1921) that the compound now named as E,E-1-[ p-dimethylaminophenyl]-5-[o-hydroxyphenyl]penta-1,4-dien-3-one (for structure diagram see Fig. 8.26) formed molecular complexes with a wide variety of guests, including ethanol, chloroform, acetic acid, m-dinitrobenzene, p-dimethylaminobenzaldehyde (PDMB), benzene, 4-methoxybenzaldehyde (anisaldehyde), and 2,4,6-trinitrotoluene; Heilbron and Buck used the name 4 0 -dimethylamino-2-hydroxydistyryl ketone, which we abbreviate for our use here as DHDK. Indeed Heilbron and Buck noted that ‘‘the ketone is very difﬁcult to obtain in the free state as it tenaciously retains traces of solvent;’’ diffraction-quality single crystals of neat DHDK have not yet been obtained (cf. deoxycholic acid, Section 6.3.1; TATM Section 8.6). Thus the crystal structure of neat DHDK is not known but those of its complexes with ethanol (DADYUC) and chloroform (DADYOW) (isomorphous, 2 : 1), m-dinitrobenzene (1 : 1) (DADZIR) and PDMB (1 : 1) (DADZOX) have been reported (Herbstein, Kapon, Reisner and Rubin, 1984); also crystal data for the acetic acid (DADZAJ) and methanol (DADZEN) complexes. The DHDK molecule can take up a number of conformations, although these are not all equally probable; the two so far reported are shown in Fig. 8.26. The DHDK molecule has three functionalities – the hydroxyl and carbonyl groups can act as hydrogen bond donors HO

HO

O N CH3 CH3

O

CH3 N CH3

Fig. 8.26. The s-trans,trans (on left) and s-cis,trans (on right) conformations of DHDK. The ﬁrst of these conformations is found in the {DHDK[0.5X]} clathrates and in {DHDK p-dimethylaminobenzaldehyde}, and the second in {DHDKm-dinitrobenzene}. The single bond about which there is a difference of conformation is marked. (Reproduced from Herbstein, Kapon, Reisner and Rubin, 1984.)

T HE HE IL BR ON C OM PLEXES

457

and acceptors respectively, while the dimethylaminophenyl and hydroxyphenyl rings can act as donors and acceptors respectively in -* charge transfer compounds. Thus it is possible that the 1 : 1 TNT and TNB adducts are -* charge transfer compounds in which the dimethyl-aminophenyl ring acts as donor and TNT or TNB as acceptor; structures were not determined because of poor crystal quality. One can envisage hydrogen bonding of hydroxyl and carbonyl groups to form DHDK dimers or chains; in addition guests with suitable hydrogen bonding capabilities could link with the DHDK molecules. All these possibilities are realized in the structures determined. Centrosymmetric dimers of DHDK are formed by head-to-waist hydroxyl-carbonyl hydrogen bonding, the DHDK molecules being in the s-trans-trans conformation. These dimers form isomorphous 2 : 1 clathrates with ethanol and CHCl3 as guests (Fig. 8.27). It is possible that the 1 : 1 acetic acid complex is isostructural but the structure has not been determined. There are only van der Waals forces between DHDK dimers and between DHDK dimers and guests, so these complexes are analogous to the clathrates of tri-othymotide (Section 8.2). The {DHDK[m-dinitrobenzene]} complex, although a tunnel inclusion complex, is of a kind not yet encountered elsewhere. The molecules are arranged in sheets, with the DHDK molecules linked in chains by head to waist hydrogen bonds (Figs. 8.28 and 8.29). The remaining space in the sheets has a sinuous rather than linear shape and the m-dinitrobenzene molecules ﬁt in rather neatly, with van der Waals interactions both to each other and to the DHDK hosts. These sheets are then superimposed in an offset manner which leads to the enclosure of the guest molecules in tunnels. The interactions between host molecules are a combination of hydrogen and van der Waals bonding.

C

A

C

A

Fig. 8.27. Stereodiagram of the {DHDK[0.5X]} crystal structure, where X ¼ C2H5OH or CHCl3. The guest molecules, which are disordered and not shown, are enclosed in the cavities centered at 0,1/2,0 and analogous positions. The hydrogen bonds are shown as dashed lines. (Reproduced from Herbstein, Kapon, Reisner and Rubin, 1984.)

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

458

C

B

A

z x

Fig. 8.28. DHDK-m-dinitrobenzene (DADZIR) crystal structure viewed down [010] showing the molecules (host and guest) located in the (201) planes. The DHDK molecules are linked by carbonyl . . . hydroxyl hydrogen bonds. The host . . . guest interaction is via van der Waals forces. The arrangement within the sheets is shown in Fig. 8.29. (Data from Herbstein, Kapon, Reisner and Rubin, 1984.)

B(666)

A(674) B(665)

B(764) b

A(665)

A(566) A(664) B(655)

[102]

0 B(656) A(556)

A(655)

Fig. 8.29. The {DHDK[m-dinitrobenzene]} structure showing sheets of molecules lying in the (201) planes. The two crystallographically independent molecules of each type are designated A and B. The reference molecules are denoted as 555, translations along the crystal axes being speciﬁed by adding or subtracting integers from the reference code, as in the ORTEP system. The rectangle shows the unit cell of the pg plane group. The hydrogen bonds are denoted by thin lines. Note the s-cis, trans conformation of DHDK. (Reproduced from Herbstein, Kapon, Reisner and Rubin, 1984.)

GOSSYPOL AND ITS INCLUSION COMPLEXES

459

DHDK

PDMB

B

A

0

y x carbonyl...hydroxyl H-bond (2.723Å)

Fig. 8.30. DHDK-p-dimethylaminobenzaldehyde (DADZOX) crystal structure viewed down [001]. The packing unit is the DHDK . . . PDMB pair linked by a carbonyl . . . hydroxyl hydrogen bond. The DHDK molecules are not hydrogen bonded to one another. The PDMB molecules have been emphasized. (Data from Herbstein, Kapon, Reisner and Rubin, 1984.)

Finally there is the {DHDKPDMB} structure (Fig. 8.30) (PDMB ¼ pdimethylaminobenzaldehyde), which is the most difﬁcult of the DHDK complexes to categorize in terms of the classiﬁcation used here. There is a hydrogen bond between DHDK hydroxyl and PDMB carbonyl; in addition the DHDK molecules are arranged so as to form the walls of tunnels which contain the guest molecules. However, it is hardly a classical tunnel inclusion complex; possibly dipole–dipole interactions, both host–host and guest–guest, play an important role in determining the overall arrangement. 8.5 Gossypol and its inclusion complexes Gossypol (8.5; 1,1 0 ,6,6 0 ,7,7 0 -hexahydroxy-5,5 0 -diisopropyl-3,3 0 -dimethyl[2,2 0 -binaphthalene]-8,8 0 -dicarboxaldehyde) is a yellow pigment isolated from cotton seed kernels as the racemate; formation of enantiomers is due to restricted rotation about the central bond. Gossypol was named by Marchlewski (1899), its formula determined by Adams, Morris, Geismann, Butterbaugh and Kirkpatrick (1936), and synthesized by Edwards (1958) (see also Adams, Geismann and Edwards, 1960). Gossypol has three possible tautomeric forms – aldehyde, lactol and quinoid – but has so far always appeared as the aldehyde in the crystalline state. It has antitumor, antiviral and antifertility properties. Enantiomeric gossypol ([]D19 ¼ þ445(10) ) has been isolated from Thespesia populnea (Bhakuni, Dhar and Sharma, 1968; King and de Silva, 1968) and is the ﬁrst example of a natural - 0 -dinaphthyl derivative showing optical activity due to restricted rotation. The chiral material has also been obtained by chromatographic separation of the racemate (Clark, 1927; Matlin, Belengeur, Tyson and Brookes, 1987). The crystallography of Gossypol and its inclusion complexes has been comprehensively reviewed (Gdaniec, Ibragimov and Talipov, 1996). ‘‘Gossypol’’ gives 147 hits in the October 2002 version of the CSD.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

460

O

OH

OH

HO

OH OH

HO

O

8.5

The ideal symmetry of the molecule would be C2–2, with the two fold axis normal to the central bond (Fig. 8.31). The torsion angle about this bond would be expected to be 90 ; in practice deviations of up to 15 from the perpendicular conformation are found. There are two strong intramolecular hydrogen bonds (O(3)–H . . . O(2) and O(7)–H . . . O(6)), forming six-membered rings, and two weaker ones (O(4)–H . . . O(3) and O(8)–H . . . O(7)), forming ﬁve-membered rings and participating weakly in threecenter hydrogen bonds. The polymorphism of gossypol has been discussed by Ibragimov and Talipov (1994) and we follow their notation; seven polymorphs in all have been identiﬁed. Two of these were prepared by recrystallization from suitable solvents. Monoclinic P1 (volume per molecule ˚ 3; Z ¼ 4; space group P21/c; Talipov, Ibragimov, Dadabaev, Aripov and V ¼ 627.9 A ˚ 3; C2/c, Sadykov, 1986; listed by CSD as BEMLOU 03 and 04). Monoclinic P2 (V ¼ 645.4 A Z ¼ 32) is not listed by the CSD. Five polymorphs (P3–P7), identiﬁed by their powder diffraction patterns (but without assignment of unit cells), were prepared by removal of guest molecules from various complexes. In addition, P3 was obtained (in rather intriguing fashion) as ‘‘monocrystals’’ from the decomposition of the CH2Cl2 complex of gossypol ˚ 3 (this volume includes empty tunnel space, see p. 467; C2/c, Z ¼ 8; Talipov, (V ¼ 710 A Ibragimov, Nazarov, Aripov and Sadykov, 1985; this is listed by the CSD as BEMLOU 02,

C2 C22

C26

C3

C29

C8

C30

C14

C28

01

C13

08

C21

C5

C4

C3 C11

C6 C10

C2

C20 C19

C16

C9

C1 C12

C15

C7

C3∗

C1∗ C2∗

C4

C24 C23 C25

05 C17

C18

C4∗ C6∗

C5∗ C27

07

C7∗ 06

Fig. 8.31. The spatial formula of gossypol. The hydrogen bonds are denoted by dashed lines. The crystallographic numbering is shown. The di-n-propyl ether guest shown has cross-hatched atoms (Reproduced from Gdaniec, 1991a.)

GOSSYPOL AND ITS INCLUSION COMPLEXES

461

12 and 22). The CSD also lists monoclinic BEMLOU and triclinic BEMLOU 01. Although some interesting relationships appear to be implied by these results, we shall hardly consider them further because of lack of direct relevance to our concerns. About 100 molecular inclusion complexes have been prepared from racemic gossypol by recrystallization from various solvents (Ibragimov and Gdaniec, 1992). Single crystals have been grown for about 70 of these and crystal data determined; cell dimensions may vary somewhat from one report to another but we have not attempted to impose any uniformity. Enough crystal structures have now been reported to demonstrate the wealth of variety found in the arrangements of the components and to outline features of the main structural families. Ibragimov, Talipov and Aripov (1994) remark that ‘‘the total number of various gossypol clathrate isostructural groups discovered by us to date is 20.’’ There are indications that enantiomeric gossypol also forms molecular complexes (for example, with acetone but not with acetic acid) but these have not yet been explored in any depth (or, perhaps, reported in any detail). We shall classify the crystalline molecular complexes of racemic gossypol in terms of 1. gossypol : guest ratio ( 2 : 1, 1 : 1, 1 : 1.5, 1 : 2); 2. gossypol packing unit; 3. structural sub-family (tunnel, clathrate or layer type complexes); and give examples of nine different structural types. In most of the complexes studied until now, the ‘‘packing unit’’ is the centrosymmetric dimer made up of two gossypol enantiomers, with two fairly strong O(5)–H . . . O(3) (or O(1)–H . . . O(7)) hydrogen bonds ˚ ). (Parenthetically we note that such dimers cannot be ‘‘packing between them (d 2.8 A units’’ of enantiomeric gossypol). These dimers may then be hydrogen bonded to one another to form more extended arrays of various types, and may also be hydrogen bonded to the guests. There are often intermolecular hydrogen bonds of about the same strength as the intradimer bonds, so that some care must be taken with the descriptions. A few complexes have been found to contain individual gossypol molecules which then form more extended hydrogen-bonded arrays. The complexity of the arrangements can make clearcut assignment to a particular structural class difﬁcult. Disorder of the guests can also complicate descriptions. 2 : 1 layer inclusion complexes of the gossypol : m-xylene type: Triclinic complexes of this isomorphous group are formed with o-, m- and p-xylene, ethylbenzene and p-chlorotoluene as guests; the crystal structure of the m-xylene and CCl4 complexes have been reported (Fig. 8.32; Ibragimov, Talipov, Aripov and Sadykov, 1990; Ibragimov, Talipov and Zorky, 1994). There are close similarities in cell edges and angles among all the crystals (Table 8.8). In general (see below) the cell angles provide a ﬁner means of discrimination among the slightly differing structural types than cell edges; the gossypol complexes provide excellent examples of the value of cell dimensions in suggesting evidence of structural differences in advance of execution of full structure analyses. Of course, comparisons of this kind can only usefully be made among reduced cells. It is possible to identify the centrosymmetric dimers noted above as the ‘‘packing unit,’’ but there are other intermolecular hydrogen bonds of about the same strength as the intradimer bonds, leading to the formation of inﬁnite columns of gossypol

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

462

molecules along [010]. Thus the term ‘‘packing unit’’ has formal rather than physical signiﬁcance. The CCl4 guests are enclathrated between the host molecules and it is perhaps a matter of taste whether this structure type is to be described as a clathrate or a layer arrangement. ˚ , deg., A ˚ 3) for 2 : 1 gossypol : guest complexes of the Table 8.8. Crystal data (reduced cells, A ˚ , angles 0.01–0.03 , volumes 2(gossypol) : m-xylene type. S.u.’s of cell edges are 0.001–0.007 A 3 ˚ 0.4–1.0 A . The data have been ordered according to decreasing cell volumes within a group Guest

a

b

c

Cell volume

2(gossypol) with Ethylbenzene; VEVSUK10 m-xylene*; JIDSOE o-xylene; VEVSIY p-chlorotoluene; VEVTIZ p-xylene; VEVSOE

8.451 8.478 8.505 8.575 8.406

14.195 14.087 14.072 14.060 14.079

14.411 14.399 14.395 14.269 14.213

114.89 115.39 115.51 115.48 115.82

102.55 104.89 105.76 107.11 92.20

92.21 93.20 93.37 93.22 104.76

1513 1475 1466 1451 1443

gossypol with CCl4; CUVLAG Paraldehyde; VEVTEV

8.847 8.97

14.015 12.95

14.304 14.69

102.16 101.2

91.12 91.1

105.79 90.5

1663 1674

˚ 3 by Ibragimov, Talipov, Aripov and Note: the cell volume for the CCl4 complex is given erroneously as 1547 A Sadykov, 1990.

Intercalated carbon tetrachloride guests

C

Layers of H-bonded gossypol hosts

B

A

z y

Fig. 8.32. Triclinic 2(gossypol)[CCl4] projected down [100] (CUVLAG01). Hydrogen bonds are shown (as dashed lines). (Data from Ibragimov, Talipov and Zorky, 1994.)

GOSSYPOL AND ITS INCLUSION COMPLEXES

463

2 : 1 layer inclusion complex gossypol: 0.5(benzene). The crystals (Gdaniec, Ibragimov and Talipov, 1990b) are triclinic (space group P1, Z ¼ 2) with a ¼ 11.241(3), ˚ , ¼ 98.89(2), ¼ 99.86(2), ¼ 98.91(2) , b ¼ 14.986(4), c ¼ 17.380(4) A 3 ˚ V ¼ 2800(2) A (reduced cell; CUVKIN; JIDTIZ). There are two crystallographically independent gossypol molecules in the asymmetric unit, A and B, with dihedral angles between naphthyl rings of 88.2(1) ) and 79.1(1) respectively. Centrosymmetric dimers of the familiar type are formed between pairs of A molecules and between pairs of B molecules. These dimers are linked into columns along [211] by ˚ ) hydrogen bonds (the O(1A)–H . . . O(8B) and O(8B)–H . . . O(4A) (d ¼ 2.77, 3.17 A corresponding bonds with A and B labels interchanged do not occur). 2 : 1 layer inclusion complexes of the gossypol: 0.5(amyl acrylate) type. Complexes of this isomorphous group are formed with amyl acrylate and amyl acetate crystals (Gdaniec, Ibragimov and Talipov, 1990a). The crystals are triclinic (space group P1, Z ¼ 2) with (for amyl acrylate, VEVMOY) a ¼ 14.425(2), b ¼ 15.519(1), ˚3 ˚ , ¼ 97.89(1), ¼ 117.80(1), ¼ 67.01(1) , V ¼ 2992.3(14) A c ¼ 16.409(2) A ˚ (reduced cell a ¼ 14.425(2), b ¼ 15.519(1), c ¼ 16.029(7) A, ¼ 77.78(2), ¼ 64.90(3), ¼ 67.01(1) ). There are two crystallographically independent gossypol molecules in the asymmetric unit, A and B, with dihedral angles between naphthyl rings of 97.6(1) ) and 105.5(1) respectively. Two A molecules related by a centre of symmetry form the dimer identiﬁed previously, but two additional gossypol molecules, of the B type, are hydrogen bonded to the gossypols of the dimer (d(O5A)– H . . . O(8B) ¼ 2.983(7), d(O8B)–H . . . O(8A) ¼ 2.813(5), d(O1B)–H . . . O(4A) ¼ ˚ ). Amyl acrylate guests are hydrogen bonded to A and B gossypols 3.125(5) A ˚ ). Presumably it is appropriate to describe this as a clathrate (d ¼ 2.75, 2.98, 3.01 A type structure (Fig. 8.33). 2 : 1 clathrate inclusion complexes of the gossypol:0.5(ethyl acetate) type. Crystallographic data have been reported for fourteen complexes of this group, the guests being ethyl acetate (VEVTUL*), n-butyl acetate (VEVVAT)*, acetylacetone, methyl propionate (VEVTOF*), ethyl acetoacetate (VEVWUO)*, acetyl acetone, methyl acrylate, ethyl bromoacetate (VEVVEX) (Ibragimov, Talipov and Gdaniec, 1990), ethyl acrylate (KIVCEX, given as 1 : 1), acetylacetone (VEVWIC, KIVCIB), propyl butyrate, di-n-propyl ether (KIVCAT*) and butyl ethyl ether (KIVCUN, given as 1 : 1) (Gdaniec, 1991a) (asterisks indicate that crystal structures have been reported). The isomorphous crystals are monoclinic, space group C2/c, Z ¼ 8, with the a parameter ˚ , from varying from 11.01 to 11.54, b from 30.54 to 30.77, c from 16.47 to 17.09 A ˚ 3. The complexes with isobutyl 90.1 to 92.4 , and cell volumes from 5601 to 5928 A acetate (VEVVUN) and methyl (S)-(–)-2-chloropropionate (KIVDAU*) as guests have very similar cells but the space groups are P21/n and the enantiomorphic C2;3 presumably the differences in arrangement are small. The packing unit is not the hydrogen-bonded dimer noted above but instead bimolecular layers are formed containing molecules of the same chirality sense, which are hydrogen bonded within the layers through the three hydroxyl groups of each molecule. These layers interact by van der Waals forces and there are no hydrogen bonds between them. Guest molecules having a carbonyl group in a chain of limited length (around seven 3

space group C2 in the original paper but C2/c in CSD.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

464

atoms) can be accommodated in cavities formed between the layers, possibly in disordered fashion; the carbonyl group is hydrogen bonded to O(5) of the gossypol. The gossypol: 0.5(ethyl acetoacetate) structure is shown in Fig. 8.34. One wonders whether the gossypol molecules which complex with the chiral methyl-(S)-(–)-2-chloropropionate guest in the enantiomorphic C2 unit cell, have undergone spontaneous resolution on crystallization, giving all the layers the same sense of chirality. As there are two gossypol molecules in the asymmetric unit, presence of both enantiomers is allowed despite the enantiomorphism of the space group, nor is there any indication from the cell dimensions of such an effect. A full crystal structure analysis would be needed for clariﬁcation of this point. A

gossypol A dimer

gos sypol B

two guest molecules

x y C

B

Fig. 8.33. Gossypol : 0.5(amyl acrylate) structure viewed down [010] of the triclinic cell. Guest molecules emphasized; dashed lines are H bonds. (Data from Gdaniec, Ibragimov and Talipov, 1990a.) C

B

A

Fig. 8.34. Projection of the gossypol : 0.5(ethyl acetoacetate) structure down [100] of the monoclinic cell. The disordered guest molecules, which are hydrogen bonded to gossypol, are emphasized. Two hydrogen bonded bimolecular layers of gossypol molecules are shown; these interact by van der Waals forces. (Data from Ibragimov, Talipov and Gdaniec, 1990.)

GOSSYPOL AND ITS INCLUSION COMPLEXES

465

1 : 1 tunnel inclusion complexes of the gossypol : acetone-type. Cell dimensions have been given for 16 complexes in this group (Ibragimov, Gdaniec and Dadabaev, 1990; Table 8.9). The crystals are all triclinic, space group P1, Z ¼ 2. The unit cells reported by the original authors are, except where noted otherwise below, reduced cells but with unconventional choices of origin; a conventional reduced cell has, inter alia, all interaxial angles obtuse or all acute and we have made the necessary changes in Table 8.9. The cell dimensions indicate that there are two groups of isomorphous complexes, and an additional miscellaneous group. The dihedral angles between the nearly planar naphthyl moieties are 82.9, 83.9, 83.0 and 86.0 in VEVRJX, VEVROD, VEVRUJ and JEGWAT respectively, suggesting that the latter differs somewhat from the other three. The packing unit is the centrosymmetric dimer, with the nearly planar naphthyl moieties approximately ˚ in mutually orthogonal, and intramolecular hydrogen bond lengths of 2.76 and 2.80 A ˚ , deg., A ˚ 3) for 1 : 1 gossypol : guest complexes. S.u.’s of Table 8.9. Crystal data (reduced cells, A ˚ ˚ 3. Within the groups the cell edges are 0.001–0.007 A, angles 0.01– 0.03 , volumes 0.51.0 A data have been ordered according to decreasing cell volume. Asterisks denote, as before, that full structure analyses have been reported Guest

a

Group I (gossypol-acetone type) 1-butanol; VEVNIT 11.090 2-methyl-1-propanol; 10.780 VEVPAN 2-butanone; VEVNAL 10.775 1-propanol; VEVNEP 10.841 prop-2-enol; VEVNOZ 10.861 acetone;* CUVKEJ 10.665 acetonitrile;* JEGWAT 10.938

b

c

Cell volume

11.090 11.204

14.510 14.399

102.60 103.19

110.90 107.53

101.10 101.61

1554 1545

11.114 11.073 11.035 11.135 10.982

14.421 14.205 14.142 14.379 14.162

102.95 102.32 101.60 103.53 102.01

108.74 109.87 110.49 108.67 112.24

101.23 101.13 100.45 102.28 102.75

1526 1500 1496 1494 1453

Group II (gossypol-butanal type). There seem to of structures. Pentanal; VEVPOB 10.343 11.643 3-methyl-1-butanol; VEVPER 10.048 11.677 1-butanal* VEVRUJ 10.190 11.335 3-buten-1-al; VEVPIV 10.258 11.271 Group III (Miscellaneous) Dioxane LOQSEP trichloroacetic acid; VEVRAP methacrylic acid; VEVPUH cyclohexanone* ; VEVROD tetrahydrofuran* ; VEVRJX 1-methylethanol; VEVNUF

10.905 11.178 10.996 10.803 10.788 10.585

11.055 11.425 11.065 11.157 10.979 11.152

be differences between the two pairs 14.928 15.426 14.665 14.455

108.83 110.08 106.96 106.47

106.47 107.64 103.74 102.41

95.40 94.69 98.93 98.97

1597 1585 1527 1523

13.772 13.139 13.452 14.692 13.880 14.017

107.07 107.39 98.24 104.61 99.89 101.53

96.72 97.07 107.09 104.73 103.87 108.80

98.68 95.06 94.30 103.34 102.04 97.64

1546 1575 1536 1573 1518 1500

References: Leading references are Talipov, Ibragimov, Tischenko and Aripov, 1989; Gdaniec, Ibragimov and Dadabaev, 1990; Ibragimov, Talipov and Zorky, 1994; Ibragimov, Gdaniec and Dadabaev, 1990; details can be obtained through the REFCODES.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

466

the VEVRJX and VEVROD structures respectively. There is a guest molecule ˚ in the VEVRJX and VEVhydrogen bonded to O(1) of each host (d ¼ 2.64, 2.78 A ROD structures respectively). The arrangement is shown in the stereodiagram of the VEVROD structure (Fig. 8.35), which can be taken as a prototype of this group of structures. This packing unit, somewhat modiﬁed, persists in the other structures of this group; Ibragimov, Gdaniec and Dadabaev (1990) consider that there are threecentered hydrogen bonds between such packing units but the intermolecular distances indicate that these are surely very weak. Comparison of the detailed structures shows considerable variability in overall arrangement resulting from accommodation of rather different guests in a single basic structure type. 1 : 1 tunnel inclusion complexes of the gossypol : chloroform type. Crystallographic data have been reported for ﬁve complexes of this group, the guests being chloroform (Gdaniec, Ibragimov and Talipov, 1990b; CUVKUZ*), diiodomethane, 1,2-dichloroethane, 1,2-dibromoethane and isovaleric acid ((CH3)2CHCH2COOH)* (Gdaniec, Ibragimov and Dadabaev, 1990). The isomorphous crystals are monoclinic, space group C2/c, Z ¼ 8, with a varying from 28.22 to 28.84, b from 8.95 to 9.16, c ˚ , from 107.8 to 109.7 , and cell volumes from 6235 to 6615 A ˚ 3. from 25.80 to 26.88 A The packing unit is again the centrosymmetric gossypol dimer, and there is no host– guest hydrogen bonding. Isovaleric acid forms centrosymmetric dimers in its complex, thus explaining how it can be incorporated as a guest in the same structural group as the hydrophobic halomethanes and haloethanes. The overall arrangement is (roughly) one of gossypol dimers in ( 101) planes, interleaved by planes of guest molecules,

host guest H-bond

gossypol

cyclohexanone

x z y

Fig. 8.35. Stereodiagram of gossypol[cyclohexanone] projected down [110], as a representative ˚ ) is shown of the gossypol[acetone] group of structures. The host-guest hydrogen bond (2.775 A as a dashed line, and the guests are emphasized. (Data from Ibragimov, Gdaniec and Dadabaev, 1990.)

GOSSYPOL AND ITS INCLUSION COMPLEXES

467

giving an intercalate type complex. The gossypol dimers form columns along [101] ˚ ); because the hydrophilic linked by O(1)–H . . . O(8) and O(8)–H . . . O(4) (d ¼ 2.94 A groups of the gossypol molecules are located within the columns, there is no hydrogen bonding between columns. 1 : 1 tunnel inclusion complexes of the gossypol : dichloromethane type. The guests CH2Cl2 and CH2Br2 form isomorphous 1 : 1 complexes with gossypol (for CH2Cl2 ˚ , ¼ 113.05(2) , Z ¼ 8, C2/c; a ¼ 21.320(4), b ¼ 19.129(6), c ¼ 15.765(2) A Ibragimov, Talipov and Aripov, 1994; JIDTOF). These are tunnel inclusion complexes which contain the centrosymmetric dimers so characteristic of the gossypol family of complexes. It is remarkable that these two complexes decompose (lose solvent at room temperature) by a single crystal to single crystal mode to give the P3 polymorph of gossypol (see p. 460). The volume decrease is 4% for the CH2Cl2 ˚ , a reduction of 3.2%) and 9.4% complex (due primarily to a change of c to 15.267 A for the CH2Br2 complex (reduction of c by 4.9%). A view down the tunnel axis is shown in Fig. 8.36. 1 : 1 inclusion complexes of gossypol with methyl acetate and acetic acid. These two examples are isomorphous (P 1, Z ¼ 2): ˚ , 92.34, 91.90, 98.71 , cell volume ¼ GOSPOL (acetic acid): 6.924, 14.276, 14.706 A 3 ˚ . 1434 A ˚ , 92.23, 91.70, 98.69 , cell VEVVIB (methyl acetate): 6.976, 14.313, 14.727 A 3 ˚ volume ¼ 1452 A . 1 : 1.5 clathrate inclusion complex of gossypol : 1.5(benzaldehyde). This has a triclinic ˚ , ¼ 73.62(1), ¼ 88.29(1), cell with a ¼ 10.959(2), b ¼ 11.418 (2), c ¼ 14.116(2) A 3 ˚ ¼ 87.73(1) , V ¼ 1693.0(5) A , space group P1, Z ¼ 2 (Gdaniec, Ibragimov and Talipov, 1991; cell is reduced). The dihedral angle between the naphthyl rings of the gossypol molecule is 86.1(3) . The two gossypol molecules in the unit cell are ˚ ) to form the familiar centrosymmetric hydrogen bonded (d(O(5) . . . O(3 0 ) ¼ 2.90 A dimers, and these are packed around two different kinds of centrosymmetric cage; there are no hydrogen bonds between dimers. The larger of the cages (T2) contains two benzaldehyde molecules related by a centre, and the second (T1) contains a single

B

C

0

B

A

C

0

A

Fig. 8.36. The diagram on the left shows the {gossypol : [CH2Cl2]} complex viewed down the axis of the tunnel which contains the halomethane guest. The diagram on the right shows the P3 gossypol polymorph obtained (as a single crystal) after loss of guest from the {gossypol[CH2Cl2]} complex. The tunnels shown as blank areas in fact contain atmospheric gases. (Adapted from Ibragimov, Talipov and Aripov, 1994.)

468

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

y x z

Fig. 8.37. Stereodiagram of gossypol1.5[benzaldehyde]. The hydrogen bonds are shown as dashed lines, oxygens are shown as circles, hydrogens have been omitted for clarity and the guests are emphasized. The cell in the ﬁgure is that given by Gdaniec et al. (1991), i.e. reduced but with nonstandard choice of axes. (Reproduced from Gdaniec, Ibragimov and Talipov, 1991.)

benzaldehyde in disordered array simulating a centre. The guests in the cages are hydrogen bonded to the hosts (Fig. 8.37). An alternative way of looking at this arrangement is to consider it as a cluster of two gossypols, forming a dimer. O(1) of gossypol is the donor in an hydrogen bond to the oxygen of one of the benzaldehydes in a T2 cage; the same arrangement is found on the other side of the dimer. This accounts for one benzaldehyde of the formula. The second benzaldehyde is hydrogen bonded to O(8) of gossypol, but only to one O(8) of a particular dimer, accounting for the remaining half benzaldehyde; this linkage takes up one of two alternative orientations. Overall, the second benzaldehyde is linked to one O(8) in half of the dimers and to its centrosymmetric congener in the other half, thus preserving composition and an average centre of symmetry. The clusters interact only by van der Waals forces. Analogous, but simpler, hydrogen-bonded clusters interacting by van der Waals forces are discussed in Chapter 12. 1 : 2 clathrate inclusion complex of gossypol : 2(salicylaldehyde). Triclinic crystals with a 1 : 1 ratio of gossypol to salicylaldehyde (2-hydroxybenzaldehyde) were obtained from neat salicylaldehyde while monoclinic crystals with a 1 : 2 ratio were obtained from salicylaldehyde/benzene mixtures. The structure of the triclinic 1 : 1 crystals (RIDNOH; Gdaniec, Talipov and Ibragimov, 1995) is not discussed here. The 1 : 2 monoclinic crystals (Gdaniec, 1991b; a ¼ 11.130(2), b ¼ 29.542(5), c ¼ 11.744(2) ˚ , ¼ 98.45(1), V ¼ 3820(1) A ˚ 3, space group P21/n, Z ¼ 4; JINFAN) have an interA esting structural relation to the gossypol : 1.5(benzaldehyde) hydrogen-bonded cluster. The gossypol molecules form the familiar centrosymmetric dimers; there is no hydrogen bonding between dimers. The hydroxyl oxygen of one of the salicylaldehyde guests (A in Fig. 8.38) is the acceptor in a bifurcated hydrogen bond from hydroxyl O(8) ˚ ), while the carbonyl oxygen of the second of one gossypol of a dimer (d ¼ 2.81 A salicylaldehyde guest (B in Fig. 8.38), is hydrogen bonded to O(1) of this gossypol, two orientations being found. This gives the 1 : 2 gossypol: salicylaldehyde ratio. The difference between gossypol : 1.5(benzaldehyde) and gossypol : 2(salicylaldehyde) is that

TRIS(5-ACETYL-3-THIENYL )M ETHANE (T AT M) AS HOST

469

B

A

Fig. 8.38. Diagram of one-half of the dimeric cluster of composition gossypol : 2[salicylaldehyde]. Hydrogen bonds are shown as dashed lines. The two crystallographicallyindependent guests are denoted as A and B respectively; B takes up two coplanar orientations in a 2 : 1 ratio. (Reproduced from Gdaniec, 1991b.)

both O(8)’s of the dimer in the latter are linked to salicylaldehydes, while only one of the two O(8)’s of the dimer is linked to benzaldehyde in the former. Disorder of orientation and arrangement complicates the situation.

8.6 Tris(5-acetyl-3-thienyl)methane (TATM) as host 8.6.1 Introduction When the host molecule is rigid, as has been the situation in most of the complexes considered previously, the possibilities of mutual host–guest adaptation are severely limited. However, the preparation of many inclusion complexes of the ﬂexile (conformationally labile) host molecule tris(5-acetyl-3-thienyl)methane (TATM; 8.6), which has a tripod shape, and determination of a number of their crystal structures, now provides information (limited but indicative) about the mutual adaptation of a host and its guests (Herbstein, 1997a). Very few other examples of this type have yet been encountered.

8.6.2 Chemistry of TATM and its inclusion complexes TATM (C19H16O3S3; indexed in Chemical Abstracts under ‘‘Ethanone, 1,1 0 ,100 (methylidyntri-4,2-thiophendiyl) tris’’; CSD name ‘‘tris(5-acetyl-3-thienyl)methane’’) was ﬁrst synthesized by Yakubov, Sudarushkin, Belenkii and Gold’farb (1973); these authors reported that the sublimed compound was an amorphous solid (m.pt. 50–58 C) which gave crystalline 2 : 1 adducts with benzene, ethanol and pyridine. An impressive list of inclusion complexes is due to Bin Din and Meth-Cohn (1977), who extended the earlier work and noted that ‘‘a systematic study has so far not revealed a solvent which is not

470

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Scheme: formal representation of the TATM molecule, with those bonds emphasized about which torsion can occur. H1 attached to C1 is below the plane of the page and the apex C1 of the trigonal pyramid C1 C2 C8 C14 is pointing away from the observer. Positions of ring hydrogens have been distorted for convenience in drawing. The particular conformation illustrated here and in Fig. 8.39 is for Molecule A in the {TATM[1/2CCl4]} complex. The line formula of the Scheme is somewhat misleading as the molecule is not planar but has the tripod shape shown in Fig. 8.39. Torsion of ﬁve membered rings about the (H)CC bonds (t1, t2 and t3 are deﬁned as H1–C1–C=C for each of the three rings) is one type of conformational variable and the second depends on whether the carbonyl oxygens are syn or anti to S in the rings; these torsion angles t4(S1–C4–C6–O1) and analogues (t5 and t6)) are all 0 or 180 . The conformations of the methyl groups, for which there is little experimental information, have not been included. C19H191,192,193

O3 C18

τ6

C16 S3

3

H17 C17

H3

C15 C14

H15

τ3 H11 C11 C8

H131,132,133C13 C12

H1 C3 τ1 1 C 1 C2 τ2

2 C 9 C10 S2 τ5

C5 H5 H9

S1 C4

τ4 C6

O1

C7H71,72,73

O2

8.6

incorporated’’ (my italics). This conclusion has been substantiated in later work (Sidhu and Ripmeester, 2001). Bin Din and Meth-Cohn (1977) made a variety of TATM analogs by replacement of the acetyl groups with functionalities such as OCOCH3; only the methyl ester showed any promise of clathration ability, while attempts at resolving a racemic mixture of 2-butanol with TATM were unsuccessful. A correlation of the thenavailable experimental data (crystal structures, TATM conformations) for the TATM inclusion complexes has been made (Herbstein 1997a) and this analysis is now brought up to date. The guests are collected together, classiﬁed in terms of host : guest ratio and chemical nature of the guest, in Table 8.10. Only binary TATM systems are considered here. It would be interesting to see if TATM could act as an acceptor for guests with hydrogen bonding capabilities; this has so far only been done for TATM2H2O.

8.6.3

Conformations taken up by the TATM molecule in the various crystallographic structure types

The conformation of the TATM molecule in various crystalline inclusion complexes provides one potential source for classiﬁcation; another is the variety of crystal structures

TRIS(5-ACETYL-3-THIENYL )M ETHANE (T AT M) AS HOST

471

Table 8.10. Crystalline {(TATM)x[Guest]y} inclusion complexes, classified according to host– guest ratio and chemical nature of the guest. TATM host–guest inclusion complexes have so far been reported in the literature with more than 60 different types of guest; nine different kinds of crystal structure have been reported, with 12 different guests. Bold type denotes complexes for which crystal structures have been reported. The dynamics of the (deuterated) guests has been studied by NMR for many of these complexes (Sidhu et al., 1996) Host–Guest ratio 1:2 water 1:1 cyclo-nonanone 2:1 C6H5R with R ¼ F, Cl, Br, I, CH3, C2H5, CH(CH3)2 (cumene); o-, m- and p-xylene, mesitylene benzene, naphthalene cyclohexane (2 polymorphs), cycloheptane, cycloo¨ctane, cycloo¨ctene methanol, ethanol, iso-propanol, sec-butanol, tert-butanol, n-decanol acetone, methyl ethyl ketone, methyl phenyl ketone methyl phenyl ether halocyclohexanes (X ¼ F, Cl, Br), CH2X2 (X ¼ Cl, Br, I), CHCl3, CCl4, 1,3-dichloropropane (5 polymorphs), also 1,3-dihalopropane (halo ¼ F, Br), 1,2-dichloroethane (2 polymorphs), 1,4-dichlorobutane pyridine, piperidine, triethylamine ethyl acetate, methyl cyanide, acetic acid, nitromethane, dimethyl sulphoxide, HCON(CH3)2, decalin, acetonitrile, dimethylformamide. 3:1 t-Butylbenzene, n-hexane, 1,5-dichloropentane, 1,6-dichlorohexane 4:1 1,8-dichlorooctane, 1,9-dichlorononane, 1,10-dichlorodecane Notes: Preparation of complexes has been reported by Yakubov, Sudarushkin, Belenkii and Gold’farb (1973), Bin Din and Meth-Cohn (1977). Roos and Dillen, (1992), Pang and Brisse (1994b), Pang and Brisse (1994a), Sidhu and Ripmeester (2001, 2003), Sidhu, Enright, Udachin and Ripmeester (2004).

(see next section) and whether these are isomorphous, isostructural or indifferent. Analysis should hopefully lead to uncovering the relation that must exist between these two structural aspects, but this largely remains to be achieved. Structural information is available for 30 crystallographically independent TATM molecules in ten different types of crystal structure (including the dihydrate). Speciﬁcally, the following questions can be asked, and answered, from an analysis of the published crystallographic results: 1. Is there a correlation between the TATM conformer and the crystal structure of the inclusion complexes, i.e. is the same TATM conformer found in all the members of a group of isomorphous crystals? The answer is ‘Yes’. 2. If so, then which TATM conformers occur in the various groups of isomorphous inclusion complexes, and what is the range of TATM molecular structural variation

472

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Fig. 8.39. Ball and stick model of TATM molecule as found in its CCl4 complex (only one of the two independent molecules in the asymmetric unit is shown). The view is along the methine C–H bond, the hydrogen being behind the plane of the page. The hydrogens have been inserted in calculated positions. Notice that two oxygens (of C¼O groups) are syn to S and one anti.

3.

(speciﬁcally torsion angles) found within the several groups? This is answered below. What is the range of structural variation when there is more than one TATM molecule in the crystallographic asymmetric unit? This is answered below.

Potentially one can also hope to study how the nature of the guest inﬂuences the conformation taken up by the host, but this is not generally possible at present because the guests are disordered in most of the crystal structures that have been determined. Repetition and extension of the crystal structure determinations at low temperatures should be rewarding. The crystals included in Table 8.9 are all racemic and so absolute optical conﬁgurations are not required; nevertheless, meaningful comparison of the geometrical structures taken

TRIS(5-ACETYL-3-THIENYL )M ETHANE (T AT M) AS HOST

473

up by TATM in its various inclusion complexes requires comparison of conformers of the same optical conﬁguration. The enantiomer chosen (arbitrarily) for intercomparison has been drawn (see Scheme) so that H1 (attached to C1) is below the plane of the page and the apex C1 of the trigonal pyramid C1C2C8C14 points away from the observer. The torsion angles 1, 2 and 3 are deﬁned (again arbitrarily but consistently) as 1 ¼ (H1C1C2¼C3) (C3 linked to S1), and correspondingly for 2 and 3. The TATM molecule will be achiral only for some special values of the torsion angles 1, 2 and 3; as these were not found, the TATM molecule is chiral. The torsion angle with the smallest absolute value has been taken as 1 (it is found that j 1j0 ) and rings 2 and 3 follow in clockwise sequence with the enantiomer oriented as described above. Further distinction among conformers depends on whether the carbonyl oxygens are syn (designated S) or anti (designated A) to sulfur in the rings; experimentally it is found that the torsion angles 4(S1–C4–C6 ¼ O1) and analogs, ( 5 and 6) are either 0 (syn) or 180 (anti). The results show that when there is more than one molecule in the asymmetric unit (i.e. in crystallographic groups III and IV), then analogous torsion angles in the crystallographically independent molecules do not differ by more than 10 (answer to x3 above). Also, analogous torsion angles within a group of isomorphous structures (i.e. in crystallographic groups III, IV, VII and VIII, and in TATM2H2O)) do not differ by more than 10 (answer to x2 above). Representative values for three speciﬁc inclusion complexes are given in Table 8.11. In fact, four conformations have so far been found for the TATM molecule considered as an entity: (a) Conformation 1, with 1 0 , 2 105 , 3 160 and SSS for the three acetyl groups (C1–SSS). The guests are ethyl acetate, ethanol, cyclohexane (polymorph A in Group II), 1,3-dichloropropane (polymorphs 1, 3, 4 and 5), 1,2-dichloroethane (polymorphs 1 and 2) and n-hexane. (b) Conformation 2, with 1 0 , 2 130 , 3 150 and SSA for the three acetyl groups (C2–SSA). The guests are benzene, CCl4, cyclohexane (polymorph B in Group III), cycloheptane, cycloo¨ctane and 1,3-dichloropropane (polymorph 2).

Table 8.11. Torsion angles (degrees) in the TATM host molecule as found in some of its inclusion complexes Inclusion complex

1

2

3

4

5

6

Conformation of carbonyl with respect to ring sulfur

Conformation 1 TATM0.5(ethyl acetate) 7.0 102.9 157.0 2.2 1.1 0.6 SSS Conformation 2 TATM0.5(benzene) 16.2 126.2 148.2 3.5 1.3 178.9 SSA Mol. A Conformation 3 TATMcyclononanone 7.3 101.8 15.2 0.8 10.3 4.3 SSS at 220K.

474

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

Conformation 3, with 1 0 , 2 100 , 3 15 and SSS for the three acetyl groups (C3–SSS). The guest is cyclononanone. (d) Conformation 4, with 1 0 , 2 24 , 3 100 and SSS for the three acetyl groups C4–SSS). This is the conformation found in TATM2H2O.

(c)

The overall conformation of the TATM molecule is determined by the values of the ring torsion angles 1, 2 and 3 (presumably the major factor), and by the values of the torsion angles 4, 5 and 6 of the acetyl group. We had earlier contended (Herbstein, 1997a) that C1 and C2 belong in the same well of the map of potential energy as a function of 2 and 3, and thus refer to one set of ring conformations. The additional examples that have since accrued suggest that C1 and C2 are indeed separate, and this applies with greater force to the overall conformations C1–SSS and C2–SSA. Syn and anti conformations of carbonyl O with respect to S appear, from the statistics of occurrence, to be of approximately equal energy but it is not known what factors govern the appearance of one or other conformation in a particular molecule, nor is it known why the other possible conformations of the acetyl group (SAS, ASS, AAA, AAS, ASA and SAA) do not appear. A molecular mechanics study is sorely lacking. 8.6.4

Crystallography of the inclusion complexes of TATM

Ten different kinds of crystal structures have been reported in the literature, with twelve different guests (Table 8.12). The shape of one example of the TATM molecule is shown in Fig. 8.39. The terms ‘‘clathrate,’’ ‘‘cage’’ and ‘‘tunnel’’ have been used to describe different varieties of these complexes. Structure analyses of the ethyl acetate complex (representative of our Group I) by van Rooyen and Roos (1991a), and of the polymorph A and polymorph B complexes of cyclohexane (representatives of our Groups II and III) by Pang and Brisse (1994b), show clearly that these are all tunnel complexes, with the linear tunnel axis of Groups I and II along the shortest cell dimension and the zigzag tunnel axis of Group III along the longest. The cyclohexane guest of the Group II (polymorph A) complex is located about a center of symmetry and is ordered; the cyclohexane of the Group III (polymorph B) complex is at a general position and takes up three orientations in 40 : 35 : 25 ratio. The cycloheptane and cycloo¨ctane molecules of the Group III complexes take up two orientations in approximate 2 : 1 ratio. Further distinctions can sometimes be made within a group – for example, the benzene and CCl4complexes are both in Group III, but the benzene molecules are ordered (only the second example of ordering of guests among the published crystal structures) while the CCl4 molecules have partially disordered arrangements in which one Cl atom is ordered and the three remaining Cl atoms are trigonally disordered in two orientations with 2 : 1 ratio. It is perhaps not surprising that the three alicyclic guests cyclohexane (Group III – polymorph B), cycloheptane and cycloo¨ctane form isomorphous crystals but the common features causing the benzene and CCl4 complexes to crystallize in this structure type are not clear. The structures of the {TATM0.5(1,3-trichloropropane)} polymorphs can be described in somewhat similar terms (Sidhu, Enright et al., 2005) but details of the resemblances are often obscure. The triclinic hexane complex (Group IV) and the monoclinic cyclononanone complex (Group V) are tunnel inclusion complexes. The ﬁrst has the tunnel axis along [111]

TRIS(5-ACETYL-3-THIENYL )M ETHANE (T AT M) AS HOST

475

˚ , degrees, A ˚ 3) for some inclusion complexes of TATM. Table 8.12 Crystallographic data (A Compositions are expressed as {TATM[n(guest)]}. Triclinic cells have been reduced. S.u.’s of cell ˚ , of angles 0.01–0.04 and of cell volumes 0.4–2 A ˚ 3. Analyses lengths are 0.002–0.006 A were at room temperature unless stated otherwise b

c

Cell volume

11.229 10.907

12.329 12.306

99.05 97.23

106.43 106.63

98.42 96.87

1057 1012

10.372 10.194

12.488 12.795

81.49 79.09

71.26 72.74

84.95 84.89

1010 1054

13.560 13.684 13.729

14.197 14.235 14.227

89.68 88.90 89.40

76.60 77.46 77.15

75.50 78.77 76.24

2089 2170 2157

13.734 14.013

14.177 13.986

89.22 89.46

76.84 77.15

76.01 75.22

2154 2198

12.647 12.684

12.694 12.704

20.604 85.89 20.572 102.71

74.31 103.95

86.36 91.35

3173 3128

10.994

19.464

13.417

90

109.4

90

2708

12.690

12.743

13.738

90

109.5

90

2100

12.715

12.723

13.893

90

109.97

90

2113

Group VII: P2/n, Z ¼ 8 0.5(1,3-dichloropropane), 173K, polymorph 2; SEUR05

14.319

13.499

22.328

90

104.08

90

4186

Group VIII: P2/n, Z ¼ 8 0.5(1,3-dichloropropane), 173K, polymorph 3; SEUR05

12.731

12.762

25.937

90

93.88

90

4204

Group IX: C2/c, Z ¼ 8 0.5(1,3-dichloropropane), 173K, polymorph 5; SEUR05

17.500

18.465

14.982

90

119.43

90

4217

n (guest), Refcode, reference

a

Group I: tunnel axis along [100], P1, Z ¼ 2 0.5(ethyl acetate) JIYVIW; RR91a 8.229 0.5 (1,2-dichloroethane) 173K, 8.033 polymorph 1; SERP02 Group II: tunnel axis along [100], P1, Z ¼ 2 0.5(ethanol) VUJZOP; DR92 0.5(cyclohexane), polymorph A at 220K; YIRVAW; PB94b

8.335 8.622

Group III: tunnel axis along [001], P1, Z ¼ 4 0.5(benzene) JIZFED; RR91b 11.538 11.638 0.5(CCl4) LEKREY; PHW94 0.5(cyclohexane), polymorph B 11.668 YIRVAW01; PB94b 0.5(cycloheptane) at 220K [c] YIRVIE 11.721 0.5(cyclooctane) at 220K YIRVOK 11.914 , Z ¼ 6 Group IV a and b: P1 a. 1/3(n-hexane) KUGZAN; RD92 b. 0.5(1,3-dichloropropane), 173K, polymorph 1; SEUR05 Group V: P21/c, Z ¼ 4 cyclononanone at 220K WIKCOI; PB94a Group VI: P21/c, Z ¼ 4 0.5(1,2-dichloroethane), 173K, polymorph 2; SERP02 0.5(1,3-dichloropropane), 173K, polymorph 4; SEUR05

Notes: (1) Space groups for the ethanol and ethyl acetate complexes were originally given as P1, but Marsh (1994) has corrected these to P 1 (see VUJZOP01 and JIYVIW01); (2) the complexes of Groups I and II are not isomorphous; however, there are resemblances between the two structure types, and both have tunnels along [100]. Similar remarks apply to Groups IVa and IVb. References: DR92 – Dillen and Roos (1992); PB94a – Pang and Brisse (1994a); PB94b – Pang and Brisse (1994b); PHW94 – Pang, Hynes and Whitehead (1994); RD92 Roos and Dillen (1992); RR91a – Rooyen and Roos (1991a); RR91b – Rooyen and Roos (1991b);SERP02 Sidhu, Enright et al., 2002; SEUR05 – Sidhu, Enright et al., 2005.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

476

(possible disorder not mentioned) and the second along [100] (guest disordered over two orientations in 75 : 25 ratio). ˚ , 88.98, 89.57, 80.70 , P1, The TATM.2H2O complex (triclinic, 8.761, 10.793, 21.794 A Z ¼ 4) has two (ordered) waters as part of the framework and two (disordered) waters in tunnels.

8.6.5

Formation of the inclusion complexes

The different overall conformations of TATM inferred above will occur in TATM solutions in relative proportions given by the Boltzmann distribution; these proportions will depend on temperature but not on the nature of the solvent. The solution will become supersaturated on cooling and the appropriate inclusion complex will begin to crystallize. For example, if the solvent is benzene then {TATM[1/2(benzene)]} will crystallize and the solution will become depleted in molecules with Conformation C2– SSA; the Boltzmann distribution will be continuously re-established by conversion of molecules with the other conformations and this process will continue until the appropriate amount (determined by its solubility) of crystalline inclusion complex has been formed. What happens with cyclohexane as solvent? Here it is presumed that nuclei of cyclohexane with the differently shaped conformers C1–SSS and C2–SSA will be formed and these will give rise to the two polymorphic forms of {TATM[1/2C6H12]} designated above as Polymorph A of Group II and Polymorph B of Group III. Pang and Brisse (1994b) report that Polymorph B was obtained by relatively rapid cooling (1 C/h) and A by slow cooling (5 C/day); this suggests that B is metastable with respect to A, in ˚ 3). Presumably accordance with the respective volumes/formula unit (B ¼ 539 A Ostwald’s rule of successive reactions (e.g. Findlay, Campbell and Smith, 1951) applies to this system but this has not been explicitly stated. In terms of this description the overall process of formation of a crystalline inclusion complex can be divided into three stages: 1.

2. 3.

Selection of appropriate TATM conformer from the ensemble of conformers, requiring recognition between solvent molecule and the appropriate TATM conformer, i.e. the determining factor is host-guest interaction. Formation of nuclei from the TATM-solvent aggregates, requiring predominantly host conformer–host conformer recognition. Growth of nuclei to form crystals.

Thus the formation of crystalline inclusion complexes containing TATM molecules of different conformations (depending on the solvent partner) does not present any conceptual difﬁculties. This description, with the guest (solvent) molecule plucking out the appropriate TATM conformer from the Boltzmann distribution, is the converse of that given when a rigid host is used in selectivity experiments with a solution of, or containing, a mixture of guests. This description also provides a possible explanation for the occurrence of an amorphous sublimate; the presence of more than one conformer in the condensing sublimate prevents crystallization.

TRIS(5-ACETYL-3-THIENYL )M ETHANE (T AT M) AS HOST

477

8.6.6 Dynamics of guest molecules in the complexes Deuterium NMR (labeling of guests) has been applied to these systems to study guest dynamics down to 112K (Sidhu et al., 1996). There is sixfold rotation of benzene in its TATM complex, with an activation energy of 4.1(4) kJ/mol, and no minimum in relaxation time down to 112K. These results are compatible with the crystal structure noted above. o-Xylene and p-xylene are rigidly held in their TATM complexes, with rapid rotation of the methyl groups. Dimethylsulfoxide is also held rigidly, but with rapid rotation of the methyl groups. Mesitylene occupies two sites in the TATM structure, but the motion of the methyl groups was not established. Acetonitrile and nitromethane both have a precession motion, with an activation energy of 11.5(5) kJ/mol. The behavior of the deuterated guest in triclinic {TATM0.5(1,2-dichloroethane)} was also studied (Sidhu, Enright et al., 2002). Correlation of NMR and XRD measurements led to a model in which the trans conformer of 1,2-dichloroethane performs 180 ﬂips through the centre of symmetry of the guest and about an axis perpendicular to the Cl–C–C–Cl plane. 8.6.7 Other examples The host–guest complexes of E,E-1-[ p-dimethylamino-phenyl]-5-[o-hydroxy-phenyl]penta-1,4-dien-3-one (the Heilbron complexes (Herbstein, Kapon, Reisner and Rubin, 1984); see Section 8.4) are an example of selection by the guest of conformationallydistinct states of the host from solution, as shown by the fact that the host molecules have the s-trans, trans conformation in some complexes and the s-cis, trans in others; however, the number of such complexes of known crystal structure is limited, and generalization is not yet possible. 8.6.8 Summary Analysis of the published crystallographic data shows that the TATM molecules in a particular group of isomorphous host–guest inclusion complexes (with different guests) all have the same conformation, with numerical values of ring torsion angles not differing by more than 10 within the group of crystals. The same holds for comparisons between different host molecules in a particular inclusion complex when there is more than one molecule in the crystallographic asymmetric unit. This could be taken to imply that there is a 1 : 1 correlation between ring conformations and crystal structure but this is an oversimpliﬁcation. The situation is complicated by the fact that, while the ring conformations are the primary factor in determining the energy of the TATM molecule, the conformations of the three acetyl groups (syn or anti relation of carbonyl oxygen to ring sulphur) are an essential component in determining the overall molecular shape, which is more important than ring conformation in determining the crystal structure of the inclusion complex. Thus the correlation is between overall molecular conformation (i.e. the combination of the conformations of rings and acetyl groups) and crystal structure. The syn and anti conformations of the acetyl groups appear to have similar energies from the statistics of their occurrence but only two of the possible combinations of ring conformation–acetyl group conformation have so far been encountered. It is not clear

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

478

whether this is because the available sample is unrepresentative of the population as a whole or because other factors contributing to overall molecular energy have not yet been recognized. 8.7

(5,10,15,20)-Tetraphenylmetalloporphyrins and complexes

8.7.1

Introduction

, , , (or 5,10,15,20)-Tetraphenylmetalloporphyrins4 form very many molecular complexes (the , , , notation is due to Fischer and the 5,10,15,20 notation is that recommended by IUPAC (Smith, 1984)); TPP is the abbreviation used for the dianion of 5,10,15,20-tetraphenylporphyrin itself and thus the metalloporphyrins are designated as (TPP–M2þ) (with obvious extensions for metal ions of different charge); the formula of (TPP–M2þ) is C44H28N4M. Many substances listed as ‘‘complexes,’’ are either coordination complexes or inclusion complexes comprised of coordination complexes with non coordinated guests; sometimes the same molecule behaves as a ligand and as a guest in an inclusion complex. (TPP–M2þ) molecules, often as ‘‘complexes,’’ have been extensively investigated from many points of view, including comprehensive crystallographic studies (Scheidt and Lee, 1987); the November 2002 Version 5.24 of the CSD (272066 entries) gave some 600 entries for TPP complexes and analogs. Many crystal structures have been reported using the conventional approach to their description, but the most substantial corpus of material is that accumulated by Strouse and his coworkers over almost a decade. The Strouse group has determined the structures of some 300 ‘‘complexes’’ (of all kinds), many at low temperatures (mostly around 100K but two at 15K). The extent of this contribution is shown by the following papers relevant to the content of this chapter: 1.

2.

3.

4.

Byrn, Curtis, Hsiou, Khan, Sawin, Tsurumi and Strouse, 1990 (B90); cell dimensions were given for 65 isostructural TPP complexes, and 52 packing diagrams were shown. Byrn, Curtis, Goldberg, Hsiou, Khan, Sawin, Tendik and Strouse, 1991 (B91): Crystal data were reported for 45 complexes, and ‘‘a detailed analysis [was made] of the molecular packing in over 100 TPP-based clathrates;’’ 56 packing diagrams were shown. Byrn, Curtis, Hsiou, Khan, Sawin, Tendik, Terzis and Strouse, 1993 (B93). Crystal data were provided for 75 new porphyrin-based clathrates, and the molecular packing was analyzed in over 200 tetraarylporphyrin-based lattice clathrates; some 150 packing diagrams were shown. Byrn, Curtis, Hsiou, Khan, Sawin, Terzis and Strouse (1996); this is an extensive summary review of earlier material.

By 1993, the structures of some 480 ‘‘porphyrin-based lattice clathrates’’ had been reported (Table 8.13, taken from Table I of B93). 4 In more general terms the host materials are tetraarylmetalloporphyrins (TAP), where the aryl groups may be substituted. We consider only the neutral (TPP–M2þ) species, but the reader should be aware of extensive additional material not covered here for reasons of space. There are related series where the host is TPP– Mnþ(n ¼ 3–6) and appropriate counterions. Examples of Mnþ are Mn3þ, Fe3þ, Co3þ, Rh3þ, Au3þ, Sn4þ, Ce4þ, U4þ, Nb5þ, Mo6þ, W6þ; there also some examples with Co, Fe, Feþ.

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

479

Table 8.13. Crystallographic symmetry of porphyrin-based lattice clathrates for which X-ray structural data are available Crystal symmetry

Z

number

Crystal symmetry

Z

number

triclinic

1 2

139 81

orthorhombic

monoclinic

2 4 8

56 132 10

2 4 8

1 18 8

tetragonal

2 4 8

20 9 3

rhombohedral

6

3

B93 have commented that ‘‘Although the TPP molecule lacks any functionality that might be expected to dictate the relative disposition of neighboring molecules, one ﬁnds that the host structure is strongly conserved in porphyrin-based clathrates.’’ Perhaps the most remarkable features of the coordination complexes are the variety of metals that can be incorporated in the TPP macrocycle, and the catholic nature of the ligands/guests. The M2þ species include M ¼ 2H, Mg, Mn, Fe, Co, Ni, Cu, Zn, Mo, Ru, Pd, Ag, Cd, Sn. The ligands (actual or potential) include heterocyclics (pyridine, piperidine, 4-picoline, acridine, isoquinoline, 1,4-dioxane, trioxane), aromatic esters (methylbenzoate, tetramethylpyromellitate), quinones (anthrone, 9-xanthone, bianthrone), aldehydes (benzaldehyde, also with various substituents), aliphatic alcohols (2-propanol, hexanol, 6methyl-5-hepten-2-ol) and phenols. The guests include aromatic hydrocarbons (benzene, anthracene, phenanthrene, 1,2-benzanthracene, 2,3-benzoﬂuorene, coronene) and substituted aromatics (halobenzenes, toluene, the xylenes, 1,2,4-trimethylbenzene, mesitylene, ethylbenzene, styrene, phenylacetylene). Although most of the guests have an aromatic functionality, this is not a requirement and the impression is that the hosts are very versatile indeed and able to adapt their packing arrangement in the crystal to the shape of the guests and, perhaps, to particular types of host–guest interaction. Some of the compounds noted above as ligands also appear as guests. Classiﬁcation of the second component as ligand and/or guest is reconsidered at the end of this section after surveying the structural results. Discussion of the structural chemistry of the metalloporphyrin complexes (using ‘‘complex’’ in its most general sense) raises a number of issues, some formal, as in their classiﬁcation, and some actual, as in their structure and behavior. The point of view taken in this book (see Chapter 2) is that binary adducts (alternatively, molecular complexes and compounds) are ‘‘crystalline two-component phases in which the properties of the components are very largely conserved.’’ This implies that there are no covalent bonds between the components and is shown in its purest form in Chapter 10 (‘‘Packing Complexes’’). However, this pure concept breaks down in Chapter 12 (‘‘Hydrogen Bonded Molecular Compounds and Complexes’’), and Chapter 11 (‘‘Donor–Acceptor Molecular Compounds (Essentially Localized Interactions)’’), where we admit the importance of partial bonds between the components. A similar process occurs in the metalloporphyrin complexes, where there is bonding (of varying strength) between metal

480

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

and ligand in the ﬁve- and six-coordinate species (the four-coordinate species do not have ligands); it is only when guests are present that one has inclusion complexes in the strict sense. However, the structural resemblances across the whole group are so strong that it is logical to treat all these species together, but only after they have been deﬁned separately. The structural consequences have been neatly summarized by B90; p. 1871: . . . the materials . . . include 4-, 5- and 6-coordinate species, all of which exhibit the same porphyrin framework. In the structures of the 4-coordinate materials, solvate molecules occupy the open channels. With the 6-coordinate materials, the axial ligands occupy the channels. In both cases the metal atom resides on a crystallographic inversion centre. [This applies speciﬁcally to the triclinic (Z ¼ 1) and some monoclinic crystals (FHH).] In the 5-coordinate materials, the single axial ligand and one solvent molecule occupy alternate sites in the channel. . . . to a large extent the packing is controlled by the centrosymmetric TPP molecule . . .

Strouse and coworkers have found it convenient to describe the large number of structures that they have investigated in terms of non-standard body-centred triclinic cells containing 2 formula units per cell, and unusual choices of monoclinic angles for some monoclinic crystals. The host–guest relationship is then illustrated using a ‘‘lattice section’’ through these cells, generally in the plane of the porphyrin ring. Lattice sections for {(TPP–Mn2þ)(toluene)2} and {(TPP–Mg2þ)(4-picoline)2} are compared in Fig. 8.53, cell dimensions being given in Table 8.22. The problem with this approach is that, using lattice sections alone, it is often difﬁcult to be certain whether a particular material is a coordination complex, or an inclusion complex based on a combination of coordination complex and included guest. A deﬁnitive decision can only be made on the basis of the complete structure analysis, usually determined by the Strouse group and available from the CSD, but seldom directly from the four papers noted above. We have preferred, in general, to follow most earlier authors and use a conventional crystallographic approach, emphasizing the advantages of using reduced cells for describing triclinic crystals, and have given standard descriptions for the other systems. We shall compare the two approaches for a few examples. We give many cross-references to the Strouse papers, noting, but not using, their classiﬁcations. Each group of related crystal structures deserves detailed analysis, and individual attention should also be given to exceptional examples. This has been done here but only partially; perhaps a full treatment will attract a dedicated author. Although these ‘complexes’ were described in the earlier studies as ‘‘extremely air sensitive,’’ it appears that decomposition was generally due to loss of guest (or solvent) molecules and later workers have grown crystals from solution and carried out diffraction studies without special precautions beyond enclosing crystals in capillaries or a plastic coating. 8.7.2

Crystallography of (5,10,15,20)-tetraphenylmetalloporphyrin coordination complexes

8.7.2.1 Introduction We start by considering the crystallography of the {host TPP-ligand} species as four-, ﬁve- and six-coordinate coordination complexes, organizing the crystal structures into isomorphous or isostructural groups on the basis of published crystallographic results. We then extend this treatment to the inclusion complexes, followed by some cross-correlation. Most of the available results are for triclinic crystals. The reader is reminded that,

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

481

although a triclinic unit cell can be chosen in many ways, it is only the ‘Niggli reduced cell’ that is unambiguously deﬁned.5 Thus we have quoted results for reduced cells, making transformations where necessary. There are two types of triclinic cell, Type (I) with the origin chosen so that the three interaxial angles are acute, and Type (II), with the three interaxial angles obtuse; for more detail and references see Herbstein (1997b). The two types are not interconvertible. We have followed the convention that a < b < c where possible. However, many structure analyzes are reported in terms of nonconventional cell choices; in order to avoid confusion, we have followed the original authors in their choice of cell unless stated otherwise. Original estimates of precision are used when required (not often), even if these may sometimes appear to be over optimistic. The crystallographic classiﬁcation is initially based on cell dimensions and space groups. These provide a necessary, but not sufﬁcient, basis for classiﬁcation because molecular arrangements are appreciably, but not entirely, determined by the packing of the (TPP–M2þ) moiety. Thus it is essential to examine the crystal structure to determine the mode of interaction between the (TPP–M2þ) moiety and the second component, i.e. is this a ligand linked to the metal, giving a coordination complex or a guest, without special linkage to the metal, giving an inclusion complex? Strouse et al. have called many of their structures ‘‘clathrates;’’ the CSD have distinguished between coordination metalloomplexes (explicit metal–ligand linkages) and ‘‘clathrates,’’ which encompasses both weaker metal–ligand linkages and inclusion complexes. We have treated the two latter groups separately. One must also note that the second components are disordered in some crystals and thus clearcut classiﬁcation is not always possible. A number of variables have to be taken into account. One is the nature of the metal ion; we restrict ourselves to uncharged hosts so the metal ion is formally M2þ. Another variable is the nature of the second component, which can be a ligand, thus giving a coordination complex, or the guest, in an inclusion complex. Some of the coordination complexes can also contain guests, so structural classiﬁcation can be quite complicated, especially when based on unit cell dimensions rather than full crystal structures. Much of our information comes from the Cambridge Structural Dataﬁle (CSD; Version 5.24 of November, 2002; 272 066 entries), where reduced cells and packing diagrams are given. Atomic coordinates are available for most entries, thus enabling re-examination of brieﬂyreported structures. The metal–ligand distances (exempliﬁed for Zn) fall (approximately) ˚ , and weaker with d(Zn–O/ into two groups – stronger binding with d(Zn–O/N) 2.2 A ˚ . We classify both as coordination complexes; longer distances imply inclusion N) 2.5 A rather than coordination. We ﬁrst discuss the true coordination complexes. 8.7.2.2

The four-coordinate coordination complexes

The four-coordinate (TPP–M2þ) neat host molecules (i.e. without ligands or guest molecules) crystallize in three isomorphous groups of crystals: Tetragonal crystals for M ¼ Ni, Cu, Co (Madura and Scheidt, 1976), Pt, Pd, 2H (Hamor, Hamor and Hoard, 1964, TPHPOR10; Stone and Fleischer, 1968; 5 Reduced cells can be deﬁned in a number of ways; we choose not to elaborate but refer the reader to authoritative sources such as the International Tables for Crystallography.

482

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

˚ , c: 13.89–14.04 A ˚ , space group I 42d (No. TPHPOR1X), Fe with a: 15.04–15.13 A 3 ˚ 122), Z ¼ 4, volume per formula unit : 788–798 A , molecular symmetry S4 4 (see Table XXVIa of Scheidt and Lee (1987) for details and references). Triclinic crystals for M ¼ 2H (Barker, Stanley and Fronczek, 2002, TPHPOR11), Zn, Ag, Cr, Mn; A full range of solid solutions is formed between TPP–Ag2þ and TPP–2Hþ (Donnay and Storm, 1967) with crystal data (Z ¼ 1, space group P1) given below. The three triclinic (TPP–M2þ) four-coordinate coordination complexes are ˚ , deg., A ˚ 3) are for reduced cells, but with nonisomorphous. The cell dimensions (A standard choice of origin.

Mnþ Reference; Refcode

a

b

c

Cell volume

2Hþ; SL67; TPHPOR01 Zn2þ; SME86; ZZZTAY02 Ag2þ; SME86; DOWRAI

10.420 10.382 10.503

12.410 12.421 12.485

6.440 6.443 6.351

99.14 98.30 97.73

101.12 101.15 100.68

96.06 96.47 97.15

799 798 801

References: SL67 – Silver and Tulinsky, 1967; SME86 – Scheidt, Mondal, Eigenbrot et al., 1986.

Triclinic crystals for M ¼ Cd. The reduced cell has a ¼ 10.096, b ¼ 12.446, ˚ 3, ˚ , ¼ 79.95, ¼ 75.81, ¼ 81.24 , volume per formula unit 800.6 A c ¼ 13.438 A space group P1, Z ¼ 2 (Hazell, 1986).

Only (TPP–2Hþ) is common to the ﬁrst two groups. As the volumes per formula unit for ˚ 3 (triclinic)), this ˚ 3 (tetragonal) and 802 A the two polymorphs are not very different (792 A datum gives only a weak indication that the tetragonal crystals are the more stable. The volume occupied by the (TPP–M2þ) host molecule (in the unit cell) can be taken as ˚ 3to a ﬁrst approximation, irrespective of the nature of the metal ion. An exception is 800 A ˚ 3 in its triclinic perhaps provided by neat (TPP–Zn2þ), which has a molar volume of 798 A 3 ˚ in a monoclinic form produced by high temperature crystallization crystals, but 841 A from 1,3,5-triisopropylbenzene (B93); a molar volume difference of 5% for polymorphs is unusual but not unprecedented. In the tetragonal crystals (which are not centrosymmetric but are racemic) the non4 symmetry with the pyrrole rings planar host porphyrin macrocycle molecule has S4 ˚ off tilted at 12 to (001). The carbons linked to the phenyls are displaced by 0.4 A (001). The planes of the phenyl rings, which librate about the C–C bonds with an amplitude of 9 , are tilted at 80 to (001). The structure consists of layers of molecules ˚ , mutually shifted in (or about) the (001) plane; succeeding layers are separated by 3.5 A by a/4 and are related by a two fold axis at z ¼ 1/8 along [100]. The triclinic (Z ¼ 1) crystals have a structure with crumpled layers about (010); all (TPP–M2þ) host molecules are translationally equivalent and the macrocycle is only slightly distorted from planarity. The ring dihedral angles have values of 90–60 in the triclinic (Z ¼ 1) group. Thus the tetragonal and triclinic (Z ¼ 1) groups can be described as having layer structures, although of rather different kinds. The metalloporphyrin macrocycles are appreciably distorted from planarity in the tetragonal polymorphs but hardly at all in the triclinic (Z ¼ 1) polymorphs. The roles of intramolecular (the nature of the metal atom) and intermolecular interactions (‘‘packing effects’’) in determining the relative stabilities of

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

483

the two structural groups do not yet appear to have been sorted out. This is important for understanding the thermodynamics of the formation of the molecular complexes and the nature of the products of their thermal decomposition. (TPP–Cd2þ) has a weak dimer structure and so is probably not directly comparable with the other structures. 8.7.2.3

The ﬁve-coordinate coordination complexes

The entries in Table 8.14 have been arranged in groups of isomorphous or isostructural crystals. The cell dimensions of the ﬁrst pair of entries suggest that these two crystals are closely isomorphous. It is clear from Fig. 8.40 that {(TPP–Zn2þ) 9-xanthone} (HALWAS) is a ﬁve-coordinate coordination complex and not an inclusion complex. The ﬁve-coordinate coordination complexes have common geometrical features. The four links from the metal atom to the equatorial nitrogens are very similar; in HALWAS they ˚ . The metal atom is displaced from the plane through are 2.055 (twice), 2.058 and 2.063 A ˚ . The angle ¼ Neq–M–Xax the equatorial nitrogens towards the ligand by here 0.218 A is 98.28 ; there are four such angles but we shall only give one value. The Zn–O distance ˚ in the 9-xanthone complex is appreciably shorter than the values found in the of 2.205 A bianthrone and dibenzosuberone complexes (see below) and attests to stronger bonding ˚ ), in accord here. The anthrone complex has a very similar structure (d(Zn–O) ¼ 2.226 A with the appearance of Fig. 26 of B93, which has the caption ‘‘Stage 2 ‘Hybrid’ clathrates.’’ We have placed the entries for 3-nitroaniline and 5-octanoic lactone next because of similarities in axial lengths despite differences in interaxial angles. There is some similarity between the lattice sections for these two complexes in Fig. 21 of B93. The crystal structure of {(TPP–Zn2þ)(3-nitroaniline)} has been obtained from HAMLAI. It is a ﬁve-coordinate coordination complex with Zn linked to the amino group of ˚ , while the distances to the equatorial nitrogens are 3-nitroaniline (d(Zn–N) ¼ 2.314 A ˚ ˚ . Perhaps surprisingly, the bifunctional 1.967, 2.018, 2.046, 2.058 A); ¼ 0.244 A 2,5-hexanedione ligand has only one of its carbonyl groups linked to Zn (crystal structure ˚ ; d(Zn–N) ¼ 2.041, 2.056, 2.059, 2.088 A ˚; from HAMGUX), with d(Zn–O) ¼ 2.261 A ˚ ¼ 0.188 A and ¼ 99.37 . The reduced cells show that the next four entries are isostructural. The pair Grandlure III/IV and II6 are closely isomorphous, despite the differences in the chemical formulae of the guests; the lattice sections shown in Fig. 19 of B93 (captioned ‘‘ ‘normal’ stage 2 clathrates’’) are similar. The Grandlure I clathrate (lattice section in Fig. 17 of Byrn et al. (1996)) has a different arrangement. 4-Chlorophenol and 4-methylcyclohexanone have similar lattice sections (Fig. 19 (B93)) but the inter-axial angles differ appreciably. 6

Glossary of chemical names: 1. 2. 3. 4. 5. 6. 7.

eugenol is 1-allyl-4-hydroxy-3-methoxybenzene linalool is 3,7-dimethyl-1 : 6-octadien-3-ol trans-anethole is p-propenyl-phenyl methyl ether grandlure I is (1R,2S)-( þ )-cis-isopropenyl-1-methylcyclobutane-ethanol grandlure II is (Z)-3,3-dimethyl-1,–cyclohexane-ethanol grandlure III is (Z)-3,3-dimethyl-1,–cyclohexane-acetaldehyde grandlure IV is (E)-3,3-dimethyl-1,–cyclohexane-acetaldehyde

The last four entries are sex pheromones of the boll weevil; their Zn TPP complexes have been used as slow release formulations of these pheromones (Byrn et al., 1996).

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

484

Table 8.14. Crystal data for triclinic and monoclinic (TPP–Mnþ) five-coordinate coordination ˚ , deg., A ˚ 3) are for reduced cells. Italicized volumes indicate that complexes. The cell dimensions (A the cell dimensions were measured at low temperature (nominally 100K) Mnþ

Ligand

Triclinic, Z ¼ 2, space group P1 Zn2þ (anthrone) HAMDAA (9-xanthone) HALWAS Zn2þ Zn2þ 3-nitroaniline HAMLAI; ˚ d(Zn–N) ¼ 2.314 A Zn2þ 5-octanoic lactone HAMJAG; ˚ d(Zn–O) ¼ 2.234 A 2,5-hexanedione HAMGUX; Zn2þ ˚ d(Zn–O) ¼ 2.261 A Zn2þ 1-hexanol 4-chlorophenol; HAMFUW; Zn2þ ˚ d(Zn–O) ¼ 2.376 A Zn2þ 4-Cl-Ph-vinylidenecarbene GAMCAY Zn2þ phenethylpropionate Grandlure III/IV Zn2þ Zn2þ Grandlure II Mg2þ (2-propanol)2 HAMBEC 145K (see text) Mg2þ (H2O)(acetone)2 133K GEPBUY (see text) Mg2þ (H2O)(2-picoline)2 DUJKUO (see text) Zn2þ 6-methyl-5-hepten-2-ol 4-methylcyclohexanone Zn2þ HAMHIM; ˚ d(Zn–O) ¼ 2.306 A

a

b

c

Cell volume

11.138 11.100 12.358

12.798 12.850 12.781

15.307 15.500 14.943

81.21 80.05 103.54

85.56 86.14 111.03

80.11 78.89 106.92

2121 2136 1950

11.202

12.671

14.516

100.47

95.52

102.80

1956

12.677

11.300

14.204

94.45

96.13

100.54

1979

10.407 10.428

10.864 10.479

19.366 18.506

89.93 88.58

76.06 81.62

77.96 79.98

2076 1970

10.667

12.514

18.091

86.94

72.90

78.51

2262

11.187 10.818 10.882 11.154

11.310 11.097 10.906 12.519

18.731 19.375 19.924 16.564

77.27 94.73 94.99 104.87

87.79 100.29 100.86 108.35

73.37 105.59 105.00 101.84

2214 2184 2220 2016

10.694

12.925

15.631

105.18

90.27

102.27

2033

10.328

13.321

16.607

87.23

82.65

86.60

2260

10.377 10.791

11.026 10.804

19.627 18.035

91.40 93.18

102.29 94.27

102.94 102.35

2132 2043

10.931

90

102.57

90

4032

10.896

90

102.70

90

4033

15.478

90

109.80

90

4093

Monoclinic, Z ¼ 4, space group P21/a or orientational variant Zn2þ (3-penten-2-ol) (4) HALXOH; 10.553 35.812 ˚ d(Zn–O) ¼ 2.267 A Zn2þ 2-phenylethylamine (4) 10.688 35.499 HAMMIR 128K; ˚ d(Zn–N) ¼ 2.193 A 3-methylcyclohexanone (4) Zn2þ 15.405 18.245 P21/n Fe2þ NO Scheidt and Frisse, 1975; 13.48 13.48 ONFTPP

9.755

Tetragonal, Z ¼ 2, I4/m

References: All data (except where noted) were taken from B93: triclinic crystals from Tables III and IV; monoclinic crystals from Table V.

The (TPP–Mg2þ)(X)} complexes are particularly interesting, and illustrative of complications that may arise. The crystal structure determination for X ¼ [propan-2-ol]2 shows that this is a ﬁve-coordinate coordination complex, where the liganded species is a ˚ ); d(Mg–O) ¼ 2.076 A ˚ ). Cell hydrogen-bonded propan-2-ol dimer (d(O . . . O) ¼ 2.740 A

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

TPP

485

Zn

d(O–Zn) = 2.205 Å 9-xanthone TPP

1Zn–O=C = 164.37° 1N–O=C = 94.35°

y x

z

Fig. 8.40. Projection of crystal structure of (TPP–Zn2þ)(9-xanthone) down [001] (note that the crystal data were taken from HALWAS and have a non-standard choice of origin in the ﬁgure, but not in the table; indulgence is requested for the confused state of the literature).

dimensions (for a body-centred cell) were given in Table IV (B93) under the heading ‘‘triclinic Z ¼ 2 clathrates (stage 2), expanded a.’’ The structure was solved (HAMBEC) ˚ , 111.12 101.72 101.84 , Z ¼ 1), in a primitive triclinic cell (11.155 12.519 16.595 A where the cell edges are similar to those of the reduced cell (Table 8.14) but the interaxial angles differ. When X ¼ (H2O)(acetone)2, the water oxygen is linked to Mg (d(Mg– ˚ ) and to the two acetone molecules by hydrogen bonds (d(O . . . O) ¼ 2.71, O) ¼ 2.054 A ˚ ) (McKee and Rodley, 1988; GEPBUY). Thus the water oxygen is three-coord2.81 A inate. The structure for X ¼ (H2O)(2-picoline)3 is analogous (Ong, McKee and Rodley, ˚ , The values are 0.33 A ˚ (HAMBEC), 0.45 A ˚ (GEP1986); < d(Mg–N) > ¼ 2.088 A ˚ (DUJKUO). Although the compositions suggest that these complexes BUY) and 0.41 A could be six-coordinate, the ligands have composite structures resulting in ﬁve coordinatecomplexes, with nonplanar macrocycles. These complexes provide good examples of the dangers involved in the use of lattice sections. The structural diagrams (for example, those in Figs. 1–3 of McKee and Rodley, 1988) show the nature of the ligands very clearly, whereas this is not at all obvious from the corresponding lattice sections (Figs. 21 and 23 of B93, although Fig. 30 is somewhat more transparent). The (TPP–Zn2þ)(2-phenylethylamine)2 complex is a ﬁve-coordinate coordination ˚ to the four equatorial nitrogens, complex with distances of 2.086(twice), 2.079, 2.063 A ˚ ˚. and 2.193 A to the axial nitrogen of the ligand; ¼ 0.331 A 2þ The three complexes (TPP–Zn )(X), where X ¼ 4-nitro--picoline-N-oxide, 9-anthraldehyde and 5,12-naphthacenequinone are ﬁve-coordinate coordination complexes but, because of disorder, have cell dimensions isostructural with those of the sixcoordinate coordination complexes and are more conveniently discussed in the next section.

486

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

8.7.2.4 The six-coordinate coordination complexes For those complexes with triclinic unit cells, the (TPP–M2þ) macrocycles are translationally equivalent and located at crystallographic centres of symmetry when Z ¼ 1, and this also holds for a single (possibly disordered) ligand in the unit cell. When Z ¼ 2 there are no symmetry requirements for (TPP–M2þ) macrocycle or ligand. There are a number of monoclinic structures where the (TPP–M2þ) macrocycles are located at crystallographic centres of symmetry but are not all translationally equivalent, and a few of lower symmetry. There are a very few orthorhombic and tetragonal complexes. Our classiﬁcation is mostly based on the many families of isomorphous crystals. The triclinic complexes with Z ¼ 1. Scheidt and Lee (1987) summarized all the information available to them in terms of the reduced cells (although the standard setting of axes with a b c was not used), making transformations where necessary. We have incorporated these, and other, cells into Table 8.15 after transformation to the standard settings. Table 8.15 has been split into three parts; Part A has monofunctional ligands and host : ligand ratio 1 : 2, and Part B bifunctional ligands with host : ligand ratio 1 : 1; some miscellaneous examples are placed in part C. Part A is further divided into two groups, the ﬁrst with stronger metal–ligand interaction, and the second with weaker. The ﬁrst six compounds in Table 8.15 (Part A, Group I) are isomorphous. Remembering that the TPP ˚3 ˚ 3, one sees that the ‘‘ligands’’ add 110 185 A molecule has a molar volume of 800 A (per ‘‘ligand’’) to the unit cell volumes (for triclinic, Z ¼ 1 structures). The available structure analyses7 show that the ‘‘ligands’’ occupy axial coordination positions and extend roughly normal to the plane of the core; the in-plane bonding is generally stronger than the out-of-plane bonding (for example, equatorial d(Mg–N) in {(TPP–Mg2þ)[piperidine]2} is ˚ whereas the axial value is 2.39 A ˚ ). These closely isomorphous structures have 2.07 A closely similar lattice sections, as given in the Byrn et al. papers (#1 Fig. 5 (B90); #2–7 Fig. 3 (B90); #8 Fig. 3 (B90)). The next three structures are isostructural rather than isomorphous. Examination of the crystal structure of {(TPP–Mg2þ)[4-picoline]2} (HAMFAC) shows that this is a six-coordinate coordination complexes. These triclinic unit cells are all Type II, i.e. in the standard setting all angles are either obtuse or 90 . After the ninth entry onwards, we encounter a group of four isomorphous crystals which are Type I, i.e. all the angles are acute in the standard setting. We have made some attempt to group together similar unit cells, but it is difﬁcult to do this in an entirely consistent manner. These examples illustrate the delicacy of the balance among the various factors determining the crystal structure; similar molecules often, but not always, crystallize in isomorphous crystals. The effect on the crystal structure of changing the metal atom can be investigated in the pairs {(TPP–M2þ)[pyridine]2} (M ¼ Fe, Mg) and {(TPP–M2þ)[THF]2} (M ¼ Fe, Zn), and the triple {(TPP–M2þ)[piperidine]2} (M ¼ Fe, Co, Mg). The differences in cell edges do not exceed 1–2% and in angles 2 . However, note the striking differences between {(TPP– Mg2þ)[picoline]2} and {(TPP–Fe2þ)[picoline]2}). Similar behavior is found among the 7

Parenthetically we note that the crystal structure of {(TPP–Cd2þ)[dioxane]2} was reported in the non– centrosymmetric space group P1 with an unsymmetrical disposition of dioxane ligands and a large thermal (or disorder) displacement of Cd normal to the mean core plane (Rodesiler, Grifﬁth, Ellis and Amma, 1980). Scheidt and Lee (1987, p. 58) have pointed out that the cell dimensions and overall structure ﬁt so well with those of the other members of the isomorphous group that re-examination seems desirable.

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

487

inclusion complexes (next section), e.g. the pair {(TPP–M2þ)[toluene]2} (M ¼ Zn, Mn). The effects of changing the ligand while maintaining the identity of the metal can be appreciably larger (see the triple {(TPP–Fe2þ)(L)2 (L ¼ pyridine, piperidine, 4-picoline)) in Table 8.15. The {(TPP–M2þ)[THF]2} (M ¼ Zn, Fe) are six-coordinate coordination complexes, ˚ and d(Fe–O) ¼ 2.351 A ˚ . {(TPP–Mg2þ)[methylbenzoate]2} with d(Zn–O) ¼ 2.380 A ˚ . {(TPP– (JIVSAI) is a six-coordinate coordination complex, with d(Zn–O) ¼ 2.390 A 2þ Zn )[o-chloroaniline]2} (JIVNIL) is a six-coordinate coordination complex, with d(Zn– ˚ and f ¼ 91.27 . These are all on the lower border of Group II (weaker Nax) ¼ 2.460 A interaction) crystals. The crystal structure of {(TPP–Zn2þ)[bianthrone]} (HAMDUU) is shown in Fig. 8.41. Both moieties are translationally equivalent and located at independent centers of symmetry (i.e. Z ¼ 1, as described at the beginning of this section). The Zn–O distance of ˚ is similar to the values given for {(TPP–Zn2þ)[1,5-dihydroxyanthraquinone]} 2.572 A ˚ ). B91 (p. 6551) describe these ˚ (2.58 A) and {(TPP–Zn2þ)[ p-diacetylbenzene]} (2.50 A materials as ‘clathrates’ and ‘‘porphyrin sponges containing ‘cross-linking’ ligands.’’ A lattice section is shown in Fig. 7 of B93, with the following caption: ‘‘Double-row clathrates. The bianthrone clathrate has been included among these structures with the 2 : 1 [guest : host] stoichiometry because the single molecule occupies channel sites in two adjacent channels. Each anthrone moiety ﬁlls the role of a guest species.’’ The CSD uses the term ‘‘TPP–Zn(II)-bianthrone clathrate’’ (our emphasis). In our view these are incorrect descriptions of the structure. The bianthrone molecule is here a bifunctional ligand, and the material is a six-coordinate coordination complex, with the ligand crosslinking between (TPP–Zn2þ) moieties. The three (TPP–Zn2þ) complexes with substituted anthraquinones have very similar cell dimensions. Lattice sections are given for 1,5-diaminoanthraquinone ((Fig. 3 (B93)) and 1,5-dihydroxyanthraquinone (Fig. 10 (B91)), the ligand being described as ‘‘crosslinking,’’ and for 1,8-dihydroxyanthraquinone (Fig. 1 (B91), This suggests that the 1,8-dihydroxyanthraquinone moiety is disordered, but this is not shown in the lattice section, which presents a ﬁve-coordinate situation; coordinates for oxygens are not given in JIVMIK so this point cannot be pursued. Presumably, the anthraquinone moieties behave as cross-linking ligands in the same way as bianthrone. This has been shown directly for 1,5-dihydroxyanthraquinone, using the structural results given in JIVMAC. The link to Zn is via the hydroxyl oxygen and not the carbonyl oxygen; here equatorial ˚ and axial d(Zn–O) ¼ 2.584 A ˚ , with < N–Zn–O ¼ 90.7 . Careful d(Zn–N) ¼ 2.041 A inspection of Fig. 10 (B91) is in accord with this description. Thus links from Zn to carbonyl oxygen appear to be weaker than those to hydroxyl or amino groups. {(TPP–Zn2þ)[nitrobenzene]2} (JIVPIN) is a six-coordinate coordination complex, with ˚ , < N–Zn–O ¼ 90.1 . {(TPP–Zn2þ)[benzenethiol]2} (JIVNAD) is a d(Zn–O) ¼ 2.655 A ˚ , < N–Zn . . . S ¼ 93.18 ; Zn six-coordinate coordination complex, with d(Zn–S) ¼ 3.08 A ˚ ; < C–S . . . Zn ¼ 101.62 . to equatorial N distances are 2.041, 2.044, 2.050, 2.056 A The three complexes HALTUJ, JIVNEH and JIVPEJ are actually ﬁve-coordinate coordination complexes which crystallize in disordered fashion in unit cells isostructural with those of the six-coordinate coordination complexes. We illustrate for JIVPEJ (Fig. 8.42). As noted in the caption to that ﬁgure, problems remain in the reﬁnement of the structure, and this also appears to be the situation with HALTUJ and JIVNEH. However, disorder is not shown in the JIVNEH and JIVPEJ lattice sections of Fig. 2 (B91).

˚ , deg., A ˚ 3) are for reduced cells, Table 8.15. Crystal data for triclinic (TPP–Mnþ) six-coordinate coordination complexes. The cell dimensions (A ˚ 3, space group P transformations having been made where necessary; these cells have Z ¼ 1, unit cell volumes (¼ formula unit volumes) 1100 A 1. Note that structure determinations were often carried out in nonreduced cells. Italicized volumes indicate that the cell dimensions were measured at low temperature (nominally 100K). References in brackets Mnþ

Ligand

a/

b/

c/

V

Part A: Triclinic, Z ¼ 1, space group P1; ratio of host to monofunctional ligand is 1 : 2. ˚) Group I: Coordination complexes with stronger metal-ligand (X) interactions (d(M–X) 2.2 A Mg2þ Fe2þ

(pyridine)2 (3) HAMFAC (pyridine)2 FUXTUN (2,4)

Zn2þ

(THF)2 DOBGOQ (5)

Mg2þ

(piperidine)2 CULXIQ (1,9)

Fe2þ

(4-picoline)2 JIVMEG; 128K (2)

Fe2þ

(piperidine)2 TPPFEP (1, 7)

Zn2þ

(3-methoxy-pyrazine)2; HAMJUA

Fe2þ

Mg2þ

(dimethylphenyl-phosphine)2 GIFJAG (2, 11); (tri-n-butyl-phosphine)2 KACGJE (2, 11); (4-picoline)2 CULXEM (10);

Fe2þ

(THF)2 PHTPFE (6)

Fe2þ

9.619 102.12 9.423 101.70 9.572 102.71 9.944 101.78 9.511 100.28

11.000 103.92 10.560 104.96 11.115 103.78 11.463 104.59 11.128 104.77

11.891 113.95 11.998 111.95 11.720 115.01 11.914 115.60 12.016 113.52

1046.8

9.797 101.02 10.737 93.37 10.305 105.83 12.039 98.13 10.146 65.63 9.688 64.95

11.113 105.67 10.962 108.85 11.149 111.61 12.499 116.39 11.210 76.32 11.354 76.08

12.071 113.70 11.041 111.52 12.341 100.75 12.528 109.79 11.643 67.42 11.804 65.16

1089.6

1008.4 1022.0 1106.4 1069.8

˚, d(Fe–N) ¼ 2.026 A but designated ‘‘clathrate’’ by CSD

1121 1201

˚ d(Fe–P) ¼ 2.284 A

1492

˚ d(Fe–P) ¼ 2.345 A

1109 1055.0

Cd2þ

(dioxane)2 PHPNCD (1,7)

Co2þ

(piperidine)2 PTPORC (9);

9.845 65.50 9.934 64.98

11.327 77.41 11.494 75.01

11.614 65.84 11.830 64.45

1073.5 1100

˚ ). Group II: Coordination complexes with weaker metal–ligand (X) interactions (d(M–X) 2.5 A These complexes have been called ‘clathrates’ by the CSD. Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Mg2þ Zn2þ Cd2þ Zn2þ Zn2þ

(2-acetyl-pyridine)2 HALXEX (3) (o-chloro-phenol)2 (2) (o-chloro-aniline)2 JIVNIL 123K (2) (o-methyl-aniline)2 HAMMEN (2); (aniline)2 (3) HAMCIH 123K (2,4-dichloro-phenol)2 JIVNOR 15K (3) (2,4,5-trichloro-phenol)2 HALWEW 15K (3) (methyl benzoate)2 JIVSAI (2) (methyl benzoate)2 SEMRIL (1) (methyl benzoate)2 JIVSOW (2) (acetophenone)2 JIVRIP (2) (o-hydroxy-acetophenone)2 JIVPOT (2)

10.545 110.85 10.716 113.40 10.781 113.74 10.731 113.94 10.822 109.44 10.753 106.83 8.883 92.74 11.052 106.37 10.994 106.93 10.998 107.72 10.601 111.19 10.228 111.54

10.670 107.69 10.826 106.39 10.980 107.31 11.017 106.53 11.125 112.46 10.912 110.25 11.874 104.53 11.236 109.44 11.125 109.25 11.025 109.56 10.643 107.75 10.595 106.71

12.238 101.51 11.480 102.21 11.560 102.47 11.783 101.94 11.360 103.37 11.302 103.48 12.040 111.12 11.410 105.57 11.605 104.89 11.874 104.27 12.325 100.93 12.333 99.59

1153 1090

˚ d(Zn–O) ¼ 2.493 A

1104

˚ d(Zn–O) ¼ 2.460 A

1135

˚ d(Zn–N) ¼ 2.522 A

1087

˚ d(Zn–N) ¼ 2.470 A

1106

˚ d(Zn–O) ¼ 2.479 A

1133

˚ d(Zn–O) ¼ 2.496 A

1175

˚ d(Mg–O) ¼ 2.390 A

1180

˚ d(Zn–O) ¼ 2.619 A

1191

˚ d(Cd–O) ¼ 2.795 A

1162

˚ d(Zn–O) ¼ 2.516 A CSD gives ‘‘clathrate’’ ˚ d(Zn–O) ¼ 2.512 A (to carbonyl). CSD gives ‘‘clathrate’’

1134

Table 8.15. (Continued) Mnþ

Ligand

a/

b/

c/

V

Part B: ratio of host to bifunctional ligand is 1:1 ˚ ), and have been called ‘‘clathrates’’ by the CSD. These coordination complexes have weaker metal–ligand (X) interactions (d(M–X) 2.5 A Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ

Zn2þ

Zn2þ Zn2þ

1,5-diamino-anthraquinone HAMKUB 123K (3) 4-diacetyl-benzene (2) bianthrone 128K HAMDUU x(3) # (tetramethyl pyromellitate) HALVAR (3) (4-nitro--picoline-N-oxide) at 123K HALTUJ (1)

1,8-dihydroxyanthraquinone JIVMIK (2) 9-anthraldehyde JIVNEH (2) 5,12-Naphthacenequinone JIVPEJ (2)

10.760 105.78 8.745 105.27 12.738 98.89 10.164 62.12 8.136 105.60

10.853 107.49 10.085 102.12 12.965 103.31 11.319 73.66 9.819 104.00

11.364 111.78 12.196 105.99 8.159 98.76 11.876 79.37 12.804 94.60

1060

10.578 106.72

10.794 105.61

11.559 109.49

1088

10.924 102.97 10.668 105.08

11.591 103.72 11.691 106.21

9.696 105.06 10.285 103.46

1097

˚. d(Zn–N(H)) ¼ 2.614 A CSD gives ‘‘clathrate’’

1044 1270 1157 944.4

1123

d(Zn–O) ¼ 2.572 ˚ ; see text. A d(Zn–O) ¼ 2.540 ˚ . CSD gives ‘‘clathrate’’ A Disordered but CSD gives d(Zn–O) ¼ 2.527 ˚ , and classiﬁes as A ‘‘5-coordinate coordination complex.’’ Guest disordered, no conclusion possible. Guest disordered, no conclusion possible. Guest disordered; CSD gives ‘‘clathrate’’

Zn2þ

1,5-dihydroxyanthraquinone* JIVMAC (2)

Part C.

Miscellaneous

Zn2þ

(methyl 4-nitrobenzoate) (3)

Fe2þ

(NO)(4-methyl piperidine) NIPORF (3)

10.590 107.37

10.857 104.79

11.294 111.29

1054

11.468 100.54 11.550 87.83

20.357 105.55 17.236 74.38

2460

T r i c l i n i c P 1 Z¼2 11.204 96.85 10.668 87.07

2042

˚, d(Fe–N(O)) ¼ 1.741 A ˚ d(Fe–N(H)) ¼ 2.463 A

For illustration we give both Niggli and Delaunay reduced cells for {(TPP–Co2þ)[piperidine]2} Co2þ

(piperidine)2 Niggli (9);

Co2þ

(piperidine)2 Delaunay (8);

9.934 11.494 9.934 11.503

11.830 67.73 11.830 101.49

78.01 64.46 101.99 115.64

1126 1126

* anthraruﬁn x HAMDUU is listed as a ‘clathrate’ by the CSD, but is clearly a six-coordinate coordination complex. No CSD entry found for {(TPP– Zn2þ) (3-methyl-2-cyclohexenone)2} (Fig. 6 of B93 suggests two orientations for 3-methyl-2-cyclohexenone, as noted in caption). References: (1) B90; (2) B91; (3) B93; (4) Li, Coppens and Landrum, 1988; (5) Schauer, Anderson, Eaton and Eaton, 1985; (6) Reed, Mashiko, Scheidt, Spartalian and Lang, 1980; (6) Rodesiler, Grifﬁth, Ellis and Amma, 1980); (7) Radonovich, Bloom and Hoard, 1972; (8) Scheidt, 1974a; (9) McKee, Ong and Rodley, 1984; (10) Sodano, Simmoneaux and Toupet, 1988; (11) Belani, James, Dolphin and Rettig, 1988; (12) Scheidt, Brinegar et al., 1977.

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

492

3A (TPP-Zn2+)

bianthrone

d(Zn–O) = 2.572 Å x

B

z y

d(Zn–N) = 2.037, 2.051 Å

Fig. 8.41. The crystal structure of {(TPP–Zn2þ)(bianthrone)} at 128K, viewed down [001]. There are chains of (TPP–Zn2þ) and bianthrone moieties along [010] linked by bonds between Zn and carbonyl oxygen. Both moieties are at crystallographic centers of symmetry. There are resemblances to the arrangement in {(TPP–Zn2þ)(dibenzosuberone)3} (Fig. 8.43) but also appreciable differences. (Data from HAMDUU.) Table 8.16. Crystal data for monoclinic (TPP–Mnþ) six-coordinate coordination complexes. The ˚ , deg., A ˚ 3) are for reduced cells, transformations having been made where cell dimensions (A ˚ 3, space group P21/n unless stated necessary; these cells have Z ¼ 2, unit cell volumes 2000 A otherwise. Italicized volumes indicate that the cell dimensions were measured at low temperature (nominally 100K). The original cell dimensions come from Table V of B93, except for (1) McKee and Rodley, 1988; (2) McKee, Ong and Rodley, 1984 Mnþ

Ligand

a

b

c

Cell volume

Cu2þ Zn2þ

(picoline)2 HALWUM; 145K (2-methoxy-3-isobutyl-pyrazine)2 P21/c HAMBON; ˚. d(Zn–N) ¼ 2.925 A (acetophenone)2; HALZOJ (phenethylpropionate)2 (methanol)2 (1); GEBPIM (methanol)2(acetone (1) GEPBOS (1-methylimidazole)2 (2); ˚ CULXAI, d(Mg–N) ¼ 2.227 A

10.125 14.774

15.372 10.968

13.547 15.791

99.91 92.99

2077 2555

10.708 8.738 13.302 10.01 20.764

20.653 26.960 12.868 17.75 9.659

10.819 11.066 11.039 12.74 ˚3 4164 A

102.27 2338 99.60 2567 113.29 1736 110.7 2118 Tetragonal P42/n, Z ¼ 4

Mg2þ Zn2þ Mg2þ Mg2þ Mg2þ

The two complexes with phosphine ligands are pseudo-octahedral six-coordinate coordination complexes of the usual type. Only some of the complexes crystallizing in monoclinic space groups and listed in Table V of B93 are six-coordinate coordination complexes. These are given in Table 8.16, together with other relevant examples. Other entries in Table V, such as those for transanethole and 4-thiocyanatonitrobenzene are actually four-coordinate inclusion complexes (Table 8.18).

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

493

3C

1.343 Å

1.225 Å

2.656 Å

z x

A 0 y B

Fig. 8.42. Projection of JIVPEJ {(TPP–Zn2þ)[5,12-naphthacenequinone]} down [100]. There are chains of (TPP–Zn2þ) and [5,12-naphthacenequinone] moieties along [001] linked by Zn . . . O1 ˚ ). The [5,12-naphthacenequinone] moiety takes up two orientations as shown interactions (2.656 A by the ostensible presence of four carbonyl oxygens, instead of two. The oxygens of the second ˚ away from the Zn, too far for meaningful interaction. Furthermore, one C¼O orientation are 4.512 A ˚ , but the other is long at 1.343 A. Thus further study distance has the acceptable value of 1.225 A seems desirable.

The methanol and 1-methylimidazole complexes are regular six-coordinate coordination complexes; the ligand in the methanol-acetone complex is this hydrogen-bonded pair, with methanol linked to Mg. The Mg–O distances are 2.220 (methanol complex) and ˚ (methanol-acetone complex). 2.188 A 8.7.3 Crystallography of (5,10,15,20)-tetraphenylporphyrin inclusion complexes 8.7.3.1

Crystallography of four-coordinate (5,10,15,20)-tetraphenylporphyrin inclusion complexes There are three different groups of {(TPP-M2þ)[guest]2} structures which come into this overall category–(1) triclinic, Z ¼ 1 (Table 8.17); (2) triclinic, Z ¼ 2 (Table 8.18);

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

494

Mn tetraphenyl porphyrin

Mn hidden C

B

0 toluene

z

A

y x

Fig. 8.43. The packing in {TPP–Mn2þ}[toluene]2 viewed down [101]. The included toluene molecules have been increased in size and lightened in colour. (Data from Kirner, Reed and Scheidt, 1977.)

(3) monoclinic, Z ¼ 2 (Table 8.19). Strouse and coworkers use the term ‘clathrates’, while we prefer to restrict this word to its original usage. All the complexes in Table 8.17 have a 1 : 2 host guest ratio, apart from {(TPP–2Hþ)[ p-xylene]} (SEMNUT). The crystal structure of triclinic {(TPP–Mn2þ)[toluene]2} has been determined at 98K (Fig. 8.43) and has two toluene molecules, related by the center of symmetry at the centre of the ˚ from the mean plane of the macrocycle. The structural macrocycle, at distances of 3–3.4 A unit is the centrosymmetric combination (toluene)(TPP–Mn2þ)(toluene), where the toluene plane is nearly parallel to the plane of the TPP core. In Table 8.17 the entries #2–8 form an isomorphous group, which is in accord with the corresponding lattice sections given in Figs. 5, 6 and 7 (B90); a diagram has not been found for {(TPP–Zn2þ)[ p-xylene]2}. Perhaps surprisingly, the unit cells of {(TPP– M2þ)[toluene]2} (M ¼ Mn, Zn) and {(TPP–Zn2þ)[2-ﬂuorotoluene]2} have remarkably similar dimensions. We note in the table four entries for different M, but all with m-xylene as guest; this follows Table 2 of B91, except that we compare reduced cells whereas they compared body-centred cells. We have chosen the anthracene complex, which is somewhat more closely packed than the others of this group, to illustrate the packing arrangement in these complexes (Fig. 8.44). The (TPP–Zn2þ) moiety is located at Wyckoff positions (a) (0,0,0) and the anthracene molecule at (d) 1/2,0,0. The plane of the anthracene molecule is not parallel to the plane of the porphyrin ring, and a charge transfer interaction would require substantiation by spectroscopic techniques. It seems more reasonable to describe this as an inclusion complex where anthracene is held by pairs of phenyls from translationallyrelated (TPP–Zn2þ) moieties.

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

495

˚ , deg., A ˚ 3) for triclinic (TPP–M2þ) four-coordinate inclusion complexes, Table 8.17. Crystal data (A ˚ 3, space group P with Z ¼ 1, unit cell volumes (¼ formula unit volumes) 1100 A 1. The cell dimensions are for reduced cells. References in brackets Mnþ

Guest

Type II 2Hþ Mn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2 þ* Cd2þ Zn2þ Zn2 þ* Zn2þ* Zn2 þ* Cu2þ 2Hþ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ

triclinic unit cells [p-xylene] SEMNUT (1) (toluene)2 TPPMNT10 (1) (toluene)2 ZNPORT (1) (2-ﬂuorotoluene)2 HAMLOW (3) (indene)2 HAMJEK(3) (indole)2 HAMJIO (3) (o-xylene)2 SEMPEF (1) (m-xylene)2 JIVRUB (2) (m-xylene)2 SEMNON (1) (p-xylene)2128K JIVPUZ; (2) (ethylbenzene)2 SEMMAY (1) (styrene)2 HAMKAH (1) (m-xylene)2 JIVPAF 128K (2) (m-xylene)2 SEMNIH (1) phenanthrene SEMMUS (1) anthracene HALYAU (3) coronene HAMGAD (3) benzacephenanthrylene HALYUO (3) 1,2-benzanthracene HALYIC (3) 2,3-benzﬂuorene HALZEZ (3) (bromobenzene)2 JIVNUX 193K (2) (phenyl-acetylene)2 SEMNAZ (1) Zn2þ Zn2þ (1,2,4-trimethyl-benzene)2 SEMMEC (1) Zn2þ (anisole)2 HALTIX (3) Zn2 þ* (3-methyl-anisole)2 SEMROR (1) Zn2 þ* (m-ethylvinyl-benzene)2 (1) Zn2þ 2,5-dimethyl-2,4-hexadiene (1) Zn2þ (3-hydroxy-acetophenone)2 JIVREL (2) Zn2þ (phenylisocyanate)2 HAMFIK 145K (3) (nitrobenzene)2 JIVPIN Zn2þ

Type I triclinic unit cells (4-vinyl-anisole)2(3) Zn2þ Zn2þ (phenazine)2 HAMMOX (3) Zn2þ (acridine)2 JIVVAL 128K (2) (1,5-cyclo-octadiene)2 SEMPIJ (1) Zn2þ Zn2þ 9,10-bis(phenethynylanthracene) x HAMDEE 128K(3) Zn2þ ((bicycloheptene)-COOH)4 JIVVEP (2)

a

b

c

V

7.879 10.487 10.502 10.480 10.541 10.766 10.550 10.926 10.992 10.076 10.932 10.408 9.924 10.172 9.529 9.458 10.491 10.372 10.593 10.590 10.758

10.418 11.320 11.349 11.390 11.162 11.040 10.980 10.995 11.174 11.297 11.487 11.613 10.570 10.749 10.715 11.990 10.570 10.901 11.146 11.182 11.047

12.956 11.465 11.404 11.462 11.912 11.902 12.057 12.067 11.796 11.885 11.488 11.648 11.984 12.020 11.790 10.655 12.497 11.971 11.651 11.530 11.501

103.73 107.80 107.65 107.85 106.81 106.71 105.83 105.52 105.65 108.30 106.91 106.69 104.46 104.28 106.13 103.52 110.77 108.21 107.37 106.54 106.90

102.19 110.63 110.48 109.95 112.62 114.38 114.34 114.55 113.42 109.92 105.88 110.18 109.54 110.21 103.49 105.19 104.59 106.60 105.51 104.60 106.75

97.66 103.34 103.87 103.50 102.23 102.70 101.12 103.56 105.19 101.43 110.58 103.45 97.45 98.73 104.38 106.30 101.61 107.25 110.88 111.85 110.20

991 1122 1119 1134 1153 1138 1148 1168 1164 1134 1173 1174 1115 1154 1060 1056 1187 1110 1114 1111 1107

10.359 10.837

10.768 11.162

11.611 12.359

106.61 99.73

104.29 108.95

105.40 116.51

1121 1175

10.726 11.18 11.340 10.851 11.416

11.350 11.48 11.506 11.370 11.644

11.360 11.68 11.590 11.995 10.465

107.85 107.29 106.33 108.28 109.62

105.31 111.75 107.24 99.10 104.37

109.63 107.38 111.19 114.19 107.49

1131 1180 1212 1210 1152

10.439

10.686

11.584

107.79

103.52

107.39

1097

10.792

11.110

11.329

107.72

104.44

109.12

1127

10.630 11.145 11.106 11.147 9.855

18.941 11.355 11.284 11.518 10.291

11.542 11.616 11.664 11.632 13.022

75.39 66.19 67.41 60.44 79.98

74.30 76.63 71.74 82.45 77.00

71.11 72.11 70.80 62.75 81.33

1203 1244 1245 1146 1259

11.674

11.676

12.751

86.00

63.69

77.14

1518

Notes: x Table II of B93; ‘‘layered’’ clathrate, see Fig. 27. References: DR92 – Dillen and Roos (1992); PB94a – Pang and Brisse (1994a); PB94b – Pang and Brisse (1994b); PHW94 – Pang, Hynes and Whitehead (1994); RD92 Roos and Dillen (1992);RR91a – Rooyen and Roos (1991a); RR91b – Rooyen and Roos (1991b); SERP02 Sidhu, Enright et al., 2002; SEUR05 – Sidhu, Enright et al., 2005.

496

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

C Zn 0B Zn anthracene

Zn A x

Zn y z

Fig. 8.44. The packing arrangement in the triclinic (Z ¼ 1) {(TPP–Zn2þ) [anthracene] fourcoordinate inclusion complex (HALYAU). A ‘‘lattice section’’ version of this diagram is given in Fig. 3 of B93. (Data from HALYAU.)

When a centrosymmetric guest such as anthracene is replaced as guest by a noncentrosymmetric molecule such as phenanthrene, and the latter occupies the same site, then it is necessarily disordered, as B93 pointed out in the caption to their Fig. 4. A related example is provided by (TPP–Zn2þ)(9,10-bis(phenylethynyl)-anthracene), where the reduced cell has appreciably different dimensions from the other entries in Table 8.17; the lattice section shown in Fig. 27 (B93) has been described as that of a ‘‘layered’’ clathrate. Comparison of Figs. 8.44 and 8.45 shows that these two inclusion complexes are isostructural, the stacked arrangement of (TPP–Zn2þ) and anthracene moieties (vertical direction in the two diagrams) being the same. The arrangement in a horizontal direction is different because of the difference in size between the two guest molecules. Triclinic HALTIX (guest anisole) has an analogous structure; here the two anisole molecules are related by the center of symmetry; this also holds for HAMMOX (guest: phenazine; Fig. 7 of B93), and JIVVAL (guest: acridine, Fig. 7 of B91). Both are described as. ‘‘double-row clathrates’’ When the guest is 3-methylanisole, the methyl and methoxy groups are disordered (B90, p. 1866; Fig. 6) but the composition remains 1 : 2. The last entry in Table 8.17 has an unusual (but not unprecedented) composition. B91 (p. 6550) have already noted that pairs of hydrogen-bonded dimers of bicycloheptenecarboxylic acid are formed. These dimers constitute the guest species in a four-coordinate inclusion complex (Fig. 8.46). However, there is a complication, because there is also a ˚ ). Thus weak interaction between Zn and one of the carboxyl oxygens (d(Zn–O) ¼ 2.89 A

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

497

C Zn 9,10(bis(phenylethenyl)anthracene 1.198 Å 0

A

z x

y

3B

Fig. 8.45. The packing arrangement in the triclinic (Z ¼ 1) {(TPP–Zn2þ) [9,10-bis (phenylethynyl)anthracene] four-coordinate inclusion complex (HAMDEE). The location of the triple bond is indicated by its bond length. A ‘‘lattice section’’ version of this diagram is given in Fig. 27 of B93. (Data from HAMDEE.)

{(TPP–Zn2þ)[bicycloheptenecarboxylic acid]4} comes somewhere between a fourcoordinate inclusion complex and a six-coordinate coordination complex. Carboxylic acid dimers are also found when the guests are o- and m-toluic acid, but without the additional interaction. Another example is {(TPP–Zn2þ)[3-hydroxyacetophenone]2}, where the hydrogen-bonded 3-hydroxyacetophenone dimer is shown in Fig. 8.47. Similarly in {(TPP–Zn2þ)[o-isopropylphenol]2}, where the guest molecules are hydrogen bonded as a linear pair; these situations were shown clearly in Figs. 5 and 4 of B91, but not mentioned in the text. We also note that the cell dimensions for JIVREL and the three isomorphous {(TPP–M2þ)[methyl benzoate]2} complexes (M ¼ Mg, Zn Cd) (Table 8.15) are very similar. Nevertheless, the ﬁrst of these is an inclusion complex and the other three are six-coordinate coordination comples. Structure cannot necessarily be inferred from composition or similarity of cell dimensions. The second to the seventh entries of Table 8.18 are isomorphous to a fair approximation; this is conﬁrmed by comparison of crystal structures, and is in accord with the similar lattice sections shown for these complexes in Fig. 29 of B93. The last four entries also form an isostructural group. These two groups (and some other entries) are treated ˚ together by B93, with the title ‘‘ ‘Herring-bone’ monoclinic Z ¼ 2 clathrate with a 19 A chain’’), without taking into account that the b axes differ for these two groups. This is also not immediately obvious from the lattice sections. (TPP–Zn2þ)(diphenylacetylene) (HAMHUY; Fig. 8.48) is a monoclinic analog of the (TPP–Zn2þ) (anthracene) structure, with the (TPP–Zn2þ) centred at 0,0,0 and the guest at 1/2,0,0. The two guest molecules in the 1 : 2 structures are related by centers of symmetry, as is shown in the layered structure of HAMCAZ; the oxygens of the 4-thiocyanato˚ from the Zn, and the sulfurs are even further. In the nitrobenzene guests are more than 4 A

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

498

bicycloheptene carboxylic acid dimer

N bicycloheptene Zn

O d (Zn–O) 2.89 Å

z x y

Fig. 8.46. The {(TPP–Zn2þ) macrocycle sandwiched between two [bicycloheptenecarboxylic acid] dimers. The equality of the O . . . O distances shows that the hydrogens of the dimers are disordered. The line linking Zn and oxygen shows the weak secondary interaction; hN–Zn–O ¼ 89.7 . The macrocycle is located at a center of symmetry, while the carboxylic acid dimer does not have crystallographically imposed symmetry. Data from JIVVEF. ˚ , deg., A ˚ 3) for monoclinic (TPP–M2þ) four-coordinate inclusion Table 8.18. Crystal data (A ˚ 3, space group P21/c. The cell dimensions are for complexes, with Z ¼ 2, unit cell volumes 2000 A reduced cells. Data from Table V of B93 Mnþ 2þ

Zn Zn2þ Zn2þ Cr2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ Zn2þ

Guest

a

b

c

V

1,4-diisopropylbenzene HAMGIL (benzene)2 SEMLUR (toluene)2 ZNPORT01 (toluene)2 CRPORT; Scheidt and Reed, 1978 (1-methyl-1,4-cyclohexa-diene)2 HAMJOU diphenylacetylene; 128K; HAMHUY (4-ﬂuorobenzaldehyde)2 HALYEY; 145K (4) (o-toluic acid)2 HALVEV; 145K (4) (m-toluic acid)2 HAMBUS (trans-anethole)2 P21/a HALWIA; 145K (4-thiocyanatonitrobenzene)2 P21/a HAMCAZ (mesitylene)2 HAMCED 128K

12.466 10.867 10.430 10.518 10.389 10.536 10.215 10.981 10.036 10.171 11.095 10.010

10.134 15.819 15.229 15.778 16.239 15.804 15.689 16.392 21.253 21.261 19.375 20.282

17.633 12.641 13.246 13.425 13.567 12.636 13.856 13.451 10.899 11.855 11.986 11.966

98.66 102.65 98.88 101.02 101.67 102.52 102.04 107.01 98.10 106.44 109.20 103.52

2202 2120 2073 2188 2241 2054 2172 2316 2302 2459 2433 2362

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

499

CH3

C O 1.218 Å 2.843 Å

OH 1.366 Å

OH O x z y

Fig. 8.47. The hydrogen-bonded dimer of 3-hydroxyacetophenone as found in the four-coordinate inclusion complex {(TPP–Zn2þ)[3-hydroxyacetophenone]2} (JIVREL).

(TPP–Zn2+) A

1.216 Å

diphenylacetylene 0

B

x z

y

Fig. 8.48. The (monoclinic) structure of HAMHUY viewed down [001]. The herringbone arrangement of the moieties is clearly shown.

HALYEY structure the 4-ﬂuorobenzaldehyde molecules are disordered and detailed interpretation is difﬁcult; however, there are no short oxygen–metal distances. HALWIA (Fig. 8.49; see Table V and Fig. 32 of B93, where it is called a ‘‘Z ¼ 2 clathrate with sheet structure’’) also illustrates the monoclinic structure, and shows that there is no meaningful

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

500

3A

0

B x

z y

Fig. 8.49. The (monoclinic) structure of HALWIA viewed down [001]. The herringbone arrangement of the moieties is clearly shown. This diagram is very different from the lattice section given in Fig. 32 of B93.

˚. interaction between ether oxygen and Zn, the distance between these atoms being 4.809 A These are all inclusion complexes. 8.7.3.2

Crystallography of ﬁve-coordinate (5,10,15,20)-tetraphenylporphyrin inclusion complexes

In this overall category, we distinguish between two chemically different groups (Table 8.19). In the ﬁrst, the second component (i.e. not TPP–M2þ) functions both as ligand and guest. In the second there is a solvent molecule (i.e. not a ligand) which is the guest. Both types are formally inclusion complexes; it is rare for a moiety to ﬁll two different structural roles in a particular inclusion complex but a number of examples appear at various places in this book. {(TPP–Cd2þ)[picoline]3} is an example where it is not possible to derive structure from composition or cell dimensions. A lattice section is shown in Fig. 14 of B93 (caption : ‘‘Normal’’ Z ¼ 2 stage 1 clathrates), from which it appears that there are two crystallographically-different kinds of picoline molecule in the unit cell, but their structural role can only be inferred from an examination of the crystal structure obtained from the CSD (Fig. 8.50). This shows that HALXIB is a ﬁve-coordinate {(TPP–Cd2þ) (4-picoline)} coordination complex with two additional independent 4-picoline guests at general positions; the macrocycle has a slightly convex shape, bowed towards the ligand nitrogen. HALTOD is a ﬁve-coordinate {(TPP–Zn2þ)(pyrazine)} coordination complex with an additional guest pyrazine molecule (at a center of symmetry). The only noncentrosymmetric crystals reported among the TPP ‘‘sponges’’ are those with (R) or (S )-2-amino,2-phenyl ethane as ligand. The Zn2þ (HALWOG), Mg2þ (HAMHOS) and

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

501

˚ , deg., A ˚ 3) for (TPP–M2þ) five-coordinate inclusion complexes, with Table 8.19. Crystal data (A one molecule acting as ligand and a second as guest Mnþ

Ligand/Guest

a

b

c

(i) Five-coordinate coordination complexes with included guest which has identity as that of the ligand Triclinic (reduced cell), Z ¼ 2, space group P1 Zn2þ (pyrazine)1.5 HALTOD 11.23 11.51 16.48 (4-picoline)3 HALXIB 12.275 12.594 17.975 Cd2þ Zn2þ (4-nitromethyl benzoate)2 11.302 11.468 20.358 HAMKOV

V

72.61 114.26 105.55

2027 2503 2459

the same chemical

89.0 95.30 96.86

85.96 94.34 100.54

˚ ), while nitro O is 3.25 A ˚ away There is a close approach to benzoate O (d(Zn–O) ¼ 2.574 A Monoclinic, space group P21; Z ¼ 2, Zn2þ ((S)-2-amino,2-phenyl ethane)2 HALWOG ((R)-2-amino,2-phenyl ethane)2 Co2þ Mg2þ ((R)-2-amino,2-phenyl ethane)2 HAMHOS

10.823

20.606

11.083

90

103.50

90

2403

10.761 10.743

20.506 20.583

11.083 11.135

90 90

103.61 103.67

90 90

2377 2392

(ii) Five-coordinate coordination complexes with included guest which has a different chemical identity from that of the ligand (piperidine)(o-xylene) 13.504 14.753 11.863 102.94 94.76 91.04 Cd2þ DOFXOL Co2þ (1,2-dimethyl-benzimidazole) 13.610 15.014 12.267 92.87 91.33 104.77 (benzene)2 DMIPCO 1-methyl-imidazolebenzene Co2þ 10.633 18.827 21.750 90 100.37 90 Scheidt, 1974b P21/c; IMTPCO

2294 2419 4283

DOFXOL: Rodesiler et al., 1985; DMIPCO: Dwyer et al., 1974. 2-amino, 2-phenyl ethane is called phenethylamine in B93. References to the monoclinic crystals from B93 (Table V) and triclinic crystals from Tables III and IV.

Co2þ complexes with (R)- (or (S))- 2-amino,2-phenyl ethane as ligand/guest are isomorphous and are described as ‘‘Z ¼ 2 clathrates with sheet structures’’ in Table V(b) of B93); lattice sections are given in their Fig. 32. Structure determinations show that the three isomorphous chiral (TPP–M2þ)( 2-amino,2-phenyl ethane)2 complexes (exempliﬁed by HALWOG) are ﬁve-coordinate coordination complexes, with equatorial ˚ and axial d(Zn–N) ¼ 2.256 A ˚ . However, the d(Zn–N) ¼ 2.092, 2.065, 2.049 and 2.061 A second 2-amino,2-phenyl ethane molecule is also in an axial position with ˚ . The Zn atom is displaced from the plane of the four equatorial d(Zn–N) ¼ 2.858 A ˚ towards the closer amino nitrogen. The same situation is found in nitrogens by 0.177 A ˚ ; axial d(Zn–O) ¼ 2.574 HAMCOV (equatorial d(Zn–N) ¼ 2.030, 2.040, 2.055, 2.058 A ˚ ; the second (guest) 4-nitromethyl benzoate oxygen is also in an axial position with A ˚ ; Zn atom is displaced from the plane of the four equatorial nitrogens d(Zn–N) ¼ 3.251 A ˚ somewhat similar situation is by 0.124 A towards the closer axial oxygen, f ¼ 97.36 ). A found in {(TPP–Zn2þ) (dibenzosuberone)3} (Fig. 8.49), where the difference between the ˚ , and we there classify the complex as six coordinate. Here two Zn–O distances is 0.2 A ˚ leads us to prefer a description as a ﬁve-coordinate inclusion the difference of 0.6 A complex; perhaps an ‘in-between’ description would be better, as we have suggested for

502

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

B

4-picoline guest B

N7

N5 Cd

4-picoline guest A N6

Five-coordinate {(TPP–Cd2+)(4-picoline)} y z x

A

Fig. 8.50. The {(TPP–Cd2þ) (4-picoline)3} structure (HALXIB) viewed down [001]; many atoms have been removed for clarity. The (TPP–Cd2þ) moiety is seen edge-on, showing that the Cd is ˚ , and that the4-picoline ligand is in an axial displaced from the plane of the macrocycle by 0.009 A position. The other two 4-picolines are crystallographically independent and occupy guest sites between the other (TPP–Cd2þ) moieties (which are not shown).

{(TPP–Zn2þ) [bicycloheptenecarboxylic acid]4}. B93 collated the bis(4-nitromethylbenzoate) and tris(dibenzosuberone) complexes together in their Table III(e) and Fig. 18 under the heading ‘‘Stage 1 Z ¼ 2 clathrates with a doubling of the cell in the chain direction.’’ The (TPP–Zn2þ)(methyl 4-nitrobenzoate)2 complex is a ﬁve-coordinate coordination ˚ to the four equatorial nitrogens, complex with distances of 2.030, 2.040, 2.055, 2.058 A ˚ to the carbonyl oxygen of the ligand; ¼ 0.124 A ˚ and f ¼ 97.36 . and 2.574 A DOFXOL and DMIPCO are both ﬁve–coordinate coordination complexes with solvent species ﬁlling cavities between the host macrocycles. 8.7.3.3

Crystallography of six-coordinate (5,10,15,20)-tetraphenylporphyrin inclusion complexes

In this overall category, we again distinguish between two chemically different groups. The ﬁrst has two coordinated ligands, and there is a third moiety of the same chemical type which is a noncoordinated guest (Table 8.20(i)). The second has a solvent molecule (i.e. not a ligand) which is the guest (Table 8.20(ii)). We illustrate the structural arrangement in the ﬁrst of these groups via {(TPP–Zn2þ) (dibenzosuberone)3} (Fig. 8.51). We earlier described this complex as an ‘‘in-between’’ ﬁve-coordinate inclusion complex, but one can consider the two similarly-located dibenzosuberone molecules to be both liganded to the metal, despite the difference of ˚ in the Zn . . . O distances. The Zn atom is displaced by 0.069 A ˚ from the plane of 0.2 A the four equatorial nitrogens towards the closer dibenzosuberone oxygen. Thus we

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

503

˚ , deg., A ˚ 3) for triclinic (TPP–M2þ) six-coordinate inclusion complexes; Table 8.20. Crystal data (A Z ¼ 2, space group P1. The cell dimensions are for reduced cells Mnþ

Ligand/Guest

a

b

c

(i) Six-coordinate coordination complexes with included guest which has the same chemical identity as the ligand Zn2þ (dibenzosuberone)3 15.510 11.863 19.858 106.89 93.99 106.23 HALXAT (2) 9.473 10.327 13.546 80.26 77.79 77.78 Fe2þ (pyridine)4 (1) DAJJAZ 11.010 11.623 12.095 77.30 71.15 85.47 Fe2þ (isoquinoline)4 JIVTOX 128K (1) (ii) Six-coordinate coordination complexes with included guest which has a different chemical identity from that of the ligand Fe2þ (piperidine)2toluene (1) 10.128 11.743 11.772 113.57 92.20 105.20

V

3311 1255 1429

1222

References: (1) B91; (2) B93.

C

0

B

dibenzosuberone ligand

2.736 2.544

dibenzosuberone guest

y

z x

3A

Fig. 8.51. Crystal structure of {(TPP–Zn2þ) (dibenzosuberone)3} (HALXAT), projected down [010]. The two Zn . . . O distances are shown; the dibenzosuberone ligand has light shading and the dibenzosuberone guest dark shading. The guest is held between phenyls of adjacent TPP moieties.

504

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS 3C

isoquinoline guest molecules 0 A

d (Fe–N) in-plane1.987, 2.005 Å out-of-plane 2.011 Å
isoquinoline ligand

z

x y

6-coordinate (TPP–Fe2+)(isoquinoline)2 coordination complex 3B

Fig. 8.52. Crystal structure of (TPP–Fe2þ)(isoquinoline)4 at 128K, viewed down [100], showing that this material is an inclusion complex, with the six-coordinate (TPP–Fe2þ)(isoquinoline)2 coordination complex acting as host (isoquinoline as ligand lightly shaded, and isoquinoline as guest with dark shading). A lattice section is shown in Fig. 2 of B91.

describe the complex as a six-coordinated coordination complex with the remaining dibenzosuberone molecule as guest. B93 describe this material in the quite remarkable ˚ 14.35 31.99 38.68 , V ¼ 3312 A ˚ 3, Z ¼ 2, I 1. Their unit cell 29.199 35.088 25.923 A Fig. 18 (captioned ‘‘Stage 1, Z ¼ 3 clathrate with a doubling of the unit cell in the chain direction’’) clearly shows two different kinds of dibenzosuberone molecule. They also draw attention to a resemblance between the {(TPP–Zn2þ) (dibenzosuberone)3} and {(TPP–Zn2þ) (eugenol)2} (Table II; lattice section in Fig. 11). The different compositions make this unlikely. Unfortunately, {(TPP–Zn2þ) (eugenol)2} is not listed in the CSD. An analogous arrangement is shown in {(TPP–Fe2þ)[isoquinoline]4} (Fig. 8.52) and {(TPP–Fe2þ)[pyridine]4}, which are isostructural. We describe the ﬁrst. The Fe–N bonding is essentially equally strong in-plane and normal to the plane (to the isoquinoline nitrogen). That there are two kinds of isoquinoline is shown clearly in Fig. 2 of B91; similarly for pyridine in Fig. 7 of that paper. The situation is similar in {(TPP– Zn2þ)[bicycloheptene-COOH]4} (see Fig. 2 of B91). However, the lattice sections do not allow one to decide which moiety is coordinated and which is guest.

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

505

8.7.4 Comparative crystallography of the (5,10,15,20)-tetraphenylporphyrin coordination and inclusion complexes The cell dimensions of a representative six-coordinate coordination complex {(TPP– Fe2þ)[4-picoline]2} are compared with those of a representative four-coordinate inclusion complex {(TPP–Zn2þ)[toluene]2} in Table 8.21. There is an overall similarity between cell axes and inter-axial angles, which shows that the packing is primarily determined by interactions between the large TPP macrocycles with the disposition of the ligand or guest having a subsidiary but non-negligible effect. {(TPP–Zn2þ)[toluene]2} is the only example reported of a tetraphenylmetalloporphyrin complex crystallizing in two polymorphic forms, triclinic and monoclinic. Comparison of the volumes per formula unit should give an indication of their relative stabilities. The molar volume in the triclinic polymorph has been measured (Kirner, Reed and Scheidt, ˚ 3 (Table 8.17), while that in the monoclinic polymorph is 1977) at 298K as Vtricl ¼ 1119 A 3 ˚ at (nominally) 100K (Table 8.20), The contraction on cooling of the Vmono ¼ 1036 A triclinic polymorph can be estimated from the values of cell volume for the isomorphous ˚ 3 at 293K and 1092 A ˚ 3at 98K). Using the {(TPP–Mn2þ)[toluene]2} (Vmono ¼ 1122 A 3 8 ˚ 3. Thus ˚ found for the Mn analog, we estimate Vtricl at 100K as 1089 A contraction of 30 A the monoclinic polymorph is appreciably more closely packed than the triclinic and is presumably the thermodynamically stable polymorph at 100K and also at room temperature, if there are no phase changes between 100 and 298K. The description of the complexes in terms of a –* interaction between the metalloporphyrin as acceptor and toluene as donor is considerably reinforced by the resemblances found between the structure of triclinic {(TPP–Zn2þ)[toluene]2} and that of monoclinic {(TPP–Cr2þ)[toluene]2} (CRPORT; Scheidt and Reed, 1978); both have the macrocycle sandwiched between two toluenes, all planes being approximately parallel. Thus there are many examples where a description in terms of charge transfer interaction is supportable. However, the example of {(TPP–Zn2þ) anthracene} should be taken as a warning – here the arrangement of the moieties in the unit cell is such that we have preferred to describe this complex as an inclusion complex. However, {(TPP–Zn2þ) anthracene}, and many analogous complexes, are black or deeply coloured, and conﬁrmation of the mode of interaction between the components by spectroscopic study is surely required before descriptions based only on arrangement can be regarded as established. Table 8.21. Comparison of crystal data for (i) a six-coordinate coordination complex and a fourcoordinate inclusion complex; (ii) the two polymorphic forms of {(TPP–Zn2þ)[toluene]2} Mnþ Fe

2þ

Zn2þ Zn2þ

Guest (4-picoline)2 JIVMEG; 128K (toluene)2 (toluene)2*

b

c

V

9.511

11.128

12.016

100.28

104.77

113.52

1070

10.502 10.43

11.349 15.23

11.404 13.55

107.65 90.0

110.48 99.9

103.87 90.0

1119 2073

a

* Space group P21/a, Z ¼ 2. 8 ˚ 3 at 300K and Much the same contraction is obtained for {(TPP–Zn2þ)[1,5-cyclooctadiene]2} – 1181 A ˚ 3 at (nominal) 100K (see Table I of B90), i.e. a contraction of 34 A ˚ 3. 1147 A

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

506

8.7.5

Questions of nomenclature and description

We ﬁrst compare the reduced and body-centered (Z ¼ 2; abbreviated as I-cell) unit cells for {(TPP–Mn2þ)[toluene]2} (Table 8.22). The I-cell is here delineated by the lattice points 110; 10 2 and 010 of the reduced cell. There is only one reduced cell but the I-cell can be deﬁned in many different ways. We next compare the reduced cells for {(TPP–Mn2þ)[toluene]2} and {(TPP–Mg2þ) [4-picoline]2}; although the cell edges are similar the cell angles are different, the ﬁrst having all obtuse angles (Type II) and the second all acute (Type I). Nevertheless, sections through the I-cells of the two crystals are very similar (Fig. 8.53; Fig. 5 of B90) because of the resemblances in the packing of the TPP macrocycles. The difference lies in the disposition of the molecules of the second component to the plane of the paper. This is the only hint that the ﬁrst material is a 4-coordinate inclusion complex and the second a pseudo-octahedral six-coordinate metal complex, as already noted above. A similar diagram (B93, see Fig. 21 on p. 9491) for the vinylidene carbene adduct {(TPP– Fe2þ)(C¼C( p-ClC6H4)2)} gives no hint that this is in fact a ﬁve-coordinate species (Mansuy, Battioni, Lavallee, Fischer and Weiss, 1988) and not an inclusion complex. Thus section diagrams must be approached with some care. Table 8.22. Comparison of reduced and body-centered cells for {(TPP-Mn2þ)[toluene]2}, and the reduced cell dimensions for {(TPP-Mg2þ)[4-picoline]2} Mnþ

Guest

a

Mn2þ (toluene)2 reduced triclinic cell (Z ¼ 1) Mn2þ (toluene)2 I-centred triclinic cell (Z ¼ 2) Mg2þ (4-picoline)2

Mn+2 (Toluene)2

b

c

V

10.487 11.320 11.465 107.80 110.63 103.34 1122 13.541 21.591 11.320

64.11

48.90

73.80 2244

10.146 11.210 11.643

65.64

76.32

67.42 1109

Mg+2 (4-picoline)2

Fig. 8.53. Comparison of the lattice sections for {(TPP–Mn2þ)[toluene]2} and {(TPP–Mg2þ) [4-picoline]2}. (Reproduced from B90.)

(5,10, 15,20)-TETRAPHENYLME TALLOPORPHYRINS AND COMPL EXES

507

How do the ‘‘tetraphenylmetalloporphyrin sponges’’ (referring only to the inclusion complexes, not the coordination complexes) ﬁt into the general scheme of nomenclature used in this book? The term ‘‘clathrates’’ was used in one of the ﬁrst papers from the Strouse group (B90), with the addition that the guests were located in channels. In our usage, ‘‘clathrate’’ and ‘‘channel’’ are mutually exclusive, and certainly the descriptor ‘‘clathrate’’ for the sponges has little connection with the meaning originally introduced by Powell (see Chapter 2). In 1993 the term ‘‘intercalate’’ and the associated notion of ‘‘staging’’ were added to the description, leading to an even more confused and contradictory situation. Again, the terms ‘‘intercalate’’ and ‘‘staging’’ are rather removed from their stricter deﬁnitions derived from the graphite intercalation complexes (see Chapter 9). We believe that there is little to be gained, and much to be lost, by extending accepted terms beyond their original meanings. The tetraphenylmetalloporphyrin sponges are ‘‘inclusion complexes;’’ further reﬁnement of this nomenclature should be based on detailed examination of individual structures. Strouse and coworkers have called these complexes ‘‘lattice clathrates’’ and described them in terms of the inclusion of guests in channels, providing reasons9 and many partialunit cell packing diagrams to support this contention. However, it would appear that there is much to be said for returning to the original point of view of Scheidt and coworkers in which, in some complexes, the guest molecules are described as linked to the metalloporphyrin ring system by delocalized –* charge transfer forces with perhaps some localized contribution from the metal atoms in a direction normal to the plane of the TPP ring system, while others are better described as having the guest molecules included within the host arrangement. 8.7.6 Can ‘‘sponge’’ structure be inferred from the chemical nature of the second component? An important question is whether one can predict the structure of the TPP sponges from the chemical nature of the second component; here we intend ‘‘structure’’ to mean whether one is dealing with a coordination or inclusion complex and, if the former, whether the coordination complex is four, ﬁve or six coordinate. A parallel, but more limited, question is to ask whether a particular second component will behave as ligand or guest. The known structures provide the database for answering these questions. Some clear-cut answers can be given. 1. Guests do not have any functional groups capable of interacting with the metal cations. Thus the list of potential guests includes: Benzene, polymethylbenzenes, aromatic hydrocarbons (phenanthrene, coronene, anthracene, indene), substituted benzenes (ethylbenzene, m-ethylvinylbenzene), bromobenzene, 1,5-cyclooctadiene, 1-methyl-1,4-cyclohexadiene, phenylacetylene, styrene, ethers (anisole, m-methylanisole; trans-anethole), alkenes (dimethylhexadiene), carboxylic acids (as H-bonded 9

We quote ‘‘the terms ‘lattice clathrate’ and ‘clathrate’ are used herein in the most general sense to indicate the inclusion of ‘guest’ molecules in a crystalline lattice of host molecules. No distinction is made for those cases in which there is a strong speciﬁc interaction between host and guest molecules. Similarly the term ‘intercalate’ is used to indicate the observation of two dimensional structure similar to that observed in the pure host materials. This use of the term is not intended to indicate knowledge of the mechanism of clathrate formation.’’

INCLUSION COMPLEXES FORMED BY VERSATILE HOSTS

508

2.

3.

dimers: bicycloheptenecarboxylic acid, m-toluic acid, o-toluic acid), m-nitrotoluene, m-ﬂuoronitrotoluene, 2,4-dinitrotoluene, acridine, phenazine, indole, m-hydroxyacetophenone (as H-bonded dimers). Ligands must have functional groups able to interact with the metal center of the porphyrin. Thus the list of potential ligands includes: N . . . metal interactions: pyridine and substituted pyridines, picoline and substituted picolines, piperidine, aniline, methoxypyrazine, 2-phenylethylamine. O . . . metal interactions: esters (methylbenzoate; p-ethoxybenzoate), quinones (anthraquinones, acetophenone, o-hydroxyacetophenone), aldehydes (9-anthranaldehyde, 2-nitrobenzaldehyde, benzaldehyde), phenyl isocyanate, alcohols (3-penten-2-ol, methanol). Ligand and/or guests: there are a number of examples where the second component ﬁlls two different structural roles. Prediction is particularly difﬁcult. Examples of such groups encountered among the porphyrin complexes are isoquinoline, dibenzosuberone. Other examples are scattered through this book, such as the ternary Menshutkin adducts (Section 11.12.1.3).

To summarize, the (TPP–M2þ) macrocycles form coordination complexes when the ligand has a functional group able to interact with the metal, but we do not know what factors decide whether a ﬁve- or six-coordinate complex will be formed. When the guest lacks such functional groups, then an inclusion complex can be formed in a manner similar to what is encountered with other host molecules of complicated shape. Sometimes the potential for behaviour as a ligand is inhibited by formation of hydrogen-bonded pairs, the guest species being the ‘‘dimer.’’ Particularly for the triclinic four-coordinate inclusion complexes, the varying dihedral angles possible for the four phenyl substituents confer a degree of ﬂexility on the host molecule which is reminiscent of the situation found in the TATM and Heilbron complexes discussed earlier in this Chapter. This also holds, but in less obvious form, for the inclusion complexes of the ﬁve- and six-coordinate coordination complexes.

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Chapter 9 Intercalation complexes

Literally, to intercalate means to place in between. An intercalation compound is like a book in which a further page has been added. On so doing, not only has the geometric aspect, the thickness, been changed, but also the meaning. Here, the layers are spread apart, which leads to a parametric expansion in the perpendicular direction, and the properties are modiﬁed by the play of electron transfer. These two aspects recur throughout. . . . Jean Rouxel, 1996. Sandwich, n. and v.t. 1. Two slices of bread with meat or other relish between (ham, egg, caviare, cucumber etc. also ﬁg., as in of good and bad); (usu. -man, -boy etc.) man etc. walking street with two advertisement-boards hung one before and one behind; -board, one of such boards; jj -boat in bumping race, boat rowing last in higher and ﬁrst in lower division on same day. 2.v.t. Insert (thing, statement etc.) between two of another character [perh. f. Earl of S (said to have eaten slices of bread and toast while gaming for 24 hrs)]. The Concise Oxford Dictionary, 4th Edition, 1960, p.1093.

Summary: The pristine host materials of intercalation complexes consist of two-dimensional sheets, successive sheets being linked by van der Waals interactions. Within the sheets the constituent atoms are covalently bonded and so the hosts are highly anisotropic in structure and properties. The sheets are comparatively easily pried apart and thus allow interlayer insertion of guest moieties, with consequent property changes that can be exploited for a variety of purposes. From the large variety of possible examples, we have chosen to discuss the intercalation complexes of graphite (GICs), (2H)-TaS2, and zirconium phosphates and phosphonates. Graphite in this context is amphoteric and can intercalate both electron donors (e.g. some of the alkali metals) and electron acceptors (e.g. some of the halogens). Not discussed are a large number of other intercalates, and the numerous ternary sytems are also excluded. Tantalum sulphide is a representative of a large family of transition metal chalcogenides, which intercalate metals and organic guests; its particular interest lies in the fact that the organic-guest intercalates become superconducting, albeit at very low temperatures. The zirconium phosphates and phosphonates are models for the smectic clays, are ion exchangers and catalysts; again we emphasize the organic-guest intercalates.

9.1 Introduction 9.2 Intercalation complexes of graphite (GICs) 9.2.1 Introduction 9.2.2 Alkali metals as guests (preparation at atmospheric pressure) 9.2.3 Alkali metals as guests (preparation at high pressures) 9.2.4 Alkaline earth and lanthanide metals as guests

516 517 517 520 532 533

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516

9.2.5 Halogens as guests 9.2.6 Uses, actual and potential, of GICs 9.2.7 Summary for GICs 9.3 Intercalation complexes of inorganic hosts 9.3.1 Introduction 9.3.2 2H-b-TaS2 as host 9.3.3 Zirconium phosphates and phosphonates as hosts 9.4 Concluding summary References

9.1

533 539 539 540 540 540 546 552 552

Introduction

Intercalation, or interlamellar (the less common term), complexes are formed by the insertion of atomic or molecular layers of a different (guest) chemical species (the intercalate1) between the layers of the intercalating host material (Whittingham and Jacobson, 1982; Dresselhaus, 1986; Selig and Ebert, 1980; Scho¨llhorn, 1994, 1996; Mu¨ller-Warmuth and Scho¨llhorn, 1994; Alberti and Constantino, 1996). Intercalation complexes occur in highly anisotropic layered structures where the intraplanar binding forces are much stronger than those between the planes. It has been claimed that the phenomenon of intercalation was discovered inadvertently by the Chinese in the seventh century B.C. (Weiss, 1963). The classical example of an intercalating host is graphite, for which many intercalates are known. Other examples are FeCl3, clay minerals of various kinds (including mica), and - and -zirconium phosphates. We refer to these materials as ‘complexes’ because the guest (intercalate) is enclosed between the planes of the (essentially) unchanged intercalating host (i.e. A–A interactions predominate in determining the structure). Most previous authors use the term ‘compound.’ The interlayer space is often referred to as a ‘gallery’ and the process as ‘ingestion.’ Staging, where the stage is the number of host layers per intercalate layer, is now used in the description of a wide variety of intercalation complexes, although it was originally thought to be peculiar to graphite intercalation complexes (GICs). Why staging occurs remains a mystery. Staging may be represented in shorthand fashion as follows (see also Fig. 9.5 below): Stage 1: jj jj jj Stage 3: jj jj jj jj jj jj jj jj jj

Stage 2: jj jj jj jj jj jj Stage 4: jj jj jj jj jj jj jj jj jj jj jj jj

where jj represents a host layer and an intercalate layer. It is convenient to divide intercalation complexes into three groups (following Averill, Sutto and Fabre, 1994). These differ primarily in the charges on the layers and the forces holding the complexes together. In the ﬁrst group the layers in the pristine host are neutral and are held together by van der Waals interactions; examples of such hosts are graphite, transition metal dichalcogenides, phosphorus trisulﬁdes, talc, oxyhalides and some dihalides. We discuss the ﬁrst two of these examples. In the second group the layers are 1 From the Latin intercalare, ‘‘proclaim the insertion of a day (month etc.) in the calendar.’’ ‘‘Intercalate’’ is used both as a noun and as a verb.

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charged with ions of opposite sign, and these hold the layers together by electrostatic interactions; example include layered silicates and double hydroxides. For reasons of space, we do not discuss these in detail. The third group has neutral layers with terminal hydroxy groups that use hydrogen bonding to maintain the layered structure; examples include zirconium phosphates and phosphonates (which are discussed), FeO(OH) and Al(OH)3 (which are not). The intercalation complexes to be discussed in this chapter differ in one important respect from almost all the other crystalline complexes and compounds considered in this book. Single-domain single crystals of intercalation complexes are hard (perhaps impossible) to come by, and so polycrystalline samples, often with high (but unspeciﬁed) degrees of preferred orientation and relatively low degrees of crystallinity (high mosaic spread), have to be used for study. Furthermore, the chemical compositions of the samples used for study are not always adequately established. The extremes of crystallinity encountered are illustrated in Figs. 9.1 and 9.11. Thus, it is usually difﬁcult to determine the true reciprocal lattice of the complex, and even more difﬁcult to measure precise (not to mention ‘accurate’) reﬂection intensities. The crystal structures inferred from such information therefore cannot be expected to meet the standards of reliability attained in the more usual types of analysis, and the chemical inferences drawn must be treated with some caution. Nevertheless, it is a tribute to the ability of the investigators that they have been able to infer so much from such a limited information base. The original investigators have usually reported their conclusions with suitable reserve, but this reserve has not always been honoured in later quotation of earlier conclusions. Two developments in experimental techniques are likely to change this situation for the better. The ﬁrst is the improvement in the capabilities for analysis of the structures of polycrystalline samples (Loue¨r, 1998) following the increased resolution available using synchrotron sources of X-radiation (Cheetham and Wilkinson, 1992; Cox, 1992) and the application of the Rietveld method (Young, 1993); this also holds for the new reactor and spallation neutron sources. A corollary is the increased capability of carrying out structure determinations on very small single crystals, using synchrotron sources (Harding, 1996). The second is the combination of imaging and diffraction techniques used in modern electron microscopes (Dorset, 1992; Cowley, 1992, 1993; Amelinckx, 1995). The latter certainly give improved structural results, but only for the thin crystalline portions of the sample; some care is therefore needed when possibly unrepresentative structural results are used to explain properties of bulk samples. Besides the review articles noted above and elsewhere in this Chapter, a very wideranging discussion has been given by 42 authors in 25 articles in the 837 pages of Vol. 7 (edited by Alberti and Bein, 1996) of Comprehensive Supramolecular Chemistry; this complements and supplements our much more limited coverage. 9.2 Intercalation complexes of graphite (GICs) 9.2.1 Introduction The ﬁrst graphite intercalation complexes (GICs) were prepared some 150 years ago (Schafha¨ult, 1841, see p.155), while the ﬁrst structural determinations by X-ray diffraction date back some 60 years (Hofman and Frenzel, 1932; Schleede and Ziegler-Wellman,

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1932); these materials have been the subject of active scientiﬁc and technological research in recent years (Hennig, 1952; Ru¨dorff, 1959; Croft, 1960; Ubbelohde and Lewis, 1960; Dresselhaus and Dresselhaus, 1981; Solin and Zabel, 1990; Zabel and Solin, 1990; Schlo¨gl, 1994; Okino and Touhara, 1996). The chemistry of intercalation into graphite has been reviewed (Vogel and He´rold, 1977) and more than one hundred different guests have been intercalated; Hennig (1952) lists some 50 compounds which do intercalate, and some 50 which do not. The guests can be broadly divided into the two classes of electron donors or Lewis bases (e.g. alkali metals) and electron acceptors or Lewis acids (e.g. halogens). Graphite is unique among the hosts of intercalation complexes in having an amphoteric nature. The intercalate serves as a source (donor) or sink (acceptor) for electrons, leading to small perturbations of the parent electron distribution. The primary emphasis of our discussion will be on the binary GICs (i.e. only one guest component) but it should be noted that there is an extensive literature on ternary GICs, which offer advantages of extra compositional variability (Solin and Zabel, 1988; He´rold and Lagrange, 2003). We generally follow the IUPAC recommendations on the nomenclature and terminology of GICs (Boehm, Setton and Stumpp, 1994), except that we give the formulae as {Cn[guest]}, with the graphene layers (the IUPAC name for the planar layers of carbon atoms) acting as host to the guest, the brackets often being dropped for simplicity; this notation conforms to our general notation for inclusion complexes as {host [guest]}. Thus we name complexes as, for example, ‘graphite-potassium (8/1; st.1)’; 8/1 gives the ‘ratio C:guest atom’ and st.1 refers to the ‘stage’; IUPAC nomenclature would be potassiumgraphite etc. Because the integrity of the graphene layers is retained on formation of the GIC whereas the guest can appear in nonstoichiometric amounts, we prefer to write compositions as {Cn[guest]x} where ‘n’ is integral but ‘x’ need not be. Single crystal graphite ﬂakes (as from Ticonderoga mine in New York State) have been used as host material but are often too thin to be satisfactory samples for physical measurements; highly oriented pyrolytic graphite (HOPG) is a much used host, many authors thanking A. W. Moore (Union Carbide; 1973) for the HOPG used in their experiments. This quasi-single crystalline host material provides great advantages in diffraction experiments compared to the use of polycrystalline samples. The common c-axis and random a-axis orientation of the HOPG crystallites are preserved on intercalation (Fig. 9.1). Two quotations highlight the problems to be solved. The ﬁrst is from Johnson (1967): ‘‘Generally the mechanism of formation of a lamellar graphite compound, that is the

Table 9.1. Some intercalates in graphite; more extensive lists are given in Schlo¨gl (1994) Electron donors or Lewis bases. Li, (Na),* K, Rb, Cs. Alkaline earth metals, lanthanides, alloys of these, and with alkali metals; aromatic hydrocarbons (e.g. anthracene).y Ternary complexes of alkali metals with hydrogen, with polar molecules such as tetrahydrofuran, and with aromatics such as benzene. Electron acceptors or Lewis acids. Br2 and ICl, metal halides (e.g. AlCl3, FeCl3, AsF5 and SbCl3) and oxyhalides, N2O5, SO3, H2SO4, HNO3. Notes: * see text. y Averill, Sutto and Fabre, (1994).

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penetration of a graphite crystal at many independent points on its prismatic faces by the reactant atoms or molecules, automatically results in a disordered and multiply twinned condition of the intercalated crystal.’’ The second is from Samuelson, Moret, Come´s, Fuzellier, Klatt, Lelaurain and He´rold, (1984/5): ‘‘The indexing of [GIC diffraction patterns] is complicated by the simultaneous presence of as many as six domains in the general case, and the single-domain reciprocal cell has to be decoded from the multitude of spots appearing due to the hexagonal symmetry imposed by the graphite lattice.’’ Kish graphite (crystallized from molten steel during manufacturing) is a host material of considerable potential (Liu and Lofer, 1991). Another novel host material is graphite ﬁlm prepared by heating polyimide ﬁlms at temperatures around 3000 C (Hishiyama, Kaburagi, Nakamura, Nagata and Iwasaki, 1993). Preparative methods have been discussed in

(a)

(b)

(c)

(d)

Fig. 9.1. X-ray diffraction photographs of graphite-potassiums ((a) Stage 4, (b) Stage 3, (c) Stage 2, (d) Stage 1) obtained during the intercalation reaction, with eventual formation of the Stage 1 complex. The c axis is horizontal and, although the samples were stationary, the photographs are equivalent to full rotation photographs because of the random orientation of the a axes of the crystallites. (Reproduced from Nixon and Parry, 1968.)

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a number of papers (Robert, Oberlin and Mering, 1973; Stumpp, 1977; Dresselhaus and Dresselhaus, 1981), and we shall often note those used for particular materials without going into detail. We give most attention to binary GICs with alkali metals (Csuk, Gla¨nzer and Fu¨rstner, 1988) and halogens as intercalates; the extensive literature on ternary GICs (Solin and Zabel, 1988) has already been noted. Of the varieties of GICs, those with alkali-metal donors have been most studied and their structures are best known.

9.2.2 9.2.2.1

Alkali metals as guests (preparation at atmospheric pressure) Ambient pressure preparations

It was reported in the late 1920s that molten and gaseous K, Rb and Cs reacted vigorously with graphite (Fredenhagen and Cadenbach, 1926; Fredenhagen and Suck, 1929), leading to the ﬁrst controlled preparations of GICs. As K, Rb and Cs do not directly form stable M2C2 carbides, the GICs are the stable species in these carbon–metal systems; the situation is different with Li as it forms the acetylide Li2C2. A two-zone vapour transport method (He´rold, 1955, He´rold and Saehr, 1960; Nixon and Parry, 1968; Fig. 9.2) is generally used for preparing alkali-metal GICs. The temperature difference Tgraphite – Tintercalate (brieﬂy Tg – Ti) determines the composition of the GIC formed. For example, for graphite at 250 C, stage 1 is formed with the potassium held in the temperature range 225–320 C, stage 2 when 350 < Ti < 400 and stage 3 when 450 < Ti < 480. The color of the GIC depends on the stage; for the alkali metal hosts, stage 1 complexes are yellow, gold or red, stage 2 blue, and graphite–metallic for higher stage complexes. In the carbon–potassium system, stage 1 has alternating graphene and potassium layers and composition C8K, stage 2 an alternation of a pair of graphene layers and a single potassium layer and composition C24K and stage 3 composition C36K (Figs. 9.1 and 9.3). The higher the stage, the more dilute the complex is in intercalate. Most GICs are reactive when exposed to the atmosphere (those of the alkali metals being spontaneously inﬂammable) and must be kept under vacuum or a pressure of inert gas; cooling samples to liquid nitrogen temperatures greatly improves their stability. The ﬂuorine GICs are, remarkably, air stable.

9.2.2.2 Structures of alkali-metal GICs (prepared at atmospheric pressure) We give an overview of the structural results for alkali-metal GICs (M¼Li, K, Rb, Cs; binary complexes with Na do not appear to have been obtained at ambient pressures; Table 9.2; Fig. 9.3); the emphasis is on ﬁrst-stage structures. Graphite itself (‘pristine’ graphite) is found as a stable hexagonal and a metastable rhombohedral polymorph. Both ˚ ; the polymorphs have the same characteristic hexagonal sheets, with d(C–C) ¼ 1.42 A sheets are stacked . . . ABABAB . . . in the hexagonal polymorph and . . . ABCABC . . . in the rhombohedral polymorph. The latter is rare and does not appear to have been used for making GICs. In the GICs one wishes to know the stacking arrangement of the graphene sheets and the three-dimensional location of the intercalated atoms or molecules. Possible graphite-metal arrangements in ﬁrst-stage GICs CnM have been described by the authors Gue´rard, Lagrange, El Makrini and He´rold in a series of papers (for example 1978, 1981); a useful summary for the C8M (M¼K, Rb, Cs) structures has been given by

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

T(graphite)

T(intercalant)

Graphite

intercalant

521

Fig. 9.2. Schematic diagram of the two stage vapor transport method of preparing GICs. The two vessels are kept at different temperatures. (Adapted from Dresselhaus and Dresselhaus, 1981.)

˚ ) for graphite and its metal intercalation complexes (all stage I except for Table 9.2. Crystal data (A stage II C12Li). In the designation of the layer stacking, the capital letters refer to the graphene layers and the Greek letters to the intercalate Material

a

b

c

Space group

Z

Layer stacking

Hexagonal graphite (E98) Rhombohedral graphite (E98) C6Li (GH75) C12Li (GH75) C8K (LG78) C8Rb (LG78) C8Cs (LG78)

2.46

2.46

6.71

P63/mmc

4

. . . ABAB . . .

2.46 ˚ aR ¼ 3.64 A R ¼ 39.5 4.305(1) 4.288(2) 4.956(6) 4.928(2) 4.95(1)

2.46

10.04

R 3 2/m

6

. . . ABC . . .

4.305(1) 4.288(2) 8.60(1) 8.536(3) 4.95(1)

3.706(1) 7.06(2) 21.58(3) 22.47(1) 17.76(3)

1 1

. . . AA . . . . . . AAAAA . . . . . . AAAA . . . d . . . AAAA . . . d . . . AAA . . . d

4.316(6) 4.315(10) 4.302(6) 4.29 4.32 4.314(3) 4.29 4.28 4.30 4.320(4) 16.10

4.316(6) 4.315(10) 4.302(6) 4.29 4.32 4.314(3) 4.29 4.28 4.30 4.320(4) 4.30

Ic ¼ 4.55(2) 9.90(5) 10.50(4) 9.37 9.62 9.745(8) 9.80 9.67 9.34 9.147(4) 8.50 ¼ 97

C6Ca (GC80) C6Sr (GC80) C6Ba (GC80) C6Nd (HI96) C6Sm(HI96) C6Eu (EM80) C6Dy(HI96) C6Er (HI96) C6Yb (HI96) C6Yb (EM80) C4K1.05 O0.074 (HHL96)

P6/mmm P6/mmm Fddd c Fddd P6222 or P6422 P63/mmc P63/mmc P63/mmc P63/mmc P63/mmc P63/mmc P63/mmc P63/mmc P63/mmc

Notes: (c) Nixon and Parry (1968) give the space group as Fdd2; (d) see discussion in text. References: E98 – Elmsley (1998); EM80 – El Makrini, Gue´rard, Lagrange and He´rold (1980); GC80 – Gue´rard, Chaabouni, Lagrange, El Makrini and He´rold (1980); GH75 – Gue´rard and He´rold, 1975; HHL96 – He´rold, He´rold and Lagrange (1996). HI96 – Hagiwara, Ito and Ito, (1996); LG78 – Lagrange, Gue´rard, El Makrini and He´rold, 1978.

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C8Cs

graphite

O

C6Li

a

C8K(Rb)

b

Fig. 9.3. A single graphene layer with superimposed outlines of the a and b axes of the unit cells to show the relations among the (ﬁrst stage) C6Li, C8K(Rb) and C8Cs structures. The unit cells of the C6M (M ¼ Ca, Sr, Ba, Eu, Yb) have the same outline as for C6Li but the c spacing and space group are different. Crystal data are given in Table 9.2.

Lagrange, Gue´rard, El Makrini and He´rold (1978). It is assumed that the intercalated metal atoms conform to the local symmetry of the graphene layers which are stacked . . . A . . . A . . . A . . . There are two possible coordinations for the metal atoms – 6 (hexagonal centered) or 3 (open hexagonal); for 6-coordination the possible values of n (in CnM) are 2, 6, 8, 14, 18 . . . , while for 3-coordination possible values are 3, 9, 12, 21, 27 . . . So far only C6M and C8M ﬁrst-stage GICs have been prepared at ambient pressures. Li GICS have been prepared by two methods: 1. 2.

reaction at 400 C of Li vapor and graphite in an evacuated sealed metallic tube. This gives only ﬁrst stage C6Li; reaction at room temperature of mixed graphite and Li powders under 15–20 kbar pressure, followed by annealing at 200 C; the stage obtained depends on the composition of the original mixture.

There is a striking dependence of color on stage in CnLi GICS; the ﬁrst stage is brassyellow, the second steel-blue, the third dark blue and the fourth black (Gue´rard and He´rold, 1975). In C6Li one-third of the possible metal sites are occupied in an ordered manner, and (metal and graphene) layers are stacked one above the other giving . . . AAA . . . stacking (Gue´rard and He´rold, 1975; Gue´rard, Lelaurain and Andre´, 1975); note that the designation of metal sites as , etc. is speciﬁc to the particular structure. The space group is P6/mmm with six C atoms in Wyckoff positions j (symmetry mm; x, 0, 0, etc with x 1/3) and the Li atom in b (6/mmm; 0,0,1/2). The shortest Li . . . Li ˚ and only minor electrostatic interactions are to be expected in-plane distance is 4.26 A among the neighboring metal atoms. Gue´rard and He´rold (1975) comment ‘‘Lithium intercalation is certainly favoured by its small radius which requires a small graphite plane displacement energy and perhaps because it gives a partially covalent character to the carbon–metal bond.’’

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

α

O

α

α

γ

δ α

a

α

β α

C2M

α

C6M

b

523

A δ A γ A β A α A

C8M

Fig. 9.4. (Above) On the left the graphene layer is shown together with the sites , , , of the metal atoms in the intercalate layers. The a, b edges of stage 1 C8K(Rb) are outlined. The stacking arrangement is shown on the right; the graphene layers all have the same relative lateral positions but the ﬁrst intercalate layer has K(Rb) atoms only in the positions, and so on for the rest of the sequence of intercalate layers. The z coordinates of the layers are: 0, 14, 12, 34. As explained in ˚ in the text, there are six equivalent stacking arrangements. The distance between A layers is 5.35 A C8K. (Below) The relationship of the graphene and intercalated metal layers is shown for the three compositions C2M, C6M and C8M.

The situation in the C8K(Rb) and C8Cs structures is more complicated. In any one layer, the metal () sites have a p(2 2)R0 superlattice packing arrangement (Fig. 9.4). The two dimensional cell is primitive (‘p’), with a unit cell edge twice that of the graphite hexagonal a axis (2 2), but not mutually rotated (R ¼ 0 ). A similar notation is used in surface crystallography to describe the arrangement of adatoms on a single-crystal surface. There are four equivalent metal-atom sites shown by , , , in Fig. 9.4. The stage 1 C8K (Ru¨dorff and Schulze, 1954; Lagrange, Gue´rard and He´rold, 1978) and C8Rb (Lagrange, Gue´rard, El Makrini and He´rold, 1978a) complexes are isomorphous (Table 9.2). Analysis of the diffraction patterns of quasi-single crystal samples of C8K (C8Rb) shows that all four of the interstitial sites are occupied, in an ordered manner. The absences show that the space group is Fddd (orthorhombic, centrosymmetric); the C atoms are in Wyckoff positions 32h (1/12,1/4,1/8, etc. and 1/12,1/4,5/8, etc.) and the K(Rb) atoms in 8a. The stacking is . . . AAAA . . . However, the diffraction patterns have overall hexagonal symmetry and this was explained on the basis of the occurrence of six energetically indistinguishable types of domain with stackings , , , , , . Any one sample will contain all six domain types. The shortest ˚ , indicating only weak metal . . . metal interactions. K . . . K in-plane distance is 4.92 A Analysis of the diffraction patterns of quasi-single crystal samples of C8Cs shows that only three of the , , , sites are occupied, in an ordered manner (Gue´rard, Lagrange, El Makrini and He´rold, 1978b). The systematic diffraction absences show that the space group is P6222, the twenty four C atoms are in Wyckoff positions 12k (symmetry 1;

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x 1/6, y 1/3, z 1/3 etc.) and 6i (symmetry 2; x, 2x, 0, etc, with x 1/6 and 1/3), and the three Cs atoms in three of the four positions of 222 symmetry (e.g. b; 0,0,1/2 etc). The stacking is . . . AAA . . . However, P6222 is a chiral space group and could not be distinguished from P6422, with stacking (abbreviated symbol); furthermore the stackings and are not energetically distinguishable. Thus six different types of domain are possible, with stackings , ; , ; , . All have hexagonal symmetry and any one sample will contain the six domain types. The diffraction patterns of graphite monocrystals intercalated with Cs have been studied (Parry, 1977; Clarke, Caswell, Solin and Horn, 1979, 1980). The structures of stage 1 GICs of K, Rb and Cs have been investigated by scanning tunneling microscopy in an inert gas environment (O2, N2 and H2O levels below 1 ppm; samples never exposed to air) at 293K (also Li and ternary GICs, which will not be discussed here) (Lang, Thommen-Geiser and Gu¨ntherodt, 1994). 2 2 superstructures are found ﬁrst and then, over a period of some 20 minutes, higher order (more dilute) superstructures develop as the uppermost gallery is depleted of metal. It appears that the uppermost surface layer is graphitic. For n 2, the stages are shown in Fig. 9.5; the ideal bulk stoichiometries are C12nM, while the layer stoichiometries are C12M. The periodicity normal to the carbon planes is Ic ¼ N[(n–1)d1 þ d2], where d1 is the spacing of AB layers in graphite and is taken as ˚ , while d2 (the spacing of the C(M)C sandwich) depends on the nature of the metal 3.36 A ˚ for M¼K, 5.68 A ˚ for Rb and 5.97 A ˚ for Cs (here average values are atom and is 5.40 A given which do not take the small effect of staging into account); N¼1 if the metal layers are disordered and 2 if they are ordered. The value of Ic can be determined from 00‘ reﬂections alone if the metals layers are disordered but hk0 reﬂections are also needed if ˚ (see above) while Na is not the metal layers are ordered. Li is anomalous at 3.71 A intercalated on its own. A

A

A

A

M

M

M

M

A

A

A

A

B

B

B

B

A

A

A

B

B

M B A Stage 2 Ic = 17.5 Å

M Stage 3 Ic = 12.1 Å

B A

A Stage 5 Ic = 18.8 Å

B A Stage 4 Ic = 30.9 Å

Fig. 9.5. Illustration of the arrangement of layers in stages 2–5. The periodicities are for potassium GICs.

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Fig. 9.6. Schematic diagrams of a third-stage GIC, according to the classical view of Ru¨dorff (on the left) and the pleated sheet (nonclassical) description of He´rold) (on the right). The graphene layers are represented by lines and the intercalate atoms by ﬁlled circles. (Reproduced from Csuk, Gla¨nzer and Fu¨rstner, 1988.)

The diagrams given in Figs. 9.4 and 9.5 are classical descriptions of staging, originally due to Ru¨dorff. These have now been superceded by a ‘‘non-classical’’ model with pleated sheets (Fig. 9.6), due to Daumas and He´rold (1969). It is no longer thought that the higherstage GICs have well-deﬁned, stoichiometric structures at ambient temperatures. Instead the crystal structures depend on the conditions at the time of preparation; the intercalated metals form liquid-like layers without long-range order and undergo diffusion within and between layers. At lower temperatures (say 50K), the ‘liquid’ layers crystallize and very complicated diffraction patterns ensue; an example, for C24Rb, is given by Moret and Dalle´ (1994). Alternatively, the metal atoms may be well ordered within a particular gallery, but there is little or no correlation from one occupied gallery to the next. Despite a tendency to accept a more physically realistic structural picture, most current (and the more so for earlier) descriptions are still couched in terms of ordered arrangments of intercalated atoms, and the reader should make the necessary allowances. The importance of considering the real, as opposed to the ideal, structures of GICs has been particularly emphasized by Schlo¨gl (1994), who has pointed that the fundamental problem of ‘staging’ is to understand why, for a given stoichiometry, it is energetically favorable to form a structure with a combination of highly ﬁlled and completely empty galleries rather than a low stage GIC with incompletely ﬁlled galleries.

9.2.2.3 Models of alkali metal GICs. (i) Introduction. Schlo¨gl (1994) has made a useful distinction between an integrative or phenomenological approach to the structures of GICs, which do not require a detailed knowledge of the host–guest binding interactions, and the ‘atomistic’ approach. The ﬁrst approach stresses ideal overall structures and thermodynamic measurements and parameters that ignore the detailed real structure of the GICs. The second approach attempts to integrate spectroscopic measurements, strongly inﬂuenced by the real structure, and quantum mechanical calculations of host–guest interactions. In practice it seems necessary to try to weave both approaches together, in the hope that the limitations of each will cancel rather than reinforce. Three models have been proposed for the host–guest interactions: 1. Hard sphere model (Dresselhaus and Dresselhaus, 1981). Here the metals keep their standard metallic radii; the problem is that there is not enough space (laterally) in the galleries to accommodate the metal atoms, especially in the dense GICs.

526

2.

3.

INTE RCAL ATION C OM PLEXES

Ionic model (Ubbelohde and Lewis, 1960). At its simplest level this model suggests that there is complete transfer of valence electrons from metal donors to the graphene acceptor layers. Thus, the ﬁrst-stage potassium GIC is described as {C8[Kþ]}, and correspondingly for other compositions and metals. If this is taken literally, and the ˚ , then the spacing of graphene layers are taken as planar, rigid and of thickness 3.36 A þ ˚ ˚ a C(K )C sandwich should be 6.02 A, using 2.66 A as the ionic diameter of Kþ. As ˚ . Two factors contribute to this noted earlier, the experimental value is 5.40 A discrepancy – the potassium ions nestle in the hollows at the centers of the carbon hexagons, and there may be some covalent bonding, i.e. incomplete charge transfer. This approach has been extended by Sawamura, Womelsdorf and Ermler (1991) to actually estimate the degree of charge transfer from the inferred radii of the metal atoms in the GIC, using a non-linear relationship between radius and charge transfer. The results are surprisingly plausible. More sophisticated experimental and theoretical approaches are described below. Mordkovitch (1994) has proposed a mechanical ‘elastic balls, elastic network’ model in which compression of the metal atoms is matched by an expansion of the graphite network. This depends on the negative compressibility of the graphene layers in the adirection (ka ¼ 1.65 1012 Pa1); the compressibilities of the alkali metals are Li (80), K (297), Rb (370), Cs(156) (all 1012 Pa1). Thus appreciable compression of the metal atoms is accompanied by small expansions of the graphene network. This model can be used to predict mechanical properties of the GICs but does not relate to physical and chemical properties.

(ii) Anisotropy of binding. The total cohesive energy of graphite is 715 kJ/mol, while the interlayer interaction energy is 2.09 kJ/mol (calculated) or 2.20 kJ/mol (measured) (Girifalco and Ladd, 1956). The speciﬁc heats of C8K and C8Cs have been measured over the range 1.5–5K and the Debye temperatures determined as 235(1) for C8K and 341K for C8Cs, to be compared with 421(4)K of graphite (Kondov, Mizutami and Massalski, 1982). This implies appreciably greater thermal motion in the GICs than in graphite. However, the highly anisotropic nature of these materials does not allow description of their properties by a single parameter. Therefore Debye temperatures for the alkali metal atoms in GICs were calculated, from the measured phonon spectra, for directions parallel and perpendicular to the graphene planes (Table 9.3; Moreh, Shnieg and Zabel, 1991). It was inferred from the values in Table 9.3 that the forces binding metal atoms in the GICs were much stronger in directions perpendicular to the graphene planes than parallel to these planes. This is, of course, the converse of the situation for the carbon atoms (cf. values for graphite). Finally, it was inferred that the degree of charge transfer between metal atoms and carbon planes, which governs their interaction, was much the same for all the GICs and for all the stages. (iii) Thermodynamics of alkali metal GICs The enthalpy of formation of the potassium GIC was measured by Fredenhagen and Caldebach at the time of the ﬁrst (modern) preparation of this complex in 1926; deﬁnitive values of thermodynamic parameters for Rb and Cs GICs were given by Salzano and Aronson (1966); see Table 9.4, where we cite only the results for the stage 1 reaction 8C(s) þ M(g) ¼ {C8[M]}(s) . . . . . . (1), where M is an alkali metal. However, the standard thermodynamic parameters of formation of C8M(s)

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

527

Table 9.3. Effective Debye temperatures (K) for graphite (Ludsteck, 1972) and for the intercalated alkali metal atoms in GICs at 0 K, as calculated from the phonon spectra (Moreh, Shnieg and Zabel, 1991). The Debye temperatures of the pure metals are given for comparison Complex

1300 337 115 78 62

670 893 307 192 153

335 91 56 38

(parallel)

graphite (ND, 300–1150K) C6Li C8K C8Rb C8Cs

(perpendicular)

(metal)

Note: The literature values for graphite (from speciﬁc heat and diffraction measurements) show a large spread, and the particular values cited are intended as indicative only.

Table 9.4. Thermodynamic parameters for the stage 1 reactions (1) and (3) (based on measurements of Salzano and Aronson (1966) and standard values from Emsley (1998)). Units of Hf are kJ/mol M, and of Sf J/mol M K Alkali metal

Hf for reaction (1)

Rb Cs

120.5 143.1

Sf for reaction (1) 97.5 100.4

H o(subl) for reaction (2)

So for reaction (2)

80.9 76.1

170.1 175.6

H 0f for reaction (3) 39.6 67.0

S 0f for reaction (3) 72.6 75.6

G 0f for reaction (3) 61.3 89.4

(i.e. from the elements in their standard states) are more relevant here and thus M(s) ¼ M(g) . . . . . . (2) must be added to (1) to give 8C(s) þ M(s) ¼ {C8[M]}(s) . . . . . . (3). The standard enthalpies and entropies of sublimation for Rb and Cs are also given in Table 9.4. Thus these GICs are both enthalpy and entropy stabilized with respect to the components. The entropy increases come in the main from the intercalated metal atoms and are rather larger than would be expected from the values given for the (in-plane) Debye temperatures in Table 9.3. Perhaps there is an additional disorder contribution to the entropy; although the alkali metals in the GICs are generally considered to be in-plane ordered, there is little long range order normal to the planes. The values of the enthalpies and entropies of formation (reaction (3)) are in the same range as those found for mixed stack donor–acceptor charge transfer compounds (see Section. 16.2). Following Schlo¨gl (1994) one can put forward the following Born-Haber type cycle for the formation of stage 1 potassium GIC: C þ 1=8K ¼ 1=8fC8 ½K g The partial reactions are the following: 1. 2. 3. 4. 5.

Vaporization of the guest (K) involving loss of metallic energy (endothermic). Separation of the graphite layers (endothermic). Ionization of the guest (Kþ) (endothermic). Reduction of the graphite layers (exothermic). Formation of GIC involving (to a ﬁrst approximation) gain of Coulomb energy (exothermic).

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(iv) Charge transfer in alkali-metal GICs. The ionic model has been tested by a wide variety of studies, both theoretical (discussed in this paragraph) and experimental (discussed in the next paragraph). Most of the theoretical studies concern the determination of the degree of charge transfer and, in particular, whether the use of a {Cn[Mþ]} type of formulation is justiﬁed (where n ¼ 6 for M ¼ Li, and n ¼ 8 for the other alkali metals); only Stage 1 GICs are included except for Stage 2 C24K noted below. A fundamental problem is that ‘charge transfer’ is not an observable in the quantum mechanical sense, and thus there is no unambiguous way of calculating it from the wave function; consequently care is needed in comparing values obtained from different methods of calculation. We consider only two recent calculations: (1)

(2)

an ab initio study of (inter alia) Stage 1 C6Li and C8M (M ¼ K, Rb, Cs) in which the charge density was calculated within the framework of the local-density approximation to density-functional theory (Hartwigsen, Witschel and Spohr, 1997a, b); crystal orbital (CO) calculations of Stage 1 C8K and Stage 2 C24K based on an intermediate neglect of differential overlap (INDO) Hamiltonian (Bo¨hm, Schulte and Schlo¨gl, 1996); these papers contain extensive discussions of earlier work.

The principal result of Hartwigsen et al. (1997b) is that lithium in C6Li carries a charge of þ0.5e, and the M atoms in C8M (M ¼ K, Rb, Cs) a charge of þ0.7e irrespective of the identity of M. Hartwigsen et al. (1997a) calculate bond lengths for the two independent ˚ ) and in C8M (for C8Cs 1.4301 and 1.4299 types of C–C bond in C6Li (1.4393, 1.4324 A ˚ A), and compare these values with experiment. However, it is very unlikely, because of the nature of the samples and the special precautions needed in making the nonroutine measurements required, that reported cell dimensions (from which the C–C bond lengths ˚ , so that the claimed agreement were calculated) are precise to better than 0.01 A ¨ with experiment is probably meaningless. Bohm, Schulte and Schlo¨gl (1996) calculate a charge of þ0.42e on K in Stage 1 C8K and þ0.55e on K in Stage 2 C24K. Thus the two calculations agree that charge transfer proceeds appreciably, but not completely, towards the ionic model; alternatively stated, there is some covalent bonding (more in C6Li than in C8M). We give a selection of references to illustrate how, over the years, opinion has changed about the degree of charge transfer in donor GICs. For example, 133Cs NMR spectroscopy of C8Cs suggests that the metal atoms have charges of þ0.3e (Roth, Luders, Pﬂuger and Guntherodt, 1981) whereas Auger spectroscopy suggests þ0.72e (Marchand, Fretigny, Lagues and Legrand, 1983). Calculations of total energy (i.e. kinetic þ potential (Coulombic þ exchange) þ Madelung) as a function of charge transfer have been made for Stage 1 metal GICs by Doyen-Lang, Charlier, Lang, Charlier and McRae (1993) and charge transfers of 0.95e at minimum energy were found for Li, K, Rb and Cs, and of 1.95e for Ca, Sr, Ba, Sm, Eu and Yb. Boehm, Setton and Stumpp (1994) recommend that the charge transfer be deﬁned by the average charge accepted or donated per carbon atom of the graphene layer. Comparison of X-ray photoelectron spectra for potassium metal, graphite and C8K shows that the fractional occupancy of the K 4s level in C8K is less than 0.04e (Preil and Fischer, 1984). Thus the charge is completely transferred to the graphite levels and the formula should be written as fC81 ½K þ1 g. This result is in agreement with Korringa–Kohn–Rostoker type calculations (Di Vincenzo and Rabii, 1982).

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

529

XPS 1253.6 eV

C 1s

80 K

C8Rb

C8K

graphite

292 [eV]

289

286 Binding energy

283

Fig. 9.7. High resolution carbon 1s spectra of HOPG and Stage 1 potassium and rubidium graphites. The GIC spectra are not corrected for the Fermi-level shift. (Reproduced from Schlo¨gl, 1992.)

Our assessment of the present situation is based on the conclusions reached in a review by Schlo¨gl (1992), who gives an excellent summing-up of the (often conﬂicting) results of different photoemission experiments; we give a number of quotations from this review. The experimental methods considered were ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS) and soft X-ray emission spectroscopy (SXS). Although both donor and acceptor GICs were discussed by Schlo¨gl, we consider here only the donor GICs. The emphasis was on the determination of charge transfer ‘‘which is adequately dealt with by electron spectroscopy because [this] . . . can probe the electronic structures of both host and guest.’’ Nevertheless, the results of the large body of work carried out between the 1970s and 1990s can only be described as disappointing in their lack of deﬁnitive and unambiguous conclusions. An initial reason is that mild intercalation conditions and well deﬁned samples are essential requirements for spectroscopic (and other) studies. ‘‘In photoemission spectroscopy [because it is a surface technique] the use of well-deﬁned and in situ cleaved samples [under UHV conditions] from HOPG is absolutely necessary for work on donor GICs.’’ The line proﬁle of the carbon 1s XPS emission line is strongly inﬂuenced by the presence of intercalated alkali metals; the sharp line from HOPG undergoes considerable asymmetric broadening in C8K and C8Rb (Fig. 9.7). The explanation is not clearcut, and we give some detail in order to illustrate that ‘‘the easy way of comparing spectra between pristine graphite and GICs and interpreting the differences as intercalation-induced shifts is rather dangerous.’’ The early suggestion that the broadening stems from interaction of the metal atoms with chemically nonequivalent carbons has not withstood critical

530

INTE RCAL ATION C OM PLEXES

examination, nor does it appear that the charge transfer process is responsible. This is because XPS does not directly probe the electronic ground state of the system, but results from transitions between the ground state and various superposed excited states, both sets of states being altered by intercalation, but not in a presently quantiﬁable way. Both SXS and UPS show a new peak (additional to graphite) at the high energy end of the X-ray spectrum (Fig. 9.8 below) (or the low energy end of the UV spectrum (Fig. 9.9 below)). This new peak is the conduction band peak formed by hybridization between graphite states and alkali s states. The following conclusions were drawn from SXS, UPS and XPS experiments on donor GICs: 1. 2. 3. 4. 5.

Charge transfer in dilute donor GICs can be described within the rigid band approximation. The model of intercalation-induced shifting of the Fermi edge through the graphite valence band is qualitatively correct. In concentrated donor GICs, strong nonrigid band effects can be observed. The charge transfer in these GICs is not unity; i.e. the donor atoms are not completely ionized. The charge transfer involves rehybridization of both the graphite states and the alkali s/p states and leads to a covalent alkali-graphite bond. [The basis for this conclusion is] ‘‘ . . . the indisputable fact of the absence of K 4s states in the SXS experiment may well arise from a covalent type of interaction between alkali metal and graphite, leading to a rehybridization of the graphite valence states with alkali states.’’

If there is covalent bonding between metal atoms and carbons of the graphene sheets, then this should surely become apparent in the spatial relations between such bonded atoms (bond lengths and angles, displacements of carbons from graphene sheets). However, there is no mention of such effects in the large body of crystallographic work reported. Is this because the effects do not exist or because the limitations of the crystallographic studies do not permit their detection? 9.2.2.4 Alkali-metal GICs with double layers of intercalates (‘‘Superdense GICs’’) The rationale behind the preparation of these phases is interesting (El Gadi, Herold and Lagrange, 1993). Ternary phases of compositions such as C4KH0.8 and C4KHg had been prepared and it was inferred that the double layer sheets of metal were being stabilized by comparatively large amounts of elements of moderate electronegativity – would not a small amount of an element of high electronegativity, such as oxygen, ﬁll the same role (El Gadi, Herold and Lagrange, 1993)? Quasi-ternary phases, containing ‘superdense’ intercalated metal and a small amount of oxygen as stabilizer, have been synthesized; for example, the quasi-binary GIC C4Rb has intermediate double layers of Rb, stabilized by small amounts of oxygen atoms (Herold, El Gadi, Mareche and Lagrange, 1994b) and C4K (actual composition C4K1.05O0.074) has a similar double-layer structure (Herold, El Gadi, Mareche and Lagrange, 1994a; El Gadi, Herold and Lagrange, 1994); ﬁve different phases were observed, identiﬁed via their c-axis spacings. The similar 00‘ reﬂections suggested similar layer arrangements, but the (well-deﬁned) hk0 reﬂections, are different

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

531

SXS potassium graphite C8K

265

energy

275

(eV)

285

graphite

Fig. 9.8. Soft X-ray carbon emission spectra for Stage 1 potassium graphite (top) and pristine graphite (bottom). The and bands have been deconvoluted from two measurements at different orientations. The (0001) surfaces were oriented at 80 and 20 to the incident polarized synchrotron beam. Data were taken from in situ cleaved surfaces at 78K. (Reproduced from Schlo¨gl, 1992.)

SXS

285

Fermi edge

(eV) 285 photon energy

UPS 408 eV

5 (eV) 0 binding energy Potassium graphite C8K 10

Fig. 9.9. Comparison of SXS and direct valence band spectra (UPS) for Stage 1 potassium graphite, showing the assignment of peaks and the cross-section effects in UPS. Note the symmetry of the conduction band feature containing the Fermi edge. (Reproduced from Schlo¨gl, 1992.)

532

INTE RCAL ATION C OM PLEXES

for each phase, thus indicating different K atom arrangements in the layers. The -phase was the most easily obtained of these phases; crystal data are given in Table 9.2. The purple ﬁrst stage complex of composition C4K1.25O0.63 and interplanar spacing ˚ , prepared from HOPG graphite and oxidized K (360 C, 69 hours), has intercalated 8.48 A sheets of two superimposed K layers surrounding a central O layer, which appears to be somewhat puckered. This phase is stable under ambient conditions (Goutfer-Wurmser, He´rold and Lagrange, 1995). It should probably be considered to be a ternary phase because of the relatively large amount of oxygen present.

9.2.3

Alkali metals as guests (preparation at high pressures)

9.2.3.1 Dense alkali metal GICs The limiting composition of GICs is C2M or C3M, depending on the nature of M, but it has not been possible to prepare these compositions under ambient conditions. An important recent development has been the synthesis, under pressure, of dense alkali-metal GICs (Belash, Zarikov and Pal’nichenko, 1989; Nalimova, Avdeev and Semeneko, 1992). These new materials superconduct at temperatures up to 5K. They also have striking colors – for example, Li and Cs GICs with compositions C2Li–C4Li and C4Cs were found to be bright yellow in color, somewhat lighter than the classical C6Li and C8Cs phases (Gue´rard and Nalimova, 1994). A sample prepared from HOPG graphite and metallic Li by heating at 280 C under a pressure of 50–60 kbar for 2–3 hours had the composition C72Li27, and fair agreement with the experimental X-ray diffraction pattern was found on the basis of a hexagonal cell p ˚ (Ic(C6Li) is the layer repeat found in with a ¼ (2aG 3) ¼ 8.63, c ¼ 3Ic(C6Li) ¼ 11.10 A C6Li) (Nalimova, Gue´rard, Lelaurain and Fateev, 1995). There are equilateral triangles of ˚; a Li atoms, parallel to the carbon layers, with very short Li–Li distances of 2.5 A cluster of seven Li atoms lies epitaxially on a substrate of 24 carbon atoms. This structure proposal is supported by IR and NMR evidence (Conard, Nalimova and Gue´rard, 1994); problems are caused by the limited stability of the synthsized samples. There is some evidence for the formation at high pressures and temperatures (up to 900 C, 50 kbar; DTA and XRD study) of Na GICs; depending on conditions either single or double intercalated layers of Na were obtained (Udod, Orman and Gewnchel, 1994). C6K and C4K phases have been synthesized at high pressure (8–10 kbar, 160 C; similar results for Rb) but decompose reversibly, on reduction of the applied pressure to less than 1.5 kbar, to a mixture of potassium and C8K (Fischer and Kim, 1985; Nalimova, El Gadi, Gue´rard, Lagrange, Sklovsky and He´rold, 1995). These phases, unstable under ambient conditions, contain single intercalated layers of close-packed potassium atoms. They are superconducting at helium temperatures. The phase C4K1.05O0.074 containing double layers of potassium (see above) transforms to single-layer C4K under a pressure of 10 –15 kbar (Nalimova, El Gadi et al., 1995). In contrast to the C6K and C4K phases, C4Cs does not decompose on release of pressure. Its diffraction patternpcan be explained in terms of a simple orthorhombic cell with ˚ ; there are rows of Cs a ¼ (2aG) ¼ 4.945, b ¼ (2 3aG) ¼ 8.565, c ¼ 4I(C4Cs) ¼ 23.48 A ˚ apart (Gue´rard and Nalimova, 1994). The Cs atoms in C4Cs appear to be atoms 2.46 A in a state of unusual compression as the distance between Cs atoms in C4Cs is similar to

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

533

that in the CsV phase, stable above 100 kbar (Takemura and Syassen, 1985). For com˚ , while the parison, we note that the Cs radius in metallic Cs at room pressure is 2.66 A ˚ ionic radius is given as 1.69 A. There are distinct differences between the Auger spectra of C8Cs and C4Cs (Nalimova, Semenenko, Avdeev, Gall, Mikhailov, Rut’kov and Tontegode, 1992), which have been ascribed to directional bonding between Cs atoms similar to that postulated for CsV. There is apparently much less Cs to graphene charge transfer than in C8Cs. This whole area is in a state of rapid development. 9.2.4 Alkaline earth and lanthanide metals as guests Two preparation methods were used in earlier work on the formation of stage 1 C6M GICs (M ¼ Ca, Sr, Ba, Ln): (1) (2)

direct action of metal vapour on graphite, in sealed metal tubes; heating of compressed mixtures of the powdered components (Gue´rard, Chaabouni, Lagrange, El Makrini and Herold, 1980; El Makrini, Gue´rard, Lagrange and Herold, 1980).

In a later development graphite was reacted at temperatures below 400 C with lanthanide metals suspended in molten chlorides, the advantage being the avoidance of carbide formation p (Hagiwara, Ito and Ito, 1996). The GICs are all isomorphous (Table 9.2) with a 3aGr, c 2Ic, space group P63/mmc. There are twelve C atoms in Wyckoff positions i (symmetry m; x, 0, 0, etc., x 1/3), and two M atoms in regular fashion in two of the three positions of symmetry 6 m2 (e.g. b; 0, 0, 1/4, etc.). The stacking is . . . AA . . . (Fig. 9.10). The C–C bond lengths in the graphene sheets are hardly different from those in graphite but the M–C distances are appreciably shorter than those calculated using ionic radii for Mnþ (n ¼ 2 for alkaline earths; n ¼ 2 or 3 for Ln), and approximate to the M . . . C distances found in the metallocenes (Table 9.5, where M ¼ Nd is the only example given here for the lanthanides but a more extensive compilation is available in Hagiwara, Ito and Ito (1996)). The values given in Table 9.5 suggest that there is a resemblance between the C . . . metal bonding in organometallics, now considered covalent in nature, and that in GICs. Thus an ionic model for these GICs would be inappropriate. 9.2.5 Halogens as guests 9.2.5.1

Introduction ˚ ), The bond lengths in the halogen and some binary interhalogen molecules are F2 (1.44 A ˚ ), Br2 (2.28 A ˚ ), I2 (2.66 A ˚ ), ICl (2.33 A ˚ ), IBr (2.47 A ˚ ). Comparing these values Cl2 (1.99 A ˚ in the graphene net, one sees that ICl and IBr with the center-to-center distance of 2.46 A have the most favourable sizes if epitaxial interaction of undissociated halogen is the determining factor, while Br2 and I2 are on the borderline. Furthermore, it seems unlikely that undissociated F2 and Cl2 would form stable intercalates. The facts are that ﬂuorine and bromine readily form GICs, iodine with difﬁculty, and claims and counterclaims, which we shall not discuss in detail, characterize the uncertainty about the existence of GICs of chlorine. The ﬂuorine, bromine and iodine monochloride GICs are considered separately.

INTE RCAL ATION C OM PLEXES

534

b a

g

c

A a A b b

A

a

Fig. 9.10. The crystal structures of the isomorphous stage 1 C6M GICs (M¼Sr, Ba, Ln) whose crystal data are given in Table 9.2. (Reproduced from Hagiwara, Ito and Ito, 1996.)

˚ ) calculated under various assumptions for the isomorphous Table 9.5. Values of d(C–M) (A (M ¼ Ca, Sr, Ba, Ln) complexes GIC

Ionic radius M2þ

Calculated d(C–M2þ) for ionic model

Typical d(C–M) in organometallics

Measured d(C–M) in GIC

C6Ca C6Sr C6Ba C6Nd

0.99 1.13 1.35

2.95 3.07 3.28 3.17 3.05 (Nd3þ)

2.69 2.75* 2.99 2.75

2.69 2.86 2.99 2.75

* This value is from electron diffraction; the other values are from crystal structure analyses.

9.2.5.2

Interaction of ﬂuorine with graphite

‘‘The reaction of ﬂuorine is rather the limit, leads to compounds in completely destroyed, leading to a Selig and Ebert’s (1980) excellent

different from that of the other halogens and, in which the aromatic graphite layer structure is perﬂuorocyclohexane net.’’ This statement, from review of the chemistry of graphite intercalation

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

535

compounds, represents the situation as of 1980. More recent work has provided considerable ampliﬁcation. The main point is the competition between the formation of strong covalent C–F bonds in covalent carbon ﬂuorides and weak semi-ionic C–F bonds in GICs. Two types of ‘perﬂuorocyclohexane net’ are known – white (CF)n, obtained at around 600 C and dark brown (C2F)n, obtained at 350–400 C. The structures of these covalent carbon ﬂuorides have been described by Touhara, Kadono, Fujii and Watanabe (1987) (after many earlier suggestions, starting with Ru¨dorff and Ru¨dorff (1947)); the densities of (CF)n and (C2F)n are 3.0 g cm3. Although Touhara et al. call them GICs, we do not think this appropriate and they are mentioned here only to be contrasted with the black planar-sheet ﬂuorine GICs of compositions CxF with x > 1.3 prepared by a variety of room-temperature methods (Nakajima, 1991; Groult, Devilliers, Chemla and Nakajima, 1993; Amine and Nakajima, 1993; Tressaud, 1994). The detailed nature of the ﬁnal product (composition, stage number) strongly depends on the rate of ﬂuorine intercalation and the type of graphite employed as host. Highly-puriﬁed F2 gas does not react with graphite below 300 C but addition of less than 30% (gaseous) HF gives rapid reaction even at room temperature; species derived from the HF must be removed at a later stage. Alternatively, the graphite can be added to anhydrous liquid HF, through which F2 is bubbled (Amine, Nakajima and Motoyama, 1993). Solid ﬂuorine-containing compounds of various kinds have also been used to improve the kinetics of the intercalation. As an initial example we consider the CxF GICs prepared in liquid HF at ambient temperature by chemical ﬂuorination of Stage II and III ﬂuoroarsenate GICs with F2. The cell dimensions for various compositions are given in Table 9.6; the measured density of C1.3F was 2.6 g cm3. The crystallographic, IR and ESCA results ‘‘are compatible with the proposal that the oxidatively inert, black C1.3F and its relatives are based on an sp2 carbon atom network like that of the parent graphite, to which the F atoms ˚ . However, a detailed structure are bound semi-ionically;’’ the C–F bond length was 1.7 A was not proposed (Hagiwara, Lerner and Bartlett, 1989). In earlier work (Mallouk and Bartlett, 1983; Mallouk, Hawkins, Conrad, Zilm, Maciel and Bartlett, 1985), compounds of composition CxF1-(HF) (x/ 12; e.g. C2.05F0.82(HF)0.18) were studied by Raman, NMR and IR spectroscopy. The graphene sheets were found to be very similar to those in pristine graphite, single ﬂuorine atoms were attached to carbon through weak semi-ionic ˚ . The HF moieties were most bonds, and the domain size was in the range of 50–100 A likely linked to C–F ﬂuorines through hydrogen bonds. Samples prepared by reaction (over a period of days or weeks) of ﬂowing F2 gas with HOPG or natural graphite ﬂakes at room temperature in the presence of AgF, SbF5 or WF5 appear to have more complicated structures than that of C1.3F (Nakajima, Molinier and Motoyama, 1991). The c-axis structures proposed for Stage 1 CxF GICs are shown in Fig. 9.11. It was suggested that graphene layers separated by an intercalated layer have an AA relationship while adjacent graphene layers are AB. The 00l powder patterns corresponding to different structure proposals have been calculated by Nakajima and Tamura (1995) using a procedure due to Pilyankevich (1992); reasonable agreement was obtained with the measured powder patterns. Details of the in-plane arrangement depend on the amount of ﬂuorine present. The para positions of half of the carbon hexagons are occupied at C4nF (n ¼ stage number), the meta positions

INTE RCAL ATION C OM PLEXES

536

˚ ) for planar sheet fluorine GICs and puckered sheet Table 9.6. Comparison of cell dimensions (A covalent carbon fluorides (from Hagiwara, Lerner and Bartlett, 1989) Compund

a

c

Planar-sheet ﬂuorine GICs C1.3F C2F C2F C3F C4F C6F

2.478(2) 2.472 2.459 2.459 2.458

6.40(5) 5.9 5.9 5.5 4.7

Puckered sheet covalent carbon ﬂuorides (CF)n (C2F)n

2.53–2.57 2.51

6.0 2 8.1 2

(a)

C4F ~ C2F C4F ~ C2F

6.0 Å 4.7 Å

Ic = 10.7 Å

(b)

C4F ~ C2F C2F ~ CF

6.0 Å 5.7 – 6.0 Å

Ic = 11.7–12.0 Å

C2F ~ CF C2 ~ CF

5.7 – 6.0 Å 5.7 – 6.0 Å

Ic = 5.7–6.0 Å

(c)

Fig. 9.11. Structures proposed for Stage 1 CxF GICs prepared from HOPG or natural graphite in the presence of AgF, SbF5 or WF5. The thick lines represent graphene layers, the complete circles ﬂuorine ions, and half-circles semi-ionically (sometimes called ‘‘semicovalently’’) bonded ﬂuorine. ˚ (ionic The spacing for the ionic intercalate is calculated as 3.34 A (graphene layer) þ 2.66 A ˚ . The spacing for the semi-ionic intercalate is calculated as 1.7 A ˚ diameter of F) ¼ 6.0 A ˚ (half-thickness of graphene layer) ¼ 4.7 A ˚ . The maximum spacing ˚ (r(F) þ 1.67 A (d(C–F) þ 1.33 A ˚ (d(C–F)) þ 1.33 A ˚ (r(F))} ¼ 6.06 A ˚ ; nestling of for the bi-intercalate is calculated as 2{1.7 A ﬂuorines will reduce this value. In practice, the Ic values (given on the right) are measured from 00‘ powder diffraction patterns (which are not very sharp) and the layer structures inferred from these values. (Reproduced from Nakajima, Molinier and Motoyama, 1991.)

of half of the carbon hexagons at C2.7nF and the meta positions of all the carbon hexagons at C2nF. The symmetry is hexagonal (or almost so) and a ¼ 2aG at the lower concentrations, and a ¼ aG at C2nF (see Fig. 4 of Nakajima, Molinier and Motoyama (1991)).

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

537

9.2.5.3 Interaction of bromine with graphite ‘‘The intercalation of bromine in graphite takes place at room temperature merely on immersion of the graphite in bromine liquid or vapour’’ (Eeles and Turnbull, 1965). The kinetics of absorption and desorption of liquid bromine by natural single-crystal graphite (from Ticonderaga Mine, N. Y., U. S. A.) are shown in Fig. 9.12; however, it should be noted that the time to reach the limiting composition C8Br depends very much on the nature of the graphite and its state of subdivision and can vary from that shown to more than 1000 hours (Saunders, Ubbelohde and Young, 1963a, b). The absorption and desorption curves appear to be continuous and do not show the composition steps usually associated with the appearance of particular phases (cf. the dehydration of CuSO45H2O shown in Fig. 197 of Glasstone (1947)). The structural situation is complicated; Chung (1986) lists the following phases: and " are commensurate phases, and there are incommensurate phases designated as and ’ (which are rather similar), , . The various phases have been studied by X-ray diffraction (including use of synchrotron sources; summarised with extensive references by Chung, 1986) and by electron diffraction and microscopy (Eeles and Turnbull, 1965; Heerschap, Delavignette and Amelinckx, 1964); a temperature range of 100–350K has been covered. Detailed structure analysis has been reported for the Stage 4 complex (limiting composition C28Br), using a combination of XRD and ED (Eeles and Turnbull, 1965). Reﬂections were found to be sharp in the a* and b* directions but inﬁnite in extent and unmodulated along c*. From this (and other details of the diffraction patterns) it was

Graphic-bromine compounds

80

C8Br

absorption

weight (%)

60 C14Br 40

20

0

C28Br

desorption

10

20

30

time (h)

Fig. 9.12. Change in weight as a fraction of the original weight for a sample of graphite during the absorption and desorption of gaseous bromine at room temperature. (Reproduced from Eeles and Turnbull, 1965.)

538

INTE RCAL ATION C OM PLEXES

inferred that the bromine atoms were ordered in two-dimensional layers of monoatomic thickness between the (essentially unchanged) graphene layers, with a random translational element of stacking along the graphite a direction. From the distances between bromine atoms, it was inferred that there were zigzag chains of strongly interacting bromine molecules along the [1 100] direction. Another conclusion was that the graphene layers above and below a bromine layer had an AA relationship, but that other graphene layers were in C positions. Eeles and Turnbull noted that the Stage 2 complex (limiting composition C8Br) had the same layer sequence as the Stage 4 complex and hence the additional bromines had to be accommodated by addition of bromines to the Stage 4 layer. A detailed structure for the Stage 2 (C8Br) complex was proposed by Ghosh and Chung (1983) on the basis of intensity measurements for some twenty reﬂections using synchrotron ˚ ); the value of RF, after reﬁnement, was 22%. Polymeric radiation ( ¼ 1.274 A chains of bromines were found along the graphite [1100] direction; in an overall sense, this structure was not very different from that proposed by Eeles and Turnbull. Ghosh and Chung suggested, on the basis of distances between bromine atoms, that polybromide ions (Br3, Br5) were present. The interatomic distances inferred from the structure analyses are hardly precise enough to permit ﬁrm chemical conclusions to be drawn, but the polybromide model is supported by the main intercalate Raman frequency of 242 cm1, to be compared with 323 cm1 in Br2 vapor and 300 cm1 in solid Br2. 9.2.5.4

Interaction of iodine with graphite

It had been concluded that iodine does not intercalate with graphite in the 78 to 950 C range (Salzano, 1964). However, more recent work (Hung and Kucera, 1994) has shown that it is possible to intercalate iodine into the residue compound of bromineintercalated graphite (C28Br; Juza, Jonck and Schmeckenbecher, 1957); GICs of composition CBrxIy (1 < y/x < 10) were obtained. The diffraction pattern of the GIC derived from HOPG graphite showed a large number of new peaks, all of which suggested ˚ apart; a detailed structure that the two carbon layers containing intercalates were 7.25 A has not yet been proposed. 9.2.5.5 Interaction of binary interhalogen molecules with graphite Both iodine monochloride and iodine monobromide form stage I GICs, with limiting compositions C8ICl and C8IBr; higher stage GICs have also been prepared. A stage I GIC, with approximate composition C8ICl, was prepared by the two-bulb vapor-phase method described above; analysis of the diffraction patterns gave a 3-fold or 6-fold twinned ˚ , ¼ 93.3 ). An analogous complex monoclinic superlattice (a ¼ 4.92, b ¼ 42.7, c ¼ 7.0 A prepared in liquid ICl was better crystallized but the diffraction pattern could not be analyzed (Ghosh, Gangwar and Chung, 1984). In contrast to the bromine GICs, the ICl GICs are well crystallized in the c direction, the diffraction patterns having sharp 00l peaks; analysis of intensity measurements gave vibration amplitudes in the c direction (Abe, Mizutani, Shinoda, Ihara, Asano, Harada, Inaba and Ogumi, 1995). However, no structures have yet been proposed.

INTERCALATION COMPLE XES OF GRAPHIT E (GICs)

539

9.2.6 Uses, actual and potential, of GICs Light weight rechargeable batteries are in great demand for use in portable electronic equipment (Pistoia, 1994; Besenhard, 1994). Graphite, which is a widely available and low cost material without environmental impact, has been considered as host lattice for the electrodes of such batteries in preference to inorganic substrates. Lithium metal has been used as a negative electrode but suffers from the disadvantages of high reactivity of the metal with the electrolyte, and dendritic growth on recycling. One of the proposed solutions is to use the lithium GIC C6Lix (0 x 1) as cathode, although its Faradaic capacity (370 mAh/g) is only about one-tenth of that achievable with metallic Li as electrode; indeed such batteries are now being mass produced (Nagaura and Tozawa, 1990). This idea can be extended towards the goal of a graphite-based metal-free battery. A positive electrode consisting of 80% natural graphite and 20% polypropylene has already been used in conjunction with inorganic negative electrodes (C6Liþ/MnO2 or Pb/ C24HSO 4 ). More recently the inorganic electrodes have been replaced by a blend of anthraquinone and carbon black, using either an aqueous electrolyte with 8M HBF4 or a nonaqueous system with 0.2M LiClO4 in propylene carbonate (Beck, Boinowitz, Krohn, Tormin and Ther, 1994). Some preparatory studies of the use of GICs as catalysts have been made; speciﬁcally the oxidation of ethylbenzene to styrene has been studied using Pb– and K/Bi–GICs (Klimkiewicz and Morawski, 1994). Graphite-metal compounds have been described as ‘‘more than just sponges which gradually release the intercalated species; instead they are new and most promising reagents or catalysts for both inorganic and (metal) organic reactions’’ (Csuk, Gla¨nzer and Fu¨rstner, 1988).

9.2.7 Summary for GICs Surveying the information available on GICs (and that given above is only a small fraction of the whole), one is struck by how many different materials have been prepared, the wide variety of methodologies used for their characterization, the many physical properties that have been studied, the range of theoretical methods that have been applied, and the practical uses that have evolved exploiting the unique properties of GICs. And yet, one has a feeling of disappointment, or, at least, of expectations unfulﬁlled. If one takes the simplest of the GICs, those with alkali metals as intercalates, crystal structures have been determined for a wide range of materials prepared under a wide range of conditions, but neither physical measurements nor theoretical calculations give us a clear picture of the nature of the interaction between host and guest. How much charge transfer occurs, and what is the role of covalent bonding? The discrepancy between experimental ﬁndings and understanding grows larger as the guests become more complicated. In part this is a consequence of the very complex real structures of the materials involved. The experimental investigations, structural and physical, are made on samples that deviate very considerably from the simpliﬁed models on which the interpretations are based. Perhaps one needs to repeat many of the earlier experiments on samples that have been much more carefully prepared and deﬁned than those used earlier in the ﬁrst ﬂush of enthusiastic progress, and compare these results with those from the ever-more powerful computational methods that seem to become available without respite.

INTE RCAL ATION C OM PLEXES

540

9.3 9.3.1

Intercalation complexes of inorganic hosts Introduction

A number of inorganic materials form intercalation complexes, in which the host layers are many atoms thick, contain functional groups of various types and are usually negatively charged. We ﬁrst consider overall properties which do not depend on the nature of the layers, with a few speciﬁc layer types being considered below. This group of intercalation complexes is usefully contrasted with the graphene layer type, with its singleatom thickness (in stage 1 materials) and its (at least partially) delocalized interaction with the intercalated atoms. Some inorganic intercalation complexes contain in their pristine state alkali or alkaline earth cations, possibly together with water molecules, while in the expanded state these smaller inorganic cations are replaced by larger organic cations such as tetraalkyl ammonium salts, or neutral molecules (Fig. 9.13). The layers themselves can have a variety of chemical identities (Clearﬁeld, 1994; Clearﬁeld and Constantino, 1996), which allows both a range of properties and their ﬁne tuning. It was ﬁrst reported in 1955 that smectic clays can be expanded and made permanently porous on a molecular scale (Barrer and McCleod, 1955). The induced porosity allows these materials to act as molecular sieves and as catalysts, but with the disadvantage of instability (loss of guest species) at higher temperatures. This can be overcome by introduction of pillars, preferably inorganic in character because of greater temperature stability, which hold the layers apart (Thomas and Theocharis, 1991). 9.3.2

2H- -TaS2 as host

Many transition metal dichalcogenides and disilicides TX2 (Hulliger, 1968; Wilson and Yoffe, 1969; Rouxel, 1996) form intercalation complexes, which have been widely studied. We concentrate here on the 2H polytype of tantalum disulﬁde (–TaS2) as host material;2 this has attracted interest because of its catalytic properties, because it exhibits charge-density waves and because of its intercalation capabilities. The intercalates have attracted especial interest because they are superconducting, although only at very low temperatures (Gamble, DiSalvo, Klemm and Geballe, 1970; Gamble, Osiecki, Cais, Pisharody, DiSalvo and Geballe, 1971; Gamble, Osiecki and DiSalvo, 1971). The superconductivity is considered to be two-dimensional in nature and conﬁned to the metallic layers, the intercalation having relatively little effect on the values of Tc. ˚, TaS2 is polytypic, the -polytype being hexagonal (a ¼ 3.314(1), c ¼ 12.097(1) A space group P63/mmm, Z ¼ 2); there is trigonal prismatic coordination of S about Ta with ˚ and the distance between ˚ . The TaS2 sandwich height is 3.116 A d(Ta–S) ¼ 2.468 A ˚ . Using the standard notation for the close packing of neighboring sandwiches is 2.932 A spheres, the structure of 2H–TaS2 is AbA CbC, where the capital letters refer to the sulphur atoms and the lower case letters to the metal atoms, and the van der Waals gap is shown by a space. Bonding within the layers is strong and primarily covalent; that between the layers is usually described as mainly ‘van der Waals type.’ Earlier structural 2 We also consider some results from the structurally analogous SnS2 complexes, Sn not being a transition metal.

INTERCALATION COMPLEXES OF INORGANIC HOSTS

+ = Na+, Ca2+ etc.

+

= organic cation

+

+

+

d3

+

+

d1

+

541

Out gassed parent

d2

Permanently expanded and porous clay

Fig. 9.13. The upper diagram shows the intercalation material in its pristine state, the host layer being represented by the hatched areas. The expanded material is shown in the lower part of the diagram. (Reproduced from Barrer, 1986.)

ba

Fig. 9.14. The crystal structure of 2H–TaS2, viewed in projection normal to the hexagonal axis; the smaller spheres are Ta and the larger S. The van der Waals gap, into which guest molecules are ˚ ), as well as the trigonal prismatic coordination of S intercalated, is shown (d(S . . . S) ¼ 3.501 A ˚ ; d(S . . . S) ¼ 3.314 A ˚ ; for clarity, some atoms have been omitted about Ta (d(Ta . . . S) ¼ 2.468 A from the coordination sphere). (Diagram based on data from Meetsma, Wievers, Haange and de Boer, 1990.)

studies on powder samples have been conﬁrmed by a single crystal study (Meetsma, Wievers, Haange and de Boer, 1990). A number of intercalation complexes have been prepared and crystal data determined (from polycrystalline samples; Table 9.7), as well as the superconducting onset temperatures. The latter range from 2.0–5.0K. The increase in the c-axis () resulting from the ˚ (or a multiple thereof ) from the c-axis intercalation can be obtained by subtracting 5.2 A value given in Table 9.7.

INTE RCAL ATION C OM PLEXES

542

˚ ) for intercalation complexes of 2H–TaS2, which has cell dimensions Table 9.7. Crystal data (A ˚ . The compositions are all TaS2.(intercalate), with the stoichiometry shown a ¼ 3.314, c ¼ 12.097 A in the Table. This table is based on F. J. DiSalvo, Ph.D. dissertation, Stanford University, 1971 (also see Revelli and DiSalvo, 1979), and updated using Table 2 of Rouxel (1996) and other sources Intercalate

a

c

Intercalate

a

c

butyramide stearamide thiobenzamide

–

11.0 57.0 11.9

aniline N,N-dimethylaniline N,N,N 0 , N 0 -tetraphenyldiamine 4,4 0 -bipyridyl

– – 3.335

18.15 12.45 2 9.66

NH3 1:1 Methylamine 1:0.5 Propylamine Decylamine Pentadecylamine

3.319 3.324 3.330 – 3.328

2 9.10 2 9.236 2 9.66 14.6 45.1

3.323

2 9.52

3.316

2 12.08

quinoline

–

12.08

pyridine 1:0.5 pyridine-N-oxide 2-aminopyridine 1:0.5 2-ethylpyridine 1:0.29 2-phenylpyridine 1:0.25 CsOH

3.326 3.335 3.325

2 12.02 11.97 2 12.09

Ethylenediamine 1:0.25 anthraceney 1:0.18 dibenzotetrathiofulvalene 1:0.55 tetraceney 1:0.58 pentaceney 1:0.66

3.328

2 9.64

3.328

2 11.92

3.330

2 9.28

y

15.44 31.98 30.53 35.78

Averill, Sutto and Fabre, (1994).

TaS2 LAYER

OCTADECYLAMINE 34 Å

Fig. 9.15. Structure of 2H–TaS2 intercalation complex of octadecylamine as inferred from the measured c-axis spacing. Compare Figs. 9.19 and 9.20 below. (Reproduced from Clearﬁeld, 1994.)

INTERCALATION COMPLEXES OF INORGANIC HOSTS

543

Care has to be exercised in assessing early structural studies of these complexes, although this is sometimes the only information available. For example, the location of the nitrogen of NH3 could not be reliably established in an early XRD study of {TaS2[NH3]} (Chianelli, Scanlon, Whittingham and Gamble, 1975). One of the ﬁrst complexes to be studied in some detail was Stage I 2H{TaS2[(pyridine)1/2]}; Stage II 2H-{TaS2[(pyridine)1/4]} has also been prepared, although not in completely pure form (Gamble, Osiecki, Cais, Pisharody, DiSalvo and Geballe, 1971). Care has to be taken to prepare these complexes under anhydrous and anaerobic conditions as the effects of moisture are not well understood (Lomax, Diel and Marks, 1985). Some remarkable electron micrographs of these complexes have been published (Fernandez-Mora´n, Ohstuki, Hibino and Hough, 1971). A neutron diffraction study (Riekel and Fischer, 1979) of polycrystalline samples (at 372K) of 2H{TaS2[(C5ND5)1/2]} showed the pyridine centred about z ¼ 0.5 and oriented with the molecular plane perpendicular to the TaS2 sheets and the pyridine twofold axis parallel to them (see lower right diagram in Fig. 9.16); this conclusion was based on a onedimensional Fourier synthesis alongc, using ten 00l reﬂections (Fig. 9.16). Although there is no doubt about the correctness of the inferences drawn from this pioneering study, it hardly constitutes a crystal structure determination in contemporary terms. A room temperature neutron diffraction study (Riekel, Hohlwein and Scho¨llhorn, 1976) of single crystals of the (analogous) 2H-{NbS2[(pyridine)1/2]} (with C5NH5 and C5ND5) showed that the complex had overall symmetry lower than hexagonal (deduced from the presence of additional reﬂections in the diffraction patterns), but details were not given. The location and orientation of the pyridine was the same in both structures, and also agrees with that inferred from a 2H NMR study of 2H-{TaS2[(perdeuteropyridine)1/2]} over the temperature range 280–385K (McDaniel, Barbara and Jonas, 1988). This

F2rel 100 80 60 40 20 0 100 80 60 40 20 0

NbS2 (C5D5N)0.5 single crystal

F2calc 100 N 50

N

(TaS2) ∞ c (TaS2) ∞

0 TaS2 (C5D5N)0.5 powder

(TaS2) ∞ c

100 N 50

2 4 6 8 10 12

(00l )

0

(TaS2) ∞ 2 4 6 8 10 12 (00l )

Fig. 9.16. (left) Measured F2 values (same relative scale; 372K) for the 00‘ reﬂections from a single crystal of 2H-{NbS2[(C5ND5)1/2]} and a powder of 2H-{TaS2[(C5ND5)1/2]}, showing that the structures projected onto the c axis are the same. (right) The F2 values calculated for the two models show that only that on the lower right is compatible with the measurements. (Reproduced from Riekel and Fischer, 1979.)

544

INTE RCAL ATION C OM PLEXES

study shows that appreciable molecular libration sets in above 330K about an axis parallel to [0001]. The following mode of interaction of intercalate and host has been suggested for pyridine as intercalalate: 2py ) bipy þ 2e þ 2Hþ xpy þ xHþ ) xpyHþ xpyHþ þ ð0:5 xÞpy þ xe þ TaS2 ) pyHþ ð0:5 xÞpy þ TaSx 2 The structural evidence available is not adequate for testing such a proposal. However, magnetic studies on 2H-{TX2[MCp2]0.25} complexes indicated (Dines, 1975) that intercalation was accompanied by ionization of host and guest: 1=4

0:25MCp2 þ TX2 ¼ fTX2

½MCþ p2 0:25 g

Pyrrole is another intercalate, and microcrystalline powders of {TaS2[0.5(C4NH5)]} have been prepared by standard methods (Revelli and DiSalvo, 1979) and shown to be ˚ , with an onset superconducting temperature of hexagonal, a ¼ 3.314(1), c ¼ 22.256(7) A 7.5K (Gamble, Osiecki, Cais, Pisharody, DiSalvo and Geballe, 1971). Space group and location of the intercalated pyrrole were not reported. It was surmised that the facile polymerization of pyrrole both provided the charge transfer required for the stabilization of the intercalation complex and the charge required for the conduction. The problems involved in the determination of the detailed structures of intercalation complexes have already been outlined in the Introduction to this Chapter (‘‘the high degree of disorder inherent in the ab plane of the crystals result[s] in broad peaks for the non-00l reﬂections of their diffraction patterns’’ (Wong, Evans, Barlow, Mason and O’Hare, 1994)). These authors suggest as remedies: (1) one-dimensional reﬁnement of Xray and/or neutron diffraction data to determine the orientation of the guest molecules with respect to the MS2 layers (cf. Fig. 9.16), and (2) 2H solid state NMR studies of ‘‘single’’ crystal samples. The ﬁrst three-dimensional crystal structure determination of a TX2 intercalate (2H-{SnS2[5-Co(C5H5)]0.31}) was reported only in 1991 (XRD, 177 hkl reﬂections; O’Hare, Evans, Wiseman and Prout, 1991). O’Hare et al. deduced, from the detailed form of the diffraction patterns, that ‘‘the crystal is made up of relatively well ˚ thick and prone to periodic stacking faults along the c ordered slabs, which are ca. 200 A axis. The total smeared pattern is then made up of many sharp patterns, due to the individual mosaics, superposed with different ! translations.’’ [We note that a thickness of ˚ along c (10 unit cells) is unlikely to produce sharp 00l reﬂections; perhaps 2000 A ˚ 200 A ˚ , and the doubling of c was was intended]. The unit cell was 3.62 3.62 22.36 A ascribed to a shift of SnS2 layers (compared to the pristine host) along both a and b directions; the space group was not given explicitly. The parallel orientation of the metallocene was conﬁrmed using the ten observed 00l reﬂections measured by XRD (Rparallel ¼ 0.137, Rperpendicular ¼ 0.347) and time-of-ﬂight ND (Rparallel ¼ 0.106), as in Fig. 9.16. 2H solid state NMR studies on the same material provided direct proof of the parallel orientation from measurement of the doublet splitting when the static magnetic ﬁeld was oriented normal to the (001) planes (136 and 68 kHz calculated for perpendicular and parallel orientations respectively; measured 68 kHz (O’Hare, 1992; Fig. 9.17).

INTERCALATION COMPLEXES OF INORGANIC HOSTS

(a)

545

(b)

C3

C2

B0 63 kHz

D

B0

C5 D

68 wts

135 wts

+100 +100

0 kHz

–100

+100

0 kHz

0 kHz

–100

–100

Fig. 9.17. The postulated motions for the perpendicular (a) and parallel (b) orientations of cobaltocene in 2H-SnS2 and the predicted 2H NMR spectra when the static magnetic ﬁeld is aligned perpendicular to the basal plane. The experimental spectrum is shown on the right, conﬁrming that the orientation is parallel (b). The spike at 0 ppm is an artefact. (Reproduced from O’Hare (1992).)

The crystal structure of the superconducting intercalate 2H-{TaS2[5-Co(C5H5)]0.25} (ﬁrst prepared by Dines (1975)) has been investigated by XRD using polycrystalline ˚ , P3; Rietveld proﬁle analysis, RF ¼ 6.7%, samples (Cu K1, a ¼ 3.330(1), c ¼ 23.040(8) A 25 parameters, 91 reﬂections, 1500 proﬁle points; Evans and O’Hare, 1995). The host layers are highly ordered, intercalation being accompanied by a shift of adjacent TaS2 p layers by a/ 3 along [11 20] compared to their position in the pristine structure. Neutron diffraction, which gives information about the light atoms (C, H, D) not obtainable from ˚ . Dynamics and orientation XRD, suggests that the true cell has a ¼ 6.64(2), c ¼ 22.98(5) A of the guest cobaltocenium ions were followed by variable temperature (20–330K) timeof-ﬂight neutron diffraction on the deuterated guest; the diffraction patterns show that the cobaltocenium ions have a single orientation, with the principal molecular axis parallel to the layers, at all temperatures. An earlier 2H NMR study of polycrystalline {TaS2[5Co(C5H5)]0.25} was interpreted very differently (Heyes, Clayden, Dobson, Green and Wiseman, 1987) but Mu¨ller-Warmuth (1994) has pointed out that this was due to neglect of the inﬂuence of the ﬁeld induced orientation effect on the spectra. Dines (loc. cit.) prepared thirteen 2H-{TX2[5-M(C5H5)]0.25} complexes (X ¼ S or Se, ˚ with respect to the c M ¼ Co or Cr) and found that all showed an expansion of 5.35–5.63 A axis of the host TX2; the results of the crystal structure analysis now conﬁrm Dines’ original proposal ‘‘that the structure is most likely one in which the ﬁve-membered rings of the metallocene are situated perpendicular to the sheets of the host.’’ Among other intercalate complexes are 2H-TaS2[dibenzotetrathio-fulvalene)]0.55}, which crystallizes in an orthorhombicp unit cell (determined from a polycrystalline sample) ˚ (aH is the a axis of the 2H-TaS2 with a ¼ 6.497 (¼2aH ), b ¼ 5.770 (¼ 3 aH), c ¼ 25.91 A hexagonal cell) (Sutto, Averill and Fabre, 1993). Colloidal dispersions of TaS2 intercalates have been prepared and studied (Jacobson, 1996) but are not discussed here because of our emphasis on structure.

546

9.3.3

INTE RCAL ATION C OM PLEXES

Zirconium phosphates and phosphonates as hosts

Recent work has been reviewed (Alberti and Constantino, 1991; Clearﬁeld and Constantino, 1996; Alberti, 1996)). The acronym MELS (Molecular Engineered Layered Solids) has been used to refer to layered materials based on zirconium phosphate and phosphonates. The general formula is {MIV(RXO3)2[nS]}, with MIV ¼ Zr, Ti, Ge, Sn, Pb, and X ¼ P, As; R can be OH or an organic group and S represents solvent which can be H2O; the intercalated species is in square brackets. We remind the reader of the formulae for phosphates and phosphonates. HO

OH

H

P HO

OH P

O

Orthophosphoric Acid H3PO4

HO

O

Phosphonic Acid H3PO3

Ion exchange properties had been found in amorphous zirconium phosphate during World War II (Russel, Adamson, Shubert and Boyd, 1943) and it has become the most widely investigated member of this group after single crystals were prepared by Clearﬁeld and Stynes (1964). The crystal structure of -Zr(HOPO3)2H2O, -zirconium bis(monohydrogen orthophosphate) monohydrate or -ZrP, was ﬁrst determined ˚ , ¼ 111.41(1) , in 1969 (monoclinic, P21/c, a ¼ 9.060(2), b ¼ 5.287(1), c ¼ 16.248(3) A Z ¼ 4; Clearﬁeld and Smith, 1969) and then further reﬁned by XRD (to R ¼ 0.027; Troup and Clearﬁeld, 1977) and by powder neutron diffraction, using the Rietveld method (Albertsson, Oskarsson, Tellgren and Thomas, 1977). A stereoview down [010] is shown in Fig. 9.18; there are layers of Zr atoms (essentially coplanar) and phosphate groups about the ab planes, individual layers interacting only by van der Waals forces. In pristine

Fig. 9.18. Stereoview of a portion of the crystal structure of -ZrP, viewed down the plane of the layers referred to in the text i.e. the ab plane. There are two crystallographically independent tetrahedral (T) phosphate groups in the structure; six phosphate oxygen atoms form a slightly distorted octahedron (O) about each Zr; the T–O–T arrangement is reminiscent of the smectic clays. Note the hydroxyl group, with exchangeable proton, linked to each phosphate, and the water molecules, each with one hydrogen participating in hydrogen bonding, and one not. The hydrogen bonding is only within these layers, not between them. There is van der Waals interaction between the layers and hence these can be pushed apart by the intercalated groups without the integrity of the individual layers being affected. (Reproduced from Troup and Clearﬁeld, 1977.)

INTERCALATION COMPLEXES OF INORGANIC HOSTS

547

˚ , the three phosphate oxygens -ZrP and its analogs, the interlayer spacing is 7.56 A bridge across the metal atoms and the hydroxyl, which provides the exchangeable proton, points into space between the layers. 31P MAS NMR spectroscopy of -ZrP shows only one resonance, although there are two crystallographically independent (but chemicallyequivalent) phosphate groups; this implies that the electronic environments of the two nuclei must be very similar (Clayden, 1987). There is an isostructural titanium analog ˚ , ¼ 110.20(1) , Z ¼ 4) (monoclinic, P21/c, a ¼ 8.630(2), b ¼ 5.006(1), c ¼ 16.189(3) A which has been reﬁned by Rietveld X-ray powder analysis (Christensen, Andersen, Andersen, Alberti, Nielsen and Lehmann, 1990). Among the guests intercalated in -ZrP are diamines, alkanols, glycols, urea, hydrazine, piperidine, pyridine, dimethyl formamide, dimethyl sulfoxide and the amino acids L-histidine, L-lysine and L-arginine (Clearﬁeld, 1994). The process of intercalation is complex and has been described by Alberti and Costantino (1991) together with the synthesis of the intercalated materials; the zirconium phosphate layers maintain their integrity but the interlayer spacing is changed, and the intercalated molecules take up positions and orientations dependent on their size and nature. A representation of possible arrangements of various intercalated alkylmonoamines is shown in Fig. 9.19. It should be OH groups (a)

(b)

+

H3O C5 N

C3

10.4 Å

C1 N

Plane of Zr atoms

C2

C4

16.5 Å

Pentylamine

Plane of Zr atoms

(c)

21 Å

C5 C3 60° 5.3 Å

C1

C4 C2

Pentylamine

N

Plane of Zr atoms

Fig. 9.19. Schematic representations of the most common orientations of alkylmonoamines in the interlayer region of -ZrP. The spacings between the planes of Zr atoms are inferred from the nature of the model and known molecular dimensions. The circles denote hydroxyl groups. (Reproduced from Alberti and Costantino, 1991.)

INTE RCAL ATION C OM PLEXES

548

50 45

Interlayer spacing (Å)

40 35 30 25 20 15 10 5 0 0

5 10 15 Number of carbon atoms

20

Fig. 9.20. Interlayer spacings of intercalated -zirconium phosphate as a function of the number of carbon atoms in the intercalating molecules. The lower group of points are for n-alkanols and the upper group (shifted upwards by 10 A) for n-alkylmonoamines. The formulae of the complexes formed are Zr(HPO4)22RH2O, where R¼CnH2n þ 1NH2 or CnH2n þ 1OH; the distribution of charges between anions and guests is not indicated. The data have been taken from Alberti and Costantino, 1991.

appreciated that representations such as these are inferred from measurements of interlayer spacings by XRD and knowledge of molecular dimensions; they do not have the certainty associated with crystal structure analyses, which await the provision of suitable samples and the solution of various technical problems. Measured interlayer spacings are plotted against number of carbon atoms in the alkyl chains in Fig. 9.20. If one compares the measured interplanar spacings with estimated molecular lengths, then it is clear that there are bilayers of n-alkanol (or nalkylmonoamine) guest molecules between the zirconium phosphate sheets (except for methanol, where the situation shown in Fig. 9.19(a) may apply). ‘Pillared’ -ZrP is obtained by replacing the hydroxyl of monohydrogen orthophosphate by an organic ligand, thus generating a zirconium phosphonate. If the hydroxyls on both sides of a layer are replaced by a bifunctional organic group, then the layers will be separated by organic spacers, the interlayer distance depending on the length of the organic molecule. The lateral bulkiness of the pillaring groups is limited by the ˚ 2 is available at each phosphate group. The inorganic pillaring fact that only 25 A agent, the aluminium Keggin ion [Al13O4(OH)24(H2O)16]7þ, which approximates to a ˚ , has been used with some success in -TiP prolate spheroid with dimensions 9.5 7 A but not in -ZrP (Clearﬁeld and Roberts, 1988). The X-ray diffraction powder patterns shown in Fig. 9.21 are very diffuse and the pillared samples are poorly crystalline (much less crystalline than the phosphate samples themselves, or those intercalated with n-butylamine). Porous pillared titanium phosphates (with Keggin ion as pillaring agent) retained more than 70% of their surface area ( 150 m2/g) after heating to 400 C, whereas unpillared titanium phosphates condensed to amorphous pyrophosphates. Zirconium

INTERCALATION COMPLEXES OF INORGANIC HOSTS

549

Relative intensity

above: alpha ZrP

alpha-Tip

alpha-Tip

gamma-Tip 25°

20°

15° 10° 2 theta (Cu K alpha)

5°

2°

Fig. 9.21. X-ray diffraction patterns of zirconium and titanium phosphates pillared with Keggin ion. The samples were subjected to different treatments. (Reproduced from Clearﬁeld and Roberts, 1988.)

phosphates, on the other hand, were non-porous species in which the Keggin ion pillars appeared to have partially decomposed with consequent ﬁlling of the interlayer space. Complete ﬁlling of the interlayer space would, of course, defeat the object of the pillaring, which is to ensure an environment which will allow selective molecular sieving and catalysis, in addition to enhancing the stability of the intercalates. With this in mind, one aim is to crosslink only a fraction of the functional groups; this is illustrated in Fig. 9.22. Different kinds of monofunctional groups, pendantly linked to the layers, could have the same sort of shape-selective effect (see Albertini and Constantino, 1991, pp. 160–162). -Zirconium phosphate, Zr(PO4)(H2PO4)2 H2O (Fig. 9.23; the Ti analog is also ˚ ) with many known), constitutes a second type of layered material (layer spacing 12.2 A advantageous ion-exchange and intercalation properties (despite the ‘-ZrP, -ZrP’ nomenclature these two materials are not polymorphs). The presence of two types of phosphorus, one belonging to the framework and non-exchangeable and the other more open and able to undergo exchange with phosphate and phosponate esters, was demonstrated by 31P NMR spectroscopy. Two well separated resonances were found and ascribed to chemically-distinct but equally abundant P atoms (Clayden, 1987), leading to the formulation given above. A highly crystalline sample of -ZrP has recently been prepared by hydrothermal methods and its crystal structure (monoclinic, P21, ˚ , ¼ 98.687(2) , Z ¼ 2) determined by a ¼ 5.3825(2), b ¼ 6.6337(1), c ¼ 12.4102(4) A Rietveld powder reﬁnement (Poojary, Shpeizer and Clearﬁeld, 1995). Interlayer spacings

INTE RCAL ATION C OM PLEXES

550

P

C P P

Zr P P

H

P

H

P

P P

Zr P P P

C

Fig. 9.22. Idealized representation of the cavity of a pillared zirconium phosphate in which 50% of the 4,4 0 -biphenyl pillaring groups are replaced by phosphite groups. (Reproduced from Alberti and Costantino, 1991.)

˚ are listed (Alberti and Costantino, 1991) for more than twenty varying from 12.7 to 22.9 A intercalates ranging from alkanols, alkylamines to amino acids and aromatic bases. Pillaring has also been achieved with -ZrP (Alberti, Marmottini, Marcia-Mascaro´s and Vivani, 1994). The recent study (Kijima, Sakoh and Machida, 1996) of the intercalation of 1,4,10,13tetraoxa-7,16-diazacyclooctadecane C12H26N2O4 (tdco) in -and -ZrP gives some ﬂavour of what can be currently achieved in this area. The aim of the research is use the intercalated crown ether as a medium for ionic ﬁxing or sieving. Powder X-ray diffraction showed that -ZrP could only take up about 0.1 moles of tdco even under a loading ratio of 10:1tdco/-ZrP, and that the samples always consisted of a mixture of -ZrP and {-ZrP(tdco)0.11}, whereas a new phase {-ZrP(tdco)0.37}was completely formed even under a loading ratio of 1 : 2 tdco/-ZrP. The structures inferred from the interlayer spacings are shown in Fig. 9.24.

INTERCALATION COMPLEXES OF INORGANIC HOSTS

551

O(W1) O(W2) O(8) O(7)

Fig. 9.23. Crystal structure of -zirconium phosphate, Zr(PO4)(H2PO4)2H2O. The Zr atoms are at the centres of octahedra of six oxygens, four from PO4 groups and two from H2PO4 groups; the two different P atoms are within the differently hatched tetrahedra. The two remaining oxygens of H2PO4 groups are in hydroxyls which project into the interlayer space and are hydrogen bonded to the two independent waters, themselves hydrogen bonded in chains within the interlayer space. The layers are thus linked by hydrogen bonding rather than by the weaker van der Waals linkage found in -ZrP (Fig. 9.18). (Reproduced from Poojary, Shpeizer and Clearﬁeld, 1995.)

(a)

Phosphate layer 6.8 Å Phosphate layer

(b)

Phosphate layer 9.1 Å Phosphate layer

Fig. 9.24. (a) Assumed mode of intercalation of tdco into -ZrP. It is inferred from the interlayer spacing that the tdco molecule takes up a twisted conformation. (b) Assumed mode of intercalation of tdco into -ZrP. It is inferred from the interlayer spacing that there is a double layer of tdco molecules in a planar conformation. (Reproduced from Kijima, Sakoh and Machida, 1996.)

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9.4

Concluding summary

We quote from Clearﬁeld’s (1994) article on ‘Intercalation Chemistry of Selected Layered Oxides and Phosphates’: ‘‘ . . . the ﬁeld of intercalation chemistry is expanding in many directions. What is most lacking is hard structural data on the packing arrangements and chain conformations of organic species held in the interlayer spaces. Most of our evidence is based upon changes in interlayer spacings and analysis of infrared spectra. Additional X-ray work by ab initio methods, modelling and Rietveld reﬁnements, as well as NMR structural studies are needed. Additional thermodynamic data would help deﬁne energies of layer expansion and host-guest interactions. Further pursuit of intercalation chemistry and ﬁxation of reactive species such as enzymes, photoactive molecules, conductive polymers and inorganic pillaring agents in layered hosts hold exceptional promise for development of useful new products.’’ Indeed, only small changes in wording are needed for this quotation to serve as a ‘‘Concluding Summary’’ for this chapter as a whole. References Abe, T., Mizutani, Y., Shinoda, N., Ihara, E., Asano, M., Harada, T., Inaba, M. and Ogumi, Z. (1995). Carbon, 33, 1789–1793. Alberti, G. (1996). ‘‘Layered metal phosophonates and covalently pillared diphosphonates,’’ Chapter 5, pp. 151–187, in Vol. 7 (G. Alberti and T. Bein, Editors) of Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Oxford: Pergamon. Alberti, G. and Bein, T. (1996). Editors, Vol. 7 (‘‘Solid-state supramolecular chemistry: two- and three-dimensional inorganic networks’’) of Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Oxford: Pergamon. Alberti, G. and Costantino, U. (1991). ‘‘Intercalates of zirconium phosphates and phosphonates,’’ in Chapter 5, Inclusion Compounds, Vol. 5 (Inorganic and Physical Aspects of Inclusion), edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Oxford U. P., pp. 136–176, Alberti, G. and Costantino, U. (1996). ‘‘Layered solids and their intercalation chemistry, ’’ Chapter 1, pp. 1–23, in Vol. 7 (G. Alberti and T. Bein, Editors) of Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Oxford, Pergamon. Alberti, G., Marmottini, F., Marcia-Mascaro´s, S. and Vivani, R. (1994). Angew. Chem., Int. Ed. Engl., 33, 1594–1597. ˚ , Tellgren, R. and Thomas, J. O. (1977). J. Phys. Chem., 81, 1574–1578. Albertsson, J., Oskarsson, A Amelinckx, S. (1995). Acta Cryst., B51, 486–501. Amine, K. and Nakajima, T. (1993). Carbon, 31, 553–556. Amine, K., Nakajima T. and Motoyama, M. (1993). Carbon, 32, 1067–1071. Averill, B. A., Sutto, T. E. and Fabre, J.-M. (1994). Mol. Cryst. Liq. Cryst., 244, 71–78. Barrer, R. M. (1986). J. Incl. Phenom., 4, 109–119. Barrer, R. M. and McCleod, D. M. (1955). Trans. Farad. Soc., 51, 1290–1300. Beck, F., Boinowitz, T., Krohn, H., Tormin, U. and Ther, E. (1994). Mol. Cryst. Liq. Cryst., 245, 177–182. Belash, I. T., Zharikov, O. V. and Pal’nichenko, A. V. (1989). Synth. Metals, 34, 455–460. Besenhard, J. O. (1994). Phys. Chem. Mater. Low-Dimens. Struct., 17, 457–508. Boehm, H.-P., Setton, R. and Stumpp, E. (1994). Pure Appl. Chem., 66, 1893–1901.

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Roth, G., Luders, K., Pﬂuger, P. and Guntherodt, H.-J. (1981). Physics of Intercalation Compounds, Springer Series in Solid State Science, Vol. 38, p. 150. Rouxel, J. (1996). ‘‘Layered metal chalcogenides and their intercalation chemistry,’’ Chapter 3, pp. 77–105, in Vol. 7 (G. Alberti and T. Bein, Editors) of Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. MacNicol and F. Vo¨gtle, Oxford, Pergamon. Ru¨dorff, W. (1959). Adv. Inorg. Chem. Radiochem., 1, 223–266. Ru¨dorff, W. and Ru¨dorff, G. (1947). Z. anorg. allgem. Chem., 253, 281–296. Ru¨dorff, W. and Schulze, E. (1954). Z. anorg. allgem. Chem., 277, 156–171. Russel, E. R., Adamson, A. W., Shubert, J. and Boyd, G. E. (1943). U. S. Atomic Energy Commission Report CN-508. Salzano, F. J. (1964). (1964). Carbon, 2, 73–81. Salzano, F. J. and Aronson, S. (1964). J. Chem. Phys., 45, 4551–4555. Samuelson, E. J., Moret, R., Come´s, R., Fuzellier, H., Klatt, M., Lelaurain, M. and He´rold, A. (1984/5). Synth. Met., 10, 13–19. Saunders, G. A., Ubbelohde, A. R. and Young, D. A. (1963a). Proc. Roy. Soc. Lond., A271, 499–511. Saunders, G. A., Ubbelohde, A. R. and Young, D. A. (1963b). Proc. Roy. Soc. Lond., A271, 512–519. Sawamura, M., Womelsdorf, J. F. and Ermler, W. C. (1991). J. Phys. Chem., 95, 8823–8826. Schafha¨ult, C. (1841). J. prakt. Chem., 21, 129–157. Schleede, A. and Ziegler-Wellmann, M. (1932). Z. physik. Chem., B18, 1–28. Schlo¨gl, R. (1992). ‘‘Electron spectroscopy of graphite intercalation compounds,’’ in H. Zabel and Solin, S. A. (editors) Graphite Intercalation Compounds II. Transport and Electronic Properties. Springer Verlag, Heidelberg, Berlin, New York. Springer Series in Materials Science No. 18, 53–104. Schlo¨gl, R. (1994). Phys. Chem. Mater. Low-Dimens. Struct., 17, 83–176. Scho¨llhorn, R. (1994). Phys. Chem. Mater. Low-Dimens. Struct., 17, 1–81. Scho¨llhorn, R. (1996). Chem. Mater., 8, 1747–1757. Selig, H. and Ebert, L. B. (1980). in Adv. Inorg. Chem. Radiochem., 23, 281–327. Solin, S. A. and Zabel, H. (1988). Adv. Phys., 37, 87–254. Solin, S. A. and Zabel, H. (1990). Editors ‘‘Graphite Intercalation Compounds,’’ Springer, Heidelberg-Berlin-New York. Stumpp, E. (1977). Mater. Sci. Eng., 31, 53–59. Sutto, T. E., Averill, B. A. and Fabre, J. M. (1993). Synth. Met., 55–57, 2019–2022. Takemura, K. and Syassen, K. (1985). Phys. Rev., B 32, 2213–2217. Thomas, J. M. and Theocharis, C. R. (1991). ‘‘The structural chemistry and reactivity of organic guests in layered aluminosilicate hosts,’’ in Chapter 4, Inclusion Compounds, Vol. 5 (Inorganic and Physical Aspects of Inclusion), edited by J. L. Atwood, J. E. D. Davies and D. D. MacNicol, Oxford U. P., pp. 104–135. Touhara, H., Kadono, K., Fujii, Y. and Watanabe, N. (1987). Z. anorg. allgem. Chem., 544, 7–20. Tressaud, A. (1994). Mol. Cryst. Liq. Cryst. Sci. Technol., 244, 13–28. Troup, J. M. and Clearﬁeld, A. (1977). Inorg. Chem., 16, 3311–3314. Ubbelodhe, A. R. J. P. and Lewis, F. A. (1960). Graphite and Its Crystal Compounds, Clarendon Press, Oxford Udod, I. A., Orman, H. B. and Genchel, V. K. (1994). Carbon, 32, 101–106. Vogel, F. L. and He´rold, A. (1977). Editors: Proceedings of the Franco-American Conference on Intercalation Compounds of Graphite, Mater. Sci. Eng., 31, 1–355. Weiss, Armin, (1963). Angew. Chem., Internat. Edit., 2, 134–144. Whittingham, M. S. and Jacobson, A. J. (1982). Editors ‘‘Intercalation Chemistry,’’ pp. 624, New York: Academic Press.

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Wilson, J. A. and Yoffe, A. D. (1969). ‘‘Transition metal dichalcogenides. Discussion and interpretation of the observed optical, electrical and structural properties,’’ Adv. Phys., 18, 193–335. Wong, H.-V., Evans, J. S. O., Barlow, S., Mason, S. J. and O’Hare, D. (1994). Inorg. Chem., 34, 5515–5521. Young, R. A. (1993). The Rietveld Method (IUCr Monographs on Crystallography, No. 5 pp. x þ 298, Oxford: IUCr/Oxford. Zabel, H. and Solin, S. A. (1990). Editors. ‘‘Graphite Intercalation Compounds I,’’ Springer Series in Materials Science No. 14, Springer Verlag, Heidelberg, Berlin, New York.

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Part IV Packing complexes

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Introduction to Part IV Packing complexes

[The term] packing complexes reveals the reason for the complex formation : a loose structure of the crystal of one or both components and increases in packing density (a positive value of ) which occur when a packing complex is formed. In all cases, no additional bonds appear between the molecules of the components other than those in single-component crystals. A complex is formed due to the tendency of the particles to pack as densely as possible in the crystal. In terms of energy it means that the formation of a complex is accompanied by a considerable gain in the short-range part of the energy of interaction between the molecules. A. I. Kitaigorodsky, 1984. p. 284.

Single-chapter Part IV bridges between ‘molecular complexes’ and ‘molecular compounds’, but is anchored securely with the complexes. The compass is wide and the examples are many and varied. The chapter title ‘Packing complexes’ comes from Kitaigorodsky and we echo many of the themes that he initiated in two classic volumes (Kitaigorodsky, 1973, 1984). One of the most fruitful of these is the importance of phase diagrams in the study of binary (and higher) systems.

References Kitaigorodsky, A. I. (1973). Molecular Crystals and Molecules. Academic Press, London. Xii þ 553. Volume 29 of a Series of Monographs on Physical Chemistry edited by E. M. Loebl. Kitaigorodsky A. I. (1984). Mixed Crystals. Springer–Berlin etc. Xiii þ 388. Volume 33 of the Springer Series in Solid State Science, edited by Manuel Cardona.

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Chapter 10 Packing complexes

. . . and they don’t seem to have any rules in particular : at least, if there are, nobody attends to them . . . Lewis Carroll : Alice in Wonderland

Summary. In binary packing complexes there is no preferential bonding between types of component – either between like or between unlike components. A large variety of phase diagrams and structural types are found and there are resemblances to metal–alloy systems. Correlation of phase diagrams and crystal structures can be considerably hampered by the occurrence of disorder and conformational isomerism. When the components resemble each other chemically and geometrically extensive solid solution can occur, with possibilities of order and/or disorder. A few solid solutions of the interstitial type are known; these form especially when the component molecules differ appreciably in size, and are not always clearly distinguishable from some clathrates. The best deﬁned group is that analogous to intermetallic compounds; here the molecular complex forms a phase different from those of its components, although echoes of structural features of one or both components often appear in the structure of the molecular complex, then dubbed ‘mimetic’. Molecular complexes of the fullerenes (C60, C70 and C76 ) are among the examples of ‘ordered packing complexes’ discussed here. Crystals containing ‘solvent of crystallization’ are included in this group when there is no preferential host–host or host–guest interaction.

10.1 Introduction 10.2 Components are isomers of various types 10.3 The (stereoisomeric) components are enantiomers 10.3.1 Background 10.3.2 Types of binary phase diagram found with enantiomers as components 10.3.3 Formation of conglomerates 10.3.4 Comparing the stability of enantiomorphs and racemic compounds 10.3.5 The structural chemistry of systems with isolatable enantiomers 10.3.5.1 Components are rigid molecules 10.3.5.2 Complications due to conformational isomerism of component molecules 10.3.6 Enantiomorphs and racemic compounds of nonisolatable conformers 10.3.7 Racemic enantiomorphs and noncentrosymmetric racemates 10.3.8 Solid solutions of enantiomers 10.4 The (stereoisomeric) components are diastereoisomers 10.4.1 Background 10.4.2 Diastereoisomers as components 10.4.3 Conformers as components 10.4.4 Cis-trans isomers as components

564 565 566 566 568 569 571 574 574 577 582 584 585 590 590 590 592 597

PACKING COMPLEXES

564

10.4.5 Cocrystallization of tautomers 10.4.6 Interallogon complexes 10.5 Components are positional isomers 10.6 Components have different chemical compositions 10.6.1 Substitutional solid solutions 10.6.1.1 Conditions for formation 10.6.1.2 The information desired 10.6.2 Systems with complete (or a wide range of) mutual miscibility 10.6.3 Some binary phase diagrams involving phases (primary and intermediate) with extensive composition ranges 10.6.3.1 Dibenzyl – trans-stilbene 10.6.3.2 Diphenyl sulphoxide–diphenyl sulfone 10.6.3.3 p-Dibromobenzene–p-diiodobenzene 10.6.3.4 p-Dibromobenzene–p-chloronitrobenzene 10.6.3.5 Benzoic acid–p-fluorobenzoic acid 10.6.3.6 1,2-4,5-Tetrachlorobenzene–1,2,-4,5-tetrabromobenzene 10.6.4 Evidence for nonrandom substitution in primary solid solutions 10.6.4.1 (trans-Stilbene)–diphenylmercury and tolane(1,2diphenylacetylene)–diphenylmercury 10.6.4.2 2,3-Dimethylnaphthalene–anthracene 10.6.5 Inhomogeneity of some solid solution crystals 10.7 Interblock solid solubility 10.8 Primary interstitial solid solutions 10.9 Ordered packing complexes 10.9.1 Metal coordination complexes 10.9.1.1 Components of different composition and configuration but in the same oxidation state 10.9.1.2 Components with different compositions, configurations and oxidation states 10.9.1.3 The components are oligomers 10.9.2 Complexes in which a moiety plays more than one structural role 10.9.3 Miscellaneous packing complexes 10.9.3.1 Packing complexes without specific interactions 10.9.3.2 Packing complexes with incipient specific interactions 6 10.9.3.3 Complexes of the fullerenes: mainly C60-Ih and C70-D5h References

10.1

600 603 605 605 605 605 607 608 615 615 615 617 617 617 617 618 618 620 620 622 622 623 623 624 624 624 625 628 628 634 634 667

Introduction

The complexes dealt with in this chapter are characterized by the apparent absence of a decisive chemical reason for their existence. The fact of their existence as stable crystals shows that there is a decrease in free energy on their formation from the pure crystalline components; however, the structures show an absence of dominant A . . . A (host . . . host) interactions, as in the inclusion complexes, or A . . . B (component A . . . component B) interactions, as in the molecular compounds. The name ‘packing complexes’ derives from the (certainly facile) explanation for their occurrence in consequence of the denser packing sometimes presumed possible in binary as compared to unary crystals

COMPONENTS ARE ISOMERS OF VARIOUS TYPES

565

(see discussion of Wallach’s rule below in Section 10.3.4). We limit ourselves to binary complexes because most of the information available concerns this group but many of the ideas can be carried over to multi-component complexes. There is a considerable formal resemblance to the situation found in metal-alloy systems; this has also been emphasized by Haget (1993), who presents eight phase diagrams of various kinds from earlier work of the REALM group. Solid solutions, interstitial and substitutional, are found as well as analogs to intermetallic compounds, where the structure of the complex differs from those of the individual components. In some packing complexes the structure of the complex resembles that of one of the components – these are called ‘mimetic’ complexes; there are also non-mimetic complexes, the distinction often being one of degree rather than of kind. Ordered and disordered complexes are also found; in alloys there is positional disordering, because of the relative ease of diffusion of the quasi-spherical atoms, while in molecular complexes diffusion is more difﬁcult and disorder is generally orientational. Primary interstitial solid solutions are known but are rather rare; they occur when the component molecules differ appreciably in size and their differentiation from inclusion complexes, especially clathrates, is usually a matter of convention. Solvates can often be included in this category. It is convenient to use a chemical basis for a systematic classiﬁcation, making a major distinction between systems with components of the same chemical composition (i.e. isomers of various types) and those with chemically-different components. Further division is structural, based on the difference between ordered complexes of various types on the one hand and solid solutions on the other. We also note whether there is, or is not, a resemblance between the structure of component (one or both) and molecular complex, i.e. whether the complexes are mimetic or not. In some of our examples, such as those involving co-crystallization of conformers or tautomers, the individual components are conceptual and are unlikely to be capable of isolation.

10.2 Components are isomers of various types We have ﬁrst to deﬁne the different types of isomer in terms of constitution and stereochemistry; our description follows the overviews given by Stoddart (1979) and Moss (1996). Isomers are compounds with the same elemental composition which differ in the nature or sequence of the bonding of their atoms in space. We now introduce the distinction between stereoisomers and constitutional isomers. Stereoisomers may be conﬁgurational or conformational in type. Conﬁguration relates to the particular spatial arrangement of atoms in molecules of deﬁned constitution, without differentiating among arrangements which differ only in torsion about single bonds. The term conformation relates to the different spatial arrangements of atoms in molecules of deﬁned constitution obtained on torsion about one or more single bonds. Stereoisomers (both conﬁgurational and conformational) are either enantiomers or diastereoisomers; enantiomers are non-superimposable molecules which are related as object and mirror image, while diastereoisomers are any stereoisomers which are not enantiomers of each other. One consequence of these deﬁnitions is a recommendation that terms such as optical and geometrical isomerism should be phased out (for example the cis and trans isomers of 1,2-dichloroethylene are diastereoisomers) but we shall sometimes ﬁnd it convenient to be delinquent in this respect. Conformers, frozen into particular

PACKING COMPLEXES

566

conformations in the solid state, are often diastereoisomers. An important difference between stereochemistry in solution and in the solid state is that conformers generally interconvert rapidly in solution and are hence considered as single components whereas the different conformers found in a crystal are often separate crystallographic entities distinguishable from other conformers. This last phrase (containing the caveat ‘often’) only holds if the crystal is ordered; operationally, one may not be able to distinguish the different conformers in disordered crystals. Constitutional isomers differ in the nature and sequence of the bonding between atoms of the molecule; dimethyl ether (H3COCH3) and ethanol (CH3CH2OH) are familiar examples. Positional isomers such as tautomers (e.g. the keto and enol forms of acetoacetic ester) also come into this category. O

O

HO

H3C

OEt keto form

O CH

CH2 H3C

OEt enol form

For completeness, we add that the extension of concepts of molecular stereochemistry to crystals, especially to the determination of absolute structure (the crystallographic term) and absolute conﬁguration (the chemist’s term), has been very clearly set out by Flack and Bernardinelli (1999) and Flack (2003).

10.3 10.3.1

The (stereoisomeric) components are enantiomers Background

In principle, the simplest situation occurs when the two components of the binary system are enantiomers (Jacques, Collet and Wilen, 1981; Collet, Brienne and Jacques, 1980). The background to the determination of the absolute optical conﬁguration and structure of a crystal using diffraction methods has been carefully reviewed by Flack and Bernadinelli (1999, 2000), including consideration of the nomenclature used. We remind the reader of the standard nomenclature (International Tables for Crystallography, 1983, and later editions). An object which has no symmetry is asymmetric, while it is dissymmetric if it has only proper rotation axes; both types are chiral and can exist in two non-superimposable mirror-image forms. At this point it is essential to distinguish between the chirality of molecules and that of crystals. If the object is a molecule then the two mirror-image forms are called enantiomers (Greek enantios opposite). The point group of such a molecule will be one of Cn (n ¼ 1, 2, 3, 4, 5, 6 . . . ), D2 (222), D3 (32), D4 (42), D6 (62), T (23), O (432), I (532), where we ﬁrst give the Schoenﬂies symbol and then, in brackets, the Hermann–Mauguin symbol. If the object is a crystal then the two forms are called enantiomorphs. Such an (enantiopure) enantiomorph must crystallize in one of the 65 space groups with symmetry elements only of the ﬁrst kind (the Sohncke groups), i.e. the point group of the crystal must be one of 1, 2, 222, 4, 422, 3, 32, 6, 622, 23, 432. ‘Racemic’ (l. racemus a bunch of grapes) is an adjective used to describe a composite body which contains equal amounts of enantiomers of opposite sense of chirality; if a body is racemic, then its solution will not rotate the plane of polarized light. The following

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

567

possibilities exist for a crystalline racemic composite body (a ‘racemate’); the order follows that of the phase diagrams given below in Fig. 10.1 : 1. It can be a conglomerate which is a mechanical mixture of the two enantiomorphs each in separate crystallite domains, the size of the domains depending on the conditions of formation of the conglomerate. The space group will be enantiomorphic but it will not be possible to determine the absolute conﬁguration of the crystal from the anomalous scattering of x-rays (Bijvoet effect) (Bernardinelli and Flack, 1985). 2. It can be a racemic compound, which has an arrangement of the two enantiomers different from that of one enantiomer in the enantiomorphic crystal. The space group of a racemic compound can be either (a) nonenantiomorphic, when the two enantiomers of opposite sense of chirality will be related by an improper rotation axis (there are 165 such space groups) or (b) enantiomorphic, when there is one or more pairs of enantiomers of opposite sense of chirality in the asymmetric unit of the crystal. Then the chirality derives from the arrangement of these pairs while the racemic nature derives from the equal amounts of the two enantiomers present. We ignore here, but illustrate later, possible additional complications due to disorder. If the component molecule occurs as a number of conformers, then the racemic compound may contain these in ordered or disordered array; equal amounts of both enantiomers of each conformer must be present but the different conformers may differ in amount. 3. It can be a racemic solid solution, where the arrangement of the two enantiomers will be similar to that in the corresponding enantiomorph. Such a solid solution will be disordered to a lesser or greater extent and there will be complications in the determination of the space group, with each example to be treated on its merits; however, the space group of the average structure will be nonenantiomorphic. Chiral molecules rotate the plane of polarised light. A clockwise rotation (to an observer looking through the solution towards the source) led originally to the enantiomer being designated ‘d’, with counter-clockwise rotation leading to the designation ‘l’; modern practice is to use (þ) and () instead. The conﬁguration of an enantiomer was originally designated on a relative basis by use of the preﬁxes d or l. Absolute conﬁgurations of single asymmetric centres are now deﬁned, in terms of rules originally formulated by R. S. Cahn, C. K. Ingold and V. Prelog, as R or S; this nomenclature has been extended to other kinds of molecular asymmetry (Stoddard, 1979; Prelog and Helmchen, 1982). Note that the d, l system is still used with -amino acids, cyclitols and carbohydrates. A statistical survey of the occurrence of organic racemates has been carried out by Dalhus and Go¨rbitz (2000a), using the October, 1998 release of the CSD. This contains 78 000 unique crystal structures, 65% (50 000) being centrosymmetric, and 35% (27 000) non-centrosymmetric. About 23% of the centrosymmetric group were organic racemates, i.e. some 11 500 structures in the database of 78 000. 98% of these racemates belong to the four space groups P 1(27%), P21/c (57%), C2/c (7.6%) and Pbca (6.7%). Of the 27 000 non-centrosymmetric structures 14% are found in achiral space groups; 16.6% of the achiral group are organic racemates, 93% of these being divided among the ﬁve space groups Pc (6%), Cc (22%), Pca21 (23%), Pna21 (37%) and Fdd2 (6%). Finally, a very small but interesting group is discussed later in Section 10.3.7 under ‘‘Racemic Enantiomorphs.’’

PACKING COMPLEXES

568

10.3.2

Types of binary phase diagram found with enantiomers as components

A simple and convenient representation of the behaviour of binary sytems of enantiomers is in terms of their phase diagrams (Findlay, 1951; Ricci, 1966). These are usually determined from the melting points of mixtures of various compositions; this method gives the liquidus and, if the thaw points can be determined reliably, also the solidus. Thus the results are likely to refer only to the higher-temperature region and phase transitions that occur on cooling may be missed, with the possibility of confusion when a hightemperature phase diagram is compared with crystallographic studies of samples prepared at lower temperatures. Crystals are generally grown from solution (often at unspeciﬁed temperatures) and the appropriate reference is to the ternary phase diagram, with components R, S and solvent and known temperature(s); the binary diagram is contained in the ternary diagram. A very useful discussion and collection of results is available (Jacques, Collet and Wilen, 1981). A comprehensive review of heterogenous equilibria in binary systems of enantiomers has been presented by Coquerel (2000). Our classiﬁcation (Fig. 10.1) is based on that originally given by Roozeboom (1899); the diagrams are necessarily symmetrical with respect to the components. We shall ﬁnd that the diagrams presented here are essentially schematic and more complicated situations are encountered in practice. Diagram (a) in Fig. 10.1 shows a eutectic with no mutual solid solubility of R and S; limited solid solubility of one enantiomer in the other is shown in diagram (b). Racemic compound formation is shown in (c) and (d), with different relative stabilities of racemic compound and enantiomers; possible formation of solid solutions has been ignored, for simplicity. Diagrams (e), (f) and (g) illustrate complete miscibility in the solid state (a)

(b)

Melt T

Melt T

R+S R Limited solid solution of S in R

R

S

S

Racemate (c)

(d) T

T

R

R

S

(e) T

(f) T

(g) T

Solid solution R

S

melt

Solid solution S

R

Solid solution S

R

S

Fig. 10.1. Binary phase diagrams for enantiomers; (a) and (b) formation of eutectics and conglomerates; (c) and (d) formation of racemic compounds; (e), (f) and (g) complete range of solid solutions. The diagrams are necessarily symmetrical. See text for further details.

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

569

but with different behaviour of liquidus and solidus. A ﬂat liquidus (e) indicates ideal liquid and solid solution; a melting point maximum (f) is generally interpreted as implying a tendency towards short range order in the solid; a melting point minimum (g) implies a tendency towards clustering (of like enantiomers) in the solid. Thus one would expect an optically-inactive melt to give a disordered solid solution if the phase diagram is type (e), show a tendency towards formation of a racemic compound for type (f) and a tendency towards resolution of enantiomers, perhaps as a conglomerate, for type (g). The diagrams are idealized and not all are realized as such in practice. We shall move from structurally simpler to structurally more complicated systems and choose, where possible, our illustrations from systems where both phase diagrams and structural information are available; thermodynamic data hardly exist. Problems arise when the components can occur as conformers of similar free energies, interconvertible in solution but not in the solid state, and which can pack in a more or less disordered arrangement. Thus we start with systems where the components are rigid molecules and then proceed to systems involving nonrigid conformers, following the order of the phase diagrams in Fig. 10.1. We ﬁrst discuss ordered systems and then disordered systems, and also ﬁrst systems where there is no resemblance between enantiomer and racemic compound crystal structures (nonmimetic arrangements) and then systems where there are resemblances between enantiomer and racemic compound crystal structures (mimetic arrangements) We have implicitly assumed in the above classiﬁcation that any interconversion of enantiomers occurs in solution or melt at a rate which is slow compared to the rate of crystallization; in the limit there is no interconversion. At the opposite extreme, when interconversion is rapid, then the enantiomers are in chemical equilibrium and are considered to be a single component (Berry, Rice and Ross, 1980). However, this need not prevent the formation of conglomerates, as the example of [4]helicene discussed below shows. 10.3.3 Formation of conglomerates If the phase diagram is Type (a) (Fig. 10.1), then spontaneous and complete resolution of enantiomorphs is to be expected on crystallization of an optically inactive solution; partial resolution will be obtained for a Type (b) phase diagram. Under fortunate circumstances (crystals with well-developed hemihedral faces) the enantiomorphs can be hand sorted (following Pasteur); more sophisticated separation techniques, some of industrial importance, are available (Collet, Brienne and Jacques, 1980). Some 30 examples of spontaneous resolution had been recorded by 1963 (Secor, 1963) and some 250 by Collet et al., in 1980. These numbers may suggest that conglomerate crystallization is a rare occurrence but Bernal and Kauffman (1993) have remarked that several thousand examples are in the process of being listed in the Cambridge Crystallographic Data File (see also Bernal, 1995). One of the few examples where both phase diagram and crystal structure have been reported is cis--camphanic acid (10.1). The phase diagram (Fig. 10.2) shows that there is conglomerate formation below 440K and above this temperature a plastic phase in which there is complete miscibility of the two enantiomers (Chion-Suchod and Lajzerowicz˚, Bonneteau, 1987). Crystals of the (–)-enantiomer are hexagonal, a ¼ 6.862, c ¼ 36.30 A Z ¼ 6, space group P61. Molecules related by the six fold screw axis are linked by ˚ . Crystallographic study of the plastic phase C¼O . . . HO hydrogen bonds of length 2.67 A was not possible because of experimental difﬁculties.

PACKING COMPLEXES

570

HOOC CH 3 H3C O H

(–)-cis-p-camphanic acid 10.1

O

The phase diagram of the free radical endo-4,4 0 -dimethyl-8,9,10-trinor-spiro-2,2 0 bornane (1,3-oxazolidine)-3 0 -oxyl (10.2) is similar to Type (b) but there appears to be a complete range of solid solutions formed very close to the ‘‘eutectic’’ line, with the consequence that a solid solution is formed at higher temperatures and a conglomerate, whose structure has been determined (Moutin, Rassat, Bordeaux and LajzerowiczBonneteau, 1976; SNBMXZ) at lower temperatures; solid solution and conglomerate are mimetic (Table 10.1). The solid solution is metastable at room temperature and phase separation (to the enantiomorphs) has been followed, via the diffraction effects, over a period of 230 days (Lajzerowicz-Bonneteau, Lajzerowicz and Bordeaux, 1986). 10.2 epimerizes readily in solution (but not in the solid) to give 10.3 (exo-4,4 0 (þ)-10.3 and dimethyl-8,9,10-trinor-spiro-2,2 0 -bornane(1,3-oxazolidine)-3 0 -oxyl). ()-10.3 form a mimetic pair (crystal data in Table 10.1). Although 10.2 and 10.3 are not isomorphous, they nevertheless form a solid solution which is isomorphous with the solid solution of the enantiomers of 10.2. The limiting composition of the 10.2/10.3 solid solution is probably close to the value given in Table 10.1; a complete range of solid solutions is not possible. It has been noticed on a number of occasions that so-called spontaneously resolved crystals in fact gave optically inactive solutions. A classic example is (–)(2S,3R)phenylglyceric acid (PhCH(OH)C(OH)HCOOH) (i.e. the threo form), whose active and inactive forms were carefully studied by non-diffraction crystallographic techniques (Goldschmidt, 1915). The inactive form was shown to be a conglomerate, lamellarly twinned on (001) and not a true racemic compound, and this was conﬁrmed in later x-ray studies (Furberg and Hassel, 1950; Cesario and Guilhem, 1975; PHGLYA). The crystals (P21, Z ¼ 2) consist of layers of hydrogen-bonded molecules parallel to (001), there being only dispersion forces between the layers. Analogous results have been reported for glutamic acid hydrochloride (P212121, Z ¼ 4; Dawson, 1953; LGLUTA01), where Liquid

T (K)

500 Plastic phase

480 460 440 D D

crystals + L crystals L

Fig. 10.2. Phase diagram for cis--camphanic acid. The compositions investigated by DSC are shown. (Reproduced from Chion-Suchod and Lajzerowicz-Bonneteau, 1987.)

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

571

˚ , deg.) for some mimetic enantiomer– Table 10.1. Comparison of crystallographic parameters (A racemic compound pairs of 10.2 and 10.3. (%) is defined below (Section 10.3.4) Compound

a

()-10.2 (þ)-10.2 0.57()10.2/ 0.43()-10.3 ()-10.3a

12.320 12.306 12.401

()-10.3

b/

8.57

9.880 9.802 9.922 10.53 98.22 10.40 96.72

8.79

V/mol

(%)

Space group

Z

Refcode

270.5 267.8 275.0

1.02

Pnma p212121 Pnma

4 4 4

FICHEE SNBMXZ FICHI

11.88

262.0

4.33

P21/c

4

BUCNAO

6.03

273.6

P21

2

BUCNES

c 8.889 8.879 8.940

Reference: (a) Bordeaux, Gagnaire and Lajzerowicz, Jeanine, 1983.

O N

O N

O

CH3 CH3

O H 3C

CH3

Molecule A

B = Epimer of Molecule A

10.2

10.3

the same crystals are obtained from active and inactive solutions (Quene´ and Jellinek, 1959) (the macroscopic resemblance between crystals of l- and dl-(sic)-glutamic acid hydrochloride had been pointed out much earlier (Kaplanova, 1917) (also for the hydrobromides; the hydroiodides do not show similar behaviour). In hexahelicene (P212121, Z ¼ 4; De Rango, Tsoucaris, Declercq, Germain and Putzeys, 1973; HEXHEL) the observed lamellar twinning on (001) (Green and Knossow, 1981) has been accounted for by calculations of interfacial energies for various putative composition planes (Ramdas, Thomas, Jordan and Eckhardt, 1981). 10.3.4 Comparing the stability of enantiomorphs and racemic compounds Relatively few concomitant phase diagrams and crystal structures are available but Brock, Schweitzer and Dunitz (1991) have found over 120 examples where crystal structures of both enantiomorph and racemic compound were reported in the Cambridge Structural Database (CSD; January, 1989 version). Whether a crystal composed of homochiral enantiomers will have a greater or lesser density than the corresponding racemic compound was ﬁrst considered by Wallach (1895) on the basis of a comparison of crystal densities. Using a sample of eight pairs, Wallach concluded that the packing was more dense in the racemate than in the enantiomorph. Indeed, there does seem to be a widely held notion that ‘‘right- and left-handed objects usually can be packed in a box better than all right- or all left-handed objects’’ (Roberts and Caserio, 1964), although it is not clear whether Wallach’s experiments are the basis for this statement. Wallach’s conclusion has been questioned by Jacques, Collet and Wilen

572

PACKING COMPLEXES

(1981; see pp. 23–31), using samples of 12 and 14 pairs. More recently, Brock et al. (1991) extended this to a sample of more than 120 well authenticated, temperature-matched pairs, volumes per molecule being calculated from measured cell dimensions. Instead of densities it was found more convenient and precise to use the parameter deﬁned as follows : ð%Þ ¼

100½ðV=ZÞA ðV=ZÞR

0:5½ðV=ZÞA þ ðV=ZÞR

Here (V/Z) is the volume per molecule in the unit cell and the subscripts refer to Enantiomorph (A ¼ antipode) and Racemate). Positive values of imply denser packing in racemate than in enantiomorph, and conversely. The distribution of values for the 120 pairs referred to above is shown in Fig. 10.3, the mean value being þ 0.56(22)%. In other words, a collection of left- and right-handed objects does not, in general, pack more densely than those of one kind alone. When the Brock sample was limited to those examples where the enantiomers can be resolved (i.e. the racemic melt is a two component system), then on average the racemic crystals were about 1% denser than their chiral counterparts. However, the last word has not been said as the distribution shows hints of bimodality and skewness and there are a few striking outliers (appreciably denser packing for dl as opposed to d alone, and conversely). Detailed analyses of structure have been published for one outlier pair with ¼ 6.0% (T ¼ 193K for both crystals) and two others with ¼ 2.9% and 0.9% (T ¼ 122K for both pairs); in all three pairs the racemate is monoclinic (P21/c, Z ¼ 4) and the enantiomer orthorhombic (P212121, Z ¼ 4). The ﬁrst compound is 1-hydroxy-3-phenyl-2-propenyl) dimethylphosphonate (S-enantiomer ROPRET and racemate ROPRAT; Blazis et al., 1997). The second and third pairs are (R)-( þ )-3-hydroxy-3-(3 0 -chlorophenyl)propionic acid (R is ROPPAN; RS is YUHFEM) and its Br analog (R is ROPPER and RS is YUHFOW; the enantiomorphs of this pair are isomorphous (Larsen and Marthi, 1997) as are the racemates (Larsen and Marthi, 1995)). The structures are not mimetic in any of the pairs, but the principal hydrogen bonding arrangements have close similarities, with the differences residing in the weaker interactions. A striking difference for the ﬁrst compound is that the atomic displacement parameters (ADPs) of the phenyl C atoms are about twice as large in the S-enantiomer as in the racemate. Larsen and Marthi have used measured enthalpies of fusion as a basis for discussion of their systems, but a more comprehensive thermodynamic study would be desirable. We note that the analog of for -molecular compounds was generally found to be close to zero, with some outliers, but a detailed statistical analysis was not made (Herbstein, 1971). We shall also ﬁnd in the next paragraphs that the structural chemistry of these systems can be quite complicated and that a ﬁner toothcomb than simple comparison of values is needed. A more fundamental approach to the problem implied by Wallach’s ‘‘rule’’ is to compare thermodynamic parameters for enantiomorph–racemate pairs. This has been done, to a limited extent, by measuring enthalpies of solution, at 298.15K, of enantiomorph-racemic compound pairs (Matsumoto and Amaya, 1980) (Table 10.2); the Hsoln values are all dl l – Hsoln ] is the standard enthalpy of endothermic. The value of (Hsoln) [ ¼ Hsoln formation of the crystalline racemic compound from the pair of crystalline enantiomorphs of opposite sense of chirality. The racemic compound is enthalpy stabilized for all the

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

573

pairs in Table 10.2, except for threonine. The values of ((Hsoln) are a few kJ/mol and are generally smaller than the enthalpies of formation found for -molecular compounds (Fig. 16.1). Some comments are in order because it seems clear that, although the method is sound in principle, the available results need both extension and critical examination. The problem is the correct comparison of the solution enthalpies of enantiomorph and racemate. Alanine is noted below (Section 10.3.5.1(b)) as giving a mimetic enantiomorph–racemic compound pair and is the only example where straightforward comparison of crystal structures and H values is justiﬁed. There are complications for the other pairs in Table 10.2. There are two polymorphs of enantiomorphic glutamic acid ( : Lehmann and Nunes, 1980; : Lehmann, Koetzle and Hamilton, 1972a), an anhydrous racemate (Dunitz and Schweitzer, 1995) and a racemic monohydrate (Ciunik and Glowiak, 1983; CADVUY). Threonine is discussed below (Table 10.7). l-Valine (P21, Z ¼ 4; Torii and Iitaka, 1970; LVALIN) has two molecules of differing conformation in the asymmetric unit. dl-valine has monoclinic (P21/c, Z ¼ 4; Mallikarjunan and Thyagaraja Rao, 1969) and triclinic (Dalhus and Go¨rbitz, 1996; 25

Number

20 15 10 5 0 –6

–4

–2

0

2

4

6

8

Bin number

Fig. 10.3. Histogram of values for 129 enantiomorph-racemate pairs. Bin number 6, for example, represents values between 6 and 5 %. (Adapted from Brock, Schweitzer and Dunitz (1991).)

Table 10.2. Measured values (kJ/mol) of the standard enthalpy of solution of enantiomorphDL L racemic compound pairs, and derived values of (Hsoln) [ ¼ Hsoln Hsoln ] Compound

L Hsoln

DL Hsoln

(Hsoln)

alanine glutamic acid threonine valine tartaric acid histidine

7.36(15) 24.53(0) 9.78(3) 2.87(1) 16.12(38) 13.6(1)

9.35(7) 28.56(12) 9.61(6) 5.16(0) 25.64(7) 15.1(2)

2.0(2) 4.1(2) þ0.17(13) 2.3(1) 9.4(3) 1.5(2)

574

PACKING COMPLEXES

VALIDL) polymorphs. There are resemblances between the two dl-valine polymorphs. is not given because of the complications stemming from the two conformations and the two polymorphs. Anhydrous tartaric acid is (of course) enantiomorphic (d-tartaric acid, Albertsson, Oskarsson and Sta¨hl, 1979; TARTAC04–07) while the only racemic structure known is that of the monohydrate (Parry, 1951; TARTDL). l-Histidine has two polymorphs with similar unit cells; one is orthorhombic (P212121, Z ¼ 4; Madden, McGandy and Seeman, 1972; LHISTD10) and the other monoclinic (P21, Z ¼ 2; Madden, McGandy, Seeman, Harding and Hoy, 1972 LHISTD01/2). The racemic compound (P21/c, Z ¼ 4; Edington and Harding, 1974; DLHIST) has a different molecular conformation from that in the enantiomorph and so the relationship is non-mimetic. Thus one has misgivings about the appropriateness of the (Hsoln) values given for those pairs where the identity of the samples used does not appear to have been adequately established, nor is it clear how to interpret the results when polymorphism is involved, nor when there are conformational changes. Alanine is probably the only fully appropriate example. More thermodynamic measurements (including speciﬁc heats), on clearly deﬁned samples, would be very valuable for furthering our understanding of enantiomorph– racemate stabilities. 10.3.5

The structural chemistry of systems with isolatable enantiomers

As we have noted earlier, some stereoisomers are geometrically stable under normal experimental conditions even in solution while others racemize rapidly. Very few racemize in the solid state. This leads us (following Brock et al., 1991) to make the operational distinction between situations where individual stereoisomers can, or cannot, be isolated. Our ﬁrst section will deal with a comparison between enantiomorphs and racemic compounds of rigid molecules, and then discuss complications due to the occurrence of conformers of the enantiomers. Molecules which are enantiomeric in solution because of rapid interconversion of conformers can become diastereoisomers in the solid state if different conformations are frozen in. Brock et al. (1991), in the survey discussed above, found 64 pairs where the crystal structures of racemate and enantiomorph had been reported, the sample being limited to compounds with resolvable, not rapidly interconverting, enantiomers. This group has been further analyzed by Marthi, Larsen, Acs, Balint and Fogassy (1994), who found ‘‘great resemblance between the packing of the racemate and the corresponding enantiomers’’ for 14 of these pairs. Extrapolation leads one to expect that about one quarter of enantiomer–racemate pairs will show appreciable resemblances in packing. Our discussion below includes alanine, tyrosine and carvoxime of the Group of 64, and some other examples. 10.3.5.1 Components are rigid molecules (a) Nonmimetic enantiomorph–racemic compound pairs. The enantiomorph and racemic compound of [7]helicene form a nonmimetic pair; ˚, the enantiomorph (HPTHEL) has space group P21 (a ¼ 14.02, b ¼ 15.09, c ¼ 9.22 A 3 ˚ ¼ 93.2 , Z ¼ 4, V ¼ 1948 A ; Beurskens, Beurskens and van den Hark, 1976) and ˚ , ¼ 95.7 , Z ¼ 4, the racemic compound (P21/n (a ¼ 20.83, b ¼ 11.50, c ¼ 8.11 A

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

575

˚ 3; van den Hark and Beurskens, 1976, HPTHEL01; Joly, Defay, Martin, V ¼ 1933 A Declercq, Germain, Soubrier-Payen and Meerssche, 1977, HPTHEL02). ¼ 0.75% for the [7]-helicene pair. The phase diagram would be expected to be of Type (c) or (d) (Fig. 10.1). There is no resemblance between the structures of -l-arabinose (10.4) (m. ˚ , V ¼ 609 A ˚ 3, Z ¼ 4, space pt. ¼ 158 C; a ¼ 6.50(3), b ¼ 19.41(10), c ¼ 4.83(2) A group P212121; Hordvik, 1961; ABINOS) and -dl-arabinose (m. pt. ¼ 161 2 C; ˚ , ¼ 99.45(6) , V ¼ 610 A ˚ 3, Z ¼ 4, space a ¼ 5.925(4), b ¼ 7.820(3), c ¼ 13.354(6) A group P21/c; Kim and Jeffrey, 1967; ABINOR); ¼ 0.15% for the -arabinose pair. Presumably the factor determining the nonmimetic nature of this pair is the different spatial requirements of the two hydrogen-bonding schemes, and this also holds for other enantiomorph–racemic compound pairs among the carbohydrates (Jeffrey, 1990). The phase diagram would be expected to be of Type (d) (Fig. 10.1). OH 5 3

HO

4 2

1

O

OH

HO

b-L-arabinose (10.4) - 1a2e3e4a- tetrahydroxypyranose

(b)

Mimetic enantiomorph–racemic compound pairs. -Alanine (10.5) presumably has a Type (c) phase diagram because the melting point of the enantiomorph is 314 (dec.), while that of the racemic compound is 295–6 (dec.). In the enantiomorphic crystal (Simpson and Marsh, 1966; Destro et al., 1988; LALNIN, XRD); Lehmann, Koetzle and Hamilton, 1972b (ND)) there are strings of hydrogen-bonded l molecules along [001] related by two fold screw axes while in the racemic compound (Donohue, 1950; Subha Nandhini et al., 2001; DLALNI, XRD) a particular string of l molecules is essentially identical to that found in the enantiomorph, but the adjacent string is related by a glide plane and thus contains d molecules. Analogous situations are found for other organic acids (Pedone and Benedetti, 1972; Benedetti, Pedone and Sirigu, 1973; also see Table 10.3).

H 3C H 3N

CH3 CH3

+

H –O C 2

CH3 10.5

O HO

S

O O 10.6

O (–)-10.7

PACKING COMPLEXES

576

An excellent illustration of the resemblances that can be found between enantiomorph and racemic compound structures is provided by ( þ )-(ZZZBLS01) and ()-endo-camphorcarboxylic acid (10.6) (Fig. 10.4; Lalancette, Vanderhoff and Thompson, 1991; KIGCAE) where there is no rotation about the carboxyl to ring bond and the molecule thus behaves as a rigid body (Table 10.3). Another carefully studied example is (7aS)-2,3,7.7a-tetrahydro-7a-phenylthio-1Hindene-1,5(6H)-dione (10.7) (Brock, Kwiatowski, Watt and Sayed, 1992), where the molecules also behave as essentially rigid bodies. The common motif in the closely related 10.7 structures (Table 10.3) is a double layer of enantiopure molecules; adjacent double layers are related by inversion centres in the racemate (KUHLAA) and by 21 screw axes in the chiral crystals (KUHLEE). The melting points of the enantiomorph and racemate are 350–1K and 397–9K respectively, i.e. phase diagram is type (d).

˚ , deg.) for some mimetic Table 10.3. Comparison of crystallographic parameters (A enantiomorph–racemic compound pairs. The type of phase diagram (Fig. 10.1) is suggested where possible V/mol

(%)

5.82 5.784

106.1 107.7

6.81

5.91

209.7

21.12

6.91

5.83

212.7

10.849

6.751 94.96

14.248

259.9

ZZZBLS01 LVT91 KUHLAA BK92 KUHLEE BK92

10.712

7.136

256.0

24.729

327.2

7.334

6.724 95.07 7.203 91.27 7.359

24.613

DMBPHA HSS63

7.234

15.120

DCLPHA HKM76

5.065

17.946

Compound

Refcode/ reference

a

b/

dl-alanine l-alanine Type (c) dl-tyrosine

DLALNI LALNIN

12.05 12.343

6.05 6.032

DLTYRS MR73 LTYROS MNR72, F73 KIGCAE LVT91

20.84

l-tyrosine

Endo-camphorcarboxylic acid ()-10.6 (þ)-10.6 (R,S)-()-10.7 (S)-()-10.7 Type (d) 1,12-dimethyl[4]helicene ()10.11b (80K) ()-Decachlorophenanthrene

7.349

c

Space group

Z

1.9

Pna21 P212121

4 4

1.43

Pna21

4

P212121

4

P21/c

4

P21

2

P21/c

4

332.1

P212121

4

12.165

332.7

Pbcn

4

18.554

421.6

Pbcn

4

1.53

1.5

Results obtained from powder samples (LTYROS02, DLTYRS01) should be viewed with some reserve. References: BK92 – Brock, Kwiatowski, Watt and Sayed 1992; F73 – Frey et al., 1973; HKM76 – Herbstein, Kapon and Merksamer, 1976; HSS63 – Hirshfeld, Sandler and Schmidt, 1963; LVT91 – Lalancette, Vanderhoff and Thompson 1991; MR73 – Mostad and Rømming, 1973; MNR72 – Mostad, Nissen and Rømming, 1972.

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

(a)

577

(b)

b b

c

a

a

c

Fig. 10.4. (a) A partial packing diagram for (þ)-endo-camphorcarboxylic acid (10.6) showing the helical hydrogen bonded chains viewed normal to the helix axis, which is along [010]. One of the two helices, which pass along the bc cell faces, has been removed for clarity. (b) A partial packing diagram for ()-endo-camphorcarboxylic acid, showing two of the four hydrogen bonded helices, (þ) enantiomer on the right and () enantiomer on the left. (Reproduced from Lalancette, Vanderhoff and Thompson, 1991.)

10.3.5.2

Complications due to conformational isomerism of component molecules

(a) Nonmimetic enantiomorph–racemic compound pairs. CH3

H3C

CH3

N

O

Cl 10.8

Some of the complications that can occur with conformationally non-rigid molecules are illustrated by 3-(o-chlorophenylimino)camphor (10.8; enantiomorph CPIMCM, Baert, Foulon and Fouret, 1975; racemate RCPICM10, Foulon, Baert and Fouret, 1979). The binary phase diagram shows a complete range of solid solutions, with a minimum at the 1 : 1 composition (cf. Fig. 10.1(g)). However, a racemic compound is obtained on crystallization from solution, so the lower-temperature portion of the phase diagram differs from that found at higher temperatures. The enantiomer ˚ , V ¼ 1500 A ˚ 3, crystallizes in space group P212121 (a ¼ 16.48, b ¼ 12.32, c ¼ 7.39 A ˚, Z ¼ 4) and the racemic compound in P21/a (a ¼ 13.80, b ¼ 10.44, c ¼ 10.46 A ˚ 3, Z ¼ 4). There is no resemblance between the two unit cells. ¼ 105.1 , V ¼ 1455 A

PACKING COMPLEXES

578

The molecular arrangements differ considerably, with different conformers present. The crystals of the (þ) enantiomer have an ordered arrangement of one conformer C. The racemic compound contains a disordered arrangement of two other conformers A and B, with a 72% probability of A being found at a particular site, and a 28% probability of B. Each conformer is present as equal amounts of both enantiomers. Comparison of molecular volumes in the racemic compound and enantiomorph shows that packing is more efﬁcient in the former ( ¼ 3.0%). The () form is described as ‘‘a true but disordered racemate’’ (Kroon, van Gurp, Oonk, Baert and Fouret, 1976). (b) Mimetic enantiomorph–racemic compound system. The carvoxime (10.9) system has been extensively studied and illustrates a number of important points; the rather tortured path leading to our still-incomplete current understanding is set out in the references given with Table 10.4. Structures of three different phases (racemic compound, ()-enantiomorph and 0.4(þ)-0.6()-solid solution have been reported; their cell dimensions (Table 10.4) are similar, showing that the system is mimetic. The essential feature common to the three crystal structures is the occurrence of pairs of molecules linked by hydrogen bridges as shown in 10.9a. The principal variable feature is the conformation of the isopropenyl group with respect to the six-membered cyclohexene ring. Complications arise from the fact that the two enantiomers (C(4) is asymmetric) exist as different conformers in the different crystal types, the isopropenyl groups being free to rotate about C(4)–C(8); the numbering follows that of the references). The details of the three crystal structures can now be described in terms of this background. C7H3 C1

H

N OH

H H

4

C

H H

10.9

H C

8

9

C H2

O

H

H

O

N

N

10.9a

H3C10

We start with the simplest structure, that of the racemic compound (Fig. 10.5). Here the six-membered hydrogen-bonded ring has a crystallographic centre of symmetry. There is one carvoxime molecule in the asymmetric unit and no disorder (neither methyl group shows rotational disorder (!)), although the isopropenyl group, attached equatorially to the cyclohexene ring, does show appreciably more thermal motion than the rest of the molecule. The (–)-carvoxime enantiomorph has two crystallographically independent molecules in the asymmetric unit with different conformations of the isopropenyl group (Fig. 10.6); there is a pseudo-center of symmetry in the hydrogen-bonded ring as opposed to the crystallographic center in Fig. 10.5. The true mirror-image relationship between (þ) and () enantiomers is shown in Fig. 10.5 and is to be compared with the pseudo-mirror image relationship of the two conformers (I and II) (of the same enantiomer) of ()-carvoxime in Fig. 10.7 (see also the Newman projections of Figs. 10.5 and 10.7). Thus the ()-enantiomorph molecules take up three different conformations – one in the racemate and two in the ()-enantiomorph.

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

579

˚ , deg, A ˚ 3) for the three phases in the (þ)-() carvoxime system; all Table 10.4. Crystal data (A three have four molecules in the unit cell. The units of Hfus and Sfus are kJ/mol and J/mol deg respectively. The enantiomorph-racemate pairs are mimetic Phase

a

racemic compound CARVOX01; BF75, OK76 enantiomorph LCARVX; KvG76 mixed crystal 0.4( þ )–0.6( ) CARVOX02; BFOK78

b/ 9.856

11.848 98.95

10.24

11.67 103.1 11.84 99.1

9.87

c

V/mol

space group

m.pt. C

Hfus

Sfus

8.480

244.5

P21/c

92

15.2

44.8

8.54

248.5

P21

72

22.2

64.4

8.48*

244.5

P21

–

–

–

* misprinted as 9.48 in the original paper. References: BF75 – Baert and Fouret, 1975; BFOK78 – Baert, Fouret, Oonk and Kroon, 1978; KvG76 – Kroon, van Gurp, Oonk, Baert and Fouret, 1976; OK76 – Oonk and Kroon, 1976.

methyl B

1.314 Molecules related by centre of symmetry

N O 2.798

y A

x

C9

C5

C10

C3

0

NOH HON

H(C4)

Fig. 10.5. (upper diagram) : Carvoxime racemate : projection along [001] of the structure of ()carvoxime showing the two enantiomers related by a crystallographic centre of symmetry and linked by hydrogen bonds between the oxime groups. (lower diagram) : The Newman projection along the C(4)–C(8) bond of racemic carvoxime is shown on the left. The mirror-image relationship between the two enantiomeres in the racemic compound is shown on the right. (Data from Kroon, van Gurp, Oonk, Baert and Fouret, 1976.)

PACKING COMPLEXES

580

B 1.318

Molecules are crystallographically indpendent 2.807

N O 2.793

y A

x

0 1.328

Fig. 10.6. Carvoxime ()-enantiomer : projection along [001] of part of the structure showing the two crystallographically independent ()-enantiomers of the asymmetric unit linked by hydrogen bonds between the oxime groups. Molecule I is at the top right and molecule II at the lower left. There are also differences in the conformations of the six-membered rings. The two I–II pairs in the unit cell are related by a twofold screw axis.

C5

C3

C5

H(C4)

C3

H(C4)

NOH HON

Fig. 10.7. (upper diagram) Newman projections along the C(4)–C(8) bond of the ()-carvoxime molecules molecule I of ()-carvoxime on the left; molecule II of ()-carvoxime on the right. The large qualitative differences among the Newman projections are quite clear; torsion angles are given in the original papers. The Newman projection (Fig. 10.5) of the carvoxime of the racemate is a third conformation. (lower diagram) The pseudo mirror-image relationship between the two independent molecules, I and II, of ()-carvoxime. (Reproduced from Kroon, van Gurp, Oonk, Baert and Fouret, 1976.)

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

581

The small but signiﬁcant differences in cell dimensions between enantiomorph and racemic compound are ascribed to these differences in molecular shape; the mirror-image molecules in the racemic compound pack somewhat more tightly than do the conformers of the enantiomorph. The composition of the mixed crystals was estimated from the structure analysis (Kroon, van Gurp, Oonk, Baert and Fouret, 1976) as 40% (þ) and 60% (); the structure is essentially that of the racemic compound, but with 15% of the ( þ ) molecules in the B sites (deﬁned by Kroon et al.) replaced by () molecules that have, however, the conformation of the I molecules in ()-carvoxime rather than that of the ()-molecule in the racemate. Differences in Newman projections for (þ) and () molecules in the mixed crystal are similar to those given above for enantiomorph and racemate. Details of the distributions among the sites are not known nor whether phase transitions occur in the racemic compound on heating from room temperature to the melting point. It is surprising that the structure of the mixed crystals resembles that of the racemate – surely disorder would have been anticipated. This is one of the yet-unsolved puzzles presented by this system; the provenance of the racemate is another. Here the phase diagrams (Fig. 10.8) do not help to resolve the inconsistencies. The last word about this system has yet to be written. Another example of the effects of conformational differences in a mimetic system is provided by 3-(1-phenylpropyl)-4-hydroxycoumarin (10.10; generic name phenoprocoumon; Valente, Trager and Lingafelter, 1976). The cell dimensions of the ˚ 3, P21, Z ¼ 4; ˚ , ¼ 92.58 , V ¼ 373.5 A ()-enantiomorph (11.752, 17.751, 7.171 A ˚ , ¼ 92.30 , PPRHCM) and those of the racemic compound (11.407, 18.005, 7.177 A ˚ V ¼ 367 A3, P21/n Z ¼ 4; PRCOUM) are similar and this suggests that enantiomorph and racemic compound are isostructural. The racemic compound contains successive layers of () and (þ) molecules. The ()-enantiomorph contains one layer almost identical with the () layer of the racemic compound while the () molecules in the second layer (a)

(b)

365

S 4

96

8

92

355 12

88

T/K 16 (+) 345 0.0 (–)

4 0.5 (±)

8

12

16

(–)

1.0 (+)

Fig. 10.8. (a) The binary solid–liquid equilibrium diagram for the system (þ)/()-carvoxime; the experimental points were determined by Adriani in 1900, the solid lines show the calculated phase diagram and the dot-dash line is the equal G curve. (b) the ternary solubility diagram for the system (þ)/()-carvoxime-hexane, determined by Jacques and Gabard in 1972. (Reproduced from Baert, Fouret, Oonk and Kroon (1978), where full references are given.)

582

PACKING COMPLEXES

adopt a different conformation involving a 180 rotation about the bond between coumarin ring and asymmetric carbon, with the result that the packing in this layer is similar to that in the ( þ ) layer of the racemic compound. The already high thermal motion of the molecules in the racemic compound is appreciably increased in the enan˚ axis tiomorph. Where the racemic compound has hydrogen bonding along the 7 A between molecules of the same conﬁguration, the enantiomorph shows similar hydrogen bonding between molecules of the same conformation. The relative bulkiness of the coumarin ring (cf. Section 10.3.7 below) presumably plays an important role in making possible the resemblances in packing found in the two types of crystal. The camphoroxime system (Baert and Fouret, 1978) provides a somewhat similar situation. O

O

∗ OH 10.10: The asymmetric carbon atom is indicated by an asterisk.

10.3.6

Enantiomorphs and racemic compounds of nonisolatable conformers

Some overcrowded molecules, such as [4]helicene (BZPHAN, 10.11a) and 1,12-dimethyl[4]helicene (DMBPHA, 10.11b), are chiral by virtue of their non-planarity; both these examples racemize rapidly in solution at room temperature but not in the solid, while higher helicenes, to which the same principles apply, racemize less rapidly or not at all in solution, the rate depending on temperature and the material under consideration. 10.11a crystallizes in space group P212121 and thus spontaneous resolution has occurred on crystallization (Herbstein and Schmidt, 1954). A racemic compound of 10.11a is not known but 10.11b crystallizes as a racemic compound (Hirshfeld, Sandler and Schmidt, 1963) and the two structures are related in a similar way to those of l- and dl-alanine. R R

10.11a: R = H; 10.11b: R = CH3.

Decachlorophenanthrene (Fig. 10.9; Herbstein, Kapon and Merksamer, 1976; DCLPHA) is isostructural with 10.11b (compare cell dimensions in Table 10.3). One would expect the enantiomers of both these molecules to crystallize in space group P212121, but this has not been tested because neither has yet been resolved. Restricted rotation about a single bond can lead to chirality of a molecule. The enantiomers racemize rapidly in solution but are stabilized in the crystal. An example (among many) of an enantiomorph resulting from such a situation is given by tartronic acid (HMALAC01, at 123K, 10.12; van Eijck, Kanters and Kroon, 1965; Roelofsen et al., 1978, at 300K), which crystallizes in space group P212121, Z ¼ 4. The structure consists of

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

583

Fig. 10.9. Stereodiagram of the crystal structure of decachlorophenanthrene viewed down [100]; b is vertical and c horizontal. The unit cell is outlined. In the horizontal slices parallel to (010) the molecules are related by screw axes and translations and hence all have the same sense of chirality. Parallel slices, as one moves along [010], are of alternating sense of chirality, each slice being related to the next by inversion centres and c glide planes. (Reproduced from Herbstein, Kapon and Merksamer, 1976.)

parallel inﬁnite chains of molecules, each chain generated by a screw axis and held together by hydrogen bonds between pairs of carboxyl groups. The molecule deviates slightly but signiﬁcantly from Cs(m) symmetry and is thus chiral in the crystal; the two carboxyl ligands are stereoheterotopic (ligands which cannot be superimposed by rotation about a Cn axis, or by rapid changes in conﬁguration or conformation, are heterotopic). Such ligands in stereoisomerically different environments are stereoheterotopic—see Stoddart (1979) for more detail. The space group is enantiomorphic and spontaneous resolution of enantiomers has taken place on crystallization; of course, racemization will be immediate on dissolution. The situation is analogous to that in [4]-helicene (10.11a) discussed earlier. In diﬂuoromalonic acid (10.13; P21/c, Z ¼ 4; Kanters and Kroon, 1972; DFMLON) the angle between the F-C-F plane and those of the two carboxyl groups are 25 and 46 respectively. The two carboxyl ligands are stereoheterotopic in the crystal; the ‘‘frozen-in’’ molecular conformation is chiral but the crystal is, of course, racemic.

O

HO

H

C

C

OH

OH

F

O

O

F

C

C

OH

OH

O

difluoromalonic acid (10.13)

tartronic acid (10.12)

H Cl Cl H2 N

HO NH2

HO

H COOH COOH

2,2’-dichlorobenzidine (10.14) meso -tartaric acid (10.15)

584

PACKING COMPLEXES

The 2,2 0 -disubstituted diphenyls and analogs provide a similar situation; for example, in 2,2 0 -dichlorobenzidine (10.14; Pnca, Z ¼ 4; Smare, 1948; CLBZID) the chiral molecules have (space group imposed) C2–2 symmetry in the crystal, their conformation being cis with an angle of 72 between the two phenyl ring planes. However, the space group is centrosymmetric and thus the crystal is racemic. A similar situation occurs in meso-tartaric acid (10.15) which would have symmetry Cs-m if eclipsed or Ci 1 if staggered (the conformation usually assumed). However, the molecules have gauche conformations in the triclinic monohydrate (TARTMM, P1, Z ¼ 2) and in the triclinic (TARTAM, P 1, Z ¼ 2) and monoclinic (P21/c, Z ¼ 4) anhydrous forms and are thus chiral in the crystals. Bootsma and Schoone (1967) remark that ‘‘The crystals are racemic compounds and their lack of optical activity is caused by intermolecular compensation of the ‘conformational antipodes’. ’’ 10.3.7

Racemic enantiomorphs and noncentrosymmetric racemates

Although the phrase ‘racemic enantiomorphs’ appears to involve a contradiction in terms, it is applicable when the asymmetric unit in an enantiomorphic crystal is made up of a number (one or more) of pairs of enantiomers of opposite sense of chirality (some disordered exceptions to this deﬁnition are noted below). Bernal (1996) has coined the term ‘kryptoracemic crystallization’ for this phenomenon and noted its rarity; one example is known among organometallics, four among coordination compounds and some twenty odd among organic compounds. These numbers are supported by an incomplete search carried out by Dalhus and Go¨rbitz (2000a) who found 17 examples among some 24 000 unique crystal structures (all with space groups containing only symmetry elements of the ﬁrst kind) reported in the October, 1998 release of the CSD containing some 78 000 unique structures; see also Section 10.3.1. The crystal (if not twinned) will have an absolute (crystal) structure determinable by (now) standard methods; the solution derived from that crystal will not rotate the plane of polarized light. A striking example is o-tyrosine (10.16; dl-2-hydroxyphenylalanine; P21, Z ¼ 4; Mostad, Rømming and Tressum, 1975; DTYROS); there are two molecules in the asymmetric unit, one d and one l. The enantiomers are in the zwitterionic form shown in the formula, with an intramolecular hydrogen bond between an NH of the ammonium group and the hydroxyl oxygen. There is intermolecular hydrogen bonding between the other two NH groups and the two oxygens of the carboxylate group and also an OH . . . O hydroxyl– carboxylate hydrogen bond. The two enantiomers are related by a noncrystallographic or local centre of symmetry. Another example is the quasi-racemic compound formed by ( þ )-3-bromophenoxypropionic acid (10.17a) and ()-3-methoxyphenoxypropionic acid (10.17b), which crystallizes in space group C2, with Z ¼ 8 (Karle and Karle, 1966; MPBOPA); the asymmetric unit is thus the quasi-centrosymmetric pair of enantiomers (ignoring the difference between bromine and methoxy) hydrogen bonded through their carboxyl groups. As the phase diagrams of the three binary systems formed by the combinations of ( þ )- and ( )-3-X-phenoxypropionic acid (X ¼ Br, OCH3) are very similar (Fredga and Andersen, 1964), it is likely that the true racemic compounds are isomorphous with the quasi-racemic compound whose crystal structure has been reported. Brock et al. (1991) give another seven examples (BIJVEV, CEHBUM, CUMFEV, DCPENT, FAXMIA, SSESOX), including dl-methylsuccinic acid (DLMSUC) discussed below.

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

585

The second phrase ‘noncentrosymmetric racemates’ presents no conceptual difﬁculties because the two enantiomers can be related by a mirror (or glide) plane, or an axis of rotoinversion. This will be an exact crystallographic relation; it is not necessary for a center to be present. The crystal will have an absolute structure determinable by standard methods; the solution derived from that crystal will not rotate the plane of polarized light. NH+3

–OOC C H2C

X

H

CH3 C

H O

COOH

HO 10.17 (a, X = Br; b, X = OCH3) 10.16 (o -tyrosine)

As already noted, the occurrence of conformers can introduce complications. ()-2-Amino-1-phenyl-1-propanol hydrochloride C6H5C*H(OH)CH(NHþ 3 )-(CH3)Cl crystallizes from an optically inactive solution in space group P21 with 4 molecules in the unit cell (Hebert, 1979; NEPHCL). This appears to be another example of a racemic enantiomorph; however, the two molecules deﬁned as enantiomers on the basis of their behaviour in solution have different conformations in the crystal, one extended trans and the other folded into a gauche form, and are thus in fact diastereoisomers in the solid state. The same material can behave in different ways depending on conditions of crystallization. For example, dl-methylsuccinic acid (H3CC*H(COOH)CH2(COOH)) has two polymorphic forms (DLMSUC02, triclinic P 1, Z ¼ 4 and monoclinic (P21, Z ¼ 4; DLMSUC01, Schouwstra, 1973b). Their structures are related as, in both, each molecule is linked to its neighbors in the adjacent unit cells by planar pairs of hydrogen-bonded carboxyl groups, forming two chains of d-molecules and two chains of l-molecules. In the monoclinic crystal (the racemic enantiomorph) the stacking of the chains results in a structure in which crystallographic 21 axes are combined with pseudo-inversion centers. In the triclinic crystal (the racemic compound) crystallographic inversion centers are combined with pseudo-21 axes; a number of variations on this theme recur. There is a second monoclinic polymorph (C2/c, Z ¼ 8; Schouwstra,1973a; DLMSUC). For completeness we note that a two-molecule asymmetric unit of an enantiomorphic crystal need not be racemic; for example, levopimeric acid C20H30O2 crystallizes in space group P212121, with eight molecules of the same sense of chirality in the unit cell (Karle, 1972; LEVPIM10), and an analogous situation occurs in enantiomorphic [7]helicene (P21, Z ¼ 4; Beurskens, Beurskens and van den Hark, 1976), where a racemate has also been reported (P21/c, Z ¼ 4; van den Hark and Beurskens, 1976; Joly et al., 1977). 10.3.8 Solid solutions of enantiomers The general conditions for the formation of solid solutions between two molecules of different types were set out by Kitaigorodsky (1984) and require that the crystals of the two components be isomorphous (i.e. similar cell dimensions and same space group), the

PACKING COMPLEXES

586

molecules be isosteric (i.e. they occupy (almost) the same regions of space; ‘congruent’ is also used) and that there should be compatibility of the hydrogen-bonding schemes or other special interactions between the two components. These requirements will be considered in a general sense in Section 10.6.1 but now we restrict ourselves to solid solutions of enantiomers. Although crystals of enantiomers have identical cell dimensions and space groups (apart from sense of chirality), one would not expect complete or even appreciable solid solubility because the enantiomeric molecules are not congruent, and their hydrogen-bonding schemes (or the like) will not necessarily be compatible. However, the greater the approach to congruence, the greater the degree of mutual solid solubility that is to be expected. One, almost trivial, possibility is that the particular atoms or groups causing the asymmetry are mutually interchangeable (e.g. methyl and chlorine) as they have similar volumes and are without special intermolecular bonding requirements. An example does not yet appear to have been reported. Another possibility, different in degree rather than kind, is when the chirality derives from an asymmetric centre which is part of a larger molecule; thus the enantiomers differ little in overall shape, the crystal packing being determined by moieties bulkier than the chiral groups, which are found to be completely or partly disordered. (R,S)-(2-chloro-2ﬂuoro-2-nitroethyl)-p-toluenesulphonate (Chekhlov, Chepakova, Brel and Martynov, 1990) is a representative example. Crystals obtained from a racemic hexane solution have space group P212121 with 4 molecules in the unit cell, the overall arrangement of the molecules in the cell being chiral; however, two of the molecules are R and two S, hence the crystal is racemic (‘‘its solution will not rotate the plane of polarized light’’). The bulkier toluenesulphonate portions of the molecule take up ordered positions in the unit cell and determine the overall structure, while the asymmetric portions of the molecule are disordered; possibly there are separate domains in the crystal which contain only (R) or only (S) molecules, as discussed by Zorkii and Nesterova (1986, 1990) for C16H16O4Se and 3-bromobicyclo[3.3.1]non-2-en-4-one. In 2-exo-norbornalol-p-toluenesulphonate (10.18; P 1, Z ¼ 2; Altona and Sundaralingam, 1972; NORBOR10) the toluenesulphonate portions again determine the overall structure, and there is a rather complicated disorder of the chiral norbornalol portion, the ratio of enantiomers on a particular site being about 3 : 1 or 1 : 3. O

O O

S O 10.18

CH3

H N

1-adamantyl

1-adamantyl 10.19

In 1,3-diadamantylaziridinone (10.19; C2/c, Z ¼ 8; Wang, Paul, Talaty and Dupuy, 1972) the packing is determined by the bulky adamantyl groups and the aziridinone ring is disordered; at any particular site the ratio of enantiomers is 2 : 1. Another example giving a racemic solution is (O2NClFC–CH2O)2CH2 (Chekhlov, Solov’ev, Brel, Kartavtseva, Chepakova and Martynov, 1988; SEFVOS). The space group is P41212, Z ¼ 4 and the molecules have symmetry C2 2; the chloroﬂuoronitromethyl group is disordered over two orientations with occupancies 0.75 and 0.25.

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

O

O

H5C2

CH3

H N

CH3 C

H5C2

H

H

CH2

CH2

N

O

587

O

H

N H

10.20

10.21

A somewhat similar situation occurs in dihydrothymine (10.20) where determination of the crystal structure (Pcab, Z ¼ 8; Furberg and Jensen, 1968; DHTHYM) shows that the material is a racemic compound. However, the enantiomers are not segregated to particular sets of sites in the cell but are disordered at the 8 equivalent positions, with a 3 : 2 (or 2 : 3) ratio of enantiomers in any particular position. This suggests that short range order may be present. The molecular structure of dihydrothymine is such that all the atoms of the d and l molecules, including the methyl groups, can be brought into coincidence except for the asymmetric carbon and its adjacent CH2 group. This also holds for 2,4-dioxo-3,3-diethyl-5-methylpiperidine (10.21), where the system has some unique features. The compound is a hypnotic and is marketed under the name Methyprylon (formerly Norludane). Early work (Vogler and Koﬂer, 1956) showed that the commercial material, supposedly a racemate but which was always found to give solutions of weak optical activity, could be separated into enantiomers by a laborious series of recrystallizations (e.g. 20 kg of starting material gave, after about 400 crystallization stages, 3 g of (þ)- and 2 g of ()-enantiomer). The melting point diagram (Fig. 10.10; Kuhnert-Brandstatter, Schleich and Vogler, 1970) showed that the enantiomers crystallized in two polymorphic forms, one (I) melting at 84.5 C and the other (II) at 79.5 C. The binary system formed is between the stable polymorph of one enantiomer (say (þ)-I) and the less-stable polymorph of the opposite 86 I

I

II

II

84 82 80 °C 78 76 74 +120°

+80°

+40°

0°

–40°

–80°

–120°

Fig. 10.10. The melting point diagram of the (þ)- and ()- enantiomers of 2,4-dioxo-3,3-diethyl-5methylpiperidine. The abscissa gives the optical rotation of the dissolved sample and this is assumed to be linearly proportional to the amount of enantiomer present. (Reproduced from KuhnertBrandstatter, Schleich and Vogler, 1970.)

PACKING COMPLEXES

588

Fig. 10.11. (Upper stereopair) One enantiomer of 2,4-dioxo-3,3-diethyl-5-methylpiperidine. (Lower stereopair) The superposed enantiomers of 2,4-dioxo-3,3-diethyl-5-methylpiperidine. All the atoms coincide in space except for one carbon and some of the hydrogens (whose locations are less precisely determined). (Reproduced from Oberha¨nsli, 1982.)

enantiomer (thus ()-II). The unit cells of the two polymorphs are similar (I : a ¼ 13.122, ˚ , V ¼ 1038 A ˚ 3; ˚ , V ¼ 1047 A ˚ 3; II : a ¼ 12.354, b ¼ 12.302, c ¼ 6.828 A b ¼ 11.690, c ¼ 6.828 A both P212121, Z ¼ 4; Oberha¨nsli, 1982; REFCODES are BEPHUV–Z) and so are their crystal structures. The cell dimensions of intermediate compositions were linearly proportional to the optical rotation of the dissolved sample. The close structural resemblance between the two polymorphs and the nature of the binary system are both most unusual. The superposed enantiomers, as determined from the crystal structure analysis, are shown in Fig. 10.11. In view of the resemblances already noted between the molecular structures and arrangements of 10.20 and 10.21, it would be interesting to see whether dihydrothymine gives a similar binary phase diagram. CH3 H3C

O N CH3

∗ R

CH3

a R = C(O)NH2 b R = OH c R = COOH d R = CH2OH

H

10.22 (the asymmetric carbon atom is indicated by an asterisk).

THE (STEREOISOMERIC) COMPONENTS ARE ENANTIOMERS

589

An extensive study has been made of a series of derivatives of the free radical 2,2,5,5tetramethylpyrollidine-1-nitroxide (10.22), which are all chiral because of the asymmetric carbon at the 3-position. One non-mimetic and three mimetic situations have been encountered (Table 10.5). The enantiomorph and racemic compound of 10.22a are not mimetic and this is explained by the differences in the hydrogen-bonding schemes. The enantiomorph has a full set of N–O . . . H–N hydrogen bonds, and these also appear between four of the eight molecules in the unit cell of the racemic compound, with the other four being linked into two sets of dimers with hydrogen bonds between oxygens and NH’s of amide groups. The molecular volume is smaller in the enantiomorph than in the racemic compound (contrary to some speculations noted above) and one could guess that it is more stable (thermodynamically) than the racemic compound and that this is due to the hydrogen bonding. Appropriate measurements of the free energy, enthalpy and entropy of formation of the racemic compound are not known for this system. The crystallization of enantiomorph and racemic compound together in the same solution is not unusual and many examples of co-temporaneous crystallization of metastable and stable polymorphs are known (Bernstein, Davey and Henck, 1999).

˚ , deg, A ˚ 3) for various derivatives of 10.22. Melting Table 10.5. Summary of crystal data (A points in C Compound

10.22a Enantiomorph (non-mimetic) Racemic compound 10.22b Enantiomorph solid solution (mimetic) 10.22c Enantiomorph solid solution (mimetic) 10.22d Enantiomorph Solid solution

a

b

c

V

Z

Space group

Remarks and notes

Refcode/ Reference

(a)

TMPYRO CL75

6.551

10.156 107.9

8.098

512.7

2

P21

7.983

25.349

2162

8

P21/c

9.953

10.840 99.7 6.678

13.940

926.5

4

P212121

10.091

6.666

13.968

939.6

4

8.089

10.097

12.404

1013

8.037

10.119

12.488

6.766

9.949 114.6 10.02 114.2

6.743

RTMPRO

Cmcm

m.pt. 126 (b) m.pt. 126

TMXPYO CLCJ76 Not given

4

P212121

See text

1016

4

Pnma

CXPYRO10 LCL76 RCXPYO

8.121

497.0

2

P21

Mimetic

8.085

498.5

2

P21 or P21/m

(c)

TMXPYP CLBCJ78 RHMPYO

Notes: (a) Racemic compound and enantiomorph crystallize from the same solution. (b) No diffuse scattering from solid solution crystals. (c) Solid solution has 60 : 40 composition. References: CL75 – Chion and Lajzerowicz, 1975; CLBCJ78 – Chion, Lajzerowicz, Bordeaux, Collet and Jacques, 1978; CLCJ76 – Chion, Lajzerowicz, Collet and Jacques, 1976; LCL76 – Lajzerowicz, Chion and Lajzerowicz, 1976.

PACKING COMPLEXES

590

The phase diagram of 10.22b shows a complete range of solid solutions (similar to the schematic diagram of Fig. 10.1(g)). The symmetry of the asymmetric unit in the racemic solid solution (space group Cmcm) is mm2 and this is achieved by a disordered packing of four molecules at each site, each molecule having an occupancy factor of 1/4. The absence of diffuse scattering in the diffraction photographs suggests that there is negligible short range order in the disordered arrangement. The absolute conﬁguration of the ( þ )-enantiomer was determined as R from measurements of circular dichroism (Collet, Jacques, Chion and Lajzerowicz, 1974). An enantiomorph and a racemic solid solution are also obtained for 10.22c, suggesting that there should be a complete range of solid solutions. The binary diagram could not be determined because of decomposition of the materials at high temperatures but the ternary diagram (CHCl3 as solvent) is compatible with this suggestion. However, the solid solution crystals show marked diffuse scattering and this has been interpreted (Lajzerowicz, Chion and Lajzerowicz, 1981) in terms of a two-dimensional ordering of enantiomers within layers, which have an almost random stacking. The correlation area ˚ 2 and contains about 140 molecules. The absolute conwithin a layer is about 60 95 A ﬁguration of the ( þ )-enantiomer of 10.22c was shown to be R by measurement of Bijvoet differences stemming from oxygen atoms (Wetherington, Ament and Montcrief, 1974). The two enantiomers of 10.22d give an incomplete range of solid solutions (as illustrated in Fig. 10.1(b)); the limiting composition, for which details are given in Table 10.5, was determined to be 60 : 40 from measurements of the speciﬁc rotation on dissolution. The chiral space group was preferred because of the optical activity of the solution obtained from the crystals.

10.4 10.4.1

The (stereoisomeric) components are diastereoisomers Background

As background we give an impression of the incidence of conformer and tautomer complexes obtained from statistical analyses of the 1987 CSD release (Chernikova, Belsky and Zorkii, 1990; Padmaja, Ramakumar and Visamitra, 1990); we have already noted the later study of Dalhus and Go¨rbitz (2000a). About 50 000 unique structures remain for analysis after culling. The asymmetric unit contains more than one molecule in about 10% of homomolecular organic crystals, with a rather uneven distribution among the space groups (Sona and Gautham, 1992; Gautham, 1992). Of this subgroup, 17% were conformers and 2% tautomers. Thus we should expect the 50 000 organic crystals to include 850 examples of conformational isomerism and 100 examples of tautomeric isomerism. It is, of course, highly unlikely that it will be possible to isolate individual conformers or tautomers because of their lability in solution, and their binary adducts will be stable only in the solid state. 10.4.2

Diastereoisomers as components

Budesonide (10.23) (11,21-dihydroxy-16,17-propylmethylenedioxy-1,4-pregnadiene3,20-dione exists as (22S; SHBUXP10) and (22R; RHBUXP10) epimers (Albertsson,

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

591

Oskarsson and Svensson, 1978). These form a complete range of solid solutions, the shape difference between the two epimers being rather small and the packing in the crystals being determined by hydrogen bonding between the bulk portions of the molecules, which are minimally changed by epimerization. The n-propyl chain is equatorially oriented to the dioxolane ring in both epimers and is thus -axial to the steroid; the chains take up two disordered orientations (in roughly equal amounts) and this enhances the similarity of the overall arrangement. The cell dimensions of the solid solutions have been measured as a function of composition; a decreases by 1.5% as the epimeric composition goes from pure (22S) to pure (22R), b decreases by 4% and c increases by 5%, with the cell volume only ˚ 3). Diffraction peak breadths are 1 at the ˚ 3; 22S : 2284 A changing slightly (22R : 2259 A 1 : 1 composition compared to 0.2 at the composition extremes, hinting at disorder or internal strains about the 1 : 1 composition. OH

O HO C

D

O E

A

B

O

22

H

O 10.23

Pipitzol (C15H20O3), isolated from the roots of Perezia michoacana as a mixture of and diastereoisomers (10.24a [3R-(3,3a,7,8a)]- and 10.24b [3R-(3,3a,7,8a)]1,2,3,7,8,8a-hexahydro-5-hydroxy-3,6,8,8,-tetramethyl-4H-3a,7-methanoazulene-4,9-dione), gives an : co-crystal (space group P1, Z ¼ 1 þ 1; Evans, Yee, Garcia-Garibay and Trotter, 1994; HATZUX), as does the analogous mixture of the acetates (C17H22O4) (space group P212121, Z ¼ 4 þ 4; Soriano-Garcia, Walls, Toscano and Lo´pez-Celis, 1986; DUXYEA). The - and -pipitzol molecules are enantiomeric at three carbon centres, but have the same (R) conﬁguration at one carbon atom. There is hydrogen bonding of / pairs (related by a pseudo-center of symmetry) in the triclinic crystals but this is not possible in the crystals of the acetates because of the absence of acceptors. The crystal structures of -pipitzol benzoate (not relevant in the present context) and -pipitzol acetate have been determined (Soriano-Garcia, Toscano and Walls, 1986; DIRNUN); the latter is orthorhombic (P212121, Z ¼ 4) but with different cell dimensions from DUXYEA. Thus ( þ )-pipitzol acetate is not a ‘‘mixed crystal’’ of the separate acetates but a phase rule compound. An even more striking example, with four independent molecules in the asymmetric unit of the crystal is provided by 4-hydroxy-6-methoxy-5,9,13,13-tetramethyl-2oxotetracyclo[6.5.0.01,8.08,12]tridecane-7-one (10.25; Soriano-Garcı´a, Walls, Yuste, Sa´nchez-Obrego´n, Ortı´z, Dı´az, Toscano and Barrios, 1990; TADRIZ; monoclinic P21, ˚ , 96.73(2) ), which was prepared by UV irradiation Z ¼ 8, 7.883(2) 14.347(2) 27.673(6) A of O-methylmethoxyperezone, and obtained as a minor product. The carbon skeleton

PACKING COMPLEXES

592

of the molecule consists of a system of fused cyclohexenone (A), cyclobutane (C) and cyclopentane (D) rings. Furthermore, the A ring is fused to an oxetane (B) ring. The four asymmetric carbon atoms C(1), C(4), C(8) and C(12) are marked by asterisks. Diastereoisomers (I) and (III) have the (1R, 4S, 8R, 12S) conﬁguration, and (II) and (IV) (1S, 4R, 8S, 12R). The A/B, A/C and C/D ring junctions are cis, except for the A/B and A/C junctions in molecules (II) and (III) which are trans. The ﬁve membered rings have envelope (I), half chair (III) and intermediate between half chair and -envelope conformations ((II) and (IV)). There is no disorder. Thus there are two pairs of diastereoisomers, but all four have different conformations. There are four intermolecular hydrogen bonds, between (I) and (II), and between (III) and (IV). The crystal structure of the major product from irradiation of O-methylmethoxyperezone is orthorhombic (Soriano-Garcı´a, Walls, Yuste, Sa´nchez-Obrego´n, Ortı´z, Dı´az, Toscano and Barrios, 1989; VARVIX) and thus TADRIZ should be considered a phase rule compound. 3′ 12′

8′

11′

6′

A

7′

B 3′

4′

H

15

10′

C O 1′

5′

OR

2

9′

O

15′

3

OR

2′

1′ 2′

9

O

12

8

10

C O1

H

5

7

B 3

4

13′

11

6

A

H

14′

10.24a: R = H or COCH3

B

A

2

H 13

14

10.24b: R = H or COCH3

HO

4∗

1

O

CH3

1∗ 8∗

O

C 12∗

CH3

D H3C

H3C

O 10.25

10.4.3

Conformers as components

, Z ¼ 2; Pinkerton, Schwarzenbach, Hubert-Pfalzgraf and Riess, In Nb2(OCH3)10 (10.26; P1 1976), the molecules are centrosymmetric dimers located about independent crystallographic centres of symmetry, and with octahedral coordination about the Nb atoms. However, the dimers differ in the conformations of the methyl groups; in one conformer equatorial methyls on a particular Nb atom are up-down (as shown) and in the other they are up-up. A somewhat more complicated situation is found in H3B(H3C)2P–P(CH3)2BH3 (10.27; P21/c, Z ¼ 6; Carrell and Donohue, 1968), where the unit cell contains two trans

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

593

isomers, at crystallographic centers of symmetry, and two d-gauche and two l-gauche isomers at general positions. An analogous situation occurs in the crystals of trans-1-(trans1-hydroxy-4-methyl-cyclohexyl)-4-methyl-1-cyclohexanol (10.28; P21/n, Z ¼ 6), where the centrosymmetric trans isomer (at a crystallographic centre of symmetry) and the D- and L-gauche enantiomers are stabilized by an extensive set of hydrogen bonds between the conformers (Bruss, Larsen, Walsh, Fait, Mundy, Ekeland and Fitzgerald, 1987; FUJREH). H3C

O

CH3

BH3

O Nb O

O

Nb

O

P O

O

H3C

O

CH3

H3C

O

H3C

CH3

CH3 BH3 10.27

(Newman projection of trans isomer)

10.26 (methyls omitted on axial and bridging oxygens for clarity)

CH3 OH OH

H3C CH3 OH OH 10.29

H3C 10.28

The constitutional isomer {(1S,3R)-1-[(1S)-1-hydroxy-3-methylcyclohexyl]-3-methyl-1cyclohexanol} (10.29) also crystallizes with all three rotamers occurring together in the unit cell, stabilized by intermolecular hydrogen bonding; the chirality of the space group (P1, Z ¼ 3) follows from that of the parent molecule (Bruss et al., 1987; DIJWUO10). In l-N-acetyl histidine monohydrate (space group P1, Z ¼ 2; Kistenmacher, Hunt and Marsh, 1972; ACHIST20) the molecule is found as the zwitterion, with protonation of the imidazole ring. There are two conformers in the asymmetric unit and these differ in the torsion angles about the C C bond; the ‘‘open’’ conformation has 0 and the ‘‘closed’’ conformation 180 (Fig. 10.12). Some ring compounds show conformational effects. One example is the antibiotic cycloheximide (P21, Z ¼ 4; Sayers, Schindler and Sundaralingam, 1977; CHEXIM10), where the two molecules in the asymmetric unit have the same sense of chirality but different conformations. The substantial difference is between the chair and twist-boat conformations of the dimethylcyclohexanone rings, but there are also differences between torsion angles in the glutarimide portion of the molecule (Fig. 10.13). The energy difference between chair and twist-boat forms is less in cyclohexanone than in cyclohexane because of the trigonal carbon in the former. Sayers et al. (1977) quote a number of other examples among nucleosides, nucleotides and steroids where the two independent molecules in the asymmetric unit have different conformations.

PACKING COMPLEXES

594

(a)

(b)

protonated imidazole ring

44 deg. torsion angle

172.3 deg. torsion angle

carboxylate carboxylate z

z x

yx

y

protonated imidazole ring

Fig. 10.12. The two conformations of the L-N-acetylhistidine molecule in L-N-acetylhistidine monohydrate. The ‘‘closed’’ conformation is shown in (a) and the ‘‘open’’ conformation in (b). (Data from Kistenmacher, Hunt and Marsh, 1972.)

C15 C15

N

N

C8

C8 C16 C16

Molecule A

Molecule B

Fig. 10.13. End-on views of the two crystallographically independent cycloheximide molecules showing the chair (A) and twist-boat (B) conformations of the dimethylcyclohexanone rings. (Reproduced from Sayers, Schindler and Sundaralingam, 1977.)

Another example is octamethylcyclotetrasilazane ((CH3)1SiNH)4; P2/c, Z ¼ 4, Fig. 10.14; Smith and Alexander, 1963; OTETSI), which has an eight-membered ring. One crystallographically independent molecule is located at a centre of symmetry and has a chair conformation, while the other is on a two fold axis and has a cradle conformation. Both enantiomers of the cradle conformer are present. There is complete segregation of the three types of differently shaped molecule, each packing into its own stack in the crystal. Among analogous compounds, chair conformations have been reported for ((CH3)2GaOH)4 (Smith and Hoard, 1959) and ((CH3)2SiO)4 (Steinﬁnk, Post and Fankuchen, 1955; OMCSIO) and a cradle conformation for ((CH3)2PN)4 (Dougill, 1961; MTETPN). Conformers are also found among large ring compounds such as cyclononylamine HBr (P21/n, Z ¼ 8; Bryan and Dunitz, 1960; CYNAMB), where the asymmetric unit contains one molecule of each conformer, and 1,8,15,22-tetraa¨za-2,7,16,21-tetraoxacycloo¨ctacosane, which has a 28-membered ring and is a cyclic dimer model for Nylon 66. The unit cell

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

C(1)

595

C(5)

C(2) Si(4∗)

C(3) Si(1)

Si(3)

N(3)

Si(2)

C(7)

N(2) C(4)

N(1)

N(4) N(3*)

N(2)

Si(4)

Si(1) C(8)

C(6)

Chair

Cradle

Fig. 10.14. Diagrams of the two conformers of [(CH3)2SiNH]4. The chair form (left) is centrosymmetric and the cradle form (right) has symmetry C2(2). (Reproduced from Smith and Alexander, 1963.)

O

O

N

H

O

O

H

O O

O O

H N N

O H

O

N

H N

Fig. 10.15. There are appreciable differences in the molecular shapes of the cyclohexaglycyl molecule in its various crystals. This is exempliﬁed by superposition stereodiagrams for four different conformations. (Reproduced from Duax, 1988.)

(P21/c, Z ¼ 4) contains two pairs of centrosymmetric conformers, each at independent centers of symmetry (Northolt, 1970; CHMADP). An even more complicated situation is found in cyclohexaglycyl hemihydrate (P 1, Z ¼ 8) where the 18-membered ring takes up four different conformations, which are shown superposed in Fig. 10.15 and separated in Fig. 10.16. Conformer (a) is stabilized by intramolecular hydrogen bonding, which does not occur in the other conformers (Karle and Karle, 1963; CYHEXG). A similar type of stabilization is found in the 18-membered ring of the polypeptide

gly–gly–D-ala–D-ala–gly–gly ·3H2O. However, only a single conformer is found in these crystals (P212121, Z ¼ 4; Karle, Gibson and Karle, 1970; GGAAGG). The crystals of 5,7,12,14-tetramethyl-1,4,5,8-tetraazacyclotetradecane dihydrate are triclinic, space group P 1, Z ¼ 3, and the asymmetric unit contains one-half of the

PACKING COMPLEXES

596

(a)

(b)

(c)

(d)

Fig. 10.16. Stereodiagrams of the four conformers found in the unit cell of cyclohexaglycyl hemihydrate. The spheres of increasing size show C, N and O atoms. Conformers (c) and (d) lie at crystallographic centres of symmetry and there is one of each type in a unit cell; conformer (b) occurs twice, as two enantiomers, in the unit cell; conformer (a) occurs four times, as two crystallographically independent pairs of enantiomers, in the unit cell. Conformer (a) appears to have an approximate centre of symmetry. (Reproduced from Karle and Karle, 1963.)

centrosymmetric 5SR,7RS,12RS,14SR-1,4,5,8-tetraazacyclotetradecane molecule (A below), one 5SR,7RS,12SR,14RS-1,4,5,8-tetraazacyclotetradecane molecule (B below) at a general position, and three waters unequally distributed over six sites (Tahirov, Lu, Liu, Chi and Chung, 1995; YUHWED). The A and B molecules have different conformations of the macrocycles and different conﬁgurations of the four chiral carbons. The crystal is stabilized by amine–water hydrogen bonds. The occurrence in a triclinic crystal, space

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

(a)

(b) methyl

methyl

N

N

methyl

N

N

N

N

methyl methyl

N methyl

597

methyl

N methyl

Fig. 10.17. A perspective view of the two diastereoisomers A (located about a centre of symmetry) and B (at a general position). (Reproduced from Tahirov, Lu, Liu, Chi and Chung (1995).)

group P 1, of two asymmetric molecules of one type at general positions (related by the center at the cell origin) and a centrosymmetric molecule of a second type, centred at the origin, is a feature common to many complexes and further examples will be presented. Analogous situations are found in some other space groups.

10.4.4 Cis-trans isomers as components No phase diagrams appear to have been reported when the two components are geometrical isomers but certain features can be anticipated on general grounds. For a binary system the two geometrical isomers (E, Z) will be the components and these would be expected to have different crystal structures (be different phases in the language of the phase rule). The EmZn molecular complex will be a third phase and knowledge of the structures of all three phases and of the mutual interactions between their components would be needed for a thorough understanding of the system. We give a few examples to illustrate some of the possibilities. 1. 2-(N-nitrosomethylamino)acetamide (10.30) has an ordered arrangement of E and Z isomers in 1 : 1 ratio (P21/n, Z ¼ 8; Templeton, Templeton and Zalkin, 1973; NSMACM). There is no segregation of like isomers to particular chains or sheets and hydrogen bonds link E to E, E to Z and Z to Z. O–

O– N N

N

O +

O

N+

H3C

H3C

NH2 E

10.30

NH2 Z

The structures of the individual components do not appear to have been determined. 2. 2,5-Dimethyl-3-hexene-2,5-diol (10.31) crystallizes in P1, with two cis molecules at general positions, related by the center of symmetry, and a third moiety at the center. This moiety is predominantly the trans compound, but there appears to be a small admixture of the hexane analog (Ruysink and Vos, 1974; CTHXDL).

PACKING COMPLEXES

598

H3C

CH3

H3C HO

CH3 OH

cis-, trans- 10.31

The background (Dunitz, 1979) to the brief report (Ermer, Dunitz and Bernal, 1973) about the analogous complex with composition (cyclodecane-cis-1,6-diol)2-(cyclodecanetrans-1,6-diol) is given here in slightly abbreviated form (with permission from Professor J. D. Dunitz; see the original for complete references) : In 1952 Prelog and Schenker tentatively assigned the conﬁgurations of the two cyclodecane-1,6diols melting at 152 and 144 C as trans and cis respectively . . . Several years later we became interested in these diols as possible candidates for a neutron diffraction study. Preliminary X-ray examination showed that both crystals were monoclinic, space group P21/c, with Z ¼ 4 (trans isomer, m.pt. 152 C; CDECOL10) and Z ¼ 6 (cis isomer, m.pt. 144 C). Now Z ¼ 4 neither demands nor precludes any molecular symmetry, but Z ¼ 6 implies four molecules in general positions plus two in special positions, the inversion centers; only the trans isomer can have the molecular symmetry thereby imposed. The obvious conclusion is that the previously assigned conﬁgurations should be reversed. However, when the detailed structure of the higher melting isomer (once deemed trans, now cis) was worked out, the four molecules in the unit cell were found to occupy two independent pairs of inversion centers and to be indubitably trans after all. What about the other isomer – once deemed cis, then trans, now by elimination cis? Analysis of the lower melting crystals showed that the four molecules in general positions have the cis conﬁguration, the two in special positions the trans. In other words, this crystal form is actually a molecular compound of the cis and trans isomers in the ratio 2 : 1. This molecular compound seems to be always formed by crystallization from a solution containing both isomers. When the pure cis isomer was ﬁnally prepared . . . it proved to be isomorphous with the 2 : 1 compound [the cell dimensions are (ﬁrst cis, then 2 : 1 ˚, cis : trans VENZOD) : a ¼ 6.665(6), 6.679(8), b ¼ 18.074(4), 18.074(4), c ¼ 14.351(8), 14.314(10)A ˚ 3, P21/c, Z ¼ 6], the two formally centrosym ¼ 119.77(6), 119.64(8) , V ¼ 1500(2), 1502(3) A metric molecules at the special positions of the space group being disordered.

But there was to be a sting in the tail (Ermer, Vincent and Dunitz, 1989). The cis molecules disordered across the centres of symmetry of the pure cis crystals have a different conformation from those in the general positions (which is the same as that found in the 2 : 1 cis : trans complex); thus, to quote Ermer et al. ‘‘In a sense . . . the crystalline cis compound [VENZIX] can be regarded as a molecular compound – between two species of molecule with different conformations but having the same constitution and conﬁguration.’’ It could have been classiﬁed in our Section 10.4.2. A ﬁnal quotation – ‘‘The denouement of this intricate story is that the tentative chemical assignments of Prelog and Schenker are correct after all.’’ ++ H2N C

S

S

NH2 C

Ni N H

N

N

H2

H2 10.32

SO42–

N H

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

599

3. -Dithiosemicarbazide Ni(II) sulphate has two independent sets of cations in the unit cell (A2/a, Z ¼ 8), with the Ni atoms of the trans cations at centres of symmetry and those of the cis cations (10.32) on two fold axes (Grœnbæk-Hazell, 1968; NIDTSS10). 4. Crystal structures are not known for any of the individual components in the previous examples but there are (at least) two systems where complete information is potentially available. The syn (rectangular prisms, m.pt. 179–181 C) and anti (hexagonal prisms, m.pt. 200–5 C (dec.)) isomers of 3-(4-bromophenyl)-6,7-dihydro-2hydroxyiminibenzofuran-4(5H)-one (10.33) and its 1 : 2 molecular complex (m.pt. 174– 8 C) have all been prepared; only the crystal structure of the complex (Pbca, Z ¼ 8) has been reported (Ansell, Moore and Nielsen, 1971; BHDBZF10). The ¼ N– groups are disordered, with hydrogen bonding to carbonyl oxygens of other molecules possible for both orientations. The cyclohexanone ring appears to be planar, suggesting that both ring inversion isomers are present in disordered array. The possibilities of this system have not yet been exhausted because the molecules are chiral and so one can envisage study of the enantiomeric species as well; the molecular complex mentioned above is, of course, racemic. O

O H

H

R

R

OH N anti

N

O

O

OH

syn R = p-bromophenyl 10.33

Ph O O

CH2OH H N O

C

O

C

Ph N

HO

H

O

O

O

CH2

O O Ph

(Ia)

HO

H

N

C C

H

O

CH2

OH CH2

N

O O Ph

(Ib) The formulae of the trans (Ia, 10.34) and cis (Ib, 10.35) isomers.

5. Co-crystallization of cis and trans stereoisomers1 of N,N’-bis(2-phenyl-hydroxymethyl1,3-dioxan-5-yl)ethanediamide. The pure trans-isomer, isolated by repeated fractional crystallization from the reaction mixture, crystallizes in P21/c, Z ¼ 2, with a centrosymmetric 1 cis and trans refer to the mutual location of the 2-phenyl and 5-hydroxymethyl groups in the 1,3-dioxan rings.

PACKING COMPLEXES

600

Fig. 10.17(A). ORTEP diagrams (30% probability ellipsoids) of (above) the Z-shaped trans-isomer, as found both in the pure compound and the 1 : 1 hydrogen-bonded adduct, and (below) the maximally extended cis-isomer, as found in the 1 : 1 hydrogen-bonded adduct. (Diagrams adapted from Ross et al., 1996.)

Z shape for the molecule (Ross et al., 1996; ZIVRIF; Fig. 10.17A). The cis-isomer could only be isolated in 1 : 1 association with the trans-isomer, the adduct being the immediate product obtained from the reaction mixture. This phase rule compound also crystallized in P21/c, Z ¼ 4, where the cis- and trans-isomers are at independent centers of symmetry (ZIVREB). The trans-isomer has essentially the same shape as in the pure compound while the cis-isomer has a maximally-extended shape. There is intermolecular hydrogen bonding in both compounds; unfortunately melting points were not reported.

10.4.5

Cocrystallization of tautomers

Crystals of isocytosine (10.36; P21/n, Z ¼ 8; ICYTIN; Sharma and McConnell, 1965) contain an ordered arrangement of the two tautomers shown below, with the base pairs bonded in the same way as are cytosine and guanine in DNA. Co-existence of the tautomers in the crystal suggests that they have similar stabilities in solution. O

O

H

H

H N

H

N

N

NH2

H

N

NH2

H 10.36

Anthranilic acid (2-aminobenzoic acid, 10.37) : there are three polymorphic forms, with a transition point between I and II at 81 C. In the lower-temperature orthorhombic form (I) (ﬁrst studied crystallographically more than 100 years ago (Haushofer, 1877)) there are two crystallographically independent molecules in the asymmetric unit (P21cn, Z ¼ 8; AMBAC10; Brown, 1968); one of these is neutral and the other a zwitterion, the

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

601

distinction being established via the bond lengths in the two moieties, the locations of the hydrogens and the hydrogen-bonding scheme. O

OH

–

O

O

NH+3

NH2

10.37

The earlier x-ray diffraction results have been conﬁrmed by neutron-diffraction (Brown and Ehrenberg, 1985; AMBACO07). The higher temperature polymorphs II (Pbca, Z ¼ 8; Boone, Derissen and Schoone, 1977; AMBACO03) and III (P21/a, Z ¼ 4; Hardy, Kaska, Chandra and Zink, 1981; AMBACO06)) each have one neutral molecule in the asymmetric unit. Polymorphs II and III have structural resemblances but there is a quite different packing of the hydrogen-bonded moieties in I, which is the only one of these structures relevant in the present context. The phase relationships in anthranilic acid have been critically reinvestigated (Ojala and Etter, 1992). 2-Pyridinecarboxylic acid (10.38) crystallizes in space group C2/c, Z ¼ 8 (Hamazaki et al., 1998; PICOLA02), all molecules appearing as neutral entities, with zigzag chains of N–H . . . N and O–H . . . O hydrogen bonds. However, the protons are disordered about the two fold axis and center of symmetry, and a high-resolution 15N-CP/MAS NMR spectrum showed two separate signals for protonated and nonprotonated nitrogen. These results were interpreted to indicate that the neutral molecules and zwitterions are arranged alternately in local domains on the NMR time scale. Low temperature neutron diffraction should provide useful emendation.

O

–

O

N H N O

+

O H 10.38

A situation similar to anthranilic acid is found in 8-(N,N-dimethylamino)naphthalene-1carboxylic acid (P21/n, Z ¼ 8; Schweizer, Procter, Kaftory and Dunitz, 1978; NANPCX), where zwitterion and neutral molecule are easily distinguished by their atomic arrangements. The zwitterion has an intramolecular hydrogen bond between COO and NH3þ ˚ ) while the carboxyl and amino groups are perpendicular to the plane of (N . . . O ¼ 2.45 A

PACKING COMPLEXES

602

Fig. 10.18. Stereodiagram of the hydrogen-bonded pair (H-bonds shown by open double lines) consisting of a neutral molecule (in front) and a zwitterion (behind), in the crystal structure of 8-(N,Ndimethylamino)naphthalene-1-carboxylic acid. (Diagram kindly provided by Prof. M. Kaftory.)

the naphthalene nucleus in the neutral molecule. The two moieties (Fig. 10.18) are hydrogen ˚ ) and this pair forms the packing unit in the structure. bonded (d(O . . . HO) ¼ 2.60 A -6-Deoxytetracycline hydrohalides (the hydrochloride (DTETC) and hydrobromide (DXTETB) are isomorphous) : in these crystals (P21, Z ¼ 4; Stezowski, 1977) the asymmetric unit contains two molecules of hydrohalide, one water molecule and one ethanol molecule. The relevant portions (ring A and its substituents) of the two crystallographically independent molecules are shown in the insert (10.39); the tautomeric and conformational differences were identiﬁed via bond lengths and hydrogen positions. (H3C)2NH+

(H3C)2NH+ O–

O H NH2+

O

O

O–

NH2+

O H

10.39

Another example is 3-methyl-1-phenyl-5-pyrazole (10.40; 10.41, P21/c, Z ¼ 8; Bechtel, Gaultier and Hauw, 1973a; PMPZOL), where keto and enol forms are linked in alternating ˚; fashion in inﬁnite chains by strong hydrogen bonds (d(O–H . . . O¼C < ) ¼ 2.48 A ˚ ). The delicacy of the balance is illustrated by the fact that, although d(N–H . . . N ¼ 2.80 A 1-phenyl-5-methyl-3-pyrazole also has two molecules in the asymmetric unit (10.42; Pbca, Z ¼ 16), both are in the enol form (Bechtel, Gaultier and Hauw, 1973b; PMPYZL). Ph HO

Ph

Ph

N

O

N

N N

CH3 10.40

H

H3C

N N OH

CH3 10.41

10.42

THE (STEREOISOMERIC) COMPONE NTS ARE DIASTEREOISOMERS

603

Cytosine-5-acetic acid (10.43) : in the examples shown above the two tautomers were arranged with long-range order, but cytosine-5-acetic acid (P21/c, Z ¼ 4; Marsh, Bierstedt and Eichhorn, 1962; CYACET) is disordered in the sense that the experimental results show one-half of a hydrogen atom attached to each of O12 and N3. This was interpreted to mean that both neutral and zwitterionic forms of the molecule were present in the crystal in equal amounts. The implications of this conclusion for the intermolecular hydrogen bonding were not explored in detail but one presumes that there must be some shortrange order. H

H

N

O

CH2 N

H

H

N

CH2

O

3

(N3)+

O H

HO12

H2N

H2N

O O12

–

10.43

In the above examples the tautomerism is due to transfer of a hydrogen, but in the bromohydrin of 7,7-dichlorobicyclo[3.2.0]hepten-6-one (10.44; C2/c, Z ¼ 16; Glen, Murray-Rust, Riddell, Newton and Kay, 1982; BAXGAI) there is also ring-chain isomerism. The two isomers constitute the two molecules in the asymmetric unit; there is no evidence for disorder. Br

Br

O HO

OH O

Cl

Cl

Cl

Cl

10.44

10.4.6 Interallogon complexes Kilbourn and Powell (1970) showed that the green crystals of dibromobis(benzyldiphenylphosphine)Ni(II) (P 1, Z ¼ 3; DBBZPN) actually contain two different stereochemical forms – a trans square planar molecule at a center of symmetry at the origin of the triclinic cell and two tetrahedral molecules at general positions, related by the center of symmetry. The fairly widespread occurrence of crystallographically analogous arrangements has already been noted (Section 10.4.2). The term ‘allogon’ (Greek allos other, different; gonia angle) was proposed to describe isomers which differ in the arrangement of the same number of bonds from a given central atom; the crystals are thus of an interallogon (molecular) complex. Formation of interallogon complexes could be observed, at least in principle, for the following combinations of stereochemistries : Coordination number

4 : square planar/tetrahedral 5 : trigonal bipyramid/square pyramid 6 : octahedral/trigonal prismatic.

PACKING COMPLEXES

604

There are additional possibilities for higher coordination numbers. Obvious requirements are similarity of free energies of formation of the different allogons in solution and a lower free energy for the crystalline interallogon complex compared to the sum of those of the individual crystalline allogon phases. An example with coordination number 5 is the pentacyanonickelate ion in tris(ethyldiamine)chromium(III) pentacyanonickelate(II) sesquihydrate {[Cr(NH2CH2CH2 NH2)3][Ni(CN)5]}1.5H2O; P21/c, Z ¼ 8; Raymond, Corﬁeld and Ibers, 1968; EDCRCN). The two crystallographically independent Ni(CN)5 ions, both at general positions, have different ligand arrangements about the central Ni atoms, one being a regular square pyramid and the other a distorted trigonal pyramid. These differences seem to be due to packing effects and are unlikely to be retained in solution. An example with coordination number 8 is tetrakis(dithioacetato)-vanadium(IV) [V(CH3CS2)4], which crystallizes in space group P2/c with Z ¼ 4, the two independent molecules in the asymmetric unit each being located on a crystallographic two fold axis (Fanfani, Nunzi, Zanazzi and Zanzari, 1972; TDTACV). One has symmetry D2d (42m) with chelation along the m edges of the dodecahedron (Fig. 10.19), while the other has C2(2) symmetry with chelation along two m and two g edges. The second arrangement is energetically unfavourable (Hoard and Silverton, 1963). It is hopefully not stretching the nomenclature too far to describe the 1 : 1 molecular complex of Tylolupenol A acetate and Tylolupenol B acetate as an interallogon complex. The source material was obtained by esteriﬁcation of tylolupenol, a crystalline substance extracted from the roots of Tylophora kerrii Craib. X-ray analysis of the acetate showed the crystals to be triclinic (space group P1) and to contain, in ordered array, one molecule of each of D : C-friedolup-8-en-3-ol acetate (molecule A) and D : C-friedolup-9(11)en-3-ol acetate (molecule B) (Nakai, Shiro, Tozyo and Ishii, 1985; COYSOY). These

a

A

A

g m b b B

B

B

m

b

b m

m a A

B g

A

2m) dodecahedron, showing equivalent trapezoids, BAAB, lying in the Fig. 10.19. The D2d (4 . The labelling of vertices mutually orthogonal mirror planes and interlocking in agreement with 4 (ligand sites) and of edges of the polyhedron shows how these sort into symmetry equivalent classes; e.g. the 18 edges are distributed among four classes : a(2), b(4), m(4) and g(8). The polyhedron centre (the site of the central atom M) is the point of intersection of three mutually orthogonal and a pair of twofold axes. Each of these latter passes through the symmetry axes, the unique 4 mid-points of two opposed b edges. (Reproduced from Hoard and Silverton, 1963.)

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

605

differ in that there is a double bond from C(9) to C(8) in molecule A but from C(9) to C(11) in molecule B, with consequent differences in the detailed conformations of analogous rings. These results suggest that tylolupenol itself consists of a 1 : 1 mixture of the corresponding alcohols. CH3

CH3

H3C

H3C

H3C H3C

CH3

H3C

H

H

H3C

CH3 R

H CH3

H H3C

CH3

R

CH3

H3C

Molecule A: R = OCOMe tylolupenol A: R = OH

H CH3

Molecule B: R = OCOMe tylolupenol B: R = OH

10.5 Components are positional isomers One example has been reported where the two components of the ordered molecular complex are positional isomers – this is Fe3(CO)11P(C6H5)3 (10.45), which crystallizes in space group C2/c, with Z ¼ 16 (Dahm and Jacobson, 1968; PHOFEC10). The asymmetric unit consists of two positional isomers, in which the triphenylphosphine moieties are attached to different iron atoms. (OC)3

(CO)4

(OC)3

C O

Fe Fe Fe

(CO)2PPh3

C O

Fe

C O Ph3P(CO)3

C O

Fe Fe (CO)3

10.45

It was suggested that interconversion of the two isomers in solution could occur by a process of breaking and reforming Fe–Fe bonds, accompanied by migration of CO groups. 10.6 Components have different chemical compositions 10.6.1 Substitutional solid solutions 10.6.1.1

Conditions for formation

In substitutional solid solutions, the molecules of component B added to component A replace A molecules at their sites in the crystal structure. This substitution produces minor changes in the cell dimensions of the A phase but there is no change in overall crystal structure until a certain composition is reached beyond which no more B can dissolve in phase A. This solid solution of B in A is called a primary solid solution. As a ﬁrst approximation the substitution of A by B may be taken to occur at random; ‘short-range

606

PACKING COMPLEXES

order’ appears if there is a greater probability of a particular molecule having unlike rather than like neighbors, while the converse situation is called ‘clustering’. If diffusion is sufﬁciently rapid, then a disordered substitutional solid solution may undergo a transformation at lower temperatures to a phase with long-range order (often called a disorder to order transition or superlattice formation). An extension of the argument allows one to discuss ternary solid solutions – in the present context, the solution of E in the molecular complex CD. The general conditions for complete mutual solid solubility (miscibility) of molecules A, B were set out by Kitaigorodsky (1984) and we adapt them as follows : 1. The molecules of the components should be isosteric, i.e. there should be close similarity between their volumes and shapes. In crystals containing isotropic units (e.g. metals) the volume difference between the components is one vital parameter determining whether two substances will be appreciably mutually soluble in the solid state. The generally accepted rule of thumb is due to Hume-Rothery and Raynor (1954) and states that where the atomic diameters of solvent and solute atoms differ by more than about 15% (using solvent as basis) solid solution is very restricted. This difference expressed in terms of ˚ , volume per atom atomic volumes is about 50%. For example, the FCC metals Cu (a ¼ 3.615 A ˚ 3, at 25 C), Ni (a ¼ 3.542 A ˚ , VA ¼ 186.1 A ˚ 3) and Au (a ¼ 4.078 A ˚ , VA ¼ 284.1 A ˚ 3), VA ¼ 197.9 A taken pairwise, are all completely miscible at high temperatures. Ordered alloys are formed at lower temperatures in the CuAu system while there is a miscibility gap in the Au-Ni system; Cu and Ni form a complete range of solid solutions over the whole temperature range. A linear dependence of cell parameter on composition is known as Vegard’s Law (Vegard and Dale, 1928), and a linear dependence of cell volume on composition as Zen’s Law (Zen, 1956). Both hold more in the breach than the observance. In crystals containing anisotropic molecules the situation is much more complicated because differences in shape (including handedness) as well as in molecular volumes must be taken into account. The fulﬁlment of special bonding requirements, such as hydrogen bonding, corresponds in these systems in some respects to the chemical interactions that occur in intermetallic alloys. Kitaigorodsky (1984, pp. 81–85) has suggested calculation of a ‘‘coefﬁcient of geometrical similarity’’ for molecules; this has more recently been called a ‘‘coefﬁcient of molecular homeomorphism’’ (Haget, Bonpunt, Michaud, Negrier, Cuevas-Diarte and Oonk, 1990). The coefﬁcient "K is calculated by superimposing the shapes of the two molecules so as to maximize intermolecular overlap; if the volume of overlapping parts is and that of the non-overlapping parts then "K ¼ {1–(/)} should be greater than 0.85 for appreciable mutual solubility (note that we use the notation of Haget et al. (1990) and not that of Kitaigorodsky (1984)).

2. The crystals of the two components must be isomorphous (if they are isostructural then there can be extensive, but not complete, mutual solid solubility). There is considerable confusion in the literature about the terms ‘‘isomorphous’’ and ‘‘isostructural’’; our usage roughly follows that of Wells (1954) but it should be noted that deﬁnitions are likely to change (Ka´lman, Pa´rkanyi and Argay, 1993a, b). ‘‘Isomorphous’’ is taken here to mean that two substances have the same, or nearly the same, crystal structures; ‘‘isostructural’’ is taken to mean that two substances have closely related crystal structures but that differences of symmetry, cell dimensions, degree of order, etc. do occur. Two questions arise : how does one determine whether two crystal structures are the same and what differences are permitted by the use of the word ‘‘nearly’’? It is often considered that two crystal structures are the same if the two unit cells have the same space group and (almost) the same cell dimensions. A criterion for similarity of unit

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

607

cell shapes (‘‘coefﬁcient of crystalline isomorphism’’) is calculated as "m ¼ {1– (m /m)}, where m is the common volume of the optimally overlapped unit cells of A and B, and m is the total volume of the non-overlapping parts, it being assumed that the two cells have the same space group and number of molecules per unit cell (Haget et al., 1990).2 It seems reasonable to expect that the degree of resemblance demanded in molecular systems, from both physical and chemical points of view, is much larger than in alloy systems. Available results (see below) show that it is usually much easier to dissolve a large amount of a smaller molecule in the crystalline framework formed by a larger molecule than vice versa, as one might expect. We shall ﬁnd below that isomorphism as measured above is not always an adequate criterion and that more sophisticated tests, based on the distribution of X-ray intensities, are sometimes required (Srinivasan and Ramachandran, 1965).

3. There must be compatibility of the hydrogen-bonding schemes or other special interactions between the two components. The requirements under this heading do not appear to have been quantiﬁed.

The description above is essentially qualitative but these ideas can be quantiﬁed by using macroscopic thermodynamic analysis of binary liquid–solid phase diagrams. One application has been to the ﬁfteen phase diagrams shared by naphthalene and ﬁve of its 2-R derivatives, where R ¼ F, Cl, Br, SH and CH3 (Oonk et al., 1991). 10.6.1.2

The information desired

As we note on a number of occasions, it is more difﬁcult to describe a disordered than an ordered structure. Some measure of the information desired may be obtained from a consideration of the simpler, and more widely studied, alloy solid solutions, where the component atoms can be taken as spherical. We ﬁrst require the variation of cell volume with composition, which is an overall parameter describing the ‘packing’ effect of changed composition and is measured from the Bragg diffraction pattern. Then we wish to have information about the local atomic arrangements, particularly about how these deviate from randomness, and whether in the direction of a preference for like neighbours (clustering) or unlike neighbors (short range order). In addition, we would wish to know how the atomic centres deviate from the positions of the average lattice; this will give some estimate of the variation of atomic radius with composition. Information about the local atomic arrangements is obtained from analysis of the diffuse (neutron or X-ray) scattering. Finally some information about possible mosaic (or domain) structure of the alloy is desirable; this is generally obtained from electron microscopy (Schwartz and Cohen, 1987). Although the variation of volume with composition has been used as a parameter for molecular solid solutions, the anisotropy of these crystals suggests that a more detailed approach, which takes into account the variation of all the cell dimensions with composition, is necessary. An early suggestion of such a treatment, but apparently without development, was made by Robertson and Ubbelohde (1939) in connection with the cell changes caused by substitution of hydrogen by deuterium. A tensorial treatment of compositional deformation (tensor elements Kl ¼ (1/l)(@l/@x)T,P; x is the composition) has 2 A full treatment is not possible here; we give three leading references – Rutherford (1997), Fa´bia´n and Ka´lma´n (1999) and Dziubek and Katrusiak (2004).

608

PACKING COMPLEXES

been developed by Chanh, Clastre, Gaultier, Haget, Meresse, Lajzerowicz, Filhol and Thomas (1988), by analogy with the tensor treatments of isobaric thermal expansion (tensor elements l ¼ (1/l)(@l/@T)P) and isothermal compressibility (tensor elements l ¼ (1/l)(@l/@P)T). Diffuse scattering measurements have been made for the primary solid solution of diphenylmercury in tolane (see below), but not, so far, for other systems (Section 10.6.2.4). Domain structure has not yet been investigated directly by electron microscopy, but indirectly by x-ray diffraction (Section 10.6.2.5). 10.6.2

Systems with complete (or a wide range of ) mutual miscibility

There are not many systems which appear or would appear to show a complete range of mutual miscibility. Perhaps the simplest are isotopically mixed systems such as benzeneh6/benzene-d6, which form a continuous series of ideal mixed crystals all across the binary phase diagram; those listed (Karl, Heym and Stezowski, 1985) have mostly been of interest for spectroscopic studies. The monoclinic crystals of p-dichlorobenzene (DCB; refcodes DCLBEN to DCLBEN11), p-dibromobenzene (DBB), p-bromochlorobenzene (BCB), p-chloroiodobenzene (CIB), and p-bromoiodobenzene (BIB) are all isomorphous (P21/a, Z ¼ 2), with the molecules located at centres of symmetry and so could be expected to show complete ranges of mutual solid solubility (BCB (Klug, 1947; BCBENZ), CIB and BIB are necessarily orientationally disordered). However, this is not so; the following pairs show full miscibility at 293K (DCB/BCB, DCB/CIB, BCB/DBB, BCB/CIB, DBB/BIB) while partial miscibility is shown by the pairs DCB/DBB, DCB/BIB, BCB/BIB, DBB/CIB and CIB/BIB (references summarised by Bonpunt, Courchinoux, Haget, Estop, Calvet, Cuevas-Doarte and Labrador, 1991). These authors have used the measured cell dimensions as a function of composition to calculate the dependence of the principal tensor coefﬁcients on composition for these binary systems, as well as the orientation of the compositional deformation tensors with respect to the cell axes. The system p-dibromobenzene/p-diiodobenzene is discussed in Section 10.6.3.3. The trans-azobenzene/trans-stilbene system at 295K ﬁlls all Kitaigorodskii’s conditions for formation of a complete range of solid solutions. However, the apparent simplicity is somewhat deceptive (Bouwstra et al., 1985). The mixed crystals were prepared by a zone-leveling technique to avoid inhomogeneities. The linear dependence of individual cell dimensions on composition accords with Vegard’s law and the similar behaviour of cell volume with Zen’s law. Structure analysis of the compositions with x ¼ 0.26, 0.46, 0.56 and 0.69 (no structure analysis) showed nonrandom substitution, which follow from the detailed structures of the neat components, where the molecules are located at two independent centrosymmetric sites A and B. A is ordered but B is disordered, with the molecules related by an approximate two fold axis. In the solid solutions site A contains both components in ordered fashion but site B contains four crystallographically different molecules. Because of the similarity of the two molecules, determination of the detailed arrangements is not easy even though both XRD and ND (only for x ¼ 0.46) were used. Among the examples of complete mutual solid solubility quoted by Myasnikova (1983) are the pairs naphthalene and -naphthol, -ﬂuoro- and -chloronaphthalene, -bromoand -chloronaphthalene, sebacic acid (C10H18O4) and dodecanedioic acid (C12H22O4), adipic acid (C6H10O4) and suberic acid (C10H14O4). Some of these examples appear to

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

609

Table 10.6. Values of eK (not emphasized) and "m (in bold type) for 2-R-naphthalene pairs (from Bonpunt, Courchinoux, Haget, Estop, Calvet, Cuevas-Doarte and Labrador, 1991) R

H

F

Cl

CH3

SH

Br

H F Cl CH3 SH Br

1.00 0.79 0.70 0.69 0.68 0.68

0.98

0.89 0.91

0.89 0.89 0.97

0.86 0.88 0.98 0.96

0.85 0.86 0.96 0.96 0.97

0.92 0.89 0.88 0.88

0.97 0.97 0.97

0.98 0.98

0.99

require further investigation. There are relatively few systems where both phase diagrams and crystal data have been reported. Calculations of "K (coefﬁcient of molecular homeomorphism) and "m (coefﬁcient of crystal homeomorphism) have been made for pairs of 2-R-naphthalenes (Table 10.6); the values of "K are all greater than 0.85, while values of "m range from 0.68 to 0.99, suggesting that it is the "m values which determine how wide the range of solid solution will be. The system naphthalene/2-ﬂuoronaphthalene ("K ¼ 0.98, "m ¼ 0.78) has been studied in some detail (Haget, Bonpunt, Michaud, Negrier, Cuevas-Diarte and Oonk, 1990). ˚, The crystals of naphthalene (at 293K, a ¼ 8.262(3), b ¼ 5.984(3), c ¼ 8.117(5) A 3 ˚ ¼ 116.02(3) , V ¼ 360.6(3) A , Z ¼ 2, P21/a) and 2-ﬂuoronaphthalene (at 293K, ˚ 3, Z ¼ 2, P21/a; FNAPTH) are ˚ , ¼ 114.92 , V ¼ 375.4 A a ¼ 8.336, b ¼ 5.915, c ¼ 8.394 A isomorphous and have very similar, although not identical, molecular arrangements (2-ﬂuoronaphthalene must be disordered). Nevertheless, the system shows a miscibility gap. The system guanine monohydrate (structure by Thewalt, Bugg and Marsh, 1971; GUANMH10)/8-azaguanine monohydrate (structure by Sloetten et al., 1968; AZGUAN01) seems to meet Kitaigorodsky’s three conditions for formation of a complete range of solid solutions. The two components are isomorphous and a mixed crystal, with a 1 : 2 ratio of guanine to azaguanine, has the same structure (Madden, 1973; QQQFGM, Z ¼ 2, P21/c). It has been noted (Thewalt et al., 1971) that guanine can substitute in the azaguanine structure by a single change in the hydrogen-bonding scheme at C(8)H [N(8) for 8-azaguanine] in the monohydrates. Determination of the binary diagram [or, more practically, a ternary (solubility) diagram] would be desirable to put the matter beyond doubt. O N

N

H N

O

N

H

H

N N N

NH2 H

guanine

N N

H

NH2

8-azaguanine

Another example is l-threonine (10.46; Janczak et al., 1997; LTHREO03) and l-allothreonine (10.47; (Swaminathan and Srinavasan, 1975a; LALTRE10), which have very similar cell dimensions and the same space groups; the two crystals are isomorphous (Srinavasan, Varughese and Swaminathan, 1974; AETHRE; Table 10.7). The crystal

PACKING COMPLEXES

610

structure of a 1 : 1 compound of l-threonine and l-allo-threonine has been determined and found to have the same structure as those of the neat components (Swaminathan and Srinavasan, 1975b); this implies that the hydrogen and methyl groups attached to C are disordered in the mixed crystal. COOH a H2NC - H b HC OH

COOH

COOH

a H2NC - H

a H2NC - H

b HOC H

b H3CC H

CH3

CH3

CH3

COOH a H2NC - H b HC CH3 CH2 CH3

L-threonine

10.46

L-allo

threonine 10.47

L-isoleucine

D-allo-isoleucine

10.48

10.49

Note that in each pair of isomers, the molecules differ in the configuration at C b.

The rather intricate relations among the stereoisomers of 2-amino-3-methylpentanoic acid (the ‘leucines’) have been resolved by Dalhus and Go¨rbitz (2000b), following earlier work by Benedetti, Pedone and Sirigu (1973) and Srinavasan, Varughese and Swaminathan (1974). There are two chiral carbons [, ] and hence four stereoisomers. The [S,S] conﬁguration is the naturally occurring L-isoleucine (10.48; structure by Torii and Iitaka (1971); LISLEU; repeated by Go¨rbitz and Dalhus, 1996)); the [S,R] conﬁguration is d-allo-isoleucine (10.49), and there are the corresponding enantiomers. The four stereoisomers can form four 1 : 1 molecular complexes, the racemates dl-isoleucine, dl-allo-isoleucine, and the diastereomers {l-isoleucine/d-allo-isoleucine} and {l-isoleucine/l-allo-isoleucine}. The structures of the 1 : 1 : 1 : 1 complex {l-isoleucine/d-isoleucine/l-allo-isoleucine/d-allo-isoleucine} and of d-allo-isoleucine were redetermined. Crystal data are given in Table 10.7. The two enantiomers of alloisoleucine were always spontaneously resolved on crystallization, and thus the structure of the racemate could not be determined. The similar cell dimensions in Table 10.7 show overall resemblances for related structures – those for {l-isoleucine/d-allo-isoleucine} and {l-isoleucine/d-isoleucine/l-allo-isoleucine/d-allo-isoleucine} can only be described as remarkably similar. The crystal structures reported in the last few years (at 150K) are now precise enough to show extremely subtle differences between one structure and its companions. These are regrettably too subtle for detailed exposition here and we must refer the interested reader to the original papers; even the non-appearance of racemic allo-isoleucine has received an explanation. There are many other studies of complexes between amino acids, which we note (with some leading references) but do not discuss for lack of space. These include complexes of l-isoleucine with hydrophobic d- and l-amino acids (Dalhus and Go¨rbitz, 1999a); l-leucine and l-valine with hydrophobic d- and l-amino acids (Dalhus and Go¨rbitz, 1999b). Diselenadithiafulvalene (10.50; Spencer, Lakshmikantham, Cava and Garito, 1975) contains approximately equal amounts of cis and trans isomers, which are not interconvertible in solution even when heated to 100 C. Crystallization shows no selectivity for either isomer. The triclinic crystals contain four crystallographically independent formula units located at centres of symmetry in the unit cell (Belsky and Voet, 1978); the S and Se

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

611

atoms are represented by a mean ‘‘atom’’ (¼1/2(S þ Se)). Separation of the isomers and determination of the phase diagram appear to be desirable (perhaps necessary) preliminaries to solving the structural problem. S

S

S

Se

Se

Se

Se

S

cis

10.50

trans

Not all reports in the literature are reliable. For example, Debye-Scherrer photographs of powder samples of benzoic acid and m-ﬂuorobenzoic acid were believed to show the formation of a complete range of solid solutions (Claeson and Baeckstrom, 1960). However, single crystal studies of the components show that these are not isomorphous (benzoic acid (Bruno and Randaccio, 1980; BENZAC to BENZAC11; m-ﬂuorobenzoic acid (Taga, Yamamoto and Osaki, 1985; COVJIG)). Problems can also arise with phase diagrams – for example, two different phase diagrams have been reported for the naphthalene/-naphthol system (Robinson, Roseel, Scott and Legge, 1970; Chanh, Bouilland and Lencretos, 1970). In some respects our knowledge of crystal structures has outrun our knowledge of phase diagrams, and certainly of the thermodynamic properties of binary systems. We give some illustrations of results where there appears to be a need for clariﬁcation of contradictions and obscurities. For example, ﬂuorene (Belsky et al., 1984; Gerkin et al., 1984) and carbazole (Gerkin and Reppart, 1986) are indeed structurally isomorphous, as is implied by the resemblance in cell dimensions (Table 10.7, but note the difference in the values of a), the atomic coordinates being in reasonable agreement. The melting points differ appreciably (388K for ﬂuorene and 518K for carbazole) and this has been ascribed to closer packing in carbazole; there are no hydrogen bonds in either crystal. A complete range of solid solutions could perhaps be expected – the phase diagram does not appear to have been reported. Phenothiazine appears to be isomorphous with ﬂuorene and carbazole on the basis of the cell dimensions (McDowell, 1976; PHESAZ01) given in Table 10.7; however, it has been claimed that this is an artifact due to disorder and that phenothiazine is really monoclinic (de Waal and Feil, 1977; PHESAZ02). The situation is further complicated by the report of another monoclinic polymorph (Bell, Blount, Briscoe and Freeman, 1968; PHESAZ). Phenothiazine and phenoxthionine (also called phenoxathiin) have been reported to form a complete range of solid solutions (Cullinane and Rees, 1940) but checking seems desirable because of the polymorphism of phenothiazine and the different space groups of the two components. Such re-examination seems even more necessary for the carbazole–diphenylene oxide system, also reported (Cullinane and Rees, 1940) as giving a complete range of solid solutions; this is not compatible with the cell dimensions (Wood and Williams, 1941) given in Table 10.7. According to early work (Wood, McGale and Williams, 1941) phenoxthionine, phenoxselenine and phenoxtellurine are isomorphous; thioxanthene (Gillean, Phelps and Cordes, 1973) and phenoselenazine (Villares, Jimene´z-Gargy, Conde Ma´rquez, 1976) should be added to this list. Isomorphism of phenoxathiine (Hosoya, 1966) and thioxanthene is conﬁrmed by crystal structure analyses. The space group of the crystals of these (nonplanar and hence

PACKING COMPLEXES

612

˚ , deg.) and space groups for various groups of Table 10.7. Comparison of cell dimensions (A molecules whose crystal structures are, or are not, isomorphous. Measurements at nominal 300K unless stated otherwise. The standard uncertainties of cell dimensions are quoted from the original papers and some may well be over-optimistic Substance

a/

b/

c/

V/mol ˚ 3) (A

Z

Space group

Remarks/ refcode

l-threonine l-allo-threonine 1 : 1 l-threoninel-allo-threonine dl-threonine l-isoleucine at 120K d-allo-isoleucine at 150(2)K dl-isoleucine at 150(2)K l-isoleucine/ d-allo-isoleucine at 140(2)K l-isoleucine/ d-isoleucine/Lallo-isoleucine/ d-alloisoleucine at 150(2)K Carbazole Fluorene Phenothiazine Phenoselenazine Phenoxathiine Thioxanthene Diphenylene oxide Phenazine

13.611 13.69 13.600

7.738 7.78 7.870

5.142 5.16 5.160

135.4 137.4 138.1

4 4 4

P212121 P212121 P212121

LTHREO03 LALTRE10 AETHRE

7.750 9.681(5)

5.160 13.956(6)

136.4 178.03(15)

4 4

Pmm2 P21

ZZZQRE LISLEU02

14.1018(1)

177.51(1)

4

P21

DAILEU01

5.2289(1) 96.332(1) 5.2438(2) 93.042(1)

13.640 5.301(3) 96.16(4) 5.2583(1) 98.033(1) 5.4102(1) 90.622(1) 5.3978(2) 92.811(1)

13.1095(3) 109.493(1) 13.2562(6) 109.897(1)

173.51(1)

2

P 1

175.71(1)

2

P 1

Reduced cell DLILEU02 XADVED

5.2493(1) 92.9433(6)

5.4006(1) 92.8639(5)

13.2778(2) 109.8571(7)

176.33(1)

2

P 1

XADVIH

7.628 8.365 7.918 7.83 7.78 7.804 15.2

18.935 18.745 20.945 20.91 20.54 21.096 5.07 100.3 5.05 109.2

5.657 5.654 5.882 5.93 5.95 6.049 11.7

213.4 230.4 243.9 242.7 237.7 249.0 221.8

4 4 4 4 4 4 4

Pnma Pnma Pnma P212121 P212121 P212121 A2/a

7.08

222.9

2

P21/a

9.6706(1)

13.200

N-oxyphenazine

14.29

4.60 108.8

7.4

231.5

2

P21/a

Anthrone

15.80

7.86

243.1

2

P21/a

Anthraquinone

15.83

3.998 101.7 3.97 102.5

7.89

242.0

2

P21/a

Y X

Z

10.51 (X = CH2 for fluorene, NH for carbazole)

10.52 (see table for Y, Z)

CRBZOL04 FLUREN01/2 Disordered PHEOXS TOXANT Probably twinned PHENAZ04 (Wozniak et al., 1991) Disordered; OXYPHE; Curti et al., 1961 Disordered; ANTRON10 ANTQUO08/ 9,11,12,13; Fu and Brock, 1998

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

613

Table 10.7. (Continued ) Compound

Y

Z

Compound

Y

Z

Phenothiazine Thioxanthene Diphenylene oxide Phenoxathiin

S S O S

NH CH2 O O

Anthrone Anthraquinone Phenazine N-Oxyphenazine

CH2 C¼O ¼ N– N

C¼O C¼O ¼ N– N-O

chiral) compounds belongs to the Sohncke family and thus spontaneous resolution has taken place on crystallization. However, racemisation surely occurs in solution. Some interesting complications can be envisaged in determining the binary phase diagrams. The anthraquinone–anthrone and -phenazine–N-oxyphenazine systems show many resemblances. Anthraquinone and anthrone are isomorphous but this is less likely for the -phenazine–(N-oxyphenazine) pair (Table 10.7). The crystal data show that the anthrone and N-oxyphenazine molecules are disordered. An extensive study of these systems (Flack and Glazer, 1970) indicates that both have miscibility gaps rather than the complete series of solid solutions suggested in earlier work (anthraquinone–anthrone, Harris, 1965; phenazine–(N-oxyphenazine), Wood, McCale and Williams, 1941). Thus in anthraquinone–anthrone there is a random distribution of disordered molecules of anthrone in the anthraquinone structure between 0–45% anthrone; then there is a miscibility gap from 45 to 88% anthrone. Anthrone itself gives diffraction patterns in which diffuse scattering indicates (incipient) doubling of the b-axis (Srivastava, 1964). As there is little change in the diffuse scattering from solid solutions of anthrone containing between 0–12% anthraquinone it was inferred that the short-range-ordered anthrone domains remain much the same as in pure anthrone and that the anthraquinone molecules are dispersed among them. The model derived for the -phenazine-(N-oxyphenazine) system (PHENBA/B/C) is similar. Up to 10% N-oxyphenazine can be substituted at random in the -phenazine structure; there is a miscibility gap between 10–52% N-oxyphenazine, and then phenazine is dispersed between the short-range-ordered domains of N-oxyphenazine in the solid solution of phenazine in N-oxyphenazine between 52–100% N-oxyphenazine. Comparison of the solubility limits suggests a kind of mirror relationship between the phase diagrams – there is up to 45% solubility of disordered anthrone in ordered anthraquinone, and up to 48% solubility of phenazine in disordered N-oxyphenazine, with an analogous relationship on the other side of the miscibility gaps. A number of crystal structures have been reported of binary systems of related (but quite complicated) molecules where the composition examined appears to have been fortuitous; these could provide starting points for more detailed studies. The major parts of the pairs of molecules are the same and hence the small chemical differences have, as noted earlier, only minor structural inﬂuence. Two examples are of (potential) solid solutions and the other of formation of a (disordered) phase diagram compound. (a) Dehydroeriolanin, C19H24O6, (10.53a) and dehydroeriolangin, C20H26O6, (10.53b) are oxidation products of the antileukemic seco-eudesmanolides eriolanin and eriolangin which differ only in the replacement of an hydrogen by a methyl group. They were ˚) isolated as a mixed crystal (P212121 Z ¼ 4; a ¼ 8.115, b ¼ 10.260, c ¼ 22.857 A

PACKING COMPLEXES

614

containing the two components in approximately 2 : 1 ratio, the two types of molecule being distributed at random over equivalent sites in the orthorhombic crystals (Bryan and Gilmore, 1975; ERLANG20). There is hydrogen bonding between hydroxyl and aldehyde oxygens. Formation of a complete range of solid solutions is conceivable but the structures of the two end members are required for this to be demonstrated. O

O

O HO CH3

CH2

O O

R

CH3

10.53a dehydroeriolanin C19H24O6: R = H; 10.53b dehydroeriolangin, C20H26O6: R = CH3

(b)

2(14-O-Benzoyl-8-methoxybikhaconine)(14-O-benzoyl-8-ethoxybikhaconine) 2(C33H47NO8)(C34H49NO8) (Parvez, Gul and Anwar, 1998; NOZVAZ). Two new C19 alkaloids (10.54) were isolated from the roots of Aconitum chasmanthum as a ‘‘crystalline mixture, which could not be separated by chromatographic techniques, although it was evident from NMR spectral data . . . that the sample was composed of two distinct compounds’’. The monoclinic cell (space group P21, Z ¼ 2) contained discrete molecules of the two compounds, occupying the same sites. There were only van der Waals interactions between neighbouring molecules. Presumably there is a complete range of solid solutions but this cannot be tested because the individual compounds are not available. OH MeO

OMe H

H

O Ph O

HH

N Me MeO

H H

OR OMe H

(1) R = CH3 (65%) (2) R = C2H5 (35%) 10.54

(c)

Glaucolide-D, C23H28O10, is a germacranolide-type sesquiterpene lactone isolated from Vernonia isoﬂora. It is orthorhombic (P212121, Z ¼ 4; a ¼ 21.57, b ¼ 12.49, ˚ ) and the crystal structure has been reported (Taylor et al., 1976; c ¼ 8.45 A GLAUCD). Replacement of the oxiranyl group of the D compound by a propenyl side chain gives the E compound, the crystal structure of which has not been reported. However, that of a mixed crystal with D : E ratio of 1 : 2 has been determined (Gopalakrishna et al., 1977; GLAUED). These crystals are monoclinic

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

615

(P21, Z ¼ 2) and the two types of molecule are disordered over the equivalent sites. There were only van der Waals interactions between neighbouring molecules. There cannot be a complete range of solid solutions as the D compound and the (D : E2) mixed crystals are clearly different phases. AcO

R

O

D O O E

O OAc O

This group of three examples may provide a neat illustration of Kitaigorodoskii’s rules for formation of solid solutions. The chemical differences between the pair of eriolangin molecules, and those between the pair of bikhaconine molecules, are too small to affect the molecular arrangements and so full miscibility seems very likely. However, in the third example, the effects of substitution are large enough to prevent complete miscibility, although not large enough to induce ordering in the 1 : 2 mixed crystal. 10.6.3 Some binary phase diagrams involving phases (primary and intermediate) with extensive composition ranges Our examples are chosen from systems where there is appreciable primary solid solution and, in some instances, formation of molecular complexes with a wide range of composition. 10.6.3.1 Dibenzyl – trans-stilbene This is a typical example of a peritectic system, with much greater primary solid solubility on one side of the diagram than on the other (Fig. 10.20 (left)); the variation of cell dimensions with composition shows that there are changes in both shape and volume of the two types of unit cell with composition (Fig. 10.20 (right); Kolosov, 1958). The ˚ 3 respectively (from cell molecular volumes of dibenzyl and stilbene are 274 and 258 A dimensions); thus the amounts of primary solid solution are in the opposite direction to what one might expect intuitively from the molecular volumes. Kolosov (1958) suggested that the more ﬂexible dibenzyl molecule might adapt itself more easily to the packing requirements of the stilbene structure, where the molecule is planar, than conversely. This again emphasises the importance of the shape factor. The crystal morphology varies from one phase to the other (Fig. 10.20 below). 10.6.3.2

Diphenyl sulfoxide–diphenyl sulfone (Ph2SO–Ph2SO2)

This system (Abrahams and Silverton, 1956) shows primary solid solution of Ph2SO ˚ 3; P21/c, ˚ 3; P21/n, Z ¼ 4) in Ph2SO2 (molecular volume 268 A (molecular volume 257 A Z ¼ 4) up to a limit of 91 mole % Ph2SO; presumably the stereochemically active lone pair in the sulfoxide substitutes without difﬁculty for the second oxygen of the sulfone. On the other hand, Ph2SO can only accommodate up to about 8 mole % Ph2SO2 in its

PACKING COMPLEXES

616

274 v

molecule 258 15.96

c

15.49

120

temp. (°C)

100

a

12.80

80

6.16

60

12.38

b 40 115°

5.73

b

20

114° 0

20 40 60 80 % stilbene in mixture

D

0

50 S % stilbene in mixture

z

z x

x y

y

––

111

––

––

––

––

110

––

110

111

110

110

–

100

–

001

201

–

–

–

001

–

201

001

–

–

001

100

Fig. 10.20. (above) The dibenzyl–stilbene system, on the left, and, on the right, the dependence of ˚, A ˚ 3, deg.) on composition for the two solid solution phases (below) In the unit cell parameters (A dibenzyl–stilbene system the dibenzyl solid solutions crystallize as needles and the stilbene solid solutions as plates. (Reproduced from Kolosov, 1958.)

structure. The crystal structures of both components have been determined, and these are ˚ , 101.12 , P21/n, clearly not isomorphous; Ph2SO has crystal data 8.347 14.092 8.917 A ˚ , 98.32 , Z ¼ 4 (Yatsenko et al., 1986; DPHSOX01) and Ph2SO2 12.225 7.830 11.328 A P21/c, Z ¼ 4 (Sime and Woodhouse, 1974; DPSULO). The binary diagram has been reported (Rheinboldt and Giesbrecht, 1946) as a continuous series of solid solutions with

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

617

a minimum melting point at 63 C, 86 mole% Ph2SO2; this is not compatible with the crystallographic evidence. Perhaps the system is really a eutectic or there are undetected solid state transformations between room temperature and the solidus temperature. 10.6.3.3

p-Dibromobenzene–p-diiodobenzene (p-C6H4Br2–p-C6H4I2)

There are three solid phases in this system which shows both a eutectic and a peritectic (Kitaigorodsky and Liang, 1960). The primary -phase is a solid solution of p-C6H4I2 in p-C6H4Br2 with a strongly temperature-dependent solubility extending up to 20 mole % at 80 C; p-dibromobenzene is monoclinic and isomorphous with the monoclinic phase of p-dichlorobenzene, whose structure is known. The primary -phase has a very narrow composition range for solid solubility of p-C6H4Br2 (up to 3 mole % at 124 C) in p-C6H4I2. The intermediate -phase has a maximum solid solubility of 50 mole % p-C6H4Br2 in p-C6H4I2 at 80 C. Approximate structures have been reported for the and phases ( has space group Pbca, Z ¼ 4, molecular symmetry 1 (Struchkov and Liang, 1959) and , containing 91% p-diiodobenzene, has space group Pccn, Z ¼ 4, molecular symmetry 1 (Liang and Struchkov, 1960). Both have layer structures, with similar arrangements within the layers but different layer stackings. Details of the mode of replacement of p-diiodobenzene molecules by p-dibromobenzene molecules in the phase are not known. 10.6.3.4

p-Dibromobenzene–p-chloronitrobenzene (p-C6H4Br2–p-ClC6H4NO2)

There are three solid-solution phases (two primary and one intermediate) in this system, separated by two eutectics (Remiga, Myasnikova and Kitaigorodsky, 1969; see also Kitaigorodski, 1984, pp. 232–235). The maximum solubility of p-chloronitrobenzene in p-dibromobenzene is 25%, and that of p-dibromobenzene in p-chloronitrobenzene 20%. The intermediate phase extends from 40 to 80% p-chloronitrobenzene in p-dibromobenzene. Only an approximate structure is available for the intermediate phase. There have been later studies of molecular alloys of binary para-disubstituted systems, including {1,4-dichloro- þ 1,4-dibromobenzene} (Oonk et al., 1995), and other paradihalogenobenzene combinations (Calvet et al., 1995). 10.6.3.5

Benzoic acid–p-ﬂuorobenzoic acid

There are three phases in this system : an intermediate solid solution phase extending from 30–90% p-ﬂuorobenzoic acid in benzoic acid, and two primary solid solutions, of up to 15%, of one component in the other (Yamamoto, Taga and Machida, 1989). The packing unit in all three phases (all have space group P21/c, with Z ¼ 4, but different cell dimensions) is the dimer formed between the two carboxylic acids, but the arrangements are different. All three phases have disorder of hydrogen and ﬂuorine in the para positions. 10.6.3.6 1,2-4,5-Tetrachlorobenzene–1,2-4,5-tetrabromobenzene An early determination showed a single solid-liquid loop and complete sub-solidus miscibility (Rheinboldt et al., 1951). Later work, using a combination of x-ray diffraction and thermal-analytical techniques (Mondieig et al., 1991) and covering a wide range of temperatures, shows the earlier results to be considerably oversimpliﬁed. The

PACKING COMPLEXES

618

500

500 L

400

400 g

XR . 293K GL . GS DTA

b+g

b

300

T /K

300

200

100

b

g+b

100

a

0 0.00 TeCB

200

0.20

0.40 0.60 Mole fraction

0.80

0 1.00 TeBB

Fig. 10.21. The phase diagram of the 1,2-4,5-tetrachlorobenzene – 1,2-4,5-tetrabromobenzene system. RX refers to isothermal XRD study at 293K; GL and GS to variable-temperature XRD studies using Guinier – Lenne´ and Guinier – Simon cameras, with analysis of peak shapes. DTA methods were also used extensively. (Adapted from van Genderen et al., 1992.)

polymorphism of the components, which considerably complicates the phase diagram, was reported separately (Mondieig et al., 1989; Herbstein, 2001). Mondieig et al. (1991) summarized their results as follows : ‘‘The polymorphism of the components of this system give rise to the ‘‘rich’’ diagram [(Fig. 10.21)]; rich because there are three invariant equilibria : a peritectic equilibrium at 422.2(9)K and two equilibria of the eutectoid type, one at 213(15)K and the other below 93K. There are twelve different regions in the T–x diagram. It may be emphasized that it is the variety of experimental techniques employed (isothermal x-ray experiments at 293K, isoplethic DTA, GL (Guinier-Lenne´) and GS (Guinier-Simon) photography) that has enabled the various phases and their limits of stability to be determined.’’ The thermodynamics of this system has been extensively discussed by van Genderen et al. (1992). 10.6.4 10.6.4.1

Evidence for nonrandom substitution in primary solid solutions

(trans-Stilbene)–diphenylmercury and tolane (1,2-diphenylacetylene)–diphenylmercury The systems (trans-stilbene)–diphenylmercury and tolane (1,2-diphenylacetylene)– diphenylmercury are both eutectics, and the primary solid solutions of diphenylmercury in stilbene (limiting composition is 31 mole% diphenylmercury) and tolane (limiting composition 14 mole%) show interesting effects of non-random substitution of stilbene (Frank, Myasnikova and Kitaigorodsky (1971) or tolane (Samarskaya, Myasnikova and Kitaigorodsky, 1968) by diphenylmercury. Stilbene (Bouwstra et al., 1984; TSTILB04) and tolane (Abramenko et al., 1988; DPHACT05) are isomorphous (both have space

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

619

Layer A

Layer B c

b b a

Layer A

Fig. 10.22. The crystal structure of tolane showing the A and B layers of molecules, which are located at two crystallographically independent sets of symmetry centres. The diphenylmercury molecules substitute exclusively in the A layers. (Reproduced from Samarskaya, Myasnikova and Kitaigorodsky, 1968.)

group P21/c, Z ¼ 4 with the molecules centred at two crystallographically independent centers of symmetry) and have a layer structure (Fig. 10.22), while diphenylmercury (Grdenic et al., 1977; DIPHHG11) has a different structure (P21/c, Z ¼ 2). The A sites have more space available and it has been suggested that even the tolane molecules in these sites are disordered (Espiritu and White (1978) (trans-stilbene generally (Bernstein, 1975), but not always (Hoekstra, Meertens and Vos (1975), shows disorder of the ethylene group). Thus it is entirely reasonable that crystal-structure analyses based on measurements of Bragg intensities show that all the diphenylmercury molecules enter the A sites even at the limiting compositions (Frank, Myasnikova and Kitaigorodsky, 1971; Samarskaya, Myasnikova and Kitaigorodsky, 1968). About 1/6 of the sites in the A layer are occupied by diphenylmercury molecules at the limiting composition in the tolane–diphenylmercury system. One should note that the precision of these analyses is rather low by current standards and the results should be regarded as indicative rather than quantitative. The system is a very favourable one for study because of the strong scattering from the diphenylmercury solute molecules in comparison with the scattering from the tolane matrix. The tolane–diphenylmercury system (principally that with 8 mole% diphenylmercury) has also been studied by measurements of x-ray diffuse scattering in the ﬁrst Brillouin zone (Semenovskaya, Smirnova and Kitaigorodsky, 1978) and by parallel theoretical analyses (Semenovskaya, Kitaigorodsky and Smirnova, 1978); these are pioneering studies for organic systems. The diffuse scattering is of the clustering type, indicating a preference for molecules of a particular type to be surrounded by neighbors of the same kind. There appears to be segregation of like molecules into thin plates, perhaps two or three molecules thick, on (001) planes – in a metal alloy these would be called Guinier–Preston zones (Barrett and Massalski, 1966). If one combines the results from Bragg and diffuse scattering then the resultant physical picture is one in which small disc-like islands of diphenylmercury molecules form on the (001) planes of the tolane solid-solution crystals. A comparable study of the solid solution of tolane in diphenylmercury would appear to be much more difﬁcult to carry out by x-ray diffraction because of the much weaker scattering of the tolane solute molecules.

PACKING COMPLEXES

620

Temperature (°C)

130

Melt 120

110

Solid solution 100

60

70

80

90

100

mol% 2, 3-DMN

Fig. 10.23. Partial phase diagram of the 2,3-dimethylnaphthalene–anthracene system, as observed by DTA. The melting point of 2,3-dimethylnaphthalene is 104.2 C and that of anthracene 215.9 C. (Reproduced from Karl, Heym and Stezowski, 1985.)

10.6.4.2

2,3-Dimethylnaphthalene–anthracene

The partial phase diagram of this system (Fig. 10.23) shows that a primary solid solution of up to 20% anthracene in 2,3-dimethylnaphthalene can be obtained from the melt; these crystals can apparently be cooled to room temperature without change. ˚, 2,3-Dimethylnaphthalene has a crystal structure (a ¼ 7.916, b ¼ 6.052, c ¼ 10.017 A ¼ 105.4 , P21/a, Z ¼ 2) in which the molecules are disordered across centres of symmetry. (Karl, Heym and Stezowski, 1985; DILKEO). Cell dimensions have been measured for solid solutions of 5,11 and 20 mol % anthracene (DILKEP/Q/R). Fluorescence and absorption spectra (at 4K) of anthracene in 2,3-dimethylnaphthalene show a fairly large residual line width of 300 cm1 which is attributed to the statistical disorder of the host molecules. Evidence for non-random arrangement of the guest molecules comes from changes in the anthracene ﬂuorescence with increasing anthracene concentration, indicating anthracene-anthracene interactions. 10.6.5

Inhomogeneity of some solid solution crystals

All of the previous discussion has been based on the assumption that solid solution crystals have the same symmetry as the pure components, with any deviations being due to departures from molecular scale randomness. However, it has been demonstrated that this assumption is incorrect for at least three primary solid solution compositions : [(E)cinnamamide–0.08(E)-2-thienylacrylamide; (E)-cinnamamide–0.15(E)-3-thienylacrylamide and (S)-asparagine–0.16(S)-aspartic acid] (Vaida, Shimon, Weisinger-Lewin, Frolow, Lahav, Leiserowitz and McMullan, 1988; Shimon, Vaida, Frolow, Lahav, Leiserowitz, Weisinger-Lewin and McMullan, 1993), thus suggesting that careful re-examination of

COMPONENTS HAVE DIFFERENT CHE MICAL COMPOSITIONS

621

(a)

c

c

2

4 1

3

(b)

c

B

(011) (001)

b

(c)

A 3

A 2

(001)

B

4 1

(011)

(011) a

A

(001)

B

3 A (011)

A (011)

Fig. 10.24. (a) Stereoview of cinnamamide unit cell seen down [100]. (b) Packing arrangement of cinnamamide showing the four different kinds of surface site at the (01¯1) face. The shaded thienyl rings are shown in the positions they would assume on substitution of a host by a guest molecule. ¯ are (c) Morphological representation of a solid solution crystal, showing the six sectors. A and A enantiomorphic sectors of P1 symmetry, while the B sectors should have Pc symmetry, with opposite polarities in the ac plane. (Reproduced from Vaida, Shimon, Weisinger-Lewin, Frolow, Lahav, Leiserowitz and McMullan, 1988.) H

H H

N

H

H

N

H

S O

O H (E)-cinnamamide

H (E)-2-thienylacrylamide

much earlier work may be necessary. We describe the results for the ﬁrst pair. Early results for (E)-cinnamamide (Leiserowitz and Schmidt, 1969) have been conﬁrmed by ˚ , ¼ 94.1 , Z ¼ 4, P21/a (Hosomi et al., 2000; later work (a ¼ 16.047, b ¼ 5.084, c ¼ 9.584 A ZZZMUR02/3). The crystal structure is shown in Fig. 10.24(a); the crystals are bounded by {011}, {100} and {001} faces. The four symmetry-related molecules are labelled 1–4 and any inequality in the occupancies of these sites by the guest (E)-2-thienylacrylamide molecules would lead to a lowering of symmetry; for example, preferential occupation of site 1 would lead to space group P1. Using the principles of additive adsorption illustrated

622

PACKING COMPLEXES

in Fig. 10.24(b) for the (0 11) face, it was argued that selectivity among the four sites would lead to formation of a solid solution crystal with six sectors, as shown in Fig. 10.24(c). X-ray diffraction analyses of a sectored crystal at 100K (with the sectors cut apart to prevent superposition of diffraction patterns) conﬁrmed that the A sectors had P1 symmetry with differential occupancy of sites 1–4. Conclusive results were not obtained for the B sector. Conﬁrmation of the reduction in symmetry on occlusion of (E)-2-thienylacrylamide in (E)-cinnamamide was obtained by topochemical (2–2) photocyclodimerization, leading to the distribution of products expected on the basis of the structural model. It was concluded that ‘‘the selective occlusion of 2-thienylacrylamide arises from a replacement of attractive C–H . . . (electron) interactions between host molecules by repulsive sulfur (lonepair electron) . . . (electron) interactions between guest and host at the crystal surfaces.’’ The often lower symmetry of solid solution crystals compared to that of the crystals of the pure component is a phenomenon known from Nineteenth Century classical crystallography, and has recently been extensively reinvestigated by Kahr and McBride (1992). The presence of growth sectors of different symmetries can be demonstrated by careful examination of the crystals with a polarizing microscope. 10.7

Interblock solid solubility

It has been suggested (Kitaigorodsky and Myasnikova, 1960a) that there are two types of solid solution – true substitutional solid solution, where the unit-cell dimensions of the solid solution will change in a regular manner with composition, and interblock solid solubility, where the solute molecules are segregated at defects or between the domains of the host crystallites and thus do not inﬂuence the cell dimensions of the host. Thus the dimensions of the unit cell in acridine–5 mole% anthracene are (slightly) different from those of acridine itself (Kitaigorodsky and Myasnikova, 1960b), whereas those of pure p-dibromobenzene and of the solid solution containing 4 mole% durene are the same (Abovyan, Myasnikova and Kitaigorodsky, 1977). The ﬁrst would be an example of true solid solution and the second of interblock solid solution. The idea is interesting but the experimental basis seems meagre, and does not seem to have increased over the past thirty years (Myasnikova, 1993). However, there is intriguing high resolution electron microscopy evidence for interblock solubility in parafﬁn solid solutions where the parafﬁns are separated by only one or two CH2 groups (Fryer et al., 1997). 10.8

Primary interstitial solid solutions

Primary interstitial solid solutions are formed when component B dissolves in the crystals of A without formation of a new phase, the molecules (atoms) of B entering interstitial sites between those of the A molecules (atoms). A necessary condition is that the B moieties should be appreciably smaller than those of A. A classic example is -iron (austenite) at 1150 C; the interstitial carbon atoms are distributed over the four octahedral sites of the FCC cell, with an average of 0.4 carbons per unit cell. The necessary and sufﬁcient conditions for recognition of the occurrence of an interstitial solid solution are (i) similarity between the diffraction patterns of the pure host crystals and those of the solid solution, and (ii) an increase in the measured density of the solid solution over that of the host material.

ORDERED PACKING COMPLEXES

A

623

B

o

R/2

R/2

Fig. 10.25. -TMA.1/6Br2–ORTEP stereodiagram of part of the structure around the twofold axis along 0, y, 1/4. Only the central member of each of the two triply catenated networks of hydrogenbonded TMA molecules is shown and only one of the Br2 orientations. There are two interstitial cavities in the structure; the larger one is occupied by Br2, as shown above, while the smaller one, in the lower part of the diagram, is empty. (Reproduced from Herbstein, Kapon and Reisner, 1985.)

Chemical analysis and location of the interstitial molecules by crystal structure analysis is desirable for conﬁrmation. Clathrate inclusion complexes and other solvates generally differ from primary interstitial solid solutions in that the complex is a different phase from the pure material; however, Dianin’s compound gives clathrates which are primary solid solutions of guest in the racemic host structure (MacNicol, 1984; see discussion in Section 7.4.2). Thus the distinctions are not always clearcut, particularly when the host molecules are much larger than those of the guests, as in many systems of biological interest. Examples of primary interstitial solid solutions among organic crystals are rare. -Quinol (p-dihydroxybenzene, hydroquinone) can form solid solutions with compositions up to 3C6H4(OH)20.08N2 (see Section 7.3.1). Trimesic acid (benzene-1,3,5tricarboxylic acid, TMA) forms crystals of composition TMApX where p ¼ 1/6 for X ¼ Br2 or acetone, and p ¼ 1/12 for X ¼ I2, resorcinol and hydroquinone (Herbstein, Kapon and Reisner, 1985). These crystals are structurally isomorphous with -TMA (Duchamp and Marsh, 1969; BTCOAC) but have higher densities than those of -TMA and slightly different cell dimensions. The structure of TMA1/6Br2 (DAZBIP) was determined and showed the Br2 molecules, disordered over a number of orientations, in interstitial positions (Fig. 10.25).

10.9 Ordered packing complexes We consider here ordered packing complexes where there is no clearcut indication of preferential bonding between like or between unlike components. The classiﬁcation is partially based on chemical composition; however, some examples with crystallographic resemblances lack chemical similarity. 10.9.1 Metal coordination complexes In interallogon complexes (Section 10.3.5) the components have the same chemical composition but different stereochemical conﬁgurations. More complicated situations are also encountered where there are differences in composition and/or oxidation state in addition to different conﬁgurations.

PACKING COMPLEXES

624

10.9.1.1

Components of different composition and conﬁguration but in the same oxidation state The Lifschitz complex of formula Ni(II)bis(meso-stilbenediamine)Ni(II)dichloroacetate crystallizes in yellow triclinic needles which have been shown (Nyburg and Wood, 1964) to be 2½OCTAHEDRALfNi½ðstienÞ2 ðdcaÞ2 g ½SQUARE PLANARf½NiðstienÞ2 þþ g ½ðdca Þ2 2ðC2 H5 OHÞ4H2 O: Ph

H2N H

C

C

Ph

O

Cl H

NH2

10.55

H

C

C _

Cl

O

10.56

[meso-stilbenediamine (10.55) is abbreviated as "stien" and the dichloroacetate anion (10.56) as "dca–"]

There are two neutral molecules (centred at 0,0,0 and 1/2,0,1/2) and one square planar cation (centred at 0,0,1/2) in the unit cell as well as ethanol and water molecules at general positions. Ni is in the (II) oxidation state in both moieties. Another example is provided by a ‘lattice adduct’ containing HgII in two different conﬁgurations – the triclinic crystals of 2{Hg(SCN)2(P(C6H5)3)2}{Hg(C6H5)2} contain two molecules per cell of four-coordinate, distorted tetrahedral {Hg(SCN)2(P(C6H5)3)2} at general positions, and one centrosymmetric two-coordinate linear {Hg(C6H5)2} molecule at the origin (Lobana, Sandhu, Povey, Smith and Ramdas, 1989; SEDGEN); from a structural point of view, this is formally similar to the situation described elsewhere in this chapter (cf. Section 10.3.3). 10.9.1.2 Components with different compositions, conﬁgurations and oxidation states The triclinic crystals of 2{NiIIIBr3[P(CH3)2(C6H5)]2{NiIIBr2[P(CH3)2(C6H5)]2C6H6 contain two molecules per cell of the ﬁve-coordinate, trigonal-bipyramidal NiIII molecule at general positions, and one centrosymmetric four-coordinate square-planar NiII molecule at the origin (cf. Section 10.3.3). The NiII species is diamagnetic and the NiIII species paramagnetic; thus, as with the interallogon complexes, care must be taken in interpreting the magnetic properties of the crystals (Meek, Alyea, Stalick and Ibers, 1969). 10.9.1.3

The components are oligomers

We have encountered four examples where the components of a packing complex are respectively a monomer and a dimer. In hydrated Co(II) 4-methyltropolonate the monoclinic cell (P21/c) contains 4 units of Co2(C8H7O2)4(H2O)2, 4 units of Co(C8H7O2)2(H2O)2 and 4 molecules of water of crystallization (Fig. 10.27; Post and Trotter, 1975; COMTRP). A tetranuclear species has also been isolated so the composition of the mother liquors must be complex. Pentaﬂuoronitrosobenzene is actually composed of a 1 : 2 ratio of monomer and cisdimer (10.57). The well-formed green crystals (P21/c, Z ¼ 10 units of C6F5NO) have monomers at centers of symmetry (and hence are necessarily disordered) and dimers at general positions (Prout, Coda, Forder and Kamenar, 1974; FNTSBZ10).

ORDERED PACKING COMPLEXES

625

B

A Co O C

Fig. 10.26. A general view of the asymmetric unit of the hydrated Co(II) 4-methyltropolonate complex (the water of crystallization has been omitted). The moiety denoted by A is dinuclear and has composition. Co2(C8H7O2)4(H2O)2, while B is mononuclear and has composition Co(C8H7O2)2(H2O)2; A has a trans disposition of water molecules and B a cis disposition. Broken lines denote hydrogen bonds between A and B; only dispersion forces operate between A molecules and between B molecules. (Reproduced from Post and Trotter, 1985). NO F

F

C6F5

O N N

F

F

O

C6F5

F 10.57 (monomer)

(cis-dimer)

An ordered complex of monomers and dimers is found in 1,3-di-t-butyl-2,2-dimethyl˚ , 106.8(1) ; C2/c, Z ¼ 12) at 1,3,2,4-diazasilastannetidine (10.655(5) 24.75(1) 17.33(1) A 153K (Veith, 1978; TBASIT). The unit cell contains four monomers on two fold axes and four dimers about centres of symmetry (Fig. 10.27). Dimerization is accompanied by small changes in bond lengths. Monomers and dimers are linked by a rather weak ˚ ). 1,10-Phenanthroline-trichloromercury also Sn . . . Sn interaction (d(Sn . . . Sn) ¼ 3.676 A belongs in this group but is more appropriately described in Section 11.6.2.3. Sodium tert-butoxide (CH3)3CONa is analogous to the examples cited above. The crystal structure (R3c, 90 units of (CH3)3CONa per unit cell; Greiser and Weiss, 1977; NABUOX; space group correction by Davies, Kopf and Weiss, 1982) has an ordered arrangement (Fig. 10.28) of six hexameric and six nonameric units (in 1 : 1 proportion), the bulky tert-butoxy groups (which are appreciably disordered) on the peripheries of these molecules preventing other than dispersion interactions. 10.9.2 Complexes in which a moiety plays more than one structural role One classic example is surely CuSO45H2O in which four of the water molecules are coordinated to the copper ion and the ﬁfth is water of crystallization. Another example is

PACKING COMPLEXES

626

(a)

monomer

Sn2

Si2

dimer Si1 Sn1

x

y

z (b)

CH3

CH3

(c)

centrosymmetric dimer 2.100

N 1.705

monomer with (horizontal) two fold axis 2.092

Sn1

N3 1.704

2.242 N1 2.392

Si1

1.804 N

Si2

Sn2 N

N2

t - butyl

y y

z x

x z

Fig. 10.27. (a) Packing of the monomers and dimers in 1,3-di-t-butyl-2,2-dimethyl-1,3,2,4diazasilastannetidine; (b) molecular dimensions of the dimer unit; (c) molecular dimensions of the monomer unit. (Data fromVeith, 1978.)

ORDERED PACKING COMPLEXES

Na

O

Na

Na O CMe3

Na Me3C

O

O

Na

O

CMe3

CMe3

CMe3 CMe3

627

Na O

Na Na

Me3C

O CMe3

Me3C

Na O

O O CMe

Na

Na

O

Na O Me3

Na

O

CMe3 3

Na

CMe3

CMe3

CMe3 A

0.25

0.75

0.75

0.25 B 0.75

–c 0.75

a

0.25

0.25 tert C Na O

Fig. 10.28. (above) The nonamer (left) and the hexamer (right) of sodium tert-butoxide; (below) Projection of the unit cell of sodium tert-butoxide down [010] showing the packing of the nonamers and hexamers (the hydrogens of the methyl groups have been omitted). (Reproduced from Greiser and Weiss, 1977.)

3/2(pyrene) : picryl bromide, described in more detail elsewhere (Section 15.5.1); one of the pyrenes is located in a mixed stack with picryl bromide while the other is intercalated, in ordered fashion, between the stacks. A somewhat similar situation occurs in 2{1,4diphenylbutadiene tricarbonyliron}(1,4-diphenylbutadiene) (de Cien, L’Huillier and Weiss, 1973; PBFCPB), which crystallizes in space group P1 with two diphenylbutadiene tricarbonyliron molecules in general positions and a centrosymmetric diphenylbutadiene molecule in a transoid conformation at the origin (cf. Section 10.3.3)). A ﬁrst crop of crystals from the synthesis of the organometallic compound gave the complex and a second the pure organometallic compound. The two components are arranged in successive (002) planes without any particularly short distances between them. A further example is tetrakis(o-phenylenediamine)Ni(II) chloridebis(o-phenylenediamine) (Elder, Koran and Mark, 1974; OPDANI). Here the Ni atom has one molecule of o-phenylenediamine coordinated to it in bidentate fashion and two molecules coordinated monodentately and there are also two molecules of ‘‘toothless’’ o-phenylenediamine not coordinated at all to Ni. An analogous situation is found in (o-phenanthroline) bis(thiourea)Cu(I)iodide (o-phenanthroline) (Hall, Kepert, Raston and White, 1977; PBTUCU).

PACKING COMPLEXES

628

10.9.3

Miscellaneous packing complexes

We include in this section two contrasting groups of packing complexes – those for whose existence there is no apparent reason, and those where some incipient linkage can be discerned. The molecules of the ﬁrst group do not have complicated shapes (and so could perhaps interlock) nor are there especially polar or polarizable substituents – thus the differences between the free energies of (AB)c and Ac þ Bc must be rather small, although no numerical values are available. In the second group there is fairly clear evidence of incipient bond formation or atom transfer and related covalent compounds or salts are known; thus it is not too difﬁcult to identify the source of the interaction between the component molecules, even though these maintain their discrete identities in the complex. Examples of the second group could have been included among the molecular compounds formed by localized charge-transfer interactions (Chapter 12) but making comparison here between the two groups is instructive. We allocate the ﬁnal section of this chapter to the molecular complexes of the fullerenes (mostly of C60 with a few examples of C70 and even C76). It would have been possible to distribute these among the two categories mentioned in the ﬁrst sentence of the previous paragraph. However, it seemed more reasonable, at the present stage of development of this part of our subject, to place them in a separate section in order to emphasize chemical rather than structural resemblances. 10.9.3.1 Packing complexes without speciﬁc interactions Among our examples in the ﬁrst group are hexabromobenzene . . . 1,2,4,5-tetrabromobenzene (HBB . . . TBB), found by chance as a minor impurity in a commercial sample of 1,2,4,5-tetrabromobenzene (Gafner and Herbstein, 1964; HBTBBZ); tolane . . . 1,1-dimethyl2,5-diphenyl-1-silacyclopentadiene (Clardy and Barton, 1972; SICPPA), obtained from the work-up of a reaction mixture that did not yield the expected Diels-Alder product; S2Fe3(CO)9 . . . S2Fe3(CO)6 (Wei and Dahl, 1965b); tetrathiafulvalene (TTF) . . . Pd (acetylacetonate)2 and the Pt analog (Siedle, Kistenmacher, Metzger, Kuo, van Duyne and Cope, 1980; FLVPDA/B) and tetrabenzoylbenzene . . . di-allene (Toda, Tanaka, Tsukada, Shimanouchi and Sasada, 1979; BBZTND). The crystal structure of C6Br6 . . . C6H2Br4 (Fig. 10.29) has a close relation to that of C6Br6; alternate (200) planes of the complex contain sheets of C6Br6 molecules in essentially the same arrangement as that in the (101) planes of C6Br6. Indeed, C6Br6 . . . C6H4Br2 decomposes at room temperature by loss of C6H2Br4 and the resulting crystallites of C6Br6 preserve this orientation with respect to the parent crystals of the complex (see Fig. 10.29 left). Thus C6Br6 . . . C6H2Br4 is a mimetic complex. The liquidus diagram (Fig. 10.29 right) gives no hint of the presence of the complex as a separate phase at temperatures above 150 C and it must appear as such only at higher pressures of the components. From the point of view of the phase rule, the complex forms a univariant system at low temperatures complex , hexabromobenzene (solid) þ vapour (mainly tetrabromobenzene) and thus has a dissociation pressure which varies with temperature. At higher temperatures the vapor will also contain appreciable amounts of hexabromobenzene and the

ORDERED PACKING COMPLEXES

b up

a

o

629

5Å

c 350

b up a c

T °C

300 250

L + C6 Br6

200 150

0

20

40

60

80

100

C6 H2 Br4 Molecular % C6 Br6 C6 Br6

Fig. 10.29. (left) C6Br6 . . . C6H4Br2 – the mutual orientation of complex (upper digram) and hexabromobenzene (lower diagram) are shown in projection down [010]. Molecules with full circles have their centres in the plane of the paper and those with open circles are translated by b/2. The relevant ˚ for both crystals; [100]complex ¼ 17.80 A ˚ ; d[1¯01]HBB ¼ cell dimensions are : [010] ¼ 4.01 A ˚ . (right) Melting point diagram for the system C6Br6/C6H2Br4 at atmospheric pressure. The 17.86 A dashed portions of the diagram are schematic only and were not observed directly. (Reproduced from Gafner and Herbstein, 1964.)

system should be treated as containing a binary compound with incongruent transitions (Ricci, 1966). In solution the system behaves like ‘‘a double salt unstable to water’’ (Glasstone, 1947). The equimolar complex of tolan and 1,1-dimethyl-2,5-diphenyl-1-silacyclopentadiene (P21/m, Z ¼ 2) has the molecules arranged in layers about (not in) the (200) planes (Fig. 10.30); each molecule has symmetry Cs(m). Each tolan molecule is surrounded by four silane molecules but the average distance between potential Diels–Alder reaction centres is ˚ so there is no hint of incipient reaction. There is no spectroscopic evidence for about 5 A charge-transfer interaction between the components, nor are complexes formed between silole and any other acetylenes. A point of resemblance to C6Br6 . . . C6H2Br4 is that tolan sublimes out of the complex at reduced pressure. This is not a mimetic complex as the neat silacyclopentadiene crystals are orthorhombic (Muir et al., 1975; MPSICP). The equimolar complex of tetrathiafulvalene (TTF) and dimethyldicyanofumarate (DDF) also has a layered structure, with the components segregated into parallel slices of the crystal (Fig. 10.31) (Mulvaney, Pang, Cramer and Hall, 1982; BILXUP). Conﬁrmatory spectroscopic evidence would appear to be necessary before accepting the assertion of the authors that this is a charge-transfer compound. In TTF : palladium diacetylacetonate (Pd(acac)2) the TTF and Pd(acac)2 molecules are segregated onto alternate (100) planes (Siedle, Kistenmacher, Metzger, Kuo, van Duyne and Cope, 1980); Raman spectroscopy shows convincingly that the TTF moieties are present as neutral molecules ( 3 which is predominantly due to the C¼C bond stretch, is

PACKING COMPLEXES

630

z

y x A

4.93Å E

C 5.03Å F

4.91Å

5.56Å B

D

Fig. 10.30. Molecular arrangement in the tolan . . . 1,1-dimetly1-2,5dipheny1-1silacyclo-pentadiene packing complex. The tolan molecules are denoted by E and F and the 1,1-dimethy1-2,5-dipheny11-silacyclopentadiene molecules by A–D. (Reproduced from Clardy and Barton, 1972.)

Fig. 10.31. Stereodiagram showing the unit cell of TTF . . . DDF viewed along the c-axis. The unique monoclinic b-axis points up in the plane of the page. (Reproduced from Mulvaney, Pang, Cramer and Hall, 1982.)

at 1517 cm1, essentially unchanged from the 1515 cm 1 found in neutral TTF, whereas in TTF þ Br it is at 1413 cm1). The equimolar complex of cyclohexasulphur and cyclodecasulphur (m.pt. 92 C) also has a layered structure with the components segregated about alternate (400) planes (Steudel, Steidel and Reinhardt, 1983). There are only van der Waals interactions between the components; the Raman spectrum of the complex is a superposition of the Raman spectra of the neat components. As there is no evidence of particular interactions between the components in these two complexes, we classify them as packing complexes. The packing complex (3-S)2Fe3(CO)9 . . . (2-S)2Fe2(CO)6 was obtained from the reaction between Fe3(CO)12 and cyclohexane sulﬁde or 3-chloropropylene sulﬁde (King, 1963) and characterized by x-ray crystal structure analysis (Wei and Dahl, 1965b). The molecular crystals (Pnma, Z ¼ 4) contain an ordered array of the two components which are held together by dispersion forces; both components have Cs(m) symmetry. This is not a mimetic complex as both components crystallize in triclinic crystals ((3-S)2Fe3(CO)9, Bard, Cowley, Leland, Thomas, Norman, Jutzi, Morley and Schlu¨ter, 1985; (2-S)2Fe2(CO)6, Wei and Dahl, 1965a). 57Fe Mo¨ssbauer spectroscopy of the dimer, trimer and complex (Dilworth, Morton, O’Connor and Silver, 1987) combined

ORDERED PACKING COMPLEXES

631

with the crystallographic results, suggests that the somewhat ﬂexible dimer is distorted by solid-state interactions in the complex, whereas the more rigid trimer remains relatively undisturbed by these interactions. Another example is the 1 : 1 complex formed between 1,2,4,5-tetrabenzoyl-3,6-di-tbutylbenzene (10.58) and meso-3,8-di-t-butyl-1,5,6,10-tetraphenyldeca-3,4,6,7-tetraene1,9-diyne (10.59); the complex crystallizes in space group I2/c, with four molecules of each type in the unit cell. The molecules 10.58 are located on two fold axes, with disorder of the t-butyl groups, and the molecules 10.59 at centres of symmetry. The dl-diallene corresponding to 10.59 does not form an analogous complex (Toda, Tanaka, Tsukada, Shimanouchi and Sasada, 1979). Ph t-Bu PhOC

C COPh

Ph

C C

C

C

t-Bu COPh

PhOC

t-Bu C

Ph

C C C

t-Bu 10.58

C

Ph 10.59

The 1 : 1 complexes of 2,5-diaryl-1,4-dithiins (10.60) with 2,4-diarylthiophenes (10.61) are also packing complexes (Kobayashi and Iwasaki, 1984; CUSTOZ). Nine varieties of complex have been obtained, with X ¼ H, Cl and CH3, and Y ¼ H, Cl and CH3. The structure with X ¼ Y ¼ H was determined; it was fully ordered and not mimetic as 2,5-diphenyl-1,4dithiin (idem, ibid; CUSTUF) has a quite different structure. There are neither hydrogen bonds nor charge-transfer interactions in any of these crystals. The 1 : 2 complex of cubylcubane and 2-tert-butylcubylcubane is triclinic (space group P 1, Z ¼ 2), with the cubylcubanes at centres of symmetry and the 2-tert-butylcubylcubane molecules at general positions (Gilardi, Maggini and Eaton, 1988; VACFIO). The cubylcubanes are in columns surrounded by the 2-tert-butylcubylcubanes, but with only dispersion interactions between them. This general arrangement has been encountered before (see end of Section 10.4.2). The 1 : 1 complex of naphthalene and 1,1 0 -bis(naphthyl)diselenide crystallizes in space group C2/c with Z ¼ 4; the naphthalenes are on centres of symmetry and the 1,1 0 bis(naphthyl)diselenide on two fold axes (Jones, Kienitz and Tho¨ne, 1994; PINTEL). This is another variant of the general arrangement encountered before (see end of Section 10.4.2). Similarly in iodobis(1,10-phenanthroline)-Cu(II)iodideS8 (Hambly, Raston and White, 1977) there are no close iodine . . . sulphur approaches and the material must be classiﬁed as a packing complex. WCl6S8 is a packing complex with alternating layers of WCl6 and S8 molecules (Cotton, Kibala and Sandor, 1989). On the other hand, [(PPh3)2N]þ[AgS9] S8 is a salt-molecule complex (Mu¨ller, Ro¨mer, Bo¨gge, Krickemeyer and Zimmerman, 1986; CONCEV20). Some other complexes of S8 are discussed in Section 11.2. The 1 : 1 complex formed between Si5Cl12 (the Si5Cl12 is present in the neopentyl form i.e. as Si(SiCl3)4) and SiCl4 (Hambly, Raston and White, 1977) is a packing complex (Fleming, 1972) and presumably the same holds for the equimolar complexes formed between Si5Cl12 (and Si6Cl14) and SiCl4, SiHCl3, Si(CH3)2Cl2 and Si(CH3)3Cl (Urry, 1964).

PACKING COMPLEXES

632

X

X

S

S

S X

X

10.61

10.60

1 : 1-Pyrene–ferrocene (Atencio, Domasevitch and Zaworotko, 2000; LONGOK) has a remarkable structure which, so far, does not have analogs. The air and water stable orange crystals, studied at 193 K, are triclinic (space group P1, Z ¼ 2, 9.5525(6), ˚ , 92.029(1), 99.634(1), 98.042(1) ); the pyrene molecules are 9.7564(6), 10.0345(7) A located about two independent centres of symmetry while the ferrocenes are in general ˚ thick, parallel positions. The two component molecules are located within slices about 6 A to (110); there are no short distances between the molecules within the layers. Atencio et al. have pointed out that it is ‘‘unexpected that pyrene and ferrocene would form binary compounds.’’ Their suggestion is that the crystals are of ‘‘a host-guest compound in which ferrocene dimers are guests inside a pyrene 2D network that is sustained by non-covalent C–H . . . stacking interactions.’’ We prefer to classify the complex as a packing complex. We conclude this section with two complexes that strikingly reﬂect the remarks of Alice given at the beginning of this Chapter. These are the 2 : 1 complexes of 9,9 0 biﬂuorenylidene (BFL; C26H16) with pyrene (C16H10) and perylene (C20H12) (Lee and Nyburg, 1985). There would seem to be no reason why formation of such complexes should be anticipated but form they do, with {2(C26H16)(C16H10)} giving wine-red crystals and {2(C26H16).(C20H12)} deep yellow crystals. C26H16 is itself deep red so the colors of the complexes perhaps hint at some interaction between the components. Melting points, phase diagrams and spectra (solution and solid state) would be of great interest but do not seem to have been reported. Nor is it known whether these are two The 9,9-bifluorenylidene molecule is not planar but twisted about the double bond, with an average angle of 39° between the planes of the two half-molecules.

˚ , deg.) for {2(9,9 0 -bifluorenylidene).pyrene} and {2(9,9 0 -bifluorTable 10.8. Cell dimensions (A enylidene).perylene} Compound

a

b

c

Z

Space group

Refcode

{2(C26H16)(C16H10)} {2(C26H16)(C20H12)}

17.846(5) 16.102(4)

15.449(3) 15.342(5)

16.27(1) 18.798(9)

95.59(3) 90.39(4)

4 4

C2/c I2/c

CUNWUD CUNXAK

ORDERED PACKING COMPLEXES 1 4

C

633

1 4

A

I

B

1 4

I

1 4

II II O

1 4

1 4

a

Fig. 10.32(a). Projection down [010] of the {2(9,9 0 -biﬂuorenylidene).pyrene} complex. The symmetry elements of space group C2/c are shown. A pair (A and B) of (homochiral) BFL molecules is shown emphasized at top centre. The alternating layers of homochiral BFL molecules about (001) are marked by lines outside the cell boundaries; I and II refer to different senses of BFL chirality. One is looking down the mixed stacks of alternating pyrenes and BFL pairs. (Adapted from Lee and Nyburg (1985).) II

I

II

I A

I

II

B

a 1 4

1 4

I

II II

I 1 4

1 4

I

II c

II I

II

I

Fig. 10.32(b). Projection down [010] of the 2(9,9 0 -biﬂuorenyliodene).perlylene complex. The symmetry elements of space group I2/c (an alternative orientation of C2/c) are shown. A pair (A and B) of (homochiral) BFL molecules is shown emphasized at top right. Alternating layers of 01)planes; I and II refer to different senses of BFL homochiral molecules lie about the (101) and (1 chirality. One is looking down the mixed stacks of alternating perylenes and BFL pairs. (Adapted from Lee and Nyburg, (1985).)

634

PACKING COMPLEXES

isolated examples or representatives of a larger family where other aromatic hydrocarbons can replace pyrene and perylene. 10.9.3.2

Packing complexes with incipient speciﬁc interactions

Our examples of packing complexes with incipient interactions between the components are chosen from the complexes of XeF2, which is a ﬂuoride-ion donor and forms salts with ﬂuoride-ion acceptors such as AsF5 and other metal pentaﬂuorides. Molecular complexes are formed with weaker acceptors, the molecular entities involved maintaining their discrete character; however, the mutual arrangement of the components indicates an attraction between negatively charged ﬂuorines of XeF2 and positively charged centres on the second component. XeF2 . . . XeF4 (Burns, Ellison and Levy, 1965) is one such example and the isomorphous pair XeF2 . . . IF5 (Jones, Burbank and Bartlett, 1970) and XeF2 . . . XeOF4 (Bartlett and Wechsberg, 1971) belongs to the same category. The structures of XeF2 . . . XeF4 and C6Br6 . . . C6H2Br4 are formally similar, with centrosymmetric molecules distributed over the same special positions of the same space group and both can be described in terms of centered sheets parallel to (001), with the components segregated on alternate sheets. Furthermore, both are mimetic complexes as has already been noted for C6Br6 . . . C6H2Br4, while in XeF2 . . . XeF4 there is a resemblance between the arrangement of XeF4 molecules in the complex and that in XeF4 itself. XeF2 . . . IF5 and XeF2 . . . XeOF4 have tetragonal structures in which the molecules of the two components are segregated onto alternate (001) planes. The distance between a ˚ and this rather short distance is interpreted ﬂuorine of XeF2 and an iodine of IF5 is 3.14 A as indicating an electrostatic interaction between these two atoms. In XeF2 . . . XeF4 the ˚ , between a ﬂuorine of XeF4 and the Xe of XeF2. The shortest F . . . Xe distance is 3.38 A structure of XeF2 . . . XeOF4 has not been reported in detail. 6 10.9.3.3 Complexes of the fullerenes : mainly C60-Ih and C70-D5h The fullerenes (Taylor and Walton, 1993; Hirsch, 1994) have excited immense interest during the past few years; originally only C60-Ih (C60 for short), and to a lesser extent C70D65h (C70 for short), were available in quantities adequate for experimental studies but this situation has changed rapidly. Moreover, modern techniques are such that the ﬁrst crystallographic study of {C76–(S8)6} (Michel et al., 1994) was carried out when the total world production of C76 was in the 10–100 mg range! Version 5.23 (April, 2002) of the CSD yields 226 hits for ‘C60-fullerene’, of which 84 concern binary adducts; the corresponding ﬁgures for C70- and C76-fullerene are 21 (10 adducts) and 2 (2 adducts). There are a number of themes in the crystal chemistry of the fullerenes and their molecular complexes, especially that of C60. The ﬁrst structures were intended to elucidate the molecular structure of C60, emphasising initially the neat compound, in which the molecule is orientationally disordered at 300K and which shows complicated ordering behavior on cooling. Then various complexes were studied in the hope that they would contain arrangements of ordered C60 molecules. Much of this early exploratory work was not carried to ﬁnal conclusions because of experimental difﬁculties, or because the center of interest had passed elsewhere. Later, after establishment of the details of the fullerene molecular structure, interest returned to supramolecular themes of arrangement

ORDERED PACKING COMPLEXES

635

of the components in the molecular complexes, and the interactions between them. The molecular complexes, which show considerable diversity of structure, are classiﬁed here in terms of the relative size of fullerene and largest additional component (many complexes are ternary), with shape and chemical nature as further factors. Where justiﬁed by resemblances, we group complexes of C70 and C76 together with those of C60; there are many examples where the C60 and C70 complexes are isostructural, but this is not an invariable rule. Many of the reports are still at the ‘Communication’ level so detail, and, in some instances, reliable detail is lacking; in particular, study at low temperatures is usually required to establish the degree of order of the components (sometimes not only that of the fullerene). When the second component is much smaller than the fullerene, the quasi-spherical shape of C60 suggests that there could be a succession of close-packed hexagonal layers of molecules with the second components in interstitial positions. A number of structures follow this pattern. Our classiﬁcation places somewhat more emphasis on structural than on chemical aspects, but we ﬁnd that the latter have an important role. We group together complexes where the most obvious feature is the three-dimensional packing of close-packed layers of quasi-spherical fullerenes, with the second component in interstitial positions (Table 10.9); here it seems justiﬁed to call the fullerene a ‘host’. We then proceed to complexes where there are single layers of fullerenes, separated by layers of the second component, and then to complexes where there are close-packed rows of fullerenes. When the size of the second component becomes comparable to that of the fullerene, then there is interspersion of the two components; when the second-component molecule has a concave shape the close packing feature is augmented by an embrace of the fullerene by the second component. Here it is convenient to group the calixarene complexes together. A number of (here concave) tetrathiafulvalenes and analogs show this feature, as do many metalloporphyrin complexes. There are a few essentially planar second-component molecules, and this leads to some differences in arrangement but interleaving of the two components remains a general feature. Calculations have been made of the energies of interaction between C60 and porphyrins (Boyd et al., 1999). Although details depend on the nature of the components and the force ﬁeld used, some 80–90% of the interaction energy derives from van der Waals interaction, and the rest from electrostatic interactions between the porphyrin molecules. It seems likely that this situation holds for most of the fullerene complexes, and that speciﬁc, directional interactions will be weak. In addition to the packing aspects of the structures of the fullerene molecular complexes, one must also consider the interactions between the components, the situation being complicated by the fact that all interactions are roughly of equal importance which is, of course, the reason why fullerene complexes are discussed in this chapter. A major conceptual division is into neutral and ionic complexes (formally ‘salts’); we do not include the salts in our discussion. The neutral complexes should presumably be classiﬁed into packing and weak charge transfer complexes but again the distinctions are not clearcut. In many of the reports of individual structures, considerable attention is given to shorter intermolecular distances between particular regions of the fullerene and the second-component, highlighting these as evidence of speciﬁc interactions; we refer the reader to the original papers for detail at this level. At present, there are a few groups of isostructural compounds (Tables 10.9 and 10.10) while the others show considerable diversity and a coherent pattern is not often discernible. Many of the complexes are in fact

636

PACKING COMPLEXES

ternary (or higher) ‘solvates’ but the tendency has been to concentrate on the relative arrangement of fullerene and second component and assume that the third component has only a space-ﬁlling role, with only a few exceptions to this rule. A comparison of packing in fullerenes and dicarbadodecaboranes has been given by Hardie and Raston (1999). We remind the reader that C60 is a weak electron acceptor with electron afﬁnity comparable to that of 1,2,4,5-tetracyanobenzene. There are two estimates of its adiabatic electron afﬁnity (see Section 13.2.5) – measurements of the charge transfer absorption energy and the redox potential give Ea ¼ (2.10–2.21) 0.1 eV (Saito et al., 1994), while give Ea ¼ 2.65(5) eV measurements of the threshold photodetachment spectra of cold C60 (Wang et al., 1991). A number of C60 complexes containing I2 or CH2I2 have been reported. Here the C60 presumably acts as donor as its electron afﬁnity ( 2.5 eV) is smaller than that of I2 (3.06 eV). Complexes are written as {donorC60} to take into account the weak acceptor properties of C60; the order has been reversed in the few examples where C60 appears to be the donor. There are 20 refcode entries in the CSD (SOCTOT to SOCTOT31) for structural studies of C60 itself; these were not included in the enumerations above. The predominant polymorph of C60 at room temperature has a face-centered cubic close packed structure, ˚ ; a minority containing spheroidal molecules of gross (van der Waals) diameter 10 A hexagonal polymorph has also been reported. The FCC crystals have a packing coefﬁcient of 0.74 so that smaller ions such as those of the alkali metals can be incorporated without marked change of structure. However, larger second components generally lead to changes in the packing arrangements. The quinol clathrates of C60 and C70 have been discussed separately (Section 7.2.1; SOMGIK to SOMGIK04). Five polymorphs of C70 have been reported (Verheijen et al., 1992) but are not listed in the CSD. Group I : fullerene considerably larger than other components Complexes based on three-dimensional close packing of layers of fullerene hosts The complexes most likely to justify description as packing complexes are the ‘solvates’ of C60 with n-pentane (Aliev et al., 1993), n-hexane and n-heptane (Ceolin et al., 1995), and cyclohexane, but these have been studied with limited degrees of completeness. However, there are a considerable number of structurally related packing complexes for which information is available (Table 10.9). The ﬁrst group of complexes is based on close packing of spherical fullerene molecules with the molecules of the smaller second component in interstitial positions. The spherical ˚ , give rise to characteristic 10 A ˚ C60 molecules, with van der Waals diameter of 10 A repeats. In some examples, the resemblance is more apparent through the reduced triclinic cells than through the higher-symmetry monoclinic cells. There is a hexagonal (or trigonal) arrangement of C60 molecules in a . . . AAA . . . packing of layers,3 with the degree of order of the second component determining the space group. The hexagonal complexes with n-heptane, HCX3, CCl4, P4 and I2 and the triclinic ferrocene complex (the latter three being air stable) form an isostructural group. The results are of varying degrees of completeness. {(P4)2.C60} was prepared both by gas–solid reaction and by co-precipitation from benzene, and {C60.(I2)2} by gas–solid reaction. The {(P4)2C60} and {C60(I2)2} complexes are isomorphous; both were studied by Rietveld analysis of synchrotron intensity measurements 3

HCP structures have . . . ABAB . . . arrangement of layers.

ORDERED PACKING COMPLEXES

637

˚ , deg) for those molecular complexes of C60 classified as packing Table 10.9. Crystal data (A complexes, some of which form isostructural groups. Temperatures are a nominal 300K unless stated otherwise. Cell angles of 90 and symmetry-related axes are omitted. Structures are not known for asterisked entries. Omission of the Refcode means that the complex has not been found in the CSD version of April, 2002 Formula/reference

a/

n-C7H16C60*x CA95 2(HCCl3)C60 JW95 2(HCBr3)C60 JW95 2(CCl4)C60 JW95 2(H2CCl2)C60 JW95

c/

Z

10.00 10.080 10.212 10.10 16.400

10.16 120 10.110 120 10.209 120 10.75 120 11.640 90

1 1 1 4

P6/mmm P6/mmm P6/mmm P6/mmm Not given

(P4)2C60 LD94; DG94 (I2)2.C60 ZC92 2(ferrocene)C70 at 130KOHB99 2(ferrocene)C60 at 143K CH92 (N,N,N 0 ,N 0 -tetramethylphenylenediamine)C60 KK02

10.084 9.962 27.752

10.105 120 9.984 120 19.603

1 1 2

see text see text C2

11.342 118.33

1

P1

10.248

2

P21 =c

TONDUV02

2(C6H5Br)C60 KM98

17.231

11.338

2

C2=m

HOSJAA

n-C5H12C60* OB94

10.101

A21ma

KOFKUG; 3D coordinates not available

PentaneC60 KF95

16.5

PentaneC70 KF95

17.33

TolueneC76 KF95

17.684

TolueneC82 KF95

18.355

4(C6H6)C60 at 104K BR94 (I2)C6H5CH3C60 at 143KBC93

9.938 65.38 19.039

9.899 95.55

10.281

b/

10.051 124.19 10.366 90.96

17.225 101.93 10.164 108.12 10.163

10.08 107.73 10.529 107.70 11.080 108.10 11.355 108.17 15.03 88.31 13.817

31.706

Space groups

Refcode

YOLTIC YOLTEY PIGWUX YOLTOI tetragonal

BEJLOR KUVNOE Reduced cell

10.14

2

P21

10.618

2

P21

11.018

2

P21

11.410

2

P21

17.425 74.83 13.479

2

P1

JUGCET11

4

Pnma

LAVNIF

ZOYSOF

˚ , Immm) from toluene–n-heptane, but composition not x Also, an orthorhombic phase (10.07, 10.22, 48.9 A established. References: BC93 – Birkett, Christides et al., 1993; BR94 – Bu¨rgi, Restori et al., 1994; CA95 – Ceolin, Agafonov et al., 1995; CH92 – Crane, Hitchcock et al., 1992; DG94 – Douthwaite Green et al., 1994; JW95 – Jansen and Waidmann, 1995; KF95 – Kawada, Fujii et al., 1995; KK02 – Konarev, Kovalevsky et al., 2002; KM98 – Korobov, Mirakian et al., 1998; LD94 – Locke, Darwish et al., 1994; OB94 – Oszlanyi, Bortel et al., 1994; OHB99 – Olmstead, Hao and Balch, 1999; ZC92 – Zhu, Cox et al., 1992.

PACKING COMPLEXES

638

from powder samples{(P4)2C60} has disordered P4 molecules located at trigonal prismatic sites in two orientations (Locke et al., 1994; Douthwaite et al., 1994). Solid state 31P MAS NMR spectroscopy of {(P4)2C60} showed that no charge transfer had occurred; there is a phase change on cooling to 20K but the low temperature structure has not yet been reported. The {C60(I2)2} complex (Fig. 10.33) has a resistivity exceeding 109 ohm cm at 300K, and shows no superconductivity above 4K (Zhu et al., 1992). The value of d(I–I) was found to ˚ (to be compared with a standard value of 2.7 A) and there was ‘‘no long range be 2.53 A order in the occupancy of the iodine sites.’’ Thus some reservations remain about structural details. Molecular dynamics in crystalline {C60(CHBr3)2} has been studied by solid state NMR (Collins, Duer and Klinowski, 2000); the C60 molecules undergo fast isotropic reorientation in the range 193–295K. Triclinic {(ferrocene)2C60} (grown from benzene) has a structure derived by small distortions from those of the two previous compounds. The ordered C60 molecules (at centers of symmetry) are packed in . . . AAA . . . layers parallel to (001), with ordered ferrocenes (in eclipsed conformation, at general positions) in interstices between the layers (Crane, Hitchcock et al., 1992; KUVNOE). Despite differences in space group, {(ferrocene)2C60} and {(ferrocene)2C70} (Olmstead, Hao and Balch, 1999) have similar structures, which are compared in Fig. 10.34. In both complexes the ferrocenes are inferred from their dimensions to be neutral, and hence there is no (or very minor) charge transfer. (a)

a

a

(b) a

a c

Fig. 10.33. {C60(I2)2} (a) basal plane projection of structure with C60 represented, in skeleton form, ˚ ) which form a simple hexagonal arrangement. The paired by the large circles (radius ¼ 3.5 A ﬁlled circles represent the iodine molecules, which do not have long range order. (b) Schematic three-dimensional view to indicate the resemblance to Stage I intercalate (see Section 9.2.2.1). (Reproduced from Zhu et al., 1992.)

ORDERED PACKING COMPLEXES

639

c

c

0 b

a

b

a

Fig. 10.34. Monoclinic {(ferrocene)2C70} and triclinic {(ferrocene)2C60} viewed down their [010] ˚ respectively). Ferrocenes are eclipsed and both componenets are ordered in axes (10.051, 10.366 A both structures. (Reproduced from Olmstead, Hao and Balch, 1999.)

There are a number of reports about the complexes of n-pentane with C60 and C70 and the relation between them is not always clear. There is a remarkable group of similar crystals for n-pentane with C60 and C70 (ﬁrst reported by Fleming et al., 1991) and of toluene with C76 and C82 where the structures have not yet been reported in detail (Kawada et al., 1995). The resemblances among the unit cells of the different compositions are surprising, with all the crystals showing a tenfold twinning which has a resemblance to a dodecahedral quasi-crystal, but was demonstrated to be true twinning. Although an orthorhombic cell can be found, it is more convenient (especially for discussion of the twinning) to retain the isostructural monoclinic cells. There are NMR measurements (Aliev et al., 1993) on complexes of composition {C60(pentane)0.88 (toluene)0.05}, which suggest the occurrence of phase transitions at low temperatures. The complex of C60 with diethyl ether has the same square-planar layers of C60 molecules as found in the n-pentane complex but the stacking of the layers is different (Oszlanyi et al., 1993). This early work clearly requires emendation. Note that the heptane complex of C60 appears to have a simple close-packed structure (Table 10.9), and that tolueneC70 has cell dimensions very similar to those of m-xyleneC60 (Table 10.12). The example of the dark-red triclinic crystals of {4(C6H6)C60} (P1, Z ¼ 2; cell dimensions in Table 10.9) illustrates how the information derived widens and deepens with continued study. These crystals were obtained by two groups (Balch et al. 1993; Meidine et al., 1992; intensity measurements at 104 and 173K respectively). The 104K data have been further reﬁned to give the following description of the structure (Bu¨rgi et al., 1994; JUGCET11) : the C60 molecules (in two disordered orientations in 55 : 45 ratio) are in inﬁnite stacks which form a regular honeycomb-like arrangement surrounding channels which contain the benzenes, one of which takes up two orientations. The C60 molecules form a defective and distorted cubic close packing in which one C60 out of three is replaced by eight benzene molecules. A domain of benzenes has dimensions of 1 nm in two directions and is inﬁnite in the third. Bu¨rgi et al. suggest that 4(C6H6)C60

640

PACKING COMPLEXES

should be described in terms of an ordered array of nanocrystalline domains of a hitherto unobserved monoclinic form of benzene stabilized by a matrix of C60 molecules, that is as a nanocomposite. This description is certainly in accord with current fashion. Large faceted translucent cherry-red crystals of a benzene-C60 complex (also with deuterobenzene) were grown for CP MAS NMR studies (He et al., 1997). The NMR study showed that there were three types of benzene molecules in the crystals – (i) a major portion of the benzene resides in a porous environment of nanometer dimensions, (ii) a minor fraction resides in a very narrow porous environment where the benzenes are freely mobile but essentially isolated, (iii) another minor fraction appears to be constrained in defect sites of the C60 sublattice. Unfortunately the composition was not reported nor was the well-resolved XRD powder pattern analyzed. However, the resemblances are such that the NMR crystals could well be {4(C6H6)C60}. One discrepancy remains to be resolved – the NMR crystals show optical activity whereas the XRD crystals are centrosymmetric. The C60–bromobenzene phase diagram was determined and the crystal structure of 2(C6H5Br)C60 where the fullerene molecules form hexagonal close-packed layers in the (001) plane, with adjacent planes separated by layers of bromobenzene (Korobov et al., ˚ . The enthalpy of (1998)). The intersphere distances within the layers are 10.00–10.16 A formation of the C60–2(bromobenzene) phase from the gaseous components was estimated as 300 kJ/mol. It was concluded that ‘‘ The solvated crystal is kept together by the short-ranged van der Waals interactions of C60 with C60 and of C60 with bromobenzene.’’ In the original paper the space group was given as C2, with determination of the Flack parameter, while it is reported as C2/m by CSD; this will introduce differences of detail but the overall structure remains unaffected. Black rod-shaped crystals of {C60(I2)C6H5CH3} were orthorhombic, with both C60 and toluene molecules in two orientations (intensities measured at 143K; Birkett et al., ˚ , close to 1993; LAVNIF). The iodine positions are probably correct (d(I–I) ¼ 2.685(2) A the standard value) but the close contacts reported between iodine and both the C60 and ˚ ) are probably to be ascribed to systematic toluene molecules (shortest C . . . I ¼ 3.09 A coordinate errors due to the disorder of the carbons of the two organic molecules. The packing could be described as having the electron acceptor iodine molecule sandwiched between the donor C60 and toluene molecules; no analogs have been reported and our classiﬁcation is clearly somewhat arbitrary. Complexes based on packing of alternating layers of fullerene host and secondcomponent guests The distinction between this and the previous group is more one of degree than of kind. {C60CH2I2(C6H6)} (Geiser et al., 1992; structure at 298 and 122K) has the C60 molecules (at centres of symmetry) arranged in close-packed layers with the other components (on two fold axes) in interstitial positions. As it was noted ‘‘in proof’’ that the C60 molecules took up two orientations (in 70 : 30 ratio), the short C . . . I distances of ˚ reported must be treated with some reserve when considered as evidence 3.29 and 3.54 A for charge transfer. {Bis(triptycene)C60(o-xylene)} (Veen et al., 1999) has sheets of close-packed ordered fullerene molecules separated by double layers of antiparallel triptycene and o-xylene molecules, with the latter ﬁlling the voids between triptycenes (Fig. 10.35). Two

ORDERED PACKING COMPLEXES

641

˚ , deg) for molecular complexes of fullerenes with layers of fullerene Table 10.10. Crystal data (A separated by layers of the second component. For other details see caption to Table 10.9 Formula/reference Complexes of C60 (C6H6)(CH2I2)C60 at 122K GK92 Bis(triptycene)C60(o-xylene) 150K; VP99 (TMDTDM-TTF*)2C603(CS2) KV97

a/

b/

c/

Z

Space group

Refcode

21.024

17.298 105.93 9.999 109.88 13.313 103.17

10.043

4

C2/c

JUVYAA

17.661

2

P21/c

CEMNUD

16.672

2

C2

DAGSUZ

19.767 15.174

Complexes of C70 (S8)6C70 at 100KBV93 BTXxC700.5CS2 NZ99

37.953 10.927

20.241 21.068

10.226 24.147

4 4

Amm2 Pbc21

LAZMEE DATQEU

Complexes of C76 (S8)6C76 at 180K MK94

10.410

20.500 98.8

19.480

2

Cm

RATCUK

x BTX is 9,9 0 -trans-bis(telluraxanthenyl); * TMDTDM-TTF is tetramethylenedithiamethyltetrathiofulvalene References: BV93 – Bu¨rgi, Venugopalan et al., 1999; GK92 – Geiser, Kumar et al., 1992; KV97 – Konarev, Valeev, Slovokhotov, Shul’ga, Roschupkina and Lyubovskaya, 1997; MK94 – Michel, Kappes et al., 1994; NZ99 – Narymbetov, Zorina et al., 1999; VP99 – Veen, Postma et al., 1999.

Fig. 10.35. Bis(triptycene)C60(o-xylene) showing close-packed layers of C60 separated by double layers of triptycene þ o-xylene. Compare with Fig. 10.36. (Reproduced from Veen et al., 1999.)

PACKING COMPLEXES

642

a

c*

b

–b

c

a

Fig. 10.36 Projections of {(S8)6C76} down [100] and [010], showing the psudo-hexagonal layers of closely packed C76 molecules (only one enantiomer is shown for clarity) interleaved by double layers of octasulfur. (Reproduced from Michel et al., 1994.)

triptycenes embrace one fullerene. ‘‘The fullerene molecules pack in an approximate hexagonal close-packed sphere pattern parallel to the bc plane with translation vectors ˚ ( ¼ b axis) and 10.147 A ˚ [ ¼ 1/2(b þ c)]’’. There is a similarity to {(S8)6C70} 9.996 A (Fig. 10.36). {Azatriptycene.C60} is placed in Table 10.11. {(S8)6C70} has densely packed layers of ordered ellipsoidal C70 molecules (crystallographic symmetry C2v) about z ¼ 0, 1/2, etc. interleaved by double layers of S8 molecules (Roth and Adelmann, 1992; Talyzin, Tergenius and Jansson, 2000; LAZMEE01). Although the 300K analysis suggested that the S8 molecules were ordered, the 100K analysis (Bu¨rgi et al., 1993) has shown that there are actually two orientations. {(S8)6C76} (Fig. 10.36) and {(S8)6C70} are isostructural, as is shown by the relationships among the cell dimensions (Michel et al., 1994; RATCUK), while a C60 complex of this composition has not been reported. The structure analysis shows that C76 is present as the D2 chiral species, the two enantiomers being superimposed, thus limiting the precision with which molecular dimensions can be determined. The ordered S8 molecules are in their usual crown conformation.

ORDERED PACKING COMPLEXES

643

{(TMDTDM-TTF*)2C603(CS2)} has a layer structure with alternating sheets of fullerene and dimers of donor TMDTDM-TTF with inserted CS2; the donor molecule has a concave conformation. The authors note that ‘‘The UV-Vis-NIR optical absorption spectrum shows a wide band at 900 nm associated with charge transfer from TMDTDMTTF to fullerene. . . . The complex is to be considered as a van der Waals compound with weak charge transfer.’’

S

S

S

S

CH3

CH3

TMDTDM-TTF

{BTXC700.5CS2} has densely packed layers of ordered ellipsoidal C70 molecules about z ¼ 0, 1/2, etc. interleaved by layers of alternating BTX and CS2 molecules (Narymbetov et al.,1999). The BTX molecules have the same conformation as in neat BTX and in the C60 analog (Table 10.11) but the two fullerene complexes are not isostructural. Te

Te 9,9’-trans-bis(telluraxanthenyl)BTX

Group II : fullerene and second component of comparable size Complexes based on close-packed rows of fullerenes separated by interspersed secondcomponent molecules One effect of increasing the size of the second component is to change the fullerene arrangement from a three-dimensional close packing, with the small second-component molecules located interstitially, to close-packed two-dimensional layers of fullerenes, separated by layers of the second component, now increased in size. This process can be extended by further reducing the dimensionality of the close-packed fullerenes to one-dimensional rows, now separated on two sides by the molecules of the second (and perhaps, the third) component. {(Octaphenylcyclotetrasiloxane)C600.5(toluene)} (Grey et al., 1999) has a structure with double column stacks of almost close-packed fullerenes enclosed in a matrix of octaphenylcyclotetrasiloxane molecules. The centroid-to-centroid distances in the ˚ ; the closest C . . . C distance between adjacent double columns range from 9.28 to 10.36 A ˚ fullerens is 3.31 A. C70 does not form a complex under similar conditions. Spectroscopic

644

PACKING COMPLEXES

˚ , deg) for molecular complexes of C60 where close-packed rows of Table 10.11. Crystal data (A fullerenes are formed. Other details in the caption to Table 10.9 Formula/reference

a/

b/

c/

Z

Triphenylsilane. C60. At 213K; WJ98 9,9 0 -trans-(bis(tellura-xanthenyl)* C60CS2 KS97 C60[Fe4(CO)4(5-C5H5)4]3(C6H6); CH93 2(Cl12Pd6)3(C6H6)C60At 130K; OG96 (octaphenylcyclotetrasiloxane) C600.5(toluene) at 123K. GH99

10.086 79.14 10.309 85.20 9.944

14.432 74.94 10.988 71.85 15.922

14.911 88.33 12.011 79.83 38.368

2

P 1

NIRLOP

1

P 1

ZUMCIT01

4

P212121

PIGPEA

12.544

50.655

24.669

8

Cmcm

NAGNAK

10.115 82.25

19.065 75.96

19.226 78.41

2

P 1

FOFKEQ

10.000

33.661

29.313

4

C2221

{C602(C26H16I4)3(toluene)}TC02

Space group

Refcode

* BTX References: CH93 – Crane and Hitchcock, 1993; GH99 – Grey, Hardie et al., 1999; KS97 – Kveder, Steinman et al., 1997; OG96 – Olmstead et al., 1996; TC02 – Tanaka and Caira, 2002; WJ98 – Waidmann and Jansen, 1998.

(UV-VIS, NMR, IR) studies of C60–siloxane solutions showed that ‘‘interactions in solution are inherently weak.’’ Air-stable {C60triphenylsilane} was prepared by recrystallizing C60 from molten triphenylsilane (m.pt. 45 C) held at 80 C. The triclinic crystals do not show any phase transitions between 298 and 108K. There are rows of disordered C60 molecules along [100] separated by triphenylsilanes, each C60 being coordinated by six triphenylsilanes (Waidmann and Jansen, 1998). The triclinic crystals of {9,9 0 -trans-(bis(telluraxanthenyl (BTX) )C60CS2} have twinbutterﬂy shaped molecules of 9,9 0 -trans-(bis(telluraxanthenyl) centered at 1/2,1/2,0; the fullerene at 00,1/2 and the CS2 at 1/2,1/2,1/2. There are close-packed rows of fullerene ˚ ) separated by the other two components. The C70 analog is along [100] ( ¼ 10.309 A discussed above (Table 10.10). Rows of C60 molecules are found in FAJFAX noted in Table 10.14, and in some other examples such as {C602(tetrakis(p-iodophenyl)ethylene3(toluene)} (Table 10.11). Pd6Cl12 is a molecule with an octahedral array of six Pd atoms that are surrounded by twelve equivalent Cl atoms in edge-bridging sites; there is no direct interaction between Pd atoms. Pd6Cl12 forms molecular complexes with a variety of small aromatics and also with C60 (Olmstead et al., 1996). In the C60 complex there are double columns of fullerenes along the [100] axis, similar to those shown in Fig. 10.41; each C60 ﬁts into a pocket formed by eight Pd6Cl12 molecules. Overall the fullerenes are enclosed in channels of Pd6Cl12. Olmstead et al. remark ‘‘In an examination of the packing in this unusual structure it is . . . not entirely clear what intermolecular forces come into play, whether the proximity of molecules is dictated by donor-acceptor interactions or simply by the efﬁcient packing of similar-sized molecules.’’ This remark applies to many other complexes described in this chapter, and elsewhere.

ORDERED PACKING COMPLEXES

645

Complexes based on three-dimensional interspersion of fullerene and the second component Despite overall resemblances, complexes of the next group (Table 10.12) deviate from the pattern described above in that there are no longer close-packed layers of C60 but rather dispersion of the second component between the fullerene spheres, and this becomes typical of most of the complexes considered below, with details of the structures depending on the nature of the second component. ˚ , deg) for those molecular complexes of C60 with layers of fullerene Table 10.12. Crystal data (A and interspersed second component. For other details, see caption to Table 10.9 Formula/reference

a/

12(CCl4)C60 JW95; GC91 12(C6H12)C60* JW95 x(C6H12)C60C70* GC91 12(C6H12)C70 JW95

27.420 28.167 28.216 28.606

2(m-xylene)C60* at 20K. RL96 tolueneC70 * AC93 m-xyleneC70 BR97 azatriptyceneC60 at 150K; VP99 C60.6SbPh3 at 130K FOF95. 2(ClAuAsPh3)C60 At 140K BO99 2(ClAuPPh3)C60 GW99, SG00, M02 3CS22C60 MN91 3CS22C60 BR97 3CS22C60 at 90KOJB00 C6H14C60* at 210K HL91 HClC¼CCl2C60* SK94 C60.1.33{S4N4)0.67(C6H6) at 153K; KV97.

23.67 21.075 21.670 13.464

b/

32.990 10.480

29.833 11.919 12.006 24.97 24.997 24.671

25.52 25.588 25.416 95.05

33.54 31.33 17.004 90.02 29.449

10.156 17.004 110.63 17.009 114.02

c/

10.02 120 10.844 33.080 12.698 11.224 120 35.874 120 35.500 120 9.98 9.984 9.872 10.113 120 10.146 24.126 119.98 24.127

Z

Space group

Refcode

8 8 8 8

P 43c F 43c Fm3m F 43c

6

P63

YOLTAU YOLSOH x JOCSOJ x YOLSUN x No 3D coordinates TEYCEF

8 8 2

Pbca Pn21a Pˆ63mc

NUDDOF CEMPAL

3

R 3

YIKVET

3

R 3

KEQKIA #

3

R 3

4 4 4

Pbnm P21nb P21/n

12

P63/m

LOHSOQ01, 02 #

MAPSUR

4

8

C2/c

FONPED; Reduced cell. Monoclinic cell

x, # Signify groups of complexes with similar structures. References: AC93 – Agafanov, Ce´olin et al., 1993; BO99 – Balch and Olmstead, 1999; BR97 – Boeyens, Ramm et al., 1997; FOF95 – Fedurco, Olmstead and Fawcett, 1995; GC91 – Gorun, Creegan et al., 1991; GW99 – Graja, Waplak et al., 1999; HL91 – Hawkins, Lewis et al., 1991; JW95 – Jansen and Waidmann, 1995; KM98 – Korobov, Mirakian et al., 1998; KS97 – Kveder, Steinmann et al., 1997; KV97 – Konarew, Valeev et al., 1997; M02 – Marsh, 2002; MN91 – Morosin, Newcomer et al., 1991; OJB00 – Olmstead, Jiang and Balch, 2000; RL96 – Ramm, Luger et al., 1996; SK94 – Spitsyna, Kushch et al., 1994; SG00 – Spitsyna, Gritsenko, et al., 2000; VP99 – Veen, Postma et al., 1999.

PACKING COMPLEXES

646

A

C

x

B

z y

Fig. 10.37. {C60.12(C6H12)} viewed down [111] showing a slice of the crystal in the (111) plane. The C60 molecules are disordered and the atom positions shown have no physical signiﬁcance. (Data from Jansen and Waidmann, 1995.)

The structure proposed for the cubic {C6012Y} crystals (Gorun et al., 1991; Jansen and Waidmann, 1995) has disordered C60 molecules in hexagonal array, not close packed but immersed in a sea of Y molecules, here cyclohexane (Fig. 10.37). The structure proposed is based on a limited set of Rietveld and single crystal measurements and reﬁned by the Rietveld method on the basis of a room temperature powder diffraction pattern. YOLSUN (C7012(C6H12) is isostructural with {C6012Y}, while JOCSOJ (x(C6H12)C60C70) is also cubic but with a different space group. Nagano and Tamura (1996) obtained the same diffraction evidence but preferred a C6013Y composition; they reported low temperature phase transitions. The structure of {2(H2CCl2)C60} was not reported. The structure of {2(m-xylene)C60} was determined at 100K and 20K with very similar results (Ramm et al., 1996), showing that the extensive disorder (of both components) was static rather than dynamic, i.e. was grown in at the time of crystallization. The structure is based on a dispersion of solvent molecules between irregularly ordered fullerene molecules. {(m-Xylene)C70} (Boeyens, Ramm, Zobel and Luger, 1997) and {tolueneC70} (Agafanov et al., 1993) have similar cell dimensions after axial transformation; the different space groups perhaps require further attention. {TolueneC70} lost toluene on heating to 380–470K. There is a second order transition at 195K, with H ¼ 932 93 J/mol (Sworakowski, Palewska and Bertault, 1994). {AzatriptyceneC60} (Veen et al., 1999) has a hexagonal arrangement in which three azatriptycene molecules embrace one C60 (Fig. 10.38) forming dimpled hexagonal mixed layers, which, suitably offset, are packed one above another in an . . . ABAB . . . stacking. The azatriptycene molecules are ordered and the C60 molecules orientationallydisordered. Crystals of C606SbPh3} (dark red rhombohedra) were grown from solutions of C60 in molten SbPh3 (m.pt. 52–55 C). The asymmetric unit contains ten C atoms (C60 has 3

ORDERED PACKING COMPLEXES

647

Fig. 10.38. {AzatriptyceneC60}, showing how three azatriptycene molecules embrace one C60; repeat of this pattern produces a dimpled mixed layer, and these are then packed one above the other to form a close-packed arrangement. (Reproduced from Veen et al., 1999.)

x

y

Fig. 10.39. {C606SbPh3} in projection down the c axis. The carbons of C60 are darkened, those of the phenyl groups of SbPh3 are cross-hatched and the Sb atoms are black. The sizes of the atoms are arbitary. (Data from Fedurco, Olmstead and Balch, 1995.)

648

PACKING COMPLEXES

Fig. 10.40. One layer of {2[Ph3 AsAuCi]C60} viewed down the c axis; the AsAuCI axis is vertical. The fullerenes (omitted for clarity) are contained in the spherical cavities. The fullerenes of the adjacent layer are located above the Cl atoms. (Reproduced from Balch and Olmstead, 1999.)

point symmetry) and a complete SbPh3 molecule (Fedurco, Olmstead and Fawcett, 1995; YIKVET). The C60 molecules are ordered and the mean lengths of the short and long ˚ respectively. The structure is based on the placing of bonds are 1.383(4) and 1.453(4) A C60 balls into phenyl ‘‘cups’’ and also has clathrate features; dispersion of the fullerenes between the SbPh3 molecules is shown in Fig. 10.39; the details of the interactions of the phenyl rings with the fullerene molecules are quite intricate. {2[Ph3AsAuCl]C60} (at 140K; Balch and Olmstead, 1999) and the corresponding phosphorus complex (Graja et al., 1999; Spitsyna et al., 2000) are isomorphous (for space group correction see Marsh (2002) ). The structure (shown partially in Fig. 10.40) has the same feature as the other examples considered here, i.e. an arrangement in which the fullerene spheres are separated by the molecules of the second component. There are six phenyl rings from six different (Ph3AsAuCl) molecules that make face-to-face contact with a particular fullerene molecule. Layers are formed in the crystal in which each fullerene in the layer is surrounded by an array of six phenyl rings. The layers are packed in an . . . ABC . . . sequence, with fullerene over the linear Au–Cl portion of the [Ph3AsAuCl] molecule; there are no fullerene . . . fullerene contacts. The structure of {3CS22C60} at 90K (Olmstead, Jiang and Balch, 2000) has CS2 molecules dispersed within a matrix of fully ordered C60. The room temperature structure has been reported twice (Morosin et al., 1995; Boeyens et al., 1997), but with different space groups. Detailed consideration of the heavily disordered structure found at 300K led

ORDERED PACKING COMPLEXES

649

Boeyens et al. to prefer the noncentrosymmetric space group, and this has been supported by Olmstead et al., who treated the 90K structure as a pseudo-merohedral twin. Although Olmstead et al. investigated the phase change at 168K, its nature – whether of ﬁrst or second order – has still to be clariﬁed. Morosin et al., reported that up to 40% of the CS2 content can be replaced by I2; the mechanism is unknown. {C60[Fe4(CO)4(5-C5H5)4]3(C6H6)} crystallizes as black needles. The crystal structure (Fig. 10.41) has been described as a three-dimensional C60[Fe4(CO)4(5-C5H5)4] host lattice with benzene molecules in interstitial positions (Crane and Hitchcock, 1993; PIGPEA). The space group is chiral but the components are both achiral ([Fe4(CO)4(543m if the cyclopentadienyl groups are assumed to C5H5)4] has ideal symmetry Td– have cylindrical symmetry (Neuman, Triunh-Troan and Dahl, 1972)) and so it is the arrangement that must be chiral rather than the components themselves. This complex illustrates the problems of classiﬁcation : charge transfer has been inferred because the strong carbonyl band is shifted to 1640 cm1, compared to 1626 cm1 for neat neutral [Fe4(CO)4(5-C5H5)4] and 1700 cm1 for the monocation; the shift is ascribed to a small degree of electron transfer to the C60 acceptor. C60 forms a series of isomorphous complexes of composition {C60(S4N4)2-x(C6H6)x} with 0 < x < 1 i.e. a complete range of solid solutions is formed (Konarev et al., 1997); different crystal habits are found depending on composition. The complex chosen for structure analysis had x ¼ 0.67; the unit cell contained 12 molecules of C60, four at inversion centers and eight at general positions; twelve fully ordered molecules of (S4N4), four on two fold axes and eight at general positions and twelve positions occupied by disordered (S4N4) and (C6H6) in ratio 1 : 2. The fullerene molecules are separated by (S4N4) and (C6H6) in interstitial positions, with resemblances to the C6012Y arrangement (Fig. 10.37).

15.39 Å

3.30 Å cp(2)

cp(3)

15.92 Å 3.36 Å 3.35 Å cp(1)

b c

15.39 Å a

Fig. 10.41. View of part of the {C60[Fe4(Co)4.(5-C5H5)4]3(C6H6)} structure. The [Fe4(Co)4 (5-C5H5)4] molecule bridges an isosceles triangle of C60 molecules (each from different stacks) through C60–cp -stacking interactions. The benzene have been omitted for clarity. (Reproduced from Crane and Hitchcock, 1993.)

650

PACKING COMPLEXES

Korobov et al. (1998) summarise thermodynamic data for some of these complexes using the following equation for their formation : C60 ðsÞ þ nYðliqÞ ¼ C60 nYðsÞ: The values of the enthalpy of formation for C602(bromobenzene)(s), C6012(CCl4)(s) and C60(C7H16)(s) are 42, 41 and nearly zero kJ/mol. Miscellaneous smaller second-component molecules {2(S8)C60} has a framework of ordered C60 molecules (i.e. the reﬁnement could be carried out to atomic resolution) with channels along [001] in which ordered S8 molecules (in crown conformation) are contained (Roth and Adelmann, 1993, HEGPAK01; Dyachenko, Yagubskii et al., 1994). {(S8)C60CS2} has a framework of disordered C60 molecules (i.e. could not be reﬁned to atomic resolution) with channels containing ordered S8 rings and ordered dumbbell shaped CS2 molecules (Roth, Adelmann and Knitter, 1993; YITCUZ). The compound is an insulator with a reddish-brown color and almost isotropic light absorption. {C60Br24(Br2)x} (Tebbe, Harlow et al., 1992) crystallizes in a pseudo-face centered cubic layer structure, with an . . . ABCABC . . . sequence of C60Br24 layers. The additional (perhaps 2) bromine molecules are disordered over 14 sites distributed about a crystallographic 3 axis. The C60Br24 molecule has Th symmetry, the Br atoms effectively covering the surface of the fullerene. Group III. Fullerene and second component of comparable size; second component has a concave shape Complexes based on three-dimensional interspersion of fullerene and a calix[n]arene second component The dark red crystals of 2(p-bromocalix[4]arene)C60 (Barbour, Orr and Atwood, 1998) are tetragonal and polar. The asymmetric unit consists of a quarter each of a calixarene and a spherically disordered C60 molecule (actual site symmetry C4–4). ˚ , deg) for molecular complexes of C60 with miscellaneous small secondTable 10.13. Crystal data (A component molecules, also complexes of halogenated C60. Other details in the caption to Table 10.9 Formula/reference

a/

b/

c/

Z

Space Group

Refcode

(S8)2C60 RA93; DY94

20.867

21.062 111.25 13.356

10.508

4

C2/c

28.654

4

Pnma

HEGPAK01, 10 YITCUZ

11.343 18.117

8 4 4

Pa 3 Pnma P21/c

EBUFAI SUDVIW SUDVOC

32.659

3

R 3

JUHJIF

(S8)C60CS2 RAK93

9.973

Complexes of halogenated C60 C60F482(mesitylene) TT01 23.229 C60Br82(Br2) at 173K BH92 24.482 18.190 C60Br6(Br2) at 173K BH92 C60Br24. Br2 at 143K TH92

12.874

16.895 11.898 96.60

References: BH92 – Birkett, Hitchcock et al., 1992; DY94 – Dyachenko, Yagubskii et al., 1994; RA93 – Roth and Adelmann, 1993; RAK93 – Roth, Adelmann and Knitter, 1993; TH92 – Tebbe, Harlow et al., 1992; TT01 – Troyanov, Troshin et al., 2001.

ORDERED PACKING COMPLEXES

651

˚ , deg) for molecular complexes of C60 with various calix[n]arenes and Table 10.14. Crystal data (A derivatives (n ¼ 3, 4, 5). See caption to Table 10.9 for other details Formula/reference Calix[n]arenes 2(p-bromocalix[4]arene)propyl etherC60 BO98 2(p-iodocalix[4]arenebenzylether)C60 BO97 calix[4]resorcinarene. C60(4 þ x)(propanol)y(odichlorobenzene) at 173K. RN98 2(p-benzylcalix[5]arene). C608(toluene); at 173K; AB99 2(1,3-diiodo-2,4,5-trimethylcalix[5]arene)8H2OHY97a (C40H40O5)2CH3OH3H2O C60HY97b (C38H36O5)4H2OC60. (5,5 0 -bis(calix[5]arene)-2(toluene) C60At 148K. WB00 calix[6]arene)2C60(toluene). At 173K. AB98 calix[6]arene)2C70. (toluene). At 173K. AB98 Hexahomo-oxa-calix[3]arenes [tribromohexahomooxacalix[3]arene]C60 TT98 2[p-benzylhexahomooxacalix[3]arene]C60, at 173K; 2(C45H27O18)C60; AB99 2(trioxacalix[3]naphthalene) C60 MA01 [tri(t-butyl)hexahomo-oxacalix[3]-arene] C60 TT98 TT98

a/

b/

c/

Z

Space group

Refcode

18.116

9.878

2

P4bm

FAJFAX

19.035

42.372

4

c2 I4

NIGPOI

18.930

27.270

4

I4/m

PUJROB

17.166

17.566 105.78

28.379

2

P21/n

JAXYIQ

18.172

18.473 89.98 13.522 74.47 15.151 108.21 30.019

16.292

2

P21/n

TUDCOK

19.913 70.44 19.731

2

P1

NIFXUV

4

C2/m

NIFYAC

12.846

4

Pnma

No refcode

13.292 76.92 22.178 23.701 18.826

25.642

P41212

NOBLEV

19.590

26.112

P41212

NOBLIZ

18.104

26.624 120 24.643 120

18

R3

SADVUO

3

R3

JAYDIW

17.217 120 14.292 90.62

6

R3

BOXQOU

2

P1

SADWAV

18.546

23.136 14.316 108.23

16.88 111.90

References: AB98 – Atwood, Barbour, Raston and Sudria 1998; AB99 – Atwood, Barbour, Nichols and Sandoval, 1999; BO97 – Barbour, Orr and Atwood, 1997; BO98 – Barbour, Orr and Atwood, 1998; HY97a – Haino, Yanase and Fukazawa, 1997a; HY97b – Haino, Yanase and Fukazawa, 1997b; MA01 – Mizyed, Ashram et al., 2001; RN98 – Rose, Barbour et al., 1998; TT98 – Tsubaki, Tanaka et al., 1998; WB00 – Wang, Bodige, Watson and Gutsche, 2000.

PACKING COMPLEXES

652

Table 10.14. (Continued ) Notes: Calix[4]resorcinarene shown below is 4,6,10,12,16,18,22,24-octahydroxy-2,14,8,20-tetrakis(2phenylethyl)-calix[4]arene. Ph

HO

OH

Ph

HO

OH

HO

OH

Ph

HO

OH

Ph

˚ ). The sizeThere are close-packed rows of C60 molecules along [001] (spacing 9.878 A shape complementarity between the calixarene and the C60 molecules allows the formation of an efﬁciently packed two-dimensional system. Rows of C60 molecules are found in a number of complexes noted in Table 10.11. The dark red crystals of 2(p-iodocalix[4]arene benzyl ether)C60 (Barbour, Orr and Atwood, 1997) are tetragonal and polar. The asymmetric unit consists of one half of a calixarene and one-quarter of an ordered C60 molecule. There are limited similarities to 2(p-bromocalix[4]arene)C60 discussed in the previous paragraph. The three calix[5]arene complexes {2(C38H34O5I2)C608H2O} (TUDCOK; Haino, Yanase and Fuzukawa,1997a), {(C40H40O5)2CH3OH3H2OC60} (NIFXUV) and {(C38H36O5) C604H2O} (NIYAC) (both Haino, Yanase and Fuzukawa,1997b) are unusual in having H2O and/or CH3OH as solvent of crystallization. Haino et al. note that ‘‘The presence of a trace amount of water and/or methanol is essential for the specimens suitable for analysis’’ but do not discuss the structural role, if any, of H2O and/or CH3OH. Our brief examination does not show hydrogen bonding to the other components but not enough information is available for a thorough check. The component arrangement in TUDCOK (Fig. 10.42) is typical of the calixarene complexes, although each has its own individual particularities (for example, NIFXUV has double rows of fullerenes extending along the [100] axis). In TUDCOK the fullerenes (ordered but with large amplitudes of thermal libration) are embraced by the calix[5]arene molecules, with hydrogen-bonded pairs of water molecules apparently not playing any structural role. The calix[5]arene molecule has the highlysymmetrical pseudo D5d structure because of positional disorder of the two iodines and three methoxy groups over the ﬁve para positions of the phenol; the phenol hydroxyls are linked by intramolecular hydrogen bonds, giving the molecule a cone conformation. The bis(calix[5]arene complex with C60 and toluene (1 : 1 : 2) has ‘‘highly disordered’’ fullerene even at 148K (Wang, Bodige, Watson and Gutsche, 2000). The bis(calix[5]arene

ORDERED PACKING COMPLEXES

653

fullerene

waters calixarenes embracing fullerenes

disordered iodine/ methyl of calixarene

z x

Fig. 10.42. {2(C38H34O5I2)C608H2O} (TUDCOK) viewed down [010]. The smaller dark spheres are C and the larger O calix[5]arene hydroxyls, with these oxygens hydrogen bonded intramolecularly. The iodines are shown as disordered over the ﬁve I/CH3 sites. The oxygens of the water molecules are the cross-hatched spheres with their size exaggerated for emphasis. One hydrogen bonded pairs is located across the origin while the others are part of a triangle of waters, whose arrangement would appear to require further examination. (Data from Haino, Yanase and Fuzukawa, 1997a.)

molecule changes its conformation from anti (uncomplexed in solution) to syn (‘clamshell’ embrace of fullerene) in the solid state; the bis(calix[5]arene molecules embrace the C60 molecules, with the two toluene molecules forming a ‘cap’. In {calix[6]arene2C60C7H8} and its isostructural C70 analog, ‘‘the calixarenes are in the double-cone conformation, and each of the associated shallow cavities is occupied by a fullerene. The overall arrangement resembles the jaws of a pincer acting on the two adjacent spheres (ellipsoids) . . . Each fullerene molecule is in close proximity to six other fullerene molecules, and is situated at the common vertex of two fullerene tetrahedra. . . . These vertex-sharing tetrahedral form a three-dimensional array interspersed with molecules of calix[6]arene and solvent’’ (Atwood, Barbour, Raston and Sudria, 1998). The brominated hexahomooxacalix[3]arene complex SADVUO (R ¼ Br) is completely ordered, while SADWAV (R ¼ t-butyl) has ordered calixarene but disordered fullerene (Tsubaki et al., 1998). Both have the fullerene embraced by the bowl-shaped calixarene, the bowl shape being enforced by intramolecular hydrogen bonding. The structure of {2[p-benzylhexahomooxacalix[3]arene]C60,} (R3, Z ¼ 3) was determined at 173K (Atwood et al., 1999). The C60 is at the cell origin and has 3 symmetry,

PACKING COMPLEXES

654

R

O

OH

OH

O

HO

O R

R R = H, t-Bu, OMe, Br, CMe2C6H4-p-OMOM Hexahomo-oxacalix[3]arene

˚ , deg) for molecular complexes of C60 with various molecules of Table 10.15. Crystal data (A concave shape. Other details in caption to Table 10.9 Formula/reference

a/

b/

c/

Z

Space group

Refcode

CTVC60 at 183K AB96 CTV1.5C600.5(C7H8)SJ94

21.630 30.131

13.200 14.638

4 4

Pnma C2/m

TAWKEH YEKBOF

o-car0C70CTV-1,2dichlorobenzene at 123K. HGR99 CTV(OBz)6C60-0.5(toluene) at 153K. MH98 {4C603(twin-TDAS)} at 100K PB00

14.749

17.122 17.436 116.33 17.771

26.354

4

P212121

GOSYOC

21.031 101.61

26.192

4

P21/n

BACQAX

2

I23 (cubic)

32.467

8

P21/n

MAGFIT, correcting POSHOU FIBVIV

12.026

2

Cm

NIXPOZ

16.762

2

C2

DAGSUZ

21.044

4

C2/c

20.799

4

C2/c

9.923

4

C2/c

YOCFOL # No coordinates UCIKEW. # No coordinates KUMMEK

10.029

4

C2/c

{C60(TMTSeF) 0.5(benzene)} DK98 {C60(TMTSeF)2(CS2)} KD97 2(BDMT-TTF)C603CS2 KV97 BDMT-TTeFC60CS2 WL94 DBTTFC60benzene at 153K. KZ01 2(BEDT-TTF)C60 IT92b, at 150K. 2(BEDT-TTF)C60 KDS97

15.567 18.849

19.388 15.407 15.174 17.059 16.257 25.956 26.639

13.410 92.71 12.934 108.39 13.313 103.17 13.502 101.50 13.311 103.02 21.889 105.08 21.836 105.30

ORDERED PACKING COMPLEXES

655

Table 10.15. (Continued ) BMDT-TTFC602CS2 SG02

13.550

C20H16S16C60CS2 IT92a 2(C1 TET-TTF)C60 * LG94

10.116 74.85 18.374

[Ni(TMTAA)C60] AA98

14.633

[Ni(OMTAA)C70] CM99

14.917

3NiLC602CS2 SD01

13.492 74.16

9.964 99.52 13.875 84.57 27.196 94.12 17.554 107.71 18.880 105.49 15.701 88.84

17.125

2

P21/m

23.081 73.24 13.683

2

P 1

4

–

18.285

4

P21/n

TODZUH. No coordinates PIGHOM #

19.564

4

P21/n

HAZQAA #

27.557 76.09

2

P 1

-

SUGBUR

# isostructural pair; C60{Cu(TMTAA)} is also isostructural (AABC99) o-carborane is 1,2-dicarbadodecaborane CTV is cyclotriveratrylene BDMT-TTF is tetramethylenedithiodimethyl-tetrathiafulvalene BDMT-TTeF is (dimethylthieneo)-tetratellurafulvalene BMDT-TTF is bis(methylenedithiotetrathiafulvalene) C1-TET-TTF is bis(methylthio)ethylenendithio-tetrathiafulvalene Ni(TMTAA) is 5,7,12,14-tetramethyldibenzo[b,i]-[1,4,8,11]tetra-azacyclotetradecinenickel(II); Ni(OMTAA) is {2,3,6,8,11,12,15,17-octamethyldibenzo-[b,i]1,4,8,11-tetraaza(1,4)-annulene}-nickel(II). NiL is 6,17-dimethyl-8,15-diphenyldibenzo[b,i][1,4,8,11]tetra-aza[14]annulenato)nickel(II) Reference: AA98 – Andrews, Atwood et al., 1998; AABC99 – Andrews, Atwood, Barbour, Croucher et al., 1999; AB96 – Atwood, Barnes, Gardiner and Raston, 1996; CM99 – Croucher, Marshall et al., 1999; DK98 – D’yachenko and Konovalikhin, 1998; HGR – Hardie, Godfrey and Raston, 1999; IT92a – Izuoka, Tachikawa, Sugawara, Saito and Shinohara, 1992; IT92b – Izuoka, Tachikawa, Sugawara, Suzuki, Konno, Saito and Shinohara, 1992; KV97 – Konarev, Valeev et al., 1997; KD97 – Konovalikhin, D’yachenko, Shilov et al., 1997; KDS97 – Konovalikhin, D’yachenko and Shilov, 1997; KZ01 – Konarev, Zubavichus et al., 2001; LG94 – Li, Gao et al., 1994; MH98 – Matsubara, Hasegawa et al., 1998; PB00 – Penicaud, Boubekeur et al., 2000; SD01 – Soldatov, Diamente et al., 2001; SG02 – Spitsyna, Gritsenko, D’yachenko and Yagubskii, 2002; SJ94 – Steed, Junk et al., 1994; WL94 – Wang, Lee et al., 1994.

with a six-membered ring located about the trigonal axis; the calixarene moieties have 3 symmetry and enshroud the fullerene from above and below. This is similar to the arrangement found in SADVUO. Complexes based on three-dimensional interspersion of fullerene and miscellaneous second components with concave shapes In {CTVC60} disordered fullerene molecules ﬁt into the dimples of the concave CTV moieties. Each fullerene has a short ˚ to fullerene neighbours. centroid-to-centroid distance of 9.87 A In (CTV15C60 .0.5(C7H8)) the asymmetric unit consists of one-half of an ordered 1 : 1 CTVC60 unit (the other half is generated by the mirror plane), one-quarter of a highly disordered C60 at a site of 2/m symmetry and possibly 1/4 of a toluene disordered over the same site symmetry. The disorder limits the precision but shows ‘ball and socket’ docking of C60 into the cyclotriveratrylene. During the preparation of the crystals it was found that C70 could be taken up from a fullerite mixture to a maximum C60 : C70 ratio of 72 : 28, and it was surmised that the C70 was accommodated in the disordered 2/m site.

PACKING COMPLEXES

656

Hexabenzoyl-CTV forms a complex of composition CTV(OBz)6C601.5(toluene), which has one C60 embraced by two CTV(OBz)6 moieties and one ‘bare’ in a space-ﬁlling role (Matsubara et al., 1998). Both C60 molecules form single close-packed rows along [100]. OCH3 OCH3

H3CO

H3CO

OCH3 OCH3 Cyclotriveratrylene (CTV)

The quaternary complex {o-carboraneC70CTV1,2-dichlorobenzene} has fully ordered o-carborane moieties hydrogen bonded to CTV, each C–H proton being involved in a bifurcated hydrogen bond to adjacent methoxy groups of the CTV, thus forming a hydrogen-bonded helix (Hardie, Godfrey and Raston,1999). The CTV cavities (the receptor sites) are directed outwards from the helices and interact as ball-and-socket with the convex fullerene, there being both shape and size complementarity. The C70 molecule is bound by – stacking to CTV. Another example of a quasi-clathrate inclusion complex is formed by C60 with 3,3 0 ,4,4 0 -tetrathiobis(1,2,5-thiadiazole) (‘‘twin-TDAS’’) which has the composition ˚ at 100(2)K; {8C606(C4S6N4)}. The irregular black crystals are cubic (a ¼ 18.8492(1) A space group I23 (no.197) (Penicaud, Boubekeur, Kotov and Yagubskii, 2000; MAQFIT). C60 is on a three fold axis and C4S6N4 has symmetry 222. There is spontaneous resolution on crystallization, but the absolute structure of the crystal used in the structure analysis was not determined. The packing unit is a group of eight C60 molecules arranged in an omnicapped tetrahedron, with the empty spaces between the (C60)8 clusters occupied by C4S6N4 molecules at the mid-points of the unit cell faces and edges. The dihedral angles between the two essentially-planar halves of the ‘‘twin-TDAS’’ molecules are close to 51 ; the ‘‘twin-TDAS’’ molecules would be achiral only if the dihedral angles were 0 or 90 (cf. Section 9.3 and Fig. 9.15). S N

C

S

C

S

S N

N

C

C S

S

N

3,3',4,4'-tetrathiobis (1,2,5-thiadiazole) (“twin-TDAS”)

ORDERED PACKING COMPLEXES

657

The complexes of fullerenes with various derivatives and analogs of tetrathiafulvalene (TTF) have been widely studied, perhaps in the hope that novel physical properties would be found, as occurs for the charge-transfer (CT) and segregated–stack (SS) molecular compounds discussed in detail in Chapters 16 and 17. Although this has not happened, this group of fullerene complexes is interesting in its own right. There is a striking conformational difference between the two situations : the TTF compounds and analogs have planar conformations in their CT and SS molecular compounds whereas they take up concave conformations in their fullerene complexes. This is analogous to the porphyrin situation. There are some spectroscopic indications of weak charge transfer interactions between TTF analogs as donor and C60 as acceptor. Perhaps the best evidence for such interactions would come from a color change on formation of the complex (cf. Section 12.1) but this is difﬁcult to observe because of the deep colour of C60 itself4; alternatively, a charge transfer band could appear in the UV-visible spectrum or there could be a change in an appropriate IR frequency. Some examples are given below. S

S

S

S

DBTTF: dibenzotetrathiafulvalene

In {DBTTFC60benzene} there is approximate close-packing of fullerenes, with each ˚ . The DBTTF moieties are arranged in C60 surrounded by six C60 molecules at 10.4 A columns along [001] with the benzenes between the columns. Efﬁcient packing of C60 and DBTTF moieties is achieved by complementarity of the convex shape of the fullerene and the concave shape of the DBTTF. There is no evidence for appreciable charge transfer. S

S

S

S

S

S

S

S

BMDT-TTF

The crystals of {BMDT-TTFC602CS2 (C8H4S4C602CS2)} have a layered structure (and could have well been placed in Table 10.10 or 10.11) where layers of C60 (on mirror planes) alternate with mixed layers of C8H4S4 (on mirror planes) and CS2 (in general positions). The donor molecules have a concave conformation. There is no evidence for charge transfer. In the black monoclinic crystals of {[BDMT-TTeF]C60CS2} the donors are boatshaped and the C60 molecules are ordered. [BDMT-TTeF] and C60 are located on two different sites, both with two fold symmetry (Wyckoff positions 4e), while CS2 is on an inversion center (4c). In its neat crystals [BDMT-TTeF] has an unsymmetrical boat conformation, unusual for a molecule of the TTF family. In the C60 complex [BDMT-TTeF] takes up a symmetrical boat conformation. The crystals are insulators 4 ‘‘All [C60] crystals tend to exhibit sixfold symmetry. In transmitted light they appear red to brown in colour; in reﬂected light the larger crystals have a metallic appearance, whereas the platelets show interference colours.’’ (Kra¨tschmer, Lamb, Fostiropoulos and Huffman, 1990).

PACKING COMPLEXES

658

and there does not appear to be any signiﬁcant electron transfer (inferred from the central C¼C bond length (Wang, Lee et al., 1995)). Despite the difference in composition, {DBTTF.C60.benzene} (UCIKEW) and {[BDMT-TTeF]C60CS2} (YOCFOL) have rather similar cell dimensions and the same space group. Are the structures similar? Unfortunately, coordinates are not available for either compound. H3C

CH3 Te

Te

S

S Te

Te

H3C

CH3

Bis(methylthieno)tetratellurafulvalene—BDMT-TTeF

The crystals of {2C602TMTSeFbenzene} (FIBVIV) have the TMTSeF molecules in a concave conformation, differing from the planar conformation found in the charge-transfer and segregated-stack molecular compounds of this material. There are two crystallographically independent molecules of C60 and TMTSeF in the asymmetric unit, and one benzene in an interstitial position. The independent molecules pack in different ways, as shown in Fig. 10.43. There are a number of examples where this happens, complicating efforts to understand, and predict, the packing arrangement. H3C

Se

Se

CH3

H3C

Se

Se

CH3

tetramethyltetraselenafulvalene (TMTSeF)

In the black monoclinic crystals of {2[BEDT-TTF]C60} (BEDT-TTF is bis(ethylenedithio)tetrathiafulvalene, also abbreviated as ET) the donors have a concave shape different from the planar shape found in the charge transfer complexes, and the C60 molecules are ordered (Fig. 10.44). The CT interactions in the crystals are via ˚ . There is a distinct absorption (max 750 nm) in C(C60) . . . S(ET) contacts of 3.4–3.6 A the UV-visible spectrum assignable to a CT band (Izuoka, Tachikawa, Sugawara, Suzuki, Konno, Saito and Shinohara, 1992; KUMMEK). S

S

S

S

S

S

S

S

bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF or ET)

The crystal structure of {2(C1 TET-TTF)C60} has apparently been determined but no details are available (Table 10.15; Li et al., 1994).

ORDERED PACKING COMPLEXES

659

Column of offset fullerences along [100], separated by TMTSeF molecules

TMTSeF molecules seen edge-on

Interstitial benzenes obscured in this view

z y Columns of C60 along [010], embraced by TMTSeF molecules

Fig. 10.43. Packing arrangement in {2C602TMTSeFbenzene} (FIBIV) viewed down [100], showing the different packing modes for the independent molecules in the asymmetric unit. (Data from Dyachenko and Konovalikhin, 1998.)

H3CS

S

S

H3CS

S

S

S

S

C1 TET-TTF; bis(methylthio)ethylenedithiotetrathiafulvalene (Chemical Abstracts name: 1,3-dithiolo[4,5-b] [1,4-dithiin], 2-[4,5-bis(methylthio)-1,3-dithiol-2-ylidene-5,6-dihydro

S

S

S

S

S

S

S

S

S

S

S

S

S

S

S

S

C20H16S16

The large concave-shaped donors in {C20H16S16C60CS2} embrace the spherical fullerene molecules with the CS2 molecules ﬁlling interstices. The spectra (Fig. 10.45) show clear evidence of a CT band at 750 nm (Izuoka, Tachikawa, Sugawara, Saito and Shinohara, 1992).

PACKING COMPLEXES

660

H3C

R1

H R2

H N

R2

N M

N

R2

N

R2

H H3C

H R1

M(TMTAA) R1 = CH3; R2 = H M(OMTAA) R1 = R2 = CH3 ML R1 = C6H5; R2 = H

b

0

a

Fig. 10.44. Upper diagram shows projection of {(ET)2C60} crystal structure down [001]; 50% probability displacement ellipsoids are shown. Lower diagram shows a partial view of the structure with shorter S(ET) . . . C(C60) contacts indicated by broken lines. (Reproduced from Izuoka, Tachikawa, Sugawara, Suzuki, Konno, Saito and Shinohara, 1992.)

ORDERED PACKING COMPLEXES

661

1·C60·CS2 Neutral 1 Abs. (arb. units)

C60

CT band

200

600 400 Wavelength/nm

1500

Fig. 10.45. UV-visible absorption spectra of {C20H16S16C60CS2} and its components. (Reproduced from Izuoka, Tachikawa, Sugawara, Saito and Shinohara, 1992.)

The ligands TMTAA, L and, especially, OMTAA have rigid saddle shapes because of the overcrowding of the four groups (methyls in TMTAA and OMTAA; two methyls, two phenyls in L) adjacent to the ortho hydrogens shown in the formula. The concave shape is here intrinsic rather than induced by the interaction as it is in, for example, the porphyrins. Thus, in {Ni(TMTAA)C60}, the large concave saddle-shaped donors embrace the spherical fullerene molecules in a layered structure, which also has fullerene-only layers (Andrews et al., 1998). The Cu(II)TMTAA and Zn(II)TMTAA C60 complexes are isostructural, as is {Ni(OMTAA)C70} where C70 is ellipsoidal (Croucher et al., 1999). In {3(NiL)C602CS2} the asymmetric unit has three different NiL moieties, one orientationally disordered over two positions and two CS2 molecules, one of which is disordered. The ‘‘architecture [as described by Soldatov et al., 2001] is surprisingly complex and entirely different from what has been observed before for analogous host complexes.’’ However, the established principles of convex C60 sockets interacting with NiL concavities still hold. In general, there are many close C . . . C contacts (some as short as ˚ ) between fullerenes and from donor to fullerene, and it is difﬁcult to identify a 3.05 A dominant interaction. Indeed, similar features are found in the 1 : 1 and 1 : 1.5 complexes of cyclotriveratrylene. Group IV. Complexes with essentially planar molecules Complexes based on three-dimensional interspersion of fullerene and miscellaneous second components of planar shape The purple blue cubes of {[HMT]2C60} (here HMT is 2,3,6,7,10,11-hexamethoxytriphenylene, not hexamethylenetetramine) have an octahedral habit. There are ordered HMT molecules at Wyckoff (b) sites of D3–32 ˚ spherical cavities that are symmetry forming a tetrahedral matrix containing 10 A occupied by partially rotationally disordered C60 molecules at tetrahedral T–23 (a) sites (Fig. 10.46; Chiang et al., 1994). This dispersed arrangement of fullerenes within a matrix resembles that described above for the cubic C6012Y crystals, although here the encompassing matrix is fully ordered. Chiang et al. considered that the HMT molecules

PACKING COMPLEXES

662

˚ , deg) for molecular complexes of C60 with various molecules of planar Table 10.16. Crystal data (A shape. Other details in caption to Table 10.9 Formula/reference

a/

2(Hexamethoxytriphenylene) CS94 OMTTFC60C6H6 ST94

30.251 10.024 77.88 13.255 101.80

2DTDSC60 SK99; SK00

b/

c/

Z 16

10.320 77.92 9.948 95.05

11.399 84.26 10.054 107.50

Space group Fd 3c

1

P 1

1

P 1

Refcode YOLVOK Reduced cell LITPUZ

Reference: CS94 – Chiang, Swirczewski et al., 1994; SK99 – Spitsyna, Konovalikhin et al. 1999; SK00 – Spitsyna, Konovalkhin et al., 2000; ST94 – Saito, Teramoto et al., 1994.

(a)

X

15.125 Å

13.099 Å (b)

Fig. 10.46. (a) 2(HMT)C60, showing packing diagram for one-half of the unit cell, with the disordered C60 spheres dispersed within a tetrahedral arrangement of HMT molecules; (b) detail of the 2(HMT)C60 arrangement. (Reproduced from Chiang et al., 1994.)

ORDERED PACKING COMPLEXES

663

were donors and C60 acceptors, but their IR and NMR spectra indicate that this effect, if existent, must be very weak. OCH3 OCH3

H3CO

H3CO

OCH3

2,3,6,7,10,11-hexamethoxytriphenylene—HMT OCH3

The black triclinic crystals of {OMTTFC60C6H6} contain layers of orientationally disordered C60 (at positions h (1/2,1/2,1/2)) interleaved by sheets of planar OMTTF (at positions f (1/2,0,1/2)), with the benzene molecules in interstitial positions a at 0,0,0 etc. (Saito et al., 1994). S

S

S

S

Octamethylenetetrathiafulvalene—OMTTF S CH3

CH3

Se

Se

S S

2-(4-thiono-1,3-dithiolan-5-ylidene)4,5-dimethyl-1,3-diselenol (DTDS)

The black prismatic crystals of {2(DTDS)C60} (LITPUZ) are triclinic, P1, Z ¼ 1 (Spitsyna et al., 1999, 2000). The structure, with layers of close-packed fullerene molecules in (100) planes interleaved by layers of pairs of DTDS molecules, could have been described together with those placed in Table 10.9 or 10.10. The center-to-center ˚ along [010] and 10.05 A ˚ along [001]. distances between fullerenes are 9.95 A Complexes based on three-dimensional interspersion of fullerene and a porphyrin second component As already noted in Chapter 8.7, porphyrins as ligands can adopt a wide variety of structures because of the possibilities of (1) changing the nature and coordination number of the metal, (2) changing the nature of the substituents attached to the porphyrin ring. Furthermore, the substitution pattern can be symmetrical or not. All of these possibilities have been exploited in the complexes of porphyrins with fullerenes. The metallo-tetraphenylporphyrins MTPP (M¼H2, Mn, Co, Cu, Zn, FeCl, etc.) are perhaps the simplest members of this family of ligands, and yield a number of complexes with

664

PACKING COMPLEXES

˚ , deg) for molecular complexes of C60 and C70 with various porphyrins Table 10.17. Crystal data (A and derivatives. For other details, see caption to Table 10.9 Formula/reference

a/

Ligand is TPP or substituted TPP H2TPPC603(toluene) BH99 14.278 69.115 14.376 CuTPPC701.5(toluene) 72.46 0.5C2HCl3 at 110K; KN01 ZnTPPC70BH99 14.481 72.623 H2TPP2C603(benzene) 19.997 at 110K. KN01 99.31 30.481 H2TPP2C604(benzene) 13.742 at 110K. KN01 2(CuTPP)C60 at 110K; 22.628 KN01 H2T(3,5-dimethylP)P 26.584 1.5 C602(toluene) BH99 12.750 H2T(3,5-dimethylP)P C704(toluene) BH99 117.94 14.650 H2T(3,5-dibutyl-P)P C60BH99 20.719 H2T(o-pivalamido-P)P C60BH99 17.186 Ni{T(p-tolyl)-P} 2C70.2(toluene) BH99 114.56 Co(II) (3,5-di-t-butyl-P) 19.971 C60 at 83K. IK01

b/

c/

Z

16.722 85.338 16.550 86.28 16.503 86.58

17.060 78.164 17.659 80.58 17.729 80.57

2

P 1

VEMNOQ

2

P 1

UBOJIE

2

P 1

VEMGOT

20.765 91.81 20.560 106.15 23.837 106.55 14.574 100.47 29.918 17.950 104.92 17.986 99.77

R 3

Refcode

2

P21/c

UBOJUQ Hexagonal axes UBOJOK

19.683

4

C2/c

UBOJIE

15.333

4

C2/m

VEMQAF

15.417 97.18 22.839

1

P 1

VEMQIN

4

Pbcn

VEMPEI

23.013

4

C2/c

VEMQEJ

21.338 103.52 11.997 90

2

P 1

VEMQUZ

2

I4

TIKHAW

28.487 120 18.626

3 9

Space group

Ligand is anti-OEP Pd(II)(anti-OEP)C60 1.5 (C6H6). at 83K. IA00

14.352 104.38

17.122 104.75

14.195 87.63

2

P 1

Cu(II)(anti-OEP)C60 2(C6H6). at 83K. IA00

14.339 104.40

17.160 104.38

14.155 87.38

2

P 1

QARPUU x Cell reduced, non-standard origin QARQAB x Cell reduced, nonstandard origin

20.968

29.520

14.797

4

P212121

QARQIJ #

20.936

29.515

14.833

4

P212121

CELVAQ #

21.06

29.31

14.841

4

P212121

CELTIW #

21.060

29.249

14.846

4

P212121

CELVUK #

Ligand is syn-OEP 2{Zn(II)(syn-OEP)}C60 2(C6H6). at 83K. IA00 2Zn(II)(syn-OEP)C60. (CHCl3) at 130K. OC99 2Co(II)(syn-OEP)C60. (CHCl3) at 130K. OC99 2Co(II)(syn-OEP)C60O. (CHCl3) at 130K. OC99

ORDERED PACKING COMPLEXES

665

Table 10.17. (Continued ) Formula/reference

a/

b/

c/

Z

Co(II)(syn-OEP)C70C6H6 (CHCl3) at 130K. OC99 Ni(II)(syn-OEP)C70C6H6 (CHCl3) at 130K. OC99 Cu(II)(syn-OEP)C70C6H6 (CHCl3) at 130K. OC99 Ru(II)(CO)(syn-OEP)C60 2(C6H5CH3) at 83K IA00 (Sc3N)@C80)Co(II) (syn-OEP)1.5CHCl3 0.5C6H6 at 130K SR99

14.359 89.88 14.412 89.58 14.402 90.09 26.019

14.628 87.45 14.723 86.99 14.654 87.45 15.838

18.782 61.10 18.882 60.56 18.836 61.38 16.805

2

P 1

CELWAR

2

P 1

CELYEX

2

P 1

CELYIB

4

Pnma

QARGEF

25.142

15.246 94.79

19.459

4

C2/m

BOJNIX

27.863

43.569

29.333

8

Ccca

GEZFIK

13.655 109.19

15.335 107.90

16.287 97.73

1

P 1

XEYZAC

13.892 67.01 22.349 15.413

14.229 83.60

15.840 65.08 20.928 21.855

1

P 1

FOPYEO

4 4

P41212 P212121

ZAPNEJ FOPZEP01

Miscellaneous Pd m-pyridyl porphyrin dimer C60 n-hexane toluene solvate {([C60]C134H150 Cl2N10Pd3)2(C6H14) 0.5(C7H8)} at 213K ST00 Porphyrin dimer C60 {C168H124O4N8Zn2} at 163K ZT01 (CuPz)2C602(C6H6) 173K. HM00 (2H-Pz)2C60toluene EY95 (NiPz)C60 123K. HM00

18.337

Space group

Refcode

x Isomorphous pair # Isomorphous quartet References: BH01 – Boyd, Hodgson et al., 2001; BH99 – Boyd, Hodgson et al., 1999; EY95 – Eichhorn, Yang et al., 1995; HM00 – Hochmuth, Michel et al., 2000; IA00 – Ishii, Aizawa et al., 2000; space group of Pd(II) complex changed to P 1; IK01 – Ishii, Kanehama et al., 2001; K01 – Konarew (2001); KN01 – Konarev, Neretin et al., 2001. Some remarkable crystallization effects were reported. OC99 – Olmstead, Costa et al., 1999. Note that Zn and Co C60O complexes with chloroform as solvate are isomorphous with the Zn complex with 2(benzene) as solvate. SR99 Stevenson, Rice et al., 1999; ZT01 Zheng, Tashiro et al., 2001. MTPP, where M ¼ Zn . . . H2 . . . is metal tetraphenylporphyrin tbp ¼ 5,10,15,20-tetrakis[3,5-di-tert-butylphenyl]porphyrin M-Pz is octakis(dimethylamino)porphyrazinatometallo(II), with M ¼ Ni2 þ , Cu2 þ , 2H þ The formula name for GEZFIK is (2-C60fullerene)-bis((25–3(pyridyl)-10,15,20-tris(3,5-di-t-butylphenyl) porphyrinato)dichloro-tri-palladium n-hexane toluene solvate. Porphyrin dimer is 2–5,5’,15,15’-bis(1,6-bis((m-phenylene)oxy(hexane)-bis(2,3,7,8,12,13,17,18-octaethylporphyrinato)di-zinc.

fullerenes. Another ligand yielding many fullerene complexes is octaethylporphyrin (OEP), where two conformations are found : syn, where the ethyl groups all point one way (say ‘down’, d8), or anti, where four point ‘up’ and four ‘down’ to give the d4u4 molecule. Crystal data for complexes of fullerenes with various porphyrin ligands are given in

666

PACKING COMPLEXES

Table 10.17; isomorphous / isostructural groups of complexes are entered together. The ﬁrst group of three MTPP complexes shows similar unit cells despite differences in fullerene (C60 or C70), M and solvent of crystallization. This also holds for complexes with OEP ligands. However, this does not always hold, and the fourth and ﬁfth entries show a striking difference when the number of solvent molecules changes from 3 to 4. Despite the differences in crystal structures among the complexes of Table 10.17, a number of structural regularities have been pointed out by the several authors. The fullerenes are not sensibly affected by complexation; in some complexes they are disordered but ordered in others, with details given in the original publications. The porphyrin ligands are known to take up two conformations, planar or warped. The planar conformation is found in the complexes discussed in Chapter 8.7; here the warped conformation (RMS ˚ ) is found in some of the complexes. Much deviation from best plane about 0.3–0.4 A attention has been given to intercomponent distances. Although details are left to the ˚ between porphyrin original publications, there is a noteworthy Zn . . . C distance of 2.89 A ˚ ), and of and fullerene in ZnTPPC70, shorter than the sum of the van der Waals radii (3.09 A ˚ 2.765(9) and 2.918(10) A between Zn and 5,6-ring junction carbons of C60 in the porphyrin dimer complex (XEYZAC). There are similar short distances (Co . . . C 2.800, Ni . . . C 2.835, Cu . . . C 2.919 A) in some of the OEP complexes (Olmstead et al., 1999). The similarity of the IR, ESR, UV-visible and X-ray photelectron electron spectra of the individual components and those of the complexes show that there is negligible (ground state) charge transfer in the solid state, and this is in concordance with the conductivities and crystal structures. Different arrangements of fullerene molecules were found in the complexes described by Konarev et al., (2001) – ‘‘a honeycomb motif in H2TPP2C603C6H6, puckered graphite-like layers in H2TPP2C604C6H6, zigzag chains in Cu(TPP)C60 1.5C6H60.5CHCl3 and columns in [Cu(TPP)]2C60.’’ Similar patterns appear in other complexes. Sun et al. (2000) remark that ‘‘A natural feature of [the structures of cocrystallates of C60 and C70 with tetraarylporphyrins and octaethylmetalloporphyrins] is the zigzag arrangement of porphyrins with the fullerenes sandwiched in the clefts . . . the unexpectedly large interaction between a curved surface and a ﬂat surface . . . is largely van der Waals in origin.’’ Using these observations as basis, a jaw-like porphyrin derivative, hinged through a {PdCl2 (bis(m-pyridyl)} group, was designed and shown to complex in solution with C60 and C70, and with C60 in the solid state (GEZFIK; Table 10.17). Boyd et al. (1999) remark that ‘‘even though fullerenes and tetraphenylporphyrins cocrystallize with great ease, one could still argue that the way they approach each other in the solid state is dictated more by size, shape and packing considerations than by . . . [a] special afﬁnity’’ [as indicated by the shorter distances noted above]. Indeed, this is the attitude we take up in this ‘‘Packing complexes’’ chapter. However, Boyd et al. (1999) argue that a ‘special afﬁnity’ should reveal itself by studies of porphyrin–C60 interactions in solution. Although electron spectroscopy is insensitive to complex formation, solutions of C60 and porphyrin in toluene show upﬁeld shifts in the 13C and 1H NMR spectra, and this was taken to be indicative of complex formation even in solution. The black, non-conducting crystals of {bis(octakis(dimethylamino)porphyrazine). C60toluene} (ZAPNET) have each C60 molecule held ‘‘between the slightly cupped ‘hands’ of a pair of dished5 porphyrazine units.’’ A three-dimensional network is formed 5

‘dished’ implies a smaller deviation from planarity than ‘warped’.

REFERENCES

667

of intersecting, almost perpendicular, linear arrays of C60 and the other molecules. Close-packed linear columns of C60 molecules run along [001]. The dished conformation of the porphyrazine molecules differs from the planar conformation found in the TCNQ mixed stack charge transfer compound, which appears to be ionic from the IR spectrum (Eichhorn et al., 1995). CH3

H 3C

H 3C

N

N

CH3

N

H3C

CH3

N

N NH

H3C

N N

N H 3C

CH3

N

CH3

HN

N

N

H 3C

CH3

N H3C

N

N CH3

H3C

CH3

Pz is octakis(dimethylamino)porphyrazine

The two octakis(dimethylamino)porphyrinatoM(II) fullerene complexes (M ¼ Cu, Ni) have different packing arrangements. The Cu(II) complex has a centrosymmetric sandwich with two slightly dished porphyrazine units enclosing one C60 molecule, whereas the second has a non-centrosymmetric 1 : 1 packing unit, the porphyrazine being strongly warped. The situation at the time of writing is that many packing complexes, weak charge transfer complexes and ionic salts have been prepared, many crystal structures determined and some physical properties (spectra, magnetic properties and conductivity (also as a function of temperature)) have been measured. Although the structures do not follow a single standard pattern, layers of close packed C60 molecules are often found with interleaved layers of the second component and interstitial solvent molecules. There are a number of examples of the second component changing its conformation to adapt to the packing requirements of the spheroidal C60 molecules. Although there are examples where there is spectroscopic evidence for weak charge transfer, some of the structural evidence for this is doubtful because disorder of the C60 molecules has not been adequately taken into account.

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Part V Molecular compounds with localized interactions

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Introduction to Part V Molecular compounds with localized interactions

In the nineteenth century convincing experimental proof was collected of interactions between molecular systems generally regarded as chemically ‘‘saturated’’, leading to more or less stable complexes. In several cases stoichiometric solid compounds could even be isolated from such mixtures . . . about the atomic arrangements in the complexes almost nothing was known until direct interferometric experiments were carried out . . . Particular importance may be attributed to complexes in which direct bonding exists between one atom belonging to the donor molecule and another atom belonging to the acceptor molecule. Complexes of this kind are above all those formed by donor molecules containing atoms possessing ‘‘lone pair electrons’’ and halogen or halide molecules. Odd Hassel, from Nobel Lecture, Chemistry, 1969.

Donor–acceptor charge-transfer interactions fall into two groups – those with localized and those with delocalized interactions between the component molecules. Part V deals with localized and Part VI with delocalized interactions. The localized interactions can be further divided into charge transfer interactions and hydrogen bonding interactions, here treated in two separate chapters. While charge transfer interactions may have received the greater attention – Nobel prizes in Chemistry to Odd Hassel for experimental studies and to R. S. Mulliken for development of theory – it would not be unfair to say that hydrogen bonding has had a greater impact on chemistry in the broader sense. Chapter 11 is the longest in the book and ranges from Hassel’s compounds with iodine as acceptor through Menschutkin’s compounds of aromatic hydrocarbons with antimony trihalides. Hydrogen bonding receives rather briefer treatment, partly because of the existence of a number of excellent texts (Jeffrey and Saenger, and Desiraju and Steiner being among the more recent) but also because we have concentrated on zero, one and two-dimensional systems and largely omitted the much more numerous three dimensional systems with their complicated and varied structures.

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Chapter 11 Donor–acceptor molecular compounds (essentially localized interactions)

Electron donors D and acceptors A are here deﬁned as all those entities such that, during interaction between a particular species of D and a particular species of A entities, transfer of negative charge from D to A takes place, with the formation as end-products either of additive combinations or new entities. The additive combinations may be 1 : 1, m : 1, 1 : n or in general m : n combinations. R.S. Mulliken (1952)

Summary: The components discussed in this chapter are linked, in the main, by localized interactions. There is a variety of donor and acceptor types ranging from n-donors and *-acceptors, through n-donors and p-acceptors, n-donors and p*-acceptors, -donors and s,p-acceptors to p-donors and *-acceptors. The ﬁrst of these categories includes some self-complexes. A distinction has been made between ‘‘pure acceptors,’’ discussed in the ﬁrst part of this chapter, and ‘‘selfinteracting acceptors,’’ discussed in the second part. The ‘‘pure acceptors’’ are involved only in donor–acceptor interaction with the donor component of the molecular compound. In the ‘‘selfinteracting acceptors’’ the principal acceptor atom (e.g. Agþ in AgClO4 or Sb in SbCl3), in addition to its donor–acceptor interaction, is also involved in interactions with other atoms of the acceptor moiety – e.g. the oxygens of AgClO4 or the chlorines of SbCl3. These additional interactions are essential to the stability of the crystalline molecular compounds. Despite widespread use of the term ‘charge transfer’ to describe these compounds, physical measurements (e.g. NQR, Mo¨ssbauer effect) suggest that there is very little actual transfer of charge in the ground state, as Mulliken often emphasized.

11.1 Introduction and classification

684

Part 1: Pure acceptors 11.2 n-Donors and s-acceptors 11.2.1 N, O, S containing ligands as donors and AgI salts as acceptors 11.3 n-Donors and *-acceptors 11.3.1 N, O, S or Se containing donors and dihalogens or halogenated molecules as acceptors 11.3.2 S containing molecules as donors and iodine molecules as acceptors (the polyiodines) 11.3.3 Physical measurements on molecular compounds of the type discussed above 11.3.4 Halogenated molecules as donors and dihalogens as acceptors 11.3.5 Self-complexes – N, O, S, Se to halogen interactions in one-component systems

687 687 688 688 706 708 712 713

684

11.4

11.5 11.6

11.7

11.8

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

n-Donors and p-acceptors 11.4.1 N, O or S containing ligands as donors and Group VA metal halides as acceptors n-Donors and *-acceptors -Donors and *-acceptors 11.6.1 Aromatic molecules as donors and dihalogens as acceptors 11.6.2 Aromatic molecules as donors and polyhalogenated methanes as acceptors -Donors and p-acceptors 11.7.1 Aluminum tribromide as an acceptor 11.7.2 Miscellany-mainly MX3 (M ¼ As, Sb; X ¼ Cl, Br) as acceptors and aromatic molecules as donors -Donors and (localized) *-acceptors

717 717 723 727 727 731 733 733 734 736

Part 2: Self-interacting acceptors 11.9

n-Donors and s-acceptors 11.9.1 N, O, and S containing ligands as donors and Ag(I) salts as acceptors 11.9.2 N, O, S containing ligands as donors and HgX2 (X¼Cl, Br, I) as acceptors 11.10 n-Donors and p-acceptors 11.10.1 N, O, S containing ligands as donors and MX3 (M¼As, Sb; X¼Cl, I) as acceptors 11.11 -Donors and s-acceptors 11.11.1 Aromatics as donors and Ag(I) salts as acceptors; also {benzene CuAlCl4} 11.11.2 Olefins as donors and Ag(I) salts as acceptors 11.11.3 Some general structural principles emerging from Sections 11.11.1 and 11.11.2 11.11.4 Acetylides as donors and Ag(I) salts as acceptors 11.11.5 Acetylides as donors and Cu(I) salts as acceptors 11.11.6 Aromatics as donors and Hg(II) salts as acceptors 11.12 -Donors and p-acceptors 11.12.1 Aromatics as donors and MX3 (M¼Sb, Bi; X¼Cl, Br) as acceptors 11.12.2 Aromatics as donors and np3 metal ions (GaI, InI, TlI, SnII, PbII) as acceptors 11.13 Summary References n n n

11.1

737 737 739 761 761 764 765 777 783 784 784 786 788 788 822 836 836

Introduction and classiﬁcation

Many chemical species can be distinguished by their tendency either to donate electrons (i.e. to be nucleophilic, or to act as electron donors, or as Lewis bases, in various different terminologies) or to accept electrons (i.e. to be electrophilic, or to act as electron acceptors, or as Lewis acids). In the limit, complete transfer of an electron from donor to acceptor leads to formation of an ionic structure. Appreciable interaction, sufﬁcient for the formation of stable crystalline molecular compounds, can occur even for partial transfer of charge and the substances considered in the following chapters are called (more or less interchangeably) charge-transfer (CT) or donor–acceptor (DA) molecular compounds.

INTRODUCTION AND C LASSIFICATION

685

Most modern theoretical treatments are based on proposals developed by Mulliken (1952a, b), which in turn rest on ideas of Weiss and Brackmann in the speciﬁc area of molecular compounds and on the more general approaches to chemical structure and reactivity introduced by many others, including G. N. Lewis and C. K. Ingold (for a review of theoretical approaches see Bender (1986)). Mulliken proposed that the wave functions of a donor–acceptor adduct in ground (G) and ﬁrst excited (E) states could be represented by: G ¼ a 0 ðD, AÞ þ b 1 ðDþ , A Þ E ¼ b* 0 ðD, AÞ þ a* 1 ðDþ , A Þ where D, A represents the no-bond structure of the adduct and Dþ, A the dative structure. It is assumed that a b, a* b* and physical measurements (e.g. NQR, Mo¨ssbauer Effect; see later for details) conﬁrm that the charge transfer in the ground state is small. This is not a contradiction of the basic premises. On the one hand, the major part of the lattice energy of crystalline CT molecular compounds comes, as Mulliken has insisted, from the contributions of dispersion and electrostatic forces of various kinds; on the other hand, the crystal structures to be described provide incontravertible geometrical evidence for speciﬁc donor–acceptor interactions and it is these interactions which determine the details of the crystal structures. The classiﬁcation used here derives from Mulliken’s (1952b) detailed classiﬁcation of donors and acceptors, but is biased towards the structural evidence obtained from diffraction analyses of crystalline molecular compounds. The structural evidence shows that it is convenient to distinguish between two types of acceptors, which we shall call ‘‘pure acceptors’’ and ‘‘self-interacting acceptors.’’ The ‘‘pure acceptors’’ are exempliﬁed by Br2 molecules in the benzene Br2 molecular compound, where the only donor–acceptor interaction is between benzene -orbitals and Br2 *-orbitals; this group of molecular compounds is described in the ﬁrst part of this chapter. The ‘‘self-interacting acceptors’’ are exempliﬁed by AgClO4 in aromatic hydrocarbon AgClO4 molecular compounds, where the vacant s-orbitals of Agþ accept not only -electrons from the aromatic molecule but also lone-pair donation from oxygen atoms of neighbouring ClO 4 ions. Both interactions are necessary for the formation and stability of these molecular compounds but it is the aromatic moiety Agþ interaction which identiﬁes them as localized interaction donor–acceptor molecular compounds; this group of molecular compounds is n n n

n n n

n n n

Table 11.1. Classification scheme for crystalline donor–acceptor molecular compounds Pure acceptors

Self-interacting acceptors

Interaction type

Example

Interaction type

Example

n!s n ! * n!p ! * ! *

dioxane AgClO4 dioxane Br2 benzoyl chloride AlCl3 benzene Br2 mesitylene NOþPF6 (localized interaction) anthracene picric acid (delocalized interaction)

n!s

pyrazine AgNO3

n!p !s !p

dioxane HgCl2 benzene AgClO4 naphthalene SbCl3

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

686

described in the second part of this chapter. Our classiﬁcation is set out in general terms in Table 11.1 and in more detail in the tables of contents. We use the following nomenclature conventions. For mnemonic reasons the donor moiety is always listed ﬁrst in the name of the molecular compound which we write as {benzene Br2} or {benzene AgClO4}. The term ‘secondary interactions’ is used as a catch-all for all bonding interactions intermediate in strength between covalent and van der Waals bonding, and will usually be indicated by ; weaker interactions are denoted by . . . ; interatomic distances are indicated as d(D A). Pioneering reviews are by Bent (1968) and Alcock (1972). Although the divisions are not sharp, as features of one structure are often partially employed in another (Nature’s principle of structural parsimony (Herbstein, 1987)), nevertheless each of these groups has sufﬁciently distinctive structural characteristics to justify separate treatment. Furthermore, there is so much information available about the delocalized ! * category that it is discussed, together with related systems, in separate chapters later. One consequence of a structurally based classiﬁcation scheme is that perhaps-expected resemblances are not always found in practice. For example, SbCl3 interacts with unsubstituted aromatics through ! p interactions, but with acetylated aromatics such as p-diacetylbenzene through n ! p interactions without participation of the aromatic ring. SbCl3 always behaves in some respects as a self-interacting acceptor but AsCl3 is a pure acceptor in its (few known) molecular compounds with aromatics. Donors can be divided into delocalized-orbital donors (the HOMOs of aromatic systems) and localized-orbital donors (the lone pair s or p electrons). A similar distinction can be applied to acceptors. The delocalized acceptors (generally substituted aromatics or heteroaromatics) employ LUMOs as acceptor orbitals. The localized acceptors are dihalogens or halogenated molecules, with * or s acceptor orbitals, nitronium salts with localized * acceptor orbitals, or metal salts in low oxidation states. For this latter group our classiﬁcation is based on foundations developed by Rundle (1957), Amma, Schmidbaur (1985) and their coworkers. The metal-ion acceptors are divided into groups with analogous acceptor orbitals (Table 11.2). Many oleﬁns and aromatics form molecular compounds with Ag(I) salts, and one example is known with a Cu(I) salt. A fair number of aromatics form molecular compounds with Ga(I), In(I), Tl(I), Sn(II) and Pb(II) salts, where the anion is a conjugate ion of a strong acid. Many crystal structures have been reported and it appears that the d10s0 ions have an 2 or 3 mode of interaction whereas the d10s2 ions have an 6 mode of interaction. This was indeed predicted many years ago by Rundle and Corbett (1957): n n n

n n n

n n n

n n n

Consider an Mþ-benzene complex with the cation on the benzene axis and therefore of symmetry C6v. The highest ﬁlled -orbitals of the benzene ring belong to the irreducible representation e1 Table 11.2. Outer electron configurations of metal ions in low oxidation states Outer electron conﬁguration of ion

Acceptor orbitals

Examples

(n 1)d10 (n 1)d10ns2

ns np3

CuI AgI HgII GaI GeII AsIII InI SnII SbIII TlI PbII BiIII

n-DONORS AND s-ACCEPTORS

687

(doubly degenerate) and the orbital of the cation must belong to the same representation to allow bonding by electron transfer from benzene to the cation. For ions such as Agþ, Hg2þ etc. the lowest acceptor orbital is an s-orbital belonging to a1, orthogonal to the upper ﬁlled -orbitals of the ring. Charge transfer is then impossible without considerable electronic promotion, so that movement of the cation to a position of lower symmetry is necessary for bonding. However, for Ga(I), In(I) and Tl(I), the lowest acceptor orbitals available are the p-orbitals, where the degenerate pair px, py belonging to e1 can accept the highest energy p-electrons from the benzene ring. Hence a symmetry C6v for the benzene-Mþ ion is by no means excluded in this case.

The results described below for the appropriate molecular compounds ﬁt these predictions very well.

PART 1: Pure acceptors 11.2 n-Donors and s-acceptors 11.2.1 N, O, S containing ligands as donors and Ag(I) salts as acceptors Silver salts form molecular compounds with molecules containing N, O, S as donor atoms and a number of crystal structures have been reported. As most of these materials appear to be on the border between metal coordination complexes and molecular compounds (for example, piperazine 2AgI (Ansell and Finnegan, 1969; PIPZAG) and morpholine AgI (Ansell, 1976; MORAG10)), we mention them only brieﬂy. In {3(dioxane) AgClO4} (Prosen and Trueblood, 1956; AGPDOX) the Agþ ions at ˚ , space group Pm3m, Z ¼ 1) are spanned by the corners of the cubic unit cell (a ¼ 7.67 A dioxane molecules along the cube edges, rotationally disordered about their O . . . O axes; thus each Agþ ion is surrounded by a regular octahedron of oxygens, with ˚ . The ClO ions are at the cube centres and are rotationally d(O Agþ) ¼ 2.46 A 4 disordered; these oxygens do not interact with Agþ. The compound is surprisingly stable and only starts to lose dioxane at 85 C; however, it is hygroscopic and the Agþ is easily reduced even in the absence of direct sunlight. Powder photographs of compounds of formula {3(dioxane) NaX} (X¼ClO4, DIOXSP01; BF4; QQQHBJ; I, QQQHBG) indicate that these are isomorphous or isostructural with {3(dioxane) AgClO4} (Barnes and Duncan, 1972; AGPDOX01){3(dioxane) NaClO4} has a more ordered form ˚ , ¼ 91.2 , space group R3) in which stable below 317.6K (rhombohedral, a ¼ 7.62 A the dioxane molecules occupy ﬁxed positions although the perchlorate ions are still disordered (Barnes and Weakley, 1978; DIOXSP); an analogous ordered form of the silver compound has not been found. It thus appears that metal-dioxane ion–dipole interactions are sufﬁcient to explain the formation of this type of compound and there is no need to invoke any special Agþ–oxygen interactions. The enthalpies of decomposition have been measured (Barnes, 1972) for {3(dioxane) AgClO4} and {dioxane AgClO4}. In {bis(2-imino-4-oxo-1,3-thiazolidene) AgClO4} (Murthy and Murthy, 1977) the Agþ is three-coordinated with two N Ag interactions to the amine nitrogens of the two ˚ ) and a weaker interaction to ring molecules of the formula unit (d ¼ 2.20(2), 2.28(2) A ˚ ); these four atoms are carbonyl oxygens of symmetry-related molecules (d ¼ 2.54(1) A n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

688

coplanar, giving triangular coordination about Agþ. A perchlorate oxygen is also weakly ˚ ). linked to Agþ (d ¼ 2.90(3) A 1,3,5-Trithian forms a 1 : 1 molecular compound with AgNO3, and monohydrates of the 1 : 1 molecular compounds with AgNO3, AgClO4 and AgBF4; (Dalziel and Hewitt, 1986) the structures of the ﬁrst three have been determined (Ashworth, Prout, Domenicano and Vaciago, 1968; TRTAGN, TRTAGH, TRTAGP). Structures are also known for the 1 : 1 compounds of dimethylbut-3-enyl methyl sulphide with AgNO3 (NMBEAG10), AgBF4 (MTBAGB10) and AgClO4 (MTBCAG10) (Alyea et al., 1981); this ligand was chosen because it was thought possible that the double bond coordinated to Agþ, but in fact the interaction is through S.

11.3

n-Donors and *-acceptors

11.3.1 11.3.1.1

N, O, S or Se containing donors and dihalogens or halogenated molecules as acceptors Summary of available results

There are many molecular compounds of I2 where lone-pair electrons of a donor atom (N, O, S, Se) are partially transferred into an antibonding *5p orbital of I2; these are n . . . * molecular compounds. Br2 behaves similarly, as do ICl and IBr. Although some of these compounds were ﬁrst prepared in the nineteenth century, major advances in understanding were not made until the theoretical studies of Mulliken (1952a, b) and Mulliken and Person (1969a, b) and the crystallographic studies of Hassel and coworkers (Hassel and Rømming, 1962; Hassel, 1970a, b). Parenthetically we note an intriguing curiosity connected with the 1969 Nobel Prize for Chemistry that Hassel shared with D. H. R. Barton ‘‘for their contributions to the development of the concept of conformation and its application in chemistry’’. Despite Hassel’s classical contributions to conformational analysis, his Nobel lecture dealt exclusively with the structures of charge transfer molecular compounds. In addition to the molecular compounds with dihalogens, there are many analogs where halogenated molecules such as halomethanes serve as electron acceptors. Evidence for CT interaction is often based on a comparison of ˚ ) (for a summary of sources see Table 11.3. Values of covalent, ionic and van der Waals radii (A Douglas, McDaniel and Alexander, 1983) Moiety

Covalent

Ionic

van der Waals

Moiety

Covalent

Ionic

van der Waals

chlorine bromine iodine

0.99 1.14 1.33 (gas phase) 1.37 (cryst. I2) 0.38 0.60

1.67 1.82 2.06

1.75 1.8 1.85 2.1 2.15

Cuþ Agþ Hg2þ

– – –

0.74* 0.81* 1.10*

– – –

– 1.26 (O2)

1.2 1.52

nitrogen sulphur

0.55 1.06 (in S8)

– 1.70 (S2)

1.55 1.80

hydrogen oxygen

* These values depend on coordination number.

n -D O N O R S A N D *-ACCEPTORS

689

experimentally determined interatomic distances with those predicted on the basis of a set of radii of various kinds, such as those in Table 11.3. Perhaps the most striking feature of the crystal structures of the present group of molecular compounds is the occurrence of short distances between donor and acceptor atoms; also, when the acceptor is a dihalogen, the distance within the molecule increases. This is shown in Tables 11.4–11.6, where the principal classiﬁcation is in terms of how the dihalogen interacts with the donor atoms. Three situations are distinguished: a. dihalogen symmetrically bonded to donor atoms (Table 11.4); b. dihalogen unsymmetrically bonded to donor atoms (Table 11.5); c. dihalogen bonded through only one of its atoms to donor (Table 11.6). There are further subdivisions according to the nature of the donor and acceptor atoms. The results for halogenated molecules (e.g. CHCl3) interacting with various donors are collected in Table 11.7. Table 11.4. Symmetrical interaction of dihalogens with donor atoms. Measurements at room ˚ , angles in degrees. Donor . . . Acceptor (Charge temperature unless stated otherwise; distances in A Transfer) Molecular Compound is abbreviated to ‘DA MC’ Interaction type

DA MC/Refcode

N I

phenazine I2 PHNAZI01

S I

N Br

n n n

d(D A) n n n

d(A–A)

Angle D A–A

Reference and remarks

Uchida and Kimura, 1984. Chains of ph I2 ph Bois d’Enghien-Peteau et al., 1968. Structural unit is mer I2 mer Marstokk and Strømme, 1968.
n n n

2.982(5)

2.726(1)

180

(merocyanine)2 I2

3.098(5)

2.750(1)

MeCN Br2 MeCN; mpt. 232K; measured at 202K; ACTNBM 1,4-dioxane Br2 DOXABR

2.84

2.328

178.4 < C¼S . . . I ¼ 99.5(7) 179.4(1)

2.71

2.31

n n n

2.78

2.29

n n n

2.82

2.28

2.67

2.02

n n n

n n n

n n n

n n n

O Br n n n

n n n

n n n

n n n

n n n

(CH3OH)2 Br2; m.pt. 207K, measured at 183K. METHOB (CH3)2CO Br2; m.pt. 265K; measured at 243K. ACETBR O . . . Cl

1,4-dioxane . . . Cl2

n n n

n n n

n n n

n n n

n n n

Hassel and Hvoslef, 1954a. I2 analogue isomorphous. Groth and Hassel, 1964a. H-bonding also present.

180

Preparation: Maass and McIntosh, 1912; Structure: Hassel and Strømme, 1959a.

Note: Raman spectra of crystalline dioxane complexes with I2, Br2 and Cl2 (all 1:1, samples at 77K) are compatible with the x-ray results (Anthonsen, 1976). NMR and NQR spectra of dioxane . . . Cl2 show that there is no phase change down to 78K (Gordeev et al., 1970).

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

690

Table 11.5. Unsymmetrical interactions of donor atoms with dihalogens. Other details as in legend of Table 11.4 Interaction type

DA MC/refcode

d(D A)

d(A–A)

N I

HMT* . . . I2 . . . NI3 HMTNTI 1-Oxa-4selenacyclohexane I2 OXSELI

2.474(8) 3.23(1) 2.755(4) 3.708(4)

2.808(1)

Tetrahydroselenophene I2 THSELI01

2.762(5)

n n n

Se .I n n n

n n n

n n n

n n n

D A–A angle n n n

2.956(3)

174.8(3) 77.4(3)

2.914(4) 3.64

179.4(3)

References and remarks Pritzkow, 1974a. Maddox and McCullough, 1966. I2 axial to Se Hope and McCullough, 1964.

* HMT is hexamethylenetetramine.

11.3.1.2

Generalizations based on the experimental results

(i) Stereochemistry of the D A interactions The D A–B (A, B halogens) arrangement is always linear or nearly so. The distance between donor and acceptor atoms varies from a small increase (ca. 10%) over the covalent bond distance (e.g. as in (CH3)3N I–I) to a small reduction (also ca. 10%) below the sum of the van der Waals’ radii (e.g. as in 3(S8) ICH3). The donor molecules do not show signiﬁcant changes of dimensions on formation of the molecular compounds, nor do the trihalogenomethanes and similar acceptors; however, the dihalogens (I2, Br2, Cl2, IBr, ICl) all show signiﬁcant lengthening compared to their gas phase dimensions. There is an experimental caveat here – halogen positions will generally be rather precisely determined in x-ray diffraction studies of these molecular compounds, and carbon (or N, S etc) positions much less so, with the consequence that C–halogen distances will have, essentially, the standard uncertainties of the C atom. Neutron diffraction may provide a means of obtaining more precise C–halogen distances in appropriate crystals. The coordination about the donor atom depends on its nature and situation: n n n

n n n

n n n

n n n

(a)

nitrogen – tetrahedral about 4-coordinated nitrogen, trigonal planar about 3-coordinated N and linear about 2-coordinated N. (b) oxygen, sulphur, selenium – the arrangement about these atoms is generally tetrahedral when there is 4-coordination and pyramidal when there is 3-coordination. O and S in ring compounds link the A atom equatorially, irrespective of whether A is in a dihalogen or a halomethane. Se in a ring compound links axially to A except for 1,4-selenothiane I2, where the bonding to both S and Se is equatorial, and in 1,4diselenane (I3CH)2, where one link is equatorial and the other axial. Oxygen with two secondary linkages forms a two-dimensional cross-linked structure in acetone Br2. The secondary linkage from sulphur forms ‘‘elbow’’ bonds (<X¼S A ca. 95–110 ) in dithizone I2 and (merocyanine)2 I2. n n n

n n n

n n n

n n n

n n n

n n n

Table 11.6. Dihalogen bonded to donor moiety through only one of its halogen atoms. Other details as in legend of Table 11.4. Some chemical formulae are given at the end of this Table Interaction type

DA MC/refcode

d(D A)

d(A–A)

angle D A–A

References and remarks

N I

(CH3)3N I2 at 253K. TMEAMI 4-picoline I2; m.pt. 356K. PICOLI HMCP* I2 HMCPZI

2.27

2.83

179

2.31

2.83

180

2.417(7)

2.823(1)

177.8(2)

HMT I2 HXMTDI

2.439(8)

2.830(1)

173.1

HMT (I2)2 HXMIOD

2.496(5)

2.791(1)

173.8(1)

HMT (I2)3 YUYNUB 9-cyclohexyladenine I2 CHXADI10 (CH3)3N ICl

2.593(6) 2.520(3)

2.746(1) 2.764(1)

177.6(2) 177.1

2.30(1)

2.54

Pyridine ICl PYRIIC10

2.29(1)

2.510(4)

178.7(3)

Pyridine IBr PYIOBR

2.26(4)

2.66(1)

180

Pyridine ICN PYCYNI

–

2.57(2)

Pentamethylenetetrazole ICl PMTTIC01

2.34

2.44

Strømme, 1959. Tetrahedral coordination about N Hassel, Rømming and Tufte, 1961. I2 at 14 to donor plane Markila and Trotter, 1974. Trigonal planar coordination about N Pritzkow, 1975. Tetrahedral coordination about N Pritzkow, 1975. Bromine analogue is isomorphous (Eia and Hassel, 1956); (ZZZHEM). Tebbe and Nagel, 1995. Van der Helm, 1973. Approximate trigonal planar coordination about N Hassel, 1958. Isostructural with I2 compound (TMEAMI) Rømming, 1972. Approximate trigonal planar coordination about N Dahl, Hassel and Sky, 1967. Approximate trigonal planar coordination about N Dahl, Hassel and Sky, 1967. Approximate trigonal planar coordination about N Baenziger et al., 1967. (PMTTIC). I bonded to N(2); ICl coplanar with donor; see note to this Table.

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

177

Table 11.6. (Continued) Interaction type

DA MC/refcode

d(D A)

d(A–A)

angle D A–A

References and remarks

O I

Dioxane (ICl)2

ca. 2.6

ca. 2.3

linear

Hassel and Hvoslef, 1956. Not known whether O I axial or equatorial Freeman et al., 1998. -polymorph (GEGNUB) –polymorph (GEGNUB01) Herbstein and Schwotzer, 1984. See note to this Table. Ahlsen and Strømme, 1974. See note to this Table. Preparation: Fromm, 1913; structure: Rømming, 1960. S pyramidal. See note to this Table. Hartl and Steidl, 1977.

n n n

n n n

n n n

n n n

n n n

S I n n n

1,3-Dimethyl-2thioimidazole I2 do. Dithizone I2 BZHTIC10

2.616

2.967

< C ¼ S I ¼ 97.7

2.607 2.664

2.984 2.918

99.7 178.4 Angle C¼S I 95.6 176.2 Angle C ¼ S I 109.9 179. Angle C ¼ S I 100.

n n n

n n n

n n n

n n n

N-methylthiocaprolactam I2 TCAPLI Benzyl sulphide I2 BENZSI

2.687

Co(py)4(NCS)2 (I2)2 PYTTCC 1,4-dithiane . . . (I2)2 DTHINI

2.797(2)

2.879

n n n

n n n

n n n

n n n

2.78(2)

2.82(1)

n n n

2.804(1)

178.8(1) Angle C ¼ S I 95.2(3). 177.9(4) n n n

2.867(2)

2.787(2)

Preparation: Husemann, 1863; structure: Chao and McCullough, 1960. Structural moiety is I2 donor I2; I equatorial to S Herbstein et al., 1986. One S I interaction is axial and one equatorial (for C4S rings) for both propellane compounds Herbstein et al., 1986. n n n

dithia[3.3.1]propellane (I2)2 FAJPUB

2.806(2) 2.852(2)

2.797(1) 2.796(1)

dithia[3.3.2]propellane (I2)2 FAJRAJ 1,4-dithiane (IBr)2 DTHIBR10

2.803(2) 2.902(2)

2.794(1) 2.767(1)

2.687(2)

2.646(1)

n n n

n n n

n n n

n n n

178.2(4)

Knobler et al., 1971

n n n

Se I n n n

1,4-diselenane I2 DSEIOD n n n

1-oxa-4selenocyclohexane ICl OXSEIC

2.829(4)

2.870(3)

180.0(3)

2.630(5)

2.73(1)

175.8(2)

Chao and McCullough, 1961. Moiety as above but I axial to Se. Knobler and McCullough, 1968. Moiety is C4H8OSe ICl; I axial to Se. Hope and McCullough, 1962. Disorder prevented detailed analysis. Shibata and Iwata, 1985. Electron diffraction Allegra et al., 1970. Pyramidal coordination about S.

n n n

n n n

1,4-selenothiane (I2)2 ZZZLSI n n n

N Br

(CH3)3N Br2

1.98(3)

2.29(1)

112(3)

S Br

C4H8S Br2 THINBR

2.724(2)

2.321(4)

178

n n n

n n n

n n n

n n n

Notes:

Chemical formulae: H Ph

N N N N(2) Pentamethylenetetrazole

N H

N

Ph

N

N

Ph

Dithizone

Benzyl sulphide H3C

S S

N

N H3C

N CH3 CH3

1,3-Dimethylimidazole

Ph

S

CH3 N

S

N-methylthiocaprolactam

H3C

P

CH3 P N

N P

CH3

CH3

Hexamethylcyclotriphazene (HMCP)

694

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

Table 11.7. Donor halogen interactions in molecular compounds of N, O, S or Se-containing donors and halogenated molecule acceptors. Other details as in legend of Table 11.4 n n n

Interaction type

DA MC/refcode

d(D A)

Remarks

N I

H3N I3N

2.53

pyridine I3N PYDTIN HMT I2 NI3 HMTNTI

2.58 2.567(6) 2.582(8)

Hartl, Ba¨rnighausen and Jander, 1968. Hartl and Ullrich, 1974. Pritzkow, 1974a. Both contacts are between I of NI3 and N of HMT. Angles N-I N 175.4, 178.6 Dahl and Hassel, 1970. C–H .N links also present (d ¼ 3.22). Tetrahedral coordination of each molecule about the other. N I–C nearly linear. Dahl and Hassel, 1970. Angle C–N I 175. Isomorphous with C2Br4 analogue Preparation: Rhoussopoulos, 1883; structure: Bjorvatten and Hassel, 1962. Angle C–N I 177 Walsh et al., 2001

n n n

n n n

n n n

n n n

n n n

n n n

n n n

HMT I3CH HEXAIF10

2.93

n n n

n n n

n n n

pyrazine I4C2 IETPYA10

2.98

(quinoline)3 I3CH; m.pt. 336K. IFOQUI

3.05

n n n

n n n

n n n

n n n

4,4 0 -bipyridine C2I4 QIHBIS 1,2-bis(4-pyridyl) ethylene C2I4 QIHCEP HMT C2I4. QIHCUF 1,4-dioxane 1,4diiodoacetylene. DOXIAC 1,4-dithiane 1,4diiodoacetylene 1,4-dithiane I3CH. DTHIOF n n n

Walsh et al., 2001

n n n

n n n

O I n n n

S I n n n

n n n

2.65

n n n

3.27

n n n

3.32

Co(py)4(NCS)2 2(I3CH). TCPYCO. (S8)3 I3CH, IFOSUL

3.361(5) 3.460(5) 3.510(5) 3.50

(S8)3 I3Sb

3.60

n n n

n n n

n n n

Walsh et al., 2001 Gagnaux and Susz, 1960. I equatorial to O; chains in crystal. Holmesland and Rømming, 1960. I equatorial to S. Bjorvatten and Hassel, 1961. Poor crystals, I equatorial to S; chains in crystal. Hartl and Steidel, 1980. Each S coordinated to three I of different CHI3 molecules Bjorvatten, 1962. I equatorial to S; (S8)3I3R (R¼CH, P, As, Sb) are isomorphous. Bjorvatten, Hassel and Lindheim, 1963. Additional Sb I and S I interactions postulated to account for stability n n n

n n n

n -D O N O R S A N D *-ACCEPTORS

695

Table 11.7. (Continued) Interaction type

DA MC/refcode

d(D A)

Remarks

Se I

1,4-diselenane 1,4diiodoacetylene

3.34

1,4-diselenane I4C2 DISTIE 1,4-diselenane 2(I3CH) IFODSE n n n

3.465

Holmesland and Rømming, 1960. I axial to Se; not isomorphous with 1,4-dithiane analogue. Dahl and Hassel, 1965.

n n n

3.514

n n n

N Br n n n

n n n

n n n

diazabicyclo[2.2.2]octane* (N-bromosuccinimide)2 CEGVUF quinuclidine Br4C FEGYEV diazabicyclo[2.2.2]octane* Br4C FEGYAR 2,3-diazabicyclo[2.2.2]octene# Br4C FEJFAB HMT (Br3CH)2, at 238K. BFHMTA pyrazine Br4C2 BEPYRZ10 1,4-dioxane oxalyl bromide at 298K. OXBDOC 1,4-dioxane . . . oxalyl chloride at 253 to 233K. OXCDOC

Bjorvatten, 1963. Angle C-I Se 178.2 . Se forms both equatorial and axial bonds to different iodines. Crowston et al., 1984.
2.332(4)

n n n

n n n

n n n

2.53 2.76, 2.88

Blackstock et al., 1987. C-Br N linear Blackstock et al., 1987.

2.91(1)

Blackstock and Kochi, 1987.

3.00

Dahl and Hassel, 1971. Also ˚ ) links. N H–C (d ¼ 3.13 A Dahl and Hassel, 1968b.

n n n

n n n

n n n

n n n

n n n

O Br n n n

O Cl n n n

Notes: * DABCO;

n n n

n n n

3.02 3.21

Damm et al., 1965. Chains of alternating donor and acceptor molecules along [111]. Damm et al., 1965. Isomorphous with bromo analogue.

3.18

# DBO, with formulae given below.

N N N N DABCO

DBO

(ii) Arrangement of the moieties in crystals (a) Individual moieties linked by Van der Waals interactions In many crystals of this kind, the structural (packing) units are donor acceptor groupings such as (CH3)3N I2 or I2 1,4-dithiane I2 (Fig.11.1); these structural units interact only through dispersion forces and thus the crystals are molecular crystals, the n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

696

C

S

2.789 2.879

4.067

Dithiane

Diiodine

B

z y

3A x

Fig. 11.1. Crystal structure of {I2 (1,4-dithiane) I2} projected onto (010). The dark circles are iodines, the intermediate circles sulphur and the smallest circles carbon; hydrogens are not shown. Dithiane molecules are located about crystallographic centres of symmetry and are in the chair form; I2 is equatorial with respect to dithiane. The I–I, I . . . S distances are shown, as well as a van der Waals contact between two iodines. (Data from Chao and McCullough, 1960.) n n n

n n n

‘molecule’ being the D A structural unit. {1,5-Dithiacyclooctane2I2} (Hope and Nicols, 1981; THOCIA) may well have a structure similar to that of {I2 1,4-dithiane I2} but atomic coordinates are not available. The D A interactions seem to be stronger (using distances between donor and acceptor atoms as the criterion) within these quasi-isolated structural groupings than when extended interactions occur, leading to the formation of chains of the type D A D A , as described in the next section. Such a situation is exempliﬁed by comparison of the {quinuclidine CBr4} (Blackstock, Lorand and Kochi, 1987; FEGYEV) (cubic, ˚ , space group P213, Z ¼ 4) and {diazabicyclo[2.2.2]octane CBr4} a ¼ 10.906(8) A (Blackstock, Lorand and Kochi, 1987; FEGYAR) structures (cell dimensions summarized in Table 11.8 below). The former has isolated D A units (Fig. 11.2) in its crystal ˚ ). One of the two structure, with rather strong and linear N Br–C links (d ¼ 2.531(6) A ˚ , which is much longer than C–Br distances reported in {quinuclidine CBr4} is 2.25 A ˚ ) (More et al., 1977; CTBROM). The the value found in Phase II of CBr4 itself (1.91(4) A discrepancy is due to inaccuracy in determining the carbon position, as noted above and ˚ . {Quinuclidine CBr4} by Blackstock et al. The other C-Br distance is normal at 1.86(2) A is unusual among CT molecular compounds in that it is enantiomorphic, although the absolute conﬁguration was not reported. NaClO3 is an example in the same space group, n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n -D O N O R S A N D *-ACCEPTORS

2.248

697

1.856 3-fold axis

2.531 Carbon tetrabromide

z Quinuclidine

y x

Fig. 11.2. Packing unit of the {quinuclidine CBr4} structure showing only the nonhydrogen atoms. Each donor–acceptor pair has three-fold symmetry about its C-Br N axis and this takes up three ˚ is an artifact due to orientations in the crystal. As noted in the text, the C–Br bond length of 2.248 A systematic error. (Data from Blackstock, Lorand and Kochi, 1987.) n n n

n n n

(a)

(b) 1.0 1.2

Absorbance

N

0.6

N CBr4

N CBr 4

Solid

0.6

Solid

0.8

0.7 0.6 0.5

0.5 0.4

0.4

0.2

Solution

Solution

0.4

0

400 Wavelength

200

600

200

300 400 Wavelength

(nm)

500

Fig. 11.3. Comparison of solution and solid-state absorption spectra of (a) {diazabicyclo[2.2.2]octane CBr4} and (b) {quinuclidine CBr4}. (Reproduced from Blackstock, Lorand and Kochi, 1987.) n n n

n n n

much studied in regard to the relation between crystal structure and optical activity (Devarajan and Glazer, 1986). Solution and solid-state absorption spectra of {quinuclidine CBr4} are virtually identical (Fig. 11.3(b)) with the latter being shifted to the red by 5 nm with respect to the former; this close similarity suggests that the D A units of the crystals are largely ˚ in {diazabicyclo maintained in solution. The N Br distances are 2.76, 2.88 A [2.2.2]octane CBr4} and solution and solid state spectra are rather different (Fig. 11.3(a)), suggesting only weak interactions in solution. Symmetrical interactions of both halogen atoms (Table 11.4) appears to be rare for I2; {merocyanine I2 merocyanine} is one example where the centrosymmetric arrangement n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

698

has an iodine molecule interacting symmetrically with the sulphurs of two merocyanine molecules. Br2 acts fairly commonly as a symmetrical acceptor (e.g. {CH3CN Br2 NCCH3}). IBr and ICl appear to act only as monofunctional acceptors, interaction always being through the iodine atom. Caution must be exercised in inferring isomorphism – for example, both {I2 1,4dithiane I2} and {BrI 1,4-dithiane IBr} have A D A moieties as structural units and also rather similar unit cells, but the structure analyses show that the moieties are arranged very differently. Comparison of the I . . . S distances in these two molecular compounds shows that IBr is a stronger acceptor than I2. (b) Unsymmetrical interactions of dihalogens There are a number of examples where weaker secondary D . . . A interactions link the D A moieties in the crystals. These can be considered as situations which are intermediate between isolated moieties ((a) above) and symmetrical linkings ((c) below). In{tetrahydroselenophene I2} (THSELI) approximately linear chains are found. The ˚ ) but there is some doubt about crystals are orthorhombic (12.804(3) 9.256(3) 7.625(3) A the space group. For convenience, we have shown in Fig. 11.4 an ordered structure in space group Pna21, Z ¼ 4, but Hope and McCullough (1964) preferred the centrosymmetric Pnma, with disorder of the tetrahydroselenophene rings. There is very little difference between the two possibilities. The striking features of the structure are the lengthening ˚ in the gas phase) and the shortening of the iodine covalent bond (compared to 2.66 A ˚ of one distance between I and Se to 2.764 A, while the other distance is close to the n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

Tetrahydroselenophene 2.914 O

A

2.764 Iodine 3.64

B

z

x

y

Fig. 11.4. A line of unsymmetrically interacting moieties in {tetrahydroselenophene I2}. The ˚ and the angles I(1)I(2) . . . Se and I(2) . . . Se . . . I(1) are 179.4(3) and Se . . . I(1) distance is 3.64 A 167.2(4) respectively. (Data from Hope and McCullough, 1964.) n n n

n -D O N O R S A N D *-ACCEPTORS

2.755

2.956 I(2)

I(1)

699

3.71 Se

O

Fig. 11.5. Chain of unsymmetrically interacting moieties along [100] in {1-oxa-4-selenacyclohexane I2}; carbons are light-dotted, oxygens dark-dotted and iodines diagonally hatched. The angles I(1)-I(2) . . . Se, I(2) . . . Se . . . I(1) and Se . . . I(1)-I(2) are 174.8(3), 82.5(4) and 77.4(3) respectively. (Adapted from Maddox and McCullough, 1966.) n n n

sum of the van der Waals radii. Thus there are distinct bimolecular {C4H8Se . . . I2} units in the crystal. In {1-oxa-4-selenacyclohexane I2} (not in CSD) the arrangement is zigzag: In the ˚ longer than the examples shown in Figs. 11.4 and 11.5, the I–I distance is about 0.3 A ˚ gas-phase value of 2.66 A and requires checking. ˚ In {1,4-diselenane I2} (DSEIOD) there are weaker secondary bonds of length 3.89 A between Se of one DA moiety and I(1) of another, the molecules being linked in helical chains about alternate twofold screw axes. Unsymmetrical chains are also found in the ternary compound {I3N I2 hexamethylenetetramine} (HMTNTI), with much stronger bonding between I3N and I2 than between I2 and HMT; there is additional bonding between iodines of I3N and nitrogens of HMT, leading to a three-dimensional arrangement of the three components (Fig. 11.6). (c) Symmetrical arrangements: When both donor and acceptor molecules are bifunctional then inﬁnite arrangements can be formed, their shape depending on the coordination at the interacting atoms. Linear chains are formed in {phenazine I2} and {dioxane Br2} and zigzag chains in {12[ane]S4I2}1 (12[ane] is 1,4,7,10-tetrathiocyclododecane (Baker et al., 1995; LINHEV) and {acetone Br2} (Fig. 11.7). In {12[ane]S4I2}1 the I–I and S . . . I distances are 2.736(1) and ˚ , indicative of rather weak interactions. Baker et al. carried out semi-empirical 3.220(3) A MO calculations on (CH3)2S . . . I2 and (CH3)2S . . . I2 . . . S(CH3)2 to study the differences between terminal and bridged molecular compounds. These calculations conﬁrmed that the principal interaction is between the thioether HOMO and the diiodine LUMO (the * antibonding orbital), with a consequent weakening of the I–I bond. A more complex arrangement, but based on similar structural principles, is found in {9[ane]S3(I2)} (9[ane]S3 is 1,4,7-trithiacyclononane) (Blake et al., 1993; PELSUX). Similar extended structures are formed by the centrosymmetrical, bifunctional donor and acceptor molecules in {pyrazine tetrabromoethylene} (BEPYRZ10) and {dioxane diiodoacetylene} (DOXIAC). Analogous structures are found in some trihalogenomethane molecular compounds, only two of the halogen atoms then interacting with donor atoms. A zigzag arrangement of moieties linked by charge transfer I . . . S interactions ˚ ) is found in {dithiane CHI3} (Fig.11.8); {dioxane CHI3}, while (d(I . . . S) ¼ 3.42 A n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

700

O

A

HMT 2.808 3.247

I2

NH3

2.14

2.583

2.475

2.566

B x y

Fig. 11.6. The ternary molecular compound {I3N I2 HMT}, shown in projection onto (001). The overall arrangement is three-dimensional as NI3 is pyramidal and the nitrogens of HMT are arranged tetrahedrally. Iodines are shown as large ﬁlled circles and nitrogens as small ﬁlled circles; carbons are the small light circles. The secondary N . . . I interactions of different lengths are shown. (Data from Pritzkow, 1974a.) n n n

n n n

not isomorphous with {dithiane iodoform}, appears to have an analogous structure, although details are lacking because of poor crystal quality. A similar chain arrangement is found in {diazabicyclo[222]octane CBr4}, where the comparison of solution and solid-state absorption spectra (Fig. 11.3) shows a clear charge-transfer band in the solid; presumably there is only weak interaction between the moieties in solution. There is also a chain arrangement in {DBO CBr4}. These molecular compounds are all isostructural, as is shown by comparison of cell dimensions and relationships among the projections (Table 11.8). These chain arrangements should be compared with the D A packing units found in {quinuclidine CBr4} (Fig. 11.2). 14 N and 81Br NQR spectra have been measured for {DABCO CBr4} over the temperature range 77–320K (Okuda et al., 1984) and provide, potentially, a means for measuring the strengths of the CT interactions. Unfortunately, this cannot yet be done as n n n

n n n

n n n

n n n

n n n

n n n

n -D O N O R S A N D *-ACCEPTORS

701

b

2.28 2.82

c

a

Fig. 11.7. Projection onto (100) of part of the {acetone Br2} structure, showing two superposed planar layers of linked bromine and acetone molecules; the O . . . Br links are shown by dashed lines and oxygens are dark-dotted, bromines cross-hatched and carbons light-dotted. The outline of the ˚ , ¼ 111.5 , C2/c, Z ¼ 4) is shown. (Reproduced from unit cell (a ¼ 7.12, b ¼ 7.48, c ¼ 12.90 A Hassel and Strømme (1959a).) n n n

˚ , deg.) for three isostructural molecular compounds. Table 11.8. Comparison of cell dimensions (A The axes of analogous projections are emphasized Molecular compound Dithiane

n n n

CHI3

a

b

6.56

21.06

DBO CBr4

8.509

DABCO

6.126

n n n

n n n

CBr4

6.101 16.80

Space group

Z

Molecular positions

4.47

104.4

P21/m

2

12.006

90

Pmc21

2

12.634

101.8

P21/m

4

Dithiane at centers; CHI3 on mirror. DBO and CBr4 molecules on alternate mirror planes Two disordered DABCO’s on independent centers; two CBr4 on independent mirrors.

c

there are some contradictions between diffraction and NQR results, perhaps because of the occurrence of a phase transition at 320K. In {diselenane 2(CHI3)}, the donor Se atoms form two secondary bonds and the diselenane molecules link across zigzag chains (Fig. 11.9(a)). A formally similar arrangement is found in {(CH3OH)2 Br2} (Fig.11.9(b)), where there are hydrogen bonds as well as O Br interactions. A common feature of these two groups of structures is that only two of the three (or four) halogens are involved in charge transfer bonding. n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

702

Fig. 11.8. Structure of the chains in {dithiane CHI3}; ﬁgured circles indicate S, cross-hatched circles I and small dotted circles C; one I does not participate in the bonding between the moieties. ˚ . Two layers are shown, projected onto (001). The unit cell dimensions The dashed links are 3.42 A ˚ , ¼ 104.4 , space group P21/m, Z ¼ 2, dithianes are on centres are: a ¼ 6.56, b ¼ 21.06, c ¼ 4.47 A of symmetry and iodoforms on mirror planes. (Adapted from Bjorvatten and Hassel, 1961.) n n n

There is a three-dimensional tetrahedral arrangement in {HMT CHI3} of the four intermolecular bonds linking each molecule to its neighbours. Three of these links are ˚ , while the fourth is a weak CH N interaction N ! I, with equal lengths of 2.93 A ˚ (3.22 A). {HMT I2} and {HMT (I2)2} both form crystals without extended linkages, ˚ ) in the ﬁrst of these although there are some weak I . . . N interactions (d(I . . . N) ¼ 3.48 A and some weak I . . . I interactions in the second (Pritzkow, 1975). {HMT (I2)3} is similar (Tebbe and Nagel, 1995; YUYNUB). (d) Octasulphur as donor and halogenated molecules as acceptors: S8 forms 3 : 1 molecular compounds with CHI3, PI3, AsI3 and SbI3, ﬁrst prepared (Auger, 1908) and examined crystallographically (Demassieux, 1909) before the First World War. The molecular compounds {3S8 CHI3} and {3S8 AsI3} are isomorphous and form an unbroken series of solid solutions (Hertel, 1931), although CHI3 and AsI3 have essentially no mutual solid solubility. The isomorphism was conﬁrmed by West (1937) and later extended to the SbI3 molecular compound (Table 11.9). The crystal structures of {3S8 CHI3} (Bjorvatten, 1966; IFOSUL) and {3S8 SbI3} (Bjorvatten, Hassel and Lindheim, 1963) have been determined and we describe them in terms of the latter (m.pt. 116–8 , sensitive to moist air). The sulphur molecules are located on mirror planes and the SbI3 molecules on trigonal axes; dimensions are given in Table 11.9. Each iodine atom has a shorter link to one S atom of a particular S8 molecule, and two longer links to two pairs of others; thus ﬁve of the eight S atoms of a sulphur molecule have close iodine neighbors. The situation is complicated by each Sb atom ˚ , all from the nearest having three additional I . . . Sb interactions at distances of 3.85 A SbI3 molecule situated along the same trigonal axis. We consider the S . . . I interactions to be more important for determining the overall crystal structure than the I . . . Sb interactions (or analogous CH . . . I interactions in {3S8 CHI3} and hence have classiﬁed SbI3, and by extension the other RI3 molecules, as ‘‘pure acceptors’’ in this group of molecular n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n -D O N O R S A N D *-ACCEPTORS

703

c sin b

b

C Å 14

I

I

I

C

3.4

Se

65

3.5

I

I

I

Å

3Å

a

2.62 c 2.78 2.29

Fig. 11.9. (above) Structure of {diselenane 2(CHI3)} projected down [100]; one I does not participate in intermoiety bonding. The dimensions of the unit cell are a ¼ 6.73, b ¼ 17.27, ˚ , ¼ 104.3 , P21/c, Z ¼ 2, m.pt. 93 C. (Reproduced from Bjorvatten, 1963.) (below) Two c ¼ 8.31 A layers of {(CH3OH)2 Br2}, viewed down [010]. This compound melts at 207K and the intensity measurements were made at 183K. Because of the limited precision of the structure analysis, only average values of crystallographically independent interatomic distances are given. The charge transfer (Br . . . O) links extend horizontally across the ﬁgure, and the hydrogen bonds (hydrogen positions were not determined) vertically. Bromines are cross-hatched, oxygens dark-dotted and carbons light-dotted. (Reproduced from Groth and Hassel, 1964a.) n n n

n n n

compounds. Fairly extensive NQR and Mo¨ssbauer effect studies have been made of this group of compounds (see Section 11.2.3.3). Second harmonic generation has been studied in {3S8 CHI3} and {3S8 SbI3} (Samoc et al., 1992); powder SHG efﬁciency is about twice as large in the CHI3 compound as in the SbI3 compound. n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

704

Table 11.9. Crystallographic data (given for the triply primitive hexagonal cell) and some results for the isomorphous molecular compounds {3S8 RI3} where R¼CH, As, Sb (rhombohedral, space ˚ , angles in degrees group R3m, Z ¼ 1). Distances in A n n n

R

a

c

d(R–I)

CH As Sb

24.32 24.60 24.817(7)

4.44 4.523 4.428(2)

2.10 2.747(2)

< I–R–I

96.56(4)

d(S I)

d(I R)

3.50(2)

3.84, 3.88

3.60(1), 3.78, 3.88

3.85

n n n

n n n

Fig. 11.10. Stereoview of the unit cell of {2S8SnI4} viewed along [001]; [100] is vertical and [010] ˚ , space group Fdd2, horizontal. The crystals are orthorhombic, a ¼ 20.89, b ¼ 21.81, c ¼ 11.40 A Z ¼ 8, m.pt. 101 C. (Reproduced from Laitinen et al., 1980.)

The above preparative results were conﬁrmed by Feher and Linke (1966), who further showed that S6 did not form corresponding molecular compounds; thus treatment of a sample of S6 with a suitable RI3 affords a method of removing unwanted S8. S8 forms 4 : 1 molecular compounds with SnI4 (Feher and Linke, 1966) and P2I4 (Feher et al., 1962) (m.pt. 66–8 ; very unstable in air) but crystal structures were not reported. 4 : 1 and 2 : 1 molecular compounds of S8 with SnI4 have also been prepared and studied by NQR (Ogawa, 1958) (see Section 11.2.3.2); the crystal structure of the 2 : 1 compound, and of a related compound, have been reported but not that of the 4 : 1 compound. Although these materials are probably better described as packing complexes, it is convenient to discuss them here and not in Chapter 10. The crystal structure of {2S8SnI4} was determined by Hawes (1962) and reﬁned by Laitinen et al. (1980) (Fig. 11.10). As no ˚ were found, it was inferred that this was a packing I . . . S distances of less than 3.8 A complex without appreciable charge transfer interactions. There is some controversy about the structure of {2SnSe8nSnI4} with Hawes (1963) claiming that the compound with n ¼ 7 is a distorted version of the sulphur complex, i.e. with similar cell dimensions and space group but with a displacement of the individual molecules from their positions in the parent complex, presumably because of the strain induced by replacement of S8 by SnSe8;n. Hawes also noted that 16% of the sulphur rings in the S8 complex could be replaced by S7Te. Laitinen et al. using a similar method of preparation, obtained a triclinic

n -D O N O R S A N D *-ACCEPTORS

705

Fig. 11.11. Stereoview of the unit cell of {2SnSe8nSnI4} seen along [001]; the [100] axis is ˚, vertical and the [010] axis horizontal. The crystals are triclinic, a ¼ 11.41, b ¼ 16.14, c ¼ 8.10 A ¼ 92.3, ¼ 110.5, ¼ 68.9 , Z ¼ 2, space group P1. (Reproduced from Laitinen et al., 1980)

S(5)

Cl(1) Cl(2) w

Cl(4)

3.189(2) Å

Cl(3) d (Cl(3)...S(6b)) = 3.36 Å d (Cl(4)...S(6h)) = 3.25 Å

S(6a) S(6h) S(6g)

S(6b)

S(6c) S(6f)

S(6e)

S(6d)

Fig. 11.12. View of the adduct {WCl4SS8}; the closer nonbonded distances are shown. The crystals ˚ , P4 21 c, Z ¼ 8. (Reproduced from Hughes et al., 1991.) are tetragonal, a ¼ 16.606, c ¼ 10.546 A

complex (Fig.11.11), which appears to differ from that of Hawes, and contains (according to evidence from Raman spectroscopy), S8 and SnSe8n, with n probably mainly 6, although there was also a small n ¼ 7 content. The deep-red, air-sensitive crystals of WCl4S9 obtained by reﬂuxing a suspension of W(CO)6 with S2Cl2 in CH2Cl2 under tungsten light irradiation, has been shown, by x-ray crystallography, to be the adduct {WCl4SS8} (Fig. 11.12) (Hughes et al., 1991). The W . . . S distance is close to the sum of the metallic radius of W and the van der Waals radius of S and is thus a normal packing interaction. The two S . . . Cl distances shown in the ﬁgure are signiﬁcantly shorter than the sum of the van der Waals radii and suggest a possible charge transfer interaction. A spectroscopic study would be of interest. (e) A diversion – an early C–H . . . O hydrogen bond Diethyl ether forms 1 : 1 molecular compounds with CHCl3 (m.pt. 182K) and CHBrCl2 (m.pt. 179K) (Andersen and Thurmann-Moe, 1964). Two polymorphs were found for {(C2H5)2OCHBrCl2} with appreciable differences in unit cell dimensions and volume

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

706

˚ 3 (ETHBME01) and 959 A ˚ 3 (ETHBME)) and hence presumably also in structure, (1111 A although both had the same space group (Pna21, Z ¼ 4). The crystal structure of ETHBME was determined, intensity measurements being made at 143K. It had been expected that there would be a link between O and one of the halogens but, in fact, the closest approach ˚ . This was called a hydrogen bond, well in was between CH and O, with length 3.10 A advance of current usage (Desiraju and Steiner, 1999). 11.3.2

S containing molecules as donors and iodine molecules as acceptors (the polyiodines)

There are a number of molecular compounds in which a molecule containing S as donor atom binds to iodine molecules. We call these polyiodines; in contrast to the polyiodides,

I4 2.796 I3 2.806

S1 A

2.825

S2

I1 dithia[3.3.1]propellane

2.797 I2 3.720

0 x

y

Fig. 11.13. The {I2dithia[3.3.1]propellaneI2} structure (FAJPUB) viewed down [001]. The large spheres are iodine, the small dark spheres sulphur, and the small light spheres are carbon; hydrogens are not shown. The chains of moieties are linked by two kinds of weak interactions – iodine to iodine, ˚ and iodine to sulphur 2.806 and 2.825 A ˚ . The covalent bonds within the iodine molecule 3.720 A ˚ ˚ ). For comparison 2.796 and 2.797 A are considerably extended above the gas phase length (2.66 A ˚ and we note that in {(merocyanine)2I2} (d’Enghien-Peteau et al., 1968) d(I–I) ¼ 2.750(1) A ˚ . (Data from Herbstein, Ashkenazi, et al., 1986.) d(S . . . I) ¼ 3.098(5) A

n -D O N O R S A N D *-ACCEPTORS

707

which are salts, the polyiodines are composed of formally neutral entities. Two groups can be distinguished, both with a limited number of examples. In the ﬁrst group the interactions are weak and there is no polarization towards the formation of quasi-charged structures. The ﬁrst example to be reported (Herbstein et al., 1986) was the bis(diiodine) adduct of dithia[331]propellane (Fig. 11.13) which is associated into pairs of adducts across crystallographic centers of symmetry, as shown in FAJPUB. ˚ between adjacent centrosymmetrically related iodines is The distance of 3.720(1) A ˚ . The I–I . . . I angle is markedly less than the van der Waals separation of 4.2–4.3 A 154.2(1) so there is an appreciable deviation from linearity. The other intra-adduct S . . . I and I–I distances are normal (Table 11.6). Thus there is no resemblance to the well-known I2 4 ions (Herbstein et al., 1983). The similar adduct {I2dithia[332]propellaneI2} does not show analogous association in its crystals. (Herbstein et al., 1986). The molecular compound {bis(morpholinothiocarbonyl) bis(diiodine)} {[OC4H8NC(S)C(S)NC4H8O] (I2)2} (Atzei et al., 1988; GIGLOX) shows an intramolecular C¼S . . . I2 arrangement and ˚ ) similar to those found intermolecular I . . . I distances (3.705, 3.758, 3.931 and 3.746(3) A in {I2dithia[3.3.1]propellaneI2}. The second group is characterized by intra-adduct polarization towards an ionic, polyiodide-type structure, but without complete separation into the discrete ions of the true polyiodides. {Dithizone I2} (BZHTIC10) shows marked polarization towards the canonical form (dithizone . . . I)þ . . . I (Table 11.6) and {(ethylenethiourea) (I2)2} (CEWMIA) is polarized towards (ethylenethiourea . . . I)þ . . . (I3) (Herbstein and Schwotzer, 1984). There are three bridged structures with very similar overall geometries, where subtle differences in bond lengths show different degrees of participation of the polarized canonical forms in the overall resonance structure. The compounds R2(I2)3, where n n n

n n n

n n n

n n n

2.745

C

3.550 2.712

2.60

2,29bipyridyl

Tris(bisiodine)

B z x

A Ribbon of interacting moieties

Fig. 11.14. Crystal structure of {(2,2 0 -bipyridyl) (I2)3} projected down [010]. The crystallo˚ , ¼ 130.8 , C2/c, Z ¼ 4. The secondary graphic parameters are a ¼ 32.15, b ¼ 4.399, c ¼ 18.24 A interactions are shown by thin lines. (Data from Pohl, 1983.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

708

R ¼ triphenylphosphine sulphide (Schweikert and Meyers, 1968; Bransford and Meyers, 1978) or ethylenethiourea (Herbstein and Schwotzer, 1984; CEWMOG), are polarized þ 0 towards (R . . . I)þ . . . I2 4 . . . (I . . . R), while {(2,2 -bipyridyl) . . . (I2)3} (Pohl, 1983; CECZAL) (Fig. 11.14) shows essentially no polarization as the bond lengths in the I2 molecules are close to standard values. On the other hand, {(dithizone)2(I2)7} is strongly polarized towards (dithizone . . . I)þ . . . I5 . . . I2 . . . I5 . . . þ(I . . . dithizone) (Herbstein and Schwotzer, 1984; BZHTID20). Physical measurements on molecular compounds of the type discussed above

11.3.3

11.3.3.1 N and S containing donors and I2 as acceptor There have been a number of measurements by various physical techniques (principally Mo¨ssbauer (129I) and NQR (127I) spectroscopy and, to a lesser extent, Raman and IR spectroscopy) on some of the molecular compounds discussed earlier. Interpretation of the experimental results gives information about the interactions linking the components. Related compounds are treated together. These results are in excellent qualitative agreement with the known crystal structures; in {phenazine I2} the iodine molecules bridge between nitrogens of successive phenazines and there is one independent iodine atom in the asymmetric unit, while in both {HMT I2} and {dithiane (I2)2} there are two crystallographically independent iodine atoms in the asymmetric unit, one bridging (IB) and linked to N (or S) and the second terminal (IT); the I2 molecules are pendant in both structures. The (e2Qq)obs values for IB and IT in the two compounds of known structure are clearly different and there is similar differentiation for the other three molecular compounds. Thus one can infer that they also n n n

n n n

n n n

Table 11.10. Experimental results from 129I Mo¨ssbauer measurements. Where two results are given for a parameter, the first refers to the bridging iodine IB and the second to the terminal iodine IT Molecular compound

Quadrupole coupling constant e2Qq(129I) (MHz)

Asymmetry parameter (mm/s)

Isomer shift @

d(D IB) ˚) (A n n n

(a) Nitrogen-containing donors (measurements at 85K) (Ichiba, Sakai, Negita and Maeda, 1971) phenazine I2 2230 30 0.06 0.93(2) 2.982(5) acridine I2 2840 20 0.13 1.64(2) 1308 20 0.16 0.29(2) HMT I2 2582 20 0.19 1.51(2) 2.439(8) 1272 20 0.06 0.28(2) n n n

d(IB–IT) ˚) (A

2.726(1)

n n n

n n n

(b) Sulfur-containing donors (measurements at 16K) (Sakai et al., 1986) thiane I2 2513 13 0.02(4) 1.54(4) 1310 13 0.02(4) 0.32(4) 2512 13 0.04(4) 1.47(4) 1,4-oxathiane I2 1475 13 0.09(4) 0.43(4) 2526 13 0.02(4) 1.47(4) 2.867(2) 1,4-dithiane (I2)2 1553 13 0.06(4) 0.50(4)

2.830(1)

n n n

n n n

n n n

2.787(2)

n -D O N O R S A N D *-ACCEPTORS

709

Table 11.11. Bonding parameters derived from the experimental results summarised in Table 11.10 – hp is the number of p electron holes; Up is the number of unbalanced p electrons; Nx, Ny, Nz are the numbers of 5p electrons in these orbitals. Where two values are given for a parameter, the upper refers to IB and the lower to IT. The electron configuration is given as 5s2 5pt. The errors of hp, Nx, Ny, Nz are estimated (Ichiba et al., 1971) as 2% while those of Up are 1% Molecular compound

hp

(a) Nitrogen-containing donors 0.91 phenazine I2 1.45 acridine I2 0.55 HMT I2 1.37 0.55 n n n

n n n

n n n

Up

Nx

Ny

Nz

t

(Ichiba, Sakai, Negita and Maeda, 1971) 0.97 2.04 2.00 1.05 5.09 1.24 1.98 1.88 0.69 4.55 0.57 2.03 1.97 1.44 5.44 1.13 1.99 1.85 0.79 4.63 0.55 2.01 1.99 1.45 5.45

(b) Sulphur-containing donors (Sakai et al., 1986) thiane I2 1.39 1.10 1.91 0.57 0.57 2.00 1,4-oxathiane I2 1.34 1.10 1.94 0.65 0.63 2.01 1,4-dithiane (I2)2 1.34 1.10 1.93 0.69 0.68 2.01 n n n

n n n

n n n

2.10 2.00 2.03 2.10 2.09 2.02

0.80 1.43 0.82 1.36 0.82 1.32

4.81 5.43 4.86 5.40 4.84 5.35

Charge on IB/IT 0.09 þ0.45 0.44 þ0.37 0.45 þ0.19 0.43 þ0.14 0.40 þ0.16 0.35

have pendant I2 molecules (note that the spectrum of {acridine I2} contained two extra peaks that were not explained; the crystal structure is not known). One notes that the (e2Qq)obs values for IB are very similar and those for IT cover only a slightly larger range. This holds also for the isomer shift (@) values while the asymmetry parameters () are close to zero for the molecular compounds with S-donors but have appreciable nonzero values for the N-donors. 127I NQR measurements (Terao et al., 1985) on the three compounds in Part (b) of Table 11.10 (and {1,3,5-trithiane I2}) lead to similar, but less detailed, conclusions; it was inferred that {1,3,5-trithiane I2} had a bridged structure analogous to that of {phenazine I2}. The bonding parameters can be analyzed quantitatively and the results are shown in Table 11.11. There are major similarities among the various derived parameters, as must indeed be the case because of the similarities among the experimental results from which they are obtained. Thus we shall treat them as a whole without attempting to account for minor differences. The picture that emerges from the 5p electron populations is that the 5px and 5py lone pair orbitals are essentially completely ﬁlled for both IB and IT in all the molecular compounds and thus the bonding orbital in the I2 molecule is 5pz. In {phenazine I2} there is a charge transfer of 0.09 e from nitrogen to iodine; this charge enters the 5*pz antibonding orbital leading to a small increase in the I–I bond ˚ as compared to 2.66 A ˚ in the gas phase. The charge transfers for the length to 2.726 A pendant I2 molecules are larger and in consequence so are the changes in the bond lengths. n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

710

The approximate charge distributions can be written as follows (where D represents a donor atom such as N, O or S): +0.05 N

–0.05 I I

N

+0.2

Symmetrical diiodine binding to phenazine

D

+0.2 I

I –0.4

Unsymmetrical diiodine binding to a donor D such as N, O or S.

The weakening of the I–I bond is also shown by a decrease in the bond stretching constant which, in {1,4-dithiane (I2)2}, has been calculated as 158 cm1 from the far IR spectrum (Hendra and Sadavisan, 1965), to be compared with 213 cm1 in free I2 (Rosen et al., 1971). Theoretical analysis based on a four electron–three-center molecular orbital treatment can reproduce the experimental results with appropriate values of the Coulomb integral of donor atom D and the resonance integral of the D . . . I bond (Bowaker and Hacobian, 1969). n n n

11.3.3.2 S8 as donor and SnI4 molecules as acceptors {4S8 . . . SnI4}, {2S8 . . . SnI4} and SnI4 have been studied by 127I NQR spectroscopy and the latter also by 129I and 119Sn Mo¨ssbauer spectroscopy (Bukshpan and Herber, 1967). There is no evidence for phase transformations in any of these materials in the temperature range 77–301K. The coupling constants and asymmetry parameters are summarized in Table 11.12. There are two independent NQR resonances for {2S8 SnI4} and SnI4 and four for 4S8 . . . SnI4; this is in accord with the crystal structures of SnI4 and {2S8 SnI4} while that of {4S8 SnI4} is not known. The differences among the various 127I coupling constants are small and the values of the asymmetry parameter are all close to zero; hence the Sn–I bonding in all of them is very similar. Analysis of the Mo¨ssbauer data for both 119Sn and 129I in SnI4 (Ehrlich and Kaplan, 1969) indicates that the Sn–I bond has about 24% -character and that 5% s-hybridization is involved in the iodine -bonding orbital; the atoms in SnI4 are essentially neutral with charges of 0.015e on each of the iodines and þ0.060e on Sn. It seems reasonable to infer also from these measurements, as from the crystal structures, that I . . . I and S . . . I interactions are very weak and that the two molecular compounds would be better classiﬁed as packing complexes (Chapter 10). n n n

n n n

n n n

Table 11.12. Parameters derived from 127I NQR measurements, which were made over the temperature range 77–301K; 77K values are given here unless noted otherwise Compound SnI4 (301K) 2S8 SnI4 4S8 SnI4 n n n

n n n

(e2Qq)obs (Mhz) 1356.36 1383.03 1364.3; 1405.0

1363.28 1402.68 1368.3; (1)

0.008 0.002 0.0; 0.03

0.000 0.039 0.0; (1)

Notes: (1) as 2 was not observed, it was not possible to calculate values of (e2Qq)obs and for the fourth iodine. (2) the Mo¨ssbauer measurements for SnI4 give a positive sign for (e2Qq)obs; the values of the isomer shift are þ1.55 mm/sec for 119Sn compared to a SnO2 source and þ0.43 mm/sec for 129I compared to a ZnTe source.

n -D O N O R S A N D *-ACCEPTORS

711

11.3.3.3 S8 as donor and RI3 (R¼As, Sb) as acceptor: The NQR spectra of AsCl3, SbCl3, SbBr3 (noted below), AsI3, SbI3 and of the molecular compounds {3S8 . . . AsI3} and {3S8 . . . SbI3} were measured more than 40 years ago (Ogawa, 1958) and also studied in a complementary Zeeman investigation (Abe, 1958) for AsI3 and {3S8 . . . AsI3}. Later a comprehensive Mo¨ssbauer study was made of AsI3, SbI3, {3S8 . . . AsI3} and {3S8 . . . SbI3} and of BiI3 (Ogawa, 1958; Sakai, 1972). Pertinent experimental information is summarized in Table 11.13. Although the NQR measurements were made over the temperature range 300–77K we give only the 77K results; there is no evidence for phase changes in this range except, perhaps, for SbI3; 45K results are quoted here and we assume these refer to the trigonal polymorph. The Zeeman measurements were made at room temperature and the Mo¨ssbauer study carried out at 85K. The (e2Qq)obs values and asymmetry parameters for all the compounds in Table 11.13, except for SbI3, fall within the range of values found for the terminal iodines IT in the compounds discussed in Section 11.2.3.2. The electron conﬁgurations and a summary of relevant molecular dimensions are given in Table 11.14. We compare the conclusions drawn about the bonding from the physical measurements with changes found in bond lengths. In crystalline AsI3 there is additional -bonding due to transfer of 5py electrons ˚ from I. This charge transfer is at the expense of the from I to the As atom at 3.467 A covalent component of the As1–I bond, which has 54% covalent character, 36% ionic character and 10% (intermolecular) character. There is only a small increase in As–I ˚ ) between gas phase and crystalline AsI3. In 3S8 . . . AsI3 the As–I bond length (0.034 A bonding is 5pz with transfer of 0.33e from As to I, the bond being 67% covalent and 33% ionic. The secondary S . . . I interactions appear to have a negligible effect on the nature of the As–I bonding. The crystal structure of {3S8 . . . AsI3} is not known. Larger effects are found when trigonal SbI3 is compared with the gas phase, where there ˚ in d(Sb–I) over the gas-phase value. However, the values is an increase of 0.15 A ˚ . The effects of of d(Sb–I) for the gas phase and monoclinic SbI3 differ by only 0.05 A secondary interactions in the sulphur molecular compounds are smaller as is shown in {3S8 . . . SbI3}, where the Sb–I bond now has 9% -character, and the increase in length Table 11.13. Summary of parameters derived from NQR and Mo¨ssbauer measurements (temperatures are 77K for NQR and 85K for Mo¨ssbauer measurements, except where stated otherwise) Compound

75

As/121Sb (e2Qq)obs (MHz)

127

I (e2Qq)obs (MHz)

@ (mm/sec)

AsI3 3S8 AsI3 SbI3 (at 45K) 3S8 SbI3

58.676(10) 99.002(10) 169.37 251.8 (250K)

1330.23–1350 1516.86–1544 895.83–911 1226.25–1209

0.1891 0.20 0.007 < 0.05 0.565 0.57 0.03 0.11

0.57 0.47 0.54 0.49

n n n

n n n

Notes: (1) The (e2Qq)obs values from the 129I Mo¨ssbauer measurements have been converted to the 127I scale for comparison with the NQR measurements. The limits of error are given as 20MHz, while for and @ the limits of error are 0.05. (2) As 75As and 121Sb have nuclear spin 3/2, the values of (e2Qq)obs and cannot be determined separately. We follow Ogawa (1958) and assume, because of the crystal structure, that ¼ 0; then (e2Qq)obs ¼ 2 meas. (3) @, the isomer shift, is given with respect to a ZnTe source.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

712

Table 11.14. Electron configurations in iodine of RI3 as deduced from NQR and Mo¨ssbauer measurements, together with a summary of relevant molecular dimensions in different environments; ˚ , angles in degrees distances in A Compound

hp

Up

Nx

Ny

Nz

t(1)

d(R–I); ˚) [d(R I)] (A References

< I–R–I

Crystal (EG80) 2.591(1) [3.467(2)] gas (M66) 2.557(5) Crystal structure not reported. gas (AB63) 2.719(2) Trigonal crystal (TZ66) 2.87(1); [3.32] Monoclinic crystal (PS84) 2.754(3), 2.768, 2.774 [3.540, 3.605, 3.880] Crystal (BHL63) 2.747(2); [3.85]

99.67(5)

n n n

AsI3

0.74

0.59

1.99

1.91

1.36

5.26

{3S8 AsI3}

0.67

0.66

2.00

2.00

1.33

5.38

SbI3

0.72

0.39

1.96

1.82

1.50

5.28

0.69

0.53

1.95

1.94

1.42

5.31

n n n

{3S8 SbI3} n n n

99.1 95.8(3) 95.1(1) 96.6(1) 100.2(1)

96.56(4)

Notes: (1) The electron conﬁguration is given as 5s2 5pt References: AB63 – Almenningen and Bjorvatten, 1963; BHL63 – Bjorvatten, Hassel and Lindheim, 1963; EG80 – Enjalbert and Galy, 1980; M66 – Morino et al., 1966; TZ66 – Trotter and Zobel, 1966; PS84 – Pohl and Saak, 1984.

˚ ) over the gas-phase value is small. The Sb–I bond in crystalline SbI3 has been (0.028 A estimated to have 36% covalent character, 42% ionic character and 22% character, but it is not clear which polymorph was used for the measurements (Pohl and Saak (1981) quote Cooke (1877/8) as reporting that monoclinic SbI3 transforms into trigonal at 367K, suggesting that monoclinic, although rarer, is the stable phase at lower temperatures). Repetition of these studies using current techniques will surely yield information of much interest. 11.3.4

Halogenated molecules as donors and dihalogens as acceptors

The phase diagrams of a number of systems containing Cl2 and various halogeno-methanes (CCl4, CHCl3, CH2Cl2, CH3Cl) have been determined from freezing-point measurements (Wheat and Browne, 1936, 1938, 1940a, b). The binary compounds found are listed in Table 11.15. The HCl–Cl2 system shows a 2 : 1 (m.pt. 121 ) and a 1 : 1(115 ) compound. No compounds were found in the CHCl3–Br2 system, which is a simple eutectic. No structures are known; it was suggested that the halogenomethanes act as donors and the Cl2 molecules as acceptors. This seems reasonable as all the evidence summarized in this

n -D O N O R S A N D *-ACCEPTORS

713

Table 11.15. Reported compositions and melting points ( C) in various halogenomethane – Cl2 systems Halogenomethane

Ratio halogenomethane : Cl2

Reference

2:1

1:1

1:2

1:3

CCl4

67

90.5

112.5

115.5

CHCl3 CH2Cl2 CH3Cl

80 – –

96.5 124.5 –

112.5 126.5 120

115 117.5 122

Wheat and Browne, 1938. idem, 1936 idem, 1940a idem, 1940b.

chapter indicates that Cl2 is a stronger acceptor than the chloromethanes. However, these results should perhaps be viewed with some caution as it has been reported that the CCl4– Cl2 system has only an eutectic at 114.4 (Abassalti and Michaud, 1975). 11.3.5 Self-complexes – N, O, S, Se to halogen interactions in one-component systems Interactions similar to those important in the formation of n–* charge-transfer compounds in binary systems also operate in many one-component (unary) crystals, which can then be described as ‘self-complexes’ (there are also ‘self-complexes’ in –* systems, which are discussed later); according to our convention, these should be called ‘selfcompounds’ but we defer here to common usage. Two excellent reviews are noted; Bent (1968) has discussed and compared donor–acceptor interactions in both unary and binary systems, while Alcock (1972) has concentrated on unary systems. Our discussion will be illustrative rather than comprehensive, and will be organized in terms of the donor-acceptor atom pairs involved in the secondary bonding. 11.3.5.1

Nitrogen . . . halogen interactions

In molecular compounds with nitrogen halogen interactions, the nitrogen is found in cyano groups or as the heteroatom in, for example, pyridine and hexamethylenetetramine. Similar combinations occur in self-complexes. The cyanogen halides (ClCN (Heiart and Carpenter, 1956), BrCN (Geller and Schawlow, 1955), ICN (Ketelaar and Zwartsenberg, 1939) and halocyanoacetylenes (XC C–C N; X¼Cl, Br (Bjorvatten, 1968), I (Borgen et al., 1962)) have been studied crystallographically, but with varying degrees of completeness. All can be represented as rod-like molecules and it is not surprising that all should be arranged in their crystals as arrays of exactly or approximately close-packed cylinders. In ClCN, BrCN and the three halocyanoacetylenes, alternate rows of molecules are antiparallel and the crystals are nonpolar; cyanogen iodide and a low-temperature form of iodocyanoacetylene are reported to form polar arrays, but more detailed study seems desirable in both examples. For all these molecules there is head-to-tail packing within the rows and all N X distances (Table 11.16) are less than the sums of the appropriate van der Waals distances. The strength of the N X interaction increases as X changes from Cl through Br to I; this also happens among the molecular compounds. The shortening has been attributed to electrostatic interactions but the more generally accepted view is that n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

714

˚ ) in cyanogen halides and halogenoacetylenes with Table 11.16. Comparison of N X distances (A sums of van der Waals radii n n n

Compound

X¼Cl

X¼Br

X¼I

Cyanogen halides X–C N Halocyanoacetylenes X–C C-C N Sum of vdW radii of N and X

3.01(1) 2.983(8) 3.33

2.87 (estimated) 2.98(2) 3.43

Not measured 2.93 3.93

there is partial charge transfer from N to halogen. In the crystals of N, N 0 -dibromoethanediimidoyl diﬂuoride there are also rather strong, essentially linear N-Br N interactions ˚ , with < N-Br N ¼ 171.1, 174.6 ) (Waterfeld et al., (d(N . . . Br) ¼ 2.863(7), 2.891(6) A 1983; BONFIT). Similar but weaker interactions are found in other crystals. Although full structures have not been reported for 2,4,6-tri-(p-chlorophenyl)-s–triazine (Belitskus and Jeffrey, 1965) and cyanuric chloride (Hoppe et al., 1957), the overall arrangements in both crystals are such that linear C N Cl–C arrangements appear probable for all three such groupings in each molecule. 2,4,6-Trichloro-1,3,5-tricyanobenzene (space group P212121, Z ¼ 4) (Britton, 1981; BAFJOH) is not isomorphous with cyanuric chloride and there is ˚ ), with a a linear arrangement only for one C N Cl–C grouping (d(N Cl)¼ 3.03 A much weaker interaction for a second such grouping and no interaction for the third potential donor–acceptor pair. Linear C N Cl–C arrangements have also been found in 2,4,6-trichloro- (CLBECN01) and tribromobenzonitrile (BRBZNT; Carter and Britton, 1972) which have similar but not isomorphous structures. Pairs of molecules are formed in trichlorobenzonitrile with each C N and ortho-Cl coordinated to the corresponding ˚ ] with an arrangement reminiscent of groups of an adjacent molecule [d(N Cl) ¼ 3.22 A that found in carboxylic acid dimers. In tribromobenzonitrile polymeric chains are formed, each N being coordinated to two Br atoms related by a mirror plane ˚ ] and the C N X angle is about 120 instead of the linear [d(N . . . Br) ¼ 3.06 A arrangement found in the cyanogen halides. ClC(C N)3 is isomorphous with the methyl analog and there are no close approaches (Witt et al., 1972). Among other crystals with appropriate N X approaches (Britton, 1967) are p-chlorobenzonitrile (Britton et al., 1979; CLBZNT) and p bromobenzonitrile (Britton et al., 1977; BRBNIT) (which are not isomorphous but have related structures), 9-dicyanomethylene-2,7-dibromoﬂuorene (Silverman et al., 1973; CYBFME20) and 1,4-dimethoxy-2,3-dicyano-5,6-dichlorobenzene (Reddy, Panneerselvam et al., 1993; LAGMOV). n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

11.3.5.2

Oxygen halogen interactions n n n

As with N X interactions, the order of increasing strength for O X interactions is Cl < Br < I; no O F interaction is found in the only relevant ﬂuorinated compound (2,3-diﬂuoro-1,4-naphthoquinone) (Gaultier et al., 1972; DFNAPQ) studied to date. Some typical O X distances are given in Table 11.17. A systematic and extended study of the secondary bonding in crystalline halogenated quinones (benzoquinones, naphthoquinones and anthraquinones) has been carried out, mainly by the Bordeaux school (Gaultier et al., 1971a); the structural arrangement in n n n

n n n

n n n

n n n

n -D O N O R S A N D *-ACCEPTORS

715

a

3.22

3.15

c

Fig. 11.15. Schematic diagram showing the O Br interactions in the crystals of 2,3-dibromo-1,4naphthoquinone; Br diagonally hatched, O small dark circles. (Reproduced from Breton-Lacombe, 1967.)

12

0

n n n

5 13

O, N u 150

C

Br

165

u (deg.)

1.60

2.40

180 4.00

3.20 r (Å)

Fig. 11.16. Polar scatter plot (r vs. ) for the nucleophiles O or N around Br. The average value of

for these contacts are 158(13) for Cl, 162(12) for Br and 165(8) for I. The crowding around 162 is especially pronounced for Br. (Reproduced from Ramasubbhu et al., 1986.)

2,3-dibromo-1,4-naphthoquinone (Breton-Lacombe, 1967; DBRNPQ10) is shown as an example in Fig. 11.15. Halogenated benzoquinones and naphthoquinones generally show O X interactions but the distances suggest that these are comparatively weak; thus it is not surprising that they do not appear when the structural arrangement is determined by hydrogen n n n

716

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

˚ ) in unary crystals Table 11.17. Some typical oxygen halogen approach distances (A n n n

Compound/refcode

Compound d(O X)

d(O X)

n n n

Type of approach: O I -HIO3; RH41 n n n

n n n

Type of approach: O Cl N-chlorosuccinimide# CSUCIM; B61 -N-(p-tolyl)-tetrachlorophthalimide TOCPIM11; HK81 -N-(p- tolyl)tetrachlorophthalimide; TOCPIM; K78 2,3,4,4-tetrachloro-1oxodihydronaphthalene (h); VM71 3-chloro-1,2naphthoquinone; CLNAPQ; C70 n n n

N,N-diiodoformamide IFORAM; P74b

2.45, 2.70, 2.95 2.565(7); 3.13(1)

N-iodosuccinimide; P90

2.580(6)

p-chloro-iodoxy-benzene; CIOBEN; A48

2.72; 2.87

KIO2F2; RH40

2.82; 2.88

3-iodo-1,4-naphthoquinone; INAPQU; GHHS71b

3.21

Type of approach: O Br 3-methoxy-5,19-cyclo-5,10secoandrosta-1(10),2,4-trien17-ol-p-bromobenzoate; CSANDR; HC68 POBr3*; OM69 oxalyl bromide (m.pt. 19.5 C) **; OXALYB; GH62 3-bromo-1,4-naphthoquinone BRNAPQ; GaHa65

2.88 2.91(1)

2.98(1)

2.973

3.22

n n n

2.93

3.08; 3.27

3.11

# N-bromosuccinimide is isomorphous * POCl3 is isomorphous ** Oxalyl chloride is not isomorphous and there are no close O Cl approaches in its crystals. n n n

References: A48 – Archer, 1948; B61 – Brown, 1961; C70 – Courseille et al., 1970; GAHA65 – Gaultier and Hauw, 1965; GH62 – Groth and Hassel, 1962; HHS71 – Gaultier, Hauw, Housty and Schvoerer, 1971; HC68 – Hope and Christensen, 1968; HK81 – Herbstein and Kaftory, 1981; K78 – Kaftory, 1978; OM69 – Olie and Mijlhoff, 1969;

bonding, as happens, for example, in 4-amino-3-bromo-1,2-naphthoquinone (Bechtel et al., 1976; BANAQP10). O X interactions have not been found among the halogenated anthraquinones. In the benzoquinone and naphthoquinone series the angle O X–C does not deviate from 180 by more than about 20 , but < C¼O X lies between 120 and 180 . Polar scatter plots of Y . . . X-C interactions (where Y is the nucleophile O or N and X is Cl, Br or I) have been presented, using the Cambridge Structural Dataﬁle as database (Ramasubbu et al., 1986); 332 Cl . . . (O, N) entries were used, 397 Br . . . (O, N) and n n n

n n n

n n n

n-DONORS AND p-ACCEPTORS

717

60 I . . . (O, N). The shorter distances, i.e. those relevant to self-complexation, are found in the region of head-on approaches (Fig. 11.16, which shows C–Br . . . (O, N) interactions, those for Cl and I being qualitatively similar). Using the same methodology, it was shown that the distribution of halogens around a carbonyl oxygen ranges from 75 to 180 , but is concentrated in the 105–140 region (especially the shorter approaches) and agrees well with an angular distribution representative of the lone pair(s) in a conventional sp2 orbital diagram.

11.4 n-Donors and p-acceptors 11.4.1 N, O or S containing ligands as donors and Group VA metal halides as acceptors Earlier work on the binary adducts of MXn [M¼Al, Ga (n ¼ 3); Ti (n ¼ 4); P, As, Sb (n ¼ 5); X¼F, Cl, Br] has been summarized by Lindqvist (1963) while the Group V adducts have also been discussed by Webster (1966). In the group of compounds of present interest only an organic ligand, such as nitrobenzene or benzoyl chloride, and metal halide are present in the adduct. A second group contains HX as well but will not concern us here because these are salts. (a) Some preparative studies of molecular compounds of AlCl3 A common experimental problem in the study of these materials is their sensitivity to moisture (‘‘even more readily hydrolyzed than AlCl3 [itself],’’ according to Jones and Ward (1966); however, they are generally well-crystallized and thermodynamically stable if adequate precautions are taken to work under dry conditions. The earliest systematic studies appear to be those of Menschutkin before the First World War (see Thomas (1941) and Olah (1973) for summaries). Phase diagrams were determined and congruently melting 1 : 1 compounds obtained of AlCl3 and AlBr3 with, severally, nitrobenzene, benzoyl chloride, benzophenone (needles up to 8 cm long were reported for C6H5COC6H5 AlCl3! (Menschutkin, 1910)) and the various isomers of XC6H4NO2 (X ¼ halogen). Later work showed that 2[C6H5NO2] AlCl3 could also be prepared. Among other crystalline compounds are 2CH3CN AlCl3, 2POCl3 AlCl3, POCl3 AlCl3 and (perhaps) 6POCl3 AlCl3 (Groeneveld and Zuur, 1958). Other ligands that have been reported to form 1 : 1 molecular compounds with AlCl3 include acetone, diethyl ketone and nitromethane (Jones andWard, 1966). Preliminary single-crystal X-ray diffraction and polarized infrared absorption studies were made of a number of compounds in this group (Gagnaux and Susz, 1961) and many crystal structures have now been reported. (b) Preparative studies of molecular compounds of Group VA halides Many compounds of oxygen-containing molecules with SbCl5 have been reported (Meerwein and Maier-Hu¨ser, 1932); among those crystallizing above room temperature are (diethyl ether) SbCl5; dioxane 2SbCl5; dimethylpyrone SbCl5; acetyl chloride SbCl5; and 2(benzoyl chloride)dimethylpyrone 2SbCl5 (prepared by adding benzoyl chloride to the dimethylpyrone SbCl5 molecular compound). (c) Structural studies of molecular compounds of Group III and V halides There are two quite distinct structural types: ionic crystals without any special interaction between cation and anion other than ionic, and molecular compounds where the donor is n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

718

linked to the acceptor by an oxygen-metal bond of varying strength. Le Carpentier and Weiss (1972c) have suggested that an equilibrium is set up between molecular and ionic moieties in solution, as illustrated here for an acyl chloride and AlCl3: RCOCI þ AlCl3 () RCOþ þ AlCl 4 This equilibrium is a consequence of the bifunctionality of the acyl chloride, which has both an ionizable chlorine and an oxygen atom with a lone pair which can complete the outer electron shell of a metallic acceptor. The validity of this proposal has been strikingly demonstrated by the determination of the crystal structures of donor–acceptor and ionic forms of the adducts between p-toluoyl chloride and SbCl5 (Chevrier et al., 1972a). The molecular compound was crystallized from CCl4 and the salt from the more polar CHCl3; the two materials were interconvertible by recrystallization from the appropriate solvent. An analogous inﬂuence of solvent polarity occurs among the –* molecular compounds (see Chapter 17). Presumably ligands without ionizable groups can form only molecular compounds, although a relevant example has not been reported. It is convenient also to list some of the ionic structures that have been determined (Le Carpentier and Weiss, 1972a, b) although they will not be discussed further here: þ [CH3CO]þSbX 6 (X ¼ F,Cl); [CH3CO] AlCl4 (Ga analog isomorphous) (Le Carpentier þ and Weiss, 1972a); [CH3CH2CO] GACl4 , [(CH3)2CHCO]þSbCl 6 (Le Carpentier and (MPOCCA; Chevrier, Le Carpentier and Weiss Weiss, 1972b); [o-CH3C6H4CO]þSbCl 6 (MPOCSB; Chevrier, Le Carpentier and Weiss (1972c)). [p-CH3C6H4CO]þSbCl 6 (1972d)). The structures of a number of AlCl3 and SbCl5 molecular compounds are known (Le Carpentier and Weiss, 1972c, d; Chevrier, Le Carpentier and Weiss, 1972a, b) all of which can be represented schematically as Cl Cl R

Cl

Cl

C

Sb Cl

MCln

O

O

M = Al (n = 3), Sb (n = 5)

Cl R

Values of d(O M) and C¼O M are summarized in Tables 11.18 and 11.19. In the ˚ and the AlCl3 molecular compounds values of d(O Al) lie in the range 1.830.02 A angle at O has a range of 4–5 about a mean of 143 the coordination about Al is distorted ˚ so the interaction in these tetrahedral. In minerals the Al O distance is about 1.79 A molecular compounds is relatively strong. The Sb O distances in the SbCl5 molecular ˚ , although the >C¼O Sb angle is rather constant compounds range over about 0.5 A around 145 , except for the dimethylformamide compound, where a lengthening of ˚ has been reported (Brun and Branden, 1962). In all these compounds d(C¼O) to 1.30 A there is a square pyramid of Cl about Sb, with the octahedron completed by the oxygen of the donor moiety. A similar geometry is found in S4N4 SbCl5, which has d(Sb N) ¼ ˚ (Neubauer and Weiss, 1960). 2.17 A The molecular compound 1,4-dioxane 2[Al(CH3)3] is an analogous example; it has overall symmetry C2h-2/m, with dioxane in the chair form (Atwood and Stucky, 1968; n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n-DONORS AND p-ACCEPTORS

719

Table 11.18. Geometrical parameters for various 1:1 AlCl3 and SbCl5 molecular compounds. ˚ , angles in degrees Distances in A Molecular compound

d(Al O)

< Al O¼C

Molecular compound

1.847(6)

141.6

1.835(2)

138.3

1.828(2)

146.6

n n n

CH3CH2COCl AlCl3 PROPAL m-CH3C6H4COCl AlCl3 ALCMTU p-CH3C6H4COCl AlCl3 ALTPCU o-CH3C6H4COCl AlCl3 ALCOTU C5H4COCl AlCl3 n n n

n n n

d(Sb O)

<Sb O¼C

ClCO(CH2)2COCl 2(SbCl5) SUCCSB C6H5COCl SbCl5

2.428

143.6

2.317

145.9

m-CH3C6H4COCl SbCl5

2.295

144.7

2.253

146.6

n n n

n n n

n n n

n n n

n n n

n n n

n n n

1.824(4)

146.2

p-CH3C6H4-COCl SbCl5 TOLCSB

1.819(5)

141.7

Cl3PO SbCl5a

2.17

145

(CH3)3PO SbCl5a HCON(CH3)2 SbCl5b (C6H5)2SO SbCl5c

1.94 2.05

145 124.5

–

–

n n n

n n n

n n n

n n n

n n n

n n n

n n n

Notes: a ˚ , < Nb O¼C ¼ 149 ; these two compounds are isomorphous with Cl3PO NbCl5, where d(Nb O) ¼ 2.16 A however, it should be noted that the interactions differ because Nb is a transition metal. b N, N-dimethylformamide. c Hannson and Va¨nngaed, 1961. n n n

n n n

n n n

TMALOX) and the two Al(CH3)3 groups linked equatorially to the oxygens of the ˚ ); there is also an incompletely studied orthorhombic dioxane (d(Al O) ¼ 2.02 A polymorph. (d) SnCl4 as an acceptor The older literature contains reports of the formation of molecular compounds between various aromatic hydrocarbons or quinones and SnCl4 and/or SbCl5. The products vary considerably in stability and crystallinity; indeed many are perhaps best described as ‘‘ill-deﬁned.’’ 2,3,10,11-Dibenzoperylene was reported to form crystalline 1 : 1 adducts with both SnCl4 and SbCl5, and 2,3-dibenzoanthraquinone forms ‘glittering violet needles’ with SbCl5 (composition 1 : 2) (Brass and Fanta, 1936). These, and perhaps other examples (Brass and Tengler, 1931a, b), may repay further study but no one seems yet to have taken up the gauntlet. Cyclohexanol forms 2 : 1 and 4 : 1 adducts with SnCl4. The crystal structure of the 4 : 1 adduct has been reported (Fournet and Theobald, 1981); there are [cyclohexanol SnCl4 cyclohexanol] molecular groupings linked to cyclohexanols of crystallization by OH O and OH Cl hydrogen bonds. The Sn atoms are at crystallographic centres of symmetry and the ﬁrst coordination shell about Sn has approximately D4h symmetry. Presumably the same molecular grouping occurs in the 2 : 1 adduct, but without ‘cyclohexanols of crystallization.’ n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

720

Mo¨ssbauer effect studies have been made (using 119Sn) of some molecular compounds of aliphatics with SnCl4 (Ichiba et al., 1968). There is little evidence for charge transfer. (e) AsI3, SbCl3 and SbI3 as acceptors The structures of {1,4-dithiane SbCl3} (Kiel and Engler, 1974; P212121, Z ¼ 4; DTANSC) and {1,4-dithiane 2SbI3} (Bjorvatten, 1966; SBIDTH) (have points of resemblance – there are weak Sb . . . S interactions in both, with considerably weaker secondary Sb . . . X interactions. There is also a 1 : 1 compound but its structure was not reported. Kiel and Engler described the {1,4-dithiane SbCl3} structure as built up by molecules of SbCl3 and S2C4H8, and these are arranged in chains along [100] (Fig. 11.17). The SbCl3 molecules have their usual pyramidal shape and the dithianes have a chair ˚ . Each Sb is conformation. The covalent Sb–Cl distances are 2.385, 2.419 and 2.438 A linked to two different sulphurs (3.065, 3.135 A). There are no other Sb . . . S limks shorter ˚ . The crystals are chiral. than 3.5 A The space group of {1,4-dithiane 2SbI3} is C2/c with Z ¼ 4; the dithiane molecules are chair-shaped and at centres of symmetry, and the SbI3 molecules at general positions (Fig. 11.18). Each Sb forms donor–acceptor links with two sulphurs of different dithiane ˚ ). Thus the coordination about Sb can be molecules (d(S Sb) ¼ 3.274(7) and 3.336(6) A ˚ ) and described as square pyramidal (three covalent Sb–I bonds (2.746, 2.767 and 2.774 A two S Sb links (3.275 and 3.337 A) or as distorted octahedral if the probable location of the lone pair is assumed to be opposite the axial covalent Sb–I bond. Each S forms two links to different Sb atoms, one in the equatorial and one in the axial direction. The Sb . . . S distances are similar to those in DTCHAC (Fig. 11.19). There are no short Sb . . . I ˚ between a sulphur and an iodine atom. interactions although there is a distance of 3.73 A Thus the overall arrangement has chains along the [110] and [110] directions in the crystal. n n n

n n n

n n n

n n n

n n n

n n n

eq Sb...S 3.065

Axial Sb...S 3.135

0

A

SbCl3

1,4-dithiane B z

x

y

Fig. 11.17. Crystal structure of {1,4-dithiane SbC13} showing the chain arrangement of moieties connected by secondary Sb . . . S interactions. (Data from Kiel and Engler, 1974.) n n n

n-DONORS AND p-ACCEPTORS

721

0 C

d(Sb–1)= 2.747, 2.767, 2.774Å d(Sb...S)= 3.275, 3.337Å

SbI3 A

1,4-dithiane B

z x

y

Fig. 11.18. The {1,4-dithiane 2SbI3} structure viewed approximately down [001] and showing the layer structure. The chains along {110] are shown in the ﬁgure. There are only van der Waals interactions between adjacent layers. (Data from Bjorvatten, 1996.) n n n

1,4-dithiacycloheptane

2.395

SbCl3 3.229

d(Sb–Cl) = 2.357, 2.395, 2.400 Å d(Sb...S) = 3.129, 3.229, 3.406 Å

3.406

z

x y

Fig. 11.19. {1,4-DithiacycloheptaneSbCl3} showing a two-dimensional layer in the bc plane. One notes that a rhombus is formed by equatorial S(2) . . . Sb secondary links to a pair of Sb atoms (3.129 ˚ ), while S1 forms an axial linkage to Sb (indicated by 3.229 A ˚ in the (not shown) and 3.406 A ˚ . (Data from Schmidt et al., 1979.) diagram). A typical covalent Sb–Cl bond is shown by 2.395 A

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

722

{1,4-DithiacycloheptaneSbCl3; DTCHAC} crystallizes in space group P21/c (Z ¼ 4); the molecules of the two components are linked by secondary Sb . . . S interactions. There are no secondary Sb . . . Cl interactions. Two dimensional slabs are formed of thickness a (Fig. 11.19). There are only van der Waals forces normal to the slabs. There is approximately octahedral coordination about Sb, with three covalent Sb–Cl bonds and three secondary Sb . . . S interactions, two from S2 and one from S1{1,4Dithiacycloheptane2SbI3} has also been reported but its structure is not known (DTANSC; Schmidt et al., 1979). {1,3,5-TrithianeSbX3} (X¼Cl, TRTHAC; Br TRTHAB; the crystals are isomorphous) is another example of a molecular compound stabilized by weak S . . . Sb interactions ˚ , space group P63mc (Fig. 11.20). The crystals are hexagonal (8.129(4) 9.141(1) A (no. 186), Z ¼ 2 for the Cl compound) (Lindemann et al., 1977). Changes in dimensions of the component molecules are not discernible but consequences of the interaction are shown by changes in the Raman spectrum (from 1000 cm 1) and the far IR spectrum 2A

O

3.26 Å

2B x z y

Fig. 11.20. Projection of {trithianeSbCl3} down the hexagonal c axis. This is a layer structure, with the trithiane molecules superimposed in columns (two, mutually rotated, are shown in the center of the diagram). The structure is polar, with the pyramidal SbCl3 molecules oriented with the Sb atoms ˚ is shown in the diagram; below the plane of the three chlorines. The Sb . . . S interaction of 3.26 A symmetry-related interactions are not shown for clarity. (Data from Lindemann et al., 1977.)

n -D O N O R S A N D *-ACCEPTORS

723

(from 400 cm1) (Schmidt et al., 1977). The adduct shows a general shift (to higher wave numbers) of Raman frequencies by 5–20 cm1, accompanied by a reduction in the number of absorptions; both effects were ascribed to the higher symmetry (hexagonal) of the adduct compared to trithiane (orthorhombic). 1,3,5,7-Tetramethyl-2,4,6,8,9,10-hexathia-adamantane (THA) forms molecular compounds with AsI3 – yellow crystals (m.pt. 109 ) of unreported composition and orange-red crystals of 1 : 1 composition whose structure has been reported (P21/c, Z ¼ 4; Kniep and Reski, 1982; BIBFOH). The coordination polyhedron of AsI3 is distorted octahedral with ˚ ); the As lone contacts to three of the six S atoms of THA (d(S As) ¼ 3.274 to 3.310 A pair is assumed to be directed towards the six-membered ring containing the linked sulphurs. There do not appear to be any close As I interactions. There are alternating layers of THA and AsI3 molecules parallel to the (100) planes. n n n

n n n

11.5 n-Donors and *-acceptors There are a number of molecular compounds with localized interactions between donor and acceptor moieties where the interaction appears to be of the n * type – among these are the 2 : 1 compounds of 9,10-diazaphenanthrene with 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) (Shaanan et al., 1982) and tetracyanoethylene (TCNE) (Shmueli and Majorzik, 1980), and the 1 : 2 compounds of TCNE with 2,3-diazabicyclo[2.2.2]octene (DBO) (Blackstock and Kochi, 1987), and DBO-oxide and DBO-dioxide ( Blackstock, Poehling and Greer, 1995). The ﬁrst two molecular compounds are isostructural but not isomorphous and are characterized by mutually perpendicular arrangements of the planes of donor and acceptor molecules. The structure of (9,10-diazaphenanthrene)2 DDQ (red monoclinic crystals; ZPHCYQ10) is shown in Fig. 11.21; the arrangement in the donor layer is remarkably similar to that found in 9,10-diazaphenanthrene itself (Van der Meer, 1972) and thus this is a mimetic molecular compound in which there is a resemblance between the structure of one of the components and that of the molecular compound (cf. Section 10.1). The interaction between the two types of layer is due to localized charge transfer of lone pair electrons from the nitrogens of the 9,10-diazaphenanthrene to acceptor * orbitals of DDQ or TCNE molecules. ˚ , 67.05(5) The crystal structure (triclinic, P 1, Z ¼ 1; 6.676(2) 8.670(2) 9.355(2) A 75.40(3) 69.84(4) ) of the dark red-brown 2 : 1 compound of 2,3-diazabicyclo[2.2.2]octene (DBO) with TCNE (Blackstock and Kochi, 1987; FEJDUT) contains discrete packing units of the formula given (Fig. 11.22). The TCNE acceptor is sandwiched between the azo groups of the azo-alkane in a manner very similar to that found for DDQ with the aromatic donor 9,10-diazaphenanthrene (compare Figs. 11.21 and 11.22). Blackstock et al. (1995) further show that the N-oxide and N,N 0 -dioxide of DBO associate with TCNE in solution (CH3CN, charge-transfer bands in the UV-vis spectra peaking at 330 and 472 nm respectively), while the crystals of (DBO-oxide)2TCNE (ZAGKOH) and (DBO-dioxide)2. TCNE (ZAGKUN) have ‘‘D . . . A . . . D sandwich structures [similar to those of (DBO)2.TCNE] in which the topology of the D . . . A . . . D interaction is effectively described as a pericyclic array, with local D . . . A cycles apparently inﬂuencing the geometry of the non-covalent interactions in the solid state.’’ n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

724

C

Shortest aza-N to DDQ-C distances are 2.85 Å.

Cl

N O

O

z

A y x

Fig. 11.21. Crystal structure of {(9,10-diazaphenanthrene)2 DDQ} showing the termolecular packing unit consisting of a DDQ molecule sandwiched between 9,10-diazaphenanthrene molecules. The planes of the two moieties are almost mutually perpendicular. These packing units are arranged in herringbone fashion in the crystal. (Data from Shaanan et al., 1982.) n n n

The 9,10-diazaphenanthrene – TCNE system is noteworthy in that two types of 2 : 1 molecular compound are formed, triclinic and monoclinic. This is an example of an isomeric molecular compound where there are polymorphic forms of the same chemical composition but these have different structures (see Section 15.11; Herbstein, 2000). In the triclinic polymorph there is localized charge transfer of lone pair electrons from the nitrogens of the 9,10-diazaphenanthrene to acceptor * orbitals of TCNE, while there is delocalized * charge transfer in the monoclinic polymorph. Another possible additional example is triethylphosphate benzotrifurazan (Cameron and Prout, 1972; BTFZEP10), where mixed stacks of the two moieties along [100] are found (Figs. 11.23 and 11.24). The oxygen atom of the phosphoryl group (O(1)) is only ˚ from the plane of the central ring of the benzotrifurazan molecule and 2.88 A ˚, 2.51 A on the average, from the six carbons of this ring; the average value of
n n n

n -D O N O R S A N D *-ACCEPTORS

725

N

2.964 N 2.883

y z

x

2,3-diazabicyclo[2.2.2]octene

2,3-diazabicyclo[2.2.2]octene

TCNE

Fig. 11.22. The termolecular centrosymmetric packing unit of formula (2,3-diazabicyclo [2.2.2]octene)2 TCNE shown with the TCNE acceptor sandwiched between the nitrogens ˚ are shown. (Data from (darkened circles) of two donor molecules. C . . . N distances less than 3 A Blackstock and Kochi, 1987.) n n n

O C

A

P

N

Mixed benztrifurazan/ triethylphosphate stack

B

z

x y

Fig. 11.23. The crystal structure of triethylphosphate benzotrifurazan at 153K; the crystal data are ˚ , ¼ 107.0 , Z ¼ 2, space group P21, with the [001] axis unique. The 7.70(2) 8.87(2) 13.13(2) A structure is seen in projection down [100], showing close packing of the mixed stacks. The P and O atoms of the triethylphosphate are superimposed. (Data from Cameron and Prout, 1972.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

726

Benztrifurazan O

Triethylphosphate

A

P C

B

x z

y

Fig. 11.24. The crystal structure of triethylphosphate benzotrifurazan at 153K. The mixed stacks of alternating triethylphosphate and benzotrifurazan moieties are shown; the polar nature of the individual stacks is evident. (Data from Cameron and Prout, 1972.) n n n

Fig. 11.25. Stereoview of the ‘‘dimeric’’ packing unit seen along a vector perpendicular to the ˚ . Nitrogens of phenazine emphasized. plane of a phenazine molecule. d(N . . . H–N) ¼ 3.115(2) A (Reproduced from Stezowski et al., 1983.)

The phosphoryl oxygen could be considered as n-donor and the benzotrifurazan molecule as *-acceptor. However, there is no charge transfer absorption band in the solution spectrum of the two components and Cameron and Prout (1972) preferred to classify this molecular compound as polarization bonded with important dipole–dipole interactions; the O . . . ring interactions are then perhaps similar to those found in crystals such

-DONORS AND *-ACCEPT ORS

727

as alloxan (ALOXAN to ALOXAN13), barbituric acid (BARBAC), parabanic acid (PARBAC) and chloranil (TCBENQ02 to 06) (Bolton, 1964). Another example where the planes of the two components are approximately mutually perpendicular is {phenazine phenothiazine} (Stezowski et al., 1983; BUNRAD; no coordinates). The binary phase diagram of the system (obtained by DSC techniques) shows formation of a 1 : 1 molecular compound (m. pt. 435.9K); there is essentially no solid solubility of phenazine in phenothiazine, or conversely. Crystals were grown by high vacuum plate sublimation techniques; their dark red color was due to a broad, unstructured absorption edge from 660 to 580 nm; both components are light yellow in color. Cell ˚ , ¼ 112.65(2) , parameters (at 297K) were a ¼ 9.072(2), b ¼ 8.872(2), c ¼ 25.934(5) A 3 ˚ V ¼ 1926.4 A , P21/c, Z ¼ 4. The molecular volume of phenazine (in the -phase) is 222.9 ˚ 3 (see Table 10.5). ˚ 3 and that of phenothiazine (in the orthorhombic phase) is 243.9 A A Thus there is a 3.2% expansion on formation of the molecular compound from these polymorphs of its components. The packing unit (Fig. 11.25) was found to consist of two phenazines in plane-to-plane arrangement, with approximately perpendicular phenothiazines linked by weak N . . . H–N hydrogen bonds. There is no potential donor to provide hydrogen bonding to the second nitrogen of phenazine, nor is there any evidence for interaction of some kind with the sulphur atom of phenothiazine. The packing arrangement does not indicate any -orbital interaction beyond that between superposed phenazines. One can argue whether {phenazine . . . phenothiazine} has been correctly located at this place in the text. Certainly {triethylphosphate benzotrifurazan} and {phenazine phenothiazine} form an interesting contrast. In the ﬁrst of these molecular compounds there are strong geometrical suggestions of charge transfer interaction but a colorless binary compound is formed from colorless components, while in the second there is spectroscopic evidence for charge transfer interaction, but no support for this from the crystal structure. These paradoxes remain to be resolved. The molecular compounds {1,4-dioxane dinitrogen tetroxide} (Groth and Hassel, 1965; NODIOX) and {1,4-dioxane oxalyl ﬂuoride} (Mo¨ller et al., 1987; FAYNOI) have isoelectronic acceptors and their triclinic crystals are isomorphous; there are chains of ˚ ) and alternating donor and acceptor molecules along [111] with short O N (2.90, 2.76 A ˚ ) distances. The common feature (Mo¨ller et al., 1987) is the nearO C (2.59, 2.61 A symmetric interaction between an electron-rich centre (O of dioxane) and the comparatively weakly linked central atoms of a 34 valence-electron system (N2O4 or C2F2O2). n n n

n n n

n n n

n n n

n n n

n n n

n n n

11.6 -Donors and *-acceptors 11.6.1 Aromatic molecules as donors and dihalogens as acceptors The color of an iodine solution depends on the nature of the solvent (Kleinberg and Davidson, 1948); for example, iodine–ethanol solutions are violet and their absorption spectra are similar to those of iodine vapour, while iodine–benzene solutions are brown. The implication is that iodine interacts with benzene in a manner that is more substantial than its negligible interaction with ethanol (Benesi and Hildebrand, 1949). Theoretical studies of this interaction were initiated by Mulliken and continue (e.g. Bruns, 1977). The geometry of the benzene I2 molecular compound formed in solution or in the vapour n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

728

phase remains controversial; in the ‘resting’ model the halogen molecule is parallel to the plane of the benzene ring, but perpendicular to this plane in the ‘axial’ model. There is a considerable body of publication, much of it contradictory, on the structures of aromatic molecules with the dihalogens Cl2 and Br2. However, rather recent studies lead to a resolution of many of the problems. The structures of the isomorphous {C6H6 Cl2} and {C6H6 Br2} molecular compounds were ﬁrst reported by Hassel and Strømme (1958, 1959c); the melting points are 233 K and 259 K respectively and the temperatures of measurement were 183 K and 223–233 K. The halogen molecules were reported to lie along the sixfold axes of the benzene rings (i.e. a very symmetrical form of the ‘axial’ model) forming an inﬁnite arrangement n n n

n n n

n n n

X2

n n n

C6 H6

n n n

X2

n n n

C6 H6

n n n

X2

n n n

C6 H6

n n n

:

The intrahalogen distances are the same as those in the gas phase, testifying to rather weak interactions, while the distances between halogen atom and center of benzene ring are ˚ for the Cl2 and Br2 compounds respectively. The crystals were originally 3.28 and 3.36 A reported to be monoclinic (space group C2/m) but re-examination (Herbstein and Marsh, ˚ for the 1982) strongly suggests that the crystals are rhombohedral (aH ¼ 8.49, cH ¼ 8.54 A chlorine compound), the correct space group being R3m. {C6H6 Br2} has been studied further by Vasilyev, Lindeman and Kochi (2001, 2002; BENZBR01, BENZBR02), who found a phase transition at 203K. Above this temperature the diffraction pattern (i.e. that found by Hassel and Strømme) was very weak; slow cooling and careful manipulation led to a single crystal to single crystal transformation to trigonal crystals which gave diffraction ˚ , space group P32212, Z ¼ 3). The patterns to high angles (aH ¼ 8.721(2), cH ¼ 8.701(2) A absolute conﬁguration (of the crystal used) was checked via the Flack parameter. The structure at 123K deviated appreciably from the axial model (the ‘A structure’ of Vasilyev ˚ et al.) and had the Br2 molecule located over a C–C bond with d(C . . . Br) ¼ 3.18 and 3.36 A (the ‘B structure’ of Vasilyev et al.). The structure of {toluene . . . Br2} was more compli˚ , ¼ 79.76(1), ¼ 80.89(1), cated (triclinic, a ¼ 5.516(1), b ¼ 11.715(2), c ¼ 13.551(3) A ¼ 85.56(1) , space group P1, Z ¼ 4). There are two crystallographically independent toluenes in the unit cell, two bromine molecules at centers of symmetry and one bromine ˚ , and molecule at a general position. The values of d(C . . . Br) lie in the range 3.01–3.17 A the bromine molecules are again positioned over the rims of the aromatic ring. Spectroscopic studies (Abe and Ito, 1978) showed that toluene and p-xylene form crystalline compounds with Cl2 and Br2 but only {toluene Br2} has been studied crystallographically. Despite the extensive IR and Raman studies (Anthonsen and Møller, 1977; Abe and Ito, 1978), there is no agreement among spectroscopists about the space groups; clearly 77K spectra of {C6H6 Cl2} and {C6H6 Br2} must be checked against noncentrosymmetric space groups, while {toluene Br2} could still be centrosymmetric at 77K.1 Vasilyev et al. give a comprehensive list of references to spectroscopic and theoretical studies. Matrix isolation spectroscopy of {C6H6 Cl2} and {C6H6 Br2} at 20K was interpreted to give a geometry where the halogen molecules do not lie along the sixfold axis of the benzene ring but are inclined to it (Fredin and n n n

n n n

n n n

n n n

n n n

n n n

n n n

1 Two errors in the literature require correction. Hassel and Stromme reported atomic coordinates for {C6H6 Cl2} (not noted in CSD) but not for {C6H6 Br2} (BENZBR), as Vasilyev et al. appear to have assumed. The statement of Herbstein and Marsh (1982) that ‘‘the spectroscopic and diffraction studies were made on the same phases’’ also requires revision. n n n

n n n

-DONORS AND *-ACCEPT ORS

729

Table 11.19. Stretching force constants for Cl2 and Br2 in different environments (units of ˚ 1) (Abe and Ito, 1978). mdyn A Molecule

Gas phase

In benzene solution

In crystalline {C6H6 X2}

Cl2 Br2

3.208 2.336

2.974 2.133

2.705 2.049

n n n

Nelander, 1974), thus supporting the off-axis model (structure B). The benzene I2 compound does not appear to be known in crystalline form, but the off-axis model described above was supported by the matrix isolation study of Fredin and Nelander and by the 16K 129I Mo¨ssbauer spectrum of iodine dissolved in benzene (Bukshpan et al., 1975; Sakai et al., 1983). The degree of charge transfer in the benzene halogen compounds has been estimated from NQR spectroscopy. Hooper (1964) found that the NQR frequency of 81Br was 321.83 Mhz in {C6H6 Br2} compared to 319.46 Mhz in crystalline Br2 (both samples at 77K). These values indicate very little charge transfer, the small decrease in the resonance frequency in Br2 being ascribed to intermolecular interactions present in the crystalline halogen but absent in the molecular compound. Later work (Kadaba et al., 1971) over an extended temperature range (15–150K) gave similar results; a break in the frequency– T curve was ascribed to a possible phase transition at 60K. A discontinuity at 120K in the curve of the 35Cl NQR frequency against temperature in {C6H6 Cl2} was ascribed to the onset of precession of the Cl2 molecules about the normal to the benzene-ring plane as the crystals warm up (Gordeev et al., 1974), but this could be evidence for a phase transition. Spectroscopic evidence for some charge transfer comes from determination of the force constants for intrahalogen stretching vibrations in different environments (Table 11.19). The weakening of the intramolecular halogen–halogen bond is ascribed to transfer of charge from benzene -orbitals to antibonding * orbitals of the halogen molecules. The 1 : 1 molecular compound of benzene and acetylene is rhombohedral at 201 and 123K (aH ¼ 8.504(1), cH ¼ 8.206(2) at 123K, Z ¼ 3, space group R3m (Boese, Clark and Gavezzotti, 2003) and is thus isomorphous with {C6H6 Br2} above 203K. Boese et al. remark that ‘‘there are no obvious peculiarities about the ADPs that might indicate static or dynamic disorder’’. However, anomalous values for the acetylene triple bond length led them to infer ‘‘an essentially dynamic disorder process in which the acetylene molecule moves along a double cone between the benzene molecules’’, also described as a wobbling or precession motion between the two rings so that the acetylene is perpendicular to them only in a time-averaged sense. Perhaps there is a phase change at lower temperatures. There are many reports of formation of ‘complexes’ of aromatic hydrocarbons with halogens; most attention seems to have been paid to pyrene and perylene as donors and Br2 and I2 as acceptors. The nature of these materials remains in doubt, especially when ratios other than 1 : 1 are reported and we shall not consider them further. However, coronene does form a 1 : 1 molecular compound with I2 and this has a structure (Shibuya, 1961; Pepinsky, 1962; Mitani, 1986; DUPCIA10) not much different from those of the {aromatic X2} compounds described above; the I2 molecule lies between stacks of superimposed coronene molecules, with both moieties at centers of symmetry in space n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

730

B 3.204

3.404

A

C

y x

z

Fig. 11.26. A layer in the {coronene I2} structure showing the zigzag chains of interacting ˚ . The unit cell (a ¼ 14.025, b ¼ 13.138, moieties. The two close I . . . C distances are 3.20 and 3.40 A ˚ , ¼ 105.05 , Z ¼ 2, P21/a) is outlined. (Coordinates from Mitani, 1987.) c ¼ 4.819 A n n n

group P21/a (Figs. 11.26, 11.27). There are very similar stacks of coronene molecules here and in neat coronene (Robertson and White, 1945; CORONE01; Fawcett and Trotter, 1966, CORONE), and the difference between the two structures is expressed in the 2 interaction between peripheral carbons of coronene and the iodines in {coronene I2}, leading to bridging between adjacent stacks and the formation of zigzag ..C . . . I– I . . . C . . . I–I . . . chains, where we use C as an abbreviation for coronene. Some measure of the interactions between the moieties can perhaps be inferred from the ˚ , the value found in intramolecular I–I distance, which is increased to 2.710(2) A ˚ crystalline iodine, where there are strong intermolecular interactions, and is 0.05 A longer than that found for I2 in the gas phase. Although precise room temperature C–C bond lengths are now available for neat coronene (Krygowski et al., 1996; CORONE02), it seems unlikely that those in {coronene I2} are precise enough to warrant comparison. 129 I Mo¨ssbauer measurements on crystalline {coronene I2} at 16K (Sakai, Matsuymam, Yamaoka and Maeda, 1983) are compatible with the crystal structure, and show that the I–I bond consists of a pure p bond, the acceptor orbital being described as the u antibonding molecular orbital of the iodine molecule. 0.06 electrons are transferred to this orbital. The B structures found for {C6H6 Br2} and {toluene Br2} ﬁt neatly with the 2 interaction found in {coronene I2}. We shall see below that an 2 interaction is also found in some of the aromatic hydrocarbon-SbCl3 compounds. n n n

n n n

n n n

n n n

n n n

n n n

-DONORS AND *-ACCEPT ORS

731

0

A

2C

3.204

3.404

2.710 3.404

3.204

2B

x

z y

Fig. 11.27. Arrangement of coronene and iodine molecules in chain of moieties along [010]. (Coordinates from Mitani, 1987.)

11.6.2 Aromatic molecules as donors and polyhalogenated methanes as acceptors The ﬁrst molecular compounds in this group appear to have been discovered by Wyatt (1936) in his studies of the phase diagrams of a number of binary systems; relevant here are the incongruently melting 1 : 1 and 1 : 2 compounds found in the benzene – CCl4 system, and the reported absence of compounds in the benzene-CHCl3 system. These results were extended by Kapustinskii and Drakin (1947), who conﬁrmed the occurrence of the 1 : 1 and 1 : 2 compounds in the benzene – CCl4 system (melting points 25 and 35 C respectively) and reported a 1 : 3 compound (m.pt. 40 they also prepared {C6H6 CBr4} (m.pt. 30.4 ) and reported incongruently-melting 1 : 1, 1 : 2 and 1 : 3 compounds in the benzene – CH2Cl2 system. Spectroscopic studies (IR and Raman) suggested that 2 : 1 (perhaps), 1 : 1 and 1 : 2 compounds do occur in the benzene – CHCl3 system (Chantry et al., 1967), in contradiction to Wyatt’s results. A variety of methods (DTA, Raman and 35Cl NQR spectroscopy) show the formation of loosely bound {benzene . . . CH3Cl}, melting at 198K (Rupp and Lucken, 1986). n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

732

CBr4 3.34 p-xylene

x z y

˚ , space Fig. 11.28. Crystal structure of {p-xylene CBr4} (a ¼ 8.48(3), b ¼ 8.89(3), c ¼ 17.46(5) A group Cmcm, Z ¼ 4) in projection down [110]. The arrows show the interactions between the ˚ between ring centres and Br. (Data from aromatic rings and the bromines, with distances of 3.34 A Strieter and Templeton, 1962.) n n n

The formation of {C6H6 2CCl4} has been conﬁrmed twice (Viennot and Dumas, 1972; Ott and Goates, 1963); the 1 : 1 compound between 1,2,4-trimethylbenzene and CCl4 melts at 229.85K (Goates et al., 1987) and its enthalpy of formation has been measured (see below). Extensive spectroscopic studies have been made of a number of crystalline {p-xylene CBr4} compounds, where the p-xylene was deuterated in various ways (Lebas and Julian-Laferriere, 1972). There are only small differences between the spectra of the pure components and those of the molecular compounds, from which it was inferred that the interactions between the components in the molecular compounds are rather weak. Only one crystal structure has been reported – that of {p-xylene CBr4} (m.pt. 53 C) (Strieter and Templeton, 1962; CTBRXY). A layer structure is formed (Fig. 11.28), with two of the four C–Br bonds directed towards the ˚ , close to that found in centers of the benzene rings; d(Br ring centre) ¼ 3.34 A {C6H6 Br2}. The liquidus curves have been determined in the phase diagrams of 1,2,4-trimethylbenzene (Goates et al., 1987) and of benzene, toluene and p-xylene with CCl4 (Boerio-Goates et al., 1985) and the detailed forms of these curves were then used to determine the standard n n n

n n n

n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

733

Table 11.20. Calculated enthalpies of formation of 1:1 aromatic hydrocarbon CCl4 molecular compounds n n n

Aromatic hydrocarbon

H m(kJ/mol)

Tm(K)

Benzene Toluene p-Xylene 1,2,4-trimethylbenzene

3.24 4.01 9.43

239.12 205.97 269.28 229.85

enthalpies of formation of the molecular compounds at their melting points, a typical reaction being C6 H6 ðs; 239:12KÞ þ CC14 ðs; 239:12KÞ ) C6 H6

n n n

CC14 ðs; 239:12KÞ

The calculated enthalpies are summarized in Table 11.20. A different method was used for {benzene CBr4}, where the vapor pressure of benzene over the molecular compound was measured in the temperature range 9–25 C (Kapustinski and Drakin, 1950). Using the Arrhenius equation, this gives the enthalpy of the reaction n n n

fC6 H6 CBr4 gðsÞ ) C6 H6 ðgÞ þ CBr4 ðsÞ as Hdiss ¼ 50.6 kJ mol1. The enthalpies of vaporization and fusion of benzene (at 278.66K) are Hvap ¼ 34.1 kJ/mol and Hfus ¼ 9.87 kJ/mol. Combining these values gives the (formal, as used above, not standard) enthalpy of formation of crystalline {C6H6CBr4} as 6.6 kJ/mol. Thus there is little difference in the stabilities of the two molecular compounds. A more useful comparison would be via the free energies of formation but entropy values are unfortunately not available.

11.7 -Donors and p-acceptors 11.7.1 Aluminum tribromide as an acceptor Aromatic hydrocarbons (ArH) form 1 : 1 and 1 : 2 molecular compounds with aluminum trichloride and aluminum tribromide. Relevant results are available only for the aluminum tribromide compounds. Compositions are generally given as ArH : AlBr3 (i.e. 1 : 1) or ArH : Al2Br6 (i.e. 1 : 2) but there is direct evidence for the nature of the acceptor species only for benzene:Al2Br6 (see below). Only one crystal structure appears to have been reported, that of the easily hydrolyzed {benzene Al2Br6} (Eley et al., 1961; ALBROB) There are layers of Al2Br6 molecules in the structure with the benzenes in interstices. There was no evidence of interactions other than those due to van der Waals forces; however, the results are not very accurate because of the experimental difﬁculties involved in the structure determination and it would be desirable to have structures of some analogs before ﬁrm chemical conclusions are drawn. NQR measurements made on this system (Okuda et al., 1972) at 301K indicate that there is very little charge transfer ( 0.01e) from benzene to Al2Br6. n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

734

Table 11.21. Thermodynamic parameters for the dissociation of 1:2 and 1:1 {aromatic hydrocarbon aluminum tribromide} molecular compounds (for reactions see below); G (at 0 C) and H values in kJ/mol and S (at 0 C) in J/mol deg. n n n

Aromatic ligand

benzene toluene p-xylene o-xylene m-xylene mesitylene

1:2 molecular compounds G(0 )

H

S(0 )

G(0 )

H

S(0 )

9.5 13.1 16.7 17.1 15.2 18.0

44.3 48.9 52.7 48.5 52.7 51.9

125 30 130 117 138 125

7.2 8.9

20.4 22.3

46 50

The reactions are: ½ArH AlBr3 ðsÞ ) 1=2½ArH Al2 Br6 ðsÞ þ 1=2ArHðgÞ ½ArH Al2 Br6 ðsÞ ) Al2 Br6 ðsÞ þ ArHðgÞ n n n

n n n

n n n

Thermodynamic parameters (Table 11.21) were measured (Choi and Brown, 1966) for a number of compounds by determining dissociation pressures at ﬁve temperatures between 0 and –45 . 11.7.2

Miscellany-mainly MX3 (M ¼ As, Sb; X ¼ Cl, Br) as acceptors and aromatic molecules as donors

Binary phase diagram studies (Shaw et al., 1968) have shown the occurrence of congruently melting equimolar molecular compounds of hexamethylbenzene with triphenylarsene (m.pt. 144 C), triphenylphosphine (145 ) and triphenylstibine (137 ). No structures have been reported. The 1 : 2 molecular compounds of benzene with AsCl3 (m.pt. –25.5 ) and of hexaethylbenzene with AsBr3 have been prepared. The ﬁrst of these has been studied (Biedenkapp and Weiss, 1968) by 35Cl NQR and it was deduced that the chlorines occur pairwise at independent sites in the unit cell but the overall structure is not known. The ˚ , Z ¼ 3) structure of {C6(C2H5)6 2AsBr3} (rhombohedral, R3, 13.356(2), 12.355(2) A has been determined; this contains discrete Br3As C6(C2H5)6 AsBr3 moieties of 3 symmetry (Schmidbaur, Bublak, Huber and Mu¨ller, 1987a; SALCIR); this was S6– called an ‘inverse sandwich’ structure. The geometries of the components in the molecular compound differ only slightly from those in the individual neat crystals; this resemblance extends even to the conformations of the ethyl groups. Furthermore, there are no weak Br . . . As interactions as in crystalline AsBr3 (Bartl, 1982). The large colourless rhombohedral crystals of {C6(C2H5)6 2AsBr3} are only slightly sensitive to air and moisture. A number of other AsBr3 molecular compounds were obtained but disorder prevented determination of the structures. Hexaethylbenzene also forms 1 : 1 molecular compounds with SbCl3 and SbBr3 (Schmidbaur, Nowak, Huber and Mu¨ller, 1987), with the structure of the former reported as orthorhombic, Pnma (no. 62), Z ¼ 4, 18.003 10.118 ˚ (FOSWUF). There are discrete C6(C2H5)6 SbCl3 moieties of C3-3 symmetry, 12.235 A ˚ . The interaction is the Sb being above the center of the benzene ring at a distance of 2.96 A thus much weaker than that in, say, hexaethylbenzene-chromium tricarbonyl, where the n n n

n n n

n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

[2.2.2] paracyclophane

735

Ga(III)Br4 Ga(III) 3.390 Ga(I)

x y z C

z B

A

x

Fig. 11.29. (upper) The ion-pair of {[2.2.2]paracyclophaneGa(I)}þ(Ga(III)Br4) seen in perspec˚ and the secondary Ga(I) to tive; the covalent Ga(III)–Br distances range from 2.306 to 2.334 A ˚ . There is a weak link between Ga(I) and Br indicating the carbon distances from 2.91 to 3.1 A formation of ion pairs. (lower) The packing arrangement of the ion pairs seen down [010]. (Data from Schmidbaur, Hager, Huber and Mu¨ller, 1987.)

˚ . A similar alternating up-down conformation of ethyl metal-to-ring distance is 1.72 A groups is found in both Br3As 6(C2H5)6 AsBr3 (SALCIR) and C6(C2H5)6 SbCl3 (FOSWUF) and also in (hexaethylbenzene)(toluene)Ga(I) tetrachloro-gallate(III)hemi (hexaethylbenzene) (Section 11.12.2). n n n

n n n

n n n

736

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

The triangular [2.2.2]paracyclophane molecule forms a 1 : 1 complex with AsCl3, where the AsCl3 coordinates weakly through As to the ring system as a whole (Probst et al., 1991; KISWUE); the crystals are orthorhombic, a ¼ 10.235(1), b ¼ 11.501(1), ˚ , Z ¼ 4, space group P212121, and the absolute conﬁguration (of the crystal c ¼ 19.330(2) A used in the analysis) was determined. The authors express their surprise at the lack of Cl3As . . . (aromatic ring) coordination, and ascribe the formation of the complex to weak van der Waals type interactions. {[2.2.2]ParacyclophaneGa}þ(GaBr4) (Schmidbaur, Hager, Huber and Mu¨ller, 1987; FIGKOV) is discussed at this point because of an overall, but incomplete, structural resemblance to {[2.2.2]paracyclophaneAsCl3}; alternatively it could be included, on grounds of chemical resemblance, in Chapter 11.12.2. The colourless, only slightly ˚ , 90.24(1) , Z ¼ 4, air-sensitive crystals are monoclinic (13.741(1) 11.856(1) 15.973(1) A P21/c) and contain ion-pairs (Fig. 11.29). The Ga(I) atom is equidistant, within narrow ˚ . However, limits, to all 18 C atoms of the arene; distances to the ring centers are all 2.65 A ˚ the Ga(I) is displaced by 0.43 A above the plane containing the three ring centers; the ˚ , and to Ga(I) being just too authors ascribe this to interaction with Br2, distant 3.388 A large to ﬁt into the inter-ring space.

11.8

-Donors and (localized) *-acceptors

Crystalline complexes have been prepared between benzene or polymethylbenzenes and NOMX6, where M may be P, As or Sb and X may be F or Cl (Brownstein et al., 1986; Kochi, 1990), and structures have been reported for {[C6(CH3)6]NOSbCl6} (COMROL10), {2[C6H5CH3]NOSbCl6} (FATFEL), {[C6(CH3)6]NOAsF6} (FATDUZ) and {[1,3,5-C6H3(CH3)3]NOPF6}. While the crystals all have different structures, there is a common feature in that much the same mutual disposition of aromatic hydrocarbon donor and the NOþ acceptor appears to be found in all of them, as illustrated for the mesitylene compound (Fig. 11.30). The bond lengths are not precise enough for one to infer the degree of charge transfer in the molecular compounds.

Fig. 11.30. View of the mutual disposition of mesitylene and NOþ moieties in the {mesityleneNOPF6} molecular compound. The N atom is probably adjacent to the ring but this has not yet been established beyond doubt. (Reproduced from Kochi, 1990.)

n-DONORS AND s-ACCEPTORS

737

PART 2: Self-interacting acceptors 11.9 n-Donors and s-acceptors 11.9.1 N, O, and S containing ligands as donors and Ag(I) salts as acceptors Silver salts form molecular compounds with molecules containing N, O, S as donor atoms and a number of crystal structures have been reported. As noted in the corresponding section (Chapter 11.2) in Part 1, many of these materials are peripheral to the major theme of this book and are thus noted only brieﬂy. {Pyrazine AgNO3} (Vranka and Amma, 1966; AGPYRZ) and {HMT AgNO3} (Michelet et al., 1981; BARPUF) (HMT ¼ hexamethylenetetramine) have somewhat similar structures. The ﬁrst compound contains kinked chains of the type n n n

n n n

n n n

Agþ

n n n

pyr

n n n

Agþ

n n n

pyr

n n n

Agþ

n n n

pyr

n n n

˚ and
n n n

n n n

Agþ

n n n

HMT

n n n

n n n

Agþ

n n n

HMT

n n n

Agþ

n n n

HMT

n n n

where Agþ and HMT lie on mirror planes, and the nitrate ions are disordered across mirror planes. Each Agþ is linked to three different HMT molecules (d(N Agþ) ¼ 2.406(5) ˚ ) and three oxygens of nitrate ions with d(N O) ¼ 2.62(1)(twice) (twice) and 2.335(6) A ˚ and 2.593(8) A. Cohesion between the sheets is by van der Waals forces. n n n

n n n

.3

Absorbance

N

N

.2 AgNO3 3.0 1.8 1.0

.1

0.42

0 400

500 Wavelength nm

600

Fig. 11.31. The charge transfer absorption bands from solutions of DBO in acetonitrile to which varying molar concentrations of AgNO3 have been added. The dashed line shows the spectrum of DBO alone; that of AgNO3 alone is rather similar. (Reproduced from Blackstock and Kochi, 1987.)

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

738

Ag DBO

Sheet A of linked molecules

C Sheet B of linked molecules

nitrate

2.487

B

A z y

x

Fig. 11.32. {DBOAgNO3} structure viewed down [010], showing the two crystallographically ˚; independent sheets A and B. In the central sheet the distances are: d(Ag . . . N) ¼ 2.298, 2.269 A ˚ . The values in the second sheet are only slightly d(Ag . . . O) ¼ 2.487, 2.509, 2.754, 2.856 A different. In each sheet only the shortest Ag . . . O distance is shown, for clarity. (Data from Blackstock and Kochi, 1987.)

A particularly detailed picture is obtained from the structure of {diazabicyclo [2.2.2]octene (DBO)AgNO3}, which shows a distinct charge transfer band in its spectrum (Fig. 11.31) (Blackstock and Kochi, 1987; FEJFEF). The canary yellow compound crystallizes in space group P21/c, with 8 formula units in the unit cell (a ¼ 19.80, ˚ , ¼ 106.9 ). The crystal is composed of sheets of interconnected b ¼ 7.45, c ¼ 13.12 A þ DBO molecules, Ag and NO3 ions. The nitrogens of the diaza group each interact with a different Agþ cation. The oxy ligands serve as multiple bridges to link the silver(I)-azo ˚ , four chromophores. Each Agþ cation is six-coordinate (two DBO nitrogens at 2.3 A ˚ ). The sheets interact by van der Waals forces (Fig. 11.32). Although oxygens at 2.4–2.9 A the layers shown are crystallographically independent, the interactions within them differ only slightly.

n-DONORS AND s-ACCEPTORS

739

11.9.2 N, O, S containing ligands as donors and HgX2 (X ¼ Cl, Br, I) as acceptors The lone pairs of O, N, S atoms in many molecules interact with HgCl2 to form addition compounds; HgBr2 forms some, while among the few HgI2 analogs reported is dioxane HgI2 (Patterson et al., 1973). In order to be able to assess the degree of ligand Hg(II) interaction it is necessary to compare ligand Hg(II) distances with those found in covalently-bonded compounds. The covalent radius of Hg(II) depends on the ˚ is used for linear bicovalent type of coordination (Grdenic, 1965); a value of 1.28 A Hg(II). Thus distances in molecular compounds should lie within a range whose lower limit is the sum of the appropriate covalent radii and upper limit the sum of the appropriate van der Waals radii (Table 11.22). These limiting values themselves have uncertainties ˚. of 0.1 A Our classiﬁcation will be based on the coordination number of Hg(II), where we include among the nearest neighbours both covalently bonded ligands and those linked by secondary interactions. In geometrical terms this gives distorted octahedral arrangements for six-coordinate Hg(II), distorted square pyramidal and trigonal bipyramidal arrangements for ﬁve-coordinate Hg(II) and distorted tetrahedral arrangements for fourcoordinate Hg(II). The distinctions are sometimes blurred because of the secondary interactions. The subject has been extensively reviewed (Branden, 1964c; Dean, 1978; Graddon, 1982). HgX2 molecules are linear in the gas phase, with dimensions given in Table 11.22. In their crystals HgCl2, HgBr2 and the yellow form of HgI2 all have structures in which each Hg is surrounded by six halogens along orthogonal axes; two trans Hg-X bonds have lengths very similar to those in the gas phase (and thus the linear HgX2 molecules are preserved), and four are appreciably longer (Table 11.22). Thus the HgX2 molecules in the solid state are linked in arrays by secondary interactions, which are often also found in the six-coordinated HgX2 molecular compounds considered in the next section. We shall to some extent infringe on the requirement imposed in Chapter 1 that ‘‘the properties of the components be very largely conserved;’’ the linear HgX2 molecule does not appear as such in all the molecular compounds to be discussed here but the advantages of considering the HgX2 compounds as a group outweigh too strict an allegiance to self-imposed deﬁnitions. n n n

n n n

n n n

˚ ) expected in molecular compounds of Hg(II) Table 11.22. Range of donor–acceptor distances (A halides together with some limiting values Type of interaction Hg Hg Hg Hg Hg Hg

n n n

n n n

n n n

n n n

n n n

n n n

O N S Cl Br I

Lower limit

Upper limit

HgX2 in gas phase

HgX2 in crystal phase

2.0 2.1 2.3 2.3 2.4 2.6

2.7 2.8 3.3 3.3 3.45 3.65

2.29 (a) 2.41 2.59

2.25, 3.34, 3.63 (all 2) (b) 2.48 (2), 3.23 (4) 2.62 (2), 3.51 (4)

References: (a) Kashiwabara et al., 1973; (b) Subramanian and Seff, 1980.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

740

11.9.2.1 Six-coordinate Hg(II) (i) Structures based on HgCl2 ribbons with weak Hg Cl interactions (bicoordinate Cl) This ﬁrst group of addition compounds contains those based on ribbons of HgCl2 molecules, with secondary Hg Cl interactions as shown schematically below, and completion of the approximately octahedral coordination by two Hg A (A¼O, N or S) interactions which run, up and down, approximately normal to the plane of the ribbon. n n n

n n n

n n n

Cl Hg Cl

Cl Hg

Cl

Cl Hg

Cl

3.2 Å

Hg Cl 2.3 Å

Cl

The HgCl2 molecule participates in these compounds almost without change from its ˚ and
n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n-DONORS AND s-ACCEPTORS

741

y

o

o

Cl t

b 0 d s

c

u

Hg a

s o

Cl

x

z

Fig. 11.33. Clinographic projection of chain in the structure of the polymeric adduct {diphenyl ˚ ). The sulphoxide HgCl2} (a ¼ 2.291(4), b ¼ 2.289(4), c ¼ 2.58(1), s ¼ 3.230(6), t ¼ 3.284(5) A ˚ ). Cl-Hg-Cl angle is 172.4(1) . The phenyl . . . Hg interactions are shown by broken lines (u ¼ 3.51(1) A (Reproduced from Biscarini et al., 1973.) n n n

von Schnering, 1974) then sheets are formed in the crystal (see below). The oxygen has a single secondary interaction in the ﬁrst of these examples and two in the second. Analogous double oxygen interactions are also found in the polymeric structure of {2,2 0 -trimethylenedipyridine-1,1 0 -dioxide (HgCl2)2} (Alshaikh-Kadir et al., 1978) which has the familiar ribbons of chlorine-bridged HgCl2 molecules. n n n

N

CH2 CH2 CH2

N

O O 2,2⬘-trimethylenedipyridine-1,1⬘-dioxide

In {cyclohexa-1,4-dione . . . HgCl2} (Groth and Hassel, 1964b; CHEXHG; a ¼ 7.57, ˚ , ¼ 108.5 , C2/c, Z ¼ 4)) the Hg atom lies on a crystallographic b ¼ 17.11, c ¼ 7.56 A

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

742

O twist-boat cyclohexa1,4-diones bridging HgCl2 ribbons

C

C Cl Hg

3.249 2.303

twisted HgCl2 ribbon

2.795

A

z

y x

Fig. 11.34. View of a single sheet of the {cyclohexa-1,4-dione HgCl2} crystal structure projected approximately down [011]. The large dark spheres are Cl, medium dark spheres Hg, smaller lighter spheres O and C. The linked HgCl2 moieties are sandwiched between the bridging cyclohexa-1,4dione molecules, giving the sheets a hydropohobic exterior. (Data from Groth and Hassel, 1964b.) n n n

˚ ,
n n n

n-DONORS AND s-ACCEPTORS

743

Hg Cl(2)

Cl(1) c

2.59 2.339 3.318

2.60 2.318 3.185

y

x

a [101]

˚ 105.28 Fig. 11.35. The crystal structure of {pyridine-N-oxide HgCl2} (7.060 10.132 6.890 A 117.04 75.35 , P1, Z ¼ 2; this is the reduced cell with a nonstandard choice of origon). The projection on (001) is on the left and shows the layers in the (010) planes, while the projection on (010), shown on the right, illustrates the structure of a layer. Hg atoms above and below the mean planes have different shadings. Although the crystals are triclinic, the a and c directions are closely equivalent structurally. Tests show that the space group is correct. The angle Cl(1)-HgCl(2) ¼ 164(1) . (Reproduced from Sawitzki and von Schnering, 1974.) n n n

For example, in {bis(thiosemicarbazide) HgBr2} (Chieh, Lee and Chin, 1978; TSCHGB) there are HgBr2 ribbons of the type shown above (at the beginning of Section 11.9.2(i)) but with a tendency towards equality of the Hg–Br links; complete equality ˚ (cf. values of d(Hg–Br) in is not yet attained as d(Hg–Br) ¼ 2.860(4), 3.436(4) A ˚ ) normal to the Table 11.22). There is a rather strong Hg–S interaction (d ¼ 2.45(1) A plane of the ribbon. The corresponding HgCl2 compound (Chieh, 1977b; CTSCHG) is isomorphous and has a similar coordination arrangement (d(Hg–S) ¼ 2.417(3), d(Hg– ˚ ). (Mono(thiosemicarbazide) HgCl2} has ﬁve-coordination Cl) ¼ 2.821(3), 3.250(3) A and is discussed later; Graddon (1982, p. 246) has confused the coordinations in the mono-and bis-liganded HgCl2 compounds. In {bis(pyridine) HgCl2} (Canty et al, 1982; ZZZLCI10) the two independent Hg–Cl distances are nearly equal at 2.754(2) and ˚ , and there is strong Hg to N bonding (d(Hg . . . N) ¼ 2.266(6) A ˚ ). The Hg–Cl 2.765(2) A ˚ ) and long ( 3.2 A ˚ ) contacts distances are close to the mean of the short ( 2.3 A encountered previously. The ribbons of Hg-centered octahedra remain. A similar structure is found in {bis(thioacetamide) HgCl2} (Rolies and De Ranter, 1977; TAMHGC) (Fig.11.36); there is a linear S-Hg-S arrangement, with stronger Hg to S interaction ˚ ) than Hg to Cl (d ¼ 3.07 A ˚ ). (d ¼ 2.39 A n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

744

b

Cl Cl

Hg

Cl

S

Hg S

Hg

Cl Cl

CH3

Cl

a

NH2

c

. Note the Fig. 11.36. {Bis(thioacetamide) HgCl2}. The crystals are triclinic, space group P1 N–H Cl hydrogen bond in the upper and lower parts of the ﬁgure. (Reproduced from Rolies and de Ranter, 1977.) n n n

n n n

HgCl2 ribbons or sheets with (2 þ 4) or (2 þ 2 þ 2) quasi-octahedral coordination are found in many crystal structures, not only those of addition compounds; for example ribbons are found in K2HgCl4H2O and sheets in NH4HgCl3 (Wells, 1975). Almost planar HgI2 ribbons are found in {bis(thiourea) HgI2} (Pnna, Z ¼ 4; Korczynski, 1968; ˚ ) and HGITUR), with the thiourea molecules coordinated to Hg (d(Hg . . . S) ¼ 2.46 A extending above and below the planes of the ribbons. However, the angle between the two covalent Hg-I bonds is 102 and no semblance of a linear HgI2 entity remains. n n n

3.86(1) I

2.84(1) I

Hg I

I Hg

I

I Hg

I

I Hg

I

Hg I

In contrast to these polymeric structures, the {bis(pyridine) HgX2} (X ¼ Br (BEJLAD), I (BEJLEH) ) compounds are monomeric with approximately tetrahedral coordination about Hg (Canty et al., 1982), but not isomorphous. n n n

(ii) Structures based on ribbons with weak Hg O or Hg S interactions Bridging in ribbons sometimes occurs through O or S atoms rather than through Cl – an essential n n n

n n n

n-DONORS AND s-ACCEPTORS

Cl

Cl

X

X Hg

Hg

(p-PhCl)

X= X

X

Cl

745

O

S

Cl

Fig. 11.37. Schematic structure of the centrosymmetric dimeric molecule {bis[(cis-4-pchlorophenylthian oxide) HgCl2}. The moiety X is linked to Hg through the oxygen of the ˚ in the bridge and 2.70 A ˚ externally. The HgCl2 thione group, with d(Hg O) ¼ 2.48 and 2.97 A ˚ and
n n n

n n n

d(Hg–Cl) = 2.331 Å

C

S

dithia[3.3.1]propellane B 2.979

Hg

HgCl2

3.212

y x z

˚ . space Fig. 11.38. {Dithia[3.3.1]propellane HgCl2} (FAJNUZ; 12.446(5) 8.680(4) 5.000(3) A group Pmmn, Z¼2), showing one sheet of HgCl2 molecules loosely linked by Hg S interactions. The Hg and Cl atoms lie in the (100) mirror plane, to which the Hg–Cl vectors are nearly normal. The largest spheres are Cl, with Hg and S intermediate in size. (Data from Herbstein, Ashkenazi et al., 1986.) n n n

n n n

requirement for inclusion of a structure in this group is that the O or S should be linked to two different Hg atoms, generally through secondary linkages which are not necessarily of equal strength; one consequence is that the Hg–Cl links will be normal to the plane of the ribbon. One of the relatively few examples studied is {bis(biuret) HgCl2(Birker et al., n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

746

1977; BURHGC) (biuret is NH2CONHCONH2), where the HgCl2 molecules are hardly perturbed and ribbons are formed containing quasi-octahedral Hg(II), with the bridging through amide oxygens of four biuret molecules. The biuret ligands are monodentate but ˚ ); the each coordinating oxygen is linked to two Hg atoms (d(Hg O) ¼ 2.76, 2.95 A ˚ Hg–Cl distance is normal at 2.30 A. The delicacy of the balance between different arrangements is shown by the occurrence of another isomer with chlorine bridging between Hg atoms (Nardelli and Chierci, 1960). Another example, but where discrete dimeric molecules are formed rather than inﬁnite chains, is {bis[(cis-4-p-chlorophenylthian oxide) HgCl2}, (McEwen et al., 1967; HGCTOX) shown in Fig.11.37. Another example, this time involving bridging through sulfur, is found in dithia[3.3.1]propellane (Herbstein et al., 1986; FAJNUZ) which forms sheets of composition C7H10S2 HgCl2. The essential structural element is a ribbon where the sulfurs ˚ and of the propellane moiety bridge between HgCl2 molecules (with d(Hg–Cl) ¼ 2.330 A ˚.
n n n

n n n

n n n

n n n

n n n

a Q

Hg C

2

Hg

02 3.3Cl 04 3.0

O 2.56

2.5

Cl

72 3.3

Cl

2.309 2.3 20

Cl

O S

3.0 81 C

C

Cl b

Fig. 11.39. Clinographic projection of the {2[(CH3)2SO] 3[HgCl2]} structure (a ¼ 6.672, ˚ , ¼ 60.0, ¼ 95.5, ¼ 90.1 , P b ¼ 9.286, c ¼ 8.764 A 1, Z ¼ 1; the reduced cell is 6.672 ˚ 8.764 9.036 A 62.87 84.77 84.50 ). One of the HgCl2 molecules and one of the oxygen-linked dimers is emphasized; both groupings are centrosymmetric. (Reproduced from Biscarini et al., 1974.) n n n

n-DONORS AND s-ACCEPTORS

747

˚ . In addition there are two centre of symmetry and hence must be linear; d(Hg-Cl) ¼ 2.30 A ˚ pairs of Cl atoms, at 3.00 A, belonging to adjacent dimer moieties and these complete the oblate quasi-octahedral coordination which is of the frequently found 2(short) þ 4(long) type. The second HgCl2 molecule, in a general position, approaches an ideal arrangement ˚ and
(iii) Ribbon structures based on the polyfunctionality of ligand molecules The prototype structure in this group is that of {bis(dioxane) HgBr2} (Frey and Monier, 1971; HGBDOX). Each HgBr2 molecule is essentially unperturbed, the coordination about Hg being completed by four oxygens of four different dioxane molecules, each dioxane being bonded to two different HgBr2 molecules. The Hg atoms are in the same plane so that sheets of composition HgBr2 (dioxane)2 are formed (Fig. 11.40). There are no weak Hg Br interactions in this structure and the oxygens are each linked to only one Hg atom. The structure of the HgCl2 analog does not appear to have been reported. The arrangement in {trans-naphthodioxane HgCl2} (Hassel and Rømming, 1956; only one projection was studied but a diagram was given later by Branden (1964c) appears to be similar in principle – each oxygen is linked to only one Hg atom. Here too the n n n

n n n

n n n

n n n

b b 1,4dioxane a HgBr2

c

Fig. 11.40. Stereodiagram of one layer in the structure of {bis(dioxane) HgBr2} viewed down ˚ , I4/m, Z ¼ 2). d(Hg–Br) ¼ 2.433 A ˚ the [001] axis of the tetragonal crystals (a ¼ b ¼ 7.454, c ¼ 12.439 A ˚ , which is only slightly less than the sum of the van der Waals and d(Hg . . . O) ¼ 2.83 A radii. The dioxanes are in the chair conformation. The layers, parallel to (001), are stacked one above the other along [001] but are mutually offset by 1/2(a þ b þ c ). Hg – partly hidden open circles, Br diagonally hatched, C cross-hatched, O dark dotted circles. (Reproduced from Frey and Monier, 1971.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

748

N

O Cl Cl

Cl Hg

Cl

Hg

Hg

Fig. 11.41. Ribbon structure in {bis(2-imidazolidinone) HgCl2}. (Reproduced from Majeste and Trefonas, 1972.) n n n

oxygens of the donor molecule interact with different HgCl2 molecules and ribbons are formed. A difference between these ribbons and those discussed in Section 11.6.2.1(ii) is that the latter are based on bicoordinate oxygens. A third example is given by the structure of {bis(2-imidazolidinone) HgCl2} ((Majeste and Trefonas, 1972; ETURHG) (2-imidazolidinone is also known as ethylene urea), where there is quasi-octahedral coordination about Hg with essential preservation of the HgCl2 molecules (d(Hg– ˚ ) and ˚ ) and formation of ribbons with weak Hg O (d ¼ 2.67(1) A Cl) ¼ 2.309(4) A ˚ Hg N (d ¼ 2.95(1) A) interactions (Fig. 11.41); the coordination about Hg is 2Cl þ 2O þ 2NH, in descending order of interaction strength. Formation of ribbons is a consequence of the bifunctionality of the organic ligand. A twisted chain structure is also found in {(S)-()-n-butyl-t-butyl sulfoxide HgCl2} (Drabowicz et al., 2001; BABNAU; absolute coﬁguration determined). This has some unusual crystallographic features; the space group is P1 and the unit cell contains 4(C8H18OS) þ 5 HgCl2. Four HgCl2 molecules are linked to four molecules of the sulfoxide by Hg–O links, Hg thus being 6-coordinate, with Hg–O distances varying from ˚ . The remaining HgCl2 molecule forms coordination bonds to Cl’s of the 2.366 to 2.533 A ˚ . The overall neighbouring HgCl2 molecules with Hg . . . Cl distances of 3.173 and 3.216 A result is a twisted chain sheathed on both sides by hydrophobic sulfoxide molecules. These chains interact by van der Waals forces. A stepped chain is found in {(S)S(S)C()589-methyl 2-phenylbutyl thioether HgCl2} (Biscarini and Pelizzi, 1988; GOKFAN) (space group P21, Z ¼ 2; absolute conﬁguration determined). The authors comment that there is ‘‘a polymeric structure in which one of the two crystallographically independent chlorine atoms unsymmetrically bridges three adjacent symmetry-related Hg atoms. The overall coordination around Hg is not simple to interpret, as the ligand arrangement cannot be described in terms of a regular polyhedron.’’ ˚ and Cl(1) at 2.315(5) A ˚ , with <S–Hg– Hg has two close neighbours, S at 2.433(4) A Cl(1) ¼ 149.8(2) ; thus no sign remains of the original linear HgCl2 molecule. Also ˚ . The sixth there are three Cl(2) neighbors to Hg at 2.677(5), 2.838(10) and 2.995(10) A ˚ ). Overall, the stepped chain is coordination site is a weak link to the phenyl ring (3.6 A sheathed by the phenyl and methyl groups. n n n

n n n

n n n

n-DONORS AND s-ACCEPTORS

749

C⬘6 C⬘5 107.0° O⬘4 O⬘3 112.3° 108.0° 108.0° C⬘7

C⬘8

Cl⬘2

Cl1

2.91A 2.76A 109.9° 2.66A O⬘2 117.2° Hg⬘ C⬘2 2.89A Cl⬘1 C1 –88° 112.8° C⬘1 O1 –67°

–176° 173°

77° C4

C⬘3

61.7°

C2 O2

C⬘4

Hg 63.0° 63.O°

C3 –176° O 3 –169° C5 –74°

Cl2 C8 –176°

O4 172°

C7

C6

Fig. 11.42. Diagram of the molecular unit in {hexaethylene glycol diethyl ether2(HgCl2)} ˚ ,
(iv) Formation of discrete molecular structures There are a number of examples where HgCl2 interacts with a particular ligand to form a discrete molecular entity of composition nLHgCl2 (n a small integer) with quasi-octahedral coordination about Hg. In earlier work complexes of polyethylene oxide had been made with HgCl2, compositions with CH2CH2O : HgCl2 ratios of 1 : 1 and 1 : 4 being obtained. However, these results will not be discussed as the structural inferences drawn from their ﬁbre diagrams appear less certain than later conclusions from analyses of single crystals of simpler analogs. Thus HgCl2 forms 1 : 1 molecular compounds with the dimethyl and diethyl ethers of tetraethylene glycol, the compositions being RO(CH2CH2O)4 HgCl2 (R ¼ CH3 (compound I; MTEGMC) (Iwamoto, 1973a), C2H5 (compound II; ETEGMC)) (Iwamoto, 1973b), and with the diethyl ether of hexaethylene glycol, the composition being {[EtO (CH2CH2O)2CH2CH2OCH2CH2(CH2CH2O)2Oet] 2HgCl2} (III) (Iwamoto, 1973c; EHXGMC). (II) was disordered but single-crystal structural results were obtained for (I) and (III), showing the Hg atoms of the HgCl2 molecules to be encompassed by 5 and 4 oxygen atoms respectively, the oxygens being arranged in planar hexagons, with one and two sites vacant; details are given for III (Fig. 11.42). The structure of {1,15-bis(2-bromophenyl)-2,5,8,11,14-pentaoxapentadecane HgCl2} (Weber, 1980; BPOHGB) is very similar to that of (I) above as is dibenzo-18-crown6 HgCl2, where the linear HgCl2 molecule in the centre of the crown ether is surrounded n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

750

N2AM

N2AM C2AM O2AM

O3 OW2 C3

C2 N4

C4M1 C4 C1 O12A C3 O1 C12A C4M2 C4A O12

C4M1 C4

HG Cl1

C1 Cl2 O1

HG

O12A Cl1

C12A

C4M2 C4A

35

O12

C5

C12

O5

O5

C6

C8

O11 C6

C6N

C6A

C10A O10

C10

C7

C11A

25A

C11

C6A

C12

O6

O11

C6N

C5

C11A

25A

O6

OW2

C2

N4

35

C2AM O2AM

O3

C10A O10

C10

C7

C8

C9

C11

C9

Fig. 11.43. Stereoview of the oxytetracycline HgCl2 interaction, viewed approximately normal to the molecular plane. (Reproduced from Jogun and Stezowski, 1976.) n n n

by six oxygens in the equatorial plane (Kawasaki and Matsuura, 1984; COCGAC). A somewhat similar distorted octahedral arrangement of oxygens about Hg is found in the dihydrate compound of zwitterionic oxytetracycline with HgCl2 ({C22H24N2O9 HgCl2 2H2O}) (Jogun and Stezowski, 1976; OXTETH10). The Hg atom is surrounded by two ˚ ; Cl Hg Cl ¼ 169 ) and four oxygens (distance of chlorines (d(Hg Cl) ¼ 2.80 A ˚ (i.e. O(3) ˚ ˚ , to OW(2) 3.025 A ˚ , and to O(3 0 ) 3.22 A Hg to O(1) is 2.80 A, to O(2am) 2.65 A of a neighbouring molecule) Fig. 11.43). There are no weaker Hg Cl interactions in any of these three structures. n n n

n n n

n n n

n n n

n n n

11.9.2.2 Five-coordinate Hg(II) Although only relatively few structures containing ﬁve-coordinate Hg(II) are known, it is possible to distinguish between those where the Hg has square pyramidal coordination and those where there is trigonal biyramidal coordination about Hg. The relation between octahedral and square pyramidal coordination is clearly shown in {3,5-dibromopyridineN-oxide HgCl2} (Genet and Leguen, 1965; HGCOPO10) where ribbons of HgCl2 molecules are found with dimensions rather similar to those encountered previously ˚ ). A ﬁfth ˚ ,
n n n

n n n

n-DONORS AND s-ACCEPTORS

751

˚ ,
n n n

n n n

n n n

n n n

n n n

Hg 2.95 C12 C11 2.95

Hg

collidine

2.18 b

a

˚, Fig. 11.44. Diagram of part of the structure of {collidine HgCl2} (a ¼ 8.15, b ¼ 17.81, c ¼ 7.44 A ˚ ; deg.) are: Hg–Cl(1) ¼ 2.455; Hg–Cl(2) ¼ 2.542; ¼ 92.6 , P21/c, Z ¼ 4). Some additional dimension (A Hg–N ¼ 2.18;
752

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

1.403

N(2)

N(3)

Cl(1)

1.333 N(1) C 1.33 3

2.512 2.7705

1.72522 7

2.366

Hg 2.4176

S

CI(2) 3.65 157.31 101.66

78.4 117.14 96.11

1191 1241 107.88

1171 125 1

LCI(I)HgS =100.31

90.94

Fig. 11.45. View of the dimer in {mono(thiosemicarbazide)dichloromercury(II)}. (Reproduced from Chieh and Cowell, 1977.)

Cl(2) b c

2.36 Hgi

Cl(1)

2.94

Hg 3.49

2.78

a Cl(11)

2.37 P C2 C1

C3

Fig. 11.46. The linear polymeric ladder structure of {trimethylphosphine HgCl2} (triclinic, P 1, ˚ . (Reproduced from Bell Z ¼ 1; MPHGCL10). Atoms of the chain are coplanar to within 0.14 A et al., 1981.) n n n

anions are arranged in a polymeric ladder (Fig. 11.46) and the distinction between an ionic and charge-transfer formulation would appear to be arbitrary. Perhaps the compound could be more reasonably described as a linear array of weakly interacting dimers of composition [Cl2HgP(CH3)3]2, containing ﬁve-coordinate square pyramidal Hg, the weak Hg Cl ˚ ) being taken into account in this description. interaction (d(Hg Cl) ¼ 3.489(4) A Br2HgP(CH3)3 appears to be isostructural with the chloro compound, but the iodo n n n

n n n

n-DONORS AND s-ACCEPTORS

753

compound is not. There is also a structural resemblance to {(tetrahydrothiophene)HgCl2} (Branden, 1964b; HGCTHS). C

Cl Polymeric ladder

Hg N

phenyl

S

B

z y

A

x

Fig. 11.47. The structure of {dehydrodithizone HgCl2}; projected down [010], the polymeric ˚ , ¼ 102.79 , ladder direction. The crystals are monoclinic, a ¼ 25.717, b ¼ 6.476, c ¼ 11.476 A ˚ ; deg.) are: Hg–Cl(1) ¼ 2.34; corrected space group C2/m, Z ¼ 4. Some important dimensions (A ˚ ; <S 0 –Hg-Cl(1) ¼ 152; Hg–Cl(2) ¼ 2.57; Hg S 0 ¼ 2.40; Hg S ¼ 3.14, 3.42; S 0 -C(ring) ¼ 1.71 A 0
n n n

n n n

Ph

Ph N N

N

± C S

N

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

754

N 2.348 2.575 Hg

S 3.418

S

2.402

2.402 3.139

S

S

Hg

y
x

CI dehydrodithizone ring

Fig. 11.48. The structure of {dehydrodithizone HgCl2}, showing detail of the polymeric ladders, projection down [011]. The two phenyl groups attached to each dehydrodithizone ring have been omitted for clarity. (Adapted from Kozarek and Fernando, 1973.) n n n

Hg Cl interactions are replaced by (rather weak) Hg S interactions in the 1 : 1 adduct of dehydrodithizone with HgCl2 (Kozarek and Fernando, 1973; DTIZHG10) (dehydrodithizone, C13H10N4S, is the meso-ionic sydnone anhydro-5-mercapto-2,3diphenyltetrazolium hydroxide). The original space group (C2) was corrected to C2/m by Marsh and Herbstein (1983) who also showed that there was residual solvent (identity not established) in the crystals. The arrangement is shown in Figs. 11.47 and 11.48; the polymeric ladder structure is not quite planar as <S 0 -Hg S is 162 . One Hg-Cl bond has lengthened appreciably to ˚ while the other has a standard value; the HgCl2 molecule is not linear,
n n n

n n n

n n n

11.9.2.3 Four-coordinate Hg(II) Four coordinate Hg(II) is found in a number of compounds of HgCl2 and HgBr2 with oxygen-containing and, especially, with sulphur-containing ligands. In the following it is convenient to distinguish between unbridged structures (i.e. with one Hg per molecule or structural unit, the latter phrase allowing for the possibility of polymeric arrangements in the solid state) and bridged structures, which range from discrete dimeric molecules to polymeric arrangements in the solid state. We ﬁrst discuss the unbridged structures. Approximately square-planar coordination about Hg is found in {cyclononanone HgCl2} (Dahl and Groth, 1971; CNONHG). In this molecular compound, where the cyclononanone molecule is in a twisted chair boat conformation of approximately C2–2 symmetry (both enantiomers are present in the centrosymmetric crystals), there are zigzag chains of composition C9H16O HgCl2 along [100]. The oxygen atoms are bicoordinate and linked to n n n

n n n

n-DONORS AND s-ACCEPTORS

755

Hg atoms of different HgCl2 molecules with
n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

Cl Hg HO testosterone

Cl

OH testosterone

two-fold axis

A similar distorted tetrahedral arrangement is found in the isomorphous structures of {bis(triphenylarsine oxide) HgCl2} (HGPARO) and {bis(triphenylphosphine ˚ , d(Hg–O) ¼ 2.32, 2.37 A ˚, oxide) HgCl2} (Branden, 1963), where d(Hg–Cl) ¼ 2.32, 2.33 A Cl–Hg–Cl ¼ 146.6 and
n n n

n n n

n n n

Cl

Cl Hg S

S

O

O 1,4-Dithioxan…HgCl2 Cl–Hg–Cl = 114°; <S–Hg–S = 115°

The structure of {1,3,5-trithian HgCl2} (ﬁrst prepared in 1870 by Hofmann and Girard) is polymeric (Fig. 11.49; Costello et al., 1966; HGTRIT) with tetrahedral coordination about Hg, the chain structure resulting from the bifunctionality of the trithian n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

756

c

C(1)

S(1) C(2)

S(2) Cl Hg

o

b

Fig. 11.49. Projection of the crystal structure of {1,3,5-trithian HgCl2} down [100] (a ¼ 4.29, ˚ , space group Pbcm, Z ¼ 4. There are zigzag polymeric chains along [001]. b ¼ 14.33, c ¼ 13.62 A (Reproduced from Costello et al., 1966.) n n n

2.396

Hg

Cl 2 2.54 S1

2.754

2.469

CI1 S2

dithia[4.3.3]propellene
x z

y

Fig. 11.50. {Dithia[4.3.3]propellene HgCl2}. The structure is viewed down the conjoining (propellene) bond. The quasi-cylindrical chains are approximately close packed along [010]. ˚ and of bond angles 0.2 . The standard uncertainties of bond lengths were reported as 0.005 A (Data from Herbstein, Ashkenazi et al., 1986.) n n n

molecule (one S does not participate in intermoiety bonding). The trithian molecule is ˚, in the chair conformation and the S . . . Hg bonds are equatorial; d(Hg–Cl) ¼ 2.44(1) A ˚ ,
n n n

n n n

n n n

n-DONORS AND s-ACCEPTORS

757

O

A

B <S–Hg–Cl2 = 146.73°

Cl2

S1

S2

2.659 Cl1 C
2.789

Hg

x

2.438

dithia[4.3.3]propellane

y z

Fig. 11.51. The quasi-cylindrical dimeric centrosymmetric structural (packing) unit of {dithia[3.3.3]propellane HgCl2 is shown in the unit cell (a ¼ 14.320(6), b ¼ 9.762(4), c ¼ 9.058(4) ˚ , ¼ 90.32(5) , P21/c, Z ¼ 4). {Oxathia[4.3.3]-propellane HgCl2} (a ¼ 14.93, b ¼ 9.42, c ¼ 8.74 A ˚ , ¼ 94.8 , P21/c, Z ¼ 4) is isostructural with {dithia[3.3.3]propellane HgCl2}; the two A centrosymmetric dimers have similar shapes. Standard uncertainties are as given in the caption to Fig. 11.48. (Data from Herbstein, Ashkenazi et al., 1986.) n n n

n n n

n n n

˚ , 115.33(5), 103.97(5) 83.18(5) ; Herbstein et al., 1986; Fig. 11.50), where the 7.552(40 A chain nature follows from the bifunctionality of the propellene moiety; the interatomic distances in the two structures are similar but not identical. A polymeric structure with a zigzag chain is found in {catena(-chloro)chloro ˚ ), and (guanosine-N7) mercury(II),} where Hg is covalently bonded to Cl (d ¼ 2.339 A ˚ ), and linked in chains by bicoordinate Cl to N(7) of guanosine (d ¼ 2.16 A ˚ ). This structure is enantiomorphic (space group P212121, (d(Hg . . . Cl) ¼ 2.659, 2.761 A Z ¼ 4) and the absolute conﬁguration of the crystal used in the analysis was determined (Authier-Martin et al., 1978; CLGUHG). Bridging leading to formation of discrete dimers is found in the isomorphous 1 : 1 HgCl2 molecular compounds with triphenylphosphine oxide (Branden, 1963; HGPARO) and triphenylarsine oxide ((Branden, 1964a; HGCPAO), where the bridging atoms are oxygen, in {1-methylcytosine HgCl2} (Authier-Martin and Beauchamp, 1977; MCYTHG) (where there are additional weak Hg O interactions), and in {oxathia[4.3.3]propellane HgCl2} n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

758

(Herbstein et al., 1986; FAJPIP) and {dithia[3.3.3]propellane HgCl2} (FAJPEL; Herbstein et al., 1986), where there are (nearly) symmetrical Cl bridges (Fig. 11.51). Similar structures are found in the 1 : 1 compounds of HgCl2 with other ligands, variability being provided by the detailed dimensions and especially by the degree of asymmetry in the bridges. Four structures with symmetrical bridges are noted immediately above, while unsymmetrical bridges are found in the HgCl2 compounds of 1,2,5-triphenylphosphole ˚ ) (Bell et al., 1980b; CLBHGC), triphenyphosphine selenide (2.60, (2.54, 2.75(1) A ˚ ˚ ) (Brotherton et al., 2.78 A) and S-methylpyrrollidene-1-carbodithioate (2.57, 2.78 A 1974; CMPRTM). The enthalpy of formation of crystalline [Ph3PO]2 . . . HgCl2 according to the following reaction n n n

2Ph3 POðsÞ þ HgCl2 ðsÞ ¼ ½ðPh3 POÞ2

n n n

HgCl2 ðsÞ

has been measured by solution calorimetry as 12.30.6 kJ/mol at 298K (Jorge et al., 1978). A one-dimensional twisted-ribbon structure is found in the compound of composition {C22H31O2S HgBr2} formed between the thiosteroid spiroxazone (7-(thio-acetyl)(17R)-spiro[androst-4-ene-17,2(3H)-furan]) and HgBr2 (Terzis et al., 1980; SBHGAF), which was studied in connection with the possible use of thiosteroids as antidotes for mercury poisoning. The ribbon has both S and Br bridging, the distorted tetrahedral coordination about Hg giving rise to a twist of the ribbon. The dimensions of the steroid molecule are hardly affected by the interaction with HgBr2 and it was inferred that it acts via direct complexation and removal of Hg rather than through a conformational change of the steroid which in turn was postulated to trigger some other defence mechanism. n n n

Steroid Steroid S

S Hg

S Hg

Hg Br

Steroid

Br

Hg Br

{Dibromo[N-(2-pyridyl)acetamide]mercury(II)} has a polymeric structure (Lechat et al., 1980; BPACHG) in which the bidentate ligands are coordinated to Hg through pyridyl-N and acetyl-O of different molecules, forming a chain structure; d(Hg N) ¼ ˚ ,
n n n

n n n

n n n

n n n

n n n

n-DONORS AND s-ACCEPTORS

759

b

Hg(I)

Cl(I) C(I) C(2) C(3) C(4) S Hg(2) Cl(3) Cl(2)

O

a sin b

Fig. 11.52. Projection of crystal structure of {1,6-dithiacyclodeca-cis-3,cis-8-diene (HgCl2)2} ˚ , ¼ 92.7 , space group P21/m, Z ¼ 2). There are mirror down [001] (a ¼ 7.29, b ¼ 17.01, c ¼ 6.20 A planes perpendicular to [010] at y ¼ 1/4, 3/4. Two of the HgCl2 molecules are emphasized for clarity. (Reproduced from Cheung and Sim, 1965.) n n n

Both tetrahedral Hg(II) and essentially undistorted HgCl2 molecules are found in the polymeric structure of {1,6-dithiacyclodeca-cis-3,cis-8-diene (HgCl2)2} (Cheung and Sim, 1965; HGCSCD10). The crystal structure (Fig. 11.52) shows that the tetrahedral ˚ ) and two S neighbors (d ¼ 2.53 A ˚ ). Hg(1) of Hg(2) has two Cl neighbors (d ¼ 2.50, 2.51 A ˚ and three further the HgCl2 molecule actually has ﬁve Cl neighbors, two close at 2.30 A ˚ . The moieties are arranged in ribbons along [010], with very away at 2.93, 3.02 and 3.21 A ˚ ) along [100] giving some degree of layer weak interactions (d(Hg. . . . Cl) ¼ 4.44 A character about (001). A combination of tetrahedral and octahedral coordination is found in {(isopropylthio)HgCl2} (Biscarini, Foresti and Pradella, 1984; CIDFAW). The space group is C2, with Z ¼ 2; the absolute conﬁguration of the crystal used does not appear to have been determined. The two independent Hg atoms are on two fold axes, one (Hg(1)) at Wyckoff position 2(a) (000) and the other (Hg(2)) at 2(b) (0,y,1/2); the other atoms are at general positions. Hg(1) has two S atoms covalently linked in a linear arrangement (d(Hg– ˚ , <S(1)–Hg(1)–S(1A) ¼ 178.2(2) ; thus the linear HgCl2 molecule has S) ¼ 2.378(6) A not been carried over to the solid state. Hg(1) forms four weaker coordinative bonds to ˚ ), leading to (distorted) octahedral coordination for Hg(1)Hg(2) chlorine (2.985, 3.342 A n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

760

P-(n-Bu)3

Cl

Cl

2.36 Å

2.30 Å

2.63 Å

3.38 Å

2.66 Å

Hg

Hg 2.71 Å 2.29 Å Cl

2.90 Å Cl

2.34 Å P-(n-Bu)3

Fig. 11.53. The weakly linked dimer of the -polymorph of {tri-n-butyl phosphine HgCl2}, showing the dimensions. The n-butyl groups have been omitted for clarity. (Adapted from Bell et al., 1980b.)

has tetrahedral arrangement of two S and two Cl atoms, covalently linked at 2.537(6) and ˚ . Two dimensional networks are stacked about (100) planes, with the alkylic 2.534(8) A tails interspersed between the layers and perhaps determining the packing arrangement. The discrete, centrosymmetric, molecules of {-[Bu3P] HgCl2} (Bu ¼ n-butyl (Bell et al., 1980b; NBUPHG10 at 300K and NBUPHG11 at 100K) also show co-existence of 4- and 5-coordinate Hg(II) (Fig. 11.53).There is ﬁvefold coordination about the central Hg and fourfold about the terminal Hg’s; one notes also the combination of highly unsymmetrical and somewhat unsymmetrical Cl bridging. The central and outer rings are approximately mutually perpendicular. The tetrameric moieties are well separated in the crystals, which have the rather low melting point of 80.5 . There is also a -polymorph (Kessler, 1977). A comprehensive 35Cl NQR study of HgCl2 molecular compounds with organic donors has been carried out by Fichter and Weiss (1976) and some comparisons between NQR spectra and crystal structures are possible. Those compounds containing essentially unperturbed HgCl2 molecules ({dioxane HgCl2}; {bis(dioxane) HgCl2}, assumed isomorphous with {bis(dioxane) HgBr2}; {cyclohexa-1,4-dione HgCl2}) all have 35 Cl NQR frequencies in the range 20–21.5 MHz. However, there are signiﬁcant differences in regard to NQR frequency and its temperature dependence among the various compounds and it has not yet been possible to explain these effects in crystallographic or molecular terms. Tetrahydrothiophene HgCl2, which has been assigned an ionic structure [ClHgSC4H4]þCl by Branden (1964c), shows a single-line spectrum ( (35Cl) ˚ ), while the frequency due to 20 MHz) due to the Cl bonded to Hg (d(Hg–Cl) ¼ 2.30 A the Cl ion was too low to be detected under the conditions of measurement. A noticeable difference was found for {1,3,5-trithiane HgCl2} where there is quasi-tetrahedral coordination about Hg; (35Cl) 15 MHz. The adducts of HgCl2 and analogs show a wide range of structural features, starting from retention of the linear HgCl2 molecule, to the disappearance of this feature and its replacement by a variety of other structural features. Presence of linear HgCl2 is an n n n

n n n

n n n

n n n

n n n

n n n

n n n

n-DONORS AND p-ACCEPTORS

761

Table 11.23. Thermodynamic quantities for the decomposition reactions of crystalline dioxane HgX2 molecular compounds at 298 K n n n

Compound

G (kJ/mol)

H (kJ/mol)

S (J/mol deg)

dioxane HgCl2 dioxane HgBr2 dioxane HgI2

22.7(4) 17.7 11.4

65.5(4) 66.6 58.3

297(5) 281 233

n n n

n n n

n n n

essential requirement for conformation to our deﬁnition of molecular compounds, The other examples stray beyond our permitted limits to different extents; however, as we have noted, there are many advantages in discussing together the whole group of mercury(II) halide adducts. Thermodynamic parameters (Table 11.23) have been determined (Barnes, 1972) for the decomposition reactions dioxane HgX2 ðsÞ ) HgX2 ðsÞ þ dioxaneðgÞ

ðX ¼ Cl, Br, IÞ:

The structure of dioxane HgI2 is not known. n n n

11.10 n-Donors and p-acceptors 11.10.1

N, O, S containing ligands as donors and MX3 (M ¼ As, Sb; X ¼ Cl, Br, I) as acceptors

11.10.1.1 SbX3 (X ¼ Cl, Br, I) as acceptor Although the ﬁrst molecular compounds of aromatic hydrocarbons with SbCl3 were made more than one hundred years ago (Smith, 1879; Smith and Davis, 1882),2 the ﬁrst systematic work was by Menschutkin (1910–1912) who studied, via binary phase diagrams, some 60 molecular compounds formed by SbCl3 and SbBr3 with alkylbenzenes, phenol, methoxy- and ethoxybenzenes, ﬂuorobenzene, naphthalene, substituted naphthalenes and other aromatics. Later work has shown that there is a fairly clear distinction, both chemical and structural, between those molecular compounds where the interaction between ligand and SbX3 is preferentially with the nitrogen or oxygen atoms of a substituted aromatic molecule (n-donor) and those where the interaction is preferentially with the aromatic ring of a ligand which is an unsubstituted aromatic hydrocarbon or one which has only alkyl substituents (-donor). Thus we shall discuss these two types of interaction separately, with the p-donors discussed here and the -donors in Section 11.11.1. Menschutkin reported stable 1 : 1, 2 : 1, 3 : 1, 4 : 1 and metastable 6 : 1 molecular compounds of aniline with SbCl3 and the structure of the ﬁrst of these has been determined (ANISBC; Hulme and Scruton, 1968); there is also a brief report of the structure of the 2 : 1 complex 2 ‘‘It was observed by one of us some time ago (this Journal, June 1879) that on melting a mixture of antimony trichloride and naphthalene, after removing the source of heat, a beautiful crystallisation commences in the still liquid mass, the minute but perfectly symmetrical clinirhombic crystals in their rapid growth performing during the process singular gyrations upon the liquid surface on which they ﬂoat.’’ The compositions given for the benzene and naphthalene molecular compounds with antimony trichloride were 2 : 3 instead of the 1 : 2 ratios of more recent work.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

762

(ANILBC; Hulme, Mullen and Scruton, 1969). There are also 1 : 1 compounds with substituted anilines (May, 1911), trans-cinnamic acid and substituted cinnamic acids, bis(p-methylstyryl) ketone, terephthaldehyde, p-acetylbenzene, o-nitrocinnamaldehyde, -methylcinnamaldehyde, p-phenyl-benzaldehyde, phenyl-benzoate, 5-methyl-1-phenyl1-hex-3-one, 5-phenyl-2,4-pentadienophenone, trans-1,2-dibenzoylethylene, chalcone (Park, 1969); {(1,3,5-triacetylbenzene) 2SbCl3} has also been reported (Park, 1969). These compounds are not particularly hygroscopic. Six crystal structures have been reported where the donor atom is nitrogen or oxygen – these are the 1 : 1 compounds of SbCl3 with aniline (noted above), terephthalaldehyde (TPHALD10) and p-diacetylbenzene (DACBZA10) (Baker and Wiiliams, 1972), and 2,2 0 -bipyridyl (Lipka and Wunderlich, 1980; BPYSBC10), the 1 : 2 compound of 1,3,5triacetylbenzene with SbCl3 (Baker, 1976) and the 3 : 2 compound of 4-phenylpyridine with SbCl3 (Lipka, 1983; PYRSBA10). In aniline SbCl3 there is trigonal bipyramidal ˚, AX4E coordination about Sb, with the lone pair (E) equatorial; d(Sb N) ¼ 2.53(4) A ˚ which is long compared to the Sb . . . N distance of 2.17 A found in {S4N4 . . . SbCl5} (Neubauer and Weiss, 1960). In {terephthaldehyde SbCl3} the coordination about Sb is remarkably similar to that in SbCl3 itself, except that the two shorter Sb . . . Cl secondary interactions in SbCl3 are replaced by Sb O interactions (two independent approaches, ˚ ). The coordination type is thus 1 : 5:1 AX6E, a distorted pentagonal both 2.932 A bipyramid with the lone pair presumably located opposite one covalently-bonded Cl in an axial position. In {p-diacetylbenzene SbCl3} the coordination about Sb is distorted octahedral AX6, with little surface area of the coordination polyhedron left over for the lone pair, which is thus probably not stereochemically active. The ﬁrst neighbour atoms to ˚ ), two O (at 2.668, Sb are three Cl (covalently bonded at 2.360, 2.385 and 2.372(2) A ˚ ˚ 2.806(5) A) and one Cl (at 3.213 A). There is also quasi-octahedral coordination about the two Sb atoms in {1,3,5-triacetylbenzene SbCl3}, with average covalent Sb-Cl distance ˚ ; one Sb has three close oxygens (at 2.76, 3.04 and 3.07 A ˚ ) and the other has one O 2.38 A ˚ ) and two more remote chlorines (at 3.42, 3.44 A ˚ ). There is no signiﬁcant (at 2.84 A n n n

n n n

n n n

n n n

n n n

n n n

n n n

Cl Cl

Cl Sb

E

Cl

Sb O

N

Cl Cl

Cl

Cl

O

Cl aniline…SbCl3

Cl Cl

Sb

O

O O

E

Cl

terephthaldehyde…SbCl3 p-diacetylbenzene…SbCl3 Cl Sb

Cl O

Cl

Cl Sb

O O

O Cl

Cl

1,3,5-triacetylbenzene…2(SbCl3)

Fig. 11.54. Schematic diagrams of coordination arrangements in p-donor SbCl3 molecular compounds. Distances between atoms are given in the text. n n n

n-DONORS AND p-ACCEPTORS

763

interaction between Sb and aromatic ring in any of these compounds. These coordination polyhedra are summarized in Fig. 11.54. The SbCl3 moiety in {aniline SbCl3} and in one of the crystallographically independent units of {1,3,5-triacetylbenzene 2SbCl3} behaves structurally as a ‘pure acceptor’ rather than as a ‘self-interacting acceptor;’ this again emphasizes that we introduce deﬁnitions and classiﬁcations for our own convenience and that Nature does not always follow the rules we may attempt to impose. 4-Phenylpyridine forms two molecular compounds with SbCl3, with compositions 3 : 2 (melts congruently at 173–176.5 ) and 2 : 1 (decomposes at 161 ). Neither of these colorless materials is markedly hygroscopic. The structure of the 3 : 2 compound contains two structural units A and B, which are linked in alternating fashion in a chain by weak ˚ ) and also laterally (d(Sb Cl) ¼ 3.23 A ˚ ) to give a Sb Cl links (d(Sb Cl) ¼ 3.59, 3.37 A sheet-like structure. The structural units A and B can be represented as shown: n n n

n n n

n n n

n n n

A:

n n n

Cl3 Sb B:

n n n

˚ NC5 H4 ---C6 H5 dðSb. . . NÞ ¼ 2:47A n n n

C6 H5 ---C5 H4 N dðSb

n n n

Sb jjj Cl3

n n n

NC5 H4 ---C6 H5

˚ NÞ ¼ 2:39 A

The SbCl3 moiety has its usual pyramidal shape in A, although the covalent Sb-Cl bond ˚ ) suggest some change in the details of the bonding pattern; lengths (2.378, 2.399, 2.505 A this is accentuated in B where the SbCl3 moiety is now T-shaped and the covalent Sb–Cl ˚ ). A similar situation occurs in bondlengths are even more different (2.361, 2.474, 2.736 A 2,2 0 -bipyridyl SbCl3 (Lipka and Wunderlich, 1980) (yellow, slightly hygroscopic crystals), which is a chelate coordination complex, the Sb . . . N distances being 2.25(1) ˚ ). In ˚ , with a T-shaped SbCl3 moiety (Sb-Cl ¼ 2.505, 2.549 and 2.588(6) A and 2.32(2) A our terms this material is not a molecular compound and would be better described as containing chelated molecules of Sb(C10H8N2)Cl3 linked by weak Sb . . . Cl interactions ˚ ). These structural differences are presumably a consequence of the small (d ¼ 3.34 A increments in basicity of the nitrogens as one passes from the anilines through 4-phenylpyridine to 2,2 0 -bipyridyl. n n n

11.10.1.2 AsCl3 as an acceptor The structure of only one AsCl3 compound has been determined, that with 2,2 0 -bipyridyl (Cameron and Killean, 1972; ASCDPY). The structure is ionic with (2,2’-bipyridyl– AsCl2)þ cations and chloride anions. There is no interaction between aromatic ring and As. This material is not a molecular compound in our present terms. Less basic ligands do not appear to have been studied. 11.10.1.3 {S8 SbCl3} This molecular compound (Mu¨ller and Mohammed, 1983), prepared by the reaction of CS2 with SbCl5 at 5 C, is considered separately as there are structural resemblances to some aromatic hydrocarbon SbX3 molecular compounds discussed later (Section 11.11.1.2). The Raman spectrum of the molecular compound was found to be the superposition of the spectra of the individual components, indicating very small mutual n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

764

octasulfur

SbCl3 dimer

z y

Fig. 11.55. Crystal structure of {S8 SbCl3} at 268K projected down [100]. The secondary interactions within the SbCl3 dimers are shown by broken lines, the S Sb interactions (distances up ˚ ) by dashed lines. The three covalent Sb–Cl distances are 2.359, 2.388 and 2.349 A. The intrato 4 A ˚ . (Data from Mu¨ller and Mohammed, 1983.) ring S–S distances range from 2.036 to 2.055(2) A n n n

n n n

perturbation. The yellow crystals are stable for some weeks at room temperature but decompose rapidly into the components on heating. There are centrosymmetric Sb2Cl6 pairs to which crown-shaped S8 molecules (ideal ˚ (to one S8) symmetry 8 2m) are linked by S . . . Sb distances of 3.33, 3.73 and 3.96 A ˚ and of 3.49 A to another S8 (Fig. 11.55). There is quasi-octahedral coordination about Sb ˚ are taken into account. There are distinct resemblances to the if distances of less than 3.5 A {diphenyl 2SbBr3} structure type shown below in Figs. 11.73 and 11.74. Although the Sb . . . S interactions are similar in {1,4-dithiane SbCl3} (Section 11.4) and {S8 SbCl3}, the important distinction is that the former has ‘‘pure acceptors’’ and the latter ‘‘selfinteracting’’ acceptors. n n n

n n n

11.11

n n n

-Donors and s-acceptors

The molecular compounds treated in this section are between acetylenes, oleﬁns or aromatics as electron donors and soft metal ions in low oxidation states as s-acceptors; speciﬁcally we consider Ag(I) and Cu(I) salts, with primacy given to Ag(I) because of the larger amount of information available about these systems. These molecular compounds exist essentially only in the solid state and dissociate appreciably in solution. Consideration of the structures suggests that the differences between aromatic and oleﬁn adducts are smaller than their resemblances; we introduce them in sequence and then compare their crystal chemistries. The earliest studies of interactions between aromatic hydrocarbons and silver salts were studies of the phase diagrams of AgClO4 (in the presence of water) with benzene (Hill, 1922), aniline (Hill and Macy, 1924), pyridine (Macy, 1925) and toluene (Hill and Miller, 1925). The following solid phases were isolated: benzene AgClO4; n n n

-DONORS AND s -ACCEPTORS

765

6(aniline) AgClO4; 4(aniline) AgClO4; 2(aniline) AgClO4; aniline AgClO4; 5(pyridine) AgClO4; 4(pyridine) AgClO4; 2(pyridine) AgClO4 and toluene AgClO4. An early study by Winstein and Lucas (1938) of the coordination of unsaturated compounds with silver ions in solution led to the synthesis of crystalline 1 : 1 adducts of dicyclopentadiene with AgNO3 and AgClO4. The 2 : 1, 1 : 1 and 2 : 3 crystalline compounds of cycloctatetraene with silver salts, and a 1 : 1 cyclo-octatriene AgNO3 adduct, were reported in 1950 by Cope and Hochstein and by 1962 some thirty crystalline compounds of AgNO3 and AgClO4 with various oleﬁns had been reported (Bennett, 1962). These early results, for both aromatics and oleﬁns, show that more than one stoichiometry is possible (perhaps even common) and thus a unique mode of interaction of Agþ with the -system of the donor is not to be expected; fortunately a sufﬁcient variety of stoichiometries has been studied to provide a comprehensive picture. More recent synthetic work with AgClO4 compounds of aromatics is summarized in Table 11.24; crystal structures of most of these compounds have been reported. The results fall into two time periods. First, there is the early work of Rundle and Amma and coworkers over the period 1950–1975; then there was a fallow period for the next twenty years, with the ﬁeld being resuscitated by Munakata and coworkers. Most compounds (oleﬁns and aromatics alike) have AgNO3 and AgClO4 as acceptor moieties but other anions of strong acids have been used, such as AlCl 4 , BF4 (Quinn and Glew, 1962; Buffagni et al., 1968), F3COO and F3CSO3 (triﬂuromethanesulphonate or triﬂate) (Gash et al., 1974). The crystalline adducts range from fairly stable in the atmosphere (decompose within a few days) to very unstable; rigorously dry conditions are often essential for preparation and preservation of the most reactive adducts. Most adducts are unstable to light (reduction of Agþ to Ag) and many to x-rays. Many of the crystalline adducts are disordered to some extent; thus details of molecular dimensions, especially in older work, should be treated with judicious reserve. Formation of an adduct with a silver salt has become an accepted method of purifying oleﬁns and aromatics, of stabilizing labile molecules and of preparing crystalline adducts suitable for crystal structure analysis (before the advent of direct methods this technique was important for determining structures of complicated molecules by heavy-atom methods; it is still important when the crystals of the parent hydrocarbon are disordered or liquid at ambient temperatures). Interactions between oleﬁns and silver salts have been used in the petroleum industry since at least the 1930s. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

11.11.1

Aromatics as donors and Ag(I) salts as acceptors; also {benzene CuAlCl4} n n n

Most compounds of aromatic hydrocarbons with silver salts are with AgClO4, especially those for which crystal structures have been determined (Table 11.24). We emphasize ﬁrst the resemblances and then discuss the differences. In the AgClO4 adducts of aromatic hydrocarbons the Agþ is four-coordinated, with a rather distorted tetrahedral arrangement of the four ﬁrst neighbors. Usually these are two C–C aromatic bonds, either in the same or in two different molecules, and two oxygen atoms of different ClO 4 ions; however, either ion can interact with Agþ ions. The one or two oxygens of a particular ClO 4 þ þ ˚ C distances lie in the range 2.4–2.5 A and the Ag O distances in the closest Ag ˚ range, with occasional outliers. Many combinations of the individual features 2.35–2.5 A of this bonding pattern are possible (and also some deviations from it) and the interatomic n n n

n n n

766

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

Table 11.24. Molecular compounds of aromatic hydrocarbons with AgClO4 (ratio hydrocarbon to silver salt given). The unbracketed entries in the table were reported by Peyronel et al. (1958) and the bracketed entries by other authors; all references except the first are to crystal structure analyses. No attempt has been made to assign priorities or achieve complete coverage 2:1

1:1

3:4

2:3

1:2

1:4

phenanthrene

naphthalene; anthracene* (benzene) RG50; SR58

(Coronene) M98

Fluoranthene M99

anthracene

Rubrene 4H2O M98

o–xylene TA75a

p-xylene

toluene (dec.25 )

(cyclohexylbenzene) HGA71

m-xylene

(1,4-benzodioxan) BB85

1- and 2methylnaphthalene (1,6-, 2,3- and 2,6dimethylnaphthalenes) B60 (acenaphthene) RA72; (acenaphthylene) RA72 (indene) R72 (1,2-diphenylethane) TA75b (diphenyl, diphenylmethane) V60 [2.2]paracyclophane M99 (2-benzene) (2–9,10diphenylanthracene) FADNUT M98

(pyrene) NOKNUW; M97 (perylene) NOKPAE; M97 (toluene) FADPEF; M98

* Needles and prisms were reported, so there are perhaps two polymorphs. References: B60 – Buffagni et al., 1960; BB85 – Barnes and Blyth, 1985. HGA71 – Hall Grifﬁth and Amma, 1971; M97 – Munakata et al., 1997; M98 – Munakata et al., 1998; M99 – Munakata et al., 1999; R72 – Rodesiler et al., 1972; RA72 – Rodesiler and Amma, 1972; RG50 – Rundle and Goring, 1950; SR58 – Smith and Rundle, 1958; T69 – Taylor et al., 1969; TA75a – Taylor and Amma, 1975a; TA75b – Taylor and Amma, 1975b; V60 – Vezzosi et al., 1960. In addition, the following solvated compounds have been prepared: 9,10-diphenylanthracene AgClO42(benzene) (k; FADNUT); rubrene.4(AgClO4).4H2O (k); benzo[a]pyrene.2(AgClO4).2(toluene) (k; FADPEF); 4(benzo[g,h,I]pyrene).4(AgClO4).toluene (l); decacyclene.2 (AgClO4).(benzene) (l).

distances are altered in a complicated way to give the lowest free-energy structures; disordered arrangements are not uncommon. In the molecular compounds of benzene and substituted benzenes with AgClO4, each aromatic molecule interacts only with a single Agþ ion while each Agþ ion interacts with two different aromatic molecules. For example, in bis(o-xylene) AgClO4 (Taylor and n n n

-DONORS AND s -ACCEPTORS

C

767

O

A

Ag perchlorate bis(o-xylene) dimer

perchlorate

o-xylene Ag+

perchlorate

z

B

x y

Fig. 11.56. An indivdual dimer of {bis(o-xylene) AgClO4}, viewed down [201] of the triclinic unit cell. The dimer is located about the centre of inversion at the origin of the unit cell; the dimer ˚, packing units shown interact through dispersion forces. The Ag O distances are 2.56 and 2.60 A ˚ ˚ the Ag C distances are 2.44 and 2.59 A to adjacent carbons in one o-xylene, and 2.49 and 2.57 A to ˚ . The precision of these rather the second o-xylene. Cl–O distances are 1.28, 1.28, 1.38 and 1.39 A early measurements is not high – compare, for example, the Cl–O distances of 1.441(1) and 1.451(1) ˚ found in {benzene AgClO4} discussed below. (Data from Taylor and Amma, 1975b.) A n n n

n n n

n n n

n n n

Amma, 1975a; OXAGPC) discrete (o-xylene) Agþ units are bridged by two tricoordinated oxygens of centrosymmetrically-related ClO 4 ions to form discrete dimeric formula units (Fig. 11.56); each Agþ interacts with a single aromatic bond in each of two ﬁrst-neighbor o-xylenes. n n n

O O

Cl

Ar O

Ag

O

Ar

O O

Cl O

Ar O

Ag Ar

However, the formation of inﬁnite chains seems to be a more common arrangement and is illustrated by the bis(m-xylene) AgClO4 structure (Taylor, Hall and Amma, 1969; n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

768

MXAGCO) which can be described in terms of chains of the type shown in the scheme below, where Ar represents the m-xylene molecule. The crystals are chiral (space group P21221), which is unusual in this group of structures and is a consequence of the arrangement of the chains as the individual structural units are achiral. Rather similar chain arrangements are found in {bis(cyclohexylbenzene) AgClO4} (Grifﬁth and Amma, 1971; CHBSPC10), {benzene AgClO4} (Rundle and Goring, 1950; Smith and Rundle, 1958) and (1,2-diphenylethane AgClO4} (Taylor and Amma, 1975b; DPEAGP), where the two phenyl rings behave as independent aromatic entities. {Bis(1,4benzenedioxan)silver(I) perchlorate} has a similar chain structure (Barnes and Blyth, 1985; DAVDIN), and is clearly a -complex, there being no interaction between Agþ and oxygen atoms; the crystals are chiral (space group C2). This is a particularly interesting example as both the -complex of silver perchlorate with 3(1,4-dioxane) (Prosen and Trueblood, 1956; AGPDOX) and the -complex with benzene are known. The {benzene AgClO4} structure has been re-determined at 18, 78 and 158K by neutron diffraction, giving roughly equal precision to all parameters (McMullan et al., 1997; AGPCBE01, 02, 03). We shall discuss only the 18K structure (orthorhombic, space ˚ , Z ¼ 4), which is the most precise group Cmcm (no. 63), 7.913(1) 7.837(2) 11.798(3) A structure considered in this chapter (and, perhaps, in this book). There is no phase change between 300 and 18K. The structure viewed down [ 1 10]is shown in Fig. 11.57. Ag and Cl are at Wyckoff position ‘c’, mm symmetry, 0,y,1/4, O1 at ‘f’ (0yz) and O2 at ‘g’ (xy,1/4), both symmetry m, C1 and H1 at ‘e’, symmetry 2, and C2 and H2 at general positions. The benzene molecules are centered at ‘a’ (000), symmetry 2/m, and the C6 rings are planar. Agþ ions are centered over C–C bonds and are slightly outside the C6 ring; these two ˚ compared to the other four. The principal effect of bonds are lengthened by 0.007(1) A þ ˚ away from Ag on the benzene molecule is to push the two nearest H atoms 0.064(1) A the C6 plane. This minor distortion allows the p– orbitals to point inward towards the metal ion. The ion is four coordinate (one to the C–C bond center, and three to perchlorate ˚ (2) and 2.785(1) A ˚ (1). The differential effects on the Cl–O bond oxygens, 2.612(1) A ˚ ) are small but signiﬁcant. The very small geometrical lengths (1.451(1) and 1.441(1) A effects of complexation found in benzene AgClO4 possibly provide a benchmark against which other reported distortions (generally measured at room temperature) should be compared. The considerable disorder (static or dynamic was not established) found in the 1958 room-temperature XRD structure is consistent with the NMR results, which show rapid benzene reorientation in the solid at room temperature (Gilson and McDowell, 1964). Thermodynamic studies have been made on {benzene AgClO4}. Vapor pressure measurements give G298 ¼ 26.9(4)kJ/mol, H298 ¼ 92.1(1)kJ/mol and S298 ¼ 399(12)J/molK, while measurements of heat of solution give H298 ¼ 33.9 kJ/mol (Tildesley and Sharpe, 1953). These results suggest that the crystals are entropy stabilized. However, the suggestion of Smith and Rundle of Agþ disorder was not conﬁrmed by the much more precise study of McMullan et al. A calorimetric study over the temperature range 8–300K (Clayton et al., 1978) showed no transitions or major anomalies in the Cp–T curve, which accords with the results of the neutron diffraction study. It was estimated that the crystals had 10 J/mol K of conﬁgurational entropy at 298K. The AgClO4 molecular compounds of acenaphthene, acenaphthylene (Rodesiler and Amma, 1972) and indene (Rodesiler et al., 1972) have been studied. In all three molecules n n n

n n n

n n n

n n n

n n n

n n n

-DONORS AND s -ACCEPTORS

769

B arrows show Ag...H interaction

y

Cl

z

O perchlorate

x

A

1 0]. Examples of the various Fig. 11.57. The {benzene AgClO4} structure viewed down [1 ˚ , slightly shorter interactions are shown. The distance of Ag from the C–C bond center is 2.467(1) A than d(Ag C). The neutron diffraction measurements permit meaningful inclusion of hydrogen atoms in the diagram. (Data from McMullan et al., 1997.) n n n

n n n

the two C¼C bonds linked to Agþ, as indicated by the arrows in the formulae, are separated by two other C–C bonds.

acenaphthene

acenaphthylene

indene

The mutual arrangement of aromatic molecules and Agþ is very similar in {acenaphthene AgClO4} (ACENAG) (Fig. 11.58), and {indene AgClO4} (INDAEP), although there are some differences in the disposition of the perchlorate ions. n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

770

To 0(5)

C(8)

C(8⬘) C(1⬘) 121.8

C(1)

1.36

103.9

2.44

Ag(1)

111.5 C(9⬘) 106.3

1.52

1.46

123.0 C(7⬘)

C(9)

C(7)

1.56

76.7 2.51

To 0(2)

1.38

C(2⬘) 103.3

1.37

C(2)

70.7 111.0

111.0 C(11⬘)

110.3 123.4

122.4

C(10⬘) 120.0

C(11)

C(6)

116.3 C(6⬘)

1.44

1.54 1.40 C(10)

1.37 C(12)

117.6 C(12⬘) To 0(2)

1.36 1.40

C(3⬘) 118.7

Ag(2)

C(3)

2.51

121.4 118.6

C(5)

C(5⬘) 72.6

2.48

To 0(4)

74.8

1.40

1.46

C(4)

C(4⬘)

Fig. 11.58. View down [001] of the {acenaphthene AgClO4} structure showing only Ag . . . C ˚ , space group Pmnb, Z ¼ 8. In this interactions (a ¼ 18.531(2), b ¼ 15.586(5), c ¼ 7.877(3) A þ view a mirror plane normal to the page bisects the Ag and perchlorate ions (latter not shown); [100] is horizontal and [010] vertical. There are two crystallographically independent Agþ and perchlorate ions in the asymmetric unit, both on mirror planes. (Reproduced from Rodesiler and Amma, 1972.) n n n

double bond

Ag

Ag

Ag Cl

double bond

Fig. 11.59. Part of the {acenaphthylene AgClO4} structure as viewed down [100]. The crystals ˚ , Z ¼ 4, space group P22121. The are orthorhombic, a ¼ 6.416(1), b ¼ 10.286(2), c ¼ 18.056(2) A silver atoms lie on the twofold axes normal to the page; the crystals are chiral but the absolute conﬁguration was not determined. There is appreciable disorder, not shown, in the structure. (Reproduced from Rodesiler and Amma, 1972.) n n n

-DONORS AND s -ACCEPTORS

771

In {acenaphthylene AgClO4} (ACYLAG), which is disordered, there is slippage along the chain (Fig. 11.59); this structure is very similar to that of {bis(m-xylene) AgClO4} if one replaces the two m-xylene molecules by one acenaphthylene molecule. In {naphthalene 4AgClO44H2O} (Grifﬁth and Amma, 1974a; NAPAGP) and {anthracene 4AgClO4H2O} (Grifﬁth and Amma, 1974b; ANTAGP) the 1–2 and analogous bonds of the aromatic molecules provide four equivalent binding sites per molecule for Agþ. However, the water molecules in these two hydrated crystals introduce appreciable changes from the bonding patterns described above for anhydrous compounds. In both the hydrated compounds Agþ interacts with one C–C bond of a particular aromatic molecule (thus each aromatic molecule interacts with four different Agþ ions) and completes its coordination requirements by Agþ O interactions with one water ˚ ) and two oxygens of different perchlorate ions molecule (d(Agþ . . . O) ¼ 2.35 A þ ˚ (d(Ag . . . O) 2.6 A). In the naphthalene compound the water molecules each interact with one Agþ ion and are also hydrogen-bonded together to form a sheet; in the anthracene compound the water molecule interacts with two Agþ ions. The Agþ . . . C ˚ ) in the naphthalene compound and normal (2.45 A ˚) distances are extended (2.6 A in the anthracene compound. Anhydrous naphthalene and anthracene molecular compounds with AgClO4 have been prepared (Table 11.24) but structures have not been reported. The structural chemistry of arene AgClO4 compounds attracted little further attention for about 25 years until its recent revival by Munakata and coworkers, who have prepared {pyrene2AgClO4}, {perylene2AgClO4}, {2(ﬂuoranthene)-3AgClO4}, (FADQAC), {[2.2]paracyclophaneAgClO4}, {9,10{3(coronene)4AgClO4} diphenylanthracene-AgClO4}2(benzene) (FADNUT), {rubrene4(AgClO4)4H2O} (FADPAB), {benzo[a]-pyrene2(AgClO4)}2(toluene) (FADPEF), {4(benzo[ghi]pyrene) 4(AgClO4)}toluene and {decacyclene2(AgClO4)}(benzene) and determined their crystal structures. References are given in Table 11.24. The motivation for their work was described as follows: ‘‘Polycyclic hydrocarbons have been selected as potential donor molecules for preparing metal ion – aromatic -donor – acceptor complexes with possible applications in electrical conductors and photosensitive devices.’’ Only time can tell whether these goals will be achieved, but there is no doubt that many remarkable crystal structures have been reported. Munakata and coworkers (1999) have classiﬁed the overall arrangements into ﬁve groups (Fig. 11.60). The linkage principles found in the simpler compounds are also encountered in these more intricate structures, but there can be additional features. ˚ ), A particular Agþ is linked to two C–C bonds in different arene molecules (distance 2.5 A ˚ ions (distance 2.5 A ), and can thus be described and to two oxygens of different ClO 4 either as 6-coordinate or as pseudo-tetrahedral. These give two-dimensional (crumpled) sheets which are then packed to give a three-dimensional supramolecular architecture. However, {9,10-diphenylanthracene.-AgClO4}2(benzene) (FADNUT) is unusual in having a monomeric structure. Some of the benzene (toluene) third components are present as space-ﬁlling solvent of crystallization (e.g. {4(benzo[ghi]-pyrene)4(AgClO4)} toluene), but there are examples where these molecules interact with Agþ (e.g. {decacyclene2(AgClO4)}(benzene)). We shall only describe {3(coronene)4AgClO4} ˚ , 89.43(2) 65.25(2) (FADQAC; triclinic, P 1, Z ¼ 1, 12.771(4) 11.224(2) 10.894(3) A n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

772

= ClO–4 M

M

M

M M

M

M

M

M

M

M

M

M

M

M

M

M

M

M

M

M

M

M

a. pillared brick

b. W-type architecture

M

M

M

M

M

M

M

M

M

M

d. triple-decker

c. double-decker

M

M

M

M

M

M

e. multidecker

Fig. 11.60. Classiﬁcation of the structure types found by Munakata et al. (1999) for the metal sandwich systems derived from assembly of Ag(I) perchlorate with polycyclic hydrocarbons. (Reproduced from Munakata et al. (1999).)

C O Ag

perchlorate Ag to C

Cl coronene at centre of symmetry

O zx y

B

coronene at general position

Fig. 11.61. {3(coronene)4AgClO4} viewed down [101]. The strips extend along [001] (see next ﬁgure) and repeat along [010], with – interactions between adjacent strips. The central coronene interacts with four Agþ cations, and the outer coronenes each with two Agþ. (Data from Munakata et al., 1998.)

-DONORS AND s -ACCEPTORS

773

Strip 1 triple-decker stack of coronenes Ag

A

O Strip 1

Cl

perchlorate

Strip 2 C

Ag

B

Strip 2

x z y

Fig. 11.62. {3(coronene)4AgClO4} viewed down [010]. Strips 1 and 2 extending along [001] only have van der Waals interactions. This view shows that each strip has an organic core and inorganic surfaces. (Data from Munakata et al., 1998.)

79.57(2) ) in some detail. One coronene molecule is at a center of symmetry, all the other moieties being at general positions (Fig. 11.59). The central coronene is planar to within ˚ but the outer coronene is bow shaped (convex towards the center), with the outer 0.018 A ˚ from the plane of the central carbons (those linked to the Agþ ions) deviating by 0.25 A hexagon. This is an unusual feature. There are a number of interesting compounds of macro-rings of aromatic molecules with silver salts (Beverwijk et al., 1970; Gmelin, 1975). For example, {([2](1,5) Naphthalino[2]paracyclophane)silver(I) perchlorate} crystallizes in space group P21/n, ˚ , ¼ 101.27(1) ) (Schmidbaur, Bublak et al., 1988; Z ¼ 4 (12.495(2) 8.546(1) 16.196(2) A SACFOR). Each Ag is connected with the naphthalene rings of two paracyclophanes and with two perchlorate ions, two oxygens of which are chelating, one monodentate and the fourth noninteracting. The cation–anion chains are linked through the organic ligands in such a way that a sheet structure is formed. The naphthalene rings are 3-bonded to the silver atoms, which are not ring-centered; the benzene rings of the cyclophanes are not

774

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

involved in the metal coordination, while the silver atoms are 3-linked to the naphthalene rings, and shifted from the centers of the rings. [23](1,4)Cyclophane (called [2.2.2]paracyclophane by Cohen-Addad et al., (1983)) forms 1 : 1 compounds with AgClO4 (chiral crystals, space group P212121; CAKDAT) and with silver triﬂate (AgCF3SO3) (space group P21/a, Z ¼ 16) (Kang et al., 1985; CUXTIY), in which the silver ions lie on the pseudo-threefold axis of the molecules at distances of ˚ ˚ from the six nearest carbons for the AgClO4 salt and of 2.40–2.69 A 2.54–2.67(2) A for the triﬂate salt, and are also each coordinated to one oxygen (d(Ag–O) ¼ 2.51(2) and ˚ respectively). 2.41 A

[23](1,4)Cyclophane

Deltaphane ([26](1,2,4,5)cyclophane also forms a 1 : 1 compound with silver triﬂate (space group P21/n, Z ¼ 4; Kang et al., 1985; CUXTAQ) with rather similar coordination ˚ above the planes of the three nearest carbons for the silver ion; the Agþ ions are 0.23 A (Fig. 11.63).

Ag

S C O F

Fig. 11.63. The structural unit in {deltaphane silver triﬂate}. (Reproduced from Kang et al., 1985.) n n n

-DONORS AND s -ACCEPTORS

775

The structure of {pentacyclo-[12.2.2.22,526,9210,13]-1,5,9,13-tetracosa-tetraene AgCF3SO3} has been brieﬂy reported (McMurry et al., 1986; DURDIF, no coordinates); the Agþ ion enters into the macro-ring and is coordinated to the four C ¼ C bonds. This latter structure is noted here rather than in the next section, where it really belongs, because of the macro-ring nature of the ligand. One (Ag(I)) structure has been reported with AlCl 4 as counterion – this is {C6H6 Ag(I)AlCl4} (Turner and Amma, 1966b; SALBEN), which is compared here with {C6H6 Cu(I)AlCl4} (Turner and Amma, 1966a; BZCATC10). The unit cells for ˚ , ¼ 95.1(3) , Z ¼ 4, {C6H6 Ag(I)AlCl4} (a ¼ 9.09(3), b ¼ 10.22(3), c ¼ 12.73(3) A ˚, space group P21/c) and {C6H6 Cu(I)AlCl4} (a ¼ 8.59(1), b ¼ 21.59(3), c ¼ 6.07(1) A ¼ 93.0(3) , Z ¼ 4, space group P21/n) appear different at ﬁrst sight but can be related. The important common feature is in the immediate surroundings of the metal atoms – the coordinations are very similar. Both structures are polymeric with 2 coordination of metal to benzene, together with interactions to two Cl atoms of one AlCl4 anion and one Cl of another anion. In {C6H6 Ag(I)AlCl4} there are inﬁnite sheets, held together by van der Waals forces, about the (100) planes (Fig. 11.64). The sheets are composed of AlCl4 tetrahedra interconnected by Ag . . . Cl links; each Agþ is linked to chlorines of three different tetrahedra in such a way that every Cl of every AlCl4 is involved in a link to n n n

n n n

n n n

n n n

n n n

n n n

sheet of AgAIC14 columns

sheet of benzene molecules 2.58

C 2.48 2.77 2.80

2.93

Ag1

AI1 O B

3A z

y

x

Fig. 11.64. Projection of {C6H6 Ag(I)AlCl4} structure down [010]. The Al–Cl distances are not ˚ , with the Ag Cl distances 2.58, 2.80 and 2.78 A. The signiﬁcantly different from 2.14 A ˚ . (Data from Turner and Agþ C¼C interaction is unsymmetrical 2, with d(Ag C) ¼ 2.48, 2.93 A Amma, 1966b.) n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

776

˚ ). Each Agþ interacts with one bond of a Agþ (d(Agþ . . . Cl ¼ 2.59, 2.77, 2.80 and 3.04 A þ ˚ benzene ring (d(Ag . . . C ¼ 2.47, 2.92 A, with the distance to the midpoint of the bond ˚ ); such asymmetry is found in many of these compounds. The benzene ring being 2.47 A extends out of the AgAlCl4 sheets, with its plane approximately normal to the Agþ ! k vector. The {C6H6 Cu(I)AlCl4} structure is based on pleated sheets lying about glide planes at y ¼ 1/4, 3/4 (Fig. 11.65). The Cuþ ion is placed asymmetrically with respect to one of the bonds of the benzene ring, and the coordination environment is completed by three chlorines of three different AlCl 4 ions. The Cu to ‘midpoint of C–C bond’ vector is nearly perpendicular to the plane of the benzene ring (angle ¼ 98 ). The overall structure is thus similar to those of the silver-salt molecular compounds, and the anion plays a correspondingly important role in stabilizing the structure. Despite the similarities between the two structures, the differences must not be disregarded. Comparing interatomic distances, one notes that the AlCl4 tetrahedra in the two structures are indeed ˚ , but other interatomic distances are appreciably shorter similar, with d(Al – Cl) 2.13 A in {C6H6 Cu(I)AlCl4} than in {C6H6 Ag(I)AlCl4}. For example, d(Cu . . . Cl) ranges ˚ , while d(Ag . . . Cl) is 2.59–3.04 A ˚ ; d(Cu . . . C) is 2.15 and 2.30 A ˚, from 2.36 to 2.56 A n n n

n n n

n n n

C

Benzene

O Cl2 Al

Al Cu Cl1

Cl3

Cl4

z B

y

Fig. 11.65. Projection of the crystal structure of {C6H6 Cu(I)AlCl4} down [100], showing the pleated sheets lying about alternate (040) planes. The 2 interactions between Cu and the benzene ring are shown by the arrows in the upper sheet in the cell. The values of d(Cu . . . C) are 2.15(3) and ˚ respectively; the Cu . . . Cl distances are – to Cl1 2.56(1), to Cl3 2.40(1) and to Cl4 2.30(3) A ˚ . The Al–Cl distances are 2.14(1) A ˚ except for Al–Cl2 (not bonded to Cu), which is 2.37(1) A ˚ signiﬁcantly shorter at 2.07(1) A. (Data from Turner and Amma, 1966a.) n n n

-DONORS AND s -ACCEPTORS

777

˚ . The bonding in the two compounds was discussed whereas d(Ag C) is 2.47 and 2.98 A by Turner and Amma but we shall not elaborate. {C6H6 Cu(I)AlCl4} is important in the Tenneco process for the puriﬁcation of carbon monoxide by formation of weak complexes with Cu(I) salts (Sneedon, 1979): n n n

n n n

nCO þ CuðIÞ ¼ CuðIÞðCOÞn The problem of poor solubility of Cu(I) salts is resolved by complexing them with aromatic solvents such as benzene or toluene. These complexes are not affected by CO2, N2 or H2 but must be protected from O2, H2O, H2S and SO2. Another situation where there are differences in the coordination around Ag and Cu are the 1 : 1 coordination polymers of [2.2]cyclophane with Ag(I)(GaCl4) (FAPCAA) and of [3.3]cyclophane with Cu(I)(GaCl4) (FAPBUT) (Schmidbaur, Bublak, Huber, Reber and Mu¨ller, 1986). Both Ag and Cu are approximately 2 bonded to aromatic rings of the cyclophanes but each Ag atom is linked to other silver atoms through two (GaCl4) anions while the coordination sphere of the Cu atom is saturated by a chelating (GaCl4) anion. Schmidbaur et al. comment ‘‘It remains an open question whether the different arene coordination of Cu(I) and Ag(I) . . . is due to the nature of the metal or to the difference in the cyclophane bridges.’’ Aromatic . . . Agþ interactions can also be important in more complicated structures: an example is Ag(I)[Cu(II)2(C8H4O4)2OH]5H2O (C8H4O4 is the o-phthalate ion) (Cingi et al., 1979; AGPHCU), where the silver ion is coordinated asymmetrically with a C–C bond of the benzene ring of the o-phthalate ion (distance of Agþ to midpoint of C–C bond ˚ ), with two water molecules (d(Ag . . . O) ¼ 2.33(3) and 2.54(3) A ˚ ) and to an is 2.43 A ˚ ); the overall coordination about Agþ is oxygen of the anion (d(Ag . . . O) ¼ 2.26(1) A distorted tetrahedral. 11.11.2

Oleﬁns as donors and Ag(I) salts as acceptors

AgNO3 is the silver salt most widely used in forming molecular compounds with oleﬁns, although AgBF4 has also been used. The 2 : 3, 1 : 1 and 2 : 1 compounds of cyclooctatetraene with AgNO3 have already been mentioned (Cope and Hochstein, 1950); norbornadiene forms 1 : 1 and 1 : 2 compounds with AgNO3 (Traynham and Olechowski, 1959; Traynham, 1961; Abel et al., 1959); linear mono-oleﬁns form 3 : 1 and 2 : 1 compounds with AgBF4 (and some other compositions as well), while butadiene forms {C4H6 AgBF4} and {3[C4H6] AgBF4} and 1,4-pentadiene forms a 1 : 1 and 2-methyl1,3-butadiene a 3 : 2 compound (Quinn, 1967). Both anhydrous and hydrated compounds can be made: for example, norbornadiene forms anhydrous compounds as above while crystallization from aqueous solutions gives {C7H8 AgBF4xH2O} (x < 2), where the water appears to be zeolitic, and {3[C7H8] 2AgBF4yH2O} (2 < y < 4), where the water appears to be structural (Quinn, 1968). Solid state studies suggested that the stability of the compounds decreases in the order SbF 6 > BF4 > ClO4 > NO3 . The stronger the acid, the more stable the compound containing the conjugate base of the acid as anion. Thus the most stable compounds would be expected to be those triﬂuoromethanesulphonic acid, the strongest monobasic acid known. This has been demonstrated in solution studies (Lewandos et al., 1976); these authors also made crystalline compounds of n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

778

mono-enes, dienes and trienes with AgCF3SO3 (i.e. silver triﬂate compounds, as already noted above). The crystal structures of the anhydrous and hydrated compounds compared below are quite complicated; in particular the oleﬁn molecules have more complicated shapes than the aromatics discussed above, leading to greater variety in the arrangement of the moieties. As before, we emphasize overall resemblances. The feature common to the structures is the interaction of the silver ion with C¼C double bonds, and structures will therefore be classiﬁed in terms of the numbers of such interactions, with Agþ . . . O interactions used as a secondary basis for classiﬁcation. Most of the crystal structures can be described as multiple sandwiches, with sheets of AgþNO 3 chains forming one part of the sandwich (the ionic part) and sheets of organic molecules acting as insulation between the charged sheets. The Agþ k interactions provide the ‘‘glue’’ between the two types of sheet. Silver ions each interacting with only one double bond are found in the 1 : 1 compounds of AgNO3 with exo-tricyclo[3.2.1.02,4]oct-6-ene (Gibbons and Trotter, 1971; TOEAGN) and with a pseudo-Diels–Alder dimer of norbornadiene (Caughlan et al., 1976; HCYTAG), in the 1 : 2 compounds of norbornadiene (Baenziger et al., 1966; BORNAG) and humulene (McPhail and Sim, 1966b; HULAGN) with AgNO3 and in the 1 : 3 compound of cis,cis,cis-1,4,7-cyclononatriene with AgNO3 (Jackson and Streib, 1967; CNTAGN10). In {trans-cyclooctene AgNO3} (Pbca, Z ¼ 8) (Rencken et al., 1988; GOJFEQ), the silver ion is coordinated almost symmetrically to the double bond (d(Ag C) ¼ 2.341(4), ˚ ), the ˚ ) and to two oxygens of different nitrate ions (d(Ag O) ¼ 2.295(3) A 2.327(4) A third oxygen being involved only in a van der Waals interaction. The conformation of the cyclooctene ring is twist-chair-chair with approximate D2 symmetry, which is also the minimum strain energy conformation of the free ring. n n n

n n n

n n n

exo -tricyclo[3.2.1.02,4]oct-6-ene

pseudo -Diels-Alder dimer of norbornadiene

The {norbornadiene . . . 2[AgNO3]} structure (space group Cmc21, Z ¼ 4) is rather symmetrical and can serve to show both the multiple sandwich arrangement of ‘‘charged’’ and ‘‘insulating’’ sheets and the arrangement of oleﬁn double bonds and oxygen atoms ˚ and the shortest around Agþ (Fig.11.66). The Agþ C distances are 2.31(5) and 2.41(4) A ˚ . These distances are fairly typical of those Agþ O distances are 2.27(4) and 2.34(4) A found in these three compounds; in particular the Agþ O distances are short enough to indicate some degree of covalence. It has been shown (Marsh and Herbstein, 1983) that the space group Cmcm is equally compatible with the atomic positions reported; the changes that would be required in the description of the structure are small and would make it more symmetrical and thus the space group change is not important in the present context. n n n

n n n

n n n

-DONORS AND s -ACCEPTORS

779

Inorganic Ag nitrate Organic bornadiene sheet

C

Arrow exemplifies interaction between sheets

O B

A

z x

y

Fig. 11.66. The structure of {norbornadiene 2AgNO3} projected onto (010). The interatomic distances are not accurate enough to distinguish among chemically similar interactions. (Data from Baenziger et al., 1966.) n n n

The silver ion is coordinated to two carbon double bonds in the same molecule in {-gorgonene AgNO3} (Hossain and Van der Helm, 1968; GORAGN10) and in different molecules in {germacratriene AgNO3} (Allen and Rogers, 1971; GRMTAG10) {cyclo-octatetraene AgNO3}, (Mathews and Lipscomb, 1959; COCAGN), in the 1 : 1 compound of the cyclo-octatetraene dimer (m.pt. 35.5 C) and AgNO3 (Nyburg and Hilton, 1959; COCDSN), in {costunolide 2AgNO3} (Linek and Nowak, 1976; COSTAG10) and in the four isostructural compounds of composition {2R AgNO3}, where R is trans-cyclodecene (Ganis and Dunitz, 1967; AGCDEC), trans-cyclododecene (Ganis et al., 1971; AGCDEG), cis-cyclodecene (Ermer et al., 1971; CDEAGN), and 1,1,4,4tetra-methyl-cis-cyclodec-7-ene (Ermer et al., 1971; TMCDAG). The structures of two hydrated compounds have been determined where Agþ interacts with two carbon double bonds; these are {pregeijerene AgNO3.H2O} (Coggon et al., 1966; PREJAG10) and {bullvalene AgBF4H2O} (McKechnie and Paul, 1968; BULAGF10). The overall structural features are the same as in the anhydrous compounds; the water molecules are ˚ ) but not coordinated to Agþ in the ﬁrst of these compounds (d(Agþ . . . OH2) ¼ 3.20 A ˚ ). The water there is strong coordination in the second (d(Agþ . . . OH2) ¼ 2.32, 2.41 A molecules play an essential role in the cohesion of the crystals of the second compound as they both occupy one of the silver-ion coordination sites and also provide a link (by n n n

n n n

n n n

n n n

n n n

n n n

n n n

780

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

hydrogen bonding to BF4) between cations and anions; the silver ions do not interact directly with the BF4 anions.

O O b-gorgonene

Germacratriene

Costunolide

Mixed situations are also found, where one Agþ interacts with one double bond and another with two double bonds. This shows that there is no great energetic advantage either to a single or a double interaction. In racemic {geijerene 2AgNO3} (Robinson and Kennard, 1970; GEIJAG10; P21/n, Z ¼ 4; geijerene is 3-isoprenyl-4-methyl-4vinylcyclohexene) one Agþ interacts with the isopropenyl and vinyl groups of a par˚ ) and completes its ticular geijerene molecule (d(Agþ . . . C) ¼ 2.39(5), 2.59, 2.54, 2.54 A distorted tetrahedral coordination (each double bond being considered to occupy a single coordination site) by interacting with oxygens from two bridging nitrate groups ˚ ). The other Agþ is trigonally coordinated to two bridging (d(Agþ . . . O) ¼ 2.42, 2.49 A þ ˚ ) and to the remaining double bond of the nitrate groups (d(Ag . . . O) ¼ 2.31, 2.48 A ˚ ). cyclohexene ring (d(Agþ . . . C) ¼ 2.30, 2.33 A n n n

* * Cyclo-octatetraene dimer

Pregeijerene

Bullvallene

Geijerene

In the molecular compound {3(1,5-hexadiene) 2AgClO4} (HDEAGC; Bassi and Fagherazi, 1965) two hexadiene molecules are in the transoid-gauche-transoid conformation and one in the centrosymmetric gauche-transoid-gauche conformation. The two double bonds of the tgt molecule are coordinated to one Agþ and one of the double bonds in the gtg molecule is coordinated to the other Agþ ion (Fig. 11.67). Thus the cation is the centrosymmetric moiety (hexadiene . . . Agþ . . . hexadiene . . . Agþ . . . hexadiene), with the outer and central hexadienes having different conformations. The perchlorate ions are disordered (rotating according to the authors) so nothing is known about how the Agþ coordination is completed. In {3(bullvallene) . . . AgBF4} (AGBULV10; McKechnie et al, 1967) double bonds of three different bullvallene molecules are coordinated to a single silver ion, giving discrete Agþ(C10H10)3 cations (Fig. 11.68; note that the three double bonds in a bullvallene molecule are chemically equivalent). Bullvallene I has two double bonds more weakly linked to n n n

-DONORS AND s -ACCEPTORS

781

Disordered perchlorate ion

O

1.31 Cl

1.34 1.33

Ag Centrosymmetric cationic packing unit

B z

x Ag...C distances range from 2.25 to 2.53 Å

y

Fig. 11.67. The crystal structure of {3(1,5-hexadiene) 2AgClO4} projected down [001]. The largest circles represent the disordered perchlorate ions. The crystals are monoclinic and the cell was ˚ , ¼ 98 , Z ¼ 4, space group P21/b). described with [001] unique (a ¼ 13.39, b ¼ 13.05, c ¼ 7.22 A (Data from Bassi and Fagherazi, 1965.) n n n

Agþ while molecules II and III each have one double bond more strongly linked to this Agþ. The BF4 ion is remote from the cation and does not interact directly with Agþ. This molecular compound, which is sensitive to light and x-rays, really belongs in Part 1 of this chapter, as the tetraﬂuoroborate ions do not interact with Agþ, as has already been noted for {bullvallene AgBF4H2O} (McKechnie and Paul, 1968). This is also probably the situation for {pentacyclo-[12.2.2.22,5.26,9.210,13]1,5,9,13-tetracosatetraene . . . AgCF3SO3} (McMurry et al., 1986; DIRDUF, no coordinates in CSD) although for the different reason that the Agþ ion is here essentially contained within the macrocycle. However, the number of examples is still too small, and uncertain, to lose the convenience of grouping together chemically similar compounds. The only example so far of AgClO4 interacting with an oleﬁn is provided by the allyl cyanide compound {CH2 ¼ CH-CH2-CN AgClO4} (Zavalii and Prots, 1987; FOBZEB) where the Agþ ions are joined in a chain by bridging perchlorate groups (d(O Agþ) ¼ ˚ ). The allyl cyanide molecules are coordinated to Agþ both through the 2.52, 2.56 A ˚ ) and the N atom (d(N . . . Agþ) ¼ 2.23 A ˚ ) and double bond (d(C . . . Agþ) ¼ 2.35, 2.43 A these interactions crosslink the chains into layers between which there are only van der Waals forces. This molecular compound can be considered to be a hybrid with both n-s and -s interactions. An apparent exception to the structures described above is the reported formation of a 1 : 1 compound of cyclobutadiene with AgNO3 (Avram et al., 1959); however, later n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

782

1.38

2.58 Ag 2.78

2.44 2.48 1.29 2.66 2.54

1.37 y z

1.50

2.69

x

Fig. 11.68. The structure of the cation in {3(bullvallene) AgBF4}. The distances of Agþ from the ˚. centres of double bonds involved in secondary linkages are shown; the cutoff has been set at 2.70 A The lengths of the double bonds are also shown, indicating that the carbon positions are not very precise. (Data from McKechnie et al., 1967.) n n n

work (Avram et al., 1961) showed that the correct formulation of the organic moiety was syn-tricyclo-[4.2.0.02,5]octadiene(3,7). Thus the compound should be formulated as {C8H8 2AgNO3}, which would be compatible with other structural results. A monomeric formulation had earlier been suggested (Fritz et al., 1960) on the basis of IR spectra. A crystal structure analysis should be decisive but has not been performed. n n n

Possible interaction between silver and the active methylene group of a chelate ring should also be noted – addition of silver salts to a solution of a metal acetylacetonate gives adducts with up to one silver per chelate ring. The crystal structures of tris(silver) dinitrate tris(acetylacetonato)nickelate(II) monohydrate (Watson and Lin, 1966; AGACNI) and of mono(silver) perchlorate iron(III) tris(acetylacetonate) monohydrate [AgClO4 Fe(C5H7O2)3H2O] (Nassimbeni and Thackeray, 1974; FACAGP) have been reported; ˚) both show four coordinated silver with close aproaches to the methylene carbon (2.3 A and to oxygens; the ﬁrst compound has approximately tetrahedral coordination about silver and the second planar. Finally, {C605(AgNO3)} is a striking inclusion complex of the fullerene in a silver nitrate network that incorporates some of the structural features described above (Olmstead, Maitra and Balch, 1999, HIFCOO; Balch and Olmstead, 1999). There is an extended network of AgNO3 moieties in which each Agþ is in contact with six oxygens

-DONORS AND s -ACCEPTORS

783

˚. from the nitrate ions, with Ag . . . O distances ranging from 2.340(12) to 2.814(12) A There is fourfold disorder of the fullerene molecule within the cavity, and one of the Agþ ˚ ) and a ions is also disordered. There is 2 interaction of Agþ to C (2.59(1) and 2.70(1) A 1 þ ˚ rare, stronger, interaction (d(Ag ) . . . C ¼ 2.213(6) A. 11.11.3

Some general structural principles emerging from Sections 11.11.1 and 11.11.2

Some general principles emerge from the preceding description of the available structural information; such differences as there are between the silver-salt compounds of aromatic and oleﬁnic ligands seem to stem mainly from the greater variability of double-bond location in the oleﬁnic molecules, and we continue to treat them together. (a) Coordination about Agþ: in the molecular compounds of aromatics with AgClO4: the silver ion interacts with one C–C bond of the aromatic molecule only in the hydrated naphthalene and anthracene compounds. In all the other compounds of this group the silver ion interacts with two different aromatic molecules, as in the compounds with benzene, o- and m-xylene, cyclohexylbenzene, 1,2-diphenylethane, acenaphthene, acenaphthylene and indene. There is always four-coordination about Agþ, with a distorted tetrahedral arrangement of coordination sites; the coordination sites additional to the C–C bonds are provided by oxygens of the perchlorate ions in the anhydrous compounds while water oxygens play an important role in the two hydrated compounds. When Agþ interacts with two aromatic molecules, the planes of these molecules are approximately perpendicular. An idealized location for Agþ could be above the centre of the aromatic bond; such completely symmetrical positioning is not found in ˚ practice and the usual situation is for the two Agþ. . . C distances to differ by 0.1–0.2 A and for the vector from the midpoint of the double bond to Agþ to be displaced by about 20 from the normal to the plane of the aromatic molecule. Most authors suggest that bonding is responsible for these displacements from the idealized situation but the variety of steric arrangements is such that a clearcut explanation does not appear possible as yet. In the molecular compounds of oleﬁns with AgNO3, one ﬁnds Agþ interacting with one double bond or with two. Two crystals are known in which one Agþ interacts with one double bond while a second interacts with two; these are {geijerene AgNO3} and {3(1,5-hexadiene) 2AgClO4}. Both three- and four-coordination have been found in the molecular compounds with oleﬁns, the coordination sites other than double bonds generally being occupied by oxygen (an exception is {3(bullvallene) AgBF4}. The mode of interaction of NO3– groups with Agþ ions varies from one molecular compound to the next; three oxygens of different NO3– groups can be involved at one extreme, as in {cyclonona-triene 3(AgNO3)} or three NO3–groups can be involved in bidentate fashion at the other extreme, as in {exo -tricyclo-oct-6-ene AgNO3}. (b) overall crystal structures: most of these silver-salt molecular compounds, albeit with aromatic or oleﬁnic moieties, have layer structures composed of sheets of Agþ and anions, separated by sheets of the organic moieties. Anions bridging between Agþ ions make important contributions to the binding within the ionic sheets, while the organic sheets are bonded to the ionic sheets through the Agþ k interactions. n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

784

In formal terms these substances are salt-molecule compounds, with the organic moiety neutral and the charge residing on Agþ and the anions. Clearly there is interaction among all three moieties but the essential points are that the type of interaction between Agþ and organic moieties is similar and consistent in this whole group of compounds, which justiﬁes their treatment together, and (b) the perturbation of the organic moiety is small.

(a)

The latter point follows from the observations that the aromatic molecules remain planar and that the changes in bond lengths and angles are small (indeed are hardly established in most of the crystal structure analyses). This situation should be contrasted with that found in the compounds formed by aromatic molecules with some alkali-metal coordination complexes; for example in bis{(tetramethyl-ethylenediamine) Li(I)} anthracenide (Rhine et al., 1975) the tetramethylethylene-diamine ligands are neutral while the anthracene moiety appears as a dianion. This hardly meets our criterion (Chapter 1) that the properties of the individual components of a molecular compound should be ‘‘very largely conserved’’ and hence such compounds, despite their interest, are not considered further in this book. Some other salt-molecule molecular compounds that do meet our criterion are considered in Chapter 17. 11.11.4

Acetylides as donors and Ag(I) salts as acceptors

Silver nitrate forms two molecular compounds with silver acetylide – {Ag2C2 AgNO3} and {Ag2C2 6AgNO3} (Shaw and Fisher, 1946) The ﬁrst of these is tetragonal and the Debye–Scherrer pattern has been reported (Redhouse and Woodward, 1964) but not the structure. The structure of the second has been brieﬂy reported (Osterlof, 1954) – the crystals are rhombohedral and the linear Ag–C C–Ag molecules lie along the long diagonal of the cell, surrounded by six Agþ and NO3 ions. Details of the interactions were not given but presumably the triple bonds act as electron donors to the Agþ ions, whose coordination spheres are completed by oxygens of the nitrate groups. Detailed crystal structure analyses are available for the compounds of silver(I) triﬂate with 1,6-cyclodecadiyne (space group P21/n, Z ¼ 4; TACXIE), 1,7-cyclododecadiyne (space group P212121, Z ¼ 4; TACXOK) and 1,8-cyclotetradecadiyne (space group Pna21, Z ¼ 4; TACYEB) (Gleiter et al., 1990). Each silver atom has a distorted tetrahedral coordination, being linked to two triple bonds and two oxygens of the triﬂate ion. There is a two dimensional sheet arrangement in the ﬁrst of these molecular compounds and three dimensional arrangements in the other two. n n n

n n n

11.11.5

Acetylides as donors and Cu(I) salts as acceptors

1,2 : 5,6 : 9,10-tribenzocyclododeca-1,5,9-triene-3,7,11-triyne forms adducts with copper(I) triﬂate, which are in the border area between molecular and organometallic compounds. A pale-yellow, air-sensitive, polycrystalline adduct Cu(C24H12)-(O2SOCF3) has been prepared, while single crystals were obtained of the related packing complex Cu(C24H12)(O2SOCF3)(C24H12) (Ferrara et al., 1987; FEHTER). The crystal structure ˚ (Fig. 11.69) showed that the copper atom was in the centre of one macrocycle (but 0.18 A ˚ above its mean plane), coordinated to the three triple bonds, which were 0.04(1) A longer than those in the uncoordinated ligand of the packing complex, which was unchanged

-DONORS AND s -ACCEPTORS

785

Fig. 11.69. The triacetylide ligand 1,2 : 5,6 : 9,10-tribenzocyclododeca-1,5,9-triene-3,7,11-triyne C24H12.

O F3C–SO3 anion

F z y

x

Cu(2+) complexed C24H12 ligand

uncomplexed C24H12 ligand

Fig. 11.70. Partial view of the crystal structure of the packing complex {Cu(C24H12)(O2SOCF3) ˚ , ¼ 105.39(1) , Z ¼ 4, space group (C24H12)} [a ¼ 11.119(2), b ¼ 12.256(2), c ¼ 28.191(2) A P21/c]. (Data from Ferrara et al., 1987.)

from the neat ligand (Irngartinger et al., 1970; TBZTDY10). The intraligand adduction is reminiscent of those found with adducts of silver salts in macrocycles containing double bonds. The crystal structure is characterized by a striking plane-to-plane juxtaposition of complexed and uncomplexed ligands (Fig. 11.70); there is a formal analogy to that of 1,4-diphenylbutadiene tricarbonyliron1/2[1,4-diphenylbutadiene] (Section 10.3.4.3). A more typical coordination occurs in the air-sensitive {Cu(C24H12)-(O2SOCF3)C6H6} (Ferrara et al., 1988; GEKZOL) (Fig. 11.71), where each copper is linked to one triple bond of the macrocycle and to two oxygens of different triﬂate ions.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

786

F F

F

F

F

F F

F

F

0 S

0

0 0

S

0

0 Cu

Cu

0

0

S

0 Cu

Fig. 11.71. ORTEP diagram of the Cu(C24H12)(O2SOCF3) moiety (crystals are triclinic, P 1, Z ¼ 2). (Reproduced from Ferrara et al., 1988.)

A similar local coordination is found in the copper triﬂate compound of 1,7-cyclododecadiyne; here, however, the overall arrangement is that of a three dimensional polymer (Gleiter et al., 1990; TACYAX). Although the 1,7-cyclododecadiyne could be expected to have some conformational ﬂexibility, there is essentially no difference between its uncomplexed and complexed conformations. The space group of the crystals is the non-centrosymmetric C2, so enantiomorphous crystals are formed; however, the absolute conﬁguration of the crystal used in the structure analysis was not determined. 11.11.6

Aromatics as donors and Hg(II) salts as acceptors

Under this heading we recall the phenyl Hg interaction found in {diphenyl sulphoxide HgCl2} (see Section 11.9.2). Solid molecular compounds of various aromatics with HgX2 (X ¼ Cl, Br, I) have been reported (Vezzosi et al., 1974) but no structures seem to have been determined. The toluene and ethylbenzene adducts of HgCl2 decomposed too rapidly for satisfactory analyses to be obtained. However, the corresponding adducts with HgBr2 and HgI2 (Table 11.25) were very stable in air, soluble in ethanol and only slowly decomposed by HCl. The toluene and ethylbenzene adducts of HgI2 showed the interesting effect of changing colour from yellow to red over a few days, apparently without change of crystal structure; no explanation has been tendered. The compound C6H6 2HgAlCl4 has been reported (Turner and Amma, 1966c) but its structure was not determined because of lack of suitable crystals. The crystal structure of {hexamethylbenzene mercuric triﬂuoroacetate} [Hg(O2CCF3)2] at 108K has been reported (P 1, Z ¼ 2; Lau and Kochi, 1985; BODYEY10). There are dimeric structural units showing 2 interaction of Hg with hexamethylbenzene (Fig. 11.72), in accordance with the predictions of Rundle and Corbett (1957). n n n

n n n

n n n

n n n

-DONORS AND s -ACCEPTORS

787

Absorbance

0.6

0.4

0.2 280

310 λ , nm

340

Hg

Hg

Fig. 11.72. (a) Charge transfer spectra of C6(CH3)6 (0.0025 M), C6H(CH3)5 (0.0025 M) and mesitylene (0.005 M) with equimolar amounts of Hg(O2CCF3)2 in CH2Cl2 at 233K; (b) ORTEP diagram of the centrosymmetric dimeric {C6(CH3)6 [Hg(O2CCF3)2]} species (crystals are ˚ . (Reproduced from Lau triclinic, P1, Z ¼ 1). The Hg . . . arene carbon distances are 2.56, 2.58 A and Kochi, 1986.) n n n

Table 11.25. Solid molecular compounds reported (Vezzosi et al., 1974) between various aromatic hydrocarbons and HgBr2 and HgI2. The ratios given are for donor : HgX2 Acceptor HgBr2

Acceptor HgI2

1:1

1:2

2:1

1:1

1:2

acenaphthene

toluene ethylbenzene acenaphthene

anthracene

pyrene pyrene:dioxane

toluene

also 2(ethylbenzene) 3HgI2. n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

788

11.12 11.12.1

-Donors and p-acceptors Aromatics as donors and MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) as acceptors

11.12.1.1 Introduction We have already noted that SbX3 acts as an acceptor for two types of donor, alkylaromatics on the one hand and aromatics with N-, O- and S-containing substituents on the other. There are chemical and structural differences between the two groups and the latter group has already been discussed (Section 11.10). The requirement for inclusion here is aromatic ring Sb (or Bi) interaction in the crystalline molecular compound, while lack of this feature leads to discussion of the molecular compound in Section 11.10. Considerable information is available for the SbX3 group with aromatics and alkylaromatics as donor, together with an important extension to analogous BiX3 molecular compounds. We shall ﬁrst outline what is available, proceeding from isolated (M2X6) dimers to more complicated (M2X6)n oligomers. These Menshutkin molecular compounds exist only in the solid state. The ﬁrst crystal structures were brieﬂy reported in the early 1960s (Beagley and Edington, 1963); interest has continued over the years with many more (and more detailed) results reported by Mootz, Schmidbaur and coworkers, and others (see references in Tables 11.28 to 11.32). The crystal structures of SbX3 molecular compounds that have been reported show both broadly-based common features, and differences in detail; this also appears to hold for the smaller number of structures known for BiX3 molecular compounds. A wide variety of physico-chemical techniques are potentially available for investigation of these compounds, but relatively little has been reported. n n n

11.12.1.2 Structures of MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) crystals Interactions between the halogen donor atoms of MX3 groups and the metal acceptor atoms (M ¼ Sb, Bi) play an essential role in stabilizing the molecular compounds and so we summarize some relevant aspects of the crystal chemistry of the MX3 compounds. A comprehensive review of the crystal chemistry of the VA element trihalides has been given by Galy and Enjalbert (1982), the structures belonging to a limited number of groups. For those relevant here (Table 11.26), it was found that -SbCl3, -SbBr3, and -BiCl3 belong to the YF3 group, while the AsBr3 group contains AsCl3, AsBr3, ‘‘-SbCl3’’ and -SbBr3. The AsI3 group contains AsI3, -AsBr3, -SbI3 and BiI3. The structures of SbCl3 (Lindqvist and Niggli, 1956; Lipka, 1979b), of two polymorphs of SbBr3 ( (Cushen and Hulme, 1964) and (Cushen and Hulme, 1962)), and of BiCl3 (Nyburg, Ozin and Szymanski, 1971) are known. Another polymorph of SbCl3 was reported by Groth (1906) but its structure is not known. Monoclinic -SbI3 is reported to be intermediate between -SbI3 and a layered molecular type. ˚ and a third at The -SbCl3 structure has two equivalent covalent bonds at 2.368(2) A ˚ ; there are secondary interactions of lengths 3.457 (2), 3.609 (1) and 3.736 2.340(2) A ˚ (2). The coordination is best described as 3 þ 2 þ 3 (bicapped trigonal prismatic), with A a three-dimensional network of secondary linkages joining the SbCl3 molecules. The covalent interactions are maintained virtually unchanged in the molecular compounds, while the pattern of secondary interactions is matched to the arene molecule. Two careful studies (references in Table 11.26) support the non-centrosymmetric space group for

- D O N OR S A N D p -A C C E P T O R S

789

˚ ) for some MX3 compounds (cf. Section 11.2.3.3) Table 11.26. Crystal data (A Compound

a

b

c

Space group

Z

Reference

-SbCl3 -SbBr3 -BiCl3 -SbBr3 AsBr3 -SbI3 BiI3 AsI3 -SbI3

8.111 8.25(1) 7.641 10.12(1) 10.17 7.48 7.5117(3) 7.193(2) 7.281

9.419 9.96(1) 9.172 12.30(1) 12.09 7.48 7.5117(3) 7.193(2) 10.902 109.93

6.313 6.68(1) 6.291 4.42(1) 4.32 20.90 20.700(1) 21.372(7) 8.946

Pnma Pnma Pn21a P212121 P212121 R 3 R 3 R 3 P21/c

4 4 4 4 4 6 6 6 4

L79 CH62 NOS71; B82 CH64 B35 TZ66 C96 EG80 PS84

Notes: -SbCl3 was reported by Lindqvist and Niggli (1956) but no x-ray work appears to have been done. There are ˚ , 9.23 A ˚ , both P213, Z ¼ 4) obtained as polycrystalline samples and cubic polymorphs of BiCl3 and BiBr3 (8.14 A of unknown structure (Wolten and Mayer, 1958). References: B35 – Braekken (1935, 1938), cited in CH62; EG80 Enjalbert and Galy, 1980; B82 – Bartl, 1982; C96 – Carmalt et al., 1996; structure from polycrystalline sample; CH62 – Cushen and Hulme, 1962 (two-dimensional analysis); CH64 – Cushen and Hulme, 1964; L79 – Lipka, 1979; NOS71 – Nyburg, Ozin and Szymanski, 1971; PS84 – Pohl and Saak, 1984; TZ66 – Trotter and Zobel, 1966.

BiCl3, but the deviations from the centrosymmetric structure are very small; Galy and Enjelbart (1982) prefer Pnma, citing a 1972 NMR study in support of their contention. Re-examination would seem desirable. 11.12.1.3 Binary molecular compounds Phase diagrams have been determined for a number of aromatics with SbCl3; the donors include benzene (Perkampus and Sondern, 1980); pyrene (Mootz and Ha¨ndler, 1985); diphenylamine and triphenylamine (Lipka, 1979a); durene, pentamethylbenzene, hexamethylbenzene, naphthalene, 2,3-dimethylnaphthalene, diphenyl, anthracene, phenanthrene (Perkampus and Scho¨nberger, 1976); benzo[b]thiophene (Korte, Lipka and Mootz, 1985). Mootz and Ha¨ndler (1985) have reported the phenanthrene–SbBr3 phase diagram. Noteworthy individual preparations include the 1 : 1 compounds of benzene and toluene with SbCl3, SbBr3 and BiCl3; and 1 : 2 compounds of benzene and toluene with SbCl3 and SbBr3 (Peyronel et al., 1968), and many other individual preparations by this group. Spectroscopic studies include applications of optical spectroscopy, nuclear quadrupole resonance and Mo¨ssbauer spectroscopy to many Menshutkin compounds, and these will be discussed below. A wide variety of molecular compounds has been reported, with the predominant composition ratio 1 : 2 and this is also the most widely investigated group. There is a fair number of 1 : 1 compounds and a much smaller number with other ratios. Some of the latter are based only on the results of chemical analyses and conﬁrmation by other techniques would be useful; this seems even more desirable for the ternary compounds (discussed separately below in Section 11.1.2.1.4). Melting points (Table 11.27) suggest that the 1 : 2 compounds are more stable than the 1 : 1 where both are present in a system,

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

790

Table 11.27 Melting points (K) of some molecular compounds of aromatics with SbCl3. Other melting points in Table 11.32 Donor benzene toluene o-xylene m-xylene p-xylene mesitylene durene pentamethylbenzene hexamethylbenzene

1:1

1:2

Donor

1:2

289 292 281 329 316

352 316 307 311 343 349 377

naphthalene anthracene phenanthrene pyrene diphenyl

359 482 378 416 345

422 466

and melting points generally increases with molecular weight of the donor, although benzene 2SbCl3 is an exception. n n n

Crystal structures of arene/MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) binary molecular compounds There are two features of the MX3 molecular compounds that hardly change from structure to structure: ﬁrstly, the MX3 molecules all have a pyramidal shape with the M–X bond lengths and the X–M–X angles having essentially invariant values (e.g. d(Sb– ˚ and
n n n

(a) Structures based on isolated M2X6 dimers In the simpler situations there are centrosymmetric (or nearly so) M2X6 dimers, as in {diphenyl 2SbBr3} (Fig. 11.73; PYRSBB10; Lipka and Mootz, 1982), {2,2 0 -dithienyl 2SbCl3} (DITHSB10; Korte, Lipka and Mootz, 1985), {diphenylamine SbCl3} (Fig. 11.78; ZZZBAM10; Lipka, n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

791

˚ , deg) for binary {arene n(MX3)} molecular compounds (n ¼ 2 Table 11.28. Crystal data (A except for the last four entries where n ¼ 1). There are three isostructural groups (a pair, a triple and a group of four). The further entries are ‘miscellaneous’ in the sense that there do not appear to be close relationships among the several crystal structures n n n

Formula/refcode

a/

b/

c/

Space group

Z

Reference

diphenyl 2SbBr3 PYRSBB10

11.305

8.183

P21/c

2

LM82

2,2 0 -dithienyl 2SbCl3 DITHSB10* naphthalene 2SbCl3 NAPSBC benzo[b]thiophene 2SbCl3 DAZZIN p-xylene 2SbCl3 (at 163 K) PXYLSB 9,10-dihydroanthracene 2SbBr3 KEFJAG pyrene 2SbBr3 PYRABR

11.188

11.645 107.66 11.116 110.6 9.368 122.7 9.39 124.35 8.44 125.4 12.396 90.75 13.001 90.00 12.564 90.33 13.21 91.60 14.198 101.27 11.10 80.4 11.387 109.6 7.884 110.1 9.599 107.09 9.415 91.08 9.905 107.09 11.54 96.7 7.750

7.561

P21/c

2

KLM85

11.989

P21/c

2

HS69

11.856

P21/c

2

KLM85

12.79

P21/c

2

HM76

7.674

P21/c

2

S90

7.634

P21/c

2

BPV72

7.220

P21/c

2

V88

7.533

P21/c

2

B90

10.803

P21/c

2

VBC92

P 1

2

D72

P 1

2

MH85

P 1

2

LM78

C2/c

4

B96

26.037

P21/c

4

L78

17.513

C2/c

4

23.44

P21/c

4

KLM79; no coordinates HH66

32.005

Pbca

8

L80

11.495

P21/c

4

FR98

23.072 19.795

P212121 P21/n

8 2

F93 F98

n n n

n n n

n n n

n n n

n n n

9.154 9.205 9.13 11.189

n n n

n n n

10.699

pyrene2BiCl3 FUNJUT

10.564

pyrene2 BiBr3 ** JEJPET

10.589

[2.2]paracyclophane2BiBr3 JOLBAN phenanthrene 2SbCl3 PHENBS* phenanthrene 2SbBr3 DEJYEW ** diphenyl 2SbCl3 BIPHSB10* pyrene 2SbCl3 DEJYAS

7.896

diphenylamine 2SbCl3 DPASBC10 triphenylamine 2SbCl3 TPASBD dibenzyl 2SbCl3 DBESBC

7.802

diphenylamine SbCl3 ZZZBAM10 1,2,3-trimethylbenzeneBiCl3 PUVLOH Benzene BiCl3 LAHJAF {[2.2.2.2]paracyclophane SbBr3} GOMWAG

11.585

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

8.990 90.7 9.015 108.39 13.498 86.4 18.423

14.066 7.46

12.746 7.343 13.024

9.197 114.98 11.631 11.962 100.58

10.44 69.1 11.862 98.32 9.341 91.41 11.789

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

792

Table 11.28. (Continued ) ˚ , 90.70 110.90 * Reduced cell (unconventional setting); for PHENBS standard settings are 8.990 10.44 11.10 A 99.60 . ** reduced cell (standard setting). References: B90 – Battaglia et al., 1990; B96 – Battaglia et al., 1996; BPV72 – Bombieri, Peyronel and Vezzosi, 1972; D72 – Demalde et al., 1972; F93 – Frank et al., 1993; F98 – Ferrari et al., 1998. FR98 – Frank and Reiland, 1998; HH66 – Hulme and Hursthouse, 1966; HM76 – Hulme and Mullen, 1976; HS69 – Hulme and Szymanski, 1969; KLM79 – Korte, Lipka and Mootz, 1979; KLM85 – Korte, Lipka and Mootz, 1985; L78 – Lipka, 1978; L80 – Lipka, 1980; LM78 – Lipka and Mootz, 1978; LM82 – Lipka and Mootz, 1982; MH85 – Mootz and Ha¨ndler, 1985; S90 – Schmidbaur, Nowak, Steigelmann and Mu¨ller, 1990; V88 – Vezzosi et al., 1988; VBC92 – Vezzosi, Battaglia and Corradi, 1992.

2.501 2.506

3.695

B

2.521

Sb

A

Br

C

y x

z

Fig. 11.73. Projection of {diphenyl 2SbBr3} structure down [001]. A linear arrangement of diphenyl and Sb2Br6 groups extends along [101]; this shows as a horizontal (projected) band in the diagram. Both the diphenyl molecules and the Sb2Br2 parallelograms are centrosymmetric and ˚ ), and the other is a secondary planar; one edge of the parallelogram is a covalent Sb–Br bond (2.521 A Sb . . . Br interaction (3.695 A). A particular Sb2Br6 group does not interact with other Sb2Br6 groups but only with phenyl rings of different diphenyls. These interactions are indicated by arrows, the ˚ . The larger dark spheres are Br and the smaller Sb; the arene Sb . . . phenyl ring distance being 3.23 A moieties are lightly shaded. Hydrogens are not included. (Data from Lipka and Mootz, 1982.) n n n

1980) and {[2.2.2.2]paracyclophane 2SbBr3} ( (Fig. 11.79; GOMWAG; Ferrari et al., 1998). In {diphenyl 2SbBr3} linear chains of diphenyl and SbBr3 are found with diphenyl and isolated Sb2Br6 moieties located about crystallographic centres of symmetry, as shown in Fig. 11.73, each Sb interacting with one phenyl ring. The Br Sb distance n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

793

Br1 Br3 2.506 2.501 Sb 3.695

C6

3.23

2.521

C1

Br2⬘ Br2

C5 C2

Diphenyl ring

y x

C4

z

C3

Fig. 11.74. The immediate environment of the Sb atom in {diphenyl 2SbBr3}. Only atoms within ˚ of the Sb are included. In this example there is ﬁve-fold ‘square’ pyramidal coordination 4.0 A about Sb. These dimers are termed ‘isolated’ because there is only one Sb . . . Br interaction of less ˚ (the actual value is 3.695 A ˚ ), and this is within the Sb2Br6 dimer; The Sb . . . C(ring) than 4.0 A ˚ . The angles subtended at distances (from C1 to C6) are: 3.66, 3.48, 3.38, 3.45, 3.63 and 3.73 A Sb are Br1/Br3 93.40, Br2/Br3 95.59, Br1/Br2 96.48, Br3/Br2 0 168.43 . (Data from Lipka and Mootz, 1982.) n n n

˚ , with all other such distances greater than 4 A ˚, within the Sb2Br6 dimer is 3.695(2) A so description in terms of isolated dimers is an acceptable ﬁrst approximation. The environment of the Sb atom is shown in Fig. 11.74, which also serves as a prototype for the other similar close environments encountered among these molecular compounds. Although the overall arrangement in the isostructural {2,2 0 -dithienyl 2SbCl3} is similar to that in {diphenyl2SbBr3}, there is not the same degree of isolation, as the ˚ , is supplemented by other such contacts intradimer Sb . . . Cl distance of 3.552(3) A ˚ . Indeed, {2,2 0 -dithienyl 2SbCl3} has ties to between dimers at 3.716 and 3.761 A {pyrene 2SbBr3} and related structures considered below. This serves as a warning that resemblance in cell dimensions and overall arrangement do not necessarily extend to the ﬁner details of the structure. The Sb atom in {2,2 0 -dithienyl 2SbCl3} is located almost ˚ ; the S Sb distances in directly above the S of the ring system, with d(S Sb) ¼ 3.31 A molecular compounds of SbCl3 with aliphatic hetero-compounds are in the range 3.06 to ˚ and hence the coordinative S Sb interaction is somewhat weaker, but not absent, in 3.3 A the dithienyl compound. In these compounds both diphenyl and dithienyl are at centres of symmetry, and hence are not twisted about the central C–C bond. A different situation occurs in {diphenyl 2SbCl3} (Fig. 11.87), where the diphenyl rings are twisted. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

794

x

z y

Fig. 11.75. The {pyrene2SbBr3} and {pyrene2BiCl3} compounds are isostructural (see Table 11.28); the ﬁrst of these is shown, viewed down [001]. The structure is also isostructural with that of {9,10-dihydroanthracene2SbBr3}. The arrows show examples of the Sb . . . arene interactions. (Data from Bombieri, Peyronel and Vezzosi, 1972.)

2.490 2.502

2.505

3.494 C

A

Sb2Br6 isolated dimer

B z

x y

Fig. 11.76. The arrangement of the isolated Sb2Br6 dimers in {pyrene2SbBr3}, showing the primary and secondary linkages between Sb and Br; pyrenes have been omitted for clarity. As the {9,10-dihydroanthracene2SbBr3} and {pyrene2BiCl3} compounds are isostructural, this diagram applies also to these compounds, with small dimensional differences. (Data from Bombieri, Peyronel and Vezzosi, 1972.)

- D O N OR S A N D p -A C C E P T O R S

ribbon of SbBr3 dimers

795

Planar 9,10dihydroanthracene B

Sb

3.50

A

O

y z

x

Fig. 11.77. Structure of {9,10-dihydroanthracene2SbBr3} viewed down [001]. The lengths of the ˚ , (to Br2) 2.502(1) A ˚ , (to Br3) 2.532(1) A ˚ ). primary covalent Sb–Br bonds are (to Br1) 2.538(1) A ˚ which is The secondary Sb . . . Br approaches are shown (there is also a longer approach of 4.035 A not included). The two arrows show the interaction of the Sb atom with two of the rings of 9,10dihydroanthracene. (Data from Schmidbaur, Nowak, Steigelmann and Muller et al., 1990.)

The {pyrene 2SbBr3} structure (Fig. 11.75) is a prototype for the four structures grouped together in Table 11.28. The Sb2Br6 dimers are indeed isolated, as is shown in Fig. 11.76, and this applies to the other isostructural compounds. The {9,10-dihydroanthracene 2SbCl3} structure (Fig. 11.77) resembles that of {pyrene 2SbBr3} (cf. Table 11.28). The arene molecule is planar in the molecular compound, although it has a fold angle of 140 in its neat crystals (Herbstein, Kapon and Reisner, 1986; Reboul et al., 1987). There is a similar occurrence of planar 9,10-dihydroanthracene in its molecular compound with 1,3,5-trinitrobenzene (Herbstein, Kapon and Reisner, 1986). The phase diagram of the diphenylamine – SbCl3 system (Lipka, 1979) shows two congruently melting compounds: 1 : 1 at 359–361 K and 1 : 2 at 354–358 K. Isolated Sb2Cl6 dimers are found in {diphenylamine.SbCl3; ZZZBAM10}, where only one of the phenyl rings is involved in a Sb ring interaction (Fig. 11.78). {Diphenylamine.2SbCl3} (see below) has chains of interacting moieties, and both phenyl rings interact with Sb (Fig. 11.88). The arrangement in {[2.2.2.2]paracyclophane2SbBr3} consists of Sb2Br6 dimers linked through Sb arene interactions to one of the four benzene rings of the paracyclophane (Ferrari et al., 1998; GOMWAG; Fig. 11.79). There are van der Waals interactions among these units which pack as in a normal molecular crystal. The [2.2.2.2]paracyclophane molecule shows some ﬂexibility. It has no symmetry here but the n n n

n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

796

C

Non-interacting phenyls

Interacting phenyls 3.528

Sb2Cl6 moieties Interacting phenyls Non-interacting phenyls

z y

x

B

A

Fig. 11.78. Structure of {diphenylamineSbCl3} projected down [010]. The three covalent ˚ , and the angles between the pairs of Sb–Cl distances (not shown) are 2.373, 2.374 and 2.390 A covalent bonds are 91.9, 94.3 and 92.6 . The secondary Sb . . . Cl interaction is shown, as well ˚ ); only one as representative Sb . . . phenyl ring interactions (arrows; Sb to ring distance 3.13 A of the two phenyls interacts with Sb. There is no Sb to nitrogen interaction. (Data from Lipka, 1980.)

gauche conformation is GþGþGþGþ; it is centrosymmetric and GþGþGþGþ in its neat crystals (Cohen-Addad et al., 1983), and centrosymmetric and GþGGþG in its molecular compound with tetracyanoethylene (Cohen-Addad et al., 1984) and in {[2.2.2.2]paracyclophane2BiBr3}(C7H8) (Ferrari et al., 1998). (b) Chain and layer structures All the SbX3 chain arrangements encountered among the present group of structures can be described in terms of two motifs. The ﬁrst is the centrosymmetric Sb2X6 pair noted above, while the second is a distorted pentagonal bipyramidal arrangement, with three covalent Sb–X bonds and three secondary X Sb links to neighbouring SbX3 moieties. Addition of a secondary link to a ring of an aromatic molecule converts the array of chains into a layer. Sometimes only two X Sb links are found and the coordination about Sb then becomes pseudo-octahedral. In {p-xylene 2SbCl3} (PXYLSB; an early low-temperature structure, determined at 163 K) there are prominent layers parallel to (100) (Fig. 11.80), and a complicated arrangement of linked Sb2Cl6 pairs (Fig. 11.81). Two Sb atoms interact with a single p-xylene molecule n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

797

Br 3.733

[2.2.2.2]paracyclophane

z

Sb

3.733

y

x

Fig. 11.79. The packing unit in {[2.2.2.2]paracyclophane SbBr3}. The covalent Sb–Br distances ˚ ; the Sb Br secondary interaction is shown on the diagram. are 2.528(2), 2.539(2) and 2.522(2) A There are also secondary interactions normal to the page between the Sb atoms and the benzene rings below (on left) and above (on right). This is approximately 2, with distance from Sb to ring ˚ . (Data from Ferrari et al., 1998.) centre 3.28 A n n n

n n n

p-xylene layer

SbCl3 layer

B

Cl1

Cl2 Cl3 Sb

A

O

y x

z

Fig. 11.80. The {p-xylene . . . 2SbCl3} molecular compound seen in projection down [001]. The segregation of organic and inorganic moieties into layers is clearly seen. The arrows represent the Sb . . . arene interaction. (Data from Hulme and Mullen, 1979.)

˚ . The closest Cl Sb from opposite sides; the distance from Sb to the ring plane is 3.09 A ˚ secondary interaction is remarkably short at 3.24 A. Despite the quite close resemblance between the cell dimensions of {p-xylene 2SbCl3} and those of {naphthalene 2SbCl3} (Table 11.28), the structures are rather different. The {p-xylene SbCl3} molecular compound has also been studied, but details do not appear to have been published. Hulme and Mullen (1976) remark ‘‘The 1 : 1 SbCl3 : C8H10 compound is very similar to the 2 : 1 n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

798

Cl3 C

A

O 3.43 Sb

2.37

2.30

2.32

Cl2 Cl1

3.24

B

z

x y

Fig. 11.81. The structure of the inorganic layer of the {p-xylene 2SbCl3} molecular compound. (Data from Hulme and Mullen, 1979.) n n n

compound in its layer-like nature, its bond distances and the antimony trichloride– aromatic interactions. Both compounds crystallize in the space group P21/c, with closely similar a, b and values. To accommodate the additional p-xylene molecule the c axis is ˚ ) than in the 1 : 1 cell.’’ Redetermination by current techniques seems longer (17.65 A desirable. The {naphthalene 2SbCl3} structure (NAPSBC; another early structure) differs from that of {p-xylene 2SbCl3} as the Sb atoms interact with individual rings of different naphthalene molecules and from opposite sides (Figs. 11.82 and 11.83). The Cl . . . Sb ˚ and the links between adjacent pairs forming a distance within the Sb2Cl6 pair is 3.66 A ˚ long; there is also a Sb . . . Cl distance of 3.83 A ˚ . Thus corrugated ribbon are 3.58 A decision whether the arrangement should be described as ‘extended SbCl3 ribbons’ or as ‘discrete Sb2Cl6 pairs’ is somewhat arbitrary. Layer structures are also found in the triclinic crystals of {pyrene 2SbCl3}, {phenanthrene 2SbCl3} and {phenanthrene 2SbBr3} (Table 11.28); however, the latter two are not isostructural despite a resemblance in cell dimensions. The ﬁrst of these has sheets of pyrene molecules and interacting SbCl3 moieties parallel to (100) (Fig.11.84). Somewhat similar SbCl3 sheets are found in {phenanthrene 2SbCl3} but here the aromaticmolecule sheets contain two phenanthrenes rather than one as in the other structures (Fig. 11.85). A consequence is that the two SbCl3 moieties interacting with the two outer rings of a particular phenanthrene molecule are both on the same side of its plane rather than on opposite sides as in most of the other structures. Single phenanthrene sheets are found in {phenanthrene 2SbBr3} (Fig. 11.86) but here the SbBr3 arrangement is rather n n n

n n n

n n n

n n n

n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

SbCl3 layer

799

Naphthalene layer A

2.367 B

3.656

3.581

C x y z

Fig. 11.82. The {naphthalene 2SbCl3} structure viewed down [010]. The naphthalene molecules are at crystallographic centres of symmetry and are seen edge-on. The alternating naphthalene and SbCl3 layers are clearly seen. Compare Fig. 11.84. (Data from Hulme and Szymanski, 1969.) n n n

Cl1 A

C

Sb2Cl2 parallelogram seen edge-on

Cl3

3.656

3.581

B z

Cl2

Sb 3.581

x y

Fig. 11.83. The {naphthalene 2SbCl3} structure viewed down [100]. The alternating naphthalene and SbCl3 layers are clearly seen. The Sb2Cl4 parallelograms (sometimes described as Sb2Cl2 or Sb2Cl6) are cross-linked to form layers. The Sb atoms are shown by open circles. (Data from Hulme and Szymanski, 1969.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

800

SbCl3 layer

Pyrene, seen edge-on

C

3.515 2.389 O B

A z y

x

Fig. 11.84. Projection of the {pyrene 2SbCl3} (DEJYAS) structure down [010] (C2/c, Z ¼ 4). The layered structure is clearly visible. The pyrene molecules lie on crystallographic two-fold axes parallel to [010] while the SbCl3 moieties are all crystallographically equivalent. The arrows show the Sb . . . ring interactions. The structure resembles that of {naphthalene 2SbCl3} (Fig. 11.82) and differs from those of {pyrene 2SbBr3} and {pyrene 2BiCl3}, which are isomorphous. (Data from Mootz and Ha¨ndler, 1985.) n n n

n n n

n n n

n n n

more complicated than in the previously-mentioned SbCl3 layers (Fig.11.84); again the SbBr3 moieties interacting with a particular phenanthrene molecule are on the same side of the phenanthrene plane. In {diphenyl 2SbCl3} (BIPHSB10; Lipka and Mootz, 1978) the two phenyl groups and the two SbCl3 groups are crystallographically independent (Fig. 11.87). One of the Sb ˚ ), with the atoms (Sb(1) participates in a centrosymmetric chain (d(Cl Sb ¼ 3.44, 3.46 A sixth coordination site occupied by one of the phenyl groups of the diphenyl molecule. The chlorine atoms above and below the plane of the chain form secondary links ˚ ) to the second type of Sb atom (Sb(2)), the coordination of which is (d(Cl Sb ¼ 3.44 A completed by three covalent Sb–Cl bonds and a ﬁfth interaction to the second ring of a diphenyl molecule. Thus Sb(1) is six-coordinated and Sb(2) ﬁve-coordinated; the torsion angle about the central C–C bond in diphenyl is 40.5 , quite different from that in the SbBr3 analog. In {diphenylamine 2SbCl3} there are dimers but these are folded (and hence not centrosymmetric) and linked in chains, with Sb atoms here interacting with both rings of the diphenylamine molecule (Fig.11.88). n n n

n n n

n n n

n n n

(c) ‘Half-sandwich’ structures The monoclinic crystals of {1,2,3-trimethylbenzene . . . BiCl3} have been described as having a layer coordination structure, built up from

- D O N OR S A N D p -A C C E P T O R S

801

c A

Sb2

3.547 Sb1 3.262

3.488

x

z

y

B

Fig. 11.85. Projection of the {phenanthrene 2SbCl3} (PHENBS) structure along [100], showing the double layer of phenanthrene molecules related by centres of symmetry. There are two crystallographically independent SbCl3 groups in the unit cell; the Sb interact with the two outer benzene rings of a phenanthrene molecule from the same side, as indicated by the arrows. Secondary Sb . . . Cl distances are shown. The Sb2Cl2 parallelograms are linked into chains along [010]. (Data from Demalde et al., 1972.) n n n

quasi-dimeric units of arene-coordinated BiCl3 fragments (Fig. 11.89; Frank and Reiland, 1998; PUVLOH). Only non-bonding arene-arene contacts are observed between adjacent layers, showing that the structure has a backbone chain of linked Bi2Cl6 parallelograms sheathed on both sides by the arene moieties. The covalent Bi–Cl distances are 2.468, ˚ . The 2.523 and 2.528 a, while there are secondary interactions at 3.293 and 3.406 A ˚ to C5 and C4 respectively). shorter Bi C interaction is 2 (distances are 3.17 and 3.24 A Because the metal arene interaction is only on one side of the aromatic ring, the arrangement was described as a ‘half sandwich’. Orthorhombic crystals of {benzene BiCl3} (Frank et al., 1993; LAHJAF) that rapidly lose benzene in vacuo, have space group, P212121 (Z ¼ 8). This is the only chiral structure so far encountered in this family of compounds, and Frank et al. determined the absolute conﬁguration of the crystal used in their structure analysis. There are two crystallographically independent BiCl3 moieties in the crystal, and similarly for the benzenes, and the Bi C interaction is weaker for one pair than for the other (Fig. 11.90). The structure was interpreted as that of a layer coordination polymer, built up from quasi-molecular BiCl3 units linked by weak chlorine bridges. Alternatively, as the n n n

n n n

n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

802

B

A

Sb2 0 Sb1

y

x

z

C

01 ]. Sb(1) and Sb(2) are Fig. 11.86. Projection of {phenanthrene 2SbBr3} (DEJYEW) down [1 rystallographically independent and have distorted six- and seven-fold coordination respectively. The arrows show the Sb . . . ring interactions, both from the same side of the phenanthrene molecule. Not all the secondary Sb . . . Br interactions have been included. (Data from Mootz and Ha¨ndler, 1985.) n n n

metal . . . arene interaction is only on one side of the arene, this can also be called a ‘halfsandwich’ structure (compare Figs. 11.89 and 11.90). The overall packing arrangements in these two structures do not differ in principle from those (based on chains and/or layers) found in the other arene . . . MX3 compounds discussed until now. Mesitylene forms isomorphous triclinic 1 : 1 compounds with MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) (Schmidbaur, Wallis et al., 1987a). Although these have also been described as ‘half-sandwiches’, there are important differences from the ﬁrst group. The crystals of {mesitylene SbBr3} and {mesitylene BiCl3} were reported to be triclinic, with unit cells of similar dimensions containing eight formula units. From a crystallographic point of view, it is interesting to note that the reported unit cells show a greater resemblance than the reduced cells (Table 11.29). Indeed, the two structures are similar but not identical; there is no evidence for disorder. The MX3 groups are in an approximate 6 relationship to the mesitylene rings, with half the metal atoms having quasi-octahedral coordination and the other half having pentagonal bipyramidal coordination; as the MX3 groups are only on one side of the mesitylene rings, these were also called ‘half sandwich’ n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

803

Sb1

Centrosymmetric chain

Sb2 40.5

Sb2 appended

x y

z

Fig. 11.87. Triclinic {diphenyl 2SbCl3} viewed down [010], showing the centrosymmetric chain of Sb(1)Cl3 groups, with appended Sb(2)Cl3 groups. The arrows show the secondary interactions of Sb with the two phenyl rings of diphenyl. Dimensions in the chain are given in the text. (Data from Lipka and Mootz, 1978.) n n n

C

A

B z

x y

Fig. 11.88. Projection down [010] of the structure of {diphenylamine 2SbCl3} (DPASBC10), showing the folded Sb2Cl6 dimers linked into zigzag chains, with both rings of the diphenylamine molecules interacting with Sb atoms. (Data from Lipka, 1978.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

804

C 1,2,3-trimethylbenzene seen edge-on

Cl Bi

Methyl

3.293

B z y x

A

Fig. 11.89. {1,2,3-trimethylbenzene . . . BiCl3} viewed down [010]. There is a striking resemblance to the analogous projections shown for {naphthalene.2SbCl3} (Fig. 11.82) and {pyrene2SbCl3} (Fig. 11.84). (Data from Frank and Reiland, 1998.)

structures. In {mesitylene BiCl3} covalent d(Bi–Cl) are very similar at 2.465(5), ˚ , with secondary d(Bi . . . Cl) ¼ 3.275, 3.302, 3.180, 3.368 A ˚ . The 2.489(4) and 2.483(5) A ˚ and 3.6 A ˚. corresponding values in {mesitylene SbBr3} are 2.5 A The overall packing in {mesitylene BiCl3} is quite different from that in the {benzene . . . BiCl3} and {1,2,3-trimethylbenzene BiCl3} despite use of the same ‘halfsandwich’ name for both (compare Figs. 11. 89 and 11.90 on the one hand with that of the hexamers of {mesitylene BiCl3} (Fig. 11.91) on the other). The hexamers of ‘half-sandwich’ {mesitylene BiCl3} lead us on to the tetramers of ‘full-sandwich’ {hexamethylbenzene 2AsCl3} (Fig. 11.96). n n n

n n n

n n n

n n n

n n n

n n n

n n n

Sandwich structures There is a remarkable group of four isomorphous structures (Table 11.30; Burford et al., 1996) based on that of the (very hygroscopic) {benzene 2SbCl3} (Mootz and Ha¨ndler, 1986). Burford et al. entitled their paper ‘‘Tethered diarenes n n n

- D O N OR S A N D p -A C C E P T O R S

805

Benzene.BiCl3 chain 3.25

O A

C Bi2 Bi1 bz1

bz2 B z

x y

Fig. 11.90. Structure of {benzene BiCl3} viewed down [100]. The two independent Bi atoms are ˚ (to designated Bi1 and Bi2, and the benzenes bz1 and bz2. The shortest Bi2 . . . C distance is 3.25 A bz2) and is shown in the diagram. The Bi1 . . . C distances (to bz1) are all (slightly) greater than ˚ , and the secondary Bi . . . Cl 3.5 A. The covalent Bi–Cl distances range from 2.444 to 2.482 A ˚ . (Data from Frank et al., 1993.) distances from 3.228 to 3.621 A n n n

A

3.368

3.275 O

3.302

B

x z

y

C

Fig. 11.91. One of the hexameric units in {mesitylene BiCl3}; there is a second, crystallographically independent hexamer with slightly different dimensions. The mesitylene molecules alternate above and below the mean plane. The distances corresponding to the secondary interactions are for this particular hexamer. There are even longer M . . . X distances between hexamers. (Data from Schmidbaur, Wallis et al., 1987.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

806

˚ , deg.) for {mesitylene SbBr3} and {mesitylene BiCl3}. Table 11.29. Cell dimensions (A Both compounds crystallize in space group P1, Z ¼ 8 (Schmidbaur, Wallis, Nowak, Huber and Mu¨ller, 1987) n n n

Compound

Reported cells

{mesitylene SbBr3} FOWYAR (1) {mesitylene BiCl3} FAPYOK10 (2) n n n

n n n

n n n

Reduced cells

a/

b/

c/

a/

b/

c/

9.401 109.27 8.716 108.64

14.200 102.94 14.150 101.24

22.759 87.94 21.740 88.88

9.401 107.29 8.716 71.36

14.200 101.76 14.150 78.76

22.501 92.06 21.740 88.88

Notes: (1) reported and reduced cells are different. The reduced cell is Type II (all angles obtuse). (2) reported cell is a non-standard orientation of the reduced cell., which is Type I (all angles 90 ).

C

A

z

x y

B

Fig. 11.92. The structure of {mesitylene BiCl3} viewed down the [100] axis. The arrows show the arene . . . Bi interactions. The central group of molecules is that shown in Fig. 11.91. This is a layer structure. (Data from Schmidbaur, Wallis, Nowak, Huber and Mu¨ller, 1987.) n n n

as four-site donors to SbCl3.’’ The prototype {benzene 2SbCl3} structure is of the layer type, with the feature that SbCl3 moieties interact with the benzene molecule from both above and below with an 6 arrangement. In this respect it resembles the {p-xylene 2SbCl3} and {C6(CH3)6 2MX3} structures (for the latter, see below). We illustrate for the {tolane . . . 4SbCl3}, the best determined of the four crystal structures (Figs. 11.93 and 11.94). Comparison of the four structures suggests that they are n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

807

Table 11.30. Four isomorphous structures. All crystallize in space group P 1; FAGFAU has 2 formula units in the unit cell and the others have 1. The triclinic cells are reduced but the ordering of the axes, where we follow reference B96, is not standard Compound

a/

b/

c/

Reference

C6H6 2SbCl3 FAGFAU

8.211 94.00 8.384 94.81 8.363 95.44 8.379 95.51

11.833 108.55 11.950 108.64 11.950 109.15 11.965 110.37

8.165 94.22 8.103 97.42 8.099 96.28 8.122 94.69

MH86

n n n

PhCH2CH2Ph 4SbCl3 DBDSBC01 PhCH¼CHPh 4SbCl3 STISBC01 PhCCPh 4SbCl3 ZOQWUX n n n

n n n

n n n

HH66, B96 HH66, B96 B96

References: B96 – Burford et al., 1996; HH66 – Hulme and Hursthouse, 1966; MH86 – Mootz and Ha¨ndler, 1986.

Tolane molecule seen edge-on C 1.178

O

3.519

A

B

z

x y

Fig. 11.93. Crystal structure of {tolane 4SbCl3} projected down [ 10 1]. The tolane molecules are ˚ . The arrows show at centres of symmetry, with the acetylene bond indicated by its length 1.178 A ˚. the interactions between Sb and phenyls, the Sb to ring centroid distances being 3.21 and 3.35 A (Data from Burford et al., 1996.) n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

808

B 3.881

Sb1

3.401 3.788 3.623

Sb2

3.813

3.519 O

A

y x

z

Fig. 11.94. Detail of the SbCl3 network in the crystal structure of {tolane 4SbCl3} projected down [ 10 1]. A number of secondary interactions not listed by Burford et al. are included. (Data from Burford et al., 1996.) n n n

determined by the interaction between benzene ring and Sb, and that the groups linking the benzene rings (none; –CH2–CH2–; –CH¼CH–; –CﬃC–) have little structural importance. These are ‘inverse sandwich’ structures, with the benzene rings coordinated at both faces. The 1 : 4 compounds of dibenzyl, and stilbene with SbCl3 were brieﬂy reported more than thirty years ago (Hulme and Hursthouse, 1966). The 1 : 2 molecular compounds of C6(CH3)6 (HMB) with SbCl3, SbBr3, BiCl3 and BiBr3 (Schmidbaur, Nowak, Schier, Huber and Mu¨ller, 1987) all crystallize in isomorphous tetragonal unit cells, where the cell dimensions of {C6(CH3)6 2SbCl3}, {C6(CH3)6 2BiCl3} and {C6(CH3)6 2SbBr3}, {C6(CH3)6 2BiBr3} are pairwise closely similar (Table 11.31); {C6(CH3)6 2AsCl3} (Schmidbaur, Nowak, Steigelmann and Mu¨ller, 1990) also ﬁts into this group; they are discussed together, the minor differences being ignored. The projection down [100] for {C6(CH3)6 2AsCl3} is shown in Fig. 11.95, and shows the hexamethylbenzene molecules sandwiched between groups of AsCl3 molecules. The 6 AsCl3 C6(CH3)6 AsCl3 moieties are arranged in tetramers (Fig. 11.95 and 11.96); there is no phase transition nor change in the disorder pattern on cooling to 123K. The structure as whole is built up by cross-linking of tetramers at the metal centres with other tetramers by double-sided arene coordination. The disorder makes some of the details of these structures suspect: for example, the unusual secondary Sb . . . Cl distance n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

809

Table 11.31. Crystal data for the similar (‘‘isotypical’’) {HMB 2MX3} molecular compounds (all crystallize in space group P42/nnm with Z ¼ 4) n n n

Formula

a

c

Reference

HMB HMB HMB HMB HMB HMB

12.683 12.581 12.599 12.950 12.915 12.644

12.379 12.315 12.315 13.015 12.966 11.967

SN87a HLK00 SNS87 SNS87 SNS87 SNSM90

n n n

n n n

n n n

n n n

n n n

n n n

2SbCl3 At 300K FOWXAQ 2SbCl3 At 123K FOWXAQ01 2BiCl3 FOWXEU 2SbBr3 FAPYUQ 2BiBr3 FOWXOE 2AsCl3 (at 233K)TADDUX

References: HLK00 – Hubig, Lindemann and Kochi, 2000; SNS87 – Schmidbaur, Nowak, Schier, Wallis, Huber and Mu¨ller,1987; SNSM90 – Schmidbaur, Nowak, Steigelmann and Mu¨ller, 1990.

Wavy sheet of hexamethylbenzenes O A

B AsCl3 moieties

x

y

C

z

Fig. 11.95. Crystal structure of C6(CH3)6 2AsCl3 seen in projection down [100]. The disorder in the AsCl3 moieties has not been removed. The C6(CH3)6 molecules interact with AsCl3 moieties above and below the benzene ring in an approximate 6 arrangement. (Data from Schmidbaur, Nowak, Steigelmann and Mu¨ller, 1990.) n n n

˚ in {C6(CH3)6 2SbCl3} is not encountered elsewhere and appears to require of 2.895(3) A independent conﬁrmation. ˚ from the centers of the benzene rings; this is the longest areneThe As atoms are 3.2 A to-metal distance observed in the series of group 15 element/hexamethylbenzene adducts ˚ ). There are other differences of detail between the analogous (As/Sb/Bi: 3.20/3.15/3.07 A compounds. For example, the three covalent d(Bi–Cl) distances are respectively 2.404(8), ˚ , considerably distorted from its gas phase structure of three 2.438(8) and 2.887(6) A similar Cl–Bi bonds; this does not appear to happen in the corresponding SbX3 molecular compounds. No explanation has been offered. If one includes the secondary interactions, then the M atoms are all 7-coordinate and are excellent examples of ‘‘split-site octahedral coordination’’ (Herbstein et al., 1989). Pentamethylbenzene gives similar adducts with n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

810

Disorder of As has been removed in upper part of diagram, showing individual HMB and AsCl3 moieties.

Cl As

Note the two disordered positions for As, the other atoms not being affected.

z

x

y

Fig. 11.96. A tetramer of AsCl3 molecules below four hexamethylbenzene molecules. There is a similar layer of AsCl3 molecules above the hexamethylbenzene molecules. The covalent As–Cl ˚ , and are considerably shorter than the bonds have lengths 2.158(2), 2.195(2) and 2.186(2) A secondary As Cl interactions not shown in the diagram. Disorder is found in all the analogous crystals. (Data from Schmidbaur, Nowak, Steigelmann and Mu¨ller, 1990.) n n n

MX3; here there must be additional disorder of the arene molecule, and the structures were ˚, not determined. Durene also forms a 1 : 2 adduct with SbCl3 (tetragonal, 17.326 24.990 A I41/acd, Z ¼ 16). This also has tetrameric chlorine-bridged Sb4Cl12 units linked to the arene, and thus is structurally analogous to the adducts described above, but not isostructural (different cell dimensions and space group). 11.12.1.5 Ternary molecular compounds A number of ternary molecular compounds have been reported; a few structures are known. The third component is presumably usually present as solvent of crystallization without interaction with the MX3 group. Examples are 2(1,4-diphenylbutadiene) 7(BiCl3) 8(p-xylene); 3(1,4-diphenylbutadiene) 4(BiBr3);(p-xylene); 3(1,4-diphenylbutadiene) 4(BiBr3)-(ethylbenzene) (all Peyronel et al., 1968); naphthalene 2(BiBr3)1/3(toluene); pyrene 2(BiBr3)xS, where S ¼ p-xylene, CH2Cl2 or diethyl ether (Buffagni et al., 1968); 4(ﬂuorene) 7(BiBr3)(p-xylene); ﬂuoranthene 2(BiBr3)x(p-xylene); acenaphthene 2(BiBr3); x(p-xylene); acenaphthene 6(BiCl3)3(toluene); (all Vezzosi et al., 1968) and 5(ﬂuoranthene) 9(SbCl3)cyclohexane (Peyronel et al., 1970). These earlier results should be viewed with some caution because more recent results for 1 : 2 compounds of perylene, pyrene (isomorphous with the BiCl3 compound), acenaphthene, phenanthrene and n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

- D O N OR S A N D p -A C C E P T O R S

811

Table 11.32. Crystal data for ternary areneMX3solvent molecular compounds. Formula

a/

{[2.2.2.]paracyclophane 2SbCl31/2(benzene)} KISXAL {[2.2.2.2]paracyclophane 2SbBr3}toluene GOMWEK* {[2.2.2]paracyclophane. 3BiCl3benzene} (KISXEP) Fluoranthene2BiBr3 0.5(p-xylene) JEJPAP** (perylene)34BiBr3 ZUVTAL** {(pyrene) [2.2]paracyclophane 2BiBr3} ZOCWOD**

14.371

n n n

12.513 90.76 12.155(3)

n n n

n n n

9.812 71.59 10.250 101.44 7.871 92.77

b/

c/

8.716 101.05 12.957 101.13 20.523(3)

24.384 7.165 112.95 29.952(5)

11.199 80.28 10.605 91.33 10.440 102.67

12.861 74.38 14.418 106.23 10.853 104.61

Space group

Z

Reference

P21/n

4

P91

P 1

1

F98

Pbca

8

P91

P 1

2

B90

P 1

2

B96

P 1

1

B95

* Reduced cell (unconventional setting). ** reduced cell (standard setting). References: B90 – Battaglia et al., 1990; B95 – Battaglia et al., 1995; B96 – Battaglia et al., 1996; F98 – Ferrari et al., 1998; P91 – Probst et al., 1991;

ﬂuorene with BiBr3 (Battaglia et al., 1990) show solvent of crystallization only in the ﬂuoranthene compound. The crystal structures (Table 11.32) of the ternary compounds fall into two groups: in the ﬁrst the third component ﬁlls the familiar ‘included solvent of crystallization’ role. However, in the second group, the arene component ﬁlls two different structural roles, in one of which it interacts with the metal atom while in the other it appears to behave only as a space-ﬁller. There are two examples known; in ZUVTAL the same arene (perylene) ﬁlls two different structural roles, while in ZOCWOD there are two different arenes, [2.2]paracyclophane interacting with BiBr3 and pyrene ﬁlling space. The arrangement in {[2.2.2]paracyclophane 2SbCl31/2(C6H6)} (KISXAL) consists of Sb4Cl12 tetramers linked through Sb . . . arene interactions to two of the three benzene rings of the paracyclophane, thus forming a set of zigzag chains along [001] (Figs. 11.97 and 11.98; crystal data in Table 11.32; Probst et al., 1991). This arrangement leaves a set of channels along [010], which contain the benzenes of crytsallization (seen edge-on in the diagram). Both tetramers and benzenes are located at crystallographic centres of symmetry. There is no Sb . . . benzene of crystallization interaction. The structure of {ﬂuoranthene2BiBr3}0.5(p-xylene) (Battaglia et al., 1990; JEJPAP) is related to this group. The triclinic crystals have centrosymmetric tetramers of loosely linked BiBr3 molecules interlayered by pairs of face-to-face ﬂuoranthene molecules. The p-xylenes, at centres of symmetry, are solvent of crystallization. The two crystallographically independent BiBr3 molecules each have three covalently bonded bromines ˚ . There are two pairs with d(Bi–Br) ¼ 2.571, 2.679, 2.695 (Bi1) and 2.601, 2.628, 2.670 A of secondary Bi . . . Br distances (bridging bromines) at longer distances (3.165, 3.494 and ˚ ). Two benzene rings of a ﬂuoranthene molecule interact with Bi1 and Bi2 3.267, 3.375 A ˚ , indicating as shown in Fig. 11.99 (pairs of closest d(Bi . . . C) are in the range 3.23–3.38 A n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

812

C InterstitiaI benzene Phenyl does not interact with Sb

O B

A

z y

x

Fig. 11.97. {[2.2.2]paracyclophane2SbCl31/2(C6H6)} viewed in projection down [010]. The two arrows show examples of the Sb . . . benzene interaction, which is 6 to a good approximation. The ˚ respectively. (Data from Probst distances between Sb and benzene planes are 3.047 and 3.050 A et al., 1991.)

2 interactions). The isolated BiBr3 tetramers can be contrasted with the interlinked tetramers found in phenanthrene2SbBr3. [2.2.2.2]paracyclophane2BiBr3toluene (GOMWEK; Ferrari et al., 1998) has centrosymmetrical paracyclophane molecules of GþGGþG conformation interacting with Bi atoms of chains of linked BiBr3 molecules (Fig. 11.100). The disordered. toluene molecules are at interstitial positions and do not interact with Bi. The Bi . . . arene ˚ . The chains are interaction is 2, the two shortest distances being 3.27(2) and 3.31(2) A made up of interacting BiBr3 moieties with twisted Bi2Br4 parallelograms; although it is out-of-order, this is an appropriate place to note the similarity of these parallelograms to

- D O N OR S A N D p -A C C E P T O R S

813

Sb1 Sb2

2.337

3.403

2.370

z

2.375 y x

3.647

Fig. 11.98. Detail of the dimensions in the inorganic tetramer in {[2.2.2]paracyclophane2SbCl3 1/2(C6H6)}. The coordination spheres about Sb are completed by interactions to two benzene rings of the [2.2.2]paracyclophane; thus Sb1 is 6-coordinate and Sb2 5-coordinate. (Data from Probst et al., 1991.)

p-xylene

Pair of flouranthene molecules BiBr3 tetramer

x z

y

Fig. 11.99. The structure of {ﬂuoranthene2BiBr3}0.5(p-xylene) viewed in projection down [010]. (Data from Battaglia et al., 1990.)

those in pyrene[2.2]paracyclophane2BiBr3 (ZOCWOD; Fig. 11.106). The structures of GOMWEK and [2.2]paracyclophane2BiBr3 (JOLBAN; Vezzosi et al., 1992) are compared in Figs. 11.100 and 11.101, emphasizing the similar structures of the inorganic chains and the modes of their interactions with benzene rings of the two cyclophanes.

814

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

Br1

Br2

Br3 Bi…arene interaction

Bi

Fig. 11.100. View of the [2.2.2.2]paracyclophane2BiBr3toluene (GOMWEK) structure, showing chains of BiBr3 molecules linked by secondary interactions between themselves, and also to benzene ˚ to Br1, 2 and 3. rings of the cyclophanes. The covalent Bi–Br distances are 2.668(2), 2.659, 2.5982 A ˚ (to Br2). The toluene solvate is not The secondary distances are 3.221(2) (to Br1) and 3.419 A shown. (Reproduced from Ferrari et al., 1998.)

The interatomic distances quoted in the captions to these ﬁgures are hardly signiﬁcantly different. Thus this pair of structures is a model illustration of ‘isostructurality.’ Perhaps the most complicated of the structures belonging to the present family is that of {[2.2.2]paracyclophane3BiCl3benzene; KISXEP} (Probst et al., 1991). The crystals are orthorhombic with the chemical moieties at general positions. The projection down [100] (Fig. 11.102) suggests a layer structure but this is misleading because of the secondary Bi . . . arene interactions to the benzene rings of the cyclophane. The BiCl3 have a ladder structure of interlinked quadrilaterals extending (roughly) along [100], with cross-links along [010] (Fig. 11.103). The cross-linked sheet is made up of interacting elements that have been encountered in many of the examples discussed above. {(Perylene)3Bi4Br12} (ZUVTAL) has perhaps the most intricate arrangement of moieties thus far encountered among the Menshutkin compounds with isolated (BiBr3)n oligomers (Battagalia, Bellito et al., 1996). The preparation was noteworthy ‘‘The compound was obtained by mixing a p-xylene 1 : 1 solution of perylene and pyrene and a solution of BiBr3 . . . In the absence of pyrene, the title compound was not obtained’’ (italics added). No explanation was offered. The asymmetric unit of the black triclinic crystals (Table 11.32) contains one perylene (a) at a general position, and half a perylene (b) centred at inversion centers. The Bi4Br12 moiety is also centred at inversion centers (Fig. 11.104). Perylene

- D O N OR S A N D p -A C C E P T O R S

815

Bi…arene interaction

Br(3) Bi Br(2)

Br(1)

Fig. 11.101. View of the [2.2]paracyclophane2BiBr3 (JOLBAN) structure, showing chains of BiBr3 molecules linked by secondary interactions between themselves, and also to benzene rings of ˚ to Br1, 2 and 3. The the cyclophanes. The covalent Bi–Br distances are 2.676(3), 2.663, 2.595 A ˚ (to Br2). (Reproduced from Vezzosi et al., secondary distances are 3.325(2) (to Br1) and 3.402 A 1992.)

Benzene of crystallization

C

z

x

A

B

y

Fig. 11.102. Structure of {[2.2.2]paracyclophane3BiCl3benzene} (KISXEP) seen in projection down [100]. The benzenes of crystallization are located in the (002) planes, and do not interact with the Bi atoms. The secondary Bi . . . arene interaction is not shown. (Data from Probst et al., 1991.)

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

816

Bi1–Bi3 ladder 3.275 2.522 Bi2

Bi1 2.524

Bi2

3.131 Bi3

Bi1

Bi2–Bi29 cross linkage

Bi3

2.449

x Bi1–Bi3 ladder z y

Fig. 11.103. The (BiCl3)n cross-linked two-dimensional polymeric sheet shown after removal of the organic moieties. (Data from Probst et al., 1991.)

interacts with Bi4Br12 in a way that is similar to the other examples described here, including interaction between two Bi atoms above perylene (a) and two below, thus interacting with the four outer rings of perylene (a) (Fig. 11.105). Perylene (b) does not show any special interaction with Bi4Br12 and appears to act just as a ﬁller of space. There are a number of examples of similar behaviour in other molecular compounds. In {pyrene[2.2]paracylophane 2BiBr3} (ZOCWOD) there are BiBr3 chains which are layered with stacks of alternating pyrene and [2.2]paracytclophane molecules (Battaglia, Cramarossa and Vezzosi, 1995). There is a secondary interaction between Bi and the benzene rings of the [2.2]paracytclophane molecules, while pyrene, which showed high atomic displacement parameters, appears to be present as an inert ‘‘ﬁller’’ (Figs. 11.106 and 11.107). The ternary compound melts without decomposition at 443K. The unusual stability of this compound compared to analogous compounds was ascribed to ‘‘the n n n

- D O N OR S A N D p -A C C E P T O R S

817

A

perylene b perylene a Br4 Bi1

Bi2

B x z

C

y

Fig. 11.104. {(Perylene)3Bi4Br12} viewed down the [010] axis of the triclinic cell. (Data from Battaglia, Bellito et al., 1996.)

remarkable effects of the transannular -electronic interactions of one benzene with another.’’ 11.12.1.6

Application of various physico-chemical methods

(a) Thermodynamics The enthalpy and entropy of formation of {benzene 2SbCl3} from the liquid components have been measured by Perkampus and Sondern (1980) by three independent methods – melting equilibrium, vapour pressure and calorimetrically 0 (enthalpy) – with good agreement. The mean values are Hcomplex ¼ 55.4 kJ/mol, 0 0 Scomplex ¼ 138.9 J/K mol. Values of Hcomplex have also been measured for a number of polymethylbenzene SbCl3 compounds (Table 11.33; Sondern and Perkampus, 1983). n n n

n n n

(b) Nuclear quadrupole resonance studies and other spectroscopies NQR spectroscopy provides a rich alternative for study of the {arenenSbX3} molecular compounds

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

818

Br2

Br5 2.597 3.451 Bi2 to Br4 2.676 Å 2.580

Bi2 Br4 Br1

Br6 Bi1

Bi1 to C9 3.10 Å C9

Bi1 to Br4 3.173 Å

x

C13

Bi2 to Br1 3.399 Å

z

Br3

y

Bi2 (obscured) to C13 3.10 Å

Fig. 11.105. {(Perylene)3Bi4Br12} showing detail of interaction between perylene (a) molecule and Bi4Br12 moiety. The perylene molecule above the inorganic moiety has been omitted for clarity. The sandwich [perylene (a)Bi4Br12perylene (a)] is the packing unit of the structure, to which perylene (b) must be added. (Data from Battaglia, Bellito et al., 1996.)

A [2.2]paracyclophane Br

3.409

3.354

B Bi

pyrene

x z

y

C polymeric (BiBr3)n chain

Fig. 11.106. Structure of {pyrene[2.2]paracylophane2BiBr3} viewed in projection down [010]. A superposed pyrene has been removed for clarity in the upper left part of the diagram, and a [2.2]paracylophane in the lower right-hand corner. The arrows show the secondary interactions between Sb and the benzene rings of [2.2]paracylophane. Battaglia et al., describe the structure as follows: ‘‘linear (BiBr3)n polymeric chains are cross-linked in a two-dimensional network in which pyrene is included; these layers are packed by means of van der Waals contacts.’’ (Data from Battaglia, Cramarosa and Vezzosi, 1995.)

- D O N OR S A N D p -A C C E P T O R S

Br

819

2.635 3.409 2.656 3.354

Bi

x

2.587

z y

Fig. 11.107. Structure of {pyrene[2.2]paracylophane2BiBr3} viewed approximately down [001]. Details of the polymeric (BiBr3)n chain. The interaction with the benzene rings, which completes the Bi coordination sphere, is not shown. (Data from Battaglia, Cramarosa and Vezzosi 1995.)

Table 11.33. Enthalpies of formation of crystalline polymethylbenzene/2SbCl3 molecular compounds from the liquid components at the melting points. Values from Sondern and Perkampus, 1983. Other melting points in Table 11.27 Polymethylbenzene

M.Pt. (K)

H0 complex

Polymethylbenzene

M.Pt. (K)

H0 complex

benzene toluene o-xylene m-xylene p-xylene 1,2,3-trimethylbenzene 1,2,4-trimethylbenzene

352 316 307 311 343 326 331

55.0 45.1 48.0 51.6 52.7 47.5 49.1

1,3,5-trimethylbenzene 1,2,3,4-tetramethylbenzene 1,2,3,5-tetramethylbenzene 1,2,4,5-tetramethylbenzene Pentamethylbenzene Hexamethylbenzene

348 367 372 375 422 467

53.5 59.0 59.6 61.0 74.8 80.4

because 35Cl, 121Sb, 123Sb, and 81Br (also 79Br) resonances can be obtained. Each crystallographically independent 35Cl and 81Br quadrupole nucleus gives a single line spectrum in the ranges 18–21 MHz and 130–145 MHz respectively, while NQR spectra of Sb contain a single line for each of the ﬁve 121Sb and 123Sb quadrupole transitions, where generally only one line for each isotope is studied. Although a wide ranging review of the combination of diffraction and NQR methods in crystal chemistry (Weiss, 1995) does not include any discussion of the {arenenSbX3} molecular compounds, these have been considered in the present context by Herbstein (2004). The number of crystallographically independent SbX3 molecules in the unit cell is shown up well both by Raman spectroscopy and by NQR. The Raman spectra in the 300 400 cm1 region (the SbCl3 region) are very similar for SbCl3 and {naphthalene 2SbCl3}, but there is a doubling of the lines for {diphenyl 2SbCl3} and {phenanthrene 2SbCl3}. We have already noted that the ﬁrst of these has one SbCl3 moiety in the asymmetric unit and the others two, and a similar correspondence is obtained (Kozulin, 1971) for other examples such as {p-xylene SbCl3}, {p-xylene 2SbCl3} and {benzene 2SbCl3}. The advantages of NQR spectroscopy appear when one compares the sensitivity of ˚ to crystallographic and spectroscopic methods. Covalent d(Sb–Cl) covers a range of 2.3 A ˚ , with s.u.’s of 0.01 A ˚ (in early work) and 0.002 A ˚ later; bond angles are in the range 2.4 A n n n

n n n

n n n

n n n

n n n

n n n

820

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

92 to 96 with s.u.’s of 1 (early work) to 0.1 later. d(C–C) in arene groups will have s.u.’s of 0.01 A or more; caution suggest that little credence should be placed on deviations of C–C bond lengths in the arene moieties from standard values. Frequencies in NQR spectra are measured with a precision of a few kHz and so the halogen NQR spectrum of a particular compound gives detailed information about small differences in chemical state among these atoms provided that frequencies can be assigned to atoms. For this a Zeeman analysis of the single crystal NQR spectrum is needed; spectra from polycrystalline samples do not carry enough information. Problems of assignment for Sb spectra arise only if there is more than one Sb atom in the asymmetric unit. Early work (Okuda, Nakao, Shiroyama and Negita, 1968; Okuda, 1971; Okuda et al., 1972) used the Zeeman effect to match particular atoms to measured frequencies, and there was also some study of the temperature dependence of the resonance frequencies; in later work (Kyuntsel and Mokeeva (2002) who give references to earlier studies) primary attention was given to the thermal behavior but correlation of crystal structure and spectra was not neglected. Parallel crystallographic and NQR spectroscopic results are available only for three {(arene)nSbCl3} molecular compounds: {naphthalene2SbCl3} (NAPSBC; Zeeman analysis by Okuda, 1971; nuclear spin–lattice relaxation times T1 over the range 77–293 K by Kyuntsel, 1998); {p-xylene2SbCl3} (PXYLSB; Zeeman by Ishihara, 1981; nuclear spin-lattice relaxation times T1 over the range 77–293 K by Kyuntsel and Mokeeva, 2001; {benzene2SbCl3}(FAGFAU; Zeeman analysis by Okuda, Nakao, Shiroyama and Negita, 1968.) There are also some partial results. The 35Cl and 121Sb NQR spectra have been measured for {ethylbenzene2SbCl3} and {diphenylmethane2SbCl3} (Kyuntsel, 2000) but crystal structures and Zeeman analyses are lacking. A Zeeman analysis has been carried out for {benzene2SbBr3} (Okuda, Terao, Ege and Negita, 1970) but the crystal structure is lacking; {benzene2SbBr3} is not isomorphous with {benzene2SbCl3}. The 35 Cl NQR spectra have been reported (Gordeev and Kyuntsel, 1992) for {diphenylamine SbCl3} (ZZZBAM10) and {diphenylamine2SbCl3} (DPASBC10) but Zeeman analyses are lacking. The fundamental structural unit in all the {(arene)nSbX3} molecular compounds reported until now is the centrosymmetric (or approximately so) (arene)2Sb2Cl6 moiety. There are three differently linked Cl atoms, which give a three-line 35Cl NQR spectrum. Zeeman analysis of single crystal NQR spectra enables assignment of frequencies to particular Cl atoms. On this basis the lowest frequency L derives from the Cl in the Sb2Cl2 parallelogram (in a few examples, this is a bent quadrilateral), the middle frequency M from the Cl with a secondary link to another moiety, and the highest frequency H to the third Cl, without secondary linkages. There is a fair correlation between L values and d(Sb . . . Cl) of the Sb2Cl2 parallelogram but hardly for M and H. The interaction of the -system of the arene with Sb is shown by Sb NQR frequencies; for 121 Sb the frequencies for the ﬁrst group of six molecular compounds listed in the previous paragraph are similar, although there are internal differences. The frequencies for the two diphenylamine compounds are in a second, lower, group. Despite the limited database, it is possible to draw some conclusions. Firstly, the qualitative correlation of the H, M and L values with the structural features shown in Fig. 5 seems to be well founded and one may risk predicting that it will hold for most of these molecular compounds. Quantitative correlation of L with d(Sb . . . Cl) seems plausible but

- D O N OR S A N D p -A C C E P T O R S

821

requires critical testing. Correlations for H and M are less convincing. The situation for 121Sb . . . arene is intriguing; it is unfortunate that the value for {benzene2SbBr3} is lacking. Clearly there is a wealth of chemical information presently locked away, and waiting to be unravelled – the many crystal structures available need to be complemented by Zeeman analyses of strategically chosen single crystal 35Cl and other NQR spectra. Some early reports indicated that the present group of molecular compounds formed highly colored crystals, possibly suggesting a high degree of charge transfer. However, measurements of the UV and visible spectra of carefully prepared crystalline arene 2SbCl3 compounds have shown (Perkampus and Scho¨nberger, 1976) that the colours are due to impurities, principally the radical ions of the aromatic components; the pure molecular compounds are colourless or slightly yellow. This agrees well with conclusions drawn from NQR and Mo¨ssbauer spectroscopy (Usanovich et al., 1974) that there is little change in electron density at the metal atoms or arene rings on molecular-compound formation. It has been suggested that there are three criteria based on NQR spectra which can be used to distinguish terminal and bridging halogens in unsymmetrically bridged molecular compounds in the absence of information from crystal structure analysis, and these have been applied to HgX2 and SbX3 molecular compounds (Wulfsberg and Weiss, 1980): n n n

1. If a series of NQR signals is split by more than the crystal ﬁeld effect (Weiss, 1972) then the lower-frequency set of resonances will belong to the more bridging halogen atoms; this is supported by the behaviour of L noted above. 2. The asymmetry parameters () will be larger for bridging than for terminal halogens; the values are smaller for unsymmetrical than for symmetrical bridging and tend to merge with the values for terminal atoms. 3. The NQR frequencies of terminal halogens decrease with increasing temperature while those of bridging halogens are less temperature dependent and may even increase slightly with increasing temperature. This has been illustrated for {4-picoline-N-oxide HgCl2} (Ramakrishnan et al., 1972). n n n

This set of criteria is likely to be more immediately applicable to the HgCl2 molecular compounds than to those of MX3 because the former show a much more deﬁnite distinction between bridging and terminal halogens than the latter. Appropriate test examples in the latter group could be {diphenyl 2SbCl3} and {p-xylene 2SbCl3}. n n n

n n n

11.12.1.7 Summary There are small differences in the detailed structures (bond lengths and angles) of the SbX3 molecules as they are found in the various molecular compounds and even in the same molecular compound when crystallographically independent. However, there is no obvious regularity in these effects, suggesting that the interactions involved are all about equally strong (or weak). It has sometimes been claimed that the dimensions of aromatic molecules in some molecular compounds differ from those in the corresponding neat crystals; more precise measurements appear necessary before expenditure of effort in explaining such putative differences. Conformational effects are, however, incontrovertible, e.g. in {diphenyl 2SbCl3} the torsion angle about the central C–C bond is 40.5 , whereas the diphenyl molecule is planar in {diphenyl 2SbBr3} and (on the average) in neat diphenyl, while 9,10-dihydroanthracene is planar in its molecular compounds with n n n

n n n

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

822

SbBr3 and 1,3,5-trinitrobenzene, but folded in its neat crystals. [2.2.2.2]paracyclophane also has different conformations in its neat crystals and in its molecular compounds with SbBr3 and BiBr3. A particular aromatic moiety can, in principle, form four different Menshutkin compounds with SbCl3, SbBr3, BiCl3 and BiBr3, and different arene/MX3 ratios are also possible. Thus, from comparisons of groups of compounds, one could perhaps hope to predict the effects of replacing Sb by Bi, and/or Cl by Br. For example, cell dimensions for the HMB/MX3 quartet are given in Table 11.31; here replacement of Sb by Bi produces a smaller perturbation than replacement of Cl by Br. Caution is needed before generalization: for example, {phenanthrene 2SbCl3} and {phenanthrene -2SbBr3} are not isomorphous, neither are {benzene 2SbCl3} and {benzene 2SbBr3}. However, the three pyrene compounds with SbBr3, BiCl3 and BiBr3 are isomorphous while {pyrene 2SbCl3} is different (data in Table 11.28). The Menshutkin molecular compounds of aromatics with MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) are relatively easily prepared and handled as single crystals despite their sensitivity to moisture. This family of compounds has the great advantage, whose potential has not yet been entirely realized, of being amenable to study by NQR spectroscopy (35Cl, 79Br, 81Br, 121 Sb and 123Sb) and Mo¨ssbauer spectroscopy (121Sb), in addition to the techniques of optical spectroscopy and crystal structure analysis. The aromatic moiety acts as an electron donor towards the MX3 moieties, which have similar mutual arrangements in all these molecular compounds. Various physical measurements agree in indicating that the actual transfer of charge is very small. The MX3 moieties form arrangements based on the interaction of six- and seven-coordinated metal atoms, the ligands being the three covalently bound halogen atoms, a ring of the aromatic molecule and halogens of other MX3 moieties linked by secondary bonding. The mutual arrangement of MX3 moieties varies from one molecular compound to the next. The arene and inorganic components of the Menshutkin compounds themselves undergo only subtle and hardly discernible changes on formation of the adducts, but the structural nature of their interaction is demonstrated by the crystal structure analyses. The arene . . . metal interaction is remarkably invariant, even to the extent of being 2 in nature in the vast majority of the examples; only a few high-symmetry donors show 6 interactions. These interactions have been interpreted by qualitative molecular orbital methods. Much less attention has been paid to the ‘self interactions’ between the MX3 moieties. Why are these sometimes localized, and sometimes extended? And what governs the type of extension that is found? How should one interpret the meager thermodynamic information available? These questions can be asked also of the compounds of silver and mercury salts discussed earlier, and of those of gallium (and its congeners) discussed in the ﬁnal section of this chapter. n n n

n n n

n n n

n n n

n n n

11.12.2 11.12.2.1

Aromatics as donors and np3 metal ions (GaI, InI,TlI, SnII, PbII) as acceptors Introduction

The outer electron conﬁgurations of metal ions in low oxidation states have been given in Table 11.2, and the complexes of d10s0 ions (CuI, AgI and HgII) and of some d10s2 ions (AsIII, SbIII and BiIII) have been discussed in earlier parts of this Chapter. Rundle and

- D O N OR S A N D p -A C C E P T O R S

823

Corbett (1957) predicted that d10s2 ions would give 6 complexes with benzene, and this prediction has proved remarkably resilient for the pure acceptors considered in Section 11.7.2. Although the benzene, sym-tri- and hexa-alkylbenzene complexes (alkyl ¼ methyl, ethyl) show 6 interactions of the metal ions with the benzene rings, the self-interacting complexes of MX3 (M ¼ AsIII, SbIII and BiIII; X ¼ Cl, Br) with (multi-ring) aromatic hydrocarbons show 2 interactions. The interactions among the oligomeric (MX3)n groups and the lower symmetry of the multiring aromatics presumably introduce complications not satisfactorily taken into account by simple theory. What of the remaining groups in Table 11.2 – GaI, InI, TlI and GeII, SnII and PbII? Ge does not form complexes with benzene and its simple derivatives, but an appreciable number of complexes are known with the other elements. MI and MII arene complexes have many features in common but there are also differences, and this is reﬂected in our discussion. At present, ‘arene’ is limited to benzene or polyalkyl-benzenes, increasing alkyl substitution in benzene strongly favouring formation of complexes, while complexes with other aromatic hydrocarbons (apart from some cyclophanes) do not appear to have been reported, and perhaps do not occur. The chemistry (preparative, NMR, crystallography) of the arene complexes of monovalent gallium, indium and thallium has been comprehensively reviewed by Schmidbaur (1985). Schmidbaur, Thewalt and Zaﬁropoulos (1984) have remarked ‘‘Over a hundred years ago [in 1881], the discoverer of the element gallium [Lecoq de Boisbaudran] reported the astonishing observation that the preparations which he termed gallium(II) halides of empirical formula GaX2 (X ¼ Cl, Br) are freely soluble in anhydrous benzene and can be precipitated from solution with ‘crystal benzene’.’’ One milestone on the path to understanding this observation was the demonstration that crystalline GaCl2 was in fact composed of Gaþ and GaIII Cl 4 ions (Garton and Powell, 1957), and this has been supplemented by analogous results for GaBr2 (Schmidbaur, Nowak, Bublak, Burkert, Huber and Mu¨ller, 1987; Ho¨nle, Simon and Gerlach, 1987). The complexes studied crystallographically can be classiﬁed into a number of groups. The invariant feature is that the MI ion always interacts in 6 fashion with a (possibly substituted) benzene ring3. Furthermore, a particular metal ion may interact with one or two benzene rings. The fundamental difference between ferrocene-type compounds on the one hand and those of the present group (and of AgI and CuI) with aromatics, on the other, is the essential role played by the partially ﬁlled d-orbitals in the bonding in the ferrocene group, whereas these orbitals are ﬁlled in the second group and hence cannot participate. All the MI (M ¼ Ga, In, Tl) complexes have [(AIII)X4] counterions, where A is Al, Ga or In. The counterions form a number of complicated arrangements, including interactions with the MI moieties, which are somewhat reminiscent of the situations found in the self-interacting {(arene)MIIIX3} complexes described in Section 11.12.1. An important chemical feature is the high sensitivity to moisture of most of the molecular compounds of aromatics with posttransition metal salts. Thus almost all of the compounds described below were prepared under pure and dry nitrogen; many of the compounds decompose under reduced pressures. The benzene complexes of Sn(II) and Pb(II) were quite extensively studied in the 1970s by Amma and coworkers, and since then further structures have been reported by 3 Bis[1,5-ditolylpentaazadienido-thallium(I)] (FAMPIS) and bis[1,3-diphenyltriazenido-thallium(I)] (FAMPOY) are examples of unary crystals where 6 Tl(I) . . . benzene interactions are important in formation of polymeric chains in the crystal structures (Beck and Stra¨hle, 1986).

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

824

Schmidbaur and coworkers. One group of Sn(II) and Pb(II) complexes has AlIIICl4 as counterion, while a second group of Sn(II) complexes has (Sn2Cl2)2þ moieties with AlIIICl 4 as counterions, coordinations being completed in both groups by secondary interactions including metal . . . benzene. Among other complexes reported (but not yet studied crystallographically) are C6H6 2TlAlCl4 and 2(C6H6) 2TlAlCl4 (Auel and Amma, 1968); C6H6 Ga(AlCl4) and C6H6 Ga(GaCl4) (Rundle and Corbett, 1957); C6H6 BiCl2AlCl4 (Peyronel et al., 1968). n n n

n n n

n n n

n n n

n n n

11.12.2.2 Ga, In or Tl to One benzene ring 1. (Hexamethylbenzene)gallium(I) tetrachlorogallate(III) tetramer[{((CH3)6C6)GaI}þ [GaIIICl4]]4. Thewalt, Zaﬁropoulos and Schmidbaur, 1984a; CUTTUG. ˚ , ¼ 91.01 , Z ¼ 4, R3m) melt at The very soft rhombohedral crystals (a ¼ 12.449 A 441 K (dec.); the structure was determined at 233(5)K. The overall structure (Fig. 11.108) may be described as consisting of four {[((CH3)6C6)GaI]þ cations and four [GaIIICl4] anions, generating a hydrocarbon surface around an inorganic skeleton. The cation and

A

Ga(III)Cl4 anion HMB seen edge-on

vectors show Ga(I)...HMB interaction

C Ga(I) cation

x z y B

Fig. 11.108. (Hexamethylbenzene)gallium(I) tetrachlorogallate(III) tetramer viewed down the [111] rhombohedral axis. The interaction between Ga(I) (open ellipsoid) and (edge-on) hexamethylbenzene is shown by the arrow; the corresponding interaction along the view axis is partially ˚, obscured. The covalent Ga(III)–Cl distances in the tetrachlorogallate anions are all close to 2.17 A ˚ in length. (Adapted from Thewalt, while the secondary Ga(I) . . . Cl interactions are 3.224 A Zaﬁropoulos and Schmidbaur, 1984.)

- D O N OR S A N D p -A C C E P T O R S

825

anion on [111] (in the center of the diagram) have crystallographic 3m symmetry, while those on the edges of the diagram have m symmetry. Each arene can be assigned to a discrete Gaþ centre as an 6 ligand. The distances of GaI to the centers of the hexa˚ . Thewalt et al. note that ‘‘The four hexamethylbenzene rings are 2.43 and 2.51 A methylbenzene rings form an efﬁcient cover around the inorganic [Gaþ GaCl4]4 framework. There are no Ga . . . Cl contacts between neighbouring ‘‘clusters’’ and the contents of a unit is to be regarded as a tetrameric species of composition (C6Me6)4Ga8Cl16.’’ 2. (Hexamethylbenzene)gallium(I) Tetrabromogallate(III) Network. CEFSEL. [{(CH3)6C6)Ga(I)þ} {GaIIIBr4}]. Schmidbaur, Thewalt and Zaﬁropoulos, 1984a. ˚ , 103.90(2) , Z ¼ 4P21/c), This material (monoclinic, 10.906(3) 13.994(5) 12.415(4) A which is stable in a vacuum at room temperature, melts at 419K. There is a complicated network of interacting {(CH3)6C6)Ga(I)þ} cations and {Ga(III)Br4} anions. Each arene can be assigned to a discrete Gaþ center as an 6 ligand, with the Gaþ cations paired through bidentate bromines, the coordination sphere about Gaþ being completed by Ga(III)Br4 anion

arrow shows HMB...Ga(I) interaction

B

A

O

y x

z

Fig. 11.109. (Hexamethylbenzene)gallium(I) Tetrabromogallate(III) Network viewed down [001]. In this ﬁgure the overall structure is emphasized; there are inorganic sheets viewed edge-on, to which arene moieties are attached on both sides. The Ga(I) atoms are identiﬁed by the associated arrows showing interactions with the hexamethylbenzenes. The covalent Ga(III)–Br distances in the ˚ , while the secondary Ga(I) . . . Br interactions range tetrabromogallate anions are all close to 2.30 A ˚ in length. (Data from Schmidbaur, Thewalt and Zaﬁropoulos, 1984a.) up to 3.5 A

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

826

monodentate bromines (Fig. 11.109). The distance of Ga(I) to the centers of the hexa˚ , with the average Ga(I) . . . C distance is 2.89(2) A ˚ . The ﬁve methylbenzene rings are 2.55 A close bromines come from one monodentate and two bidentate {Ga(III)Br4} tetrahedra. ˚ but The benzene ring of the complexed hexamethylbenzene is planar to within 0.02 A ˚ the methyl groups deviate from this plane by up to 0.14 A. The crystal structures of the tetrachloro-and tetrabromogallates are quite different; Thewalt et al.(1984) consider ‘‘that the arrangement of halogens in these compounds around GaI centers is governed largely by packing effects originating in the relative size of the halogen atoms.’’ 11.12.2.3

Ga, In or Tl to Two benzene rings

1. and 2. {Bis(benzene)gallium(I) Tetrachlorogallate(III)} Dimer3(benzene). [{(C6H6)2Gaþ}[Ga(III)Cl4]]23(C6H6). Schmidbaur, Thewalt and Zaﬁropoulos, (1983) (CEFPAE), and the isomorphous {Bis(benzene)gallium(I) Tetrabromogallate(III)} Dimer3(benzene). [{(C6H6)2Gaþ}[Ga(III)Br4]]23(C6H6). Uson-Finkenzeller et al., 1986 (DIVNOL). These two (colorless) compounds crystallize in isomorphous triclinic cells. We concen˚, trate on the bromo compound, determined at 233K (9.390(2) 10.847(2) 13.118(2) A

Br 3∗

Ga1∗ D2∗

Br4∗

Br 2∗

D1

Br1∗ Ga2

1

Ga2∗

Br1

D1∗

Br2

Br4

D2

Ga1

Br3

Fig. 11.110. The centrosymmetric [{(C6H6)2Gaþ}[Ga(III)Br4]]2 molecule; ORTEP diagram, 50% probability ellipsoids. The atom labellled Ga2 is GaI while Ga1 is GaIII. The four independent ˚ ; the secondary Ga . . . Br distances covalent Ga–Br distances range from 2.300(1) to 2.337(1) A ˚ . (Reproduced from Uson-Finkenzeller et al., 1986.) range from 3.205 to 3.803 A

- D O N OR S A N D p -A C C E P T O R S

827

85.54(1) 102.91(1) 105.62(10 , Z ¼ P 1). The structure consists of centrosymmetric dimers of composition [{(C6H6)2Gaþ}[Ga(III)Br4]]2 (Fig. 11.110), with three benzene solvate molecules not coordinated to Ga. The distances of Ga(I) to the centers of the ˚ (Ga to C 3.08 to 3.16 A ˚ ) and 3.00 A ˚ (Ga to C two coordinated benzene rings are 2.78 A 6 ˚ 3.24 to 3.36 A) (both have arrangements), appreciably longer than for Ga linked to a single benzene. The angle between the vectors from Ga to the ring centers is 124.5 Ga(I) is 6-coordinate. These crystallographic results enable one to make some comments on earlier work in this area. The (Ga2Br4)/(C6H6) pressure-composition phase diagram shows 1 : 1 and 1 : 3 phases (Oliver and Worrall, 1967), and the latter is presumably to be identiﬁed with the 1 : 3.5 compound described above. A 1 : 1 (Ga2Cl4)-(C6H6) phase giving a satisfactory chemical analysis was reported by Carlston, Griswold and Kleinberg, (1958), while Rundle and Corbett (1957) reported a 1 : 1 pseudo-hexagonal phase a ¼ 11.89, c ¼ 30.05 ˚ ) but could not obtain a structure. Schmidbaur, Thewalt and Zaﬁropoulos (1983) remark A that crystals of [{(C6H6)2Gaþ}[Ga(III)Cl4]]23(C6H6) must not be dried by lowering pressure ‘‘as any loss of benzene in vacuo leads to phase changes and deterioration of crystal quality. It should be noted that the alleged 1 : 1 complex Ga2Cl4C6H6 is reported to be obtained from GaCl2 solutions in benzene upon removal of solvent at –5 C.’’ No preparative details were given by Rundle and Corbett. It would seem that existence of a crystalline 1 : 1 phase has yet to be demonstrated. 3. Bis(mesitylene)gallium(I) Tetrachlorogallate(III) Chain Polymer. [{1,3,5-(CH3)3 H3C6]2Ga(I) (Ga(III)Cl4)]n. Schmidbaur, Thewalt and Zaﬁropoulos, 1984b; CUPJUS. This material is stable in a vacuum at room temperature; the crystals are monoclinic ˚ , 110.21(1) at 233K, Z ¼ 4, space group Cc). There are (17.717(3) 10.856(2) 12.959(2) A bent-sandwich moieties similar to those found in the benzene analog, but here these are linked through (Ga(III)Cl4) tetrahedra into polymeric chains running along [001] ˚ ; the angle (Fig. 11.111). The Ga to mesitylene ring-centre distances are equal at 2.673 A between the vectors from Ga2 to the two ring centers is 136.5 . The Ga–Cl distances in the ˚ . Ga(I) is 4-coordinate. anion range from 2.156(3) to 2.178(3) A 4. Bis(mesitylene)indium(I) Tetrabromoindate(III) chain polymer. [1,3,5-(CH3)3 H3C6]2In(I) (In(III)Cl4). Ebenho¨ch et al. (1984); COCFEF. This chain polymer structure is closely related to that of the bis(mesitylene)gallium(I) tetrachlorogallate(III) chain polymer, but the two structures are not isomorphous. The ˚, colourless monoclinic crystals (at 233K a ¼ 10.624(2), b ¼ 13.384(3), c ¼ 17.697(4) A ¼ 94.56(2) , Z ¼ 4, space group P21/n) are sensitive to air and light, and readily lose mesitylene on reduction of ambient pressure. Helical chains extend along [010]; complex cations and anions are coupled so that the tetrabromoindate(III) tetrahedra are bidentate chelate-forming on the one side and monodentate-bridging on the other. Each In(I) ˚ from In(I) to forms two 6 links to separate mesitylenes, with distances of 2.83 and 2.89 A ring center and an angle of 47.3 between the mesitylene planes. The coordination about In(I) is completed by two links to the chelated bromines with distances of 3.446(1) ˚ . In(I) is 5-coordinate. Crystals of [1,3,5-(CH3)3H3C6]2In(I) (Al(III)Br4) and and 3.503(1) A [(CH3)6C6]2In(I) (In(III)Br4) were also obtained but structures have not yet been reported. 5. (Hexaethylbenzene)(toluene)Ga(I) Tetrachlorogallate(III)hemi((hexaethylbenzene) Monomer[{(C6Et6)(C6H5Me)Ga}þGaCl4]1/2(C6Et6). Schmidbaur, Nowak, Huber and Mu¨ller, 1988; SARKEB.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

828

mesitylene layers Ga(III)Cl4 anion

Ga(I) B

Ga(I)

Ga(I)

A y x

O Ga(I)

z Ga(III)Cl4 anions removed for clarity

Fig. 11.111. Projection down [010] of the bis(mesitylene)Ga(I) tetrachlorogallate(III) structure (CUPJUS). The anions have been removed from the vertical band in the centre of the ﬁgure in order to show the secondary interaction of Ga(I) with bis(mesitylene). Other secondary interactions have not been included here but details are available from the original paper. (Data from Schmidbaur, Thewalt and Zaﬁropoulos, 1984b.)

In structural terms this is perhaps the simplest of the present group of complexes, and the only one in which Ga(I) interacts with two chemically different arenes. The colourless ˚ , not given, space transparent monoclinic crystals (9.760(1), 21.447(2), 17.754(2) A group P21/n; Z ¼ 4, measurements at 238K) melt sharply at 387K, are unstable in a vacuum and moist air but stable under a protective atmosphere. The molecules of the complex are at general positions with the uncoordinated solvation hexaethylbenzenes at centers of symmetry. Although the Ga2 to benzene ring interactions are both 6, the linkage from Ga2 to hexaethylbenzene is markedly stronger than that to toluene (Fig. 11.112). Ga(I) is 4-coordinate. Both coordinated and solvent hexaethylbenzene molecules have the alternating up . . . down conformation of the ethyl groups shown in Fig. 11.112, which is also found in other crystals containing hexaethylbenzene. 6. {[2.2]paracyclophane-gallium(I) tetrabromogallate(III)DUMVAI[(1,4-C6H4CH2 CH2)2Ga]þ(GaBr4). Schmidbaur, Bublak, Huber and Mu¨ller, 1986a. Mixing of the components in benzene gives the complex (both tetrachloro- and tetrabromogallate complexes were obtained but only the latter was examined crystallographically). The complexes were insoluble in most solvents so NMR spectra could not be obtained. In(I) and Tl(I) salts did not give complexes on treatment with [2.2]paracyclophane. The bromo complex crystallized in space group Pnma, Z ¼ 4, a ¼ 12.836(4), ˚ (note: CSD interchanges b and c but not y and z). There b ¼ 10.004(3), c ¼ 14.943(4) A are chains of interacting moieties along [010] (Fig. 11.113). Each Ga(I) center is

- D O N OR S A N D p -A C C E P T O R S

829

C13 coordinated toluene

C12

Ga1 C14

CT11 DT 3.500

CT1

C11

3.145 Ga2

3.080 2.535

D1

coordinated hexaethylbenzene

Fig. 11.112. ORTEP diagram of the monomeric molecule of (hexaethylbenzene)(toluene)Ga(I) Tetrachlorogallate(III)hemi((hexaethylbenzene); SARKEB. Ga1 is Ga(III) and Ga2 is Ga(I). The angle DT–Ga2–D1 is 137.2(1) , and that between the hexaethylbenzene and toluene planes is 38.8 . ˚ . (Adapted from Schmidbaur, Nowak, The Ga1–Cl distances range from 2.152(1) to 2.192(1) A Huber and Muller, 1988.) Br2∗

Br2 Ga1 Br3

C8

Br1

3.378 – 1

Ga2 Ga1∗

C4 C3 E C2 C1 3.474 Br3∗ C7

CS– 1 C6

– 1 2.72

Fig. 11.113. Detail of the folded Ga(I) . . . paracyclophane . . . Ga(I) chain running along [010]. Atoms Ga1, Ga2, Br1 and Br3 are situated on crystallographic mirror planes, and the paracyclophanes are at centers of symmetry. (Reproduced from Schmidbaur, Bublak, Huber and Mu¨ller, 1986a).

6–coordinated to two different cyclophane molecules (‘external’ coordination); the crystal symmetry requires that the Ga(I)–arene distances (2.72 A) are equal. The paracyclophanes are at centers of symmetry, and the angle subtended at Ga2 by the centers of adjacent coordinated benzene rings is 131.1(8) . This folding is similar to that found in other bis(arene)metal complexes. The paracyclophane geometry hardly differs from that found in crystals of the neat compound. When all interactions are considered, it becomes

830

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

clear that the overall structure is best described as a three-dimensional network. Ga(I) is 4-coordinate. 7. {[3.3]paracyclophane-gallium(I) tetrabromogallate(III). [(1,4-C6H4CH2CH2 CH2)2Ga]þ(GaBr4). Schmidbaur, Bublak, Huber and Mu¨ller, 1986b; FEFWUI. [3.3]paracyclophane forms 1 : 1 complexes with both Gaþ(GaCl4).and Gaþ(GaBr4), ˚, and the structure of the latter (monoclinic, P21/m, Z ¼ 2, 8.082(1) 15.960(3) 8.818(1) A 107.18(1) ) has been reported. The crystals are less sensitive to air and moisture than other arene complexes of Ga(I). The structure has resemblances to that of the [2.2]paracyclophane analog, but has two-dimensional sheets rather than a three-dimensional network. However, the immediate environment of Ga(I) is similar to that shown in Fig. 11.113, the angle subtended at Ga2 by the centers of adjacent coordinated benzene rings ˚ ) are equal. being 134.2 . Crystal symmetry requires that the Ga(I)–arene distances (2.76 A 8. {[2](1,4)Naphthalino[2]paracyclophane)gallium(I) tetrabromogallate(III)}. [(C20H18)2Ga]þ(GaBr4). Schmidbaur, Bublak, Huber and Mu¨ller, 1987b; GANPOA.

[2](1,4)Naphthalino[2]paracyclophane

˚ , 97.98(1) , Z ¼ 4, P21/n) The monoclinic crystals (12.353(2) 15.035(2) 12.368(2) A have a layer structure based on the interaction of Ga(I) with the linked benzene rings of the cyclophane (those on the left hand side of the structural formula shown above); the ˚ (d(Ga(I) to C range from distance from Ga(I) to the center of the benzene ring is 2.67 A ˚ ˚ 2.89 to 3.15(2) A), and that to the naphthalene ring is 2.85 A (d(Ga(I) to C range from 3.06 ˚ ), suggesting a stronger complexation with the unperturbed -system of the to 3.35(2) A former. There are also important secondary interactions between Ga(I) and two bromines ˚ for of the GaBr4 ions. The covalent bond lengths in the GaBr4 ions are (twice) 2.306(3) A ˚ the two bromines that do not interact and 2.324 and 2.338(3) A for the bromines involved ˚ ). The angle between in secondary interactions (distances of 3.310, 3.331 and 3.523(4) A the vectors from Ga(I) to the two ring centers is 124.8 . Ga(I) is 5-coordinate (Fig. 11.114). 11.12.2.4

Mixed mono- and bis(arene) complexes

1. {Hexakis[mesitylene]tetrathalliuml(I) Tetrakis(tetrabromogallate(III)) {(1,3,5-(CH3)3 H3C6]6(Tl(I))4 [Ga(III)Br4]4}. Schmidbaur, Bublak, Riede and Mu¨ller, 1985; DEXLOH. This is the only example (so far) of a mixed complex in which both mono- and bis(arene)M(I) moieties are present in the same cluster (Fig. 11.115). The triclinic crystals have centrosymmetric tetrameric units. In the monoarene cations the Tl(I) is located ˚ above the center of the mesitylene, while in the bis(arene) cation the distances are 2.94 A ˚ , with a mutual inclination of 60.5 . The cationic units are linked via 3.00 and 3.02 A III tetrahedral [Ga Br4] anions into a complicated network of thallium–bromine contacts.

- D O N OR S A N D p -A C C E P T O R S

Ga2∗

831

Br 2∗ Br 4∗ Ga1∗

Br 3

C7

Br1 * Br1

Ga1 Br 4 Br 2

C1 Br3∗ C6 Ga 2 C5

C8

C 15 C 16 C2 C 17 C3 C 18

C4 C 19

C9 C 14 C 10 C 13 C 11 C12

C 20

Fig. 11.114. {[2](1,4)Naphthalino[2]paracyclophane)gallium(I) tetrabromogallate(III)}, showing the centrosymmetric [(C20H18)2Ga]þ(GaBr4) grouping, which repeats to form the layer structure. Ga(I) is shown by ﬁlled spheres and Ga(III) by open spheres. Br1 and Br2 of the tetrabromogallate(III) ions are linked to Ga(I) while Br3 and Br4 do not have secondary interactions. (Reproduced from Schmidbaur, Bublak, Huber and Mu¨ller, 1987b.)

11.12.2.5

Sn or Pb to one benzene ring

1. The polymeric chain complex [(-C6H6)Sn2þ(AlCl4)2]nnC6H6BENZSN10. Rodesiler, Auel and Amma, 1975. ˚ , 110.08(1) , Z ¼ 4, space The crystals are monoclinic (11.282(3) 17.317(8) 12.646(6) A group P21/n); the Sn(II) environment and chain structure are shown in Figs.11.116 and ˚ , and the Sn . . . Cl 11.117. The Al–Cl distances range from 2.068(3) to 2.199(3) A ˚ . The Sn-benzene ring interaction is 6, with the distances from 2.766(2) to 3.280(2) A ˚ while the average Sn . . . C distance is 3.06 A ˚. distance to the ring center 2.74(1) A A simple molecular orbital scheme (which we do not detail) was put forward to rationalize the present structure, and its relationship to (C6H6)U(AlCl4)3Sn(I) is 7-coordinate. 2. The polymeric chain complex [(-C6H6)Pb2þ(AlCl4)2]nnC6H6. Gash et al., (1974; BZACLB). This structure is isomorphous with the Sn(II) analog described in the previous ˚ , 110.14(1) , Z ¼ 4, space group P21/n). The paragraph (11.365(1) 17.307(2) 12.707(2) A ˚ ˚. Al–Cl distances range from 2.05 to 2.21 A, and the Pb . . . Cl distances from 2.85 to 3.22 A 6 ˚ The Pb-benzene ring interaction is , with the distance to the ring center 2.77 A while ˚ . There is approximate pentagonal bipyramidal the average Pb . . . C distance is 3.11 A coordination about Pb(II), with Cl(1), Cl(2), Cl(6), Cl(3 0 ) and Cl(4 0 ) in the equatorial plane and Cl(7) and the centre of the benzene ring in the axial sites; Pb is displaced by ˚ out of the equatorial plane towards the benzene. The primed atoms are related 0.6 A

832

DONOR–ACCEPTOR MOLECULAR COMPOUNDS (a) D1

Br5 D3∗

Ga1

Ga2 T12∗

T11 Br6

Br8 Br4∗

Br2∗

Br2

– O1 Br6∗

T12 D3

Ga2∗ Br7∗

Br1∗

Br5∗

D1∗

D1

(b)

Br4

Br8∗

T11∗ Ga1∗ Br3∗

Br3

Br1

Br7

D2∗

D2

(c)

D3

2.94 Br6

T11

3.01

Br8∗

T12 Br2 Br4 D2

Br1 Br7

Br2

Br5∗

Br6∗

Br6∗

mono(arene)T1

bis(arene)T1

Fig. 11.115. (above) A general view of the mixed arene {hexakis[mesitylene]tetrathalliuml(I) tetrakis(tetrabromogallate(III)) structure. (below) Detail of the mono- and bis(arene)Tl parts of the structure. In the bis(arene)Tl part, Tl is 7-coordinate and the two distances from Tl to the midpoint of the arene ring are essentially equal, and a little longer than the distance for 6-coordinate mono(arene)Tl. (Adapted from Schmidbaur, Bublak, Riede and Mu¨ller. 1985.)

Cl(8) Al(2) Cl(5) Cl(7)

Cl(3⬘)

Cl(6) Cl(3)

Cl(2)

Cl(4⬘)

Sn C(4)

Al(1)

C(5)

Cl(1) C(3)

Cl(4)

C(2)

C(6) C(1)

Fig. 11.116. (-C6H6)Sn2þ (AlCl4)2C6H6 structure: ORTEP plot (50% probability ellipsoids) showing the sevenfold coordination about Sn(II) (two axial chlorines, four equatorial chlorines, and the center of the benzene ring). Two chlorines are not coordinated; the equatorial AlCl4 groups provide the propagating element for the chains. (Reproduced from Rodesiler, Auel and Amma, 1975.)

by symmetry elements to the unprimed and their repetition forms the Pb(AlCl4)2 chain. The second benzene is intercalated in the structure between the AlCl4 groups. The overall structure can be described as a chain where one group of AlCl4 tetrahedra is bridged by Pb ions and those of the second group act as chelating ligands forming axial and equatorial

- D O N OR S A N D p -A C C E P T O R S

interstitial benzene

CI

833

coordinated benzene

AI

Sn

z y

Fig. 11.117. Projection of the (-C6H6)Sn2þ (AlCl4)2C6H6 structure down [100], showing zigzag chains approximately along [001]. Most vectors linking the centers of the coordinated benzene rings (ﬁlled atoms) to Sn have been omitted for clarity. Two chlorines on one AlCl4 moiety are not linked to Sn but all other chlorines form secondary links to Sn. (Data from Rodesiler, Auel and Amma, 1975.)

Pb . . . Cl links. Thus both benzene metal ion and cation . . . anion interactions are important in stabilizing the structure. There are analogies to the structural arrangements in C6H6 UIII(AlCl4)3 (Cesari et al., 1971a; BNZUAL) and {[UIV(6-C6Me6)Cl2]2(-Cl3)} AlCl4 (Cotton and Schwotzer, 1985; DACRII), where the rings are -bonded to the uranium atoms. 3. The dimeric coordination complex of hexamethylbenzene with Sn2þ(AlCl4)2]. [(6 C6(CH3)6)Sn2þ(AlCl4)2]23C6H6. Schmidbaur, Probst, Stiegelmann and Mu¨ller, (1989); JAVJIZ.+ ˚ , 85.94(1) 115.59(1) 98.30(1) , The triclinic crystals (11.852(1) 11.839(1) 12.031(1) A Z ¼ 1; P 1; reduced cell, non-standard choice of origin) contain centrosymmetric [(6 C6(CH3)6)Sn2þ(AlCl4)2]2 dimers (Fig. 11.118). The difference from the polymeric chain structure [(-C6H6)Sn2þ(AlCl4)2C6H6]n appears in the mode of interaction between Sn(II) and AlCl4 moieties. Here the Sn(II) atoms are linked by bidentate bridging AlCl4 counterions, with the Sn coordination completed by 6 interaction to benzene, and bidentate interaction to another (nonbridging) AlCl4 counterion, which has no other Cl ˚ , and the Sn . . . Cl contacts. The Al–Cl distances range from 2.092(1) to 2.178(2) A ˚ ˚ distances from 2.920(1) to 3.097(1) A. The Sn-benzene ring center, distance is 2.45 A ˚ while the Sn . . . C distances range from 2.75 to 2.88 A; these are the shortest such distances so far recorded. n n n

n n n

834

DONOR–ACCEPTOR MOLECULAR COMPOUNDS Cl5 Cl7

Cl3 Al2 Cl8

Z⬘

Cl4

Cl6

Al1 Cl2 Sn Z

Cl1⬘

Cl1

Sn⬘

Al1⬘ Cl2⬘

Cl6⬘

Cl4⬘

Al2⬘

Cl8⬘ Cl3⬘

Cl Cl5⬘

Fig. 11.118. Environment of the Sn(II) atoms in the dimeric coordination complex of hexamethylbenzene with Sn2þ(AlCl4)2]. (Reproduced from Schmidbaur, Probst, Stiegelmann and Mu¨ller, (1989).)

C(4)

C(3)

C(5)

C(2) C(1) Cl(5⬘)

C(6) Cl(4) Sn

Cl(5) Cl(2) Cl(1)

Fig. 11.119. ORTEP diagram (50% probability ellipsoids) showing the local environment of the centrosymmetric (Sn2Cl2)2þ dimer in ((-C6H6)Sn2þCl(AlCl4). The two independent Sn–Cl ˚ . (Reproduced from Weininger, bonds in the dimer parallelogram have lengths 2.614 and 2.659(4) A Rodesiler and Amma, 1979.)

11.12.2.6 Sn to one benzene ring, (Sn2Cl2)2þ moiety being present 1. {((-C6H6)Sn2þ Cl(AlCl4)} dimer. Weininger, Rodesiler and Amma, 1979; CBZSNA10. ˚ , 93.65(10 , Z ¼ 4 formula The monoclinic crystals (19.624(6) 9.531(1) 7.099(1) A units, space group P21/n) have centrosymmetric (and hence planar) (Sn2Cl2)2þ moieties ˚ ) to form chains along [001], with the linked to (AlCl4) moieties (d(Al–Cl) 2.08 to 2.19 A ˚) coordination of each Sn being completed by three longer Sn . . . Cl links (2.84 to 3.32 A ˚ and an approximately 6 link to benzene, with the distance to the ring center 2.90(2) A ˚ while the Sn . . . C distances range from 3.05 to 3.39 A (Fig. 11.119). 2. {(p-xylene) Sn2þ Cl((AlCl4)2} dimer. Weininger, Rodesiler and Amma, 1979; CPXSNA10. The monoclinic crystals were described in the non-standard I2/c space group (Z ¼ 8, ˚ , 107.33 ); the local environment of the planar centrosymmetric 18.970 10.903 15.470 A

- D O N OR S A N D p -A C C E P T O R S

D1

D 2⬘ Cl4⬘

Cl5⬘

Cl8

Sn2

Al2

Sn 2⬘

Cl3⬘

Cl6

Cl1

Cl9

Cl10⬘

Cl7⬘ Al1⬘

Sn 1 Cl2

835

Cl2⬘ Cl3

Al2⬘ Cl9⬘

Cl1⬘ Cl8⬘

Cl6⬘ Sn1⬘

Al1 Cl5 Cl10

Cl4

Cl 7 D2

D 1⬘

Fig. 11.120. The centrosymmetric tetrameric [(6 (C6(CH3)6)2Sn2þCl(AlCl4)]4 molecule. (Reproduced from Schmidbaur, Probst, Huber, Mu¨ller and Kru¨ger, 1989.)

˚ ) is much the same as shown in (Sn2Cl2)2þ dimer (d(Sn–Cl) ¼ 2.616(3) and 2.684(3) A Fig. 11.119 although there is evidence for somewhat stronger Sn . . . p-xylene interaction ˚. as the Sn to ring carbon distances range from 2.92(1) to 3.27 A 6 2þ 3. Tetrameric [( -(C6(CH3)6)2Sn Cl(AlCl4)]43C6H5Cl at 238K. Schmidbaur, Probst, Huber, Mu¨ller and Kru¨ger, 1989; SANMUP. ˚ , 100.77(1) 93.62(1) Colourless triclinic crystals (12.481(2) 14.749(2) 12.899(2) A 100.98(1) , Z ¼ 1 (solvated tetramer), space group P1; reduced cell, nonstandard choice of origin) were obtained from chlorobenzene. The structure is composed of dimeric [(6-(C6(CH3)6)2Sn2þCl(AlCl4)]2 units containing crystallographically non-equivalent monomers. These dimers are cross-linked to form centrosymmetric tetramers (Fig. 11.120). The hexamethylbenzene molecules are each 6-coordinated to a particular ˚ (d(Sn . . . C) range from 2.831(3) to Sn atom, the Sn to ring center distances being 2.60 A ˚ ˚ ˚ ). The chloro3.110(5) A) and 2.73 A (d(Sn . . . C) range from 3.014(5) to 3.106(5) A benzene molecules, one of which is disordered about a center of symmetry, do not make any metal contacts. The covalent Al–Cl distances (8 independent values) range from ˚ , the Sn–Cl distances (4 independent values) within the dimer range 2.104(2) to 2.191(2) A ˚ , whereas the secondary Sn . . . Cl distances (7 independent from 2.586(1) to 2.709(1) A ˚, values) range from 2.808(1) to 3.625(2) A 11.12.2.7 Sn to two benzene rings, (Sn2Cl2)2þ moiety being present 1. Dimeric [(6 (C6H6)2Sn2þCl(AlCl4)]2C6H6. Schmidbaur, Probst, Huber, Stiegelmann and Mu¨ller, 1989; VAWCAX. ˚ , Z ¼ 8, space group The crystals are orthorhombic (19.869(1) 15.941(1) 25.954(2) A 6 2þ cations are bridged by two 1,3-bidentate tetrahedral Pbca). Two [( -(C6H6)2Sn (AlCl4)anions and by two bicoordinate Cl anions (Fig. 11.121). The angles between the planes of the pairs of coordinated benzenes are 101.9 and 99.7 , and the distances for ˚ , somewhat longer than found in Sn(II) to the ring centers range from 3.11 to 3.26 A analogous complexes.

DONOR–ACCEPTOR MOLECULAR COMPOUNDS

836

Cl14 Cl13

coordinated benzene Cl0

AlCl4

Al1

Cl1

C40 C41

Cl11 C45

Cl12

Cl5

Cl2

C42

Cl1

Cl3 Cl4 Sn1

Sn2Cl2 dimer

Sn2

Cl2

C24

C43

C31

C25 C20

C44

C30

C32

Cl22

C21

C35 Cl24

C22

Al2

C23

C33

C34

Cl21 Cl23

Fig. 11.121. ORTEP diagram (50% probability ellipsoids) showing the local environment of the (Sn2Cl2)2þ dimer in [(6-C6H6)Sn2þCl(AlCl4)]2. The four independent Sn–Cl bonds in the dimer ˚ , with angles of 78.5 at Sn and 101.5 at Cl. The parallelogram range from 2.607(2) to 2.633(2) A molecule of crystal benzene has been omitted. (Reproduced from Schmidbaur, Probst, Huber, Stiegelmann and Mu¨ller, 1989.)

11.13

Summary

Four of the groups of molecular compounds considered in this Chapter have similar overall features but differences in detail. The MX3 compounds with arenes contain only neutral moieties, the AgX compounds with arenes contain a single type of charged species, M(I)A(III)X4 compounds with arenes contain metal species in two oxidation states, and the HgX2 compounds with arenes, which show the most structural variability, fall between the limits of charged and uncharged species. Of course, the extensive networks of secondary interactions will modify formal charge distributions. The inorganic part of the AgX compounds with arenes shows little variability, and the same is true for the A(III)X4 moieties. The SbX3 moieties also maintain their pristine shapes, but BiX3 shows departures. As already noted, HgX2 shows wide structural variety. Invariance holds rather strictly for the arene . . . metal interactions –2 for the AgX and MX3 compounds and 6 in the M(I)A(III)X4 compounds. Isomorphism is rare in this family of molecular compounds – there are examples of replacement of Cl by Br, or Sb by Bi, or even Sn by Pb, that do not lead to changes of crystal structure – but it is more usual for the overall structure to change, even though recognizable structural features are carried over from one compound to the next. References Abassalti, M. and Michaud, M. (1975). Rev. Chim. Mineral., 12, 134–138. Abe, H. and Ito, M. (1978). J. Raman Spectroscopy, 7, 35–40. Abe, Y. (1958). J. Phys. Soc Japn., 13, 918–927.

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Schmidbaur, H., Bublak, W., Huber, B. and Mu¨ller, G. (1987a). Angew. Chem., Int. Ed. Engl., 26, 234–237. Schmidbaur, H., Bublak, W., Huber, B. and Mu¨ller, G. (1987b). Z. Naturforsch., 42b 147–150. Schmidbaur, H., Bublak, W., Huber, B., Reber, G. and Mu¨ller, G. Angew. Chem., Int. Ed. Engl., 25, 1089–1090 (1986). Schmidbaur, H., Bublak, W., Riede, J. and Mu¨ller, G. (1985). Angew. Chem. Int. Ed. Engl., 24, 414–415. Schmidbaur, H., Hager, R., Huber, B. and Mu¨ller, G. (1987). Angew. Chem. Int. Ed. Engl., 26, 338–340. Schmidbaur, H., Nowak, R., Bublak, W., Burkert, P., Huber, B. and Mu¨ller, G. (1987). Z. Naturforsch., 42b, 553–556. Schmidbaur, H., Nowak, R., Huber, B. and Mu¨ller, G. (1987). Organometallics. 6, 2266–2267. Schmidbaur, H., Nowak, R., Huber, B., and Mu¨ller, G. (1988). Z. Naturforsch., 43b, 1447–1452. Schmidbaur, H., Nowak, R., Schier, A., Wallis, J. M., Huber, B. and Mu¨ller, G. (1987). Chem. Ber., 120, 1829–1835. Schmidbaur, H., Nowak, R., Stiegelmann, O. and Mu¨ller, G. (1990). Chem. Ber., 123, 19–22. Schmidbaur, H., Probst, T., Huber, B., Mu¨ller, G. and Kru¨ger, C. (1989). J. Organometall. Chem., 365, 53–60. Schmidbaur, H., Probst, T., Huber, B., Stiegelmann, O. and Mu¨ller, G. (1989). Organometallics. 8, 1567–1569. Schmidbaur, H., Probst, T., Stiegelmann, O. and Mu¨ller, G. (1989). Z. Naturforsch., 44b, 1175–1178. Schmidbaur, H., Thewalt, U. and Zaﬁropoulos, T. (1983). Organometallics, 2, 1550–1554. Schmidbaur, H., Thewalt, U. and Zaﬁropoulos, T. (1984a). Angew. Chem. Int. Ed. Engl., 23, 76–77. Schmidbaur, H., Thewalt, U. and Zaﬁropoulos, T. (1984b). Chem. Ber., 117, 3381–3387. Schmidbaur, H., Wallis, J. M., Nowak, R., Huber, B. and Mu¨ller, G. (1987b). Chem. Ber., 120, 1837–1843. Schmidt, M., Bender, and Burschka, C. (1979). Z. anorg. allgem. Chem., 454, 160–166. Schmidt, M., Bender, R., Ellermann, J. and Ga¨belein, H. (1977). Z. anorg. allgem. Chem., 437, 149–154. Schweikert, W. W. and Meyers, Edward A. (1968). J. Phys. Chem., 72, 1561–1565. Shaanan, B., Shmueli, U. and Colapietro, M. (1982). Acta Cryst., B38, 818–824. Shaw, J. A. and Fisher, E. (1946). J. Am. Chem. Soc., 68, 2745. Shaw, R. A., Smith, B. C. and Thakur, Ch. P. (1968). Ann. Chem., 713, 30–39. Shibata, S. and Iwata, J. (1985). J. Chem. Soc. Dalton, pp. 9–10. Shibuya, I. (1961). Bussei, 2, 636. Shmueli, U. and Mayorzik, H. (1980). Abstract 1-A-37, ECM-6, Barcelona. Silverman, J., Krukonis, A. P. and Yannoni, N. F. (1973). Acta Cryst., B29, 2022–2024. Smith, H. G. and Rundle, R. E. (1958). J. Am. Chem. Soc., 80, 5075–5080. Smith, W. (1879). J. Chem. Soc., 35, 309–311. Smith, W. and Davis, G. W. (1882). J. Chem. Soc., 41, 411–412. Sneedon, R. P. A. (1979). L’actualite Chimique, pp. 31–45. Sondern, Chr. and Perkampus, H. H. (1983). Ber. Bunsenges. Phys. Chem., 874, 432–435. Stezowski, J. J., Stigler, R.-D., Karl, N. and Schuller, K. (1983). Z. Kristallogr. 162, 213–215. Strieter, F. J. and Templeton, D. H. (1962). J. Chem. Phys., 37, 161–164. Strømme, K. O. (1959). Acta Chem. Scand., 13, 268–274. Subramanian, V. and Seff, K. (1980). Acta Cryst., B36, 2132–2135. Taylor, I. F., Jr. and Amma, E. L. (1975a). J. Cryst. Mol. Struct., 5, 129–135. Taylor, I. F., Jr. and Amma, E. L. (1975b). Acta Cryst., B31, 598–601. Taylor, I. F., Jr., Hall, E. A. and Amma, E. L. (1969). J. Am. Chem. Soc., 91, 5745–5749.

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Tebbe, K.-F. and Nagel, K. (1995). Acta Cryst., C51, 1388–1390. Terao, H., Sakai, H. and Negita, H. (1985). Bull. Chem. Soc. Jpn., 58, 2318–2322. Terzis, A., Faught, J. B. and Pouskoulelis, G. (1980). Inorg. Chem., 19, 1060–1063. Thewalt, U., Zaﬁropoulos, T. and Schmidbaur, H. (1984). Z. Naturforsch., 39b, 1642–1646. Thomas, C. A. (1941). ‘‘Anhydrous Aluminum Chloride in Organic Chemistry.’’ A. C. S. Monograph No. 87, Reinhold, New York. See particularly Chapter 3. Tildesley, B. D. and Sharpe, A. G. (1953). Research, 6, 51S–52S. Traynham, J. G. (1961). J. Org. Chem., 26, 4694–4696. Traynham, J. G. and Olechowski, J. R. (1959). J. Am. Chem. Soc., 81, 571–574. Trotter, J. and Zobel, T. (1966). Z. Kristallogr., 123, 67–72. Turner, R. W. and Amma, E. L. (1966a). J. Am. Chem. Soc., 88, 1877–1882. Turner, R. W. and Amma, E. L. (1966b). J. Am. Chem. Soc., 88, 3243–3247. Turner, R. W. and Amma, E. L. (1966c). J. Inorg. Nucl. Chem., 28, 2411–2413. Uchida, T. and Kimura, K. (1984). Acta Cryst., C40, 139–140. Usanovich, M. I., Makarov, E. F., Kamysbaev, D. Kh., Aleksandrov, A. Yu., Sumarakova, T. N. and Amelin, I. I. (1974). Dokl. Akad. Nauk. SSSR, 217, 151–153; Chem. Abstr., 81, 113273g (1975). Uson-Finkenzeller, M., Bublak, W., Huber, B., Mu¨ller, G. and Schmidbaur, H. (1986). Z. Naturforsch., 41b, 346–350. Van der Helm, D. (1973). J. Cryst. Mol. Struct., 3, 249–258. Van der Meer, H. (1972). Acta Cryst., B28, 367–370. Vasilyev, A., Lindeman, S. V. and Kochi, J. K. (2001). Chem. Commun., pp. 909–910. Vasilyev, A., Lindeman, S. V. and Kochi, J. K. (2002). New J. Chem., 26, 582–592. Veenvliet, H. and Migchelsen, R. (1971). Z. Kristallogr., 134, 291–304. Vezzosi, I. M., Battaglia, L. P. and Corradi, A. B. (1992). J. Chem. Soc. Dalton, pp. 375–377. Vezzosi, I. M., Buffagni, S. and Peyronel, G. (1960). Ann. Chim. (Roma), 50, 343–347. Vezzosi, I. M., Peyronel, G. and Buffagni, S. (1968). Gazz. Chim. Ital., 98, 162–166. Vezzosi, I. M., Peyronel, G. and Zanoli, A. F. (1974). Inorg. Chim. Acta, 8, 229–232. Vezzosi, I. M., Zanoli, A. F., Battaglia, L. P. and Corradi, A. B. (1988). J. Chem. Soc. Dalton, pp. 191–193. Viennot, J. P. and Dumas, G. G. (1972). Compt. Rend. Acad. Sci., Paris, Ser. B, 275, 489–492. Vranka, R. G. and Amma, E. L. (1966). Inorg. Chem., 5, 1020–1025. Walsh, R. B., Padgett, C. W., Metrangolo, P., Resnati, G., Hanks, T. W. and Pennington, W. T. (2001). Cryst. Growth Des., 1, 165–175. Waterfeld, A., Isenberg, W., Mews, R., Clegg, W. and Sheldrick, G. M. (1983). Chem. Ber., 116, 724–731. Watson, W. H., Jr. and Lin, C.-T. (1966). Inorg. Chem., 5, 1074–1077. Weber, G. (1980). Acta Cryst., B36, 2779–2781. Webster, M. (1966). Chem. Revs., 66, 87–118. Weininger, M. S., Rodesiler, P. F. and Amma, E. L. (1979). Inorg. Chem., 18, 751–755. Weininger, M. S., Rodesiler, P. F., Gash, A. G. and Amma, E. L. (1972). J. Am. Chem. Soc., 94, 2135–2136. Weiss, Alarich. (1972). Fortschr. Chem. Forsch., 30, 1–76. Weiss, Alarich. (1995). Acta Cryst., B51, 523–539. Wells, A. F. (1975). Clarendon Press, Oxford, 4th Edition, see, pp. 918–926. West, C. D. (1937). Z. Kristallogr., 96, 459–465. Wheat, J. A., II and Browne, A. W. (1936). J. Am. Chem. Soc., 58, 2410–2413. Wheat, J. A., II and Browne, A. W. (1938). J. Am. Chem. Soc., 60, 371–372. Wheat, J. A., II and Browne, A. W. (1940a). J. Am. Chem. Soc., 62, 1575–1577. Wheat, J. A., II and Browne, A. W. (1940b). J. Am. Chem. Soc., 62, 1577–1578.

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Chapter 12 Hydrogen bonded molecular complexes and compounds

Although the hydrogen bond is not a strong bond (its bond energy . . . lying in most cases in the range 2 to 10 kcal/mole), it has great signiﬁcance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, the hydrogen bond is especially suited to play a role in reactions occurring at normal temperatures. It has been recognized that hydrogen bonds restrain protein molecules to their native conﬁgurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the signiﬁcance of the hydrogen bond for physiology is greater than that of any other structural feature. Linus Pauling: The Nature of the Chemical Bond (3rd Edition, pp. 449–450, 1963).

Summary: Hydrogen bonding, one of the most important secondary interactions between molecules of the same kind, is no less important among the binary adducts, and most of the same principles apply. Among the most important hydrogen bond donors are –OH, >NH, –NH2 while >C¼O, >O, –Cl and >S are important acceptors, together with charged analogs. The major structural distinction is between ‘‘appendage structures’’, where one component forms a framework to which the second component is hydrogen bonded, and ‘‘mixed framework structures’’, where both components form part of an alternating framework. The latter group can have the two components hydrogen bonded in pairs or in larger discrete groupings, the crystals being molecular crystals from a structural point of view, or in linear chains, or in layers, or in three-dimensional frameworks, where many complex arrangements are possible, especially if a third component such as water is present. Finally, the question of the circumstances under which proton transfer takes place (the formation of ions) is considered.

12.1 Introductory survey 12.1.1 Introduction 12.1.2 The characteristic features of hydrogen bonds 12.2 Application of graph theory to the description of hydrogen-bond patterns 12.3 Statistics of hydrogen bond patterns 12.4 Appendage structures (one component forms a hydrogen bonded framework, to which the second component is appended by hydrogen bonding) 12.5 Alternating framework structures (the components, in hydrogen bonded alternating array, form a mixed framework) 12.5.1 Zero-dimensional frameworks 12.5.2 One-dimensional frameworks (linear chains of alternating components) 12.5.3 Two-dimensional frameworks (layer arrangements of alternating components)

852 852 853 861 862 864 867 867 884 896

852

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

12.5.4 Three-dimensional frameworks (arrangements of alternating components in space) 12.5.5 Accounting for formation of a molecular compound 12.6 Crystal engineering with hydrogen bonds 12.7 Charged or neutral moieties – when is there hydrogen transfer between the components? References

12.1 12.1.1

901 904 905 908 911

Introductory survey Introduction

Hydrogen bonding is undoubtedly the most widespread of the speciﬁc interactions linking molecules with suitable functional groups together in the solid state (and, of course, also in the gas and liquid phases, which lie beyond the boundaries of this book). The molecules can be similar, as in ice, or different, as in the molecular compounds to be discussed in this chapter. The phrase ‘hydrogen-bonded molecular complex’ is widely used; in terms of our classiﬁcation (Chapter 1) this is appropriate only when the interactions between one of the components predominates (A . . . A), as, for example, in the gas hydrates (Chapter 7, where we prefer to emphasize the clathrate properties rather than the hydrogen bonding), while ‘compound’ is to be used when A . . . B interactions predominate. Our structural classiﬁcation, based on the nature of the hydrogen-bonded unit formed, distinguishes between two major groupings. First are the appendage structures, where the A component forms a hydrogen-bonded framework to which the pendent B component is linked by a further hydrogen bond; only a relatively few examples of these molecular complexes are known. Ferguson and coworkers (e.g. Lavender et al., 1998) have used the graphic phrase ‘‘stem and leaves motif’’ for this group1. Next are the framework structures, with the two components in alternating array; many such molecular compounds have been studied. The arrays may extend in zero, one, two or three dimensions. We use the term ‘hydrogen bonded adduct’, when these distinctions are not important. Graph theory provides a convenient way of describing hydrogen bonded arrangements and we shall introduce some of these concepts in Section 12.2. We ﬁrst apply these principles of classiﬁcation to adducts in which hydrogen bonding is the major cohesive interaction, accompanied as always by van der Waals forces. Here we choose illustrative examples for discussion and then list (but certainly not completely) other examples of the same category. There are, however, many adducts in which hydrogen bonding accompanies other types of interaction, such as covalent linkages (as in the oligomers of nucleic acids), or ion–dipole or other types of electrostatic interaction. These are usually adducts with more than two components, the structures are complicated and it is not always easy to disentangle the relative importance of the various interactions. We give only a few illustrative examples. The partners in hydrogen-bonded adducts may be neutral or charged; in the latter situation the material is formally a salt, with cation and anion linked by hydrogen bonding. 1 The same phrase was used with a different meaning by Ferguson et al. (1998). We prefer to retain the unambiguous ‘appendage structures.’

INTRODUCTORY SURVEY

853

There do not appear to be clearcut structural differences between the neutral adducts and the salts and we treat them together. Apart from a few isolated examples, we do not include salts of simple inorganic cations or anions nor those in which there is no cation–anion hydrogen bonding. Hydrates are also generally excluded for reasons of space, despite their undoubted importance. We have found it convenient to distinguish between compounds where the two components have only donor or acceptor functions and those in which each component behaves both as donor and acceptor, i.e. is amphoteric. Pyridinium picrate is a simple example of the ﬁrst group and the carboxylic acid dimer an example of the more numerous second group. The last section of this chapter is concerned with the factors which lead to complete transfer of hydrogen from one component to the other, and hence to formation of a salt. There are a number of classical treatments of the broad aspects of hydrogen bonding (Pimentel and McClellan, 1960; Hamilton and Ibers, 1968; Vinogradov and Linnell, 1971; Joesten and Schaad, 1974; Schuster et al., 1976; Jeffrey and Saenger, 1991; Jeffrey, 1997) dealing mainly with unary systems. Theoretical studies have been summarized by Scheiner (1997) and Del Bene (1998). Most emphasis has been placed on structure and physical properties and their inter-relation. Infrared spectra and dielectric properties, which can be used to identify structural types, have received particular attention. These properties, in turn, can be explained in terms of structure. The most recent monograph is ‘‘The Weak Hydrogen Bond in Structural Chemistry and Biology’’ by Desiraju and Steiner, 1999. A modern approach to strong and weak hydrogen bonding is outlined in carefully argued introductory chapters; a later chapter on ‘‘The weak hydrogen bond in supramolecular chemistry’’ is particularly relevant to our present purposes, as discussed here and in Chapter 15. There are many older records of binary molecular compounds, some predating the concept of hydrogen bonding, which we would now recognize as hydrogen bonded. For example, Plotnikow (1909) prepared well crystallized 1 : 2, 1 : 1 and 2 : 1 addition compounds of dimethylpyrone (not deﬁned more precisely) with trichloro- and tribromoacetic acids, their solutions being conducting. Bramley (1916) reported freezing point diagrams for the systems phenol–pyridine (1 : 1 and 2 : 1 compounds) and phenol– quinoline (2 : 3 and 2 : 1 compounds), and for some other systems. Similar methods showed that there was a 2 : 1 compound of camphor and salicylic acid (Le Fevre and Tideman, 1931), which had indeed been reported earlier by Leger in 1890, and of 1,8-epoxymenthane with phenols (see Section 12.5.1.2) (Baeyer and Villiger, 1902). 12.1.2 The characteristic features of hydrogen bonds The most important hydrogen bonds are formed between the following groups of atoms: O---H . . . O; N---H . . . N; O---H . . . N; N---H . . . O; N---H . . . Cl; N---H . . . S; with the donor atom mentioned ﬁrst and then the acceptor atom. The same atom can act both as donor and acceptor. These are strong hydrogen bonds. The participating atoms can be neutral or charged. Appreciably weaker hydrogen bonds occur for C–H . . . O, C–H . . . N and C–H . . . Cl (and some other) groups (Desiraju and Steiner, 1999). A hydrogen bond is said to be formed when the distance between the proton and the acceptor atom (d(X–H . . . Y))2 is less than the sum of their van der Waals radii, i.e. HB 2

X is used for the donor atom to avoid possible confusion with deuterium (D).

854

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

˚. {¼d (H . . . Y)–[r(H) þ r(Y)]} should be negative. When Y¼O, then [r(H) þ r(O)] 2.5 A When the hydrogen position is not known accurately, then the comparison has to be made between the measured value of d(X . . . Y) and [r(X) þ r(Y)]; for O–H . . . O hydrogen ˚ ; much the same values can be used for bonds this means comparing d(Od . . . Oa) and 3.1 A the N–H donor. Effective values (Table 12.1) for van der Waals radii of a number of important atoms, all singly bonded to C (H (Nyburg et al., 1987), F to Se (Nyburg and Faerman, 1985)) have been derived from statistical analyses of the structural results given in the Cambridge Structural Database (CSD). For most of these atoms it is found that the van der Waals radius in the direction of the bond (a head-on contact) is shorter than that in the perpendicular direction (a side-on contact), i.e. there is polar ﬂattening, and the atom must thus be described by a minor and a major radius. There is no polar ﬂattening in N and O and relatively little in F. The averages of the major and minor radii are quite close to the standard (spherical) values of Pauling (1963) and Bondi (1968). For H bonded to O a ˚ was deduced by Steiner and Saenger (1991) from minimum side-on contact of 1.03 A analysis of ND results for 23 carbohydrate structures. Baur (1992) has pointed out that ‘‘side-on [H . . . H] contacts in inorganic crystals can be shorter than head-on contacts, while in organic crystals the opposite is true.’’ The operational deﬁnition of a strong hydrogen bond in terms of the van der Waals radius has advantages of convenience and applicability to most of the situations discussed in this chapter. but is not in tune with the more sophisticated approaches reviewed by Desiraju and Steiner in their Chapter 1, and has been much criticized (Jeffrey and Saenger, 1991; Desiraju and Steiner, 1999). We shall use it widely as, for our purposes, its advantages outweigh its defects, which are most obvious in borderline cases, and for the weak hydrogen bonds. Hydrogen bonds can be two-centered (‘‘linear’’), three-centered (‘‘bifurcated’’) or fourcentered (‘‘trifurcated’’) (Fig. 12.1). A three-centred bond is one in which the proton forms two contacts to hydrogen-bond acceptor atoms, such that both are in the forward direction (i.e. both 1 and 2 are greater than 90 ) and both are shorter than the sum of the van der Waals radii of the atoms involved. The second acceptor atom (X) is approximately in the same plane as the donor (D), H and ﬁrst acceptor (O) atoms, and in the general direction of the external bisector of the D–H . . . O angle. ˚ ) of atoms X, singly bonded to C Table 12.1. Effective van der Waals radii (A Atom X

Spherical

Major

Minor

H, bonded to sp3 C H, bonded to sp2 C* F Cl Br I N O S Se

1.20 1.20 1.47 1.76 1.85 1.98 1.70 1.50 1.74 2.00

1.26 1.38 1.38 1.78 1.84 2.13 1.60 1.54 2.03 2.15

1.01 1.35 1.30 1.58 1.54 1.76 1.60 1.54 1.60 1.70

˚ away from proton towards C. * Centre of spheroid 0.42 A

INTRODUCTORY SURVEY

N-H...O a1 N-H a2

855

Two center or linear O Three center or bifurcated X O

N-H

X

Four center or trifurcated

Y

Fig. 12.1. Geometrical descriptions of the different multicenter hydrogen bonds. In the diagram the speciﬁc example illustrated has N as donor atom and O as the primary acceptor, with X and Y as subsidiary acceptors. Other donor–acceptor combinations are possible.

Structural details of hydrogen bonded systems are determined by x-ray and neutron diffraction; the latter method is to be preferred as the information obtained about the location of hydrogen (or deuterium) atoms is then as precise as that for the heavier atoms. Detailed statistical surveys have been made for O–H . . . O systems where the acceptor oxgen is from an ether or alcohol [XRD by Kroon et al. (1975) (196 bonds in 45 crystals of polyalcohols, saccharides and related compounds) and ND (100 bonds in 24 crystals of carbohydrates) by Ceccarelli et al. (1981)]; the samples of Kroon et al. and Ceccarelli et al. hardly overlap and thus can be combined. Such surveys have also been made for N–H . . . O¼C systems, where the acceptor oxygen is part of a carbonyl group or a carboxylate ion [combined XRD and ND data (1509 bonds in 889 organic crystals, 1357 of which were intermolecular; 1982 CSD release, 27000 entries)] (Taylor, Kennard and Versichel, 1983, 1984a, b). A parallel study (Murray-Rust and Glusker, 1984) concerned X–H . . . O< interactions, where X¼N, O and the oxygen acceptors were contained in a number of different chemical frameworks; similar analyses have been carried out for –NH2/>N–H . . . N(sp2) (Llamas-Saiz and Foces-Foces, 1990), R–O–H . . . N(sp2) (1990 CSD release, 79 000 entries, 400 hits) (Llamas-Saiz et al., 1992) and N–H . . . S (Taylor and Kennard, 1984c) systems. Almost all the crystals considered in these surveys were homomolecular. There were signiﬁcant differences between the geometries of intramolecular and intermolecular hydrogen bonds and the results given here are mainly for the latter group. Detailed studies have not yet been reported for N–H . . . Cl. Hydrogen bonding of the weaker C–H . . . O, C–H . . . N and C–H . . . Cl types (Taylor and Kennard, 1982; Berkovitch-Yellin and Leiserowitz, 1984) is discussed below. One-quarter of the H-bonds examined in the Ceccarelli study were found to be three centred. Among the 1354 intermolecular bonds in the Taylor sample, 1112 (82%) were two-centered and 242 three-centered. Among the 149 intramolecular bonds in the sample, 87 (58%) were two centred and 62 three centred. Four centre bonds were very uncommon, there being only six in the total sample of 1509; 2 of these were entirely intramolecular, while all involved positively charged nitrogen atoms. Thus two centre hydrogen bonds predominate but bifurcation is quite common, especially among intramolecular hydrogen bonds. Geometrical parameters of hydrogen bonds are deﬁned in Fig. 12.2. We ﬁrst consider hydrogen bond parameters for Od–H . . . Oa hydrogen bonds. The ˚ and a standard deviation of distribution of d(Od . . . Oa) values has a mean of 2.77 A

856

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS Donor d(SH) H

rH

R1 C

S

R2

f

u

Fig. 12.2. The geometry of hydrogen bonding illustrated for a thiocarbonyl acceptor, with S to be replaced by O for carbonyls, and appropriate changes to be made for other situations. The lone pair lobes are shown for the S (O) atom, together with the angle at the hydrogen atom (the bond is linear when this is 180 ). The H . . . lone pair directionality parameters are given by the angles (angle of elevation from the sp2 lone pair plane) and (angle of rotation from the C¼S vector in that plane). (Reproduced from Allen, Bird, Rowland and Raithby, 1997a.)

˚ (Fig. 12.3). The distribution of <(Od–H . . . Oa) values has a mean value at 165 , 0.07 A with a standard deviation of about 8 (Fig. 12.4); this is not corrected for the RamachadranKroon conical factor (Balasubramanian et al., 1970), which states that, from purely geometrical considerations and excluding energy factors, the number of D–H . . . A bonds whose bending angle lies in the range to þ @ is proportional to 2 sin @ . There is a deﬁnite tendency for the H-bonds to be close to linear, and this is accentuated by application of the conical correction. Analysis of other distributions, not reproduced here, shows that the oxygen and hydrogen atoms of the donor moiety, particularly the hydrogens, prefer to lie in or near the lone pair plane of the acceptor moiety. When the Oa atom is a single hydrogen bond acceptor, there is no tendency for the hydrogen atom to adopt any particular position within the lone pair plane; in other words, a distinct preference for hydrogen bonding in the direction of one of the equivalent acceptor lone pairs was not observed. In bonds involving alcohol type acceptors, there is a tendency for the hydrogen bond to occur on the hydrogen side of the C–Oa–H plane. Although the observed parameters cover a fairly large range, Kroon et al. (1975) suggest that the extreme conﬁgurations have energies only about 4 kJ/mol higher than that of the ˚ ;<(Od–H . . . Oa)¼165 ). optimum arrangement (d(Od . . . Oa)¼2.77 A The histogram of N . . . O distances is also shown in Fig. 12.3; the distribution is positively skewed (coefﬁcient of skewness is 0.84, as against 0 for a normal distribution) and exhibits positive kurtosis (actual value 3.49, value for normal distribution 3). The ˚ , with a standard deviation of 0.11 A ˚ , the extreme values being mean distance is 2.89 A ˚ . The mean value of the observed N–H . . . O angles is 164 (Fig. 12.3). 2.6 and 3.4 A ˚ and are close to The R–O–H . . . N(sp2) hydrogen bonds have ¼2.80(6) A linear (at hydrogen); the strength of the interactions depends on R, increasing as C(sp3) < N < C(sp2 ). The R–NH2 and R, R0 > N–H . . . N(sp2) hydrogen bonds were studied by Llamas Saiz and Foces-Foces (1990) using the January, 1989 CSD release with 70000 entries; about 300 hits were obtained for each of these hydrogen-bond types

INTRODUCTORY SURVEY

240

N

240

(a)

N

(b)

210

210

180

180

150

150

120

120

90

90

60

60

30

30

0

0 1.4

450

857

1.6

1.8

N

2.0 2.2 N–H … N

2.4

2.6

2.8

1.4 700

(c)

1.6

1.8

2.0 2.2 O–H…N

2.4

2.6

2.8

1.6

1.8

2.0 2.2 O–H …O

2.4

2.6

2.8

N

(d)

400

600

350 500

300 250

400

200

300

150

200

100 100

50

0

0 1.4

1.6

1.8

2.0 2.2 N–H …O

2.4

2.6

2.8

1.4

Fig. 12.3. Histograms of d(H . . . A) for various (X–H . . . A) systems: (a) (N–H . . . N), (b) (d(O–H . . . N), (c) (N–H . . . O), (d) (d(O–H . . . O), no distinction being made for different chemical roles of the elements. (Reproduced from Allen, Motherwell, Raithby, Shields and Taylor, 1999.)

˚ for the two types, with minimum and and was found be 3.04 and 2.95 A ˚ , and 2.70 and 3.20 A ˚ . The means depend somewhat maximum limits of 2.81 and 3.20 A on the limiting values used for the distributions. The H bonds are close to linear, with the highest concentration of interactions in the directions of the N(sp2) lone pairs; the strength of the interactions depends on R, and increases as C(sp3) < N < C(sp2). The earlier distance/angle surveys for strong hydrogen bonds have been supplemented by a survey by Allen et al. (1999), based on about 160 000 structures given in the CSD release of October, 1996. More than 10 000 N–H . . . O and O–H . . . O fragments were found, and histograms were plotted of d(H . . . O) and d(H . . . N) in O–H . . . O, N–H . . . O, O–H . . . N and N–H . . . N hydrogen bonds. Values for the peaks of the distributions d(O–H . . . O), d(N–H . . . O), d(O–H . . . N) and d(N–H . . . N) were obtained here by adding ˚ to the Allen values, giving 2.80 [2.77], 2.91[2.89], 2.87 and 3.05 [3.04 and 2.95] A ˚, 1.0 A with earlier mean values in square brackets. The limits were obtained from visual inspection of the minima in the histograms and were given as 3.20 (O–H . . . O, ˚ (N–H . . . N). Allen et al. note that the H-bond O–H . . . N), 3.25 (N–H . . . O) and 3.30 A

858

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

500 O-H...O

450

N-H...O=C<

400

Number

350 300 250 200 150 100 50 0 175

165

155 145 135 Mid-Range (°)

125

115

Fig. 12.4. Histogram of <(Od–H . . . Oa), where Oa is an ether (or alcohol) oxygen, and of <(N–H . . . Oa), where Oa is a carbonyl oxygen. The angular values have not been corrected for the Ramachandran-Kroon conical factor.

distances are dependent on chemical environment, for example ether and carbonyl oxygens are not equally good acceptors; however, their survey, in contrast to the earlier work, does not make such distinctions, i.e. their histograms represent the superposition of severally chemically-independent distributions. Both means and limits should be considered as fuzzy values, useful but not to be taken too literally. An earlier investigation of hydrogen bonding between N–H and thiocarbonyl was based ˚ , with on 650 intermolecular interactions, and showed a range of contacts from 3.2 to 3.7 A ˚ ; the values for O–H are only slightly shorter. The H is approaching S in a mean of 3.4 A directions which are likely to be occupied by lone pairs and the mean C¼S . . . H angle is 106 (Taylor and Kennard, 1984c). These earlier results have been conﬁrmed and supplemented by more extensive studies of R1R2C¼S and R1CS 2 acceptor systems (Allen, Bird, Rowland and Raithby, 1997a) and of divalent S systems (Y–S–Z acceptors and R–S–H donors) (Allen, Bird, Rowland and Raithby, 1997b); these studies were based on 1994 and 1995 issues of the CSD, with some 150 000 entries. They were derived mostly from homomolecular systems but there is no obvious reason why they should not also be relevant to the heteromolecular systems of primary interest here. An important feature was comparison of analogous C¼O and C¼S systems, with distinctions made between H–O– and H–N< donors. There are about ten times as many >N–H as –O–H donors in the sample. There are some ﬁfteen times as many C¼O as C¼S systems in Table 12.2, but the ratio in the sample is about 45 (for subgroup (b) analysis was limited to about 1/3 of the total entries in the sample, see p. 691 of Allen et al., 1997a). The fraction of acceptors forming hydrogen bonds is 2/3rds for both types (subgroups (a) and (b)); the advantage of C¼O over C¼S is shown in the competitive situation (subgroup (c)). One important goal of these surveys was to answer the question whether there is a preference for bonding in the directions of the conventionally viewed O and S sp2 lone pairs. Some of the results are summarized in Fig. 12.5. The distributions have clear

INTRODUCTORY SURVEY

859

Table 12.2. Comparison of hydrogen-bond acceptor abilities of >C¼S and >C¼O groups (taken from Table 9 of Allen et al., 1997a) nP is the number of potential hydrogen bond acceptors (S or O) in each subgroup; nb is the number of acceptors that actually form intermolecular hydrogen bonds. D–H is the average number of N, O–H donors in each structure of each subgroup Subgroup

nP

nb(C¼S) (%)

nb(C¼O) (%)

D–H

(a) One C¼S only (b) One C¼O only (c) One C¼S plus one C¼O

202 3549 81

133 (66) – 34 (42)

– 2342 (66) 58 (72)

1.97 1.62 3.37

u = 90

(a) Number of fragments

u = 90

(b)

75

100 80 60 40 20 0

60

Number of fragments

45 30

75

3000 2500 2000 1500 1000 500 0

60 45 30

15 C

S

f = 90

(c) Number of fragments

140 120 100 80 60 40 20 0

15 C

u=0

(d)

105

O

f = 90

120

2000

Number of fragments

135

1500 1000 500 0

150 165

C

S

f = 180

u=0

105 120 135 150 165

C

O

f = 180

Fig. 12.5. Symmetrized polar scattergrams for the directionality parameters for S¼O and C¼O to H–(N or O) hydrogen bonds. above and below. (Reproduced from Allen et al., 1997a.)

maxima ( 0 for both S and O (i.e. in the lone pair plane) and 107 (S) and 120 (O)) (i.e. in the conventional lone pair directions). The peaks are not especially sharp and deviations of up to 20 can be expected from the lone pair directions both in, and above and below, the lone pair mean plane. There are also qualitative differences between the N and O scattergrams (not reproduced here but shown by Allen et al. (1997a)).

860

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

The principal conclusions, based both on the CSD survey and ab initio computations, were that S in R1R2C¼S is an effective acceptor only when R1, R2 can form an extended ˚ ). The delocalized system with C¼S (one criterion for H-bond formation is d(C¼S)>1.65 A C¼S . . . H–N, O arrangement tends strongly to linearity. Univalent ¼S in a conjugative environment acts as an effective, but not potent, acceptor of hydrogen bonds, appreciably weaker than ¼O. Among the reasons are that the and components of the C¼S bond are weaker than those of the analogous C¼O bond; furthermore the electronegativity of S (2.6) is similar to that of C(2.6) and considerably lower than that of O (3.4). Thus the C¼S bond spans a wider distance range than C¼O, and will be less polar than >Cþ¼O. ˚ ) are Hence ¼S is a weaker hydrogen bond acceptor than ¼O. Longer C¼S bonds (>1.70 A ˚ more polar than shorter (1.58 A); the frequency of H-bond formation rises from 5% for shorter bonds to >70% for longer bonds. Thioethers (YSZ) are weak acceptors; of 1223 such sub-structures that co-occur with N(O)–H donors in the 1995 CSD release, only about ˚ ). The corresponding values for dialkyloxy5% form hydrogen bonds (d(S . . . H)<2.9 A ethers (YOZ) are 1900 and 30% (Allen et al., 1997b). Only 43 thiol –S–H groups were found in the 1995 CSD release. Of these 70% formed hydrogen bonds with a variety of acceptors (O, S, N, Cl, F), but the numbers were too small for a meaningful statistical analysis. ˚ (Steiner, 1998); the shortest The mean value for d(>Nsp2–H . . . Cl) bonds is 3.18 A ˚ value found is about 3.0 A. The role of C–H . . . X (X¼O, N, S, Cl) interactions in crystals has been considered by Taylor and Kennard (1982) from a statistical point of view and by Berkovitch-Yellin and Leiserowitz (1984) by detailed examination of moiety packing in a variety of representative molecular crystals. Taylor and Kennard considered 113 structures determined by neutron diffraction, in which there were 661 nearest-neighbour contacts; the mean value of HB (as deﬁned above) was essentially zero, conﬁrming the correctness of the van der Waals radii used in calculating HB. However, 46 contacts were found with ˚ , of which 42 were C–H . . . O contacts. The proton in the majority of these HB<0.3 A short contacts lies within 30 of the plane containing the oxygen lone pair orbitals. The geometrical features of these short C–H . . . O contacts were similar to those of O–H . . . O hydrogen bonds and the interactions were attractive. Thus it was concluded that it would be reasonable to use the terminology ‘‘C–H . . . O hydrogen bond’’ in crystallographic studies. There were far fewer examples of shortened C–H . . . X (X¼N, S, Cl) contacts but it was suggested that these too came into the same category. Supporting evidence for C–H . . . O and C–H . . . N hydrogen bonds has been marshalled by analysis of various crystal structures, including those of the 1 : 1 molecular compounds of thymine and chlorophenol with benzoquinone, and of barbital with urea and acetamide (BerkovitchYellin and Leiserowitz, 1984). A data set consisting of 30 carbohydrate structures analyzed by neutron diffraction has also been considered (Steiner and Saenger, 1992); about one-ﬁfth of the hydrogens were found to be engaged in C–H . . . O interactions with ˚ ; the mean value of d(C–H . . . O) was 3.5 A ˚ for interH . . . O separations of <2.5 A molecular interactions. These conclusions match those of Desiraju (1991), the C–H . . . O hydrogen bond being described as a largely electrostatic long range interaction, the length ˚ ) depends on the acidity of the hydrogen. The of which (lying in the range 3.1 to 3.8 A energy is in the 0.5–1.0 kJ/mol range and the C–H group points towards the lone pairs of the oxygen. This suggests that many, but weak, C–H . . . O interactions will contribute to

GRAPH THEORY DESCRIPTION OF HYDROGEN BOND PATTERNS

861

the cohesion of the crystal; this situation differs from that found with the stronger hydrogen bonds where a few can have a strong inﬂuence in determining the overall crystal structure. Theoretical justiﬁcation, initially for unperturbed dimers in the gas phase, but extended to the solid state has been provided by Legon and Millen (1987). Earlier reviews by Desiraju (1991) and Steiner (1996) have been expanded into their deﬁnitive treatment (Desiraju and Steiner, 1999). The -system of a benzene ring can also act as an electron acceptor. The phase diagrams of benzene, toluene and mesitylene – HCl have been reported; incongruently melting benzene–HCl, toluene–2HCl and mesitylene–3HCl being found, together with congruently-melting toluene–HCl (180K) and mesitylene–HCl (209K). Crystal structures of toluene2HCl and mesityleneHCl were determined, with the HCl molecules normal to the benzene planes, above and below for the toluene complex and only above for the ˚, mesitylene complex (Deeg and Mootz, 1993). In toluene–2HCl, d(Cl . . . ) ¼ 3.504(1) A ˚ ˚ d(Cl–H) ¼ 1.01(7) A and d(H . . . ) ¼ 2.51(8) A; similar values were found in the mesi˚ (Steiner, 1998). tylene complex. The mean value for Cl3C–H . . . Cl bonds is 3.42 A We add that there is conclusive crystallographic and spectroscopic evidence for C–H . . . A interactions where A is a strong proton acceptor and C–H forms part of a haloform molecule, HCN or an acetylene derivative (Sim, 1967).

12.2 Application of graph theory to the description of hydrogen bond patterns The patterns found in the hydrogen bonded molecular compounds and complexes are conveniently described, and sometimes analyzed, by an adaptation of the mathematical theory of graphs (Harary, 1967) to hydrogen bonding in organic crystals (Etter, Macdonald and Bernstein, 1990). Our account closely follows that of Etter et al. More detailed expositions are by Grell et al. (1999; 2002). The set of molecules to be analyzed is called an array; some or all of these molecules are hydrogen bonded. A network is a subset of an array in which each molecule in the network is connected to every other molecule by at least one hydrogen bond pathway. A motif is a special type of network, a hydrogen bonded set in which only one type of hydrogen bond is present. Graph sets are assigned ﬁrst to motifs and then to networks. A graph set is speciﬁed by a pattern designator (G), its degree (r), and the number of donors (d) and acceptors (a); ‘a’ and ‘d’ were originally presented as superscripts and subscripts but it is more convenient to write them as G(a,d)(r). The pattern designator G has four different assignments depending on whether the hydrogen bonds are intra- or intermolecular: S(self) denotes an intramolecular hydrogen bond; C(chain) refers to inﬁnite hydrogen bonded chains; R refers to rings, a cyclic carboxylic acid dimer being an example of a typical ring pattern; D (discrete) refers to non-cyclic dimers and other ﬁnite hydrogen-bonded sets, such as phenol hydrogen bonded to acetone. The parameter ‘r’ refers to the degree, being either the number of atoms in a ring or the repeat length of a chain. When there is only one hydrogen bond in a D motif, then the degree is 2 and this is taken as the default value and not speciﬁed. The parameters ‘d’ and ‘a’ refer to the number of different kinds of donors (d) and acceptors (a) used in the hydrogen bond pattern. The default values are 1.

862

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

O O

O

H O S(6)

N C(4)

R O

H

R

H

O R(2,2)(8)

O

H

O

O H

O

P

Ph Ph

D

Ph

Scheme 1

Graph sets are assigned to motifs by ﬁrst identifying the different types of hydrogen bond, one motif being generated for each type of hydrogen bond. The hydrogen bonds are then ranked by chemical priority, deﬁned by an extended version of the Cahn–Ingold– Prelog rules. The highest priority hydrogen bond, H(1), is then identiﬁed and its motif is generated by ﬁnding all occurrences of this bond in the array. A graph set is then assigned to this motif; the process is repeated until graph sets have been assigned to all the motifs. A ﬁrst-order network is then set up by listing all the motifs in order of increasing priority: N 1 ¼ Mj Mi . . . M3 M2 M1 : Rules have also been given for setting up higher order networks, which arise by combination of motifs from two different kinds of hydrogen bonds. When there is only a single hydrogen bond type in an array which consists of a discrete pair of molecules, then N1 ¼ D(2), or simply D. If one ﬁnds a centrosymmetric B–A–B discrete triple, then N1 ¼ 2D; if the two hydrogen bonds are not equivalent then N1 ¼ DD. 12.3

Statistics of hydrogen bond patterns

Allen et al. (1999) have developed a methodology for extracting from the CSD statistical data on the occurrence of hydrogen-bond patterns of various kinds between two organic molecules without any prior knowledge of the topology or chemical constitution of the motifs. This has enabled them to assess the strengths of various supramolecular synthons (the structure directing motifs involving non-covalent bonds) as a guide towards the synthesis of supramolecular structures. We use their data to assess the frequency of occurrence of the various patterns of hydrogen bonding that are found among the hydrogen-bonded molecular complexes and compounds. It should be emphasized that the methodology and results are restricted to the strong hydrogen bonds. Results are available for the graph-set group of rings (R).

STATISTICS OF HYDROGEN BOND PATTERNS N

H

O

H

N

863

H O

O N N

H

H

O

70

23

29 O

O

H

O

O

H

N

H H

N

O

H

O

N

N N

H

48

N

O

N

N

H

N

N

H

O S

N 2

N

H

N

27

N

17

C+

N

H

N

H

6

O

H

N

H

H

O

7

O

H

O

O

O

O

H

O

O

C N

H 33

65 N

H

O

O

H

N

51

Scheme II

12.3.1 Methodology We give a simpliﬁed account without technical detail. The ﬁrst step is to determine the number of occurrences Nobs (in the CSD) of a particular motif, e.g. the carboxylic acid cyclic dimer. However, the carboxylic dimer may have a large Nobs value simply because there are many carboxylic acids in the CSD, not all of which participate in dimer formation. Thus one also needs the total number of carboxylic acids Nposs appearing in the CSD. The structural probability of carboxylic dimer occurrence is then given by Pm¼Nobs/ Nposs. This process is then repeated for all desired motifs and the results tabulated. The graph set symbols of the motifs were generated as part of the process.

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

864

Table 12.3. Statistical parameters for the most frequent ring motifs found in hydrogenbonded molecular complexes and compounds. Note that Allen et al. ordered motifs in terms of decreasing Pm values. The numbers refer to the October, 1996 release of the CSD Motif

Graph set

Nobs

Nposs

Pm (%)

29 23 70 48 6 17 2 27 7 33 65 51

R(2,2) R(2,2) R(2,2) R(2,2) R(2,2) R(2,2) R(2,2) R(2,2) R(2,2) R(1,2) R(2,2) R(2,2)

876 847 408 361 206 204 199 172 158 153 135 59

3687 2541 21824 4310 354 556 218 660 290 904 3702 488

24 33 2 8 58 37 91 26 54 17 4 11

12.3.2

(8) (8) (4) (8) (10) (8) (8) (8) (8) (6) (10) (10)

Statistics of ring formation

75 ring motifs were obtained, with associated parameters; rings were limited to 20 atoms and Nobs 12 was required for inclusion. We have abstracted (Table 12.3) the motifs with Nobs 100 (with one exception), retaining (to avoid confusion) the original motif numbering of Allen et al.; diagrams of the motifs are given in Scheme II.

12.4

Appendage structures (one component forms a hydrogen-bonded framework, to which the second component is appended by hydrogen bonding)

One component forms a hydrogen-bonded framework, to which the second component is appended by hydrogen bonding without being part of the framework. Perhaps the simplest example is the formic acid . . . hydrogen ﬂuoride complex HCOOH . . . HF (NEWXAO; congruent melting point 242K) (Wiechert, Mootz and Dahlems, 1997). The structure (Pnma, Z ¼ 4) was determined at 123K, and shows chains of hydrogen-bonded formic acid molecules to which HF molecules are appended by F–H . . . O bonds. The authors point out that the formic acid chains here, with antiplanar carboxyl groups, are isomers of those found in the neat formic acid structure, where all the hydrogen bonds are reversed and the carboxyl groups are thus synplanar. Calculations suggest that the synplanar formic acid structure is some 30 kJ/mol more stable than the antiplanar structure. Weaker C-H . . . O and C–H . . . F interactions are also shown in Fig. 12.6. The description of the packing will change if these are given equal status with the strong hydrogen bonds. As the energy of a strong hydrogen bond is some thirty times as large as that of a weak hydrogen bond, it seems clear that the former are structure determining unless the number of weak H bonds is preponderant. This is the point of view we have adopted in describing moiety arrangements in this book.

APPENDAGE STRUCTURES

865

F–H...O

F Fb Formic acid chain

F...H–C O2a

H3 O1

H1 C H2

O2

O1a Appended HF molecule

Fig. 12.6. Structure of formic acid . . . hydrogen ﬂuoride. The ellipsoids correspond to 50% ˚ , showing localization of the probability. The two C–O bond distances are 1.232(2) and 1.298(2) A ˚ . The C–H . . . O proton of the carboxyl group. d(O–H . . . O)¼2.649(2) and d(F–H . . . O)¼2.556(2) A ˚. and C–H . . . F interactions are shown by dotted lines; the distances are 3.240(2) and 3.238(2) A (Adapted from Wiechert et al., 1997.)

Another relatively clearcut example is provided by the 1 : 1 complex of trans-9, 10-dihydroxy-9,10-diphenyl-9,10-dihydroanthracene with ethanol (CENMOX; Toda et al., 1984b). The crystals are triclinic, space group P1 with two formula units per cell. The substituted DHA molecules are situated at two independent centres of symmetry. These two crystallographically distinct molecules, I and II, are alternately linked by ˚ ) to form zigzag chains along [001]. The ethanol OI . . . H–OII hydrogen bonds (2.893(8) A ˚ ) and is not linked to OII molecule is an acceptor in a hydrogen bond to OI (2.767(8) A (Fig. 12.7). A somewhat similar example is provided by 1,1,6,6-tetraphenylhexa-2,4diyne-1, 6-diol : benzophenone (A . . . B; SOGHAX), where the linear framework is made up of a combination of covalent bonds within the bifunctional diol molecules and hydrogen bonds between them (Bond et al., 1991). The pendent benzophenone molecule ˚ ), which is is linked to a hydroxyl of the diol by a hydrogen bond of length (2.670(2) A ˚ ). Thus a somewhat shorter than that between hydroxyls (d(O(1A) . . . O(1B) ¼ 2.786(3) A more appropriate description for both these examples could be of A . . . B units linked by A . . . A hydrogen bonds. We have encountered relatively few other examples in this category; among these are glucitol : pyridine (SORBPY20; Kim, Jeffrey and Rosenstein, 1971), diethylstilboestrol: dimethyl sulphoxide (DESTDM10; Busetta et al., 1973), 3,5-diiodotyrosine: ˚ in addition to N-methylacetamide (where there is a short I . . . O¼C< contact of 3.03 A the hydrogen bonding) (ITYRMA10; Cody et al., 1972) and trimethylammonium hydrogen oxalate (TMAHOX; Thomas and Renne, 1975). The ﬁrst named component forms the framework in the ﬁrst three examples and the hydrogen oxalate ions in the

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

866

Linear frame work of DHDPDHA molecules appended ethanol C B

appended ethanol

OH DHDPDHA-II

2.767 DHDPDHA-I

OH OH 2.893 DHDPDHA-I

z

y x

appended ethanol

appended ethanol

DHDPDHA = trans-9,10-dihydroxy-9,10-diphenyl-9,10-dihydroanthracene

Fig. 12.7. Projection down [010] of the 1:1 appendage complex of trans-9,10-dihydroxy-9,10diphenyl-9,10-dihydroanthracene with ethanol. Hydrogen bonds are indicated by dark lines between oxygens (hydroxyls). Note that the two DHDPDHA molecules are at independent centers of symmetry. (Data from Toda et al., 1984.)

fourth. The 1 : 1 compound between testosterone and p-bromophenol also falls into this category (space group P212121, Z ¼ 4) (HOTEST10; Cooper et al., 1969). Steroid molecules related by the two-fold screw axes parallel to [010] are hydrogen bonded end˚ ), while O17 also acts as an hydrogen bond to-end by O17–H . . . O3¼C< links (d ¼ 2.71 A ˚ ); here too a more appropriate acceptor to the pendent phenolic hydroxyl group (d ¼ 2.62 A description could be of A . . . B units linked by A . . . A hydrogen bonds. Another example is the 1-(2,3-dideoxy-erythro--D-hexa-pyranosyl)-thymine – dioxane molecular complex (KINHIY) where there is an extensive network of hydrogen bonds between the thymine molecules and the dioxane is linked through one of its oxygens to a thymine ˚ ), giving C–H group through what may be a C–H . . . O hydrogen bond (d ¼ 3.182(5) A a pendent structure (De Winter et al., 1991). A similar arrangement is found in the Grossularine II – tetrahydrofuran complex (DOGJIS), where there are layers of hydrogenbonded Grossularine molecules, with pendent THF linked to them through weak ˚ ) (Carre´ et al., 1986). N–H . . . O(THF) bonds (d ¼ 3.08 A 2,2 0 -Bipyridyl (in its trans conformation) is pendent in its 1,3,5-trihydroxybenzene–2 (bipyridyl) (PUVMIC) and 4,4 0 -sulfonyldiphenol–bipyridyl (PUVMOI) molecular complexes (Lavender et al., (1998a, b), who here introduced the phrase ‘‘stem and leaves motif’’). In the ﬁrst of these (P21/c, Z ¼ 4), two hydroxyls of phloroglucinol are linked to the two nitrogens of one bipyridyl molecule to form a chain along [010], with the second bipyridyl pendently linked to the third phloroglucinol hydroxyl group, while the ˚ ). This connectivity is identical remaining nitrogen has only a weak C–H . . . N link (3.49 A to that in {1,1,1-tris(4-hydroxyphenyl)ethane–2(hexamethylenetetramine)}{H3C–C(C6H4 (OH)3(HMTA)} (RAWDEY), where half the HMTA molecules act as double acceptors

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

867

within chains and half act as single acceptors pendent from the chains (Coupar et al., 1997). In the 1 : 1 {4,4 0 -sulfonyldiphenol–bipyridyl} molecular complex, the bis-phenol molecules are linked into C(8) chains by means of O–H . . . O¼S hydrogen bonds, and the 2,2 0 -bipyridyl moieties, which act as single acceptors only, are pendent from these chains through O–H . . . N hydrogen bonds. Pairs of these chains, related by centres of inversion, are mutually interlocked via their pendent arms (a ‘‘zip-fastener architecture’’). The pendent moiety is the acceptor in all these examples. 12.5 Alternating framework structures (the components, in hydrogen bonded alternating array, form a mixed framework) In this group of molecular compounds, the components, hydrogen-bonded together in alternating array, form a Mixed Framework. When the components are hydrogen bonded into a discrete group, then the framework has zero dimensions and the crystal is a molecular crystal, irrespective of whether the components are present as neutral molecules or ions. Other possibilities are that the mixed array is linear (one-dimensional), or has hydrogen bonding in two dimensions, forming layer structures, or has three dimensional hydrogen bonding. Which of these possibilities occurs depends on the number of functional groups in each component capable of hydrogen bonding. An important principle appears to be maximal formation of hydrogen bonds but there are examples where potential hydrogen bond donors or acceptors are left unengaged. 12.5.1 Zero-dimensional frameworks Groups of two, three, four and even ﬁve linked molecules have been found in reported crystal structures. Pairs are by far the most frequent. We give some examples to illustrate each situation. 12.5.1.1 Structures with discrete pairs (A–B) of components We start by choosing examples of a hydrogen-bonded neutral molecule pair and a salt (hydrogen-bonded cation–anion pair). The salt nicotinyl salicylate (NICSAL) (Kim and Jeffrey, 1971), and the neutral-molecule compound between antipyrine and salicylic acid (salipyrine; APYSAL) (Singh and Vijayan, 1974) are viewed normal to the benzene rings (Fig. 12.8). Molecular compounds of triphenylphosphine oxide3 provide interesting comparisons of proton positioning (Haupt et al., 1977). The HCl adduct was prepared from Ph3PO and HCl in benzene (HXTPPL). The space group is P21/c and Z ¼ 4. Discrete molecule pairs were found but it was inferred from the hydrogen position in the P¼O . . . HCl bridge that the compound was better described as hydroxotriphenylphosphonium chloride, i.e. Ph3PþOH . . . Cl. The HF compound was also prepared in benzene and molecular pairs were found (TPOXHF; Thierbach and Huber, 1979). Although the space group was also P21/c, Z ¼ 4, the two compounds were not isomorphous. Here the hydrogen was attached to the ﬂuorine in an asymmetrical hydrogen bond. In the trichloroacetic acid compound 3 Etter and Baures (1988) note that Ph3PO (also abbreviated as TPPO) forms high quality crystals with many organic compounds, acting as a ‘‘crystallization aid.’’

868

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

nicotinyl cation

intermolecular hydrogen bond intramolecular O...H–O H

N y

z

O salicylate anion

Hydrogen-bonded nicotinyl salicylate

x

Intramolecular O...H–O hydrogen bond

O

N Salicylic acid

y z

Antipyrine

Intermolecular O...H–O hydrogen bond Hydrogen-bonded salicylic acidantipyrine

x

Fig. 12.8. Two examples of a pair of moieties linked by an hydrogen bond to form a discrete pair; the salt nicotinyl salicylate (NICSAL) is shown above and salipyrine (APYSAL), composed of the neutral molecules antipyrine and salicylic acid, below. For clarity only hydrogens involved in hydrogen bonding are shown. There is hydrogen transfer within the molecular compound in the ﬁrst example but not in the second. In both examples there is a single donor–acceptor interaction between ˚ , APYSAL the components. H-bond distances are: intramolecular O–H . . . O NICSAL 2.550 A þ ˚ ˚ ˚ 2.582 A; intermolecular NICSAL N . . . O 2.628 A; APYSAL O–H . . . O 2.534 A. (Data from Kim and Jeffrey (1971) and Singh and Vijayan (1974).)

with triphenylphosphine oxide (TPOTCA) the structural units are discrete hydrogen ˚ ), it is unsymmetrical bonded pairs; although the hydrogen bond is rather short (2.496(3) A with the hydrogen remaining on the carboxyl group (Golic and Kaucic, 1976). It would be useful to verify these descriptions by neutron diffraction, preferably at low temperatures.

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

869

(a) Neutral molecule pairs (single intermoiety donor–acceptor interactions) Single O–H . . . N hydrogen bonds link pentachlorophenol in neutral molecule pairs with 4-acetylpyridine (PABBAV; Mayerz et al., 1991), 3-pyridinecarbonitrile (FOMWIN; Malarski et al., 1987a), 4-methylpyridine (with singly deuterated pentachlorophenol) (GADGUN01; Majerz et al., 1990b), 4-methylpyridine (with singly hydrogenated pentachlorophenol; GADGUN02) [these two compounds are not isomorphous] (Malarski et al., 1987b), 3-oxo-azabicyclo[2.2.2]octane (Majerz et al., 1990b) and 5,6,7,8-tetrahydroquinoline (SOGXUH; Malarski et al., 1991). Single O–H . . . O hydrogen bonds are found in the compounds of p-nitrophenol with triphenylarsine oxide (DOYDAW; Lariucci et al., 1986a), diphenylmethanol with triphenylphosphine oxide (FAXRAX; Lariucci et al., 1986b), (2,4-dichlorophenoxy)acetic acid with triphenylphosphine oxide (d(O . . . O) ¼ 2.58, ˚ ) (YACNUL; Lynch et al., 1992), 1-(2 0 -hydroxy-3 0 ,6 0 -diethylphenyl)-2-bromomethyl2.61 A naphthalene with triphenylphosphine oxide (PATROR; Peters et al., 1993), triphe˚ ) and nylmethanol with dioxane (JODXUV; P 1, Z ¼ 2, d(O . . . O) ¼ 2.839(3) A ˚ tri-1-naphthylsilanol with dioxane (JODYEG; P1, Z ¼ 2, d(O . . . O) ¼ 2.736(3) A (Bourne, Johnson et al., 1991); p-carboxy-phenylazoxycyanide with dimethyl sulphoxide (CPZXCY; Viterbo et al., 1975), 2-aminophenol with 4-nitropyridine-N-oxide (NPOAPL; Cc, Z ¼ 4; ˚ ; Lechat et al., 1981). 10,11-Dihydro-5-phenyl-5H-dibenzo[a,d] d(O . . . O) ¼ 2.696(3) A cyclo-hepten-5-ol forms a 1 : 1 compound with acetone (JIDCUU; P21/c, Z ¼ 4), which is isomorphous with the 2 : 1 compound formed by the same donor with dioxane (JIDCOO) (Caira et al., 1990). The second of these compounds could also be classiﬁed as a centrosymmetric D–A–D compound belonging in the following section. Single N–H . . . O¼C< hydrogen bonds link diphenylamine in neutral molecule pairs with benzophenone (BZPPAM); the space group is P21/c and Z ¼ 4. Although there are two polymorphs, only the structure of Polymorph I has been reported (Brassy and Murnou, 1972). Single P¼O . . . H–N hydrogen bonds link triphenylphosphine oxide ˚ ), N-propionylbenzamide (VIWBEI; with N-acetylbenzamide (VIWBAE; 2.839(3) A ˚ ) and dibenzamide (VIWBIM; 2.897(3) A ˚ ; Etter and Reutzel, 1991) and with 2.836(3) A ˚ ) (GACCES; Etter and Baures, N-acetyl-p-toluenesulphonamide (P21/a, Z ¼ 4; 2.705(2) A 1988). All these examples have graph set ﬁrst order networks N1¼D. More complicated arrangements are also found. 1,8-Biphenylenediol forms two strong O–H . . . O hydrogen bonds with molecules such as O¼P(NMe2)3 (COXKUV10) 1,2,6-trimethyl-4-pyridone (CEWYIM30) and 2,6-dimethyl--pyrone (COXLEG; Hine et al., 1990) which contain R¼O groups; indeed the linkage in the latter molecular compound is so strong that it persists in solution, as shown by vapour pressure osmometry measurements (Hine et al., 1984). 1,3-Bis(m-nitrophenyl)urea forms 1 : 1 complexes with ˚ ; graph set R(1,2)(6)), triphenyltetrahydrofuran (THF; GIMROJ10; 2.995(2), 2.918(2) A ˚ ; graph set R(1,2)(6)) phosphine oxide (TPPO; GIMSEA10; 2.860(3), 2.969(2) A ˚ ; graph set R(2,2)(8)) where the two N,N-dimethyl-p-nitroaniline (GIMRUP10; 3.003 A N–H groups of the urea molecule are both linked unsymmetrically (except for the third of these examples) to the oxygen of the acceptor molecule; a similar arrangement is found in the 1 : 1 complex of (1-m-nitrophenyl)-(3-p-nitrophenyl)urea with DMSO ˚ ; graph set R(1,2)(6), (Fig. 12.9). The authors (Etter, (SILVOY; 2.880(2), 3.100(2) A Urbanczyk-Lipkowska et al., 1990) suggest that 1,3-bis(m-nitrophenyl)urea behaves primarily as a proton donor because very weak intramolecular C–H . . . O interactions inhibit its proton-accepting properties.

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

870

NO2

NO2

NO2

NO2 O

O N H

NO2

N H

N H

NO2

O N H

O

O

(a)

P Ph Ph Ph (b)

N H

N H O

H3C

S

CH3

(c)

Fig. 12.9. Similar hydrogen bonding patterns are found in the discrete 1 : 1 complexes of (a) 1,3bis(m-nitrophenyl)urea and THF; (b) 1,3-bis(m-nitrophenyl)urea and triphenylphosphine oxide; (c) (1-m-nitrophenyl)-(3-p-nitrophenyl)urea and DMSO. These are examples of ring motif 41 in the Allen et al. (1999) statistical analysis; it is not included in Scheme II because there are only 31 occurrences in the data set. (Adapted with permission from Etter et al., 1990).

Finally we mention two remarkable examples, where discrete molecule pairs are formed with all possible intercomponent hydrogen bonds – the 1 : 1 compounds between bis[2-(o-methoxyphenoxy)ethoxyethyl]ether (C22H30O7) and thiourea (MPEXTU; Suh and Saenger, 1978), and between bis[(8-quinoyloxy)ethoxyethyl]ether (C26H28N2O5) and thiourea (QUETHU; Weber and Saenger, 1980, Fig. 12.10). Each thiourea interacts with only one ether molecule, and there are no stacking interactions between quinoline groups in the second example.

thiourea

2.109 2.039

y z bis(8-quinoyloxy)ethoxyethylether

Fig. 12.10. View of the mutual arrangement of the two components in the (C26H28N2O5)–thiourea molecular compound showing how the polyether (the hydrogen bond acceptor) winds itself around the thiourea molecule (the hydrogen bond donor). The N–H . . . N hydrogen bonds are shown by broken lines. (Data from Weber and Saenger, 1980.)

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

871

(b) Salts (cation–anion pairs) Mearsinium picrate (C9H14NOþ C6H2N3O 7 ) has hydrogen bonded ion pairs packed as units in the crystal (CIJXOI10; Robertson and Tooptakong, 1985), as do fenpropimorph picrate (SENBUI; Jensen and Jensen, 1990), acridinium pentachlorophenolate (PABBEZ; Wozniak et al., 1991) and pyridinium picrate (PYRPIC03; Botoshansky et al., 1994), which is dimorphic (Koﬂer, 1944). Both phases of the latter contain hydrogen bonded ion pairs as the structural unit, with pyridinium nitrogen forming a bifurcated hydrogen bond with phenolic oxygen and an oxygen of an ortho nitro group. In Phase I (stable at room temperature) the pairs are stacked in parallel array while the antiparallel arrangement of Phase II (stable at higher temperatures) is somewhat similar to that found in mearsinium picrate. Note that the structure reported originally (Talukdar and Chaudhuri, 1976) for Phase I is wrong. Hydrogen bonded ion pairs are also found in N(6),N(6)-dimethyladeninium picrate and promethazine picrate (PROPIC10; Shastry et al., 1987). A bifurcated hydrogen bond, somewhat different from that in pyridinium picrate, is found in the neutral molecule pair 2,3-dichloro-5-hydroxy-6-cyanobenzoquinone and 2-benzamidopyridine (GESSAY; Bruni et al., 1988). A crystalline 1 : 1 molecular compound of N,N-dimethyl-p-toluidine and 1,2-benzisothiazol-3(2H)-one 1,1-dioxide (o-sulfobenzimide, Saccharin) can be prepared (with difﬁculty) and has been found to be composed of discrete, hydrogen bonded cation– anion pairs, in which a hydrogen has been transferred from the imide N of saccharin to the dimethylamino group of the toluidine moiety, followed by formation of a Nþ–H . . . O¼C< ˚ , P21/c, Z ¼ 4) (KIFYAZ; Courseille et al., 1990). An antihydrogen bond (d ¼ 2.676(3) A parallel arrangement of hydrogen bonded cation–anion pairs is found in trans-4 0 -hydroxyN-methyl-4-stilbazolium (þ)-camphor-10-sulphonate (BOJWAY; Ziolo et al., 1982) (these crystals are enantiomorphic, space group P21, with 4 ion pairs per unit cell). O

N-H S O O Saccharin

In contrast to the above examples we give two examples of true salts. The ﬁrst is ethyl 8-dimethylamino-1-naphthalenecarboxylate picrate (VIGJEA; Parvez and Schuster, 1991), in which the transferred hydrogen is located in an intramolecular hydrogen bond between protonated dimethylamino and carbonyl groups of the cation. The second, 1,8-bis(dimethylamino)naphthalene pentachlorophenolate. 2(pentachlorophenol), has an analogous proton sponge type cation. There is no hydrogen bonding between cation and anion in either of these salts but in the second the pentachlorophenolate anion and the two neutral pentachlorophenol molecules form a discrete hydrogen bonded system (TAPCES; Kanters et al., 1992). The hydroxyl donors of these hydrogen bonds are each involved in an asymmetric three center hydrogen bond with a strong O–H . . . O intermolecular branch and a weak OH . . . Cl intramolecular branch. (c) Neutral molecule pairs (amphoteric intermoiety donor–acceptor interactions) There are a number of examples where both components have donor and acceptor functions which are used in the formation of the molecule pair, i.e. both components are amphoteric.

872

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

This occurs in the molecular compound of 2-pyridone and 6-chloro-2-hydroxypyridine (left hand formula below) (PYOCHP; Almo¨f et al., 1972). Other examples involving donor and acceptor functions from both components are the 1 : 1 molecular compounds between 1-chloro-2-hydroxynaphthalene-3-carboxylic acid and dimethylformamide (right hand formula below) (JIWNIM; Czugler et al., 1991), where both intra- and intercomponent hydrogen bonds are shown in the diagram, and the 1 : 1 neutral-molecule molecular compounds between (E)-acetophenone oxime and benzoic acid (JUKJII) and (E)-benzaldehyde oxime and benzamide (JUKJOO; Maurin et al., 1993). Cl Cl 2.90 Å H N

O H

N O C

O H 2.57 Å

O

H

CH3 N

O H

O

CH3

Scheme III

In the 1 : 1 compound of 3,4-dimethoxy- and 2,4-dinitrocinnamic acids (orange crystals) the carboxylic acid groups form the familiar hydrogen bonded pairs; furthemore, superimposed antiparallel pairs interact by a –* charge transfer mechanism, thus accounting for the colour (BOGGUZ10; Sarma and Desiraju, 1985). These crystals belong both here and in Chapter 15. (d) Intermediate situations The examples given above include structural units composed of neutral molecule pairs and of ion pairs; intermediate situations are also found, as in trichloroacetic acid – pyridine-N-oxide (Golic and Lazarini, 1974), where the IR spectrum shows the same features as are found in Type A acid salts (Golic et al., 1971). The structure was ﬁrst determined by x-ray diffraction at room temperature and has been reinvestigated by neutron diffraction with the crystal at 120K (PYOTCA10; Eichhorn, ˚ 1991). The hydrogen bond is nearly symmetrical, with d(O . . . H) ¼ 1.148 and 1.284 A respectively, the hydrogen being closer to the pyridine-N-oxide oxygen. (e) Some examples of molecular recognition There is a simple demonstration of molecular recognition in the molecular compound of 2-phenyl-4-(4,6-dimethyl-2-pyrimidyl)aminomethylene-5(4H)-oxazolone and acetic acid (Fig. 12.11) (TALHIX; Leban et al., 1991) while a more complicated, but particularly neat example, is 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene–adipic acid (Fig. 12.12) (JEWNUU10; Garcia-Tellado et al., 1991); both involve >N–H . . . O¼C< and –O–H . . . N< hydrogen bonds and the interactions are amphoteric. C–H . . . O interactions occur in the second example, leading to formation of a seven-membered ring involving secondary interactions. A classical example of molecular recognition in solution is of pyrazine, quinoxaline and phenazine by Rebek’s diacid C39H43N3O8 (Rebek et al., 1987). The association constants were interpreted to show two-point hydrogen bond binding, but this was later questioned by Jorgensen et al. (1993), who suggested one-point binding from Monte Carlo

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S CH3

H3C

O

O

H

H

N

N N

CH3

873

acetic acid Ph N O

H O 2-phenyl-4-(4,6-dimethyl-2pyrimidyl)aminomethylene5(4H)-oxazolone

Fig. 12.11. Schematic diagram of the molecular compound of 2-phenyl-4-(4,6-dimethyl-2pyrimidyl)-aminomethylene-5(4H)-oxazolone and acetic acid, demonstrating molecular recognition. After Leban et al., 1991.

O 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene

O N

N O

N O

O

N O adipic acid

Fig. 12.12. Projection onto plane of the benzene ring of the discrete binary molecular unit formed by 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene and adipic acid. Hydrogen bonds are shown by thinner lines. The space group is P212121 with Z¼4. The C–H . . . O interactions in the center of the diagram are not shown explicitly. (Reproduced with permission from Garcia-Tellado et al., 1991.)

solution studies. An unambiguous demonstration of two-point binding was provided by the structure determinations of {C39H43N3O8.pyrazine.2.5(pyrazine)} (POLFUR) and {C39H43N3O8.quinoxaline.0.5-(ethanol)} (YAWJIP10; Fig. 12.13) by Pascal and Ho (1994); both crystals are triclinic, P 1, Z ¼ 4. It was shown that the Rebek-acid molecule ‘‘is quite ﬂexible, and that small changes in critical framework bond angles may be ampliﬁed into substantial displacements at the diamine binding site’’. The above examples demonstrate the formation of discrete polymolecular units from mutually compatible components, with evidence for the existence of such units in solution and demonstration of their structure in the solid state. Most of this book is concerned with the structures of binary adducts of crystallizable mutually-compatible components, generally encountered by chance. But what of design, especially with a view to controlling solid-state properties? One example of a brave attempt is given by Garcia-Tellado et al., 1991. The naphthalene compound (Scheme IV) forms triclinic 1 : 1 adducts with 1,8-octanedicarboxylic acid (JOHRAZ; P1, Z ¼ 2, thus there are two crystallographicallyindependent units of each component in the unit cell, without crystallographically imposed symmetry), and with 1,12-dodecanedicarboxylic acid (JOHPUR; P1, Z ¼ 1, thus both components are located at independent centres of symmetry); the biphenyl compounds behaves similarly with 1,12-dodecanedicarboxylic acid (JOHPOL; P1, Z ¼ 1,

874

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

0(28a)

N(51a)

N(54a)

0(47a)

0(27a) 0(46a) 0(24a)

0(50a) N(1a)

N(34a)

0(31a) N(15a) 0(43a)

0(27b)

N(51b)

N(54b)

0(28b) 0(24b)

0(31b) N(15b)

0(46b)

0(47b) N(1b)

0(50b)

N(34b) 0(43b)

Fig. 12.13. Structures of the two independent molecular units in {C39H43N3O8quinoxaline0.5(ethanol)} showing the differences in the details of their structures. The N . . . O distances are 2.761 and ˚ in the upper diagram and 2.691 and 2.661 A ˚ (all s.u.’s 0.007 A ˚ ) in the lower diagram. 2.790 A The quinoxaline molecules are held by the crab-like claws of Rebek’s diacid. (Reproduced with permission from Pascal and Ho, 1994.)

thus both components are located at independent centres of symmetry). There is amphoteric >N–H . . . O¼C< and –O–H . . . N< hydrogen bonding, linking the components in head-to-tail fashion in chains (Fig. 12.14); the hydrogen bonding motif is similar to that shown in Fig. 12.12 (but without C–H . . . O interaction). Varying mutual dispositions of the components allow more than one possibility of recognition. It is not clear whether there are interactions in solution, but this seems unlikely, The authors comment ‘‘The development of molecules that can self-assemble into new solid-state materials is an area of recognized importance. The ability to control both the formation and details of the structure of these materials offers an interesting approach to ﬁne tuning electrical or optical properties in the crystal.’’

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

875

CH3 O

N

H

N

N

H

N

O bis[(6-methylpyrid-2-yl)amino)carbonyl]naphthalene

H3C

CH3 O

N

N

H H N

N

O H3C

bis[(6-methylpyrid-2-yl)amino)carbonyl]biphenyl

Scheme IV

(f) Separation of enantiomers by formation of diastereoisomeric compunds There are now many examples where formation of discrete 1 : 1 hydrogen bonded compounds has been utilized to separate enantiomers (reviewed by Toda, 1987). For example, brucine forms a compound with o-bromophenyl-phenylacetylene-hydroxymethane which undergoes spontaneous resolution on crystallization (BAHLAX; space group P212121, Z ¼ 4; Toda, Tanaka and Ueda, 1981). Another example is the preferential formation of the diastereomeric compound between (S)-N-(3,5-dinitrobenzoyl)-1-phenylethylamine and (R)-methyl-p-tolyl sulphoxide. The space group is P21 and Z ¼ 2; an >N–H . . . O¼S< hydrogen bond is formed between the paired components, which form the packing units in the molecular crystal (Charpin et al., 1981). Bicyclic enones can be resolved by formation of speciﬁc diastereomers with the chiral donor4 molecule (–)-(R,R)-trans-4,5-bis(hydroxydiphenylmethyl)-2,2-dimethyl-1,3dioxacyclopentane; the adducting acceptor molecules tested were (–)-(R)-6-methylbicyclo[4.4.0]dec-1-ene-3-one (KODWEF) and the corresponding 3,7-dione (KODWIJ) (Scheme V). Only the (–) . . . (–) hydrogen bonded compounds are formed, and these are isomorphous (space group P212121, Z ¼ 4). Only the oxygen in the 3-position of the acceptors behaves as an hydrogen bond acceptor (Nassimbeni et al., 1991). 4 Although a host–guest terminology was used by Nassimbeni et al., we prefer to distinguish between H-bond donors and acceptors as inclusion is not involved.

876

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

(a)

(b)

Fig. 12.14. Hydrogen bonding scheme in 2,6-bis[(6-methylpyrid-2-yl)amino)carbonyl]naphthalene – 1,8-octanedicarboxylic acid (P1, Z¼2); the upper part of the diagram (a) shows a projection onto the planes of the pyridine rings and the lower part (b) a stereoview in an approximately perpendicular direction. (Reproduced with permission from Garcia-Tellado et al., 1991.) O Ph

CH3

Ph

O

O

O

O

CH3

H H Ph O

Ph

Donor

CH3 O Acceptor enones

Scheme V

CH3

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

877

The unresolved donor forms discrete-pair molecular compounds with some amines, 1, Z ¼ 2) and another with the unusual such as Donor : (n-C3H7)3N (SADFEI; P composition 2(Donor) : 3(n-C3H7)2NH (SADFAE; P21/n, Z ¼ 2), where one of the (n-C3H7)2NH molecules is disordered about a centre of symmetry and is not involved in the hydrogen bonding (Weber, Do¨rpinghaus and Goldberg, 1988). 12.5.1.2

Structures with discrete triples (B–A–B) of components

When one of the components has two functional groups which can act as acceptors and/or donors in hydrogen bond formation, and the other is monofunctional, then triples can be formed which pack in the crystal as discrete trimolecular units. It is convenient to distinguish the arrangements D – A – D and A – D – A, at least for purposes of classiﬁcation. A simple example of the ﬁrst group is pentaﬂuorophenol – dioxane – pentaﬂuorophenol (P21/c, Z ¼ 2, crystal structure determined at 138K) (DEVFOZ; Gramstad et al., 1985). The oxygens of the dioxane are hydrogen bonded, in roughly equatorial directions, to ˚ ,
878

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

cell (KOCHOZ; P 1, Z ¼ 2; Bourne, Nassimbeni and Toda, 1991). Competition experiments showed that 3,5-lutidine was more strongly adducted to 1,1,2,2-tetraphenylethane-1,2-diol than 2,6-lutidine despite the similar shapes of the two acceptor molecules. A particularly interesting situation is provided by the 1 : 2 molecular complexes of 3,5-dimethylpyridine (A) with 3,5-dinitrobenzoic acid (B) (HAXFER) and its monodeuterated analog (HAXFER01) (Jerzykiewicz et al., 1993). The all-hydrogen compound ˚, crystallizes in the triclinic space group P 1, with Z ¼ 2 (a ¼ 11.680, b ¼ 8.451, c ¼ 24.382 A 3 ˚ ¼ 95.75, ¼ 108.17, ¼ 91.48 , volume per formula unit ¼ 590.9 A ). There is proton transfer from the carboxyl group of one molecule to pyridine nitrogen, thus leading to formulation as {3,5-dimethylpyridinium 3,5-dinitrobenzoate 3,5-dinitrobenzoic acid} or {AHþBB}. There is >Nþ–H . . . O hydrogen bonding between AHþ and ˚ ), and O . . . H–O– hydrogen bonding between B and B (2.499(3) A ˚ ). When B(2.644(4 A the carboxyl of B is deuterated, the crystals examined were found to be monoclinic, P21/c, ˚ , ¼ 102.94 , volume per formula unit ¼ Z ¼ 4 (a ¼ 9.409, b ¼ 10.813, c ¼ 12.310 A 3 ˚ 586.4 A ) and the analogous hydrogen bond distances (but with deuterium) were ˚ . While the overall arrangements of {AHþBB} and lengthened at 2.739(5) and 2.526(5) A þ {AD B B} moieties are similar, there are differences of detail and this led to the suggestion that the difference in H(D)-bond distances is due to the difference in crystal structure (perhaps this phrase implies polymorphism) rather than to isotopic substitution. The difference in formula-unit volumes is suggestive. There are also 1 : 1 hydrogenated (PUHROZ; formula˚ 3) and monodeuterated (PUHROZ2; formula-unit volume 350.65 A ˚ 3) unit volume 351.04 A molecular complexes of 3,5-dimethylpyridine with 3,5-dinitrobenzoic acid (Jerzykiewicz et al., 1996; structures at 80K). These two compounds are isomorphous, with the acid hydrogen reported to be shared between carboxyl oxygen and pyridine nitrogen. Resolution of enantiomers is obtained in some of the 1 : 2 compounds of chiral 1-(o-chlorophenyl)-1-phenyl-2-propyn-1-ol (CPPOH) (Scheme VI) with achiral 1,4diazobicyclo[2.2.2]octane (DABCO) and achiral N,N 0 -dimethylpiperazine (DMP) (Yasui et al., 1989). For example, {[(–)-(R)-CPPOH] . . . DABCO . . . [(–)-(R)-CPPOH]} (chiral, P21, Z ¼ 2; VAWLAG) is formed selectively from a racemic solution of CPPOH and thus molecular compound formation with achiral DABCO effects resolution of CPPOH. However, an achiral centrosymmetric molecular compound is formed from DMP {[(þ)-(S)CPPOH] . . . DMP . . . [(–)-(R)-CPPOH] (achiral, P 1, Z ¼ 1) GERWEF10}. Racemic [(þ)-(S)-CPPOH] . . . DABCO . . . [(–)-(R)-CPPOH] (C2/c, Z ¼ 8; VAWLEK) and chiral [(–)-(R)-CPPOH] . . . DMP . . . [(–)-(R)-CPPOH] (P21, Z ¼ 2; GERWIJ10) were obtained under (unspeciﬁed) ‘‘appropriate but severe’’ conditions. Ph

OH C C H

Cl

(–)-(R)-CPPOH

Scheme VI

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

879

1,4,7,10,13,16-Hexaoxacyclo-octadecane (18-crown-6, 18C6O) and 1,4,10,13-tetraoxa7,16-diazacyclo-octadecane (diaza-18-crown-6, 18C(4O2N)) form 1 : 2 hydrogen bonded molecular compounds with a variety of ligands, showing interesting variations in the conformation of the macrocycle and the modes of hydrogen bonding. We consider ﬁrst some of the proposed conformations for the macrocycle. Strain energy calculations by molecular mechanics (Bovill et al., 1980) show that the most stable conformation (‘c’ of Fig. 12.15) is that described by the (a, a, a)(a, gþ, a)(a, g, gþ) sequence of partial conformations for the three successive non-equivalent –O–CH2–CH2–O– units of the (here assumed) centrosymmetric macrocycle (a¼anti, gþ and g are the two gauche conformations) (Fig. 12.15); this biangular conformation is found in the crystalline uncomplexed macrocycle (Maverick et al., 1980). The conformation with (ideal) D3d symmetry (‘b’ of Fig. 12.15) has partial conformations (a, a, g–) (a, a, gþ)(a, a, g) and a relative strain energy of 33 kJ/mol, due mostly to unfavourable interactions between the oxygen atoms separated ˚ . Another conformation (‘e’ of Fig. 12.15) with partial conformational sequence by 2.8 A (a, g, a)(a, g, a) (g, g, a) has a relative strain energy of 21 kJ/mol. The 1 : 2 compounds are centrosymmetric (from the space groups) and have the ligands inclined with dihedral angles of 120 ‘above’ and ‘below’ the planes of the six oxygens of 18C6O, to some or all of which the ligand donor groups are hydrogen bonded. In the 18C(4O2N) compounds the hydrogen bonding is exclusively to the nitrogens of the macrocycle. The macrocycle has approximately D3d symmetry in its 1 : 2 compounds with malonitrile (HODMLN; Kaufmann et al., 1980), 2,4-dinitrophenylhydrazine (CRHYDZ; Hilgenfeld and Saenger, 1981) and formamide (CEHGEB; Watson, Galloy, Grossie, Vo¨gtle and Mu¨ller, 1984) and the (a, g, a)(a, g, a)(g, g, a) sequence when the ligand is dithiooxamide (CEHGOL; Watson, Galloy et al., 1984) or 2,4-dinitroaniline (BAKHIE; Weber and Sheldrick, 1981). The sequence (gþ, a, a)(gþ, a, gþ)(gþ, a, a), the strain energy of which has not yet been reported, is found in the compounds of 18C6O with benzenesulphonamide (Kno¨chel et al., 1976) and 4-nitro-1,2-benzenediamine (BECVEK; Weber, 1982), and in the compounds of 18C(4O2N) with p-nitrobenzaldehyde oxime and N-hydroxybenzamide (Watson, Nagl and Kashyap, 1991). The 2 : 1 molecular compounds of N-m-chlorophenylurea (DIWMOL10; Nastopoulos and Weiler, 1988) and N-m-bromophenylurea (KIVKAB; Nastopoulos et al., 1991) with 18-crown-6 are not isomorphous although both contain discrete centrosymmetric [ligand– ˚ ) and one 18C6O–ligand] arrangements, in which there is one medium (d ¼ 2.94 (2.91) A ˚ ) N–H . . . O hydrogen bond. The macrocycle has the biangular, weak (d ¼ 3.27 (3.34) A minimum strain energy conformation in both molecular compounds. Interactions between hydrogens of methyl groups and the trigonally arranged oxygens in the two faces of 18C6O provide an opportunity for studying the formation (or not) of C–H . . . O hydrogen bonds. The crystal structure of the {O2NCH3 (18C6O) CH3NO2} complex has been determined at 298K (Rogers and Green, 1986) and at 123K (BIJWAS02; Rogers and Richards, 1987), the crystals being monoclinic (P21/n, Z ¼ 2) at both temperatures. The methyl hydrogens appear to be ordered and linked by hydrogen bonds to the oxygens of the crown ether. The {NCCH3 (18C6O) CH3CN} complex has been studied at 298K (GEFREO02; Garrell et al., 1988; Weller et al., 1989) and at 123K (GEFREO01; Rogers, Richards and Voss, 1988). The acetonitrile complex at 298K is monoclinic and isomorphous with the nitromethane complexes, but there appears to be a phase transformation on cooling as the complex is triclinic at 123K (P1, Z ¼ 2,

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

880

(a)

(b) C(11)

C(12) –64 –178

O(14)

C(1)

C(13) 67 50 C(12)

C(16) C(15) O(17) 175 C(18) 179 175 –56 –75

O(13)

O(11) 72 56

176 O(8)

C(15)

C(5)

–178 –179 O(4)

–64 –179

–178

O(1)

178 64

C(3)

C(2)

7.84 kcal mol–1 (d)

–69 O(13) 17777 –173 62

C(6)

–64

C(15) O(16)

C(18)

C(12)

C(14)

O(7) –179

3.86 kcal mol–1 (c)

C(8)

179

179

C(17)

O(7) C(6)

C(9)

64

64

C(10)

C(9)

–174

–175 –65 O(5) C(4)

179

–178

C(14)

–178

O(2)

–52

O(10)

179

–179 –171

C(3)

178

C(11)

C(9)

O(10)

C(8)

179 O(7)

C(9)

O(11) O(10) –174 C(12) 77 63

55 –172

180

177

–172 O(16)

C(6)

C(8) 180

180

–177 C(18)

172

–179

74

–61

O(7) C(6)

C(17)

O(13) 180

C(5)

O(4)

–62 173

C(3)

61 174 C(2)

0.00 kcal mol–1

C(14)

C(15)

O(13)

C(11) 61 174

176 –59 O(1) C(18)

C(15)

O(16) C(17)

4.39 kcal mol–1 O(10) C(9) –177

174

C(8) –58 –70

O(7)

176 60

–176

176

–60 –176

C(6)

O(16) 70 58 O(17)

–76

–175

C(5) O(4) O(1) –77 –177 69 C(3) C(2)

C(12)

C(14) 49 108

178

–174

177

C(18) O(1)

–174 –61 C(2)

O(4)

C(5)

C(3)

5.01 kcal mol–1

Fig. 12.15. Conformations of 18C6O as calculated by molecular mechanics; the strain energies appended are given with respect to conformation (c), the lowest energy conformation, as zero. (Reproduced with permission from Bovill et al., 1980.)

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

881

termolecular moieties located about two independent centres of symmetry). The 18C6O molecule has (noncrystallographic) D3d symmetry in all these structures. At room temperature the methyl hydrogens are rotationally disordered about the acetonitrile axis and H-bonding in the classic sense does not occur; this is corroborated by the lack of a shift in the C–H stretching frequency of the acetonitrile on complexation. At low temperature two of the three hydrogens of the acetonitrile are hydrogen bonded to 18C6O ˚ ). The differences between the two comoxygens (d(C . . . O) ¼ 3.19, 3.27; 3.27, 3.46 A plexes are perhaps due to the greater acidity of the hydrogens of nitromethane compared to those of acetonitrile, or to the lower symmetry of nitromethane. Diaza-18-crown-6 [18C(4O2N)] forms centrosymmetric 1 : 2 ‘discrete-molecule’ compounds with p-nitrophenol (GOBYOL; P21/n, Z ¼ 2), 2,4-dinitroaniline (GOBYUR; P21/n, Z ¼ 2) and salicylaldoxime (GOBZEC; P21/c, Z ¼ 2) (Watson et al., 1988b). In all these molecular compounds there are hydrogen bonds between amine or hydroxyl hydrogens and the nitrogens of the host and the crown ether has the D3d conformation. 18C(4O2N) forms ionic as well as neutral molecular compounds. For example, both tropolone (FUYSOH) and 4-hydroxy-3-methoxybenzaldehyde (FUYSUN) form 1 : 2 ionic molecular compounds in which a proton from each ligand molecule is transferred to a nitrogen of the macrocycle (Watson et al., 1988a). In the ﬁrst of these the macrocycle has the biangular, minimum strain energy conformation but the second shows a novel conformation where we list the torsion angles [73, 162, 174, 66, 96, 164, 78, 168, 117] because of their appreciable deviations from the standard values of 60, 180 . 18C6O also forms diaqua compounds in which a water molecule is hydrogen bonded, on each side of the macrocycle, to oxygens; an organic ligand is then hydrogen bonded to each water molecule. There is no direct link between organic ligand and macrocycle. Examples are {[18C6O2H2O].(3-nitrophenol)2} (CEHGUR) and {[18C6O2H2O] ( p-nitrobenzaldehyde)2} (CEHHAY); both have D3d conformations (Watson, Galloy, Grossie et al., 1984). Somewhat analogous, at least from a formal point of view, is {bis(trichloroacetato-O,O’)-Pb[18C6O]}(trichloroacetic acid), where each trichloroacetic acid molecule is hydrogen bonded to a trichloroacetate ion and not linked directly to the macrocycle (SOPRIY; Malinovski et al., 1990). 12.5.1.3 Larger discrete groupings of components There are relatively few examples. Centrosymmetric quasi-linear tetramers are formed by linking p-nitrophenol molecules to diacetamide (VIVYUU) and N-butyrylbenzamide (VIVZAB) dimers (Etter and Reutzel, 1991; Fig. 12.16), and formally-similar arrangements are found in the 1 : 1 compound of 2-aminobenzothiazole with hexamethylphosphoramide (O¼P(N(CH3)2)3) (JOLJID; Armstrong, Bennett et al., 1992) and that of 2-aminobenzothiazole with dimethylpropyleneurea (PASYEN; Armstrong, Davidson et al., 1992). All three have solid-state structures which can be described as containing B . . . A . . . A . . . B units, with the three-dot linkages representing hydrogen bonds of possibly different kinds. There may also be differences in the ways these units are arranged in their respective crystals. 1,1,2,2-Tetraphenylethane-1,2-diol (T) forms a 1 : 1 compound with 2,6-lutidine (L) (KOCHOZ; Bourne, Nassimbeni and Toda, 1991; P1, Z ¼ 2) which resembles the arrangements shown in Fig. 12.16 in the sense that the packing unit is L . . . T . . . T . . . L, and differs from the T compounds with the other lutidine isomers noted above.

882

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS O O

O p-nitrophenol

N

N

O p-nitrophenol

O H O Diacetamide H3C

O H O

CH3

N O

H

O

N

O

O

H O

H

H 3C

N-butyrylbenzamide

N H

N-butyrylbenzamide

N

CH3 Diacetamide

O

H

H

O

O

p-nitrophenol

N O

O

O

p-nitrophenol

N O

Fig. 12.16. Centrosymmetric tetramers of p-nitrophenol molecules linked to diacetamide (left) and N-butyrylbenzamide dimers (right). (Reproduced with permission from Etter and Reutzel,1991.)

In 8-dimethylamino-1-dimethylammonionaphthalene hydrogen squarate (2-hydroxy-3, 4-dioxocyclobut-1-en-1-olate) (KINKEX; Pbca, Z ¼ 8), the two squarate ions are linked across a centre of symmetry to form hydrogen bonded ‘quasi-carboxylic acid’ dimers. Each squarate transfers an hydrogen to the proton sponge to form an ordered intramolecular hydrogen bond between dimethylamino groups, the hydrogen being additionally bonded in bifurcated fashion to a carbonyl oxygen of the squarate ion; there are a number of analogous structures (Kanters et al., 1991). Somewhat similar arrangements are found in kinetin picrate (kinetin is 6-furfurylpurine) (VICPOM; Soriano-Garcia, Toscano et al., 1985) and N(6)-methyladeninium picrate (VATCEY; Dahl and Riise, 1989), with the formation of discrete groups of four hydrogen-bonded moieties as illustrated below: ðPICÞ . . . ðCATÞþ . . . ðCATÞþ . . . ðPICÞ The arrangement in 4(triphenylsilanol) – dioxane is formally rather similar (JODYAC; Bourne, Johnson et al., 1991). This can be represented as B . . . B . . . [dioxane] . . . B . . . B, with both hetero and homo hydrogen bonds (Scheme VII).

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

883

In hexamethylenetetramine : tris(phenol) (HMTTPO10; Jordan and Mak, 1970) three phenols are linked to each HMT through O–H . . . N hydrogen bonds in the form of a three˚ , space bladed propeller, and the crystal structure (trigonal, a ¼ 14.88, c ¼ 6.007 A group P3, two units of HMT : (phenol)3 per unit cell) is based on a packing of such units. The two tautomers of 3(5)-methylpyrazole form termolecular units with 1,1-bis (2,4-dimethylphenyl)but-2-yn-1-ol (P21/n, Z ¼ 4) (GERYIL; Toda, Tanaka, Elguero, Stein and Goldberg, 1988) linked in a closed loop by N–H . . . O, O–H . . . N and N–H . . . N hydrogen bonds (Scheme VIII). HOSiPh3 O

HOSiPh3

centre of symmetry

O Ph3SiOH Ph3SiOH

Scheme VII

H3C

(R)2R⬘COH

H3C

3 N

(R = 2,4-dimethylphenyl R⬘ = -C ≡ C-CH3)

5 N

N H

N

H 1,1-bis(2,4-dimethylphenylbut-2-yn-1-ol

3(5)-methylpyrazole

Scheme VIII

1,1,6,6-tetraphenylhexa-2,4-diyne-1,6-diol forms a 1 : 2 dioxane compound in which the diol hydrogen bonds to one dioxane to form an alternating . . . A . . . B . . . A . . . B . . . chain, while the second dioxane is not hydrogen bonded at all (JODXOP; Bourne, Johnson et al., 1991). We have encountered a number of examples containing parallelograms (some almost squares) of alternating N and O (or N and N, or O and O) atoms linked in different ways by hydrogen bonds. Neutral tetramolecular units are found in aniline – trichlorophenol ˚ , d(O–H . . . N) ¼ 2.78 A ˚ ) (ANCPOL; Bellingen et al., 1970), and in (d(N–H . . . O) ¼ 3.13 A ˚ ) (JARRID; Weber, Skobridis triphenylmethanol – methanol (d(O–H . . . O) ¼ 2.71, 2.71 A and Goldberg, 1989). Discrete centrosymmetric 2 þ 2 units with a roughly square arrangement of hydrogen bonds are formed in trans-9,10-dihydroxy-9,10-diphenyl-9,10-dihydroanthracene – 1,4-butanediol (DEPTAT; Toda et al., 1985). In thiomorpholine – 3, 5-dinitroimidazole a hydrogen is transferred from the pyrrole nitrogen to the nitrogen of the thiomorpholine, forming a >NþH2 ammonium cation. The ions form a four-membered hydrogen bonded ring lying on the two fold axis of the cell (space group C2/c, Z ¼ 8), with ˚ ) (JILWUW; Gzella and Wrzeciono, 1991). d(NþH . . . N) ¼ 2.936(4), 2.924(4) A

884

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

Morpholinium

Morpholinoformate 2.661 2.692

N C z x

O

y

Fig. 12.17. The eight-membered ring composed of morpholinium cations and morpholinoformate anions. The neutral moiety packs as ‘‘molecular’’ units in the crystal. (Data from Brown and Gray, 1982.)

Larger rings are also found, often constructed of a combination of covalent and hydrogen bonds. Crystalline morpholinium morpholinoformate was isolated by morpholine extraction of the yellow-orange product formed during the corrosion of metallic lead by white mineral oil; its structure (Fig. 12.17) was deduced entirely by crystallographic methods (P1, Z ¼ 2; MORPLN; Brown and Gray, 1982). It was later realized that the compound had ﬁrst been prepared in 1898 by bubbling CO2 gas through morpholine (Knorr, 1898). In the 4 : 1 compound of triphenylsilanol with ethanol, four triphenylsilanol molecules and one ethanol are linked together by homodromic hydrogen bonds (a circular pattern of hydroxyl groups all pointing in the same direction) in a ﬁve membered ring (SITKEL; Bourne, Nassimbeni, Skobridis and Weber, 1991). A rosette of trigonal symmetry has been constructed from three molecules each of N,N 0 -bis(p-butylphenyl)melamine and 5,5diethylbarbituric acid (Fig. 12.18) (KUFPIK; Zerkowski et al., 1992), and linear tape and crinkled tape motifs (see below) have been obtained from 1 : 1 combinations of other substituted melamines and 5,5-diethylbarbituric acid. These constitute particularly beautiful examples of molecular recognition via hydrogen bonding between amphoteric moieties each having both donor and acceptor functions. The bulky p-butylphenyl groups encourage the formation of isolated rosettes rather than the extended sheet structure found in the melamine– cyanuric acid molecular compound (QACSUI; Ranganathan et al., 1999; see below). A novel 3 : 2 structure has been found for the hydrogen-bonded molecular compound formed between [Ph2Si(OH)OSi(OH)Ph2] and pyridazine (1,2-diazine) (Fig. 12.19; KIRTOU; Ruud et al., 1991). 12.5.2

One-dimensional frameworks (linear chains of alternating components)

A ‘ribbon’ is deﬁned in the Concise Oxford Dictionary as a ‘‘Long narrow chain of anything’’. In structural chemistry suitable ribbons can interact laterally to form sheets

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

C(CH3)3

(CH3)3C

H H5C2

H N

H H

O

N H

H N

N

N

O

N

H H

H

H

N

C2H5 O

N H

H N

H N

N N

N

C2H5

N

O

O H

H

N

H

N

N

N

N N

N

H5C2 O

(CH3)3C

N

O

H H

N

C(CH3)3

N

O O H5C2 C2H5

(CH3)3C

885

C(CH3)3

Fig. 12.18. Schematic diagram of the rosette formed between N,N 0 -bis(4-t-butylphenyl)melamine and 5,5-diethylbarbituric acid. The crystals are triclinic (P1, two rosettes (i.e. six pairs) in the unit cell). (Adapted with permission from Zerkowski et al., 1992.)

Ph Ph

Ph Si

O

O

Ph

H H

H N

N

O Ph

N N

Ph

Ph

Si O

Si

O

Si O Ph

H

H Ph

H O

Si O

O Si Ph

Ph

Ph

Fig. 12.19. The centrosymmetric 3 : 2 adduct between [Ph2Si(OH)OSi(OH)Ph2] and pyridazine (1,2-diazine) (space group P1, Z¼1). The central [Ph2Si(OH)OSi(OH)Ph2] molecule in the schematic diagram is centrosymmetric, with <Si–O–Si¼180 (by symmetry) but not the others, which have <Si–O–Si¼144.5 . (Reproduced with permission from Ruud et al., 1991.)

(or layers). Many different kinds of ribbons are encountered among unary systems and also among the binary systems of interest here; their role in crystal engineering has been reviewed (Mele´ndez and Hamilton, 1998). The requirement for forming ribbons (linear chains) is that each component should be able to form two hydrogen bonds. This can be achieved in a number of ways. 12.5.2.1

Component A has two donor groups and the single acceptor of component B can accept two hydrogen bonds

An example is the quinol (A) – acetone (B) molecular compound, which was ﬁrst reported more than one hundred years ago (Haberman, 1884; Schmidlin and Lang, 1910); other ketones do not form molecular compounds with quinol. The crystal structure (C2/c, Z ¼ 4) (QLNAC; Lee and Wallwork, 1959) has inﬁnite chains of alternating quinol and

886

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

˚ ). Each oxygen of acetone molecules joined by O–H . . . O hydrogen bonds (d ¼ 2.74 A acetone is linked to hydroxyls of two different quinols, with the hydrogen bonds in the directions of the oxygen lone pairs. The speciﬁcity to acetone was explained in terms of matching the dimensions of the two components. A formally similar example is trans-1,2-cyclohexanediol – N-methylmorpholine-N-oxide; hydroxyl groups of two different cyclohexanediols are hydrogen bonded to the exocyclic oxygen of the ˚ ), forming N-methylmorpholine-N-oxide molecule (d(O–H . . . O) ¼ 2.677(4), 2.691(4) A ribbons along [100], with only dispersion interactions between neighbouring ribbons (BADCOY10; Chanzy et al., 1982). A one-dimensional chain but with different types of hydrogen bonding is found in 4-nitropyridine-N-oxide – 2-aminobenzoic acid (Cc, Z ¼ 4) (SOJPEM; Fuquen et al., 1991). The hydroxyl group of the carboxylic acid acts as a ˚ ), with a second link formed donor to the oxygen of the N-oxide (d(O . . . O) ¼ 2.629(5) A ˚ ), thus forming a zigzag by O to H–N of the amino group (d(N . . . O) ¼ 2.999(6) A chain structure. There is an intramolecular hydrogen bond between N–H and carbonyl ˚ ). The components are stacked alternately face-tooxygen (d(N–H . . . O) ¼ 2.675(7) A face, leading to a charge transfer interaction as shown by the red color of the compound compared to the yellow colors of the individual components (cf. the molecular compound of 3,4-dimethoxy- and 2,4-dinitrocinnamic acid (Desiraju and Sarma, 1983) discussed earlier). The crown ether, 18-crown-6, can be considered as having the triangles of three oxygens on opposite sides of the macrocycle as its two acceptor groups, with analogous behaviour for diaza-18-crown-6. Linear chains of alternating diaza-crown ether and 1,4-dihydroxybut-2-yne molecules are found in their 1 : 1 complex (GOBZIG; ˚ ) is too long for Watson, Vo¨gtle and Mu¨ller, 1988b) but the N . . . O distance (3.63 A hydrogen bonding. The authors note that the low density (measured 1.20, calculated 1.18 g cm3) could, perhaps, be ascribed to the difﬁculty of packing long linear and short cylindrical molecules closely together; there may also have been undetected solvent molecules, but this appears negated by the good agreement between measured and calculated densities. The last word is not yet in. A somewhat more complicated example is provided by the 1 : 1 molecular compound of 5-bromouridine and DMSO (space group P21, Z ¼ 2; BURDMS) (Iball et al., 1968), where the oxygen of DMSO acts as a double acceptor to two different hydroxyl donors of ˚ ) while one of its carbonyls acts as acceptor 5-bromouridine (d(O . . . H–O) ¼ 2.66, 2.74 A ˚ ), thus to an N–H group of another 5-bromouridine molecule (d(C¼O . . . H–N) ¼ 2.86 A forming a linear chain ( . . . 5-BU . . . 5-BU . . . (DMSO)2 . . . 5-BU . . . 5-BU . . . ) along the ½10 1 direction (Fig. 12.20). Similar packing arrangements, accompanied by optical resolution, are found in a number of examples. One of these is the molecular compound of (R,R)-(–)-1,6-bis (o-chlorophenyl)-1,6-diphenylhexa-2,4-diyne-1,6-diol and (–)-(R)-(Z)-benzyl-idene-2(3-methylbutyl)azane oxide, which crystallizes in space group P212121 (Z ¼ 4). The diol and nitrone molecules alternate along [100], forming an inﬁnite zigzag spiral chain, where different hydroxyls of the diol are involved in the two hydrogen bonds; ˚ (VAXFUV; Toda et al., 1989). Mutual optical resolud(O–H . . . O) ¼ 2.788, 2.780 A tion is also obtained in the molecular compound of (R)-(þ)-bis(-naphthol) and (m-tolyl)(methyl)sulfoxide (space group P1, Z ¼ 1), where inﬁnite zigzag chains are ˚ (CONPAW; Toda et al., 1984); formed along [100]; d(O–H . . . O) ¼ 2.758(2), 2.782(1) A the bis (-napthol) has a cisoid conformation with a torsion angle of 78 about the C–C

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

887

OH DMSO 5-BU

OH

C

OH OH 2.737

DMSO

OH O 2.658 S OH

5-BU

O

Br

O

N 2.855

O

O DMSO B

A

5-BU

z y

x

Fig. 12.20. Projection down [010] of the unit cell of 5-bromouridine – DMSO, showing the chains of hydrogen bonded molecules along the [101] direction. The hydrogen bonds are emphasized. (Data from Iball et al., 1968.)

bond joining the aromatic rings, and both hydroxyls participate in the hydrogen bonding. Mutual optical resolution also occurs in the molecular compound of (S)-(–)-9, 9 0 -biphenanthryl-10,10 0 -diol and (þ)-4-acetoxyazetidine-2-one (space group P212121, Z ¼ 4), where inﬁnite zigzag chains are formed along [010]; both hydroxyls and both carbonyls participate in the two nonequivalent hydrogen bonds, which nevertheless have ˚ ) (JEFRER; Toda et al., 1990). essentially the same length (d(O–H . . . O¼C) ¼ 2.91(1) A Helical chains of alternating 1,1 0 -diphenyl-2,3-dicarboxylcyclopropane and tert-butanol molecules, linked by hydrogen bonds, are found in their 1 : 1 molecular compound (P212121, Z ¼ 4) (KAXTUY; Weber, Hecker et al., 1989). The two carboxyl groups of the cyclopropane derivative are linked by strong intramolecular hydrogen bonds ˚ space group P21, Z ¼ 2) and (d(O–H . . . O¼C) both in the neat compound (2.513(5) A ˚ in the molecular compound with t-butanol. Spontaneous resolution of 2.552(5) A enantiomers has taken place on crystallization of both the neat cyclopropane derivative and the t-butanol molecular compound. Chains are also found in the 1 : 2 molecular compounds of 1,1 0 -binapthyl-2,2 0 dicarboxylic acid with methanol (CILLUE: TANDAN; Czugler and Weber, 1991; P21/n, Z ¼ 4; Fig. 12.21a) and with ethanol (CILMAN) and 2-propanol (CILMEP) (Fig. 12.21b, the 2-propanol compound being shown) and 2-butanol (CILMIT) (Weber, Cso¨regh, Stensland and Czugler, 1984). In the ﬁrst three compounds both hydroxyl groups of the

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

888

(a) B

0M1& 010 0M1

010⬘

0M2 0M2&

010 1⬘

(C∝)

R

A

0 0

BIN2 1

0∝ 010 R2 BIN1

011

(b) 011⬘

010

0P⬘

011

B C

BIN2 (c) 011 010⬘ d

011

0B &

0∝

011⬘ 0 0

0B

BIN1

0:0⬘

0

010

2 – BuOH

B

Fig. 12.21. Stereodiagrams of (a) 1,1 0 -binaphthyl-2,2 0 -dicarboxylic acid (BIN) – (methanol)2; (b) BIN – (2-propanol)2; (c) BIN – 2-butanol (P21/n, Z¼4). Crystals of (b) with ethanol and 2-propanol are isomorphous, C2/c, Z¼4. Two types of interruption of carboxylic acid dimers are shown on the right hand sides of the diagrams. (Reproduced from Weber, Cso¨regh, et al., 1984.)

alcohols are inserted into the two sides of the carboxylic acid dimer, giving what we may call a doubly interrupted dimer. In the 1 : 1 compound with 2-butanol (P21/n, Z ¼ 4; Fig. 12.21c) only one side of the carboxylic acid dimer is so interrupted. The preferred bonding pattern of carboxylic acids is the formation of dimers, although some chain

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

889

structures are known. Interruption of the dimers, as shown in these structures, is rare but not unprecedented and Weber et al. (1984) give other examples. Some of the trimesic acid channel inclusion complexes (Section 10.2) also fall into this group. Trans-9,10-dihydro-9,10-diethanoanthracene-11,12-dicarboxylic acid (Fig. 12.22) has been shown to form molecular compounds (all compositions 1 : 1 except where noted otherwise) with 27 different moieties of different chemical types (Weber, Cso¨regh, Ahrendt, Finge and Czugler, 1988) (1-butanol, t-butanol, 1-pentanol, 1-octanol, ethylene glycol (1 : 2), 2-methoxyethanol, formic acid (1 : 2), acetic acid, propionic acid, 2-chloropropionic acid, valeric acid, lactic acid, tartaric acid (2 : 1), mercaptoacetic acid, thioacetic acid (2 : 1), propionaldehyde, acetone, DMF, acetonitrile, benzyl cyanide, DMSO, THF (1 : 2), dioxane (2 : 1), o-dichlorobenzene, 2,6-dimethylnitrobenzene, 1-propanol and 2-nitrophenol (1 : 2)). Crystal structures have been reported for the neat host (SABNAK) and the 1 : 1 compounds with DMF (SABNIS; P21/c, Z ¼ 4) and 1-butanol (SABNEO; P 1, Z ¼ 2). Both have unusual arrangements in which the components are linked in hydrogen bonded chains, one pair of carboxylic acid dimers having the usual uninterrupted arrangement while the second pair is interrupted by two hydroxyl groups of butanol, or two aldehyde groups, with consequent formation of C¼O . . . HO and C–H . . . O¼C hydrogen bonds (Fig. 12.22). Pentachlorophenol (pKa ¼ 4.5) is a stronger acid than 2,4,5-trichlorophenol (pKa ¼ 6). Whereas the molecular compound aniline – 2,4,5-trichlorophenol (ANCPOL; Bellingen et al., 1971a) appears to be composed of neutral molecules, that between aniline and pentachlorophenol has been reported to be the salt anilinium pentachlorophenolate (ANLPCP; Bellingen et al., 1971b; there are inﬁnite chains of alternating cations and ˚ ). Three grounds were given anions linked by Nþ –H . . . O hydrogen bonds (2.73, 2.60 A for preferring the ionic formulation (i) the stronger hydrogen bonds compared to those in aniline – 2,4,5-trichlorophenol, (ii) the higher acidity of pentachlorophenol, (iii) the nature of the infrared spectrum (Zeegers-Huyskens, 1967). This conclusion is at variance with the pKa value quoted below (Section 12.5) and it would be useful to conﬁrm these conclusions by determining hydrogen positions, which were not found in the 1971 structure analysis. In imidazolium picrate (SEZREU; Soriano-Garcia et al., 1990; Herbstein and Kapon, 1991)), there are zigzag chains of hydrogen bonds, each ‘picrate’ oxygen being linked to H–N groups of two different imidazolium cations, which have ˚ ); presumably the effective symmmetry mm2 (d(O . . . H–N) ¼ 2.710(4), 2.825(5) A positive charge is preferentially localized on the N involved in the shorter of these two hydrogen bonds. 12.5.2.2

Component A has two hydrogen bond donor groups and component B two acceptor groups

The simplest examples are perhaps quinol – dioxane (SENYOK; Barnes et al., 1990) and 1,4-diazabicyclo[2.2.2]octane (DABCO) and 4,4 0 -biphenol (NISLOQ; Ferguson et al., 1998). [DABCO . . . biphenol] crystallizes in space group C2/c, Z ¼ 4, with DABCO disordered across centers of inversion and diphenol lying across two fold axes. Linear C(2,2)(16) chains of alternating DABCO and (non-planar) biphenol molecules run parallel to [201] (Fig. 12.23). Because of very limited conformational ﬂexibility there is no coiling of the chains.

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

890

D

A O

normal carboxylic acid dimer; d(0...0)=2.641Å) 1-butanol

hydroxyl of 1-butanol inserted in dimer

B x y Carboxylic acid group

O

O

2.741

H

2.599 2.741

z y

1-butanol x

C

Fig. 12.22. Trans-9,10-dihydro-9,10-diethanoanthracene-11,12-dicarboxylic acid is noted above in the text for its prolixity in forming 27 molecular compounds. The overall arrangement in the molecular compound with 1-butanol, projected down [001], is shown in the upper part of the diagram, with the two independent carboxyl groups (both located about centres of symmetry) interacting in different ways. Details of the interrupted hydrogen bonding scheme found for one of the carboxyl pairs (the other is a standard dimer) are shown below. Both carboxyl groups are ordered ˚ ) and C¼O (1.207 A ˚ )), hydrogens (other than (shown by different bond lengths for C–OH (1.307 A those participating in H-bonds) have been omitted for clarity, while the butanol hydroxyl H was not ˚ ); the butanol molecule has been found but is presumably located in the interaction denoted 2.741 (A emphasized. (Data from Weber et al., 1988).)

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b

4,4⬘-biphenol

DABCO

c

Fig. 12.23. [DABCO . . . biphenol] viewed approximately along [010], showing the alternating DABCO . . . biphenol chains running parallel to [201]. The oxygens of the hydroxyl groups have been emphasized. (Reproduced from Ferguson et al.,1998.)

Resorcinol – progesterone has chains of alternating donor and acceptor molecules ˚ ) (PRORES; Diderberg (space group P212121, Z ¼ 4, d(O–H . . . O¼C) ¼ 2.799, 2.818 A et al., 1975). Resorcinol also forms a 1 : 1 compound with 2,9-dimethyl-1, 10-phenanthroline (P 1 Z ¼ 2; CECBOJ; Watson, Galloy, Vo¨gtle and Muller, 1984), in which one of the hydroxyls of one resorcinol is linked in a bifurcated manner from ‘above’ to the nitrogens of one phenanthroline molecule while the second hydroxyl binds similarly from ‘below’ to the nitrogens of this phenanthroline, thus forming rows of alternating components. The planes of the two components are approximately mutually perpendicular. In 1,1,2,2-tetraphenylethane-1,2-diol – dioxane (C2/c, Z ¼ 4; JODXOP; Bourne, Johnson et al., 1991) the ﬁrst component is located on a diad axis and the dioxane at a ˚ in the linear chains of alternating centre of symmetry, with d(O–H . . . O) ¼ 2.865(4) A moieties. Analogous linear chains are found in 1,1,6,6-tetraphenylhexa-2,4-diyne-1, 6-diol – 2(dioxane) (P 1, Z ¼ 1), with the second dioxane in the asymmetric unit enclathrated between the chains and not hydrogen bonded in any way. A helical chain structure is found in cis-1-{[4-(1-imidazolylmethyl)cyclohexyl]methyl}-imididazole – succinic acid, shown schematically below (TAJVOP; Van Roey et al., 1991; Scheme IX). O H

O

O O H

O succinic acid

N

N

N

N

cis-1-{[4-(1-imidazolylmethyl)cyclohexyl]methyl}imidazole

Scheme IX

O H

H O O

892

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

The piperidine salts of p-chlorobenzoic (PIPCBZ), p-bromobenzoic (PIPBBZ) (Kashino et al., 1972) and p-toluic acids (PIPTAC) (Kashino, 1973) and pyrrolidinium p-chlorobenzoate (PYMCBZ) and p-bromobenzoate (ZZZBVP) are isomorphous (Pbca, Z ¼ 8) and pyrrolidinium p-toluate (PYMMBZ) is isostructural (P21/c, Z ¼ 4; Kashino et al., 1978). The moieties are linked by two kinds of Nþ–H . . . O hydrogen bond to form ribbons along the two fold screw axes along [001] (the ﬁrst group of salts) or [010] ˚. (the last example); the values of d(Nþ–H . . . O) range from 2.67 to 2.77 A 2-Aminopyridinium salicylate (SLCADB10; Gellert and Hsu, 1988) (Fig. 12.24) can also be classiﬁed in this group if some elasticity of deﬁnition is permitted. The two ionized moieties are linked by a pair of donor–acceptor hydrogen bonds and this unit is then joined in chains to other similar units by N–H . . . O¼C< hydrogen bonds, employing the second N–H of the amino group and the second acceptor function of the carbonyl oxygen of the carboxylate. As noted above, the two triangles of three oxygens on the opposite sides of the macrocyclic crown ether 18-crown-6 can behave as its two acceptor groups. Thus molecular compounds of composition 2(donor) – 18C6O, with molecules containing two hydrogen bond donors, can be classiﬁed in the present group; not all of the (potential) acceptor oxygens necessarily interact with the donors. Among the donors investigated in this

O3

O1

2.5

35

C13 C14

C12 C11

C15

C16

H2 2.845 O2 C17 N H 1 O1 2.699

2.914 H1 N2

H1 N2 C2

C3 C4

C6

C5

Fig. 12.24. The hydrogen bonding scheme in 2-aminopyridinium salicylate. The expected intramolecular hydrogen bond is found in the salicylate anion. (Reproduced with permission from Gellert and Hsu, 1988.)

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893

context are N,N 0 -dimethylthiourea ((P21/c, Z ¼ 2; 18C6O in D3d conformation) (BUPRAF; Weber, 1983) and N,N 0 -diformohydrazide (P21/c, Z ¼ 2; 18C6O in D3d conformation) (CEJVIW; Caira, Watson, Vo¨gtle and Mu¨ller, 1984). These two molecular compounds are isostructural but not isomorphous. The N,N-dimethylthiourea molecular compound forms a chain of the following schematic type . . . DMTU . . . 18C6 . . . DMTU . . . DMTU . . . 18C6 . . . DMTU . . . DMTU . . . 18C6 . . . in which each dimethylthiourea forms an aminic hydrogen bond (d(N–H . . . O ¼ ˚ ) to one oxygen of the macrocycle, with C–H . . . O interactions to the other 2.955(6) A two oxygens of the triangles on each side. The dimethylthioureas are linked by N–H . . . S ˚ ). Similar chains are found in the N,N 0 hydrogen bonds (d(N–H . . . S ¼ 3.394(6) A diformohydrazide molecular compound, with one N–H . . . O hydrogen bond to one oxygen of the triangle and two between adjacent diformohydrazide molecules in the chain, and in the 1 : 2 18C(4N2O) complex with 5,5-diethylbarbituric acid (GOBZAY; Watson et al., 1988b), where there are N–H . . . N and N–H . . . O links between barbituric acid and crown ether molecules, and similar links between adjacent barbituric acid molecules. The crown ether deviates from the D3d conformation as there are two successive gauche interactions with torsion angles of 66 and 55 . Optical resolution has been obtained with suitable combinations of donor and acceptor molecules. Thus, when chiral (R,R)-(–)-trans-2,3-bis(diphenyl-hydroxy-methyl)-1, 4-dioxaspiro[4,5]-decane and racemic dihydro-3-hydroxy-4H-dimethyl-2(3H)-furanone are crystallized together, optical resolution occurs because the crystalline hydrogen bonded molecular compound formed (space group P21, Z ¼ 2) contains only the (S)-(–)furanone (VAXFOP; Toda et al., 1989), the carbonyl and hydroxyl of which participate in the formation of spiral columns of alternating components along [010]. The two hydroxyl groups of the spiro compound are linked by a surprisingly short intramolecular hydrogen ˚ ; this should be checked. bond of length 2.365 A 12.5.2.3 Both components have both hydrogen bond donor and acceptor functions For example, the phase diagram of 3,5-dichlorophenol (DCP) and 2,6-dimethylphenol (DMP) shows formation of a 1 : 1 molecular compound (Bavoux, 1975). Structure analysis shows that there are chains of alternating DCP and DMP molecules along [010], the ˚ respectively (EDCTMP10; O–H . . . O hydrogen bonds having lengths of 2.83 and 2.67 A Bavoux and Thozet, 1980). This can be considered to be a mimetic structure as both DCP (DCLPHE; Bavoux and Thozet, 1973) and DMP (DMEPOL10; Antona et al., 1973) have similar one-dimensional chain structures. More complicated ribbon arrangements are found in the following molecular compounds (1) (2) (3) (4)

syn-5-nitro-2-furaldehyde oxime – urea (URNFRO; Mathew and Palenik, 1972); 1-(4-bromophenyl)-4-dimethylamino-2,3-dimethyl-3-pyrazolin-5-one – 5,5-diphenylhydantoin (DPHPZL; Uno and Shimizu, 1980); 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine – 5,5-diethylbarbituric acid (BIGCUP; Shimizu et al., 1982); 2-amino-3,5-dibromo-N-cyclo-hexyl-N-methylbenzenemethanamine – 1,2-benzisothiazol-3(2H)-one 1,1-dioxide, in which the components are ionized (BOYMEH; Shimizu and Nishigaki, 1983).

894

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

(a)

(b)

(c)

(e) (d)

Fig. 12.25. Alternating arrangements of two components in (a) linear ribbon, (b) and (c) crinkled ribbons, (d) rosette (cf. Fig. 12.16) and (e) sheet aggregate. This diagram has been adapted from Fig. 2 of Mele´ndez and Hamilton (1998), which was in turn based on Fig. 1 of Zerkowski, Seto and Whitesides, 1992).

A particularly interesting group of ‘‘linear’’ and ‘‘crinkled’’ hydrogen-bonded tapes (Fig. 12.25) has been prepared from 1 : 1 combinations of suitable derivatives of melamines and cyanuric acid, where there are three hydrogen bonds between each pair of components, thus imposing rather stringent geometrical limitations on the possible structures. The strategy (Whitesides, Mathias and Seto, 1991) for preparing the self-assembling motifs shown schematically in Fig. 12.25 was developed from ‘‘the pattern of hydrogen bonds present in the 1 : 1 complex formed from cyanuric acid and melamine.’’ This pattern, shown in Figs. 12.25(e) and 12.26, was proposed by Finkel’shtein and Rukevich (1983) on the basis of an infra-red study. Diffraction-quality crystals of cyanuric acid–melamine (CA.M) were prepared only in 1999 by a hydrothermal technique (Ranganathan et al., 1999); CA and M are both high-melting solids with limited solubility in most organic solvents. The XRD CA.M structure (QACSUI; 14.853(3) 9.641(2) ˚ , 92.26(1) , C2/m, Z ¼ 2), and that of the isomorphous trithiocyanuric acid3.581(1) A melamine compound (QACTAP), have provided full conﬁrmation of the postulated structure shown in Fig. 12.25(e). The molecules are arranged in planar layers, super˚ along [001]. There imposed in such a manner as to leave channels of diameter 4 A

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Fig. 12.26. The structure proposed for the 1:1 molecular compound of melamine (top left) and cyanuric acid (top right) on the basis of infra-red spectroscopy (Finkel’shtein & Rukevich, 1983). A representative portion of the inﬁnite sheet is shown. This structure has been conﬁrmed by XRD (see text); N–H . . . O and N–H . . . N distances are in the standard ranges of ˚ respectively. (Reproduced with permission from Mele´ndez and 2.94–2.98 and 2.85–2.88 A Hamilton, 1998.)

has been interest in polymeric melamine–cyanuric acid complexes because of their potentialities as ﬁre-retardants and lubricants; the layer structure may explain the latter property. The success of the proposed strategy has been fully proved, as is shown by the structures of 1 : 1 combinations of suitable derivatives of melamines and 5,5-diethylbarbituric acid (Fig. 12.27; an analogous isolated rosette of trigonal symmetry (Zerkowski et al., 1992) has been noted earlier in Fig. 12.18), and many other examples. Linear tapes have been found (Zerkowski, Seto, Wierda and Whitesides, 1990) in the 1 : 1 molecular compounds of 5,5-diethylbarbituric acid with N,N 0 -di-p-tolylylmelamine (JICVEW) and N,N 0 -diphenylmelamine (JICTIY) (for the latter, see Fig. 12.27 (left)), and a crinkled tape in the 1 : 1 molecular compound of 3,5-bis(N-4 0 -methoxycarbonylphenyl)melamine with 5,5-diethylbarbituric acid (KUFPIC; Zerkowski et al., 1992; Fig. 12.27 (right)).

896

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

Fig. 12.27. Left: the linear triply hydrogen-bonded tape found in the 1:1 molecular compound of N,N 0 -diphenylmelamine and 5,5-diethylbarbituric acid (Zerkowski, Seto, Wierda and Whitesides,1990). Right: the crinkled triply hydrogen-bonded tape found in the 1:1 molecular compound of 3,5-bis(N-4 0 -methoxycarbonylphenyl)melamine and 5,5-diethylbarbituric acid (Zerkowski et al., 1992). (Reproduced with permission from Zerkowski, Seto, Wierda and Whitesides (1990) and Zerkowski et al., (1992).)

12.5.3

Two-dimensional frameworks (layer arrangements of alternating components)

We distinguish between molecular compounds of neutral components and those where hydrogen transfer has occurred between the components and are thus formally salts. A highly symmetrical 1 : 1 neutral-component molecular compound is formed between tris(4-hydroxy-3,5-dimethylbenzyl)amine (‘TP’) and hexamethylenetetramine (‘HMTA’) ˚ , R (14.109(1) 26.697(5) A 3, Z ¼ 6; Fig. 12.28; HIFZIF; Bruyn et al., 1996). We quote (with some abbreviation) ‘‘The central N of TP and one N of HMTA lie on sites of threefold symmetry, and thus one third of the two molecules forms the asymmetric unit. The phenol rings are perpendicular to (00.1). Each TP is H-bonded to three HMTA molecules, and each HMTA to three TPs; all molecules lie on threefold axes. Within each layer, N–H . . . O linkages give rise to large pear-shaped rings, with three HMTA and three TP molecules. Packing of these layers occurs in a space-ﬁlling way, which precludes the formation of any channels. There are no unusually short intermolecular distances between the layers.’’ Comparison can be made with the close-packed layers found in CCP and HCP metals. Not all layer structures are as symmetrical as HMTA–TP. Planar layers are found in {thiourea – parabanic acid} (structure at 93K (TUPRBN01; Weber and Craven, 1978), space group P21/m, Z ¼ 2; no phase change between 93 and 298K); the N–H . . . S ˚ ) are shorter by 0.15 A ˚ than any of those in thiourea hydrogen bonds (d(H . . . S) ¼ 2.25 A ˚ . The crystal structure of the 1 : 1 complex of itself. The layers are separated by 3.15 A acetamide with the E, Z (cis, trans) isomer of diacetamide has been determined at 123K (a ¼ 7.695(9), b ¼ 6.443(8), c ¼ 8.918(9), ¼ 108.90(9) , P21/m, Z ¼ 2). The hydrogenbonded molecules are in sheets in (010) planes, the sheets interacting by dispersion forces (DUVHOR10; Matias et al., 1988). These two crystals are isostructural. The 1 : 1

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897

b

a

Fig. 12.28. HMTA – TP: projection down [001] showing the packing of two adjacent layers centrosymmetrically related through the origin. (Reproduced with permission from Bruyn et al. (1996).)

molecular compound between urea and 2,6-lutidine (2,6-dimethylpyridine) is an interesting example of molecular recognition in the solid state, providing a convenient method of separating 2,6-lutidine from other coal tar bases (Riethof, 1944, 1945). In the crystal (space group C2/c, Z ¼ 4, each molecule on a two fold axis) (LUTDUR; Lee and Wallwork, 1965) the planes of the two components are mutually perpendicular; there are strips of urea molecules linked by N–H . . . O¼C< bonds, with the pyridine nitrogen acting as acceptor to the second N–H group of each urea. All the hydrogen bonding possibilities are used. The layers are packed one above the other, interacting by dispersion forces. There is also a 2 : 1 compound but its structure does not appear to have been reported. In 2-thiohydantoin – 9-methyladenine (C2/c, Z ¼ 8) (BIFYOE; Cassady and Hawkinson, 1982) there are ribbons of alternating hydantoin (donor) and adenine (acceptor) molecules linked via N–H . . . N hydrogen bonds, with the ribbons linked laterally by N–H . . . N hydrogen bonds between adenine molecules, ﬁlling both donor and acceptor roles. The S and O atoms of the 2-thiohydantoin molecules do not appear to act as acceptors in strong hydrogen bonds. In 5-ﬂuorouracil – 9-ethylhypoxanthine (P21/c, Z ¼ 4) (FUREHX; Kim and Rich, 1967) there are centrosymmetric pairs of 5-ﬂuorouracils linked by two N–H . . . O hydrogen bonds, with each 5-ﬂuorouracil linked to two different 9-ethylhypoxanthines.

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

898

Thus sheets of molecules are formed in the (100) plane. Puckered layers of the components are found in 9-ethyladenine – parabanic acid, with hydrogen bonding links between parabanic acid and adenine molecules and between pairs of adenine molecules; there are no links between parabanic acid molecules nor are there any unusual carbonyl-carbonyl interactions (EADPBA; Shieh and Voet, 1976). In thiourea – hexamethylenetetramine oxide (HMTO) (Pbca, Z ¼ 8) (HMTATV; Yu and Mak, 1978) three of the four N–H groups of thiourea act as hydrogen bond donors (while the fourth is inactive) towards the formally-negative oxygen of HMTO, which is the sole acceptor atom in this molecule. This leads to the formation of corrugated layers parallel to (001). The HMT portions of the HMTO molecules project from both sides of each layer to ﬁll the space between adjacent layers; this is their only structural role. A somewhat similar arrangement of corrugated layers occurs in HMTOH2O2H2O, where again the HMTO oxygen atom is the sole acceptor of hydrogen bonds to HMTO, and the HMT portion of the molecule has only a space-ﬁlling role (HMTOXH; Mak and Lam, 1978). 1,1-Di(p-hydroxyphenyl)cyclohexane forms isomorphous 1 : 1 triclinic layer complexes with m-cresol (GEFROY), p-cresol (GEFRUE), phenol (GEFSAL) and o-cresol (GEFRIS) (Goldberg et al., 1988) (Fig. 12.29); although isomorphous, the complexes ˚ 3). have slightly different cell dimensions and volumes (1029, 1012, 1014 and 964 A Selectivity studies show the order: m-cresol > p-cresol > phenol > o-cresol, and the

H-bonded chain

B 0

ligand phenol

phenol

ligand phenol

y

phenol

ligand

A

x

Fig. 12.29. A hydrogen bonded layer in the isomorphous triclinic 1:1 complexes of 1,1-di(phydroxyphenyl)cyclohexane with m-cresol, p-cresol, phenol and o-cresol, illustrated for the phenol compound. (Data with permission from Goldberg et al., 1988.)

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899

separation of m-cresol (b.pt. 202.0 ) and p-cresol (b.pt. 201.8 ) has been demonstrated. Every hydroxyl group is involved in two hydrogen bonds. There are a number of 1 : 2 molecular compounds forming sheet structures which have the formal similarity of crystallizing in space group P21/c with Z ¼ 2, the ﬁrst component thus being located at a crystallographic centre of symmetry. Among the many examples are oxalic acid – (urea)2 (by XRD at 298K (UROXAL; Harkema et al., 1972); also by ND at 100K), succinic acid – (benzamide)2 (BZASUC) [oxalic acid – (furamide)2 (FURAOX) is a triclinic variant of this structure type] (Huang et al., 1973), 2,5-bis (2,4-dimethylphenyl)-hydroquinone – (ethanol)2 (CAMMIN; Toda et al., 1983) and -truxillic acid – (methanol)2 (JOBXON; Cso¨regh, Czugler et al., 1991). A somewhat similar arrangement is found in N2H4 – (C2H5OH)2 (m. pt. 242K), this being the only intermediate compound in the hydrazine–ethanol freezing point diagram (Corcoran et al., 1953). The crystal structure (determined at 85K, space group Pbcn, Z ¼ 4, hydrazine on a two fold axis parallel to [010]) shows that hydrazine and ethanol molecules are hydrogen bonded to one another forming inﬁnite layers parallel to (100). The hydroxyl of each ethanol forms one donor bond to hydrazine N, and accepts two N–H bonds. Each N accepts one hydroxyl H-bond and is the donor in two N–H bonds; the hydrogen bond lengths are ˚ (HYDETH; Liminga, 1967). The crystal N–H . . . O 3.041, 3.060 and O–H . . . N 2.730 A structures of both phases of oxalic acid – bis(N-methylurea) have been determined at 295K (MUROXA; Harkema et al., 1979). The phase stable up to 182K is orthorhombic (space group Pnma, Z ¼ 4); it seems that this phase can be (super)heated to at least 300K. The monoclinic phase stable at room temperature can be cooled down to 182K, where it changes to orthorhombic; it is not clear whether these are thermodynamic (equilibrium) or kinetic temperatures. Very similar mixed-component layer arrangements are found in both phases, with the layers in the mirror planes at y ¼ 1/4, 3/4 in the orthorhombic phase, and the oxalic acid molecules at inversion centres in the monoclinic phase (Fig. 12.30). The phase change is stated to be irreversible and exothermic (presumably this means the phase change ‘monoclinic to orthorhombic on cooling’). All possible hydrogen bonds appear to be formed in both phases, although there are some differences in the details of their geometries. The volume per formula unit is 1.3% greater in the monoclinic than in the orthorhombic phase, with 0.9% ascribed to the difference in distance between parallel ˚ ), and 0.4 % to small differences in atomic positions in the planar layers (3.21 and 3.24 A layers. There are some resemblances between the 1 : 1 salt of piperazine and phenylbutazone (4-n-butyl-1,2-diphenyl-3,5-dioxo-1,2-pyrazolidine) (space group P21/c, Z ¼ 2; PBZPAZ10; Singh and Vijayan, 1977) and the 1 : 2 salt of N-methylpiperazine and phenylbutazone (space group P21/c, Z ¼ 2) (Toussaint et al., 1974). In the ﬁrst of these salts there are two-dimensional sheets in (100) planes linked by N–H . . . O bonds of length 2.627(8) and ˚ ; all possible H-bonds are formed. There is a rather similar arrangement in the 2.650(8) A ˚ . Puckered layers are second salt, with N–H . . . O links of length 2.670(5) and 2.753(5) A found in dimethylammonium hydrogen oxalate (P21/c, Z ¼ 4) (DMAHOX; Thomas and Pramatus, 1974). The H2C2O4 anions are linked via strong O–H . . . O hydrogen bonds ˚ ) to form chains along [100], which are linked transversely through the (d ¼ 2.533(1) A (CH3)2NH2þ cations by N–H . . . O hydrogen bonds. Histidinium trimesate1/3(acetone) forms hydrogen bonded layers about z 0, 1/2 in which the acetone molecules are enclosed by the cations and anions of the hydrogen bonded framework structure but not

900

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

H(1)

(–100) H(4)C(1)

N(1) C(2)

(110) H(2) H(3) i

N(2 )

O(1) i

H(5)

H(5 )

N(2)

O(2) C(3) O(3)

(–101)

i

H(7)

H(6)

N(1 ) i

H(4 )

i

C(3 )

(–111)

Fig. 12.30. Hydrogen bonding in the crystal structure of monoclinic bis(N-methylurea) – oxalic acid. The arrangement in the layer at y¼1/4 is shown above, and a stereoview looking down [010] below. The thermal ellipsoids of the atoms in both diagrams are scaled to include 50% probability and hence the hydrogen atoms are largest. (Reproduced with permission from Harkema et al., 1979.)

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

901

linked to them. The L- and DL-histidinium salts are isostructural, with the former having space group P212121 (LHISTM) and the latter space group Pna21 (DLHTMS), with Z ¼ 4 in both examples (Herbstein and Kapon, 1979). 12.5.4 Three-dimensional frameworks (arrangements of alternating components in space) The spatial arrangements in these molecular compounds can be quite complicated and we shall describe only a few examples in which the components are small molecules. The ﬁrst of these is ‘hyperol’, urea – hydrogen peroxide, the room temperature structure of which was ﬁrst determined in 1941 by what was then a crystallographic tour de force, (Lu et al., 1941), and later redetermined by neutron diffraction, with crystals at 81K, thus enabling positions of all the hydrogens to be found (UREXPO11; Fritchie and McMullan, 1981). The 298 and 81K structures are essentially the same, and we shall describe only the latter. The space group is (nonstandard) Pnca, with Z ¼ 4 (Fig. 12.31). The urea molecule lies along and the H2O2 molecule across the crystallographic two fold axis along [001]. The hydrogen bonding of ﬁrst-neighbor H2O2 molecules to urea is shown in Fig. 12.32. The peroxide oxygens act both as donors (to carbonyl O) and acceptors (from N–H of the amine groups). All possible hydrogen bonds are formed. In monomethylammonium hydrogen oxalate (monoclinic, P21/n, Z ¼ 4) the ions are ˚ ) to form inﬁnite chains along [101]. linked by O–H . . . O hydrogen bonds (d ¼ 2.515(2) A Transverse linkage between these chains is by a complex network of N–H . . . O bonds to the CH3NH3þ cation (MAMHOX; Thomas, 1975). The hydrazine-methanol melting point diagram shows a 1 : 1 compound with an incongruent melting point at 226K, a 1 : 2 compound that melts at 215K and a 1 : 4 compound that melts at 203K; only the crystal structure of the latter has been reported (HYDTML; Liminga and Sørensen, 1967). Unusually, the

Fig. 12.31. Stereodiagram showing the hydrogen bonding in the crystal structure of hyperol at 81K. The [001] direction is vertical with [100] horizontal. The thermal ellipsoids are scaled to enclose 80% probability surfaces. (Reproduced with permission from Fritchie and McMullan, 1981.)

902

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

two fold axis

1.619 Å

H2O2 seen approximately edge-on

urea

2.003 Å

x

y z

Fig. 12.32. Intercomponent hydrogen bonding in hyperol, showing the immediate surroundings of a ˚ ) between H donor atoms and O acceptors are taken from urea molecule. The lengths (esds 0.001 A the 81K neutron diffraction measurements. The crystallographic two fold axis along [010] is shown. (Adapted from Fritchie and McMullan, 1981.)

crystals are tetragonal and chiral (P42, Z ¼ 2). The methanol molecules are bonded to one ˚; another and to the hydrazines in a three-dimensional network (d(N–H . . . O) ¼ 2.96, 3.03 A ˚ ; d(O–H . . . O) ¼ 2.74 A ˚ ). In estradiol – urea (P212121, Z ¼ 4) d(O–H . . . N) ¼ 2.68 A (ESOURE10; Duax, 1972) the steroid molecules are hydrogen bonded head-to-tail along [100] via hydroxyl groups; the urea molecules are interleaved, each being linked to four estradiol molecules and to two other ureas, forming inﬁnite chains along [001], and in fact giving a three-dimensional arrangement of hydrogen bonds. As Duax notes, the ureas serve to bind the sterol molecules, not to enclose them. In salicylic acid – urea (C2/c, Z ¼ 8) (SLCADC10; Hsu and Gellert, 1983) the urea molecules form centrosymmetric dimers, while salicylic acid forms intermolecular hydrogen bonds exclusively to urea; one N–H group of each urea does not participate in a hydrogen bond. The strong O–H . . . O hydrogen ˚ ) found in this structure indicates that the carbonyl oxygen of urea is a bond (d ¼ 2.54 A stronger hydrogen bond acceptor than that of salicylic acid. In quinol – urea (a ¼ 17.180(2), b ¼ 6.601(1), c ¼ 7.341(1), ¼ 94.4(1) , P21/c, Z ¼ 4) (QUOLUR; Mahmoud and Wallwork, 1975), the quinol molecules are situated at independent centres of symmetry. There are alternate sheets of mutually hydrogen bonded ureas and quinols parallel to (100); ˚ from each O atom of urea receives two hydrogen bonds of length 2.683(2) and 2.702(2) A the hydroxyl groups of quinol molecules on either side of it in the [100] direction. In addition, two of the N–H groups of urea link to O atoms of two quinol molecules in the ˚ , and a third N–H links to a quinol chain along [010] at distances of 2.980(2) and 3.049 (3) A

A L T E RN A T I N G F RA M E W O R K S T R UC T U RE S

903

C

2.927

succinic acid

2.523

2.971 two ureas B

A

z

y

x

Fig. 12.33. The primary hydrogen bonded chain in {2(succinic acid):urea}, showing the C¼O . . . H–O and C¼O . . . H–N hydrogen bonds, the two bonds of the latter kind are between ˚ ) and urea . . . urea (2.927 A ˚ ). The NH groups of urea syn to the urea and succinic acid (2.971 A oxygen are involved in the H-bonds within the primary chain. (Adapted from Videnova-Adrabinska (1996).)

˚ . The fourth N–H does not O in an adjacent chain along [001] at a distance of 3.048(2) A participate in the hydrogen bonding. Thus this is a three-dimensional structure, describable in terms of layers about (001) linked by hydrogen bonds roughly along [001]. The structure of (perdeuterated) parabanic acid – urea (P21/c, Z ¼ 4; m. pt. 456K; determined by neutron diffraction at 116K) consists of alternating tilted stacks of nearly planar hydrogen-bonded ribbons which are symmetry-related and parallel to the crystal planes (211) and (2 11) (URPRBN01; Weber, Ruble et al., 1980). Close C . . . O approaches between the ribbons provide cohesion in addition to the hydrogen bonding. Such interactions, which have been found in a number of different crystals, are not well understood. There are three-dimensional arrangements of hydrogen bonds in 18C6O–(urea)5 (CRWNUR; Harkema, Hummel et al., 1981) and 18C4O2N – (thiourea)4 (BITYUY; Weber, 1982). In the ﬁrst, two adjacent oxygens of the polyether bind to two urea molecules by N–H . . . O hydrogen bonds; the remaining urea molecules form hydrogen bonded layers, which alternate with the mixed 18C6O-urea layers. In the second, there are two intracyclic N–H . . . O hydrogen bonds, giving a biangular conformation to the macrocycle, and a three-dimensional arrangement of intermolecular hydrogen bonds.

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

904

Primary A chain

two ureas 2.927

2.971 succinic acid 2.523

Primary B chain Primary A chain

Parallel superimposed A and B primary chains

N1 Primary A chain

N2 H-bonding between O2 chains: N1...O2 3.181 A; N2...O2 3.011 Å A

z

y

x

Fig. 12.34. Cross linking of the primary chains in {2(succinic acid):urea}. Shorter bonds in the primary chain are shown. The NH groups of urea anti to the oxygen are involved in the H-bonds between the primary chains. (Data from Videnova–Adrabinska, 1996).

12.5.5

Accounting for formation of a molecular compound

It is not often that one can assemble the facts (or most of them) needed to account for formation of a molecular compound from its components. The succinic acid–urea system meets most of the requirements. Two molecular compounds are formed in this system: 1 : 1 and 2 : 1. The crystal structures of succinic acid (neutron diffraction, 77K; SUCACB10; Leviel, Auvert and Savariault, 1981), urea (Swaminathan, Craven and McMullan, 1984; Section 6.2.1.1, Fig. 6.1) and {2(succinic acid):urea} (Wiedenfeld and Knoch (1990), VEJXAJ; Videnova-Adrabinska (1996), VEJXAJ10; 5.637(4) 8.243(3) ˚ 96.80(5) , Z ¼ 2, P21/c) have been reported. The two structure determinations 12.258(3) A for {2(succinic acid) : urea} agree but the interpretations differ; we follow VidenovaAdrabinska. No structure has been given in the CSD for the 1 : 1 compound although Videnova-Adrabinska does give a postulated one-dimensional self-assembled chain (her Fig. 3). The structures of {2(succinic acid) : urea} and {2(fumaric acid) : urea} (TIPWIY) are isomorphous (Videnova-Adrabinska, 1996), but there does not appear to be a 1 : 1 {(fumaric acid) : urea} molecular compound.

CRYSTAL ENGINEERING WITH HYDROGEN BONDS

905

{2(Succinic acid) : urea} has a three-dimensional hydrogen-bonded structure in which primary chains can be identiﬁed (Fig. 12.33). Comparison of hydrogen bond lengths in the molecular compound with those in the components shows that the only substantial difference is shortening of the distance from urea oxygen to succinic acid hydroxyl ˚ ) compared to that between carbonyl oxygen and hydroxyl in the succinic acid (2.532(3) A ˚ ). The shortening (strengthening) of this H-bond is the decisive effect dimer (2.678(2) A leading to formation of the heteromolecular cocrystal rather than separate crystals of the two components. An analogous H-bond shortening is found in {2(fumaric acid) : urea}, ˚ . However, the reason with a urea oxygen to fumaric acid hydroxyl distance of 2.499(2) A why this shortening occurs is not known. The primary H-bond chains are crosslinked by weaker hydrogen bonds as shown in Fig. 12.34; these hydrogen bonds have close to standard distance values. Videnova-Adrabinska notes that ‘‘unlike the case of the ureaglutaric acid cocrystal, the three-dimensional networks of the present crystals do not contain independent two-dimensional hydrogen-bonded substructures (layers).’’

12.6 Crystal engineering with hydrogen bonds Crystal engineering is the process of designing a crystal with speciﬁc properties and then actually synthesizing the material, generally by self-assembly of components linked in speciﬁc ways. These linkages are usually provided in purely organic crystals by strong hydrogen bonds, which can be very usefully supplemented by coordinative interactions in inorganic-organic hybrid materials (Aakero¨y and Beatty, 2001). Rather than attempting a comprehensive review of this rapidly expanding ﬁeld, we give an evolving case history of a small but well-deﬁned area ‘‘Engineering crystals for excited state diffraction studies’’. The purpose of such studies is to determine the geometrical changes that occur on excitation of a particular molecule from ground to excited state, the lifetime of the excited state being in the range of milliseconds to nanoseconds. To avoid possible crystal damage because of geometrical changes on excitation, it is essential to encapsulate the targeted molecules in some suitable framework rather than irradiate neat crystals. Ideally, one would wish to design a framework containing a single molecule in each of its cavities; the inclusion complex would be studied (at low temperature) in a third-generation synchrotron with synchronization of a pulsed laser beam (the pump beam) and the timevarying x-ray source (the probe beam) to achieve a sufﬁcient concentration of molecules in the excited state (Zhang et al., 1999). We limit ourselves to discussion of benzophenone as target molecule, and a framework composed of a hydrogen bonded combination of C-methylcalix[4]resorcinarene (CMCR) and the ‘extender’ 4,4 0 -bipyridine (bipy) (there are other extenders (MacGillivray and Atwood, 2000) not discussed here; ‘spacer’ and ‘pillar’ have also been used). It will be seen that there are many twists and turns on the road between conception and ultimate success. C-methylcalix[4]resorcinarene has been found in four conformations in its various molecular complexes (Fig. 12.35). Many crystalline CMCR–bipy combinations have been prepared, generally by hydrothermal methods. Some do not include benzophenone at all (or benzil, as an alternative target molecule) even though these potential guests were present in the reaction mixture; examples are the ‘supramolecular’ compounds {CMCR2bipy}, {CMCR3bipy}, {CMCR2bipy2H2O}, {2CMCR}1.5bipy5H2O and

906

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

(a)

(b)

(c)

(d)

Fig. 12.35. The four conformations of C-methylcalix[4]resorcinarene: (a) crown or bowl, ideal symmetry C2v – mm2; (b) boat or ﬂattened cone; (c) chair; (d) saddle. (Reproduced with permission from Ma, Zhang and Coppens, 2001b.)

{CMCRbipy}3.5ethanolH2Obipy, where the parentheses enclose framework components (Ma, Zhang and Coppens, 2002). As these are of no direct interest in the present context, they have not been included in Table 12.4, where only host-guest inclusion complexes are listed. However, essentially identical hydrothermal conditions (4 mL water, 0.025 mol CMCR, 0.05 mol bipy, 0.05 mol benzophenone (or benzil); heated at 140 C for 1 day, cooled to room temperature at 20 per day) gave, in another set of experiments, the desired inclusion complexes of composition {CMCR3bipy2H2O}[benzophenone], {[CMCRbipyH2O} [benzophenone] and {(CMCRbipy)[benzophenone]} (Ma, Zhang and Coppens, 2001b), where the framework components are included in parentheses and the guest in square brackets. The ﬁrst and second of these complexes, which are both of the framework type (Fig. 12.36), were considered suitable for photochemical experiments; the complexes differ in that the ﬁrst has a single guest molecule in a cavity while the second has two. The third of these inclusion complexes has a carcerand type structure (cf. Chapter 3), and disordered guest in the cavities and appeared to be less suitable than the other two. It seems clear from these experiments that the type of complex formed (both those containing guests and those that are guest-free) depend in a subtle and not-yet-understood way on the crystallization conditions. A proposed design has yielded the desired product, but the road between beginning and end has yet to be mapped out convincingly. One can consider the CMCR-bipy-H2O-guest system in terms of phase diagrams. For example, the simplest of the ternary compounds have the composition {CMCR2(bipy)}[guest]. There are three groups of isostructural crystals; in the ﬁrst the several guests are p-chlorotoluene, ferrocene adamantone and [2.2]paracyclophane,

CRYSTAL ENGINEERING WITH HYDROGEN BONDS

907

Table 12.4. Crystal data for inclusion complexes in the CMCR-bipy-H2O-guest system. The classification is based on chemical composition, CMCR conformation in the complex and its crystal structure. Data at room temperature unless stated otherwise. The REFCODES are given where available Guest (reference)

a/

b/

c/

Space group

CMCR2(bipy)n(guest): bowl; one-dimensional wave-like polymer p-chlorotoluene (MRR99) 10.025 23.982 11.375 P21/m QAHNAO 112.71 Ferrocene (at 173K) (MSRR00) 9.730 25.440 10.825 P21/m 110.71 Adamantanone (MRR99) 9.903 24.813 10.972 P21/m QAHNAS 114.17 [2.2]paracyclophane (MRR99) 9.846 24.871 11.338 P21/m QAHNIW 105.71 7.893 29.243 10.054 P21/m CH3CN (MHA98) 99.67 7.709 29.307 9.982 P21/m CH3NO2 (MHA98) at 173K 100.55 Acetylferrocene (at 173K) 18.477 11.742 26.086 P21/n (MSRR00) 107.794 18.808 11.948 25.595 P21/n 1,1 0 -diacetylferrocene (at 173K) (MSRR00) 108.306 CMCR2(bipy)n(guest): bowl; zero-dimensional carcerand-like structure 2(Nitrobenzene) (MDRR00) 10.731 15.075 16.882 P 1 95.727 94.860 93.915 2(butanol)(MZC02) Benzophenone (MZC01) 22.824 25.799 36.354 Fddd

Z

Volume

2

1261

2

1253

2

1230

2

1336

2

1144

2

1120

4*

1347

4*

1365

2

1350

16

1338

CMCR(bipy)H2O n(guest): ﬂattened-cone; two-dimensional brick wall structure Benzophenone(MZC01) 10.072 13.735 17.338 P 1 2 1080 75.98 79.80 68.86 CMCR3(bipy)2H2On(guest): chair conformation; three-dimensional stepped network Benzophenone (MZC01a) * not 2, as given in paper. References: MHA98 – MacGillivray, Holman and Atwood, 1998; MRR99 – MacGillivray, Reid and Ripmeester, 1999; MDRR00 – MacGillivray, Diamente, Reid and Ripmeester, 2000; MSRR00 – MacGillivary, Spinney, Reid and Ripmeester, 2000; MZC01a – Ma et al., 2001a; MZC01b – Ma et al., 2001b; MZC02 – Ma et al., unpublished.

in the second acetonitrile and nitromethane, and in the third acetylferrocene and 1,1 0 -diacetylferrocene. In all three two guest molecules are included in a carcerand-like capsule, but these capsules are packed differently, as shown by the crystal data given in Table 12.4. Thus the structural situation is indeed complicated. The CMCR2(bipy) and {CMCR2(bipy)H2O} combinations are versatile hosts in the sense of Chapter 8 and both

908

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

Fig. 12.36. Three-dimensional stepped sheet hydrogen bonded network of {[CMCR3bipy2H2O] benzophenone}. The horizontal layers contain CMCR and water molecules, while the bipy act as spacers, and the benzophenone guests are contained within the channels. (Reproduced with permission from Ma et al., 2001b.)

crystallization conditions and nature of the guest determine the ﬁnal structure; one of the tasks of the future is determine the relative roles of each factor. 12.7

Charged or neutral moieties – when is there hydrogen transfer between the components?

An early attempt to deﬁne conditions for the occurrence of neutral or charged components in hydrogen-bonded molecular compounds was made by Johnson and Rumon (1965). These authors prepared 18 crystalline molecular compounds of assorted combinations of pyridine and substituted pyridines, as hydrogen bond acceptors, and benzoic acid and substituted benzoic acids, as hydrogen bond donors. The infrared spectra of the solids were then determined, with emphasis placed on the N–H, O–H and C¼O bands, most weight being given to the latter because the benzoic acid absorptions are much stronger than those of the pyridines. Detailed analysis of the spectra also permitted distinction

C H A R G E D O R N E U T R A L M OI E T IE S

909

between single-minimum and double-minimum potential wells. The pKa value of the component in water was used as the best available measure of acidity, although this is not necessarily directly applicable to the situation in the solid. Their conclusion was that neutral component B . . . H–A compounds were formed when pKa<3.8 [pKa¼pKa (base) pKa(acid)], while for pKa>3.8 salts of the type Bþ–H . . . A were formed. We summarize their results for the salts (pKa in brackets) – collidinium 3,4-dichlorobenzoate (3.99), collidinium 2,4-dichlorobenzoate (4.92), 2,6-lutidinium 3,5-dinitrobenzoate (6.47, erroneously printed as 3.88 in the original), collidinium 3,5-dinitrobenzoate (7.37, erroneously printed as 4.78 in the original), pyridinium 2,4-dinitrobenzoate (3.81), 3,5lutidinium 2,4-dinitrobenzoate (4.92), 2,6-lutidinium 2,4-dinitrobenzoate (5.28), collidinium 2,4-dinitrobenzoate (6.18), pyridinium trichloroacetate (4.34), pyridinium triﬂuoroacetate (5.00). Crystal structures do not appear to have been reported for any of these molecular compounds. However, their conclusion is in accord with the following crystalline systems where both pKa values and structural results are available – pyridinium picrate (two polymorphs (Botoshansky et al., 1994), 4.85), histidinium trimesate (3.98) (Herbstein and Kapon, 1979), nicotinyl salicylate (4.85) (Kim and Jeffrey, 1971), 2-aminopyridinium salicylate (3.86) (Gellert and Hsu, 1988), imidazolium picrate (6.57) (Soriano-Garcia et al., 1990; Herbstein and Kapon, 1991), the isomorphous piperidinium salts of p-chlorobenzoic (7.14), p-bromobenzoic and p-toluic acids (6.76) (Kashino et al., 1972; Kashino, 1973), pyrrolidinium p-chlorobenzoate (7.19) and pyrrolidinium p-toluate (6.81) (Kashino et al., 1978) and 2,6-pyrido-2,7-crown-9 picrate (3.4) (Uiterwyk et al., 1986). Some exceptions should be noted – 9-methyladeninium salicylate has a pKa value of 0.9 but is nevertheless a salt; the pKa of 9-methyladeninium (6-amino-9-methylpurine) is given as 3.9 in the tables but is labelled ‘uncertain’. Acridinium pentachlorophenolate crystallizes as an ion pair (Wozniak et al., 1991), although pKa ¼ 5.58 4.5 ¼ 1.1; anilinium pentachlorophenolate is said to crystallize as an ion pair, although pKa ¼ 4.63 – 4.5 ¼ 0.13. A better established surprise is found in dipyridinium oxalate oxalic acid (pKa ¼ 5.23 1.23 ¼ 4.00) where ‘‘one oxalic acid donates two protons to [the two] pyridine bases rather than two oxalic acids giving up one proton each!’’ (Newkome et al., 1985). A similar approach, but applied to solutions, was taken by Brezinski et al. (1991) in their IR study of the proton potential as a function of pKa in hydrogen-bonded molecular compounds of various phenols (R–C6H4OH) with trimethylamine-N-oxide (pKa ¼ 4.65). For the most basic 4-methoxyphenol (pKa ¼ 10.21; pKa¼–5.56) there are two broad bands with maxima at about 2550 cm1 ( (OH) vibration) and 1800 cm1 (2(OH) vibration). There was no continuous IR absorption. These results show that the proton is localized on the phenolic group in the OH . . . ON bond. With 4-chlorophenol (pKa ¼ 9.37; pKa¼4.72), there are indications of a double minimum but the well is much deeper at the phenol and the weight of the polar structure O . . . HþON is very small. With R¼COOC2H5 (pKa ¼ 8.50; pKa¼3.85), the minimum of the proton potential at the phenol is less deep than for the 4-chlorophenol molecular compound, and the weight of the polar structure slightly larger. These changes are accentuated for R¼NO2 (pKa ¼ 7.15, pKa¼2.50). The spectrum changes completely when R ¼ 3,4-dinitro– and shows that there is a very strong hydrogen bond in which the proton ﬂuctuates in a double minimum with a very low barrier, or in a broad ﬂat single minimum potential. In the pentachlorophenol compound (pKa ¼ 4.74; pKa¼0.09) the proton

910

HYDROGEN BONDED MOL ECULAR COMPLEXES AND COMPOUNDS

ﬂuctuates in an OH . . . ON , O . . . HþON equilibrium, as indicated by the continuum absorption. With 2,6-dichloro-4-nitrophenol (pKa ¼ 3.70; pKa ¼ 0.95) the polar structure has gained more weight. However, it was only with the picrate (pKa ¼ 0.38; pKa ¼ 4.27) that the polar structure was completely realized, the hydrogen bond no longer showing proton polarizability. A parallel study has been made with carboxylic acid/trimethylamine-N-oxide compounds in acetonitrile solutions (Bo¨hner and Zundel, 1986). Various attempts have been made to correlate pKa with hydrogen bond distances. Although some authors reported disappointing results, Lechat (1984) claimed that the ˚ ¼ 2.374 þ 0.1754 ln (0.405 pKa þ 1) reproduced the measured equation d(O . . . O) A ˚ for a number of molecular compounds where pKa distances to within less than 0.02 A ranges from 17.95 to 0. In order that the pKa values measured in solution should be applicable to the situation in the solid, it seems desirable to restrict the sample to those molecular compounds which contain discrete pairs. Approximately linear relationships between d(X–H . . . Y) and pKa are found for the available examples in both N–H . . . O and O–H . . . O systems (Fig. 12.37), but it remains to be seen whether such a simple approach will survive the addition of more experimental values. The present situation is that pKa values are lacking for relevant molecular compounds of known crystal structure, while crystal structures are not known for systems with known pKa values. We note some 2.8

d(XH … O) Å

2.7

N-H … O

2.6

2.5

O-H … O

2.4

2.3 –12 –10 –8

–6

–4

–2

0

2

4

∆pKa

Fig. 12.37. Approximately linear plots are obtained for both d(O–H . . . O) and d(N–H . . . O) against pKa for hydrogen bonded, discrete pair molecular compounds. The equations are ˚ (R2¼0.88) and d(N–H . . . O)¼0.0232 pKa þ 2.61 A ˚ d(O–H . . . O)¼0.0219 pKa þ 2.45 A 2 (R ¼0.86). The data on the ﬁgure are for the following molecular compounds: O–H . . . O (from left to right): 3-aminophenol/4-nitropyridine-N-oxide (NPNO); 3-chlorophenol/NPNO; 4-nitrophenol/ triphenylphosphine oxide (TPPO) (Moreno Fuquen & Lechat, 1992); 4-nitrophenol/triphenylarsine oxide; 4-aminobenzoic acid/NPNO; 2-carboxyl-1,3-xylyl-30-crown-9/urea (Aarts et al., 1986); oxalic acid/TPPO; trichloroacetic acid/TPPO; salicylic acid/antipyrine; trichloroacetic acid/ pyridine-N-oxide. N–H . . . O (from left to right): All have pentachlorophenol as hydrogen bond donor and 3-pyridinecarbonitrile; 4-methylpyridine; 5,6,7,8-tetrahydroquinoline; N-methylmorpholine respectively as acceptors.

REFERENCES

911

compilations of pKa values (Serjeant and Dempsey, 1978; Smith and Martell, 1982, 1989; Klofutar et al., 1967).

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Schuster, P., Zundel, G. and C. Sandorfy, C. (1976). (Eds). The Hydrogen Bond (Recent Developments in Theory and Experiments), Vol. I Theory, Vol. II Structure and Spectroscopy, Vol. III Dynamics, Thermodynamics and Special Systems. North-Holland, Amsterdam, New York and Oxford. Serjeant, E. P. and Dempsey, B. (1978). ‘‘Ionization constants of organic acids’’ in Aqueous Solution, IUPAC Data Series No. 23, Pergamon Press, Oxford. Shastry, C. I. V., Seshadri, T. P., Prasad, J. S. and Achar, B. N. (1987). Z. Kristallogr., 178. 283–288. Shieh, H.-S. and Voet, D. (1976). Acta Cryst., B32, 2361–2367. Shimizu, N. and Nishigaki, S. (1983). Acta Cryst., C39, 502–504. Shimizu, N., Nishigaki, S., Nakai, N. and Osaki, K. (1982). Acta Cryst., B38, 2309–2311. Shiro, M. and Kubota, T. (1972). Chem. Lett., pp. 1151–1152. Sim, G. A. (1967). Annu. Rev. Phys. Chem., 18, 57–80. Singh, T. P. and Vijayan, M. (1974). Acta Cryst., B30, 557–562. Singh, T. P. and Vijayan, M. (1977). J. Chem. Soc., Perkin II, pp. 693–699. Smith, R. M. and Martell, A. E. (1982). Critical Stability Constants, Plenum, Vols. 1–4, Vol. 5 (First Supplement), Vol. 6 (Second Supplement), 1989, London. Soriano-Garcia, M., Schatz-Levine, M., Toscano, R. A and Iribe, R. V. (1990). Acta Cryst., C46, 1556–1558. Soriano-Garcia, M., Toscano, R. A. and Espinosa, G. (1985). J. Cryst. Spectroscop. Res., 15, 651–662. Steiner, T. (1996). Cryst. Revs., 6, 1–57. Steiner, T. (1998). Acta Cryst., B54, 456–463. Steiner, T. and Saenger, W. (1991). Acta Cryst., B47, 1022–1023. Steiner, T. and Saenger, W. (1992). J. Am. Chem. Soc., 114, 10146–10154. Steudel, R., Rose, F. and Pickardt, J. (1977). Z. anorg. allgem. Chem., 434, 99–109. Suh, I.-H. and Saenger, W. (1978). Angew. Chem. Int. Ed. Engl., 17, 534. Talukdar, A. N. and Chaudhuri, B. (1976). Acta Cryst., B32, 803–808. Taylor, R. and Kennard, O. (1982). J. Am. Chem. Soc., 104, 5063–5070. Taylor, R. and Kennard, O. (1984). Acc. Chem. Res., 17, 320–326. Taylor, R., Kennard, O. and Versichel, W. (1983). J. Am. Chem. Soc., 105, 5761–5766. Taylor, R., Kennard, O. and Versichel, W. (1984a). Acta Cryst., B40, 280–288. Taylor, R., Kennard, O. and Versichel, W. (1984b). J. Am. Chem. Soc., 106, 244–248. Thierback, D. and Huber, F. (1979). Z. anorg. allg. Chem., 451, 137–142. Thierback, D. and Huber, F. (1981). Z. anorg. allg. Chem., 477, 101–107. Thomas, J. O. and Pramatus, S. (1975). Acta Cryst., B31, 2159–2161. Thomas, J. O. and Renne, N. (1975). Acta Cryst., B31, 2161–2163. Thomas, J. O. (1975). Acta Cryst., B31, 2156–2158. Toda, F. (1987). Top. Curr. Chem., 140, 43–69. Toda, F., Sato, A., Tanaka, K. and Mak, T. C. W. (1989). Chem. Lett., pp. 873–876. Toda, F., Tanaka, K, and Ueda, H. (1981). Tetr. Lett., 22, 4669–4672. Toda, F., Tanaka, K. and Mak, T. C. W. (1983). Chem. Lett., pp. 1699–1702. Toda, F., Tanaka, K. and Mak, T. C. W. (1984a). Chem. Lett., pp. 2085–2088. Toda, F., Tanaka, K. and Mak, T. C. W. (1984b). Tetrahedron Lett., 25, 1359–1362. Toda, F., Tanaka, K. and Mak, T. C. W. (1985). J. Incl. Phenom., 3, 225–233. Toda, F., Tanaka, K. and Mak, T. C. W. (1989). Chem. Lett., pp. 1329–1330. Toda, F., Tanaka, K., Elguero, J., Stein, Z. and Goldberg, I. (1988). Chem. Lett., pp. 1061–1064. Toda, F., Tanaka, K., Yagi, M., Stein, Z. and Goldberg, I. (1990). J. Chem. Soc., Perkin I, pp. 1215–1216. Toussaint, J., Diderberg, O. and Dupont, L. (1974). Acta Cryst., B30, 590–596.

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Part VI Molecular compounds with delocalized interactions

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Introduction to Part VI Molecular compounds with delocalized interactions

In this group of ﬁve related chapters we discuss principally molecular compounds with delocalized interaction between donor and acceptor molecules, due to electron transfer, in ground or excited states, from the highest occupied (HOMO) orbitals of the donor to the lowest unoccupied (LUMO) * orbitals of the acceptor. Thus these are –* molecular compounds (the * is often dropped for brevity). The molecular compounds are generally highly colored even though the parent molecules are colourless; this striking feature was already apparent in the ﬁrst groups of molecular compounds to have been prepared (quinhydrone by Wohler (1844), picric acid molecular compounds of benzene, naphthalene and anthracene by Fritzsche (1858)). The early stages of research on -molecular compounds were summarized by Pfeiffer (1928), whose book, despite the passage of the years, still contains much useful and interesting information. At that time there were two rival theories about the structures of -molecular compounds; one, put forward by Lowry (1924) and Bennett and Willis (1929), envisaged the formation of covalent bonds between the two partners, whereas the other, due essentially to Pfeiffer, ascribed the cohesion to secondary valence interactions (Rest-afﬁnita¨tskrafte). The ﬁrst direct evidence for the Pfeiffer proposal was provided by the ﬁnding (Powell, Huse and Cooke, 1943) that all intermolecular distances in the crystal structure of fp-iodoaniline TNB} were far too long to be ascribed to covalent bonding. Attention thus necessarily shifted to secondary interactions between the components, with major emphasis on ﬁnding an explanation for the intense colours developed in crystals and, especially, in solutions. A major advance was made by Mulliken (1952a, 1952b, 1956), following earlier suggestions by Weiss (1942) and Brackmann (1949). The essential idea was that the ground state of the molecular compound can be described by combining a (major) contribution from a no-bond wave function of the two uncharged molecules and a (rather minor) contribution from a dative structure involving transfer of an electron from donor to acceptor. In the excited state, on the other hand, the major contribution comes from the dative or charge-transfer structure. The additional, frequently intense, charge-transfer band in the spectra of solutions or suitably-oriented crystals is ascribed to excitation of the system from its predominantly no-bond ground state to its predominantly dative excited state. Mulliken’s theoretical contributions (Mulliken and Person, 1969) were primarily directed towards 1 : 1 ‘loose complexes’ in solution but donor–acceptor interactions occur also in the gas (Tamres, 1973), liquid (melt) and solid phases. In solution there will be interactions with solvent molecules while in the solid longer-range interactions must be taken into account. These additional interactions may be sufﬁcient to stabilize the ionic form as the ground state of the molecular compound. The overall subject has been extensively discussed (Briegleb, 1949, 1961; Andrews and Kieffer, 1964; Rose, 1967; Foster, 1969; Slifkin, 1971; Soos and Klein, 1976) and the crystallographic aspects reviewed in detail (Prout and Wright, 1969; Herbstein, 1971; n n n

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Prout and Kamenar, 1973; Soos, 1974; Bleidelis, Shvets and Freimanis, 1976; Andre`, Bieber and Gautier, 1976; Ponte Goncalves, 1980). A major impetus was given in 1973 by the discovery (Coleman et al., 1973) that f½TTF][TCNQ]g had a peak at 60K in its conductivity-temperature curve, with a maximum conductivity of 104S/cm1 (for comparison the conductivity of copper at 293K is 6 105S/cm1). This lead to intense activity for a number of years in the ﬁeld of ‘‘organic metals’’, many of which are not -molecular compounds in our present sense. There is so much material available that we have found it necessary to spread our discussion over ﬁve chapters. The ﬁrst of these, Chapter 13, serves as an overall introduction, with many of the topics dealt with more extensively later. Chapter 14 deals with layered molecules with intramolecular charge transfer interactions, Chapters 15 and 16 with the crystal chemistry and physics of mixed-stack compounds and Chapter 17 with segregated-stack compounds. In Chapters 13 to 16 the structure determining interaction is A B leading to mixedstack arrangements of donors and acceptors. This ﬁts our original deﬁnition of molecular compounds (Chapter 1). The structures in Chapter 17 are also stacked but there is a striking difference – donors and acceptors are in separate stacks, hence the term ‘segregated’ – the structure determining interactions are A–A and B–B, and the materials are not molecular compounds in a strict sense. Nevertheless, it is desirable to keep both groups together for historical reasons and because delocalized charge transfer is important in both. n n n

References Andre`, J. J., Bieber, A. and Gautier, F. (1976). Ann. Phys., [15] 1, 145–256. Andrews, L. J. and Keefer, R. M. (1964). Molecular Complexes in Organic Chemistry. Holden-Day, San Francisco. Bennett, G. M. and Willis, G. H. (1929). J. Chem. Soc., pp. 256–268. Bleidelis, J. J., Shvets, A. E. and Freimanis, J. F. (1976). J. Struct. Chem., 17, 930–944. Brackmann, W. (1949). Rec. Trav. Chim. Pays-Bas, 68, 147–159. Briegleb, G. (1961). Elektronen-Donator-Acceptor-Komplexen. Springer, Berlin-Go¨ttingenHeidelberg. Briegleb, G. (1949). Zwischenmolekulkrafte, G. Brown, Karlsruhe. Coleman, L. B., Cohen, M. J., Sandman, D. J., Yamagichi, F. G., Garito, A. F. and Heeger, A. J. (1973). Solid State Commun., 12, 1125–1132. Foster, R. (1969). Organic Molecular Complexes. Academic Press, London. Fritzsche, J. von, (1858). J. Prakt. Chem., 73, 282–292. Herbstein, F. H. (1971). ‘‘Crystalline -molecular compounds: chemistry, spectroscopy and crystallography’’ in Perspectives in Structural Chemistry, edited by J. D. Dunitz and J. A. Ibers, Wiley, New York etc., Vol. IV, pp. 166–395. Lowry, T. M. (1924). Chem. and Ind. (London), 43, 218–221. Mulliken, R. S. and Person, W. B. Molecular Complexes – a Lecture and Reprint Volume, Wiley, New York, 1969; also in Physical Chemistry (An Advanced Treatise), Vol. III, edited by D. Henderson, Academic Press, New York and London, 1969. Mulliken, R. S. (1952a). J. Am. Chem. Soc., 72, 600–608. Mulliken, R. S. (1952b). J. Phys. Chem., 56, 801–822. Mulliken, R. S. (1956). Rec. Trav. Chim. Pays-Bas, 75, 845–852.

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Pfeiffer, P. (1928). Organische Moleku¨lverbindungen, 2nd Edition, Stuttgart: Enke. Ponte Goncalves, A. M. (1980). Prog. Solid State Chem., 13, 1–88. Powell, H. M., Huse, G. and Cooke, P. W. (1943). J. Chem. Soc., pp. 153–157. Prout, C. K. and Kamenar, B. (1973). Molecular Complexes, 1, 151–207. Prout, C. K. and Wright, J. D. (1968). Angew. Chem. Int. Ed. Engl., 7, 659–667. Rose, J. (1967). Molecular Complexes. Pergamon Press, Oxford. Slifkin, R. M. (1971). Charge-Transfer Interactions of Bio-Molecules. Academic Press, London. Soos, Z. G. (1974). Ann. Rev. Phys. Chem., 27, 121–153. Soos, Z. G. and Klein, D. J. (1976). In Treatise on Solid State Chemistry, edited by N. B. Hannay, Plenum, New York, Vol. 3, 679–767. Tamres, M. (1973). Molecular Complexes, 1, 49–116. Weiss, J. (1942). J. Chem. Soc., pp. 245–252. Wohler, F. (1844). Ann. Chem., 51, 145–163.

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Chapter 13 Charge transfer molecular compounds with delocalized –* interaction – introduction and general survey

I now identiﬁed the Benesi–Hildebrand spectrum as an ‘‘intermolecular chargetransfer spectrum’’ of a benzene-iodine molecular complex resulting from partial transfer of an electron from the benzene to the iodine partner within the complex, which I called a ‘‘Charge-transfer Complex’’. . . . my use of the term ‘‘charge-transfer complexes’’ was not really appropriate because in the ground state there is usually only a little electron transfer. On the other hand, the name ‘‘charge-transfer state’’ is highly appropriate for the excited state, in which nearly a complete transfer of an electron has occurred. R. S. Mulliken, 1985.

Summary: About one hundred years elapsed between the preparation of the ﬁrst crystalline charge transfer molecular compound with delocalized –* interaction (anthracene picric acid) and the development of a generally accepted theory, based, in turn, on the experimental demonstration that these compounds crystallized in mixed stacks with alternation of donor and acceptor moieties. The conditions under which the moieties occur as neutral molecules (the predominant situation) or as radical ions have been deﬁned. The properties of a donor–acceptor -compound depend on the individual properties of the donor and acceptor participants, usually expressed in terms of donor ionization potential and acceptor electron afﬁnity as modiﬁed for the difference between the gas and crystalline phases. These crystalline binary sytems should be characterized in terms of their binary phase diagrams, which will show the appearance of DnAm compounds, where ‘n’ and ‘m’ are usually but not always 1. These principles can be extended to self-complexes, where donor and acceptor portions are situated within the same molecule. n n n

13.1 Introduction and historical development 13.2 Classification 13.2.1 General considerations 13.2.2 Intramolecular -compounds and self-complexes 13.3 Chemical nature of donors and acceptors 13.3.1 Introduction 13.3.2 Donors 13.3.3 Acceptors 13.3.4 Quasi-acceptors 13.3.5 Ionization potentials of donors and electron affinities of acceptors 13.3.6 Determination of degree of charge transfer

926 927 927 930 932 932 933 935 939 940 944

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13.4

Binary and quasi-binary donor–acceptor systems 13.4.1 Phase diagrams 13.4.2 Component ratios in binary donor–acceptor systems 13.5 Ternary -molecular compounds References

13.1

948 948 952 953 954

Introduction and historical development

The purpose of Chapter 13 is to provide physical and chemical background in advance of the following three more detailed chapters. We start with an overall classiﬁcation that establishes chemical and structural foundations for these three chapters. This is followed by a description of the families of donor and acceptor structures, showing the special features underlying the general description. Among the acceptors we distinguish between the classical group of acceptors, exempliﬁed by picric acid – a choice based on historical considerations – and quasi-acceptors, the majority of which appear to be ﬂuorinated hydrocarbons. In the donor–quasi-acceptor molecular compounds the interaction between components is based on quadrupolar interactions rather than charge transfer interactions. An important consequence is that these molecular compounds are not coloured. Returning to the classical charge transfer molecular compounds, measures of the strengths of the donor and acceptor interactions are given by the ionization potentials and electron afﬁnities of donors and acceptors respectively; modiﬁcation of the standard deﬁnitions applicable in the gas phase to the solid state are next discussed. We then consider the assessment of the degree of charge transfer encountered in various charge transfer molecular compounds, especially referring to the segregated stack structures. One of our constant themes has been that it is unsatisfactory to base discussion of particular donor–acceptor systems on the crystal structure of the pair obtained by crystallization from solution. Instead, it is desirable to report the phase diagram (at least a melting point diagram, but preferably a more elaborate version) of the system. This is illustrated towards the end of Chapter 13, followed by a brief discursion on ternary systems. How important have charge transfer compounds been in the standard lexicon of the contemporary organic chemist? We have tried to obtain a rough answer to this question by examining a number of standard post-Second World War organic chemistry texts, all of which have some thousand pages or more. A text that bridges between pre- and post-War periods is that of Fieser and Fieser (1961). These authors allocate just over one page (pp. 694–695) to the topic under the title ‘‘Hydrocarbon–polynitro compound complexes’’. The main features are nicely summarized – the formation of colour on crystallization of the two-component system, exempliﬁed ﬁrst for picric acid as acceptor and then extended to trinitrobenzene, trinitrotoluene, trinitroresorcinol, 2,4,7-trinitroﬂuorenone, picryl chloride and picramide. The Fiesers point out the value of some of the ‘complexes’ ‘‘in identiﬁcation and puriﬁcation of hydrocarbons and in isolation of hydrocarbons from reaction mixtures because of their superior crystallizing tendency, sparing solubility, and relatively high melting points. The derivatives often have identifying colors . . . ’’ Roberts and Caserio (1964), Hendrickson, Cram and Hammond (1970) and Streitweiser, Heathcock and Kosower (1992) cover much the same ground with similar allocations of space. However, the topic seems to have vanished from two more

CL ASSIF IC ATION

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recent books (Solomons and Fryhle (2000) and Clayden, Greeves, Warren and Wothers (2001)). A word about nomenclature – for mnemonic reasons we always place the donor molecule ﬁrst. For mixed stack compounds we join donor and acceptor by the symbol , indicating a –* charge transfer interaction, but denote segregated stack complexes as symbol to emphasize the difference between the f[donor][acceptor]g, dropping the two types. n n n

n n n

13.2 Classiﬁcation 13.2.1 General considerations For the broad group of molecular compounds where the donor–acceptor interaction appears to be structure-determining, a classiﬁcation can be set up both in structural terms and in terms of the nature of the ground state. However, there is overlap rather than exclusion between these two parts of the deﬁnition. Structurally it is possible to distinguish three types: those in which the two components are arrayed in mixed stacks, those where the components are segregated in separate stacks and those where there is an intermediate situation, either quite without stacks or with stackings of limited length. The terms ‘heterosoric’ have been suggested for mixed-stack structures, ‘homosoric’ for segregated-stack structures, and ‘nonsoric’ for those without stacks (Dahm et al., 1975); however, most authors use the English nomenclature, and so shall we. Now the ground state can be neutral or ionic (when the material is formally a salt) and one can further differentiate between salt formation due to electron or to proton transfer. We distinguish among three possible types of charge transfer; which type occurs depends on the nature of the components involved (Fig. 13.1). The ﬁrst group (Fig. 13.2), where only electron transfer is possible, can be further subdivided. It seems useful to add three further subgroups for those -compounds with neutral ground states. The ﬁrst subgroup includes most -compounds with a quinone as acceptor, including the quinhydrones; there appears to be a characteristic mode of interaction between aromatic hydrocarbons and quinones (supplemented by hydrogen bonding for the quinhydrones) which is worth emphasizing. The second subgroup is based on all other acceptors except for the quasi-acceptors, which are the basis for the third subgroup. A molecular compound based on a quasi-acceptor is structurally a mixed-stack molecular compound but lacks the characteristic charge-transfer band in its UV-visible spectrum and is not colored. The three subgroups merge into one another without sharply deﬁned boundaries.

Delocalized donor–acceptor interactions

Only electron transfer

Electron or proton transfer

Only proton transfer

Fig. 13.1. Schematic description of the various types of donor–acceptor compounds with delocalized interactions.

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Only electron transfer

Intermediate structures Ionic ground state

Segregated stacks

Ionic ground state

Neutral ground state

Radical cation salts

Mixed stacks

Radical cation, radical anion salts

Neutral ground state

Radical anion salts

Fig. 13.2. The types of molecular compound found when only electron transfer occurs.

For -compounds with ionic ground states we distinguish between proton transfer and electron transfer (Fig. 13.3). Only proton transfer occurs when the components are relatively strong acids and bases (e.g. aniline, pKb¼9.51; picric acid, pKa¼2.80) and here the binary compounds should be classiﬁed as organic salts rather than as molecular compounds. However, when the acid and/or base strength is reduced, a particular base–acid (donor–acceptor) pair may form a -molecular compound (with neutral ground state) at higher temperatures and a salt at lower temperatures. The terms ‘base/acid’ are to be interpreted in the Lewis sense for the molecular compounds and in the Lowry–Brønsted sense for the salts. For example, 1-bromo-2-naphthylamine and picric acid form red 1 : 1 crystals that melt at 180 C; these transform on cooling to a yellow compound stable below 117 C. It has been shown (Carsten-Oeser et al., 1968) that the red crystals are of a -compound while the yellow compound is presumed to be a salt (-molecular compounds are denoted ‘{donor picric acid}’ while salts are denoted ‘cation’ picrate, and similarly for analogous situations). Many other examples were studied in the 1930s by Hertel and his coworkers and have been discussed by Herbstein (1971) (see pp. 187–192). The crystal structures of -molecular compound and salt are likely to be appreciably different and so most phase transformations between them are likely to be (single crystal) ! polycrystal (see Section 16.11.3). Qualitative considerations based on spectral studies (Davis and Symons, 1965) and approximate calculations (McConnell et al., 1965) suggest that crystalline 1 : 1 mixed stack -molecular compounds are quite sharply divided into two classes, with nominally neutral or ionic ground states respectively. More elaborate calculations (Strebel and Soos, 1970) substantiate these conclusions; the situation in {TTF chloranil} near the neutralionic interface, has been considered in detail (Soos et al., 1986) and will be discussed later. The energies of the lowest charge transfer excitations for neutral (N) and ionic (I) compounds are (McConnell et al., 1965): n n n

n n n

h CT ðNÞ ¼ ðI AÞ he2 =ai h CT ðIÞ ¼ ðI AÞ þ ð2 1Þhe2 =ai

CL ASSIF IC ATION

Electron or proton transfer

Electron transfer

Proton transfer

Mixed-stack, neutral ground state

“True phenoxides”

929

Only proton transfer

Quaternary ammonium salts

Fig. 13.3. The possible types of molecular compounds that are formed when there is either electron or proton transfer, or only proton transfer. Only those ‘proton transfer salts’ that have a ‘-compound’ polymorph are included here. If, for example, there is hydrogen bonding between cation and anion, then the ‘proton transfer salt’ would belong more logically in Chapter 12.

where I and A are ionization potential and electron afﬁnity of donor and acceptor respectively (see Section 13.3.5 for discussion of these quantities), he2/ai is the averaged electrostatic attraction between neighboring donor and acceptor moieties (deﬁned to be positive) and is the Madelung constant for the structure. These formulae have been tested (Torrance et al., 1981) using the approximation that (I A), values of which are not always available, may be replaced by Eredox, the difference between the oxidation potential of the donor and the reduction potential of the acceptor. The experimental values of h CT have been plotted against Eredox (Fig. 13.4) and lie close to two separate straight lines as predicted. Thus mixed-stack molecular compounds form a class of materials which are either neutral or ionic, but which range from being near to the neutral–ionic boundary to being far away. McConnell et al. (1965) suggested that for a particular -compound the ionic ground state would be favored at high pressures and/or low temperatures. Indeed application of pressure does cause neutral ! ionic transitions (Torrance et al., 1981); critical pressures are given in Table 13.1. Furthermore {TTF chloranil} has been shown to undergo a neutral ! ionic phase change at 84K (Batail et al., 1981). General forms can be suggested for the temperature–pressure phase diagrams of mixedstack molecular compounds, based on the results reported for both electron-transfer and proton-transfer systems (Fig. 13.5). The crystal chemistry of mixed stack compounds, irrespective of the nature of the ground state, is described in Chapter 15 and some of their physical properties in Chapter 16. The segregated stack compounds can be divided into two chemical groups. In those with radical cations and closed-shell anions there is complete transfer of an electron from cation to anion; this is dictated by the requirement that the discrete closed-shell anions bear an integral charge. The same argument applies to closed-shell cation, radical anion salts. The radicals are often arranged in stacks in both types of salt. In the so-called simple salts (e.g. KTCNQ; Wu¨rster’s blue perchlorate TMPDClO4, both of which have stacked structures) each radical ion accepts (or loses) one electron; many different types of interaction between these electrons (holes) are possible along the stacks. In the so-called complex salts (e.g. Cs2(TCNQ)3) the stacks contain both radical ions and neutral molecules, which can sometimes but not always be distinguished in the crystal structures, there n n n

930

CHARGE TRANSFER MOLECULAR COMPOUNDS

(e 2/a)

3.0

(I –A ) Z

Charge transfer band

2.5

W

hCT (eV)

U

2.0

1.5

S

V

Y X

T

QR

D+ A–

D° A°

P

N D

C

1.0

K H E

A

L Simplest Theory Slope = 1

I

B F

0.5

Neutral

Ionic

0

M

–0.5

0

+0.5 +1.0 +1.5 ∆EREDOX (V)

+2.0

+2.5

Fig. 13.4. Experimental values of h CT (measured for the -compound in a KBr disk) plotted against Eredox (deﬁned in the text). The scale of Eredox is shifted with respect to that of (I A) in order to take solvation energy into account. The dashed line is the neutral–ionic boundary. The compounds are identiﬁed in Table 13.1. (Reproduced from Torrance et al., 1981.)

being generally extensive delocalization of the electrons or holes along the stacks at moderate temperatures. A new feature enters with radical cation, radical anion salts of equimolar composition, which contain segregated stacks of radical cations and of radical anions very similar to those found individually in the radical-ion closed-shell ion salts. The requirement for transfer of charge in discrete overall amounts from radical-cation stack to radical-anion stack no longer holds. This is because of the possibility of delocalization of charge between radical ions and neutral molecules within the stacks. This confers varied and interesting properties on these compounds including, as noted earlier, some remarkably high electrical conductivities. The characteristic feature is a marked anisotropy and these materials are often described as quasi-one dimensional. Structures and physical properties are discussed in Chapter 17. Finally there is a miscellaneous group of compounds, as yet limited in number, where the mixed stack or segregated stack description does not ﬁt very well. There are often incipient stacks, either mixed or segregated, but the anisotropy associated with essentiallyinﬁnite stacks is lost. These examples are considered at appropriate points within the coming chapters. 13.2.2

Intramolecular -compounds and self-complexes

Up to this point we have considered binary systems where one component is a donor and the second an acceptor. However, there is a group of compounds where donor and

CL ASSIF IC ATION

931

Melting point curve Liquid

Liquid

Temp.

Temp. Neutral

Ionic

Neutral

Solid state transition Pressure

Ionic Pressure

Fig. 13.5. Schematic representations of the T–P phase diagrams showing possible ﬁelds for the occurrence of neutral and ionic ground states for both ‘‘isomeric complexes’’ (proton transfer) and -compounds (electron transfer). In the type of phase diagram on the left there will be an enantiotropic1 I ! N transition, while for the type shown on the right there will be a I ! N transition only at higher pressures and the relationship between the two phases will be monotropic, with possible transitions above atmospheric pressure. In a third type of phase diagram (not shown) the I–N phase boundary occurs above the melting point for a range of pressures and the material is ionic at all temperatures in this pressure range; the form of the phase diagram may be more complicated at other pressures.

acceptor properties are located in different parts of the same molecule. These are called self-complexes (the term ‘autocomplexes’ is sometimes used, especially in translations from the Russian literature). Two types may be distinguished. The ﬁrst are molecules based on a cyclophane skeleton where one of the interacting units is a donor and one an acceptor. The advantage of working with molecules of this type is that donor and acceptor can be brought into propinquity in the same molecule in a ﬁxed (and determinable) orientation relationship; different mutual orientations of the same donor–acceptor pair can be obtained by synthesis of suitable cyclophanes. The interaction is thus intramolecular, although intermolecular interactions may also occur between different molecules in a crystal. This controlled and deﬁned intramolecular interaction should be contrasted with that normally occurring in solution, where it is probable that a range of orientations exists (Matsuo and Higuchi, 1968), or in the solid, where the donor–acceptor orientation depends on the overall crystal structure and where the interaction is generally within stacks rather than between pairs. These ‘intramolecular -compounds’ are discussed in detail in Chapter 14 under the title ‘‘Layered molecules’’. The second group comprises those molecules made up of linked donor and acceptor portions, the molecule as a whole being approximately planar (Bleidelis et al., 1976). Intramolecular charge transfer is possible when donor and acceptor portions are linked by 1 In a pair of enantiotropically related polymorphs one is stable over a particular temperature range (at a particular pressure, e.g. 1 atm.) and transforms into the other outside this temperature range but below the melting point; the transformation will be reversible (in theory, if not necessarily in practice). The details of the relationship will depend on pressure. In a pair of monotropically related polymorphs one is stable (at a particular pressure, e.g. 1 atm.) over the whole temperature range up to its melting point, and the other metastable. However, the metastable polymorph can often be obtained (cf. Ostwald’s rule) and may transform to the stable form below the melting point; the transformation is irreversible. The details of the relationship will depend on pressure.

CHARGE TRANSFER MOLECULAR COMPOUNDS

932

Table 13.1. Auxiliary information about the molecular compounds included in Fig. 13.4 (for acronyms see Table 13.2) Symbol

Compound

Neutral

A B

TMPD TCNQF4 Dimethylphenazine TCNQ TMPD TCNQ TMPD chloranil TMDAP TCNQ TTF chloranil TTF ﬂuoranil DibenzTTF TCNQ DEDTMSeF diethylTCNQ TMDAP ﬂuoranil TTF dichlorobenzoquinone perylene TCNQF4 perylene DDQ perylene TCNE perylene TCNQ TTF dinitrobenzene perylene chloranil pyrene TCNE pyrene chloranil anthracene chloranil HMB chloranil naphthalene TCNE pyrene PMDA anthracene PMDA anthracene TCNB phenanthrene PMDA n n n

I I

0.42 0.08

I N N N N N

I 0.13 0.17 0.29 0.34 0.36 0.39

N N N N N N N N N N N N N N N N N

Eredox/ Ionic

h CT(eV)

Pc (kbar)

0.96 0.89

Stacking

? Mixed

n n n

C D E F G H I J K L M N O P Q R S T U V W X Y Z

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

0.05

1.04

0.91 0.80

12 8 9 13 5

Mixed Mixed Mixed Mixed Mixed ? ?

0.4 0.48

0.99

19 21

? Mixed

0.5 0.55 0.84 0.87 0.99 1.05 1.14 1.35 1.36 1.57 1.62 1.91 1.92 2.01 2.38

0.97 1.08 1.38 1.33 1.55 1.53 1.57 2.00 1.97 2.36 2.17 2.47 2.42 2.50 2.95

11

? ? Mixed Mixed Mixed ? Mixed ? ? Mixed Mixed Mixed Mixed ? Mixed

1.03 0.93 0.73

18

35

a conjugated system. Intermolecular donor–acceptor interaction is possible in the crystal when the donor and acceptor portions of the self-complex are suitably oriented; for example in 1-phenyl-2-(methylthio)vinyl-2,4,6-trinitro-benzenesulphonate the interaction is pairwise (Meyers and Trueblood, 1969) while in 2-methyl-3-(N-methyl-anilinomethyl)1,4-naphthoquinone donor–acceptor stacking occurs (Prout and Castellano, 1970). This area is discussed in more detail in Chapter 15.

13.3 13.3.1

Chemical nature of donors and acceptors Introduction

Which molecules act as electron donors and which as electron acceptors in -molecular compounds? How is donor or acceptor quality measured and how is it enhanced or

CHEMICAL NATURE OF DONORS AND ACCEPTORS

933

Table 13.2. Acronyms in common use Electron donors

Electron acceptors

TDAE

BAQ

2,5-bis(methylamino)-p-benzoquinone

BTF DDQ DEQ HCBD PMDA TCNB

benzotrifuroxan 2, 3-dichloro-5,6-dicyano-p-benzoquinone 2,5-diethoxy-p-benzoquinone hexacyanobutadiene pyromellitic dianhydride 1,2,4,5-tetracyanobenzene

TCNE TCNQ TCPA TNB TNT TNP (PA)

tetracyanoethylene 7,7,8,8-tetracyanoquinodimethane tetrachlorophthalic anhydride 1,3,5-trinitrobenzene 2,4,6-trinitrotoluene 2,4,6-trinitrophenol (picric acid)

TMU TENF TNF TNAP

1,3,7,9-tetramethyluric acid 2,4,5,7-tetranitro-9-ﬂuorenone 2,4,6-trinitro-9-ﬂuorenone 11,11,12,12-tetracyanonaphthoquinodimethane

tetrakis(dimethylamino)ethylene DMA N,N-dimethylamine HMB hexamethylbenzene PD p-phenylenediamine DAD durenediamine TAB 1,3,5-benzenetriamine TMPD N,N,N 0 ,N 0 -tetramethylp-phenylenediamine TTF tetrathiafulvalene TTT tetrathiotetracene TSF tetraselenofulvalene TMTSF tetramethyltetraselenofulvalene BP 3,4-benzopyrene DBA 1,2,5,6-dibenzanthracene (dibenz[a,h]anthracene)

diminished by various substituents? Theory suggests that a good donor has a low ionization potential while a good acceptor has a high electron afﬁnity. Planarity of both donor and acceptor would be expected to enhance effective electron transfer. The broad effects of substituents have been known for many years (Martinet and Bornand, 1925); electrondonating substituents increase donor strength, and electron-withdrawing substituents diminish it, and conversely for electron acceptors. Nature, number and location of substituents are all important factors. There have been a number of qualitative studies of these questions and some results are summarized below; a quantitative approach would require measurement of thermodynamic parameters for the various molecular compounds but not enough information is yet available to permit a quantitative discussion. Donor and acceptor are really relative terms since a particular compound can act as a donor in some circumstances and as an acceptor in others. An extreme example is provided by aromatic hydrocarbons which usually behave as reasonably strong electron donors, but act as electron acceptors in the presence of the very powerful donor tetrakis (dimethyl-amino)ethylene (Wiberg, 1968). Acronyms for some donors and acceptors are given in Table 13.2. 13.3.2 Donors Various types are shown in Fig. 13.4. Aromatic hydrocarbons are the classic donor type; indeed formation of molecular compounds between aromatic hydrocarbons and picric acid

934

CHARGE TRANSFER MOLECULAR COMPOUNDS

or sym-trinitrobenzene provided for a long time the most widely used laboratory method for identiﬁcation and puriﬁcation of aromatics. Shinomiya (1940a) found the following order for the ability of aromatic hydrocarbons to form molecular compounds with polynitrobenzenes: naphthalene, pyrene, ﬂuoranthene > acenaphthene > benzene, phenanthrene > ﬂuorene > anthracene, chrysene. Complete planarity of the hydrocarbon is not essential as the acceptor can usually ﬁnd a reasonably planar region with which to interact; many -molecular compounds are formed by helicenes and substituted helicenes, e.g. hexahelicene 4-bromo-2,5,7trinitroﬂuorenone (Mackay et al., 1969); trithia[5]heterohelicene TCNQ (Konno et al., 1980). Electron donating substituents such as alkyl groups (if not too bulky), methoxy groups and, particularly, amino and dimethylamino groups considerably enhance the donor strengths of aromatic hydrocarbons. Tetramethylphenylenediamine (TMPD) is a powerful donor, forming molecular compounds with ionic ground states with acceptors such as chloranil and TCNQ. 2,7-Diaminopyrene is also a strong donor with a tendency to give molecular compounds with ionic ground states. Some qualitative studies have been made of the effects of various substituents in naphthalene on compound formation with various polynitrobenzenes (Shinomiya, 1940b). The following sequence was found for the effect of a substituent (in a given position in the naphthalene ring) on molecular compound formation: n n n

n n n

NH2 > CH3 > OH > C2 H5 > OCH3 > C1 > Br > OC2 H5 > H > COOH > COOCH3 > OC6 H5 > CN > COOC6 H5 > NO2 : Substitution in the 1-position tended to favor molecular compound formation while substitution in the 2-position sometimes hindered. Somewhat similar comparisons have been made for the picric acid compounds of polymethylbenzenes and of polyhydroxybenzenes and naphthalenes, and of some aromatic hydrocarbons (Baril and Hauber, 1951). For benzene derivatives the tendency to compound formation is greater the larger the number of methyl substituents and the more symmetrical their disposition in the ring. Methyl groups were found to be even more effective in side chains than in the ring, a perhaps surprising result. Unsaturation in the side chains produced very explosive picrates! However, it should be appreciated that these considerations are intrinsically qualitative as they rest on the formation of crystalline molecular compounds, without taking into account their structures, which may be very varied. Polycyclic hydrocarbons forming molecular compounds can be divided into the following groups: (i) Planar aromatic hydrocarbons, e.g. benzene, naphthalene, anthracene, phenanthrene, pyrene, perylene. (ii) Nonplanar aromatic hydrocarbons, e.g. the helicenes, heterohelicenes, 9,10-dihydroanthracene. (iii) Substituted aromatic hydrocarbons, e.g.

CHEMICAL NATURE OF DONORS AND ACCEPTORS

935

NH2

(H3C)2N

N(CH3)2

2,7-diaminopyrene

TMPD NH2

(iv) Heteroaromatics and related compounds, e.g. N

S N

acridine

S

S

S

S

tetrathiafulvalene (TTF)

H phenothiazine

X

X

X X tetra-X-tetracene: X = S thia Se selena Te tellura

N

O

H 1,2,3,4-tetrahydro1-oxocarbazole

N OH carbostyril (lactam form)

Heteroaromatic donors, mainly with nitrogen and oxygen substitution, have been known for many years while sulphur-containing molecules have become very important recently. Tetrathiafulavalene (TTF) and derivatives act as donors in many radical-cation salts and, of course, in {[TTF][TCNQ]} (see Chapter 17 for formulation), arguably the most-widely studied of the ‘organic metals’. The effects of chemical modiﬁcation of TTF will be illustrated later (Chapter 17). Another important donor containing sulphur is tetrathiatetracene; Se and Te analogs have also been prepared (Sandman et al., 1982). Among other donors are various metallocenes, including ferrocene, dibenzene chromium and tricarbonylchromium anisole, porphyrins and coordination complexes (e.g. metal oxinates with Cu(II), Pd(II) and Ni(II) as the metal atoms). 13.3.3 Acceptors Acceptors are conveniently grouped on the basis of fundamental structures to which substituents have been appended in various ways. The fundamental structures are ethylene, p- and o-benzoquinone, cyclopentadienone, benzene, naphthalene and ﬂuorene. The most important electron-withdrawing substituents are nitro, cyano, halo, anhydride, furoxan and furazan groups. We give below a selection of proven and potential acceptors. Synergistic interaction of various substituents seems to be an important factor in the formation of electron acceptors. For example, maleic anhydride, phthalic anhydride and

CHARGE TRANSFER MOLECULAR COMPOUNDS

936

hexachlorobenzene do not form stable -compounds with aromatic hydrocarbons while tetrachlorophthalic anhydride (TCPA) is a powerful electron acceptor. Unsymmetrical substitution, as in DDQ, enhances the effectiveness of electron acceptors, presumably because dipole and polarization interactions also contribute to the stability of the molecular compounds, in addition to the charge transfer interactions. (a) Substituted oleﬁns Examples are TCNE, TCNQ and hexacyanobutadiene (HCBD). Of these TCNQ is undoubtedly the most prominent and occurs not only as the radical anion in many charge transfer salts and organic metals but also as a neutral acceptor in many mixed stack -molecular compounds (for some other formulae see Section 17.2.3). O O

O

O R'

NC

CN

NC

CN

CN

NC

O

O

O

CN

O

O

CN

NC

TCNE

HCBD

NC

R NC

R

CN CN

CN

R

NC

CN NC

a: R = R' = H; b: R = NO2, R' = H; c: R = R' = NO2.

CN

NC

TCNQ

CN TNAP

(b) Substituted aromatic hydrocarbons Substituted polynitrobenzenes (e.g. TNB, picric acid) are the best known members of this group but polynitro naphthalenes and ﬂuorenes also form molecular compounds. Anhydrides of benzene and naphthalene polycarboxylic acids are important acceptors, as well as polycyanobenzenes. X O2N

NO2

O O2N

C O

X = H, OH, CONH2 NO2 X O2N

NO2 Y NO2

X = H, OH, CH3, Cl, Br, I, NH2, (N ≡ N); Y = H; X = Y = OH.

2

CHEMICAL NATURE OF DONORS AND ACCEPTORS

O2N

NO2

NO2

O2N

NO2 NO2 O2N

NO2

O O N

O

N

N

N

N

N

O O

O

N

N

N

N

O N

O

O

N

benzotrifuroxan ( BTF).

NC

CN

NC

CN

N N

CN

N CN

CN NC

CN

NC

CN

NC

CN

NC

CN TCNB

CN X

X

O

O

O O

O

O X

O

O

X

O

X = H, F, Cl, Br or I X = Cl: TCPA X

X

X

X O

O

various anhydrides

O

X

O O

O O

O

O

mellitic trianhydride

X

X

O

O

X X = H: PMDA

O

937

CHARGE TRANSFER MOLECULAR COMPOUNDS

938

(c) Unsubstituted and substituted quinones Most attention has been paid to the tetra-substituted p-benzoquinones (see also Section 17.2.3 (v)), the less stable o-benzoquinones having been largely ignored; ﬂuorenones, naphthoquinones, phenanthraquinones and anthraquinones have also been studied. Two vicinal triones are relatively new, powerful acceptors and have been shown to form 1 : 1 molecular compounds with pyrene (Gleiter and Schanz, 1980). We have already noted that the quinhydrones (Section 15.7.1), and {aromatic hydrocarbon quinone} molecular compounds (Section 15.6) are best treated as separate groups. n n n

O

O

O

X'

X

X'

NO2

O2N

O a: X = X' = F, Cl, Br, I, CN or CH3. b: X = Cl; X' = CN. O

O

O

X

O

O

Cl Cl

O O Cl

Cl

O Cl

O

O

O

O

Cl

Cl Cl

O

Cl

Cl O

O

O O

X

O

X

X

X X = Cl, CN

R

O O R

R' a: R = NO2, R' = H. b: R = H, R' = NO2.

R' Substituted o-benzoquinones and phenanthraquinones

O

O

O

O O

O

O

O

O

O O

O

1,2,3,5,6,7-s-hydrinacenehexone 1,2,3,6,7,8-pyrenehexone

(d) Cyclopentadienone systems The last of the molecules shown in this section is of particular interest because it contains an asymmetric carbon atom (asterisked); the presence of the carboxyl group allows resolution into enantiomers which can be used for the formation of diastereoisomeric -complexes with nonplanar overcrowded aromatic hydrocarbons. The resolved aromatics can then be recovered (Newman and Lutz, 1956).

CHEMICAL NATURE OF DONORS AND ACCEPTORS

R'

939

R

Cl

Cl

Cl

R

R

Cl Cl Cl

O a: R = R⬘= H; b: R = NO2, R⬘= H; c: R =R⬘= NO2.

O Cl

Cl

Cl R'

R

Cl Cl Cl O2N

O2N

O NO2

R

NO2

R O a: R = R⬘= H; b: R = NO2, R⬘= H; c: R = R⬘= NO2.

OC∗H(CH3)COOH

(e) Chelates Chelates act as acceptors in some -molecular compounds; examples are bis(diﬂuoroborondimethylglyoximato)Ni(II) (on the left), metal bis(dithiolene) (on the right, where M ¼ Ni, Pd, Pt) and bis(cis-1,2-triﬂuoro- methylethylene-1,2-dithiolato)Ni(II). The chemistry of the dithiolenes and related species and their metal complexes has been comprehensively reviewed (Mueller-Westerhoff and Vance, 1987). F

F B O

O N

N

R

S

Ni N

R

M N

O

S

R

S

S

R

O B

F

F

13.3.4 Quasi-acceptors Three groups of molecular compounds are known which are structurally similar to the mixed stack -donor–acceptor molecular compounds but do not show charge transfer bands in their absorption spectra. The donors are regular donors of the -compound series and thus any difference in properties must derive from the second component, which we call a quasi-acceptor.

CHARGE TRANSFER MOLECULAR COMPOUNDS

940

The ﬁrst quasi-acceptor type is a halogenated aromatic hydrocarbon; the perﬂuorinated molecules hexaﬂuorobenzene, octaﬂuoronaphthalene and decaﬂuoro-biphenyl are the best known examples, especially C6F6, and the structures of their molecular compounds will be described later (Section 15.9.1). Decachloropyrene perhaps behaves in a similar way but other examples are not known. O CH3

O

CH3 H

N

N

CH3

N O

O

N CH3

N

O

CH3

N

N

H

1,3,5,7-tetramethyluric acid (TMU)

caffeine

CH3 N

N

O

N N

CH3

O 1,3-dimethylalloxazine

The second type is based on the purines 1,3,7,9-tetramethyluric acid and caffeine; some pyrimidines may play a similar role. Mixed stack molecular compounds of aromatic hydrocarbons and heteroaromatics with TMU and caffeine have been prepared (WeilMalherbe, 1946; Booth and Boyland, 1953) and some crystal structures are known (Section 15.9.2). These have mixed stack structures but there is no charge transfer band in solution or solid state spectra. Pyrene, TCNE and DDQ form 1 : 2 molecular compounds with 1,3-dimethylalloxazine but the varying nature of the ﬁrst component suggests that further study is needed before these can be reliably classiﬁed. The third group is based on the ﬂavins as quasi-acceptors. Various iosalloxazine derivatives have been reported to form molecular compounds of different types with electron donors such as phenols. The chemistry and structures of these molecular compounds are discussed in Section 15.7.2. 13.3.5

Ionization potentials of donors and electron afﬁnities of acceptors

The ﬁrst ionization potential (or energy) of a molecule is deﬁned as the energy which is required to remove an electron from the highest occupied molecular orbital (HOMO) of the neutral molecule in its ground state and is denoted I1. It is thus the enthalpy of the reaction D ! Dþ þ e (infinitely separated):

CHEMICAL NATURE OF DONORS AND ACCEPTORS

941

The electron afﬁnity (EA) of a molecule is deﬁned as the difference in energy between the ground state of the neutral molecule plus an electron at rest at inﬁnity, and that of the negative ion. It is thus the enthalpy of the reaction A þ e ! A The electron afﬁnity of a stable negative ion is deﬁned as positive, although this contradicts the usual thermochemical sign convention. The difference in energy between the lowest vibrational level of the ground state of the neutral molecule and the corresponding level of the cation or anion is termed the ‘adiabatic ionization energy’, or ‘adiabatic electron afﬁnity’, respectively. The energy difference between the energy level of the ground state and that part of the potential curve to which, on applying the Franck–Condon principle, transition is most likely to occur is denoted the ‘vertical ionization energy’ or the ‘vertical electron afﬁnity’ as the case may be. Photoelectron spectroscopy, for example, gives the vertical ionization energy. Experimental and calculated values of ionization potentials and electron afﬁnities have been tabulated (Blaunstein and Christopherou, 1971; Rosenstock et al., 1980). Reasonably accurate values of ionization potentials have been available for many materials for some time; in the last few years many new values have been obtained and there has been a marked increase in accuracy stemming from widespread application of photoelectron spectroscopy (Eilfeld and Schmidt, 1981). Selected values for donors of interest here are given in Table 13.3. There has been considerable confusion about the correct absolute values of electron afﬁnities and two rather different sets of values were proposed at one point (Briegleb, 1964; Batley and Lyons, 1962). However, these can be correlated and put on an absolute scale (Chen and Wentworth, 1975) and absolute electron afﬁnity values have been calculated for about 150 electron acceptors from measurements of charge transfer spectra and half-wave potentials (Table 13.4, which also includes some more recent values). It is illuminating to compare typical values of I1 and EA for organic donors and acceptors with those for alkali metals and halogens. For a typical organic donor I1 7 eV, whereas for Li I1 ¼ 5.4 eV and for Cs I1 ¼ 3.4 eV; for the best organic acceptors EA 2.8 eV, while EA for ﬂuorine is 3.4 eV and for iodine 3.2 eV. Thus it is somewhat more difﬁcult to form cations from organic donors than from alkali metal atoms, and also somewhat less advantageous to form anions from organic acceptors than from halogen atoms. The values of ionization potential and electron afﬁnity given in Tables 13.3 and 13.4 refer to isolated gaseous molecules and we shall denote them as IG and EAG respectively. However, the appropriate ionization potentials for molecules in crystals (IC) will be less than those for isolated molecules because of polarization effects in the crystals. Similarly the electron afﬁnity of a molecule in a crystal (EAC) will be greater than that of a molecule in the gas phase because of polarization. Thus we can write IC ¼ IG – P, where P is the polarization energy; similarly EAC ¼ EAG þ P*, where both P and P* are positive quantities. P and P* depend on the polarizabilities of the molecules involved as well as on the crystal structures. Gutmann and Lyons (1981) have given a detailed discussion; the following values (Table 13.5) for P (for a single charge) are quoted from them and other sources. A comprehensive set of values of P has been determined by ultraviolet photoelectron spectroscopy (examination of line widths of the spectra) for 44 organic

CHARGE TRANSFER MOLECULAR COMPOUNDS

942

Table 13.3. First -ionization potentials (eV) for some aromatic hydrocarbons and other molecules. Values from Schmidt (1977) unless stated otherwise. Method is photoelectron spectroscopy (PES) unless stated otherwise Molecule

I1

Molecule

I1

Molecule

I1

benzene naphthalene

Perylene (CS77) Ovalene (BL62)

6.97 6.71

Coronene (BL62) Diphenyl (R81)

7.29 7.95

Biphenylene (BCS74)

7.61

hexamethylbenzene (R80)

7.8 (CTS)

tetracene

9.24 8.15 8.12 (adiabatic) (SSI81) 7.41 7.36 (adiabatic) (CBS72) 6.97

6.83

TDAE

6.5

pentacene

6.61

Tetrathiofulvalene (R80) Graphite (BL62)

4.9

6.28 (ETR)

phenanthrene

7.86

chrysene

7.59

triphenylene phenothiazine1

7.88 6.54 (ETR)

benzo[c]phen-anthrene N,N,N 0 ,N 0 -tetramethylbenzidine (CS77)

7.60 6.48 (ETR)

N,N-dimethyl-pphenylenediamine (BCS74) 1,2,7,8dibenzochrysene Pyrene (CS79)

anthracene

7.20 7.41

Notes: PES photoelectron spectroscopy (molecule in gas phase); accuracy 0.02 eV for I < 10 eV; vertical ionization potential is measured. CTS charge transfer spectrum (molecule in solution). ETR electron transfer reactions (molecule in solution); adiabatic ionization potential is measured. References: B74 – Boschi et al., 1974; BL62 – Batley and Lyons, 1962; C72 – Clark et al., 1972; CS77 – Clar and Schmidt, 1977; CS79 – Clar and Schmidt, 1979; R80 – Rosenstock et al., 1980; SSI81 – Sato et al., 1981.

solids (Sato, Seki et al., 1981); the values of P ranged from 0.9 to 3.0 eV. Planar condensed aromatic hydrocarbons appeared to have a common value of 1.7 eV. These values refer to the crystals of the pure components and somewhat different values would be expected to apply to these molecules in the crystals of the charge transfer molecular compounds. Measurements of photoelectric emission thresholds for neutral and ionic charge transfer compounds give values of P for anthracene and perylene in some of their molecular compounds as well as in their neat crystals (Batley and Lyons, 1968) and these values are also included in Table 13.5. Taken at face value these numbers would appear to mean that the donor qualities of anthracene are enhanced (by 0.2–0.4 eV) in its PMDA and TCNQ charge transfer molecular compounds compared to its behaviour in its neat crystals while those of perylene are diminished in its chloranil and PMDA -compounds. Analogous values for electron acceptors (P*) are hardly available as measurement of the solid state electron afﬁnity is very difﬁcult. Nevertheless the electron afﬁnity of PMDA in PMDA molecular compounds has been estimated as 3.6(3) eV (Stezowski et al., 1986).

CHEMICAL NATURE OF DONORS AND ACCEPTORS

943

Table 13.4. Electron affinities (eV). Most of the values have been taken from the more extensive collection in Table III of Chen and Wentworth (1975); these are charge transfer spectrum (CTS) values except where noted otherwise (PDS photodetachment spectra, E1/2 half wave potentials) Molecule

EA

Molecule

EA

Molecule

EA

p-benzoquinone

1.83 2.62

1.09 (PDS) 2.57

p-bromanil

2.48

TCNB

2.00

DDQ (CS77) p-chloranil p-iodanil

hexacyanobenzene p-ﬂuoranil hexacyanobutadiene

2.56 2.45 3.09

duroquinone

3.13 2.48 2.43 (E1/2) 1.67

2,4,7-trinitroﬂuoren-9-one 2,4,5,7-tetranitroﬂuoren-9-one 2,4,5,7-tetranitroﬂuorenemalononitrile TCNE TCNQ tetraﬂuoro-TCNQ

2.17

o-bromanil

Hexaﬂuorobenzene (SH80) o-chloranil

2.82

2,5-diﬂuoro-TCNQ (SF79)

tetranitromethane

1.63

2,3-dicyano-5,6dicyano-7-nitro-1, 4-naphthoquinone TNB

1.73

TNT 1,4,5,8naphthalene tetracarboxylic acid anhydride

1.67 2.28

TCPA mellitic trianhydride

1.72 2.38

tetrabromophthalic anhydride PMDA dibromo-PMDA

2.24 (E1/2) 2.56 2.77 2.84 3.22 (E1/2) 3.02

1.72 2.04 2.23

References: CS77 – Clar and Schmidt, 1977; SF79 – Saito and Ferraris, 1979; SH80 – Sowada and Holroyd, 1980.

Table 13.5. Values of polarization energy P (in eV) for aromatic hydrocarbon molecules in their neat crystals (values from Gutmann and Lyons (1981), except where noted otherwise) and in some -molecular compounds (values from Batley and Lyons (1962), except where noted otherwise) Molecule in its neat crystals

P

naphthalene phenanthrene tetracene chrysene pyrene coronene anthracene

1.3, 1.4 2.1, 2.1, 1.7, 2.4, 1.8,

Molecule in some -molecular compounds

P

anthracene PMDA anthracene TCNQ perylene PMDA perylene chloranil

2.16 2.39 1.81 1.57

1.7 (SSI81) 1.57 (S81) 1.7 (SSI81) 1.6 (SSI81) 1.7 (SSI81) 1.61 (KSS82)

n n n

n n n

perylene

1.9, 1.6 (SSI81)

n n n

n n n

References: KSS82 – Karl, Sato, Seki and Inokuchi, 1982; S81 – Silinski, 1981; SSI81 – Sato, Seki and Inokuchi, 1981.

944

13.3.6

CHARGE TRANSFER MOLECULAR COMPOUNDS

Determination of degree of charge transfer

The degree of charge transfer (Z) from donor to acceptor, giving compositions DZþAZ (where 0 Z 1), is a quantity of prime importance in the discussion of delocalized charge transfer molecular compounds. The lattice energy, the conductivity, the nature of a possible Peierls transition, the type of ESR spectrum, are all heavily dependent on this parameter. A number of methods of general applicability have been used for determining Z. One method relies on diffraction studies and uses the differences in bond lengths between neutral and ionic forms of donor and acceptor moieties; two other methods rely on spectroscopic studies, one using the dependence of selected stretching frequencies on moiety charge, while the other uses the dependence of the oscillator strength of the charge transfer band on moiety charge. Photoelectron spectroscopy has been used to demonstrate the presence of two charge states but is not suitable for quantitative determination of Z. The most accurate method is based on analysis of diffuse x-ray (or neutron) scattering and will be discussed in Chapter 17. Dependence of moiety bond lengths on charge is shown in Table 13.6 for some donor and acceptor moieties. Clearly TMPD becomes more quinonoid and TCNQ more benzenoid on passing from neutral molecule to ion; this is in accordance with theoretical calculations for TMPD (Haddon, 1975) and TCNQ (Johanson, 1975). Four equations have been proposed for estimation of Z from changes in various bond lengths in TCNQ ((1) Flandrois and Chasseau, 1977; (2) Umland et al., 1988 extending an earlier proposal of Coppens and Guru Row, 1978; (3) Kistenmacher et al., 1982; (4) derived here from values in Table 13.6): ZTCNQ ¼ 7:25ðb cÞ 8:07ðc dÞ 1 ZTCNQ ¼ 26:24 29:92½ða þ cÞ=ðb þ dÞ

ð1Þ ð2Þ

ZTCNQ ¼ 19:83 41:67c=ðb þ dÞ ZTCNQ ¼ 1:374 þ 8:13fðb þ dÞ ða þ cÞg

ð3Þ ð4Þ

There seems little reason to prefer one or other of these equations at the available levels of precision of bond length measurements. One should note that all the equations assume a linear dependence of Z on dimensions, which is surely an over simpliﬁcation. The values of the coefﬁcients depend on the bond lengths used for neutral and ionic moieties, only one set being available for the neutral molecule but a number for the ionic moiety as it appears in different closed-shell salts; presumably it would be best to take a weighted average of the latter but such sophistication seems premature at the available levels of precision. It is possible to identify the most sensitive parameters (‘discriminators’) from the dimensions given in Table 13.6. We illustrate some of the problems by using {[TTF][TCNQ]} as an example, its crystal structure having been determined at a number of temperatures. We have used bonds (a) and (b) of TTF as standards although it has been suggested by Mayerle et al., (1979) that the ring double bond (d) is more sensitive, based ˚ in {[TTF][TCNQ]} and 1.336 A ˚ in TTFI0.71. Parenthetically, on values of 1.323(4) A we had considered TTFClO4 for use as our reference cation because four independent values are available for each bond length; however, using the ring double bonds as an ˚ , with a clearly example, we ﬁnd values of 1.292(20), 1.305(15), 1.306(17) and 1.321(13) A unacceptable spread.

CHEMICAL NATURE OF DONORS AND ACCEPTORS

945

Table 13.6. Dimensions of neutral and ionic forms of representative donor and acceptor moieties. The ionic forms are for salts where the counterion is a closed shell ion with an assumed integral ˚ ) are not corrected for thermal motion and have been averaged single charge. The bond lengths (A assuming D2h symmetry. Values in brackets are experimental standard uncertainties divided by 1 ðn 1Þ2 where n independent values have been averaged. l ¼ lion–lneutral. Equations showing the dependence of moiety charge (Z) on bond lengths (a, b, c, d ) are given; the constants have dimensions such that Z is dimensionless. The values of a etc. in the equation for Z are those for the species under consideration Moiety

Bond

l (neutral molecule)

l (ion)

l

TMPD

a b c

A (IK79) 1.390(5) 1.397(5) 1.418(6)

B (dBV72) 1.363(2) 1.428(2) 1.345(2)

0.026(5) þ0.031(5) 0.073(6)

a b c d

C (CK71) 1.349(3) 1.757(2) 1.730(2) 1.314(3)

D (YN80) 1.404(10) 1.713(3) 1.725(4) 1.306(8)

þ0.055 0.042 0.005 0.008

a b c d C N

E (LST65) 1.346(3) 1.448(2) 1.374(3) 1.441(3) 1.140(2)

F (HSV72) 1.373(1) 1.423(3) 1.420(0) 1.416(8) 1.153(2)

0.027(3) þ 0.025(3) 0.046(2) þ 0.025(6) þ 0.013(3)

a b

Me2N

c

NMe2

ZTMPD ¼ 10.85 7.69(c þ a b) TTF S S

Sc b d a S

ZTTF ¼ 3.835 9.174(b a) TCNQ NC

c a

NC

b

CN d CN

See text for equations for ZTCNQ. Notes: A. TMPD0 at 298K; B. TMPDClO4 at 110K; C. TTF0; D. TTFClO4; E. TCNQ0 at 300K, libration corrected; F. Rb TCNQ at 113K. References: CK71 – Cooper, Kenny, Edmonds, Nagel, Wudl and Coppens, 1971; dBV72 – de Boer and Vos, 1972; HSV72 – Hoekstra, Spoelder and Vos, 1972; I79 – Ikemoto, Katagiri, Nishimura, Yakushi and Kuroda, 1979; LST65 – Long, Sparks and Trueblood, 1965; YN80 – Yakushi et al. 1980.

We illustrate possible use of discriminator bonds (a) and (b) of TTF and (c) and (d) of TCNQ by plotting these in Fig. 13.6, together with ‘standard’ values (300K) for the neutral and ionic moieties. The differences between paired bond lengths in the neutral and ionic moieties are only a few times the standard uncertainty of the measurements. If we make the approximation (permissible in terms of the available precision) that bond lengths are not dependent on temperature, then using mean values we calculate that jZTCNQj ¼ 0.41 (eq. 1), 0.37 (eq. 2), 0.44 (eq. 3) and 0.39 (eq. 4). Although the internal agreement is satisfactory, the accepted value of jZj (from X-ray diffuse scattering

CHARGE TRANSFER MOLECULAR COMPOUNDS

946

TTF 1.42 1.40

Bond (a)

cation

TCNQ 1.46

1.38

Bond (d) 1.44

1.36

neutral neutral

1.42

anion

neutral

1.42

anion

1.34 1.75

1.40

1.74

1.38

1.73

1.36

1.72

Bond (b)

cation 1.71

Bond (c)

0

100

neutral 0

100 200 300 T (K)

200 300 T (K)

˚ ) of two discriminator bond lengths in each of Fig. 13.6. The ordinates show measured values (A the TTF and TCNQ moieties of {[TTF][TCNQ]} at 300K (Kistenmacher et al., 1974) and at 100, 60, 53 and 45K (Schulz et al., 1976). The standard values deduced for these bonds in the anionic and neutral species are shown at the left and right extremes of the temperature scale and the measured values at the appropriate temperatures. The horizontal broken lines show the bond lengths corresponding to Z ¼ 0.59 deduced from x-ray diffuse scattering measurements. See text for discussion.

(Section 17.7)) is 0.59. It is clear that much higher precision is required for all bond length measurements if meaningful conclusions are to be extracted. The spectroscopic methods have been applied mainly to TTF and TCNQ, and we summarize the conclusions in Table 13.7. Again a linear dependence of Z on frequency is assumed. For example, resonance Raman measurements of the frequency of the exocyclic C¼C bond stretch ( 4) show this to be 1454 cm1 for neutral TCNQ (Van Duyne et al., 1979) and 1379 cm1 for TCNQ (Matsuzaki, Kuwata and Toyoda, 1980). Linear interpolation gives ZTCNQ ¼ –0.01333 C¼C þ 19.39. As the resolution of the spectroscopic methods is 1–3 cm1, a precision of 0.01 in Z can be expected. However, solid-state (crystal ﬁeld) effects can alter vibration frequencies by 10 cm1. We also note that (C N) is very sensitive to the degree of charge transfer, in contrast to d(C N). Photoelectron spectroscopy using deconvolution of N-1s and S-2p spectra demonstrates the presence of neutral and charged moieties in segregated stack molecular compounds. This is illustrated for {[TMTTF][TCNQ]} in Fig. 13.7 (Tokumoto, Koshizuka, Murata, Kinoshita, Anzai, Ishiguro and Mori, 1982; Tokumoto, Koshizuka, Anzai and Ishiguro, 1982). Unfortunately the method does not give reliable quantitative results (Ritsko et al., 1978).

CHEMICAL NATURE OF DONORS AND ACCEPTORS

947

Table 13.7. Determination of degree of charge transfer by spectroscopic techniques (neutral species) cm1

(ionic species) cm1

(Charge transfer)/frequency relationship

TTF Raman, ag 3, predominantly C¼C stretch 1515 (S80) 1413 (MMT80)

ZTTF ¼ –0.00980 C¼C þ 14.85.

TCNQ Resonance Raman, 4 exocyclic C¼C stretch 1454 (VD79) 1379 (MKT80)

ZTCNQ ¼ –0.01333 C¼C þ 19.39

TCNQ IR Absorption C N stretch 2227 (CB81) 2183 (CB81)

ZTCNQ ¼ –0.02273 C N þ 50.61

TMTTF-TCNQ

TMTTF+

S 2p

TMTTF0

170 165 BINDING ENERGY (eV)

EMISSION INTENSITY (ARB. UNITS)

EMISSION INTENSITY (ARB. UNITS)

References: CB81 – Chappell et al., 1981; MKT80 – Matsuzaki, Kuwata and Toyoda, 1980; MMT80 – Matsuzaki, Moriyama and Toyoda, 1980; S80 – Siedle et al., 1980; VD79 – Van Duyne et al., 1979.

TMTTF-TCNQ

N Is

TCNQ– TCNQ0

405

400 BINDING ENERGY (eV)

Fig. 13.7. Core level XPS spectra for {[TMTTF][TCNQ]} after data processing. Observed spectra are given by dotted lines, simulated spectra by full lines, and the individual moiety spectra by chain lines. The latter are obtained from TMTTF, {[TMTTF][(DDQ)2]}, TCNQ and K-TCNQ. (Reproduced from Tokumoto et al., 1982.)

It has also been suggested that the value of Z can be obtained from measurement of the oscillator strength ( f ) of the charge transfer band (Jacobsen and Torrance, 1983). The relation between them is f ¼ f82 mc CT j RDA j2 Zg=h ¼ 3:254 105 CT j RDA j2 Z ˚ ) between the centers of the donor and acceptor molecules where RDA is the distance (A and CT is the excitation energy of the charge transfer band in cm1. The oscillator strength is measured from Z 4mc 2 ð Þ cos2 d ; f ¼ Ne2 1

948

CHARGE TRANSFER MOLECULAR COMPOUNDS

where N is the number of DA pairs per unit volume and is the angle between the direction of light polarization and the transition dipole moment (Wooten, 1972). Results obtained by this method are given in Section 17.4 to demonstrate that a neutral to ionic phase transition occurs in {TTF chloranil}. Some care is needed in using the values of Z derived by these methods as systematic errors can occur. Cross checking of one method against another is always desirable. n n n

13.4 13.4.1

Binary and quasi-binary donor–acceptor systems Phase diagrams

Most charge transfer molecular compounds have been prepared by what are essentially hit-or-miss techniques – mix the components in a particular ratio in a suitable solvent and hope that the binary compound will crystallize. However, careful studies, involving determination of the phase diagram of the system, are now becoming more common. Ideally both the binary phase diagram, which covers a wide range of temperatures, and the ternary (D-A-solvent) phase diagram, at a particular or limited number of temperatures, should be determined, but this has rarely been done. The ternary phase diagram will give more reliable results in the lower temperature regions where solid–solid transitions are likely to be slow. In older work melting point diagrams were determined, perhaps with the addition of thaw points; in modern work use of differential scanning calorimetry (DSC) has greatly improved both the precision and the reliability of the results. Quite complicated binary diagrams can sometimes be obtained, as exempliﬁed by that of carbazole/ 2,4,7-trinitroﬂuoren-9-one (Fig. 13.8; Krajewska and Pigon, 1980); we maintain our D/A nomenclature despite the converse usage in Fig. 13.8. This shows such typical features as a 1 : 1 molecular compound with congruent melting point and a 1 : 2 molecular compound

500 T (K)

450

TNF

2:1

1:1

carbazole

mole per cent

Fig. 13.8. Phase diagram for the carbazole-TNF system. Liquidus and eutectic lines; peritectic lines; --ø--ø-- phase transition line. (Reproduced from Krajewska and Wasilewska, 1981.)

B I NA R Y A N D Q UA S I- B I NA R Y D O N O R – A C C E P T O R S YS T E M S

I

IX

140

L

II

Temperature, °C

A II

30

10

20

30

10

20

30

10

20

30

10

20

30

I

100 I

20

P P

P

P

10 P

120 I

949

II

I,I I

A

80 II II,II II

60 P

I

II

A

40 A A 0

20

40 60 Mol %

80

100

2

Fig. 13.9. (a) on left: Phase diagram for the mixed donor system (phenanthrene/anthracene)–picric acid: x single phase from Debye–Scherrer patterns; two phase from Debye–Scherrer patterns. Mol.% anthracene runs from zero on the left to 100% on the right. Greek letters (, , ) indicate phases stable at increasing temperatures; (b) on right: Debye–Scherrer patterns (Cu K) from the phases found in the phase diagram. In order from top to bottom these show (i) the three phases of phenanthrene-picric acid and solid solutions (ii) the three patterns from the phases of intermediate solid solution I (iii) the three patterns from the phases of intermediate solid solution II (iv) the two patterns from anthracene-picric acid and solid solutions. The very simple patterns of P and I have been interpreted as indicating that these are plastic phases (see Section 16.5). (Reproduced from Koizumi and Matsunaga, 1974.)

with incongruent melting point (in some systems ratios other than 1 : 1 or 1 : 2 are found but these are relatively rare). The 1 : 1 compound is more stable than the 1 : 2 compound, which is the usual situation. The composition ranges of both compounds appear negligibly small (although it should be remembered that the methods used are generally not sensitive to composition differences of less than 1%). The 1 : 1 compound shows a solid state transition at about 460K; transitions below room temperature are also often found (see Chapter 16). Despite the improvements in methodology, controversy has not been entirely eliminated; for example, a phase diagram has been reported for the pyrene/picryl chloride system which shows DA, D4A3, D2A and D4A compounds (only DA melts congruently) (Bando and Matsunaga, 1976) while other workers could ﬁnd only DA and D3A2 compounds (Krajewska and Wasilewska, 1981). Sluggishness in the attainment of equilibrium and problems of identiﬁcation of incongruently melting compounds from small breaks in the liquidus curves can give rise to many difﬁculties. The binary phase diagram summarizes an appreciable amount of information about a system, and is always a desirable preliminary to a detailed study of the structure and/or

CHARGE TRANSFER MOLECULAR COMPOUNDS

950

L

L

S 200

t /°C

200 S

S

100

S

100 S

Py-TNB

Mol%

Py-TNP FI-TNB

FI-TNP

Mol%

Fig. 13.10. Phase diagrams for the mixed acceptor systems pyrene–(TNB, TNP) and ﬂuoranthene– (TNB, TNP) (TNP ¼ 2,4,6-trinitrophenol or picric acid). The crystal structure of pyrene TNB is known. (Reproduced from Inabe et al., 1981.) n n n

properties of a particular charge transfer molecular compound. Many such diagrams are available for mixed stack systems (for examples, see Herbstein, 1971; D’Ans and Kaufmann, 1956; Koﬂer, 1956; Radomska and Radomski, 1980a, b). There do not appear to be any phase diagrams for segregated stack systems but there are some for ‘‘complex isomers’’ e.g. 1-bromo-2-naphthylamine/picric acid (Hertel, 1926); 4-bromo-1-naphthylamine/ 2,6-dinitrophenol (Hertel and Van Cleef, 1928); o-bromoaniline/picric acid (Komorowski et al., 1976). Although the donor : acceptor ratio appears to be ﬁxed at a ratio of small integers in the charge transfer molecular compounds, it is possible to replace to a considerable extent one donor by another, and the same holds for suitable pairs of acceptors. Thus about 60% of the phenanthrene molecules can be replaced by anthracene in the {phenanthrene TNB} compound, and about 20% of the anthracene molecules in {anthracene TNB} can be replaced by phenanthrene (Lower, 1977). Similar extensive mutual solid solubility of anthracene and phenanthrene has been found in the (anthracene–phenanthrene)/TCNB (Wright et al., 1976) and (anthracene–phenanthrene)/picric acid (Koizumi and Matsunaga, 1974) systems. In the ﬁrst of these there is complete mutual solid solubility of the two donors and the crystal structures of {anthracene TCNB} and {phenanthrene TCNB} are isostructural at room temperature (there is disorder of the phenanthrene molecule). In the second system (Fig. 13.9) the situation appears to be more complicated; in addition to limited solid solubility of anthracene in {phenanthrene picric acid} and of phenanthrene in {anthracene picric acid} two intermediate phases with fairly wide composition ranges appear. Only the crystal structure of {anthracene picric acid} is known (Herbstein and Kaftory, 1976). Among the mixed acceptor systems there are some (Fig. 13.10) with a full range of solid solubility at lower temperatures as well as at higher temperatures; in accordance with these phase diagrams the {pyrene picric n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

B I NA R Y A N D Q UA S I- B I NA R Y D O N O R – A C C E P T O R S YS T E M S

200

t /°c

L

L

L

S

100

951

S S

0 Py-NPA

Py-DNF

200

Mol%

L

L

S

S

Py-TNT

FI-TNT

L

t /°c

S

100

0 FI-TNT

FI-TNP

Ph-TNP

Ph-TNB

Mol%

Fig. 13.11. Phase diagrams for the systems Py-(NPA, DNF); Py-(DNF, TNT); (Py, Fl)-TNT; Fl-(TNT, TNP); (Fl, Ph)-TNP; and Ph-(TNP, TNB). Py ¼ pyrene; Fl ¼ ﬂuoranthene; Ph ¼ phenanthrene; TNP ¼ 2,4,6-trinitrophenol (picric acid); NPA ¼ 2-nitrophthalic anhydride; DNF ¼ 2,4-dinitroﬂuorobenzene. (Reproduced from Inabe et al., 1981.)

acid} and {pyrene TNB} compounds were reported to be isomorphous at room temperature, and also the pair {ﬂuoranthene picric acid} and {ﬂuoranthene TNB} (Herbstein and Kaftory, 1975a). Other systems (Fig. 13.11) show complete miscibility only at high temperatures and complicated diagrams at lower temperatures. There are many indications of solid state transitions. Some information about relevant crystal structures is noted in the captions to these diagrams; references are given in Chapter 15. The phase diagrams for the mixed acceptor systems (Fig. 13.10 and 13.11) are compatible with the more limited information available from crystallographic studies despite the different temperature ranges of the two types of study. It is not known whether there is ordered or random substitution of one donor (or acceptor) for another in the mixed stacks of these molecular compounds. n n n

n n n

n n n

CHARGE TRANSFER MOLECULAR COMPOUNDS

952

One ternary mixed-donor system has been studied – (anthracene, acridine, phenazine)/ PMDA (Karl et al., 1982). The three individual molecular compounds ({anthracene PMDA}, {acridine PMDA}, {phenazine PMDA}) are isomorphous (triclinic, P 1, Z ¼ 1; Table 15.2, Group 1a). Complete miscibility was found for all donor ratios over the temperature range 500–120K, the molecular compounds melting around 500K. n n n

n n n

13.4.2

n n n

Component ratios in binary donor–acceptor systems

Most crystalline -molecular compounds, be they mixed stack or segregated stack in structure, have a 1 : 1 donor : acceptor ratio and this has been the most extensively studied group, both in regard to crystal structures and physical properties. Many 1 : 2 and 2 : 1 compositions have been reported, and most of these occur as incongruently-melting compounds in systems where the 1 : 1 composition is the most stable. However, there are examples where the 1 : 2 (or 2 : 1) molecular compound appears to be the more stable e.g. (benzo[c]pyrene)2 TMU (Weil-Malherbe, 1946); relative stabilities of the different compositions in such systems do not appear to have been investigated. There are also reports of compositions other than 1 : 1, 1 : 2 or 2:1 (Table 13.8); these should be viewed with caution if based on chemical analyses alone. However, there are structural explanations for some unusual compositions. For example, in both n n n

Table 13.8. Some examples of compositions other than 1 : 1, 1 : 2 or 2 : 1 reported for -molecular compounds Donor (D)

Acceptor (A)

D:A

Reference

Bromodurene Tetralin Pyrene N,N-dibenzyl-m-toluidine Triphenylmethanol Phenanthrene Fluorene 1-Naphthylamine 2-Naphthylamine Phenanthrene Naphthalene 1-Naphthol p-Phenylenediamine Dibenzo[c,d]phenothiazine Benzene 1,4-Diphenylbutadiene Tetrathiotetracene(TTT) TTT TTT

BTF Nitrobenzodifuroxan PMDA TNB TNB p-Dinitrobenzene TNB 2,3-Dinitrophenol 2,3-Dinitrophenol 1,2,4,6-Tetranitrobenzene 1,2,4,6-Tetranitrobenzene Tetryl p-Benzoquinone DDQ o-Chloranil TNF o-Chloranil o-Bromanil TCNE

3:2 1:3 1:3 3:2 3:2 3:1 3:4 3:2 3:2 2:3 3:2 3:2 2:5 3:2 3:1 3:1 3:1 3:1 3:1

B60 BC58 HS69 KMC39 KHM12 K08 HKR76 S40b S40b S40a S40c S40c S09 M64 PJF17 OW46 M65 M64 M64

References: B60 – Bailey, 1960; BC58 – Bailey and Case, 1958; HKR76 – Herbstein, Kaftory and Regev, 1976; HS69 – Herbstein and Snyman, 1969; K08 – Kremann, 1908; KHM12 – Kremann, Hohl and Muller, 1912; KMC39 – Kent, McNeil and Cowper, 1939; M64 – Matsunaga, 1964; M65 – Matsunaga, 1965; OW46 – Orchin and Woolfolk, 1946; PFJ17 – Pfeiffer, Jowleff, Fischer, Monti and Muuly, 1917; S09 – Schlenk, 1909; S40a – Shinomiya, 1940a; S40b – Shinomiya, 1940b; S40c – Shinomiya, 1940c.

TERNARY -MOLECULAR COMPOUNDS

953

(pyrene)3 (picryl bromide)2 (Herbstein and Kaftory, 1975b) and (TMTTF)1.8 TCNQ (Kistenmacher et al., 1976) the molecules present over and above the 1 : 1 composition are included in the structure without participating in the charge transfer interaction, i.e. they are present as ‘‘molecules of crystallization’’. The remarkable structure of {(ﬂuorene)3 (TNB)4} is discussed in Section 15.4. The segregated-stack radical-cation, radical-anion salts seem all to have equimolar compositions but the Mn(TCNQ)m salts, where M is a closed-shell cation, have a wide range of compositions depending on the nature of the cation. There are good structural explanations for compositions such as Cs2(TCNQ)3 (see Section 17.4.6) or N-(n-butylpyridinium)4(TCNQ)7 (see Section 17.4.2.3). n n n

n n n

n n n

13.5 Ternary -molecular compounds There are a number of molecular compounds which contain three components and we can distinguish three situations: (i) Noninteracting third component, where the third component appears to be present essentially as ‘‘molecules of crystallization’’ and does not participate in the charge transfer interaction. However, no relevant structures have been reported so some reserve must be maintained about examples such as azulene BTF(propionic acid)0.5 (Bailey, 1960); 2,2 0 ,4,4 0 hexamethylstilbene (picric acid)2benzene (Elbs, 1893); 1-naphthol hexachloro-1-indenone1/2X where X ¼ benzene or acetic acid (Pfeiffer et al., 1924); phenanthrene TNBx(benzene) and tetrabenznaphthalene picric acid. ethanol, where the third component may be present zeolitically in both examples (Herbstein, Kaftory and Regev, 1976). (ii) Interacting third component: one example where all three components interact is Koﬂer’s (1944) 1 : 1 : 1 ternary compound {1-naphthylamine pyridine picric acid}, the structure of which has been determined (Bernstein et al., 1980; see Section 15.11.4). A second example is the ordered ternary compound {3,3 0 -dimethylthioazolinocarbocyanine TCNQ 2,4,7-trinitroﬂuorenone} (Kaminskii et al., 1974), with mixed stacks of alternating TCNQ and TNF moieties. The pseudo-binary systems with mixed donors or acceptors presumably should be classiﬁed in this group. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

Table 13.9. Examples of TNB molecular compounds formed by a particular donor and by its potassium salt. Melting points in C Donor

o-Aminobenzoic Acid m-Aminobenzoic Acid p-Aminobenzoic Acid 1-Anthrol

TNB molecular compound

TNB molecular compound of K salt

Crystals

M. Pt.

Crystals

M. Pt.

orange needles

192

red red-brown plates

151 161

deep-red needles red-brown needles red needles black needles

114 118 115(dec) 275

Notes: All the compounds are 1 : 1 (Sudborough and Beard, 1910) except for the K salt of anthrol. TNB which has composition C14H9OK {C6H3(NO2)3}2 (Cadre and Sudborough, 1916). n n n

954

CHARGE TRANSFER MOLECULAR COMPOUNDS

(iii) There is another group of molecular compounds where the third component, although not participating in the charge transfer system, exerts a profound inﬂuence on the structure and its properties. These are the benzidine TCNQ.solvent compounds discussed in Section 15.7.3.3, which have both charge transfer and inclusion characteristics. (iv) Finally we draw attention to a group where both a particular donor, and its potassium salt, form molecular compounds with TNB (Table 13.9). As both neutral compounds and the salts are highly colored, it seems probable that charge transfer interactions occur in both. These pairs of compounds could provide an opportunity to compare the donor characteristics of molecules and their anions. n n n

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Chapter 14 Layered molecules with intra-molecular donor–acceptor interactions

. . . lock’d in ﬁerce embrace . . . Unknown.

Summary: Layered molecules (in the present context) are donor–acceptor cyclophanes in which the mutual orientation and/or location of the donor and acceptor ring systems can be altered in order to investigate the conditions for maximum overlap and hence charge transfer. The enhancement of charge transfer in pseudogeminal as opposed to pseudo-ortho cyclophanes has been demonstrated by comparison of UV-visible spectra for many diastereoisomeric pairs. Crystal structure determinations show that there is superposition of donor and acceptor moieties in the paracyclophane series, with appreciably more distortion in [2.2] than in [3.3] paracyclophanes. Charge transfer interactions persist in triply and quadruply layered donor–acceptor paracyclophanes but the orientation effects are lost. The charge transfer spectra of syn and anti diastereoisomers in the metacyclophane series are remarkably similar; crystal structure analyses show considerable intramolecular distortion and mutual displacement and nonparallelism of the donor and acceptor moieties. The ideas developed in the cyclophane studies are beginning to be applied to other areas of chemistry. 14.1 Introduction 14.2 Molecules of the paracyclophane type 14.2.1 Molecules derived from [n.n]paracyclophanes 14.2.2 Systems related to [n.n]paracyclophanes 14.2.3 Multi-layered systems 14.3 Molecules of the metaparacyclophane type 14.4 Molecules of the metacyclophane type 14.5 Some other systems 14.6 Concluding summary References

959 961 961 972 974 976 980 984 986 986

14.1 Introduction We have already emphasized that the more stable –* charge-transfer molecular compounds have equimolar ratios and that the most striking feature of their crystal structures is the alternating arrangement of donor and acceptor molecules, planes essentially parallel, in mixed stacks. However, the mutual donor–acceptor arrangements in the crystals, under which heading we include the aspects of D A interplanar distance, orientation and overlap, is not free of inﬂuence from neighbouring stacks and separation of the various n n n

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

960

contributory factors can be troublesome. Thus study of charge transfer in an intramolecular situation has many advantages because the donor–acceptor arrangement is well-deﬁned. This approach appears to have been suggested ﬁrst by Cram and Day (1966), who synthesized 14.1 (the [2.2] compound); the corresponding [3.3] (Shinmyozu, Inazu and Yoshino, 1977) and [4.4] (Cram and Day, 1966) compounds have also been reported. Cram and Day (1966) anticipated that 14.2 and 14.3 would differ because of the possibility of interannular hydrogen bonding in 14.3 but not in 14.2 (Fig. 14.1). Such hydrogen bonding has not yet been encountered. However, in the early 1970s Staab pointed out a more important feature – that 14.2 and 14.3 differ in the mutual orientation of the -systems of donor and acceptor moieties and thus permit a direct test of the validity of Mulliken’s ‘‘overlap and orientation’’ principle for a D A pair. Many cyclophanes suitable for this purpose have been synthesized in the last decade, principally by Staab and coworkers in Germany but also in Japan and elsewhere (Schroff, van der Weerdt et al., 1973; Schroff, Zsom et al., 1976) and we survey these results, which have been reviewed (Schwartz, 1990). The cyclophane systems needed were obtained by extensive synthetic programmes which will not be discussed here despite their many novel features. The UV-visible absorption spectra of many diasteroisomeric pairs were measured in dilute solution, with Beer’s law checked to ensure that the spectra were truly those of intramolecular species. Solutions in rigid glasses allow low-temperature spectroscopy while determination of the crystal structures gives details of molecular structure (the rings are generally deformed in these strongly interacting systems) and also shows if there are appreciable intermolecular interactions in the crystals. Approximate molecular orbital calculations aid in the interpretation of the results. The reader should be warned that what started out as a simple and clearcut means of testing Mulliken’s ‘‘overlap and orientation’’ principle has developed complications; Staab, Dohling and Krieger (1991) remark ‘‘that a general and strict correlation between CT absorption and ground-state stabilisation by CT interaction (which is still widely taken for granted in organic chemistry) cannot be expected.’’ This will be illustrated towards the end of this chapter. n n n

p(CH2) X O

O

p(CH2) O

X O q(CH2) 14.2

X

X q(CH2) 14.3

Fig. 14.1. Schematic diagram of the pseudo-ortho (14.2) and pseudo-geminal (14.3) diastereoisomers of [n,m]paracyclophane quinhydrones (X¼OH) and related molecules. The methylene linkages between the rings can be equal but are not required to be so; n ¼ p þ 2 and m ¼ q þ 2, where p and q have integer values 0. The para mode of bridging is shown for both rings but meta bridging, and mixed meta-para bridging, are also found, as are other types of ring. 14.1 has X ¼ H, p ¼ q ¼ 0; 14.2 and 14.3 have X ¼ OH and p ¼ q ¼ 0.

MOLECULES OF THE PARACYCLOPHANE T YP E

961

14.2 Molecules of the paracyclophane type 14.2.1 Molecules derived from [n.n]paracyclophanes The experimental results show that para- and metacyclophane systems differ in important respects and we consider them in separate sections, starting with the paracyclophanes. Nomenclature and schematic structures are summarised in Fig. 14.1. Initial emphasis was placed on the quinhydrone systems; analogous crystalline intermolecular systems have been extensively studied (Section 15.7.1). The pseudo-ortho (14.2) and pseudogeminal (14.3) diastereoisomers were synthesized (Rebafka and Staab, 1973, 1974), followed by other syntheses and studies of physical properties (Staab and Rebafka, 1977; Staab, Herz and Henke, 1977; Staab and Haffner, 1977; Staab and Taglieber, 1977). The absorption spectra of the diastereoisomeric pair 14.2 and 14.3 are shown in Fig. 14.2 and it is clear that the charge transfer band centred at ca. 500 nm is much more pronounced for the pseudogeminal than for the pseudo-ortho isomer, and thus the charge-transfer interaction is appreciably stronger when the donor and acceptor moieties are parallel rather than when they are 60 apart. This conclusion is reinforced by a number of other measurements. For example, NMR results (1H NMR, d6-DMSO solution, coalescence of singlets at ¼ 4.14 and 3.98 above 161 C) shows that there is exchange of oxidation states between the two rings with simultaneous proton exchange in 14.3 but not in 14.2 (Rebafka and Staab, 1974). As the crystal structure of 14.3 has not been reported, it is not known whether there is interannular hydrogen bonding in this molecule. The pseudo-ortho conﬁguration of the compound obtained in a synthesis of the paracyclophane diene quinhydrone (rings linked by double rather than single bonds) was inferred from the essential identity of its charge

HO

Ig E

O OH

O

4 O

OH

HO

O

3

2 250

300

350

400

450

500

550

600

650

700

[nm]

Fig. 14.2. Absorption spectra (dotted 14.2, full 14.3) of the diastereoisomeric [2.2]paracyclo-phane quinhydrones (solvent CH3OH). (Reproduced from Rebafka and Staab, 1974.)

962

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

transfer absorption with that of 14.2 (Stobbe, Kirchmeyer, Adiwidjajaj and Meijere, 1986). The orientation dependence of the charge transfer excitations in the [2.2] and [3.3] quinhydrone paracyclophanes has been explained in terms of Hu¨ckel molecular orbital theory (Vogler, 1983a,b), and good agreement obtained with experiment. The enhancement of the charge-transfer band in the pseudogeminal [2.2]paracyclophane donor–acceptor diastereoisomer (14.3) over that in the corresponding pseudoortho diastereoisomer (14.2) is a quite general phenomenon (see spectral parameters summarized in Table 14.1). The [2.2]paracyclophane quinhydrones have the disadvantage, in the present context, of very strong interannular interactions, with marked deforma˚ between their mean planes, compared to the tions of the rings and distances of 2.9 A ˚ 3.2 A found in the crystalline quinhydrones. These complicating features do not appear in the [3.3]paracyclophane quinhydrones (Staab and Herz, 1977b; Staab, Herz, Krieger and Rentea, 1983); in these diastereoisomeric pairs the CT interaction is also strikingly greater in the pseudogeminal than in the pseudo-ortho diastereoisomer. One of the objectives of the synthetic programmes was the preparation of cyclophanes with very strong donor and acceptor moieties. One such molecule would contain TMPD as donor and TCNQ as acceptor. Paracyclophanes with TCNQ as acceptor and donors of various kinds have been reported (Staab and Knaus, 1979; Staab, Knaus, Henke and Krieger, 1983; Tatemitsu et al., 1978). They show the same orientation effects as described above for the quinhydrones. The importance of the methoxy substituents in enhancing the donor strength is shown by the much stronger CT absorption in the compound with a p-dimethoxybenzene donor group and TCNQ acceptor group than when the donor is a benzene ring (Staab, Knaus et al., 1983). The converse situation where TMPD is donor and there are various acceptors has been achieved in the [2.2] series (Staab, Reimann-Haus et al., 1983) and also in the [3.3]paracyclophane series (Staab, Gabel and Krieger, 1983), where speciﬁcally the pseudo-ortho and pseudogeminal diastereoisomers of N,N,N 0 ,N 0 -tetramethyl[3]-(2,5)p-benzoquinone[3]paracyclophane-5,8-diamine were prepared and the crystal structure of an analog to the latter compound (in which the p-benzoquinone group was replaced by p-dimethylcyanobenzene) has been determined. One diastereoisomer with the desired TMPD–TCNQ combination has been synthesized – the pseudogeminal N,N,N 0 ,N 0 tetramethyl[3]-(2,5)tetracycanoquinodimethane[3]paracyclophane-5,8-diamine (Staab, Hinz, Knaus and Krieger, 1983). Its absorption spectrum shows a particularly broad CT band stretching over the region from 600–1600 nm. The trans-annular coupling is so strong (because of low ID and high EA values) that there is no longer any localization of valence electrons in the two rings and the spectrum does not show features of the TMPD and TCNQ spectra at short wavelengths, such as are found in weaker donor-acceptor systems. There is little dependence of the absorption spectrum on solvent polarity, the C N stretching frequency in TCNQ is 2216 cm1 and there is no ESR spectrum; all these facts point to a neutral ground state for the molecule rather than the ionic ground state that might have been anticipated (cf. Section 15.10.2). The TCNQ moiety is also neutral in the corresponding pseudo-ortho diastereoisomer ( CN ¼ 2220 cm1). Another such strong donor-acceptor pair is TTF and TCNQ where considerable progress has been made in the synthesis of the separate systems (TCNQ as before, TTF as below) but the desired combination in the same cyclophane (14.4) has not yet been reported. However, [3]tetrathiafulvaleno-[3]paracyclophane (14.5.1) and an analogous

MOLECULES OF THE PARACYCLOPHANE T YP E

963

Table 14.1. Comparison of spectral parameters for charge-transfer absorption bands of various donor–acceptor cyclophanes in pseudogeminal and pseudo-ortho configurations (note that this distinction does not hold when the donor is a benzene ring). The max values are in nm Donor moiety

Acceptor moiety

Cyclophane Pseudogeminal max/"

Pseudoortho max/"

Solvent

Ref

p-Dimethoxybenzene (DMB) DMB Benzene DMB

TCNQ

[2.2]para

695/3225

730/258

CHCl3

SKHK83

[3.3]para [3.3]para [2.2]para

705/3450 530*/795 483/1329

670/117

CHCl3 CHCl3

475/3000 466/360 462/324

DMB

BQ

TMPD TMPD

BQ BQ

[3.3]para [4.4]para [2]para crown (3) [2]para crown (3) with Naþ [2.2]para [3.3]para

438/160 498/142 500*/100 445/97

SK79 SKHK83 SHH77

DMB DMB DMB

TCNQ TCNQ p-benzoquinone (BQ) BQ BQ BQ

TMPD p-Dihydroxybenzene (quinol) quinol p-trimethylsiloxybenzene DMB

TCNQ BQ

[3.3]para [2.2]para

1050/3160 495/1600 515/170

SH83 CH3OH SR77

BQ BQ

[3.3]para [2.2]para

500*/105 430/205

dioxane CHCI3

SHKR83 SHH77

pyrazine

[2.2]para

462/3210 444/1710 500*/116 440/405

460/103

CF3COOH

SA81

benzene benzene benzene DMB

BQ BQ BQ p-dinitrobenzene

[2.2]para [3.3]para [4.4]para [2.2]para

340/597 406/407 288/1290 468/414

* shoulder

#

CHCl3 CHCl3

478/874

577/1930 538/2455

SDK83 SDK83 SSK83 SSK83

595/160 CH2CI2 537/76 387/1480#

475/120

CHCl3

SR83 SGK83

CD66 SIY77 CD66 SH77

2nd CT band

References: CD66 – Cram and Day, 1966; SA81 – Staab and Appel, 1981; SDK83 – Staab, Do¨hling and Krieger, 1981; SGK83 – Staab, Gabel and Krieger, 1983; SH77 – Staab and Haffner, 1977; SH83 – Staab, Hinz, Knaus and Krieger, 1983; SHH77 – Staab, Herz and Henke, 1977; SHKR83 – Staab, Herz, Krieger and Rentea, 1983; SIY77 – Shinmyozu, Inazu and Yoshino, 1977; SK79 – Staab and Knaus, 1979; SKHK83 – Staab, Knaus, Henke and Krieger, 1983; SR77 – Staab and Rebafka, 1977; SR83 – Staab, Riemann-Haus, Ulrich and Krieger, 1983; SSK83 – Staab, Starker and Krieger, 1983.

[4.4] compound have been synthesized (Staab, Ippen et al., 1980) and crystal structure analyses (brieﬂy) reported for both compounds; surprisingly the latter compound was found to be the isomer 14.6 rather than 14.5.2. The [2.2]tetrathiafulvalene isomers 14.7 and 14.8 have been synthesized but only the second was obtained in pure form (Ippen, Tao-pen, Starker, Schweitzer and Staab, 1980).

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

964

CN

NC (H2C)n

S

S

S

(H2C)n S

14.5.1: n = 3 14.5.2: n = 4

14.4 S

S

NC

S

(CH2)n

S

(CH2)n

CN

S

S

S

S

14.6

Its structure has been conﬁrmed crystallographically; the molecule has a step-like anti conformation. The [3.3]tetra-thiafulvalenes (14.9 and 14.10) have been synthesized but not completely puriﬁed. Black needles of a complex of composition [3.3]tetrathiafulvalene:(TCNQ)4 were obtained and shown to be triclinic but the structure was not reported. Conductivity measurements gave values of about 10 2 S/cm along the needle axis at 300K the conductivity at 40K is ten orders of magnitude less than at 400K!

(H2C)n

S

S

S

S

S

S

(H2C)m

S

S

S S

S S

S

S

(CH2)m

(CH2)n S

S

14.7: n = 0; 14.9: n = 1.

14.8: m = 2; 14.10: m = 3.

Sometimes there are complications. For example, the pyrazine moiety acts as an acceptor in the diastereoisomeric 12,15-dimethoxy-4,7-diaza[2.2]paracyclophanes (pseudogeminal and pseudo-ortho) (Staab and Appel, 1981); however, there are only small differences, which are solvent dependent, between the absorption spectra of the two diastereoisomers in the CT region of the spectrum. Thus a straightforward explanation in terms of ring overlap is no longer possible, as already noted in the Introduction. The generalization that there is greater CT interaction in pseudogeminal than in pseudoortho diastereoisomers breaks down for [4.4]paracyclophanes and those with longer

MOLECULES OF THE PARACYCLOPHANE T YP E

965

methylene bridges (Staab, Do¨hling and Krieger, 1981; Staab, Starker and Krieger, 1983). Crystal structure analysis of pseudogeminal-6,9,16,19-tetramethoxy[4.4]paracyclophane (Staab, Do¨hling and Krieger, 1983) and pseudogeminal-7,10,18,21-tetramethoxy[5.5]paracyclophane (Staab, Starker and Krieger, 1983) shows that the interannular dis˚ respectively. There is no distortion of the rings and presumably tances are 4.01 and 5.11 A there is little CT interaction at such large distances. Further comparison of the relative strengths of the donor–acceptor interaction in the two diastereoisomers can be made through emission spectra and zero-ﬁeld splitting (ZFS) parameters (Hausser and Wolf, 1976); in these experiments the molecules are held at 1.3K, either in rigid glasses or as their crystals. The diastereoisomers used were those of 4,7-dicyano-12,15-dimethoxy-[2.2]-paracyclophanes (Schweitzer, Hausser et al., 1976) and 12,15-dimethoxy-4,7-diaza[2.2]-paracyclophanes (Staab, Herz and Henke, 1977). Crystal structures have been determined for the ﬁrst pair of compounds by Irngartinger and Merkert but details do not appear to have been published. Emission spectra were used as follows: the characteristic properties of the excited triplet state of CT compounds originate from the fact that the two triplet excitons have a high probability of being, at a given time, in two different orbitals separated in space, i.e. one in the HOMO of the donor and the other in the LUMO of the acceptor. Consequently the exchange integral is diminished, with the energy of the ﬁrst excited triplet state being reduced less than that of the corresponding excited singlet state. Thus large spectral overlap occurs between phosphorescence (triplet to ground state transition) and ﬂuorescence (ﬁrst excited singlet to ground state transition) spectra. Furthermore, the absolute red shifts of the emission spectra in CT-cyclophanes are larger than those in CT molecular compounds because of the stronger interannular interactions in the cyclophanes. The ESR method is to be preferred to emission spectroscopy because the ZFS parameters (the D values) are more sensitive than emission spectra to differences in CT interaction. The larger the separation between the two triplet electrons, the smaller is jDj; small jDj values thus correspond to larger CT interactions. The trend in jDj values shown in Table 14.2 is entirely compatible with the absorption spectra and also with the results of Hu¨ckel MO calculations (Vogler, Ege and Staab, 1977). However, it is not clear why the jDj values from the crystals are lower than those from the rigid glasses. The spectroscopic and other results mentioned above are reinforced by the detailed molecular geometries obtained from crystal structure analyses (note that in some instances structures of analogs have been reported rather than those of the immediatelyrelevant molecules, presumably because of difﬁculties in obtaining suitable crystals of the molecules of primary interest). Only a limited number of representative structures are discussed here. The pseudogeminal and pseudo-ortho diastereoisomers of 4,7-dimethoxy[2](2,5)tetracyanoquinodimethane[2]paracyclophane (Staab, Knaus, Henke and Krieger, 1983) are shown in Figs. 14.3 and 14.4, the actual molecular structures showing a remarkable resemblance to schematic formulae such as 14.1. The geometries of the two diastereoisomers are very similar (apart from the mutual positioning of the substituents), even in respect to the distortions introduced by the interannular interactions. Thus it is probable that these geometries can be taken as representative of all diastereoisomeric pairs in the [2.2]paracyclophane series.

966

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

Table 14.2. Zero Field Splitting (ZFS) parameters measured by Optical Detection of Magnetic Resonance (ODMR); all measurements at 1.3K. n-Octane and PMMA are rigid glasses. The jDj values are given in units of cm1. Compound

a. 2,5-dimethylpyrazine b. 1,4-dimethoxy-2,5dimethylbenzene c. 4,7-diaza[2.2]paracyclophane (Combination a-b) d. 1,4-dicyano-2,5dimethylbenzene e. 4,7-dicyano-12,15dimethoxy[2.2]-paracyclophane (Combination b-d)

Component

Paracyclophane

Donor

Pseudogeminal

Acceptor

Remarks Pseudoortho

0.177

n-octane n-octane

0.116 0.0967

0.1022

0.1229

n-octane PMMA

0.0313 0.0213

0.0642 0.0259

PMMA single crystal

The results of crystal structure analyses of [3.3]paracyclophanes are similar to those in the [2.2] series, and we shall give only one example – pseudogeminal 14,17dimethoxy[3](2,5)-p-benzoquinone[3]paracyclophane (Staab and Knaus, 1979; Fig. 14.5). There is almost exact overlap of the two rings as in the [2.2] series but less ring distortion. This perhaps explains the somewhat higher extinction coefﬁcients found for [3.3] than for [2.2]cyclophanes (Table 14.1). The methylene bridge is disordered in some of the crystal structures in this group (for example, Fig. 14.5) but not in all of them. When both rings of the [nn]paracyclophane are the same and both are paradisubstituted in the same way, then the pseudogeminal diastereoisomer will be centrosymmetric while the pseudo-ortho diastereoisomer will have a C2(2) axis normal to the mean ring planes (these symmetries can be exact or approximate). If the rings are different then both diastereoisomers will have twofold axes (or even lower symmetry). If the molecules are chiral, there is a possibility of spontaneous resolution if the compound crystallizes in a Sohnke space group (cf. Section 11.2.2.1). This has so far been reported, for paracyclophanes, only for pseudogeminal-N,N,N 0 ,N 0 -tetramethyl[3](2,5)-pbenzoquinone[3]paracyclophane-14,17-diamine (space group P21, Z ¼ 2, molecular symmetry C11; Staab, Gabel and Krieger, 1983; BUVRIT). The metacyclophane (see Section 14.4 below) syn-15,18-dimethoxy[3]-p-benzoquinone[3]metacyclophane also crystallizes in space group P21, Z ¼ 2; Staab, Herz, Do¨hling and Krieger, (1980). Correlation of absolute conﬁguration and optical rotation has not been reported for these two compounds but has been effected for a metaparacyclophane (see Section 14.3 below). A rather detailed comparison of the effects of various factors on donor–acceptor interactions in paracyclophanes has been made possible by the synthesis of a series of [2.2], [3.3] and [4.4] paracyclophanes all containing 1,2,4,5-tetracyanobenzene as acceptor and with a variety of donor moieties (Staab, Wahl and Kay, 1987). As crystal structures have been determined for most of these molecules, the comparisons can be

MOLECULES OF THE PARACYCLOPHANE T YP E

967

1.572

TOP VIEW

N

methoxy dicyano

1.579

z y methoxy

1.579

SIDE VIEW 1.510

N dicyano z

y x

Fig. 14.3. Top and side views of the pseudogeminal diastereoisomer of 4,7-dimethoxy[2](2,5)tetracyanoquinodimethane[2]paracyclophane (BUZROD). Note the close superpositioning of ˚ . Full molecular donor and acceptor moieties, and also their appreciable deformation. Distances in A dimensions of all crystal structures discussed in this Chapter are given in the original papers. (Data from Staab, Knaus, Henke and Krieger, 1983.)

968

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

Fig. 14.4. Stereoview view of the pseudo-ortho diastereoisomer of 4,7-dimethoxy[2](2,5)-tetracyanoquinodimethane[2]paracyclophane (BICFAU01). The overall molecular structure is very similar to that of the pseudogeminal diastereoisomer in Fig. 14.3. (Diagram produced using data from Staab, Knaus, Henke and Krieger, 1983.)

made for systems of well-deﬁned geometry. The spectroscopic results are summarized in Table 14.3. The crystallographic results (Staab, Krieger, Wahl and Kay, 1987) follow the pattern established previously – considerably more distortion in the [2.2] (FIPLOF, FIPLUL, FIPMAS) than in the [3.3]paracyclophanes (FIPMEW, FIPMIA, FIPMOG), while distortion is negligible in the [4.4]paracyclophanes; almost complete eclipse of the donor and acceptor ring systems in the [2.2]paracyclophanes but with some mutual lateral shift of rings in [3.3]paracyclophanes and rather more variability in [4.4]paracyclophanes; substituents are coplanar with associated rings except for the methoxy groups in the tetramethoxy-substituted [2.2]paracyclophanes where the methyl groups are roughly normal to the ring planes. As Staab, Krieger, Wahl and Kay, (1987) point out, these changes can be followed qualitatively by changes in the colour of the crystals and more quantitatively by changes in max and " of the charge transfer absorption bands (Table 14.3). For example, in the [2.2]paracyclophane series, the benzene donor is weakest while increasing the donor strength by substitution of four methyl groups or two methoxy groups leads to a deepening of the colour of the solutions; however, four methoxy groups cannot be coplanar, thus reducing the mesomeric effect and the donor strength. If the dimethoxy donor is kept constant while the methylene chain length is increased, then the colour weakens from deep violet to dark red to orange as one passes from the [2.2] to the [3.3] and then to the [4.4]paracyclophane. The paracyclophanes discussed above are intramolecular charge-transfer molecular compounds and, as such, have a donor face and an acceptor face (Janus-like molecules) Thus one can anticipate formation in the crystals of stacks of the following type: D

A

D

A

D

A

D

A

These occur in some crystals but not in others; certainly this type of stacking is not a feature of the crystal structures comparable in importance to the – D A D A D A – arrangement

MOLECULES OF THE PARACYCLOPHANE T YP E

969

p-dimethoxy portion 1.412

1.382

1.518

1.497

1.227 p-benzoquinone portion x z

y

0

A

dimethoxy above

benzoquinone below

B

x y

Fig. 14.5. (upper) Perspective view of the pseudogeminal diastereoisomer of 14,17-dimethoxy[3](2,5)p-benzoquinone[3]paracyclophane (CECTIN). The molecule has a twofold axis normal to the mean ˚ . There is some disorder, not shown, in the methylene bridges. Note the ring planes. Distances in A close superpositioning of donor and acceptor moieties, and also some deformation. ˚ , I41cd, Z ¼ 8. (Data (lower) Packing diagram viewed down [001]; tetragonal, 15.891(2), 13.223(2) A from Staab, Herz, Krieger and Rentzea, 1983.)

970

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

Table 14.3. Colours and parameters for charge transfer absorption bands in spectra of [2.2], [3.3] and [4.4]paracyclophanes, with 1,2,4,5-tetracycanobenzene as acceptor moiety and various donors. The data in this Table are taken from pp. 556–557 of Staab, Krieger, Wahl and Kay, (1987). Asterisks indicate shoulders Donor Moiety

1. 2. 3. 4. 5. 6. 7. 8.

[n.n]

Benzene p-dimethoxybenzene 1,2,4,5-tetramethylbenzene 1,2,4,5-tetramethoxybenzene benzene p-dimethoxybenzene 1,2,4,5-tetramethylbenzene p-dimethoxybenzene

Colour

[2.2]

Charge-transfer band

yellow deep violet red orange red

[3.3] dark red [4.4]

orange

max(nm)

"

395* 520 440 380* 416 508 434 495

437 240 537 1318 1288 347 575 89

found in the mixed stacks of most intermolecular donor–acceptor molecular compounds (see Chapter 15). However, we note that this sort of stacking is found in many of the donor– acceptor complexes discussed in Chapter 3. One may venture the suggestion that ternary molecular compounds could be formed with stacks having the following arrangement: D

A

D' A

D

A'

D

A

D' A

D

Synthesis of such molecular compounds does not appear to have been attempted – a neat balance of donor and acceptor strengths would appear to be needed for success; however, it should be noted that [3.3]paracyclophane forms a 1 : 1 : * molecular compound with TCNE (Bernstein and Trueblood, 1971; PACTCN10) (see also Section 15.4), so the suggestion may not be entirely fanciful. It has been argued that cyclophanes containing donor (or alternatively acceptor) moieties in both rings would not be likely to form mixed stacks with added acceptor (donor) molecules but that segregated stacks would be favored (Staab, Gabel and Krieger, 1987). This proposal has so far been tested only for pseudogeminal-5,8,14,17-tetrakis(dimethylamino)[3.3]paracyclophane, which is formulated as TMPD TMPD

and which we shall denote for convenience as [TMPD-(CH2)3]2. This material forms a black 1 : 2 molecular compound of metallic appearance with TCNQ, the roomtemperature conductivity along the ‘‘longer crystal axis’’ being 1.5 S/cm, about 106 times as large as that of TMPD TCNQ (in which there is a mixed stack arrangement of ionized moieties). The crystal structure has not yet been reported. n n n

MOLECULES OF THE PARACYCLOPHANE T YP E

971

The compound [TMPD-(CH2)3]2 would be expected to undergo oxidation in four stages, the ﬁrst giving an analog of Wu¨rster’s blue cation. Cyclic voltametry shows that oxidation occurs at potentials of 0.242, 0.102 and 0.249 V (two unresolved stages); these values should be compared with potentials of 0.206 and 0.378 V for TMPD and 0.081 and 0.242 V for 2,5-dimethyl-TMPD. Thus oxidation to the radical cation is more facile in [TMPD-(CH2)3]2 than in the other two compounds. Fast electron exchange has been demonstrated in the radical cation according to the following scheme: TMPD +•

TMPD

TMPD

TMPD

+•

The very rigidly linked [2.2.2.2](1,2,4,5) cyclophane quinhydrone (14.11; Staab and Schwendeman, 1978) is strongly deformed, the interannular distance (as judged from the crystal structures of the corresponding cyclophane (Hanson, 1977; CYLOPH) and the ˚ , compared to about 3 A ˚ in 14.3; the rings are tetraquinone (Krieger, 1978) is about 2.69 A boat-shaped in both reference molecules, with the substituent groups pointing away from the transannular region rather than towards it as in the paracyclophanes. Nevertheless the absorption spectrum is very similar to that of 14.3 (for the CT band, m ¼ 491 nm and " ¼ 1280, compared to 492 nm and 1600 for 14.3). Another surprising feature is that there is no hydrogen exchange between donor and acceptor moieties, even on heating to 140 C; perhaps this difference from the behaviour of 14.3 is due to a different type of deformation in 14.11 which increases the distance between hydroxyl and quinone oxygens beyond the limit for which exchange is possible.

CN O

O

HO

OH

14.11

NC

C

NC

C

CN

14.12

Crystal structures have been reported (Mizuma, Miki, Kai, Yasuoka and Kasai, 1982) for 14.12 (as its benzene solvate, P 1, Z ¼ 2; BICDUM) and for the 14,17-dimethoxy derivative of 14.12 (Fdd2, Z ¼ 16; pseudo-ortho diastereoisomer; BICFAU). The molecular structures show the distortions familiar from earlier work on cyclophane systems; in particular the six-membered rings have boat forms and the C(CN)2 portions are slightly twisted away from coplanarity with the ring. The packing in both crystals is based on head-to-tail stacking of the molecules (cf. previous paragraph). The solvent molecules in the benzene solvate do not participate in the stacking but are located in sheets about the (100) planes, interleaving double sheets of stacks of cyclophane molecules.

972

14.2.2

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

Systems related to [nn]paracyclophanes

Enhancement of the CT absorption was obtained in intramolecular quinhydrones with oligo-oxaparacyclophane structures (14.13; Bauer, Briaire and Staab, 1983). The effect was most marked for n ¼ 3; the CT absorption in the region of 500 nm was rather weak for the neat molecules but was strongly enhanced when the Naþ crown ether complex was formed, the conclusion being that the complexation had forced the donor-acceptor quinhydrone pair into a more parallel alignment. The crown ether portion of the molecule can be adjusted to be selective for a particular cation, while clathration of the cation is shown by enhanced spectral absorption; thus the principle of a cation-selective ligand with a ‘‘built-in’’ charge-transfer indicator has been demonstrated. O O CH2

OCH3 O O

CH2

n

O CH3O 14.13 Note: the –CH2–O–CH2– group is repeated n times (for n ≥ 1).

Some work has also been done on cyclophanes containing naphthaleno systems, including synthesis of intramolecular quinhydrones based on [2](1,4)naphthaleno[2]paracyclophane (Herz and Staab, 1977) and [2.2](1,4)naphthalenophane. The syn and anti isomers 14.14 and 14.15 of the latter type have very similar absorption spectra, both showing broad CT bands between 500 and 700 nm (Staab and Herz, 1977a; not reproduced here). It was inferred that in these molecules direct donor–acceptor interaction through space was less important than the interaction through the strongly coupled [2.2]paracyclophane portions of the molecules. The spectra of 14.16 and 14.17 (Fig. 14.6) show even broader CT bands than 14.14 and 14.15. O

O

OH

OH O HO

O

HO 14.14 (syn isomer, dec 260 °C)

14.15 (anti isomer)

The crystal structure of 14.16 (space group Cc, Z ¼ 4) has been reported (Mizuma, Miki, Kai, Tanaka and Kasai, 1982; BIMNOA). One of the six-membered rings in the

MOLECULES OF THE PARACYCLOPHANE T YP E

973

5 Charge transfer bands 4 Log epsilon

14.20

14.16

3

14.17 2 2,5-dimethyl-TCNQ

14.12

1 300

700

500

900

Wavelength nm

Fig. 14.6. Electronic spectra (in CH2Cl2) of the two-layer molecules 14.12, 14.16 and 14.17, the three-layer molecule 14.20 and 2,5-dimethyl-TCNQ. (Adapted from Yoshida et al., 1978.)

naphthaleno portion is boat-shaped while the other, which protrudes, is planar. The crystals contain head-to-tail stacks of molecules. NC

NC

NC

NC CN

CN

CN 14.16

CN 14.17

(Note: some double bonds have been omitted in the TCNQ moieties).

Some work has been done on systems where the two rings have different sizes, one six-membered and the other seven-membered; para systems are discussed here and meta and mixed systems later. The [2]paracyclophane[2](3,7)p-tropoquinonophane (14.18) shows little evidence of CT absorption, and this is also true of the corresponding [3.3] compound (Kawamata, Fukazawa, Fujise and Ito, 1982a,b). However, there is strong charge transfer when the seven-membered ring is positively charged and so acts as a strong electron acceptor; for example [2.2](1,4)tropylioparacyclophane tetraﬂuoroborate (14.19) has a broad CT band centred at about 350 nm, with "m about 3100 (Horita, Otsubo, Sakata and Misumi, 1976; O’Connor and Keehn, 1976).

974

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

O

+ O

BF4–

O

14.18

14.2.3

14.19

Multi-layered systems

Considerable effort has been invested in the synthesis of multilayered systems and, so far, triply and quadruply layered molecules are known. In the triple-layer molecules 14.20–14.25 there are rather similar CT bands (14.21 and 14.23 have essentially identical spectra), which do not depend on the mutual orientation of donor and acceptor moieties (Staab, Zapf and Gurke, 1977; Machida, Tatemitsu, Sakat and Misumi, 1978; Staab and Zapf, 1978). 14.20 has the absorption maximum of its CT band in the 600 nm region (Fig. 14.6) but replacement of the TCNQ moiety in these molecules by p-benzoquinone leads to appreciable bathochromic shifts to the 450–500 nm region. On the basis of the spectroscopic results Machida, Tatemitsu, Sakat and Misumi (1978) inferred that ‘‘a sandwiched benzene ring functions as a sort of conductor for intramolecular donor–acceptor interaction and not as an insulator.’’ Presumably this is the reason why there is a distinct CT absorption for 14.20 but only a barely noticeable shoulder for 14.12 (Fig. 14.6). The generalisation holds also for the triple-layer charged tropylium system 14.24 (Horita, Otsubo, Sakata and Misumi, 1976). Thus it is intriguing to note that the CT interaction in 14.25 is weak (Tatemitsu, Otsubo, Sakata and Misumi, 1975). Unfortunately details of the absorption spectra have not been published for the p-dicyano triple-layer analogs (Yoshida, Tatemitsu, Sakata, Misumi, Masuhara and Mataga, 1976) of 14.21–14.23 (where the p-benzoquinone group has been replaced by p-dicyanobenzene), which appear to be the only other comparable group of molecules to have been synthesized. CN NC

CN CN

14.20

MOLECULES OF THE PARACYCLOPHANE T YP E

O

975

O

O

O

O

O MeO

MeO MeO

OMe OMe

OMe 14.21

14.22

pseudogeminal isomer 1

+

14.23 pseudo-ortho isomer 2

O –

BF4

O

14.24

14.25

There are four-layer systems (Staab and Zapf, 1978) with a p-benzoquinone moiety at one end as acceptor and a p-dimethoxybenzene moiety at the other end as donor, separated by two benzene rings. These compounds show intense CT absorption bands in the 350–550 nm range (a: m ¼ 447 nm, " ¼ 2500; b: m ¼ 450 nm, " ¼ 2490); the intramolecular nature of the absorption was checked from the concentration dependence of the spectra. Not only are the intensities of the CT bands higher than those of the comparable triple-layered [2.2]paracyclophane quinhydrones but they also show a distinct bathochromic shift, indicating overall enhancement of the donor strength of the -electron system interacting with the acceptor p-benzoquinone moiety. These molecules were synthesized as a diastereoisomeric pair but there was no evidence from their spectra of any dependence of the absorption on the mutual orientation of donor and acceptor. Thus the triple- and quadruple-layer systems behave differently in this regard from the simpler [2.2] and [3.3] paracyclophane quinhydrones. Simple Hu¨ckel molecular orbital theory breaks down when four-layer cyclophane double-quinhydrones are considered, the states being dominated by important (nearly ﬁrst order) conﬁguration interaction (Vogler, 1983b). The crystal structure of 14.25 has been reported (Toyoda, Tatemitsu, Sakata, Kasai and Misumi, 1986; FEFYIY) and also that of the compound in which the p-benzoquinone

976

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

moiety is replaced by bromobenzene (Koizumi, Toyoda, Miki, Kasai and Misumi, 1986; DOHXAZ); the crystals are isomorphous, Pbcn, Z ¼ 4, and the molecules have twofold axes along the O . . . O (Br . . . H) vectors. The outer benzene rings are deformed to boats and the inner ring has a twist shape in these triply layered molecules. A similar pattern of distortions for inner and outer rings is found in the centrosymmetric quadruply layered tetramethyl [2.2]cyclophane C40H14 (Mizuno et al., 1977; MPCPHT10).

14.3

Molecules of the metaparacyclophane type

The [2.2] metaparacyclophane quinhydrones and derivatives are conveniently treated here because they act as a bridge between the paracyclophanes, which they resemble in rigidity, and the metacyclophanes, to which they are perhaps closer in geometrical structure. 12,15-Dimethoxy[2](2,6)-p-benzoquinono[2]paracyclophane (14.26; DALTOZ) and 13,16-dimethoxy[2](2,5)-p-benzoquinono[2]metacyclophane (14.27) were ﬁrst reported by Staab, Jo¨rns and Krieger in 1979 and, in more detail, some years later (Staab, Jo¨rns, Krieger and Rentzea, 1985). The quinhydrone analog of 14.27 has also been reported (Tashiro, Koya and Yamamoto, 1983). 14.26 has a broad CT band from 400–630 nm (m ¼ 490 nm, " ¼ 590, in CHCl3), whereas the CT band of 14.27 is blue-shifted by about 70 nm (m ¼ 420 nm, " ¼ 825, in CHCl3). O

O OMe OMe

MeO

O

14.26

MeO

O

14.27

14.26 crystallizes in three polymorphic forms, two racemic and one enantiomorphic (P212121, Z ¼ 4) and the stereochemical implications derived from the crystal structure of the latter have been investigated in particularly thorough fashion (Staab, Jo¨rns, Krieger and Rentzea, 1985). The meta-bridged quinone unit shows a much greater deformation from planarity than the para-bridged aromatic moiety (Fig. 14.7). The carbonyl group is located above the aromatic ring in a manner similar to that found in binary CT molecular compounds where the acceptor is a quinone, and also in self-complexes such as naphthoquinones (cf. Section 15.6). The spontaneous resolution of 14.26 into chiral crystals was exploited by handseparation of enantiomorphs under the microscope (the Pasteur method) and measurement of optical rotatory dispersion (ORD) and circular dichroism (CD) in CHCl3 solution (Fig. 14.8). In principle, at least, the absolute conﬁgurations of the crystals could

MOLECUL ES OF THE METAPARACYCLOPHANE TYPE

para bridge

1.377

977

p-dimethoxy portion

1.554

meta bridge

z x

p-benzoquinone portion

1.224 y

C

A

B

z y

Fig. 14.7. Molecular and crystal structure of 14.26 (DALTOZ). (upper): Perspective view of the ˚ ) in the two portions of the molecule are shown, as well as molecule. The different C–O distances (A a typical bridging C–C distance. Bond angle deformation is preferred to alteration of bond lengths. (lower): Packing arrangement shown in projection down [100]; hydrogens omitted for clarity. ˚ , P212121, Z ¼ 4. (Data from Staab, Jo¨rns, Krieger and Orthorhombic; 7.698(1) 8.205(1) 24.025(2) A Rentzea, 1985.)

be determined by the Bijvoet method using anomalous scattering from the oxygen atoms and then related to the signs of the optical rotation; however, this has not yet been done and is a challenging task, as has been demonstrated, for example, by Rabinovich and Hope (1980). Furthermore, ‘‘these systems offer, apparently for the ﬁrst time, the

978

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

(+) O

40

OMe

30 MeO

O

20

[u]·10–3

10 A 0 300 10

400

500

600

l[nm]

B

20

30

40 (–)

Fig. 14.8. Circular dichroism of two enantiomorphic single crystals (of unknown optical purity) in CHCl3 solution (concentrations 2.8 106 (A) and 2.1 106 g/ml (B) respectively). The molar rotations (in deg. at 20 ) were []460 5215 (A) and þ 5811 (B); []334 35164 (A) and þ 41720 (B). (Reproduced from Staab, Jo¨rns, Krieger and Rentzea, 1985.)

opportunity of measuring ORD and CD related to a charge-transfer chromophore with well-deﬁned and rigid donor–acceptor orientations’’ (Staab, Jo¨rns, Krieger and Rentzea, 1985). 14.26 and 14.27 are, of course, isomers which differ in that the aromatic ring is para bridged in the ﬁrst of the pair and meta bridged in the second. The crystal structure of 14.27 has not been reported but those of 5,8,12,15-tetra-methoxy[2.2]metaparacyclophane (DALTUE) and the corresponding bis-quinone {[2.2](2,5)-(2,6)-p-benzoquinophane (DALVAN) have been determined (Staab, Jo¨rns, Krieger and Rentzea, 1985). All three molecules have similar overall shapes, and it is reasonable to assume that this holds for 14.27 as well. There have also been a number of investigations of compounds of the [3.3]metaparacyclophane series and both quinhydrone isomers have been synthesized (as the methoxy derivatives 14.28 and 14.29) (Staab, Jo¨rns, Krieger and Rentzea, 1985). In the corresponding benzene compounds it was inferred (Staab and Knaus, 1979) from NMR spectra that the rings were not parallel, thus accounting for the rather ill-deﬁned CT bands in the UV-visible spectra. Deﬁnitive evidence about molecular structure comes from the crystal structure analysis of 14.28 (Fig. 14.9; DALVER).

MOLECUL ES OF THE METAPARACYCLOPHANE TYPE

979

p-dimethoxy portion

O4 para bridge

O3 1.536 O2

meta bridge p-benzoquinone portion

y x

O1 z

A

B

C

y z

Fig. 14.9. Molecular and crystal structure of 14.28 (DALVER). (upper) Perspective view; distances ˚ . The torsion angle O1–O2–O3–04 is 141.5 . in A (lower) Pseudo-hexagonal close packing of molecular stacks viewed along [100]; monoclinic, ˚ , ¼ 114.87(2) , P21/c, Z ¼ 4. (Data from Staab, Jo¨rns, Krieger and 8.555(1) 25.697(3) 8.370(1) A Rentzea, 1985.)

980

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

OMe

O

O OMe

MeO

O

MeO 14.28

O

14.29

The two rings are inclined at an angle of 12.6 , the individual rings being only mildly deformed; one bridge shows disorder of a methylene group over two sites (occupancy of major site 85%) similar to that encountered earlier (see Fig. 14.5). The spectrum of 14.28 has a CT band similar to that of 14.26 (m ¼ 485 nm, " ¼ 560, in CHCl3); however, there is also an absorption at shorter wavelength (m ¼ 375 nm, " ¼ 620, in CHCl3) which was ascribed to a second CT transition analogous to that found in the electronic spectra of pseudo-ortho [3.3]paracyclophane quinhydrones. The CT band of 14.29 is blue-shifted by about 120 nm (m ¼ 365 nm, " ¼ 800, in CHCl3), analogous to the behaviour of the 14.26 and 14.27 diastereoisomers. The rather complicated and distorted geometrical structures of the molecules in this series prevent explanation of the spectra by the simple HMO model that worked fairly well for the [2.2] and [3.3]paracyclophane quinhydrones. The analogous compounds containing tropoquinono rings have also been reported (Kawamata, Fukazawa, Fujise and Ito, 1982a,b); the spectra are very similar to those of the para compounds (e.g. 14.18), with ill-deﬁned CT bands. 14.4

Molecules of the metacyclophane type

The anti- and syn-isomers of a number of [2.2]metacyclophanes, where both donor and acceptor groups are suitably-substituted aromatic moieties, have been investigated (Staab, Schanne, Krieger and Taglieber, 1985); the corresponding quinhydrones are also available (Staab, Reibel and Krieger, 1985). Crystal structures have been reported for representative molecules and there are appreciable geometrical differences between anti and syn isomers. The structure of anti-5,8-dimethoxy-13-nitro[2.2]metacyclophane (Staab, Schanne, Krieger and Taglieber, 1985; DAVHAJ) is shown in Fig. 14.10 and that of syn-13,16dimethoxy-[2](2,6)-p-benzoquinono[2]metacyclophane (Staab, Reibel and Krieger, 1985; DEBZEP) in Fig. 14.11. Meo x

OMe Meo x

OMe x

X = COOMe, CN, NO 2

O

O x

MeO

OMe

SYN

O

O Meo

OMe

ANTI

The anti-isomer shows little overlap of donor and acceptor portions and the tilt between them is relatively small at 15 . On the other hand, although the two rings of

MOLECULES OF THE METACYCLOPHANE TYPE

981

O1

1.563

p-dimethoxy portion O2

PERSPECTIVE VIEW

C16

2-meta bridges y N1 nitrobenzene portion

x

z

nitrobenzene portion

SIDE VIEW

meta bridges

z p-dimethoxy portion x y

Fig. 14.10. Molecular structure of anti-5,8-dimethoxy-13-nitro[2.2]metacyclophane (DAVHAJ). ˚. (upper) Perspective view of molecule; the torsion angle O1–O2–C16–N1 is 178.95 ; distances in A (lower) Side view. A stereoview of the molecule is shown in the original paper. (Data from Staab, Schanne, Krieger and Taglieber, 1985.)

the syn molecule appear to be appreciably overlapped in plan view, the side view shows that there is a tilt angle of 33 between them and that there are close interannular approaches only on one side of the molecule. Despite these geometrical differences, the spectra of the anti, syn pair of diastereoisomeric quinhydrones are remarkably similar (Fig. 14.12; Staab, Reibel and Krieger, 1985) and this holds also for other analogous pairs; investigation of the solvent dependence of the ﬂuorescence from various molecules showed that the long wavelength absorption bands were indeed charge-transfer bands (Staab, Schanne, Krieger and Taglieber, 1985).

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

982

PERSPECTIVE VIEW p-dimethoxy portion

O4

O3

1.557

O2

p-benzoquinone portion

x y

O1

z

p-benzoquinone portion

O1

O2

SIDE VIEW 1.557 O4 O3 p-dimethoxy portion

x

y

z

Fig. 14.11. Molecular structure of syn-13,16-dimethoxy[2](2,6)-p-benzoquinone-[2]metacyclo-phane (DEBZEP). (upper) Perspective view of molecule; the torsion angle O1–O2–O4–O3 is 9.81 ; ˚ . (lower) Side view. A stereo view of the molecule is shown in the original paper. distances in A (Data from Staab, Reibel and Krieger, 1985.)

The similarity of the CT absorption bands from anti and syn donor–acceptor metacyclophanes despite the very different disposition of donor and acceptor moieties has been explained in terms of Hu¨ckel molecular orbital theory (Vogler, Schanne and Staab, 1985).

MOLECULES OF THE METACYCLOPHANE TYPE

983

lg e O

O

O

O OMe MeO

MeO

OMe

4.00

3.00

2.00

1.00 250

300

350

400

450

500

550

l (nm)

Fig. 14.12. The charge-transfer spectra (in CHCl3) of the anti -syn isomer pair of quinhydrones shown as inserts at the top of the diagram. (Reproduced from Staab, Schanne, Krieger and Taglieber, 1985.) lg ε

O MeO

O OMe

O

lg ε

O MeO

HO

OMe

4

4

3

3

2

2

300

400

500

λ (nm)

O

300

O OMe

400

O

O MeO

500

OH

λ (nm)

Fig. 14.13. Comparison of the spectra of the syn and anti diastereoisomers of the two [3.3]metacyclophanes shown as inserts at the top of the ﬁgure. Replacement of one methoxy group in each donor moiety by an hydroxyl has little effect on the spectra. (Reproduced from Staab, Herz, Do¨hling and Krieger, 1980.)

Quinhydrones of the [3.3]metacyclophane series and related molecules have also been studied (Staab, Herz and Do¨hling, 1979; Staab and Do¨hling, 1979; Staab, Herz and Do¨hling, 1980; Staab, Herz, Do¨hling and Krieger, 1980). Spectra of anti and syn pairs of isomers show marked resemblances (Fig. 14.13). The spectrum of syn-15,18-dihydroxy[3](2,6)-p-benzoquinone[3]meta-cyclophane is very similar to that of pseudogeminal 14,17-dihydroxy[3](2,5)-p-benzoquinone-[3]

984

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

O

O

HO

lg ε

O

OH

O

HO

OH

4

3

2

300

400

500

600

λ (nm)

Fig. 14.14. Comparison of the UV-visible absorption spectra (in dioxane) of the pseudogeminal 14,17-dihydroxy[3](2,5)-p-benzoquinone[3]paracyclophane (on the left of the insert in the upper portion of the diagram) and of syn-15,18-dihydroxy[3](2,6)-p-benzoquinone[3]metacyclophane (on the right). (Reproduced from Staab, Herz, Do¨hling and Krieger, 1980.)

paracyclophane (Fig. 14.14). The overlaps of donor and acceptor portions of these two molecules are not very different, thus accounting for the similarity of their spectra; the structure of syn-15,18-dihydroxy[3](2,6)-p-benzoquinone[3]metacyclophane is shown in Fig. 3 of Staab, Herz, Do¨hling and Krieger (1980) while that of pseudogeminal 14,17-dihydroxy-[3](2,5)-p-benzoquinone[3]paracyclophane is in Fig. 14.5. The crystal structures of two syn isomers have been reported – of syn-15,18dimethoxy(2,6)-p-benzoquinono[3.3]metacyclophane (Staab, Herz, Do¨hling and Krieger, 1980; MXBQMP) and of syn-6,9-dimethoxy-15,18-dinitro-2,11-dithia[3.3]metacyclophane (Staab, Schanne, Krieger and Taglieber, 1985; DAVGUC). As would be expected, the molecules of the [3.3]metacyclophane series are less distorted (but some distortion remains) than those of the [2.2]metacyclophane series. 14.5

Some other systems

We give a few examples of other systems where the principles discussed above are being applied in order to illustrate how one may expect the particular features of cyclophane systems to be exploited in the future. The electron transfer properties of the verticallystacked porphyrin-quinone(1)-quinone(2) cyclophane, an analog to compounds involved in the primary process of biological photosynthesis, have been studied in order to determine which structural factors favour a consecutive, stepwise electron transfer and which an integrated process relying on electron coupling (Staab, Tercel, Fischer and Krieger, 1994). During the course of the synthesis of compound 14.30, the crystal structure of 14.31 (which is a substituted pseudo-ortho[3.3]-paracyclophane) was determined (WIHMIJ); the molecular structure resembles that shown in Fig. 14.5.

SOME OTHER SYSTEMS

985

Cl 0 pseudo-ortho [3.3]paracyclophane

0 Cl

Cl 0

0Me

Me0

Et

0Me

Cl

Et

Me

Me N NH

Me

HN

Me0

Me00C

N

C00Me

Me Et

Et

14.30

14.31

Another system (Cowan, Sanders, Beddard and Harrison, 1987), involving different dispositions of pyromellitimide (an electron acceptor) and porphyrin rings (the cofacial pair acting as an electron donor), demonstrates that ‘‘mere proximity between donor and acceptor is not a sufﬁcient condition for electron transfer. There is also a strong geometrical requirement.’’ Picosecond ﬂuorescence measurements show (by marked quenching of the ﬂuorescence) that there is rapid electron transfer from the excited porphyrin pair to the pyromellitimide electron acceptor in 14.32 whereas there is relatively little ﬂuorescence quenching in 14.33, and hence slow electron transfer. A rather similar rigid triple-ring molecule with a porphyrin sandwiched between two parallel p-benzoquinone units has also been reported (Weiser and Staab, 1984). There are clear analogies to triple-layer CT cyclophanes. Another triple layer system is the crystalline green cationic acceptor–donor–acceptor system prepared by Simonsen et al. (1998), with butane-1,4-diyl linkers; there are four PF6 counter-anions and three MeCN molecules of solvation. The acceptors are bipyridinium moieties and the donor is based on TTF. Crystal structure analysis shows a rather distorted molecule without particularly close interactions. Presumably shorter linker units are needed to enforce geometrical constraints. N

O

O

O

O

O

O

O O

N

O

N

O

O

N O O N NH O

O O

NH

N

N H N

HN N

N H N

HN O

N O

O

O

O

O

O

O (2) N NH

HN N

(1)

14.32

14.33

INTRA-MOLECULAR DONOR–ACCEPTOR INTERACTIONS

986

14.6

Concluding summary

Thus, in summary, the measurements on the cyclophane intramolecular donor–acceptor compounds have conﬁrmed, for many two-layer molecules, a marked dependence of the degree of charge transfer on the mutual orientation of the donor and acceptor moieties. The charge transfer is greater when the long axes of the moieties are parallel than when they are inclined at an angle of 60 . For two-layer molecules the situation in the [2.2]paracyclophanes is complicated by the very strong interaction between the adjacent rings, but the orientation effect is just as marked in the [3.3]paracyclophanes where the distance between the rings is similar to non-bonded distances found in the corresponding crystalline compounds. Charge transfer interaction persists through the rings in three- and four-layer molecules but the orientation effect is lost. The orientation effects are not marked in systems such as the tropoquinophanes and the higher [n.n]cyclophanes (n > 3), where the CT interaction is rather weak. In the [n.n]metacyclophane series the geometrically-different anti and syn isomers give remarkably similar CT absorption spectra, a result which has been explained by HMO theory. One may anticipate that a wealth of information remains to be uncovered by spectroscopy at very low temperatures of molecules in rigid glasses, and that these results will eventually be interpreted by ab initio calculations based on the detailed geometrical structures obtained from diffraction studies. In addition one should note that cyclophanetype molecules lend themselves to study of a variety of secondary interactions between moieties in deﬁned geometrical situations, and this is likely to be an important growth area in future research. References Bauer, H., Briaire, J. and Staab, H. A. (1983). Angew. Chem. Int. Ed. Engl., 22, 334–335. Bernstein, J. and Trueblood, K. N. (1971). Acta Cryst., B27, 2078–2089. Cowan, J. A., Sanders, J. K. M., Beddard, G. S. and Harrison, R. J. (1987). J. Chem. Soc., Chem. Comm., pp. 55–58. Cram, D. J. and Day, A. C. (1966). J. Org. Chem., 31, 1227–1232. Hanson, A. W. (1977). Acta Cryst., B33, 2003–2007. Hausser, K. H. and Wolf, H. C. (1976). Adv. Magn. Reson., 8, 85–121. Herz, C. P. and Staab, H. A. (1977). Angew.Chem. Int. Ed. Engl., 16, 394. Horita, H., Otsubo, T., Sakata, Y. and Misumi, S. (1976). Tetr. Letts., pp. 3899–3902. Ippen, J., Tao-pen, C., Starker, B., Schweitzer, D. and Staab, H. A. (1980). Angew. Chem. Int. Ed. Engl., 19, 67–69. Kawamata, A., Fukazawa, Y., Fujise, Y. and Ito, S. (1982a). Tetr. Letts., 23, 1083–1086. Kawamata, A., Fukazawa, Y., Fujise, Y. and Ito, S. (1982b). Tetr. Letts., 23, 4955–4958. Koizumi, Y., Toyoda, T., Miki, K., Kasai, N. and Misumi, S. (1986). Bull. Chem. Soc. Jpn., 59, 239–242. Krieger, C. (1978). Unpublished. Machida, H., Tatemitsu, H., Sakata, Y. and Misumi, S. (1978). Tetr. Letts., pp. 915–918. Mizuma, T., Miki, K., Kai, Y., Tanaka, N. and Kasai, N. (1982). Bull. Chem. Soc. Jpn., 55, 2026–2028.

REFERENCES

987

Mizuma, T., Miki, K., Kai, Y., Yasuoka, N. K. and Kasai, N. (1982). Bull. Chem. Soc. Jpn., 55, 979–984. Mizuno, H., Nishiguchi, K., Toyoda, T., Otsubo, T., Misumi, S. and Morimoto, M. (1977). Acta Cryst. B33, 329–334. O’Connor, J. G. and Keehn, P. M. (1976). J. Am. Chem. Soc., 98, 8446–8450. Rabinovich, D. and Hope, H. (1980). Acta Cryst., A36, 670–678. Rebafka, W. and Staab, H. A. (1973). Angew. Chem. Int. Ed. Engl., 12, 776–777. Rebafka, W. and Staab, H. A. (1974). Angew. Chem. Int. Ed. Engl., 13, 203–204. Schroff, L. G., Weerdt, A. J. A.van der, Staalman, D. J. H., Verhoeven, J. W. and de Boer, Th. J. (1973). Tetr. Letts., pp. 1649–1652. Schroff, L. G., Zsom, R. L. J., Weerdt, A. J. A. van der, Schrier, P. I., Geerts, J. P., Nibbering, N. M. M., Verhoeven, J. W. and de Boer, Th. J. (1976). Rec. Trav. Chim. Pays-Bas, 95, 89–93. Schwartz, M. H. (1990). J. Incl. Phenom., 9, 1–35. Schweitzer, D., Hausser, K. H., Taglieber, V. and Staab, H. A. (1976). Chem. Phys., 14, 183–187. Shinmyozu, T., Inazu, T. and Yoshino, T. (1977). Chem. Letts., pp. 1347–1350. Simonsen, K. B., Thorup, N., Cava, M. P. and Becher, J. (1998). Chem. Commun., pp. 901–902. Staab, H. A. and Appel, W. (1981). Liebig’s Ann. Chem., pp. 1065–1072. Staab, H. A. and Do¨hling, A. (1979). Tetr. Letts., pp. 2019–2022. Staab, H. A. and Haffner, H. (1977). Chem. Ber., 110, 3358–3365. Staab, H. A. and Herz, C. P. (1977a). Angew. Chem. Int. Ed. Engl., 16, 392–394. Staab, H. A. and Herz, C. P. (1977b). Angew. Chem. Int. Ed. Engl., 16, 799–801. Staab, H. A. and Knaus, G. H. (1979). Tetr. Letts., pp. 4261–4264. Staab, H. A. and Rebafka, W. (1977). Chem. Ber., 110, 3333–3350. Staab, H. A. and Schwendemann, V. (1978). Angew. Chem. Int. Ed. Engl., 17, 756–757. Staab, H. A. and Taglieber, V. (1977). Chem. Ber., 110, 3366–3376. Staab, H. A. and Zapf, U. (1978). Angew. Chem. Int. Ed. Engl., 17, 757–758. Staab, H. A., Do¨hling, A. and Krieger, C. (1981). Liebig’s Ann. Chem., pp. 1052–1064. Staab, H. A., Do¨hling, A. and Krieger, C. (1991). Tetr. Letts., 32, 2215–2218. Staab, H. A., Gabel, G. and Krieger, C. (1983). Chem. Ber., 116, 2827–2834. Staab, H. A., Gabel, G. and Krieger, C. (1987). Chem. Ber., 120, 269–273. Staab, H. A., Herz, C. P. and Do¨hling, A. (1979). Tetr. Letts., pp. 791–794. Staab, H. A., Herz, C. P. and Do¨hling, A. (1980). Chem. Ber., 113, 233–240. Staab, H. A., Herz, C. P. and Henke, H.-E. (1977). Chem. Ber., 110, 3351–3357. Staab, H. A., Herz, C. P., Do¨hling, A. and Krieger, C. (1980). Chem. Ber., 113, 241–254. Staab, H. A., Herz, C. P., Krieger, C. and Rentzea, M. (1983). Chem. Ber., 116, 3813–3830. Staab, H. A., Hinz, R., Knaus, G. H. and Krieger, C. (1983). Chem. Ber., 116, 2835–2847. Staab, H. A., Ippen, J., Tao-pen, C., Krieger, C. and Starker, B. (1980). Angew. Chem. Int. Ed. Engl., 19, 66–67. Staab, H. A., Jo¨rns, M. and Krieger, C. (1979). Tetr. Letts., pp. 2513–2516. Staab, H. A., Jo¨rns, M., Krieger, C. and Rentzea, M. (1985). Chem. Ber., 118, 796–813. Staab, H. A., Knaus, G. H., Henke, H. -E. and Krieger, C. (1983). Chem. Ber., 116, 2785–2807. Staab, H. A., Krieger, C., Wahl, P. and Kay, K-Y. (1987). Chem. Ber., 120, 551–558. Staab, H. A., Reibel, W. R. K. and Krieger, C. (1985). Chem. Ber., 118, 1230–1253. Staab, H. A., Reimann-Haus, R., Ulrich, P. and Krieger, C. (1983). Chem. Ber., 116, 2808–2826. Staab, H. A., Schanne, L., Krieger, C. and Taglieber, V. (1985). Chem. Ber., 118, 1204–1229. Staab, H. A., Starker, B. and Krieger, C. (1983). Chem. Ber., 116, 3831–3834. Staab, H. A., Tercel, M., Fischer, R. and Krieger, C. (1994). Angew. Chem. Int. Ed. Engl., 33, 1463–1466. Staab, H. A., Wahl, P. and Kay, K-Y. (1987). Chem. Ber., 120, 541–549. Staab, H. A., Zapf, U. and Gurke, A. (1977). Angew. Chem. Int. Ed. Engl., 16, 801–803.

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Sto¨bbe, M., Kirchmeyer, S., Adiwidjaja, G. and Meijere, A. de, (1986). Angew. Chem. Int. Ed. Engl., 25, 171–173. Tashiro, M., Koya, K, and Yamato, T. (1983). J. Am. Chem. Soc., 105, 6650–6653. Tatemitsu, H., Natsume, B., Yoshida, M., Sakata, Y. and Misumi, S. (1978). Tetr. Letts., pp. 3459–3462. Tatemitsu, H., Otsubo, T., Sakata, Y. and Misumi, S. (1975). Tetr. Letts., pp. 3059–3062. Toyoda, T., Tatemitsu, H., Sakata, Y., Kasai, N. and Misumi, S. (1986). Bull. Chem. Soc. Jpn., 59, 3994–3996. Vogler, H. (1983a). Tetr. Letts., pp. 2159–2162. Vogler, H. (1983b). Z. Naturforschung, 38B, 1130–1135. Vogler, H., Ege, G. and Staab, H. A. (1977). Mol. Phys., 33, 923–932. Vogler, H., Schanne, L. and Staab, H. A. (1985). Chem. Ber., 118, 1254–1260. Weiser, J. and Staab, H. A. (1984). Angew. Chem. Int. Ed. Engl., 23, 623–625. Yoshida, M., Tatemitsu, H., Sakata, Y., Misumi, S., Masuhara, H. and Mataga, N. (1976). J. Chem. Soc. Chem. Comm., pp. 587–588. Yoshida, M., Tochiaki, H., Tatemitsu, H., Sakata, Y. and Misumi, S. (1978). Chem. Lett., pp. 829–832.

Chapter 15 Crystal chemistry of mixed-stack p–p* molecular compounds

Wie aus zahlreichen Versuchen hervorgeht, vereinigen sich die Nitroko¨rper der aliphatischen wie aromatischen Reihe mit den verschiedenartigsten organischen Verbindungen zu mehr oder weinigen tieffarbigen Additionsprodukten. Besonders gut charakterisiert sind vor allem die Verbindungen aromatischer Di-und Trinitroko¨rper mit aromatischen Kohlenwasserstoffen, Amine und Phenolen. Wie ein statistische Ueberschicht der bis heute dargestellten, etwa 700 Moleku¨l-verbindungen der Nitroko¨rper zeigt, haben diese in den allermeisten Fa¨llen, ganz unabha¨ngig davon, wieviele Nitrogruppen die nitroide Komponente entha¨lt, auch unabha¨ngig von der Zusammensetzung der benzoiden Komponente, die denkbar einfachste Zusammensetzung A1B1, indem auf 1 Moleku¨l des Nitroko¨rper 1 Moleku¨l des Kohlenwasserstoffs bzw. seiner Derivate kommt. Rund 85% der Verbindungen, von dene wenige aufgeza¨hlt seien, entsprechen diesen Typus. Paul Pfeiffer, 1927 (p. 336).

Summary: The room-temperature crystal structures of many mixed stack charge transfer molecular compounds can be grouped into a relatively small number of crystallochemical families. Although the mixed stack arrangement predominates, there are structures which deviate to a greater or lesser extent from such an arrangement, for reasons which are often not clear. We ﬁrst review these maverick structures and then classify the more common mixed stack arrangements into a number of structural groups. Compounds with quinonoid acceptors sometimes have special structural features because of the mode of interaction of the carbonyl groups with aromatic rings. In the quinhydrone family the (aromatic ring) carbonyl interaction is supplemented by hydrogen bonding between carbonyl and hydroxyl oxygens and this leads to considerable structural homogeneity. Many CT compounds where the –* interaction is supplemented by hydrogen bonding show special structural features and physical properties different from those with only –* interaction. The mixed stack compounds with ionic ground states generally resemble those with neutral ground states in structural terms but have different physical properties. In the isomeric compounds the possibility of having both electron and proton transfer leads to variations on the mixed stack theme. n n n

15.1 15.2 15.3 15.4 15.5

Introduction Nonstacked structures containing structural groups of limited size The crystallochemical families found for 1 : 1 p–p* molecular compounds Packing arrangements in n : m p–p* molecular compounds Some special features of packing arrangements in p–p* molecular compounds 15.5.1 Crystals where one of the components is also found in interstitial positions 15.5.2 Noncentrosymmetric crystals of -molecular compounds

990 993 994 1001 1005 1005 1007

990

CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

15.5.3 Acceptors based on polynitrofluorene 1009 15.5.4 Resolution of helicenes by formation of diastereoisomeric charge transfer molecular compounds with enantiomeric acceptors 1010 15.6 Structurally important interactions between polarizable and polar groups 1011 15.7 Mixed-stack crystals with both charge transfer and hydrogen bonding interactions 1013 15.7.1 The quinhydrones as a crystallochemical family 1013 15.7.2 Molecular compounds of the flavins 1022 15.7.3 Other crystals with both charge transfer and hydrogen bonding interactions 1026 15.8 Mixed-stack crystals with both delocalized and localized charge transfer interactions 1030 15.9 Donors and acceptors with special chemical features 1032 15.9.1 Fluorinated aromatics as quasi-acceptors 1032 15.9.2 1,3,5,7-Tetramethyluric acid (TMU) as quasi-acceptor 1040 15.9.3 Acceptor is a metal coordination complex 1040 15.9.4 Donor is a metal coordination complex 1042 15.9.5 Donors based on phenazine 1044 15.10 Mixed-stack donor–acceptor molecular compounds with ionized ground states 1047 15.10.1 Mixed-stack closed shell charge transfer salts 1047 15.10.2 Ion-radical salts 1048 15.11 Isomeric (polymorphic) molecular compounds 1052 15.11.1 Type 1 – isomerism due to different types of interaction without change of moiety structure 1052 15.11.2 Type 2 – isomerism due to electron transfer 1054 15.11.3 Type 3 – isomerism due to proton transfer or to –* electron transfer 1055 15.11.4 Isomerism stabilized by both charge (–*) and proton transfer (CPT compounds) 1058 15.12 Self-complexes 1059 15.13 Conclusions 1064 15.13.1 Structural variety in –* molecular compounds 1064 15.13.2 How should the packing arrangements in –* molecular compounds be described? 1065 15.13.3 Structural consequences of –* interactions 1066 (Note. The components in the ground states of these molecular compounds are taken to be neutral unless explicitly stated otherwise). References 1068

15.1

Introduction

Most –* molecular compounds have 1 : 1 donor acceptor (D A) ratios and the components crystallize in alternating array in mixed stacks, the stacks being close packed in a quasi-hexagonal arrangement of (approximate) cylinders (Fig. 15.1). We remind the reader of our conventions – donors always come ﬁrst in the formulation and are linked to the acceptor by , indicating a –* charge transfer (CT) interaction; we have not been very strict in our usage of this indicator. Most donor and acceptor molecules are disk-like in shape, i.e. their cross-sectional area is appreciably greater than their thickness. ˚ and thus the The molecular thickness of aromatic donor and acceptors is about 3.5 A n n n

n n n

n n n

I NT RO D UC T I O N

991

˚ for. . . . DADA. . . . stacks. The interplanar periodicity along the stack axis should be 7–8 A spacing, measured along the normals to the planes of the approximately parallel disks, ˚ less than the sum of the thickness of the components; this is is often found to be 0.1–0.2 A interpreted as evidence for a D A interaction along the normal to the component planes, or stack axis (see below), which is additional to the ubiquitous van der Waals interactions. There are a number of facts in support of this contention. Firstly, one can compare the transannular atom-to-atom distances, found from crystal structure analyses (Staab et al., 1983) in pseudo-geminal-5,8,14,17-tetramethoxy[3.3]paracyclophane and its quinhydrone analog pseudo-geminal-14,17-dimethoxy-[3](2,5)p-benzoquinone-[3]paracyclophane (see Chapter 14 for discussion of these compounds). The molecules have identical ˚ closer in the latter than in the former molecule, conformations but the two rings are 0.13 A in conformity with the existence of charge transfer interactions between the rings in the latter molecule but not in the former. A second line of evidence comes from comparison of Young’s modulus values in the direction of the stack axes, which are about ten times larger for crystals of -molecular compounds than for those of comparable aromatic hydrocarbons (Danno et al., 1967). Thus we choose to emphasize the mixed stacks as the essential and characteristic feature of the packing arrangements in -molecular compounds. The simple mixed stack description works remarkably well for most of the structures so far reported; however, it tends to break down when donor and acceptor molecules differ appreciably in disk (face) area or when there is additional bonding (e.g. hydrogen bonding or dipolar interactions) between the components. There are some crystals of this type where the structure can equally well be described in terms of layers of donor and acceptors. The extremes of packing type within the stacks can be described as ‘‘overlapped disks’’ (Fig.15.1(a)) and ‘‘slipped disks’’ (Fig.15.1(b)). However, intermediate situations are also found and there have been a number of essentially similar proposals (Fritchie and Arthur, 1966; Goldberg and Shmueli, 1973b; Visser et al., 1990) for a quantitative description of the arrangement within the stacks; we have adapted the proposal of Visser et al. (1990) to mixed stack compounds where the components lack symmetry. Right-handed orthonormal axial systems L, M, N are deﬁned for the donor and acceptor molecules (or convenient portions, such as benzene rings); with L along the longest molecular axis, n n n

(a)

(b)

Stack Axis

(c)

Stack Axis

Fig. 15.1. Schematic representation of different types of stacking in crystalline mixed stack -compounds: (a) overlapped disk stacking, (b) slipped disk stacking and (c) quasi-hexagonal arrangement of stacks.

992

CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

M perpendicular to L and in the best molecular plane, and N at right angles to the plane. The offset of the centre of gravity of the donor from the center of gravity of the acceptor is then given in terms of the components along the L, M and N axes of the acceptor (an arbitrary choice). A simpliﬁed situation for centrosymmetric molecules projected onto their mean planes is shown in Fig. 15.2. Results for a few molecular compounds are summarized in Table 15.1. Unfortunately most authors describe molecular overlap and calculate interplanar distances on a less well-deﬁned basis. ˚ along the stack axis may require amendment in two The repetition period of 7 A ways : (a)

there are a number of crystals (Table 15.3) where the stack periodicity is doubled to ˚ and the arrangement along the stack is 14 A -------D1 A1 D2 A2 D1 A1 D2 A2------˚ | 14 A | The subscripts here refer to positional and/or orientational differences between donor (and acceptor) molecules, not to chemical differences. The causes of the ordering

Table 15.1. Examples of different stacking arrangements in mixed stack molecular compounds: I is {phenazine TCNQ} (Goldberg and Shmueli, 1973c; TCQPEN10); II is {dibenzop-dioxin TCNQ} (Goldberg and Shmueli, 1973b; TCQBDX); III is {anthracene TCNQ} ˚ and angles in deg (Williams and Wallwork, 1968; TCQANT). Distances in A n n n

n n n

n n n

Parameter

I

II

1. 2. 3. 4. 5.

8.57 38 1.85 1.89 3.38

7.04 11 0.51 0.48 3.46

Repeat distance along stack axis Angle between stack axis and plane normal Mutual offset along L Mutual offset along M Interplanar spacing

III 7.00 0 0.0 0.0 3.50

M N

N N

L

N

Fig. 15.2. {Phenazine TCNQ}, showing donor and acceptor molecules in a mixed stack projected onto their common mean plane. The long (L) and short (M) in-plane axes of TCNQ are shown. (Reproduced from Goldberg and Shmueli, 1973b.) n n n

NONSTACKED STRUCTURES

993

along the stack direction are not always clear; interactions between adjacent stacks are sometimes invoked. Higher degrees of ordering (i.e. periodicities greater than ˚ ) do not appear to have been encountered. 14 A (b) there are a number of crystals where the concept of inﬁnite stacks no longer applies; instead the stack length is limited to one, two or three pairs. These ﬁnite stacks can be arranged in different ways. These ideas will be illustrated in more detail and also extended to -molecular compounds with D : A 6¼ 1.

15.2 Nonstacked structures containing structural groups of limited size The smallest structural group of limited size is the donor–acceptor pair, not incorporated in a stack. Such arrangements are found in {benz[a]-anthracene PMDA} (Foster et al., 1976; BZAPRM10) and {1,10-phenanthroline TCNQ} (Goldberg and Shmueli, 1977; TCQPAN10). The overall crystal structures can be described in terms of mutually shifted layers of donors and acceptors. Analogous donor–acceptor pairs are found in the crystal structures of tryptamine picrate (TRYPIC) and dl-tryptophan picratemethanol (TPTPCM) (Gartland et al., 1974). The red colour of these crystals attests to the occurrence of charge transfer interactions within the donor–acceptor pairs; neighbouring pairs are linked by hydrogen bonds and not by –* interactions.1 n n n

n n n

H tryptamine: R+ = –CH2CH2NH3+

N H

R+

tryptophan: R+ = –CH2CH(CO2H)NH3+

In {(9-ethylcarbazole)2 TCNE} (Lee and Wallwork, 1978; ETCZCE) the structure ˚ between donor and consists of centrosymmetric DAD units, with a distance of 3.24 A acceptor molecules. These sandwiches are arranged in face-centred pleated sheets, with mean plane (010); however, the pleats are alternately parallel to (021) and (021); there being an angle of 60 between these planes. Successive sheets are related by a c glide plane perpendicular to [010]. The analogous arrangement found in {(acridine)2 PMDA} (Karl, Binder et al., 1982; BIWVUY) is shown in Fig. 15.3. Centrosymmetric ADA sandwiches are found in the 1 : 2 compound of a Ni(II)etioporphyrin with 2,4,5,7-tetranitroﬂuorenone (P21/n, Z ¼ 2) (Grigg et al., 1978; ETPNFL); and in {2,7-bis(methylthio)1, Z ¼ 1) (Nakasuji, Sasaki et al., 1,6-dithiapyrene- (tetrahydrobarreleno-TCNQ)2} (P 1988; SANYOV). Effectively-isolated DAD triads are found in (toluene)2 tetraphenylporphyrinato-M(II) molecular compounds (M ¼ Cr, Mn, Zn; see Chapter 8 and Section 15.9.4). In the 2 : 1 compound of N,N,N 0 ,N 0 -tetramethylbenzidine and chloranil n n n

n n n

n n n

n n n

1 Mixed stacks are found in three tryptophan metabolite–picric acid molecular compounds; their red colour shows that there is charge-transfer interaction (Nagata et al., 1995).

994

CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Fig. 15.3. The crystal structure of {(acridine)2 PMDA} at 120K, showing a stereoscopic view down [100] of one layer of the structure ([001] is vertical and [010] runs from left to right). The tilt of the acridine molecules with respect to the PMDA molecules can be seen clearly. (Reproduced from Karl, Binder et al., 1982.) n n n

the two benzene rings of the benzidine moiety have an interplanar (twist) angle of 31 and the chloranil is sandwiched between two parallel rings of successive benzidines, the second ring of each benzidine molecule not participating in the charge transfer interaction (Yakushi, Ikemoto and Kuroda, 1971; TMBCAN). There are a number of analogous structures where the ground state is ionic and these are discussed in Section 15.10. No overall explanation has yet been put forward for these exceptional structures.

15.3

The crystallochemical families found for 1 : 1 p–p* molecular compounds

The crystal structures of most of the 1 : 1 –* molecular compounds can be grouped into a limited number of crystallochemical types; we use number of formula units in the unit cell (Z ); space group and stack axis direction as criteria for this classiﬁcation, restricting ˚ (however, some exceptions are ourselves at this point to stack axis periodicities of 7 A ˚ ). The cell admitted when the donor or acceptor molecule is thicker than the usual 3.5 A dimensions in directions normal (or approximately so) to the stack axis are determined mainly by the cross-sectional dimensions of the stacks and their mode of arrangement. As noted above, there is generally quasi-hexagonal close packing of the stacks, all stack axes being parallel. A few exceptions have been found to this rule; for example, in {pyrene pbenzoquinone} (Bernstein et al., 1976; PYRBZQ) (tetragonal, space group P41, Z ¼ 4) ‘‘slipped disk’’ stacking of the usual kind is found but the stacks are arranged in layers one stack thick, successive layers being related by the 41 axes (Fig. 15.4). No explanation has n n n

C4

2.8

8

C11

C4 C1 C2

b

C9

995

O4

C11

2.4

5

3.4

9

O4 C2

O4

2.8 8

T HE CRYSTALLOCHE MICAL FAMILIES

2.4

C9

9

01

a 0

1

2Å

Fig. 15.4. Part of the {pyrene p-benzoquinone} structure, viewed down [001]. The stack axes are alternately along the [100] (open circles) and [010] (full circles) axes of the tetragonal unit cell, and the layers are related by the fourfold screw axis along [001]. Some short distances between ˚ would now be considered as stacks are shown. In particular, the (C)–H . . . O¼C distance of 2.49 A evidence for a weak hydrogen bond. (Reproduced from Bernstein et al., 1976.) n n n

been put forward for this unusual arrangement, which is chiral (but the absolute conﬁguration of the crystal used in the analysis was not determined). A distorted version of this structure type is found in {9-methoxy-5,11-dimethyl-6Hpyrido[4,3-b]carbazole TCNQCH3CN} (P21/c, Z ¼ 4) (Viossat, Dung and Daran, 1988; GEZKIF), where there are mixed stacks with axes approximately along [110] and [110], arranged in successive layers about z 0 and 1/2. A similar arrangement is found in ˚ , Z ¼ 16, space group I41/a) (Bravic 1,3-indandione (tetragonal, a ¼ 14.361, c ¼ 13.631 A et al., 1976; INDDON); which can be considered to be a self-complex, with the two parts of the molecule having donor and acceptor properties respectively. It seems probable that there are both dipole–dipole and –* interactions. Most of the other structures can be classiﬁed as shown in Table 15.2; the scheme is based on that developed earlier (Herbstein, 1971; see Table 20) but the numbering of the groups has been changed to match the usual crystallographic hierarchy – triclinic, monoclinic, etc.; primitive, centred unit cells; molecules at special positions, molecules at general positions. Structures have been determined for most but not all of the compounds listed. The most proliﬁc acceptor and donor components are TCNQ and TTF. There are 1161 hits for TCNQ in the October, 2002 issue of the CSD, and 253 for TTF, both numbers including derivatives and covering binary adducts of all kinds. Table 15.2, which includes only mixed-stack structures, has 48 examples with TCNQ as acceptor and 16 with TTF as donor. n n n

996

CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.2. Classification of 1 : 1 –* molecular compounds into structural groups. In each group the donors that form molecular compounds with particular acceptors are listed; in general only the most recent reference is given. Alternative orientations (e.g P21/c instead of P21/a with alternative stack axis) are not listed separately. Acronyms are listed in Table 14.2. Z is the number of formula units in the unit cell Acceptor

Donors

Group 1a: Triclinic, P1, Z ¼ 1, stack axis [001] TCNE C6(CH3)6, (Sahaki et al., 1976; MBZTCE; Maverick et al., 1978; MBZTCE10) [3,3]paracyclophane (Bernstein and Trueblood, 1971; PACTCN10); ferrocene (Adman et al., 1967; FERTCE); [2,2]metacyclophane (Cohen-Addad, Renault et al., 1988; GEBREK). 2,5-dimethyl-TCNQ Octamethylene-TTF (OMTTF) (Chasseau and Leroy, 1981; BESPEU). ﬂuoranil TTF (Mayerle et al., 1979; TTFFAN); durene (Dahl and Sørensen, 1985); N,N-dimethylaniline (disordered over two orientations) (Dahl, 1981b; BAPLEJ). chloranil Pd(II)oxinate (Kamenar et al., 1965; CLAQPD); bis(8-hydroxyquinoline) (Prout and Wheeler, 1967; HQUCLA); perylene (Kozawa and Uchisa, 1983; CAFWAH); N,N,N 0 ,N 0 -tetramethylbenzidine (TMBD) (Yakushi et al., 1973; MBZDCN). Perylene (Kozawa and Uchida, 1979; PERPBQ); acceptor disordered 2,5-dibromo-3,6at inversion center. dichloro-pbenzoquinone TCNB Pd(II)oxinate (Kamenar, Prout and Wright, 1966; PDHQCB); TMPD (Ohashi et al., 1967; TPDTCB); biphenyl (Pasimeni et al., 1983; BUHSIG); acridine (disordered) (Marsh, 1990; KARKAP01). TCNQ Naphthalene (Shaanan et al., 1967; TCQNAP); chrysene (Munnoch and Wright, 1974; CHRTCQ); d14-p-terphenyl (Lisensky et al., 1976; TCQDTP10, ND); phenazine (Goldberg and Shmueli, 1973b; TCQPEN10); Cu(II)oxinate (Williams and Wallwork, 1967; TCQCUH); Pt(II)oxinate (Bergamini et al., 1987; FEFCAU); bis(1,2-benzoquinonedioximato)-Pd(II) (Keller et al., 1977; BCDPDQ); bis(1,2-benzoquinonedioximato)Ni(II) (Keller et al., 1977; ZZZATV); bis(propene-3-thione-1-thiolato)Pt(II) (Mayerle, 1977; PRTTCQ); dibenzofuran (may be ordered in P1) (Wright and Ahmed, 1981); TMTSF (Kistenmacher et al., 1982; SEOTCR); dibenzotetrathiafulvalene (DBTTF; ¼ 0.47e) (Kobayashi and Nakayama, 1981; Emge, Wijgul et al., 1982; BALNAD); 9,9-trans-bis-(telluraxanthenyl) (Lobovskaya et al., 1983); E-DMDBTTF (Shibaeva and Yarochkina, 1975); Octamethylene-TTF (OMTTF) (Chasseau et al., 1982; BESPEU); 2,2 0 ,5,5 0 -tetramethoxystilbene (Zobel and Ruban, 1983; TMXSTQ10). Tetrakis(methylthio)TTF (Mori, Wu et al., 1987; FIJYEC). Bis(ethylenedithio)TTF (Mori and Inkuchi, 1986; FAHLEF). There is also a monoclinic polymorph.

T HE CRYSTALLOCHE MICAL FAMILIES

997

Table 15.2. (Continued ) Acceptor

Donors

2,5-diﬂuoro-TCNQ PMDA

DibenzoTTF (Emge, Wijgul et al., 1982; BITROL) Anthracene (Robertson and Stezowski, 1978; ANTPML at 153 and 300K); phenazine (Bulgarovskaya et al., 1982; Karl, Ketterer and Stezowski, 1982; BECNUS02); acridine (disordered) (Binder et al., 1982; BIHBUP10) {previous three examples isomorphous}; tetracene (Bulgarovskaya et al., 1987a; FILHOK). p-xylene (Dahl, 1975a; PXYHFB); TMPD (Dahl, 1979; MPAHFB); C6(CH3)6 (at 233K) (Dahl, 1973; MBZFBZ01). Pyrene (Collings et al., 2001; ECUVIH). Perylene (Schmitt et al., 1969; PERNIT).

C6F6

octaﬂuoronaphthalene bis(cis-1, 2-preﬂuoromethylethylene-1,2dithiolato)Ni(II) 2,3,5,6-tetracyanohydroquinone p-dinitrobenzene

Pyrene (Bock, Seitz et al., 1996; TEXPOB10) TTF (Bryce, Secco et al., 1982; BIRDIP).

Group 1b: Triclinic, P1, Z ¼ 2, stack axis [001] TCNQ Acenaphthene (Tickle and Prout, 1973c; ACNTCQ); 5-pheny1-,3-thiaselenole-2-thione (Kaminski et al., 1979; PTSTCQ); dibenzothiophene (Wright and Ahmed, 1981; BAHFEV). phenothiazine (Toupet and Karl, 1995; PTZTCQ01). PMDA Phenothiazine (Anthonj et al., 1980; PTZBMA). TCPA d8-naphthalene (Wilkerson et al., 1975; DNPCPH at 120K). TNB Pyrene (Prout and Tickle, 1973b; PYRTNB); acepleiadylene (Hanson, 1966; APANBZ); tetrabenznaphthalene (Herbstein et al., 1976); dibenzothiophene (Bechtel et al., 1977; DBTTNB); TTF (Bryce and Davies, 1987; GASGUC); phenanthrene-chromium tricarbonyl (De et al., 1979; CPCTNB); 12-imino-12H-benzimidazo [2,1-b]-[1,3]benzothiazine (Viossat et al., 1995; ZAYQEV). TCNB 2,3,6,7-tetramethoxythianthrene (Bock, Rauschenbach et al., 1996; RIKYUF) picric acid Tetrabenznapthalene (Herbstein et al., 1976; ZZZAHA). 3,5-dinitrobenzoic acid Phenothiazine (Fritchie and Trus, 1968; PHTNBA). BTF 13,14-dithiatricyclo[8,2,1,14,7]tetradeca-4,6,10,12-tetraene (Kamenar and Prout, 1965; BOXTET). 2,6-dichloro-N-tosyl-1,4Pyrene (Shvets et al., 1980; PYTQIM). benzoquinonemonoimine octaﬂuoronaphthalene Triphenylene (Collings Roscoe et al., 2001; ECUVON). Group 2a: Monoclinic, P21/a, Z ¼ 2, stack axis [001] TCNE h10-and d10-pyrene (Larsen et al., 1975; PYRTCE); [2.2] (9,10)-anthracenophane (Masnovi et al., 1985; DIRKIY). Perylene (Ikemoto et al., 1970; PERTCE10)

998

CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.2. (Continued ) Acceptor

Donors

TCNB

anthracene (below 200K) (Stezowski, 1980; ANTCYB11); pyrene (Prout, Morley et al., 1973; PYRCBZ at 178 and 300K); C6(CH3)6 (Niimura et al., 1968; CYBHMB); p-phenylenediamine (PD) (Tsuchiya et al., 1973; PDTCNB); biphenylene (Stezowski et al., 1986; Agostini et al., 1986; DURYUK);, durene (Lefebvre et al., 1989; KARHAM). Perylene (Yamachi et al., 1987). Perylene (Tickle and Prout, 1973a; PERTCQ); pyrene (Prout, Tickle and Wright, 1973; PYRTCQ); dibenzo-p-dioxin (Goldberg and Shmueli, 1973b; TCQBOX); 1,2-di(4-pyridyl)ethylene (Ashwell et al., 1983; BUKXOU) (red, non-conducting crystals; black crystals were also reported); 6,13-diacetyl-5,14-dimethyl-1,4,8,11-tetraazacyclotetradeca-4,6, 11,13-tetraenenickel(II) (Lopex-Morales et al., 1985); 4, 6, 8-trimethylazulene (Hansmann et al., 1997a; ROJYUK) (donor disordered at inversion center). Bis(ethylenedithio) TTF (Mori and Inokuchi, 1987; FAHLEF01); monoclinic polymorph. OMTTF (Chasseau and Hauw, 1980; OMTFNQ). 2,7-bis(methylthio)-1,6-dithiapyrene (Toyoda et al., 1993; PIGYUK).

HCBD TCNQ

Dimethoxy-TCNQ (tetracyano-2,6napthoquinodimethane (TNAP) PMDA

1,8-4,5-naphthalene tetracarboxylic dianhyride Pyromellitic dithioanhydride N,N 0 -dimethylpyromellitic di-imide) 1,4-dithiintetra carboxylic N,N 0 -dimethyldiimide p-benzoquinone ﬂuoranil chloranil

BTF

pyrene (above 160K) (Herbstein and Snyman, 1969; Allen et al., 1989; PYRPMA); carbazole (disordered) (Stezowski, Binder and Karl, 1982; BIWVOS); biphenylene (red, stable above 400K. (Stezowski, Stiegler and Karl, 1986; DURZAR). Antharacene (Hoier et al., 1993; WABWEB); dibenz[a,h]anthracene (Zacharias, 1993; BZANTC10). Anthracene (Bulgarovskaya et al., 1974; TPYMAN); acridine (Bulgarovskaya et al., 1976; ACRTMA); dibenzothiophene (Bulgarovskaya et al., 1978; PMTABT); (all three isostructural). Anthracene (Bulgarovskaya et al., 1977; PMEANT). Acridine (Yamaguchi and Ueda, 1984; space group correction by Marsh, 1986; CEJTAM). TTF (Frankenbach et al., 1991; SIVBAA). Perylene (Hanson, 1963; PERFAN). Pyrene (Prout and Tickle, 1973c; PYRCLN); 9-methylanthracene (Prout and Tickle, 1973a, MANTCB) (disordered); TTF (Ohashi et al., 1967; Mayerle et al., 1979; TTFCAN). copper oxinate (BTF is disordered) (Prout and Powell, 1965; ZZZGDI)

T HE CRYSTALLOCHE MICAL FAMILIES

999

Table 15.2. (Continued ) Acceptor

Donors

benzo[1,2-c;4,5-c 0 ]bis[1,2,5]-thiadiazole4,8-dione 1,4,5,8-naphthalenetetrone 3,3 0 ,5,5 0 -tetrachlorodiphenoquinone octaﬂuoronaphthalene

TTF (Gieren et al., 1984; CIYNUT)

C6F6 bis(diﬂuoroborondi methylgloximato)Ni(II)

Pyrene (Herbstein and Reisner, 1984; CEKBUP) Anthracene (Starikova et al., 1980; ANPHXN). Naphthalene (Potenza and Mastropaolo, 1975; NPOFNP); tolan (Collings, Batsanov, et al., 2001; OCAYIA). anthracene (Collings, Roscoe, et al., 2001; ECUTUR). dimer of o-diethynylbenzene (Bunz and Enkelmann, 1999; JOCRIC); Perylene (Boeyens and Herbstein, 1965a; ZZZLJY) Anthracene (Stephens and Vagg, 1981; BADZOV).

Group 2b: Monoclinic, P21/a, Z ¼ 4, stack axis [001] TCNB N,N-dimethylphenylenediamine (Ohashi, 1973; DMPTCN); perylene (Bock, Seitz et al., 1996; REHMUM). PMDA Phenanthrene (Evans and Robinson, 1977; PENPYM). TNB s-triaminobenzene (Iwasaki and Saito, 1970; NIBZAM); p-iodoaniline (Powell, Huse and Cooke, 1943; IANNOB); tricarbonylchromium anisole (Carter et al., 1966; CCATNB); 3-formylbenzothiophene (Pascard and Pascard-Billy, 1972; TNBFTB); DBTTF (Lobovskaya et al., 1983). picric acid Anthracene (Herbstein and Kaftory, 1976; ANTPIIC). TCNQ dithieno (3,2-b 0 ;2 0 ,3-d)thiophene ((Zobel and Ruban, 1983; Bertinelli et al., 1984; CAPTOC); dithieno [3,4-b : 3 0 ,4 0 d]thiophene (Catellani and Porzio, 1991; VIGTAG); 2,4,7-trinitroﬂuorenone C6(CH3)6 (Brown, Cheung et al.,1974; TNFLMB). 2,4,6-trinitro-anisole pyrene (disordered over two orientations) (Barnes et al., 1984; CILRAQ). Group 3a: Monoclinic, P21/a, Z ¼ 2, stack axis [010] TCNE Perylene (Ikemoto et al., 1970; PERTCE10); DBTTF (Lobovskaya et al., 1983). TCNB Hydroquinone (Bock, Seitz et al., 1996; REHNAT) TCNQ bis (ethylenedithio)TTF (Mori and Inokuchi, 1987; FAHLEF01) (also triclinic isomer with segregated stack). TCNQF4 Trans-stilbene (Sato et al., 2001; QILZOA). PMDA Benzene (Boeyens and Herbstein, 1965a; ZZZKSM); naphthalene (orange polymorph) (Bar-Combe et al., 1979; NAPYMA); perylene (Boeyens and Herbstein, 1965b; PERPML); trans-stilbene (Kodama and Kumakura, 1974a; PYMAST); chrysene (Bulgarovskaya et al., 1987b; FILHIR).

1000 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.2. (Continued ) Acceptor

Donors

ﬂuoranil

Pyrene (Bernstein and Regev, 1980; PYRFLR); chrysene (Munnoch and Wright, 1975; CHRFAN). Pyrene (Shchlegova et al., 1981; C1–BAZDAH, Br–BAZCUA).

3,3 0 ,5,5 0 -tetrahalodiphenoquinone (halo ¼ Cl,Br)

Group 3b: Monoclinic, P21/a, Z ¼ 4, stack axis [010] TCNQ (tetramethyl)porphyrinato)Ni(II) (Pace et al., 1982; BEGLUU); dibenzotellurophene (Singh et al., 1984). TNB Naphthalene (Herbstein and Kaftory, 1975a; PVVBKP); azulene (Hanson, 1965a; AZUNBZ; Brown and Wallwork, 1965); skatole (133K) (Hanson, 1964; SKINIB); indole (133K) ) (Hanson, 1964; INTNIB). picric acid Naphthalene (Banerjee and Brown, 1985; PVVBHJ01). picryl chloride 9-isopropylcarbazole (Cherin and Burack, 1966; ZZZMCI). picryl bromide ﬂuoranthene (Herbstein and Kaftory, 1975a; FLABPC). BTF Perylene (Boeyens and Herbstein, 1965a; ZZZMHI); Benzene (Boeyens and Herbstein, 1965a; ZZZLDA). Group 4a: Monoclinic, C2/m, Z ¼ 2, stack axis [001] PMDA naphthalene (ordered yellow form) (Le Bars-Combe et al., 1979; NAPYMA01); 9,10-dibromoanthracene (Bulgarovskaya, Belsky et al., 1987; FILHEN). TCNE Naphthalene (Shmueli and Goldberg, 1974; CYENAP01). TCNB naphthalene (above 68K) (Kumakura et al., 1967); anthracene (above 200K) (Stezowski, 1980; ANTCYB12); phenanthrene (donor disordered) (Wright et al., 1978; PHTCBZ); -naphthol (NAPTCC10), -naphthol (BNATCB10) (both Couldwell and Prout, 1978). TCNQ Anthracene (Williams and Wallwork, 1968; TCQANT); benzidine (Yakushi et al., 1974a; BZTCNQ); N-methyl-phenothiazine (Kobayashi, 1973, 1987; TCQNMP10); dithienylethene (Zobel and Ruban, 1983; CAPTAO); trans-stilbene (Zobel and Ruban, 1983; STILTQ10); carbazole (donor disordered) (Mitkevich and Sukhodub, 1987). TMPD (Hanson, 1965b; QMEPHE) C6F6 Anthracene (ZZZGMW); pyrene (ZZZGKE) (both Boeyens and Herbstein, 1965a); durene (Dahl, 1975b; DURHFB). octaﬂuoronaphthalene Phenanthrene (Collings, Batsanov et al., 2001; ECUVED) Note: {4,6,8-trimethylazulene TCNE} is a rare example crystallizing in space group P2/m, Z ¼ 4, stack axis [010] (Hansmann et al., 1997b). n; n n

PACKING ARRANGEMENTS IN n:m – * M OL ECULAR COMPOUNDS

1001

We cite three examples of structures of the 1 : 1 mixed stack type which crystallize in a space group other than those listed in Table 15.2. {5,8-Dimethoxy-2,11dithia[3,3]paracyclophane TCNE} crystallizes in space group C2/c, Z ¼ 4, with mixed stacks along [010] (Cohen-Addad, Consigny et al., 1988). Both components lie on two fold axes; the donor molecule is chiral and so are individual stacks as successive donors are related by translation; the space group is, of course, centrosymmetric. The interplanar spacings between TCNE and p-dimethoxyphenyl and phenyl rings are respectively 3.15(1) ˚ , indicating, as would be expected, that p-dimethoxyphenyl is a stronger and 3.33(1) A donor than phenyl. {TTF m-dinitrobenzene} also crystallizes in space group C2/c, Z ¼ 4, but the mixed stacks lie along [100], with TTF at centres of symmetry and mdinitrobenzene on two fold axes (Bryce et al., 1988). There is little overlap of components and their planes are mutually inclined at 8 ; nevertheless, the black color of the crystals suggests appreciable charge transfer (in the excited state). The low conductivity along the stack axis ( 109 S/cm) and other physical properties show that the ground state is neutral. {Chrysene TNB} crystallizes in space group Pna21, Z ¼ 4, with both components in general positions; there are mixed stacks along [001] (Zacharias et al., 1991; VIGKIF {3-Methylchrysene TNB} (VIGLAY) is isomorphous, with disorder of the donor. ˚ , except a few The structures in Table 15.2 all have stack axis periodicities of 7 A ˚ examples where donor and/or acceptor thickness is greater than 3.5 A. Although {trans˚ stack axis periodicity, stilbene PMDA} (Kodama and Kumakura, 1974a) has a 12.48 A the arrangement of the components justiﬁes its inclusion in Table 15.2; both molecules lie about centres of symmetry, but there are stepped stacks, with each phenyl group of the donor being overlapped on one side only by an anhydride portion of the PMDA acceptor. However, in about 10% of 1 : 1 donor acceptor molecular compounds the stack axis ˚ , a possibility already noted in Section 15.1. A somewhat random periodicity is 14 A selection of examples is given in Table 15.3. Possibly some of these crystals have order-disorder transitions leading to doubling of the stack periodicity as occurs in {pyrene PMDA} (Herbstein and Samson, 1994); but this has hardly been investigated. n n n

n n n

n n n

n n n

n n n

n n n

n n n

15.4 Packing arrangements in n : m p–p* molecular compounds D : A ratios of 1 : 2 or 2 : 1 are found in a rather small fraction (roughly 5%) of the crystal structures that have been reported. Other ratios (e.g. 3 : 2, 3 : 4) are much less common. The pyrene-picryl chloride system is remarkable in that ﬁve molecular compounds with mole ratios of 4 : 1, 3 : 1, 2 : 1, 1 : 1 and 1 : 3 respectively have been reported on the basis of a DSC study (Bando and Matsunaga, 1976) (but see Section 13.4 for conﬂicting results). Crystal data have been reported only for the 1 : 1 compound (Herbstein and Kaftory, 1975a). The 1 : 2 (or 2 : 1) compounds are generally found in one or other of two structural groups. In the ﬁrst group the donor (say) has a much larger cross-sectional area than the acceptor and can thus behave as a bifunctional donor, with two acceptor molecules sandwiched between each pair of donors. This arrangement is found in {copper oxinate2 (TCNB)2} and in {copper oxinate (picryl azide)2} (Bailey and Prout, 1965; n n n

2

n n n

Copper oxinate is bis (8-hydroxyquinolinato)Cu(II).

1002 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

˚ periodicity along the stack Table 15.3. 1 : 1 donor-acceptor molecular compounds with 14 A axis; see also Section 15.5.1. Only the higher symmetry space group is given when the systematic absences do not unequivocally determine the space group Z

Crystal structure reported?

P1

2

No

13.94

P1

2

No

[101]

13.8

P1

2

Yes*

n n n

[001]

13.93

P1

4

No

n n n

[001]

14.5

P21/n

4

Yes*

[001]

13.7

P21/c

4

No

[001]

13.83

P21/c

4

Yes

[001]

14.57

P21/c

4

Yes

[001]

13.72

P21/c

4

Yes

[001]

14.61

P21/c

4

Yes

[001]

13.7

P21/c

8

No

[001]

13.02

C2/c

4

Yes

[001]

13.84

C2/c

4

Yes

n n n

[001]

14.4

A2/a

8

No

n n n

[001]

14.54

A2/a

8

No

[001]

14.13

Pcmm

8

No

[100]

14.0

Amam

4

No

[100]

14.63

Pnca

4

Yes

[001]

14.53

P21/c

4

Yes

[201]

14.73

P21/n

4

Yes

Molecular compound

Stack axis along

Stack axis periodicity ˚) (A

{naphthalene picryl chloride} (Herbstein and Kaftory, 1975a); {naphthalene picryl bromide} (Herbstein and Kaftory, 1975a); PVVBHG {pyrene dicyanomethylene-croconate} (Doherty et al., 1982); BEFGIC {pyrene picryl chloride} (polymorph II) (Herbstein and Kaftory, 1975a) {pyrene PMDA} (below 160K) (Herbstein et al., 1994) {phenanthrene TNB} (Herbstein and Kaftory, 1975a) {benzo[c]phenanthrene DDQ} (Bernstein et al., 1977); BZPCBQ {4-(2-hydroxyethyl)carbazole DDQ} (Qi et al., 1996); TEJGUK {2,3,7,8-tetramethoxythianthrene TCNQ} (D’yachenko et al., 1977); Hinrichs and Klar, 1982; MXTTCQ {(pyrene)3 (picryl bromide)2} (Herbstein and Kaftory, 1975b); PYRBPC {guiacol picric acid} (yellow polymorph) (Herbstein, Kaftory and Regev, 1976); ZZZAHG01 {anthracene TNB} (at 173K) (Brown et al., 1964); ANCTNB {trithia[5]heterohelicene TCNQ} (Konno et al., 1980); THLCTC {triphenylene picryl chloride} (polymorph II) (Herbstein and Kaftory, 1975a); PVVBEY01 {triphenylene picryl bromide} (polymorph II) (Herbstein and Kaftory, 1975a); PVVBEV {benzene picric acid} (Herbstein, Kaftory and Regev, 1975); ZZZAGV {C6(CH3)6 picryl chloride} (Powell and Huse, 1943)x {resorcinol p–benzoquinone} (Ito et al., 1970); BZQRES {5,10–dihydro-5,10-diethylphenazinium TCNQ} (Dietz et al., 1982); BEWBUA {dipyrido-1,3,4,6-tetraazapentalene TNF} (Groziak et al., 1986); FARMAM n n n

[001]

13.81

n n n

[001]

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

Space group

n n n

n n n

PACKING ARRANGEMENTS IN n:m – * M OL ECULAR COMPOUNDS

1003

Table 15.3. (Continued ) Molecular compound

Stack axis along

Stack axis periodicity ˚) (A

Space group

Z

Crystal structure reported?

{-2,7-bis(methylthio)-1,6dithiapyrene TCNQ} (Nakasuji et al., 1987); FUDTON01

[100]

15.08

P21/c

4

Yes

n n n

Notes: * two independent pyrenes at inversion centers; acceptor at general position. x diffuse scattering ignored. The C6(CH3)6 picryl bromide and picryl iodide molecular compounds are similar but the diffuse scattering is more complex. n n n

PAZQCU). In these two molecular compounds the stacks can be represented schematically as shown below and thus are essentially 1 : 1 in character; consequently the stack ˚ , as before. Analogous situations are found in axis periodicity will be about 7 A {bis(N-isopropyl-2-oxy-1-naphthylidene-aminato)Cu(II) (TCNQ)2} (Matsumoto et al., 1979; IPONTC) and in {9,10-dihydroanthracene (TNB)2} (Herbstein et al., 1986; ZZZAGS10). Relative donor and acceptor sizes cannot be the only factor in determining the stability of these 1 : 2 compounds as palladium oxinate forms a 1 : 1 compound with TCNB (Kamenar et al., 1966; PDHQCB). n n n

n n n

Donor A

A Donor

A

A

The second group of molecular compounds is characterized by stacks of -----DAD DAD DAD DAD----˚ (3 3.5 A ˚ ). type (for a 2 : 1 composition). The stack axis periodicity will be about 10.5 A A striking example is found in the {(perylene)3 TCNQ} compound (Fig. 15.5) (Hanson, 1978; TCQPER); the role of the perylene molecule outside the stacks is discussed below (Section 15.5.1). Rather similar stack arrangements (but without the additional interstitial molecules) are found in the isomorphous pair {benzo[c] pyrene (TMU)2} (Damiani, Giglio, Liquori and Ripamonti, 1967; TMUBZP10) and {coronene (TMU)2} (Damiani, Giglio, Liquori, Puliti and Ripamonti, 1967) and in {stilbene (TNB)2} (Bar and Bernstein, 1978; STINBZ), {DBA (TNB)2} (Zacharias, 1976), {(HMTSF)2 TCNQ} (Emge et al., 1982; BOWSUB), {(BTT)2 TCNQF4} (Sugano et al., 1988; SAJMEV) (BTT is the hexaradialene benzo[1,2-c : 3,4-c 0 : 5,6c 0 0 ]trithiophene), {(HMB)2 TCNE} (IR study, crystal structure has not been reported; Hall and Devlin, 1967), and {(TTM-TTF)2 TCNQ} (Mori, Wu et al., 1987; FIJYAY; there is also a 1 : 1 compound FIJYEC). n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

1004 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

x

y

Fig. 15.5. Projection down [100] of the {(perylene)3 TCNQ} crystal structure showing – DADDAD– stacks and interstitial perylene molecules. The crystals are triclinic and the stack axis ˚ . (Reproduced from Hanson, 1978.) periodicity is 10.422 A n n n

Charge-transfer mean axis

(111)

(010)

B iii C

iv A

TCNE(2)

C A i (i) x, y, z (ii) 1 + x, y, 1 + z (iii) 1 − x, 1 − y, 1 − z (iv) −x, 1 − y, −z

ii

(000) TCNE(1)

(101)

Fig. 15.6. Intermolecular arrangement in {[2.2.2]paracyclophane TCNE}; the molecules are projected onto the plane deﬁned by the barycentres of the phenyl rings. (Reproduced from CohenAddad et al., 1984.) n n n

One method of forcing the formation of ---DADDAD--- type stacks is to use a cyclophane donor where the two potential donor portions have very different donor strengths. Thus in {(5,7-[12]-paracyclophanediyne)2 TCNE}, the TCNE acceptor is sandwiched between benzene rings of two different donor molecules, with an interplanar distance of n n n

SPECIAL FEATURE S O F PACKING ARRANGEM ENTS

1005

˚ , while there is no interaction between triple bonds and TCNE (Harata et al., 1972; 3.27 A PCDTCN). In contrast, mixed stacks of the usual type are found in {1,5naphthaleno(2)paracyclophane TCNE}, with the distances between TCNE and ben˚ (Irngartinger and zene and naphthalene planes essentially equal at 3.464 and 3.457 A Goldman, 1978); a similar situation is found in {[2.2.2.2]paracyclophane TCNE} (Cohen-Addad et al., 1984; COMHOB). An unusual variant on mixed stacking is found in {[2.2.2]paracyclophane TCNE} (Cohen-Addad et al., 1984; COMHIV), where only two of three benzene rings participate in charge transfer interactions with TCNE (Fig. 15.6). In the molecular compounds considered up to this point, the donor molecules have all been planar or approximately so. However, in the isomorphous {transazobenzene (TNB)2} (ABTNBA) and {N-benzylideneaniline (TNB)2} (ABTNBB) (Bar and Bernstein, 1981) there are angles of 42 and 48 between the planes of the phenyl rings in the donor molecules and thus there is some disruption of the stacking leading to a tendency to form DAD units. This tendency reaches an extreme in {(N,N,N 0 ,N 0 tetramethylbenzidine)2 chloranil} (Yakushi et al., 1971; TMBCAN) where isolated (nonstacked) DAD sandwiches are found (see Section 15.2). Finally we note that {trans-4-methylstilbene (PMDA)2} has a rather complicated disordered structure (Kodama and Kumakura, 1974b; PYMSTL). n n n

n n n

n n n

n n n

n n n

n n n

n n n

15.5 Some special features of packing arrangements in p–p* molecular compounds 15.5.1 Crystals where one of the components is also found in interstitial positions Perhaps some thirty -molecular compounds with compositions other than 1 : 1, 1 : 2 or 2 : 1 have been reported (for earlier work see Table 12 of Herbstein, 1971). Some of these compositions require authentication but crystal structure analysis does provide explanations for the unusual compositions of {(pyrene)3 (picryl bromide)2} (Herbstein and Kaftory, 1975b; PYRBPC) and {(perylene)3 TCNQ} (Hanson, 1978; TCQPER). In these two compounds there are respectively 1 : 1 and 2 : 1 donor acceptor stacks of the usual types, with the additional molecules in interstitial positions where they do not participate in the charge transfer interaction (see Fig. 15.5). There are a number of examples of interstitial donors among the molecular compounds of the ﬂavins and these are noted in Section 15.7.2. The fact that a particular component can play two (or more) different roles in a crystal structure is not new; a classical example already noted is CuSO45H2O where four water oxygens and two sulphate oxygens are coordinated octahedrally about Cu and the ﬁfth water molecule is present as solvent of crystallization (Beevers and Lipson, 1934). It is possible that {(coronene)3 TCNQ} (Truong and Bandrauk, 1977) has a structure similar to that of {(perylene)3 TCNQ}. {5,6-Dihydropyrimidino[5,4-c]carbazole}3 TCNQ2H2O also comes into this general group. There are mixed. . . . DADDAD . . . stacks (TCNQs at centers of symmetry) with additional donor molecules in interstitial positions. The two types of donor are mutually hydrogen bonded and also to the water molecules (Dung et al., 1986; DULFAR). {Phenothiazine (PMDA)2} (Brierley et al., 1982) is another example with 1 : 1 donor acceptor stacks, with the additional PMDA n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

1006 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

separating the stacks from one another. The stacking arrangements in the 1 : 1 stacks are appreciably different in {phenothiazine PMDA} and in {phenothiazine (PMDA)2}. {(TMTTF)1.3 (TCNQ)2}, which is a segregated stack molecular compound (Chapter 17), is mentioned here because the additional 0.3 molecule of TMTTF is inserted interstitially between the stacks of TMTTF and (TCNQ)2 with its molecular plane parallel to the stack axis (Kistenmacher et al., 1976; SEOTCR01). The isostructural -compounds {bis(3,6-dibromocarbazole) tris(PMDA)} ((Bulgarovskaya et al., 1989; VILFIF) and {bis(N-methyl-3,6-dibromocarbazole) tris(PMDA)} (Dzyabchenko et al., 1994; WEXKEP) and the (not isostructural) {3,6-dibromocarbazole bis(PMDA)} (Bulgarovskaya et al., 1989; VILFEB) show interesting resemblances and differences. The crystals are all triclinic and were reported in reduced cells, albeit with unconventional choices of origin. All three have 1 : 1 mixed donor acceptor stacks, with, however, different modes of overlap and differing dispositions of the additional PMDA molecules. In the isostructural pair there are sheets of donor acceptor stacks (stack axis [001]) arranged in the (002) planes, interleaved by sheets of stacks of PMDA molecules, located at crystallographic centres; these PMDA molecules are roughly coplanar with the components in the stacks. Thus VILFIF and WEXKEP could be said to have compositions {donor PMDA}0.5(PMDA). In VILFEB3 the additional PMDA molecules are located at two independent sets of symmetry centres with markedly different orientations with respect to the mixed stacks, although both have their molecular planes parallel to the stack axes. Thus VILFEB could be said to have composition {(3,6-dibromocarbazole) PMDA}[0.5(PMDA1) þ 0.5(PMDA2)], where ‘1’ and ‘2’ refer to crystallographically independent PMDAs. This arrangement has similarities to that found in (perylenium)2PF62/3(THF) shown in Fig. 17.6 and is also related to that of {(perylene)3 TCNQ}. One might guess that triclinic {(ﬂuorene)3 (TNB)4} (Hertel and Bergk, 1936; Herbstein, Kaftory and Regev, 1976; ZZZAGP) has 1 : 1 stacks with the additional TNB molecules inserted interstitially; however, the crystal structure (Mariezcurrena et al., 1999; ZZZAGP02) shows a remarkable arrangement of mutually-perpendicular 1 : 1 and 1 : 2 stacks (Fig. 15.7). The 1 : 1 stacks, with orientationally-disordered ﬂuorene about inversion centers, are similar to those found in {4-methylchrysene TNB} (Zacharias et al., 1991; VIGLEC) while the 1 : 2 stacks resemble those in {1-methylchrysene (TNB)2} (Zacharias et al., 1991; VIGKOL). Placing this structure description here is clearly somewhat arbitrary. The structure of the ternary compound {benzidine TNB}1/2(C6H6) (Yakushi, Tachikawa et al., 1975; BDTNNB) is somewhat different from those described above. Benzidine and TNB form mixed stacks rather similar to those found in {benzidine TNB} itself as crystallized from CHCl3 (Tachikawa et al., 1974; BNZTNB); however, there is some alteration in the mutual positioning of the stacks so as to leave channels in which the benzene molecules of solvation are accommodated at centres of symmetry with their molecular planes approximately perpendicular to those of the components in the stacks. The benzene molecules are quite strongly contained within the channels and require application of a vacuum for their removal. Other similar examples are discussed later. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

3 VILFEB is incorrectly given a 2 : 3 composition by the CSD and incorrectly named as ‘bis(PMDA) 3,6dibromocarbazole PMDA solvate’.

SPECIAL FEATURE S O F PACKING ARRANGEM ENTS

1007

y O

z (a) O y

x

(b)

˚, Fig. 15.7. Triclinic {(ﬂuorene)3 (TNB)4} (a ¼ 7.596(7), b ¼ 27.69(2), c ¼ 7.276(11) A ¼ 93.117(9), ¼ 91.114(11), ¼ 82.374(8) ; this is the Niggli reduced cell in a non-standard setting)) showing (above) the 1 : 1 stacking arranged along the [001] axis, and (below) the 1 : 2 stacking arranged along the [100] axis. Atomic displacement ellipsoids are at an arbitrary level. (Reproduced from Mariezcurrena et al., 1999.) n n n

15.5.2 Noncentrosymmetric crystals of -molecular compounds The vast majority of -molecular compounds crystallize in centrosymmetric space groups. Some of the exceptions are listed in Table 15.4, where a separation has been made between the noncentrosymmetrical crystals with enantiomorphic (Sohncke groups) and non-enantiomorphic space groups (see International Tables for X-ray Crystallography, 1965, Vol. I, pp. 41–43, for further discussion). The components in the listed crystals are achiral;4 thus the chirality for the ﬁrst group, or lack of a centre for the second group, results from the details of the mixed-stack donor–acceptor arrangement. These crystals may well have interesting physical properties. The example of {1,5diaminonaphthalene chloranil} (Tamura and Ogawa, 1977; CANANP) is worthy of note because the component molecules are centrosymmetric; the noncentrosymmetric structure probably results from a compromise between the requirements of hydrogen bonding between different stacks and charge-transfer interactions within stacks. The 1,6-diaminopyrene – bromanil system (Fujinawa et al., 1999) has a number of points of interest. Firstly, the compound is polymorphic and the thermodynamically stable n n n

4 This holds, for some examples, only if the component molecule is planar (a situation not always realized in practice) or there is disorder.

1008 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.4. -Molecular compounds which crystallize in non-centrosymmetric space groups Molecular Compound/reference/refcode

Space Group

Z

Crystal Structure Reported ?

2

Yes

2

Yes

2

Yes

2

Yes

2

Yes

n n n

2

Yes

n n n

4

Yes

4 4 4

Yes Yes No

4

Yes

4

Yes

4

Yes

2

Yes

2

Yes

2

Yes

2

Yes

2

Yes

4

Yes

4

Yes

4 4

Yes Yes

I. Enantiomorphic Space Groups 1. benzo[c]pyrene (TMU)2 (Damiani, Giglio, P1 Liquori and Ripamonti, 1967); TMUBZP10. P1 2. coronene (TMU)2 (Damiani, Giglio, Liquori, Puliti and Ripamonti, 1967) 3. 7,8-benzoquinoline TCNQ P21 (Shaanan and Shmueli, 1980); BZQTCQ10. 4. 1-acetylskatole TNB (Surcouf and Delettre, P21 1978); ASKNBZ 5. TTF 2,7-dintro-9-ﬂuorenone (Soriano-Garcia P21 et al., 1989); KARHOA. P21 6. 2-methylchrysene TNB (Zacharias et al., 1991); VIGKUR. P212121 7. 5-methylchrysene TNB (Zacharias et al., 1991); ZEGKIF10. P212121 8. carbazole TNB (Bechtel et al., 1976); CBZTNB P212121 9. perylene TNB (Hertel and Bergk, 1936); ZZZOZO. 10. anthracene BTF (Boeyens and Herbstein, 1965a); P212121 ZZZTOS. P212121 11. hydroquinone naphthaquinone (Thozet and Gaultier, 1977a); NPQHRQ. 12. acenaphthene 3,5-dimethylpicric acid P212121 (Chantooni and Britton, 1998); PUNYUS. 13. pyrene p–benzoquinone (Bernstein et al., 1976); P41 PYRBZQ. (or P43) n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

II. Non-enantiomorphic Space Groups Pc 1. pyrene TMU (Damiani et al., 1965); MURPYR. 2. N,N 0 -dimethyldihydrophenazine TCNQ Cm (Goldberg and Shmueli, 1973a); TCQMHP. Cc 3. trans-4-methylstilbene PMDA (disordered) (Kodama and Kumakura, 1974); PYMSTL. Pn 4. 1,5-diaminonaphthalene chloranil (Tamura and Ogawa, 1977); CANANP. Pn 5. 1,6-diaminopyrene bromanil (Fujinawa et al., 1999); QADGEH. Pca21 6. phenanthrene DDQ (Herbstein et al., 1978); PANCYQ. 7. benz[a]anthracene PMDA (Foster et al., 1976); Pna21 BZAPRM10. 8. chrysene TNB (Zacharias et al., 1991); VIGKIF. Pna21 9. 3-methylchrysene TNB (Zacharias et al., 1991); Pna21 VIGLAY; disordered. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

SPECIAL FEATURE S O F PACKING ARRANGEM ENTS

1009

delta-polymorph crystallizes in the noncentrosymmetric space group Pn (QADGEH). This polymorph resembles {1,5-diaminonaphthalene chloranil}. The other (metastable) polymorph (triclinic P 1, Z ¼ 4; QADGEH01) appears to have an intriguing structure but poor crystal quality prevented a deﬁnitive determination of its structure. Both polymorphs have interesting physical properties that we shall not discuss. We have deliberately excluded from consideration here molecular compounds where one or both of the components are themselves chiral; for example, crystals of some ﬂavin compounds (Section 15.7.2) lack centres of symmetry but are not included because the ﬂavin molecules are chiral and also because the charge-transfer interactions are probably weaker than the hydrogen bonding in these crystals. n n n

15.5.3 Acceptors based on polynitroﬂuorene Four acceptors of this type (2,7-dinitroﬂuoren-9-one, 2,4,7-trinitroﬂuoren-9-one, 2,4,5,7tetranitroﬂuoren-9-one and 2-(2,4,5,7-tetranitroﬂuoren-9-ylidenene)-propane-dinitrile) have been found to form donor-acceptor compounds with a variety of aromatic hydrocarbons (Table 15.5). An early use was the formation of molecular compounds with Table 15.5. Some molecular compounds of aromatic hydrocarbons with acceptors based on substituted polynitrofluorenes. These are all mixed stack structures Molecular compound

Space group

Reference/refcode

1. 1,12-dimethylbenzo[c]phenanthrene 4bromo-2,5,7-trinitroﬂuorenone 2. hexahelicene 4-bromo-2,5,7trinitroﬂuorenone 3. 2,6-dimethylnaphthalene 2,7dinitro-9-ﬂuorenone 4. TTF 2,7-dinitro-9-ﬂuorenone

Details not given Details not given P1

Ferguson et al., 1969

5. Hexamethylbenzene 2,4,7trinitroﬂuorene-9-one 6. 1-ethylnaphthalene 2,4,5,7tetranitroﬂuorene-9-one 7. 2-ethylnaphthalene 2,4,5,7tetranitroﬂuorene-9-one 8. 3,6-dimethylphenanthrene 2,4,5,7tetranitroﬂuorene-9-one 9. chlorobenzene 2-(2,4,5,7tetranitroﬂuorene-9-ylidene)propanedinitrile) 10. (chlorobenzene)2 2,4,5,7tetranitroﬂuorene-9-one 11. TTF 2-(2,4,5,7-tetranitroﬂuorene-9ylidene)-propanedinitrile) 12. benzonitrile 2,7-dicyano-9dicyanomethylene-4,5-dinitroﬂuorene

P21/a

n n n

n n n

n n n

n n n

n n n

n n n

P21/c

n n n

P21/c

n n n

n n n

n n n

n n n

n n n

P21

P21/n P21/c

P212121 Pna21 P21

Ferguson et al., 1969; HELFLU. Suzuki, Fuji et al., 1992; PARBIT. Soriano-Garcia et al., 1989; KARHOA. Brown et al., 1974 Baldwin and Baughman, 1993; LAVFOD. Shah and Baughman, 1994; LESZIS. Baldwin and Baughman, 1993; LAVFUJ. Batsanov, Perepichka et al., 2001; TIJTIP. Batsanov, Perepichka et al., 2001; TIJTOV. Perepichka, Kuz’mina et al., 1998 Batsanov and Perepichka, 2003.

1010 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

overcrowded aromatic hydrocarbons such as hexahelicene (cf. Mackay, Robertson and Sime, 1969). More recent examples have some of the nitro groups replaced by cyano groups (Perepichka, Kuz’mina et al., 1998) or by butylsulfanyl, butylsulﬁnyl or butylsulfoxyl substituents (Perepichka, Popov et al., 2000). Presumably there is a synergistic effect between electron-withdrawing nitro and carbonyl (dicyanoethylene) groups, such as is also found between halogens and carbonyl groups (cf. 1,4-benzoqunone and chloranil). The two chlorobenzene molecular compounds are unusual in their mode of preparation (see original paper for details) and in the role of chlorobenzene as apparent donor, although it is usually considered a weak acceptor, All these crystal structures are of standard inﬁnite mixed-stack type without aberrant features; overlap of the donor is over the polynitroﬂuorene ring without the carbonyl (or dicyanoethylene) substituent appearing to play an important role. 15.5.4

Resolution of helicenes by formation of diastereoisomeric charge transfer molecular compounds with enantiomeric acceptors

An acceptor of the type discussed in the previous section has an interesting application. Resolution of the helicenes (Martin, 1974) is an interesting example of the use of charge transfer interactions. Helicenes are nonplanar because of intramolecular overcrowding and hence exist in enantiomeric forms. The ﬁrst steps towards their resolution were taken in 1956(!) when Newman and Lutz synthesized and resolved TAPA (2-[2,4,5,7-tetranitro9-ﬂuorenylidene-aminoo¨xy]propionic acid; Fig. 15.8; see also Newman and Lednicer, 1956). R(–)TAPA forms a red complex in solution when mixed with racemic hexahelicene and M(–)hexahelicene5 can be recovered from the solution. These results imply that the P( þ )hexahelicene R(–)TAPA diastereoisomer is more stable in solution than the M(–)hexahelicene R(–)TAPA diastereoisomer. These principles have been adapted to n n n

n n n

CH2OH H O N

C

CO2H

H

OH OH

H NO2

O 2N

OH

H

X

O2N

H

H

H 3C

N

H3C

N

NO2 (a)

O

N N

H O

(b)

Fig. 15.8. Enantiomeric electron acceptors used in the resolution of helicenes by formation of diastereoisomeric charge transfer molecular compounds (a) TAPA and related compounds : X ¼ methyl, R(–)TAPA; X ¼ ethyl, R(–)TABA; X ¼ isopropyl, R(–)TAIVA; X ¼ butyl, R(–)TAHA. 5 The absolute conﬁgurations (e.g. that of TAPA (Kemmer et al., 1976)) were determined after Newman’s pioneering studies and have been added here for completeness.

INTERACTIONS BE TWEEN POLARIZABLE AND POLAR GROUPS

1011

[10] [8]

[12]

start

uv 280 nm

[6]

[14]

10

20

30

40

50

60

70

80

90 (min)

Fig. 15.9. Resolution of a mixture of the racemates of the [6]-, [8]-, [10]-, [12]-and [14]-helicenes. The microsilica column contained 25% R(–)TAPA covalently linked to the silica; the mobile phase was 25% dichloromethane–cyclohexane; U ¼ 0.26 cm/sec. In all instances the more strongly retained enantiomer was the P( þ )helicene. Similar results were obtained for the [7]-, [9]-, [11]-and [13]helicenes. [5]-Helicene was resolved only by a multipass technique. (Reproduced from Mikes et al., 1976.)

high performance liquid chromatography with great success (Mikes et al., 1976; Numan et al., 1976), (Fig. 15.9). The HPLC results conﬁrm the deduction from the solution experiments that the P(þ)hexahelicene R(–)TAPA diastereoisomer is the more stable. Later work has shown that riboﬂavin, adenosine and adenylic acid coated on microsilica particles can also be used as the stationary phases. The M(–)helicenes are more strongly retained on riboﬂavin. Measurements have been made (in tetrachloroethane solution at 248K, using 1H NMR) of the stabilities of the (P)-[7]-thiaheterohelicene S(þ)-TAPA and (P)-[7]-thiaheterohelicene R(–)TAPA diastereoisomeric molecular compounds (Nakagawa et al., 1982); the P S diastereoisomer was found to be the more stable by DDH ¼ 1.03 kJ/mol and DDS ¼ 1.40 J/mol K. A1H NMR survey of the structures of the two diastereoisomers was said to indicate that the components packed better in the P S than in the P R diastereoisomer. Analogous crystal-structure comparisons do not appear to have been made. n n n

n n n

n n n

n n n

n n n

n n n

15.6 Structurally important interactions between polarizable and polar groups The juxtaposition of polar groups (such as >C¼O or R > C¼C < R 0 ) in acceptors and polarizable groups (such as benzene rings) in donors leads to dipole-induced dipole interaction between them. This interaction, ﬁrst emphasized in the present context by Prout and Wallwork (1966), can be an important or even dominating inﬂuence in determining mutual donor-acceptor arrangement in unary and binary crystals (see also Gaultier et al., (1969)). {Perylene ﬂuoranil} (Hanson, 1963; PERFAN) has a typical overlap n n n

1012 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

diagram (Fig. 15.10(a)) which is also found in the molecular compounds of perylene with 2,5-dibromo-3,6-dichloro-p-benzoquinone (Kozawa and Uchida, 1979; PERPBQ) and TCNQ (Tickle and Prout, 1973a), and in {(perylene)3 TCNQ} (Hanson, 1978) (Fig. 15.10(c)); and also in the unary crystals of 1,4-naphthoquinone (Gaultier and Hauw, 1965; NAPHQU) and 1,4-anthraquinone (Dzyabchenko and Zavodnik, 1984; COBBIE04) (Fig. 15.10 (d) and (e)). Aromatic ring carbonyl interactions are also important in forming the DAD triples in {(TMBD)2 chloranil} (Yakushi, Ikemoto and Kuroda, 1971) (Fig. 15.10(f)) and in the mixed stacks of chrysene ﬂuoranil (Munnoch and Wright, 1975; CHRFAN) and {1,5-diaminonaphthalene chloranil} (Tamura and Ogawa, 1977; CANANP). Direct overlap of donor and acceptor is also found in solvent-free and in solvated benzidine TCNQ (see Section 15.7.3.2). One should note the close dimensional correspondence between donor and acceptor molecules in all these molecular compounds; the distance between the centres of the benzene rings in a diphenyl-like portion of perylene or benzidine is closely equal to the O---O distance in the halo-anils or the distance between the centres of the extra-ring double bonds in TCNQ. n n n

n n n

n n n

n n n

n n n

n n n

(a)

(b)

(c) C1

F

(d)

(e)

O

O

O

O

O

O

O

O

(f )

C N O Cl

Fig. 15.10. Patterns of overlap which result from interactions between polarizable and polar groups (a) perylene ﬂuoranil; (b) pyrene chloranil; (c) perylene TCNQ in (perylene)3 TCNQ; a somewhat similar overlap diagram is found in perylene TCNQ; (d) 1,4-naphthaquinone; (e) 1,4anthraquinone; (f) (TMBD)2 chloranil. n n n

n n n

n n n

n n n

n n n

n n n

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1013

Aromatic ring polar group overlap is less pronounced but still obvious in the molecular compounds of pyrene with chloranil (Prout and Tickle, 1973c; PYRCLN) (Fig. 15.10(b)), ﬂuoranil (Bernstein and Regev, 1980; PYRFLR), p-benzoquinone (Bernstein et al., 1976) and 2,6-dichloro-N-tosyl-1,4-benzoquinonemonoimine (Shvets et al., 1980; PYTQIM), and in {acenaphthene chloranil} (Tickle and Prout, 1973a) and {acenaphthene TCNQ} (Tickle and Prout, 1973b; ACNTCQ). We end this section by stressing the obvious – there are many molecular compounds in which interaction between polarizable and polar groups could occur but does not. This is the situation for such molecular compounds as {HMB chloranil} (Jones and Marsh, 1962; CLAHMB), {TMBD chloranil} (Yakushi et al., 1973; MBZDCN), {anthracene 3,3 0 ,5,5 0 -tetrachlorodiphenoquinone} (Starikova et al., 1980; ANPHXN) and {pyrene 3,3 0 ,5,5 0 -tetrachlorodiphenoquinone} (Shchlegova et al., 1981; BAZDAH). Although there is no direct aromatic ring carbonyl overlap in the P21/n polymorph of 2,3-dichloronaphthazarin (Rubio et al. 1985; DCDHNQ01), nevertheless the molecules are arranged in stacks containing symmetry centres that are situated such that the quinoid part of one molecule partially overlaps a benzenoid part of a neighbouring symmetry-related molecule, the interplanar distance ˚ . Consequently this polymorph forms a self-complex in the solid state; being 3.40(3) A spectroscopic data indicate that such close associations also exist in solution. Finally, we note that in the few crystal structures that have been reported for molecular compounds with polynitroﬂuorenones (TNF and TENF) as acceptors, the acceptor behaves as a polynitroaromatic and aromatic ring carbonyl interactions do not seem to be important. n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

15.7 Mixed-stack crystals with both charge transfer and hydrogen bonding interactions 15.7.1 The quinhydrones as a crystallochemical family 15.7.1.1

Crystal structures

Quinhydrones (Patil et al., 1986) are molecular compounds formed by polyhydroxyaromatics (as donors) and aromatic quinones (as acceptors); quinhydrone itself is {hydroquinone p-benzoquinone} (hydroquinone is also called quinol or 1,4-dihydroxybenzene). We deﬁne members of the quinhydrone structural family as having crystal structures involving two speciﬁc interactions between the components n n n

(i) hydrogen bonding between hydroxyl and carbonyl groups (ii) charge transfer interaction between donor and acceptor ring systems. The crystal structures appear to be determined by an interplay between these factors, whereas the UV–visible spectroscopic properties are a consequence of the charge transfer interactions, which often show themselves structurally by a superposition of the carbonyl group of the acceptor over the (possibly substituted) aromatic ring of the donor. A consequence of this deﬁnition is that every molecular compound composed of a polyhydroxyaromatic and an aromatic quinone is not necessarily a quinhydrone. Donor : acceptor ratios of 2 : 1, 1 : 1 and 1 : 2 (and, exceptionally, 1 : 3) are known and can be seen to depend on the nature of the components. Much of the systematic preparative work dates back 60–80 years; we quote some of these results (Siegmund, 1908;

1014 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.6. Quinhydrones reported to be formed between polyhydroxy-aromatics and aromatic quinones Donor

D/A Ratio

(a) With p-benzoquinone as acceptor: phenol 2:1 p-chlorophenol 2 : 1, 1 : 1 p-bromophenol 2 : 1, 1 : 1 p-nitrophenol 1:1 1,2-dihydroxybenzene 2 : 1, 1 : 1 1,3-dihydroxybenzene 1:1

Donor

D/A Ratio

1,4-dihydroxybenzene(quinol) 1,2,3-trihydroxybenzene 1-naphthol 2-naphthol p-methylaminobenzene 2-naphthylamine

1:1 1:3 2 : 1, 1 : 1 2 : 1, 1 : 1 1:1 2 : 1, 1 : 1

(b) With other acceptors: 1-naphthol -naphthoquinone; 1-naphthol phenanthrenequinone n n n

n n n

Meyer, 1909; Kremann et al., 1922) in Table 15.6, which does not give a complete survey of the known compounds. This type of information, taken together with that about crystal structures in Table 15.7 (which is hopefully more comprehensive), shows both what has been learned and what gaps remain. The methods used include crystallization from solutions of the mixed components and determination of binary phase diagrams. Two aromatic amines are included among the donors because their molecular compounds may resemble the quinhydrones in structure. Similarity of intercomponent interactions leads to striking resemblances among many of the crystal structures and justiﬁes treatment of the whole group as a single crystallochemical family. The known crystal structures (Bernstein, Cohen and Leiserowitz (1974) and later work) can be grouped as shown in Table 15.7. In this classiﬁcation we have emphasized the importance of donor-acceptor stacking and distinguished between 1 : 1 and 1 : 2 (or 2 : 1) compositions of the stacks. This means that quinhydrones with overall compositions 1 : 2 (or 2 : 1) are classiﬁed according to the D : A ratio in the stack and not in terms of overall composition. The structural features of Group A are conveniently introduced by reference to the two polymorphs of quinhydrone ( triclinic, P 1, Z ¼ 1; , monoclinic, P21/c, Z ¼ 2). In these crystals a combination of charge-transfer interactions along [100] and hydrogen bonding along [120] gives molecular sheets, one molecule thick, parallel to (001). In the triclinic polymorph (Fig. 15.11(a)) all the molecular sheets are identical, whereas in the monoclinic polymorph (Fig. 15.11(b)) the direction of the hydrogen bonds in successive sheets changes from [120] to [1 20] in accord with the introduction of the c glide plane. The arrangements in the two polymorphs are formally similar to those found in the triclinic and monoclinic polymorphs of p-dichlorobenzene (Herbstein, 2001). The volume per formula unit in both quinhydrone polymorphs is less than the sum of the volumes (in their respective crystals) of the two components; the reduction is 9% for the triclinic polymorph and 7% for the monoclinic polymorph, suggesting that the former is the more stable at room temperature and pressure. Analogous reductions are found for almost all the quinhydrones but none is as large as that found for -quinhydrone; the only exception we have found is {(2,5-dimethylhydroquinone)2 (2,5-dimethyl-p-benzoquinone)} (CIKRAP), where there is a volume increase of 1.4%. The orientations of the stacks alternate in {resorcinol p-benzoquinone} (BZQRES) (space group Pnca, Z ¼ 4) (Fig. 15.11(c)) and the structure thus resembles that of n n n

n n n

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1015

Table 15.7. Classification of the quinhydrones according to relationships among their crystal structures Type I: with DA stacks Group A: (donor : acceptor ratio 1 : 1). -quinhydrone (Sakurai, 1968; QUIDON01) and -quinhydrone (Sakurai, 1965; QUIDON); resorcinol p-benzoquinone (Ito et al., 1970; BZQRES); hydroquinone 1,4-naphthaquinone (Thozet and Gaultier, 1977a; NPQHRQ); 2-phenyl- (or 2-chlorophenyl)-benzhydroquinone 2phenyl- (or 2-chlorophenyl)-benzoquinone (Desiraju et al., 1979; PBZQHQ); durohydroquinone duroquinone [duroquinhydrone] (Patil et al., 1986; Pennington et al., 1986; FADCES), Group B: (donor : acceptor ratio 1 : 1, donor is a phenol). p-chloro- (or p-bromo-)phenol p-benzoquinone (isomorphous) (Shipley and Wallwork, 1967b; BNQCLP, BNQBRP). Group C: (donor : acceptor ratio 2 : 1; additional donor bridges between DA stacks) (hydroquinone)2 2,5-dimethylbenzoquinone) (Patil et al., 1984; CISCOW); (hydroquinone)2 duroquinone) (Pennington et al., 1986; FADCIW). n n n

n n n

n n n

n n n

n n n

n n n

n n n

Type II: (with --DAD-- or --ADA-- as repeat units in the stacks) Group D1: (donor : acceptor ratio 2 : 1). {(phenol)2 p-benzoquinone} [phenoquinone] (Sakurai, 1968; PHENQU); ({p-chloro(or p-bromo-) phenol}2 p-benzoquinone} (these two molecular compounds are isomorphous) (Shipley and Wallwork, 1967b; BNQDCP, BNQDPB). Group D2: (donor : acceptor ratio 1 : 2). {(1,3,5-trihydroxybenzene) (p-benzoquinone)2} (Sakurai and Tagawa, 1971; PHLBZQ); {1,4-dihydroxynaphthalene (1,4-naphthoquinone)2} (Artiga et al., 1978b; NPQNHQ); {-naphthol (2,3-dichloro-1,4-naphthoquinone)2} (Thozet and Gaultier, 1977b; CNQNPO); {(2,5-dimethyl-1,4-dihydroxybenzene) (2,5-dimethyl-1,4-benzenoquinone)2} (Patil et al., 1984). n n n

n n n

n n n

n n n

n n n

n n n

Notes: Cell dimensions have been reported for {(p-cresol)2 p-benzoquinone} and {-naphthoquinonequinhydrone} (ZZZOXY) (Anderson, 1937); the structure of {-naphthol 2-methyl-1,4-naphthoquinone} has been brieﬂy described (Berthelon et al., 1979). n n n

n n n

monoclinic -quinhydrone; polymorphism has not been reported. There is also a remarkable resemblance (Herbstein, 1971, see p. 317) between the structures of {resorcinol p-benzoquinone} and {anthracene TNB} (Brown, Wallwork and Wilson, 1964; ANCTNB). There is superpositioning of carbonyl groups over aromatic rings in - and -quinhydrones (Fig. 15.11(d)) and this is also found in {p-ClC6H4OH C6H4O2}, phenoquinone, {resorcinol C6H4O2} and {(p-ClC6H4OH)2 C6H4O2} (C6H4O2 is p-benzoquinone). Two structures in this group have noteworthy features. {Hydroquinone 1,4naphthoquinone} has a structure (Thozet and Gaultier, 1977a; NPQHRQ) based on hydrogen bonding and charge-transfer interactions, with aromatic ring-carbonyl superpositioning. Individual sheets are analogous to those in -quinhydrone but four crisscrossed sheets are packed in each b-axis period. The crystals are chiral (space group P212121) although the components are not. The structures of 2-phenylquinhydrone and 2-(p-chloro)-phenylquinhydrone are based on the usual principles of hydrogen bonding and charge transfer interaction but are such that quinol and quinone components cannot n n n

n n n

n n n

n n n

n n n

n n n

1016 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

(a)

(b)

a

b

o [101up]

a9 o

b 1Å (c)

o

O

b C up

2Å

4

2.7

OH

O

a/2

OH

Fig. 15.11. (a) Triclinic () quinhydrone in projection down [001]; (b) monoclinic () quinhydrone in projection down [101]; (c) {resorcinol p-benzoquinone} in projection down [001]; the resorcinol molecules are seen edge-on and the p-benzoquinone molecules are seen slightly tilted. The overlap diagram typical of many quinhydrones showing superposition of carbonyl group on aromatic ring is illustrated in the lower left portion of the diagram. Hydrogen bond lengths (d(O . . . O)) are ˚ in -quinhydrone and 2.71 A ˚ in the -polymorph. (Reproduced from Herbstein, 1971.) 2.739 A n n n

be distinguished in the crystal because of disorder (space group P21/c, Z ¼ 2); it was suggested that the crystals could be conglomerates of regions with true space group symmetry either P21 or Pc (Desiraju et al., 1979). The same structural principles apply in Group B as in Group A, except that the molecules are hydrogen bonded in pairs (Fig. 15.12) rather than ribbons because of the monofunctionality of the phenols. The structures of {(hydroquinone)2 (2,5-dimethyl-p-benzoquinone)} (CISCOW) and {(hydroquinone)2 (duroquinone)} (FADCIW) form a separate group in which the equimolar DA stacks are preserved with the second hydroquinone molecule bridging between the stacks; the details of the hydrogen bonding by which the bridging is effected differ in the two crystals. We ﬁrst illustrate for {(hydroquinone)2 2,5-dimethyl-p-benzoquinone)} (Fig. 15.13); there is carbonyl-aromatic ring overlap within the stacks and the stacks are linked together by hydrogen bonding between hydroquinone and benzoquinone to give sheets analogous to those already noted in - and -quinhydrones. The interstitial hydroquinones hydrogen bond between hydroquinones of the stacks to give cohesion in the third dimension. On the other hand, the stacks in {(hydroquinone)2 (duroquinone)} are not hydrogen bonded into sheets but the cohesion is given by the bridging hydroquinones n n n

n n n

n n n

n n n

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

(a)

1017

c sin a

b up

C O Cl

a sin g c sin a (b) a down

b sin g

Fig. 15.12. Projections of the crystal structure of {p-chlorophenol p-benzoquinone} down (a) [010], (b) [100]. In (b) two hydrogen-bonded donor–acceptor pairs are shown, related by a centre of symmetry; one of these pairs has been omitted in (a) for clarity. (Reproduced from Herbstein, 1971.) n n n

which link four stacks by HQ--HQ and HQ--DQ hydrogen bonds (Fig. 15.14); there is no carbonyl-aromatic ring overlap within the stacks. Thus the ﬁrst structure is essentially a true quinhydrone in terms of its resemblance to - and -quinhydrone while the second is noted here for reasons of chemical rather than structural resemblance. The 2 : 1 and 1 : 2 quinhydrones of Group D have somewhat similar structures and we describe that of phenoquinone ({(phenol)2 p-benzoquinone}; Fig. 15.15). The components are hydrogen bonded in groups of three, the minor component being ﬂanked on each side by a molecule of the major component. The stacks have composition n n n

----DAD DAD DAD---˚ ; the D---A interplanar and thus the characteristic periodicity along the stack axis is 11 A distances are somewhat shorter than the D---D distances. Aromatic ring-carbonyl overlap occurs in phenoquinone, there is partial overlap in {(2,5-dimethylhydroquinone)2 (2,5dimethyl-p-benzoquinone)} (CIKRAP) but none in {1,4-dihydroxynaphthalene (1,4naphthoquinone)2} (NPQNHQ) nor in {-naphthol (2,3-dichloro-1,4-naphthoquinone)2} (CIQNPO). In the latter the -naphthol molecule is disordered across a centre of sym˚ ) are also important. metry and Cl---O interactions (d ¼ 2.95 A The {1,3,5-trihydroxybenzene (p-benzoquinone)2} compound (PHLBZQ) has an interesting structure in which there are independent branched zigzag chains of molecules n n n

n n n

n n n

n n n

1018 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Fig. 15.13. Stereoview of the {(hydroquinone)2 (2,5-dimethyl-p-benzoquinone)} structure, seen approximately down [001]; hydrogen bonds are shown as broken lines; all three component molecules are at independent centres of symmetry, with some symmetry-related molecules omitted to simplify the diagram. Ribbons of hydrogen-bonded hydroquinone 2,5-dimethyl-p-benzoquinone extend along the [101] direction as shown in the lower ac plane of the cell. The aromatic ringcarbonyl overlap occurs between superimposed ribbons of this type. The ribbons are linked by the ‘‘interstitial’’ hydroquinone molecules shown in the centre of the (100) faces. (Reproduced from Patil, Curtin and Paul, 1984.) n n n

n n n

Fig. 15.14. Stereodiagram of the crystal structure of {(hydroquinone)2 (duroquinone)} showing linking of four DA stacks by hydrogen bonding to the interstitial hydroquinone in the center of the cell. (Reproduced from Pennington et al., 1986.) n n n

in each molecular layer (Fig. 15.16). Two of the acceptor molecules bridge between different hydroxyl groups of the donor while the third p-benzoquinone is linked through one of its carbonyl groups to the third hydroxyl, while the second is unlinked; this arrangement accounts for the composition. The chains interact only by dispersion forces

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

(a)

1019

(b) O

3.16

b

O

3.32

3.28

3.42

3.25

c

3.32 3.42

a

a (c)

Fig. 15.15. Phenoquinone (a) projection down [001], (b) projection down [010], (c) overlap diagram showing superimposed DAD hydrogen-bonded triples; note the aromatic ring-carbonyl overlap. (Reproduced from Sakurai, 1968.)

0

c⬘

c

b⬘

Fig. 15.16. {1,3,5-trihydroxybenzene (p-benzoquinone)2} projected onto the mean molecular plane. The zigzag hydrogen-bonded ribbons, one of which has been shaded, extend along the axis labelled c. There is no hydrogen bonding between neighbouring ribbons in the b 0 direction. (Reproduced from Sakurai and Tagawa, 1971.) n n n

so that the crystal structure is a two-dimensional analog of the intersecting but non-bonded three-dimensional networks found in the quinol clathrates (Chapter 8) and some other crystals such as -trimesic acid (Section 9.3) and adamantane-1,3,5,7-tetracarboxylic acid (Ermer, 1988; GEJVEW).

1020 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

The equimolar molecular compound of 6-hydroxydopamineHCl and its oxidized p-quinonoid form is a quinhydrone (Andersen et al., 1975; DOPAQC). The compound ˚, crystallizes in a monoclinic unit cell with a ¼ 6.815, b ¼ 13.108, c ¼ 20.365 A ¼ 95.43 , space group P21/n, Z ¼ 4. The component cations stack alternately along [100], with an angle of 3.8 between ring planes and interplanar spacings of 3.42 and ˚ , somewhat longer than in most quinhydrones. The two components are respect3.49 A ively colourless and yellow in their neat crystals and the red colour of the molecular compound is credibly ascribed to a charge transfer interaction. There is no carbonylaromatic ring overlap. OH

OH O

HO

O

OH CH2

CH2

CH2

CH2

NH3+

NH3+

The asymmetric unit consists of the two cations shown and two chlorides as counterions.

Crystal structures have been reported for a number of cyclophane quinhydrones (see Chapter 14 for details and references); for example, a stacked structure was found for pseudogeminal 14,17-dimethoxy[3](2,5)-p-benzoquinone, with an

AD AD AD AD ˚ , about arrangement along the stacks and an average intermolecular separation of 3.42 A ˚ larger than the intramolecular transannular separation (see Fig. 14.5). Hydrogen 0.23 A bonding between moieties in different stacks seems unlikely for steric reasons. 15.7.1.2

Thermodynamic studies of quinhydrones

A number of measurements have been made of thermodynamic parameters for various quinhydrones. The enthalpy of formation of a crystalline molecular compound of composition DmAn is deﬁned as DH f ðDm An Þ ¼ HðDm An Þ fmHðDÞ þ nHðAÞg; where the enthalpies H(DmAn) etc. refer to the crystalline materials at the same (speciﬁed) temperature. Analogous equations and conditions apply to free energies DGf (DmAn) and entropies of formation DSf (DmAn). Available results for DHf (DmAn) are summarized in Table 15.8. We ﬁrst consider the results for quinhydrone. Three polymorphs of hydroquinone and two of quinhydrone are now known and thus speciﬁcation of polymorph, with regard to both quinhydrone and hydroquinone, is required; Suzuki and Seki (1953) checked that they used -hydroquinone but do not report which quinhydrone polymorph was used, while the converse situation applies to the results of Artiga et al. (1978a, b). The values of the crystal densities suggest that triclinic quinhydrone is stable with respect to monoclinic at room temperature but the quantitative situation is not known, nor is it known whether

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1021

Table 15.8. Values of Hf(DmAn) (kJ/mol) for some quinhydrones as measured by a variety of methods Molecular Compound

–Hf(DmAn)

Method

Quinhydrone

20.2 (303K); 22.6 (297K) 19.7; 20.6(1) (295K) 33.9 23.2 (297K)

Dissolution (Artiga et al., 1978a; Suzuki and Seki, 1953) vapour pressure (Nitta et al., 1951; Kruif et al., 1981). Combustion (Schreiner, 1925) calculated from G, S (Schreiner, 1925) Estimated (Suzuki and Seki, 1953) Dissolution (Artiga et al., 1978a, b); vapour pressure (Kruif et al., 1981) Dissolution (Artiga et al., 1978b); vapour pressure (Kruif et al., 1981) vapour pressure (Kruif et al., 1981)

{hydroquinone 1,4naphthoquinone} {1,4-dihydroxynaphthalene (1,4-naphthoquinone)2} {1,4-dihydroxynaphthalene 1,4-naphthoquinone} n n n

n n n

n n n

22.0 (0K) 6.1 (303K) 8.0(2) (320K) 8.6 (303K) 9.6(4) (320K) 11.6(2) (330K)

the two polymorphs are enantiotropically or monotropically related. Artiga et al., report that triclinic quinhydrone is thermally stable up to its melting point at 443K, suggesting that the relationship for quinhydrone is monotropic. The precision reported for the various measurements is 1–3%, but intercomparison of the DHf values suggests that systematic errors can occur, apart from the uncertainty about which polymorph was used. The value of DHf for quinhydrone at 297K is about –21(2) kJ/mol, presumably applying to the more stable -polymorphs of hydroquinone and quinhydrone. The value of DHf at 0K was estimated Suzuki and Seki (1953) by correcting the 297K value via speciﬁc heat values measured by Lange (1924) and ‘‘put in order’’ by Schreiner (1925); as the speciﬁc heats were measured at rather large temperature intervals, these corrections are somewhat uncertain. The free energy and entropy of formation of quinhydrone at 297K were measured by an EMF method (Schreiner, 1925) and the following values obtained : DGf ¼ 15:3kJ=mol

DSf ¼ 26:3J=mol K:

The corresponding values from vapour pressures (Kruif et al., 1981) [–13.8(1) kJ/mol and –23(5) J/mol K] are in good agreement. One may conclude that the components are more strongly bound in crystalline quinhydrone than in the separate crystals of hydroquinone and p-benzoquinone, and that there is a concomitant reduction in the entropy, presumably because of a reduction in the amplitudes of thermal vibration. The negative value of DSf implies that quinhydrone becomes more stable with respect to its separated components as the temperature is lowered, it being assumed that DHf and DSf are only weakly temperature dependent; this is also the situation for anthracene picric acid (see Chapter 16). A value of DGf (330K) of –8.6(1) kJ/mol. has been calculated for {1,4-dihydroxynaphthalene 1,4-naphthoquinone} (crystal structure does not seem to have been reported) from vapour pressure measurements (Kruif et al., 1981) with DSf (330K) calculated n n n

n n n

1022 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

as –9(5) J/mol K. The situation is similar to that found for quinhydrone but the molecular compound is less stable with respect to its components than is quinhydrone. Speciﬁc heats have been measured for {1,4-dihydroxynaphthalene (1,4-naphthoquinone)2} and its components from 4–300K and DSf (297K) calculated as 7.7 J/mol K, leading to a value of DGf (297K) of 10.9 kJ/mol (Artiga et al., 1978b). Vapor pressure measurements (Kruif et al., 1981) give DGf (320K) ¼ 12.9(10) kJ/mol., DHf (320K) ¼ 9.6(4) kJ/mol, and DSf(320K) ¼ 10(10) J/mol K. The positive value of DSf implies that {1,4-dihydroxynaphthalene (1,4-naphthoquinone)2} becomes less stable with respect to its separated components as the temperature is lowered, contrary to the situation in quinhydrone. The energies of complexation have been calculated for some of these molecular compounds using atom-atom potentials (Wit et al., 1980); the results were qualitatively correct but not very accurate. This is not surprising as atom-atom potentials hardly seem ﬁtted to the quantitative representation of hydrogen bonding and charge transfer interactions. n n n

n n n

15.7.1.3 Spectroscopy Polarized absorption (polymorph not speciﬁed) (Nakamoto, 1952) and reﬂection spectra (monoclinic polymorph) (Anex and Parkhurst, 1963) have been measured from small single crystals of quinhydrone. Nakamoto (1952) interpreted his results in terms of enhanced absorption, due to charge transfer, when the radiation was polarized normal to the ring planes of the two component molecules but Anex and Parkhurst (1963) claimed that the appropriate polarization direction is along the stack axis and not along the ring normals, a result veriﬁed by both techniques used by them. They point out that Mulliken’s theory in fact suggests that the polarization vector for the charge transfer band should lie along the line joining the centres of the components. However, the occurrence of crisscrossed stacks in monoclinic quinhydrone (Fig. 15.10(b)) forces the polarization to lie along the average normal to the molecular planes, which is the stack axis. Measurements on the triclinic polymorph, where all plane normals are parallel, and inclined to the stack axis, would provide the decisive test. A measurement of this kind made on triclinic {anthracene PMDA} (ANTPML) shows unequivocally that the moment of the principal charge transfer transition lies along the anthracene to PMDA center-to-center vector or [001] axis and not along the plane normal (Merski and Eckhardt, 1981) (cf. Section 17.3). Polarized single-crystal spectra of {resorcinol p-benzoquinone} have been studied by Amano (quoted by Ito et al., 1970). Intense charge transfer bands were observed with light polarized along [100] while the crystal was almost transparent to light polarized along [010]. The orthorhombic crystal structure requires the charge-transfer moment to be along the stack axis as in monoclinic quinhydrone. n n n

n n n

15.7.2

Molecular compounds of the ﬂavins

The ﬂavo co-enzymes, which are the non-protein parts of ﬂavoenzymes, are widely involved in oxidation-reduction processes in the cell. The two forms most commonly found in biological systems are ﬂavin mononucleotide (FMN or riboﬂavin 5 0 -phosphate) and ﬂavin adenine dinucleotide (FAD), whose molecular structures are given in Fig. 15.17.

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1023

FAD FMN H

Riboflavin (Vitamin B2) H Lumiflavin H CH2 10

H3C H3C

6

N N 5

(CHOH)3 1 N

CH2O

O PO O–

O PO O–

CH2 N N

O O

NH O

HO

N

NH2 N

OH

Fig. 15.17. The molecular structures of several ﬂavins. In iso-alloxazine the substituents at C(7), C(8) and N(10) are all hydrogens.

The iso-alloxine or ﬂavin nucleus, which is common to all forms, is the site of electron exchange and is shown in the air-stable, fully oxidized or quinoid form. It is reduced enzymatically by one or two electrons to either the semiquinoid or the hydroquinoid state. Since many of the substrates, including reduced pyridine nucleotide, DPNH, are aromatic or quasi-aromatic, it is possible that the electron interchange reaction occurs by formation of an intermediate, transient, charge transfer complex (Szent-Gyorgi, 1960). In consequence considerable effort has been applied to the preparation of complexes between electron donors and ﬂavins in various oxidation states. Cationic, neutral and anionic species can be obtained depending on the pH of the system (Kosower, 1960; Tollin, 1968). Neutral and charged ﬂavoquinone complexes have been obtained, as well as charged ﬂavosemiquinone complexes. A fairly complicated series of equilibria has been shown to exist between the fully oxidized and fully reduced forms of ﬂavins (Kuhn and Stroeble, 1937), each intermediate being characterized by ‘‘excellent crystallizing power, vivid colours and sharply deﬁned composition.’’ The best results were obtained with riboﬂavin where the equilibria can be represented as : flavin ! verdoflavin ! chloroflavin ! rhodoflavin ! leucoflavin. All the crystalline intermediates were paramagnetic (bulk susceptibility measurements), ionic (Naþ or Cl ions were necessary), and supposed to be composed of different mixtures of the various ﬂavin oxidation states. Most studies to date of complexes of ﬂavins are based on visible and ESR spectra of solutions but some crystalline compounds have been prepared. For convenience, neutral and charged species will be described together. The neutral crystalline compounds are usually orange to orange-red, while the protonated complexes range from green through

1024 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

deep red to black. Charge transfer interaction between donor and ﬂavin acceptor has been suggested for certain compounds, although this may not always have been appropriate. Neutral crystalline molecular compounds of 2,3- and 2,7-naphthalenediol with riboﬂavin have been prepared (Fleischmann and Tollin, 1965a) with phenol : ﬂavin ratios of 2 : 1, although spectroscopic analysis indicated that the solution compositions were 1 : 1. There was an extra band in the spectra of mineral oil suspensions of powdered crystals, and this has been ascribed to charge transfer. Various indoles, such as 5-methylindole, carbazole and tryptophan, gave neutral 1 : 1 crystalline compounds with lumiﬂavin but not with riboﬂavin. Protonated complexes such as lumiﬂavin-tryptophan-HCl-H2O have also been obtained. Although the crystalline complexes are more highly colored than the parent ﬂavins, the diffuseness of the additional bands in the spectra makes it difﬁcult to decide whether there is indeed a charge transfer interaction (Pereira and Tollin, 1967). Crystalline complexes have also been prepared with compositions phenol : ﬂavin : HCl, where the phenols include hydroquinone, 4-chloropyrocatechol, resorcinol and 1,2- and 1,4-dihydroxynaphthalene and the ﬂavins riboﬂavin, lumiﬂavin and 9-methylisoalloxazine (Fleischmann and Tollin, 1965b). The spectra suggest charge-transfer interactions between the components. Mention must also be made of the paramagnetic semiquinone salts and complexes ﬁrst prepared by Kuhn and Strobele (1937) and studied later by Fleischmann and Tollin (1965c), who showed that iso-alloxazine derivatives in concentrated hydroiodic acid were reduced to the semiquinone state and that some crystalline ﬂavin hydroiodides could be obtained; ESR measurements showed that the latter had 100% unpaired spins. Riboﬂavin hydroiodide (no analysis given) gave pink crystalline platelets, while lumiﬂavin hydroiodide (composition FH22HI) was a dark-brown solid which could not be recrystallized. Black crystals (red in thin section) were obtained from saturated solutions of riboﬂavin in hydroiodic acid to which various phenols (e.g. hydroquinone, 2-naphthol, 2,3-, 1,7-, 2,7-, 1,5- and 1,4-dihydroxynaphthalene) had been added; a typical composition was FH3þI2,3-dihydroxynaphthalene. There were no indications of charge transfer interactions in the spectra (Tollin, 1968). A number of crystal structures have been determined (Table 15.9) and comparison shows many common features. 1. 2.

3.

There is always an extensive array of hydrogen bonds which is probably the primary factor in determining the overall arrangement. Most structures contain inﬁnite stacks of donor and acceptor molecules but two have ﬁnite DAAD sequences (Fig. 15.18). The interplanar distances range from 3.3 to ˚ and there is some correlation between colour of the crystals (a rough measure of 3.5 A charge transfer, in the absence of spectroscopic results) and interplanar distance. However, the nature of the moieties is probably a more important factor here and it seems clear that the protonated ﬂavins are appreciably stronger acceptors than the neutral ﬂavins (in contrast one may note that picric acid molecule and picrate ion have similar acceptor strengths). In four of the compounds (out of eight) there are additional donor molecules in interstitial positions outside the mixed stacks, with the planes of the interstitial molecules approximately normal to those in the mixed stacks. The arrangement is similar to that encountered in a few mixed stack donor–acceptor molecular compounds

Table 15.9. Some structural details for crystalline flavin molecular compounds. Reports of crystal structure determinations after 1975 have not been found. Complex/reference/refcode

Colour of Crystals

Interplanar ˚) Spacings (A

Space Group

Z

Stacking Type

Interstitial Donors?

1. Adenine riboﬂavin. 3H2O (Fujii et al., 1977); ADRBFT10 2. (Naphthalene-2,3-diol) lumiﬂavin (Wells et al., 1974); LUMNPO20 3. 5 0 -Bromo-5 0 -deoxy-adenosine riboﬂavin3H2O (Voet and Rich, 1971); RIBBAD10 4. (Naphthalene-2,3-diol)2 (10-propyl-isoalloxazine) (Kuo et al., 1974); PALXND10 5. (Naphthalene-2,3-diol)2 lumiﬂavin3H2O (Fritchie and Johnson, 1975); LUNMPO10 6. (2,6-Diamino-9-ethylpurine)2 (lumiﬂavin)2 C2H5OHH2O (Scarbrough et al., 1976, 1977); LUFAEP 7. Quinol lumiﬂavin chloride (Karlsson, 1972); LUMIHQ 8. Quinol riboﬂavin(HBr)2(H2O)2 (Bear et al., 1973); BIBHQN10

dark yellow

3.4–3.5

P21

4

No

yellow

3.46; 3.48

P21/c

4

inﬁnite mixed stacks ditto

Yes

orange-brown

3.45; 3.54

P212121

4

ditto

No

orange

3.38; 3.46

A2/a

8

ditto

Yes

reddish-orange

3.3

P1

2

ditto

Yes

deep red

3.4

P21/c

4

DAAD sequence (cf. Fig. 15.17)

No

n n n

green

P21/c

8

black

P21

4

blackish

P21/c

4

DAAD sequence (see Fig. 15.17) One stack of inﬁnite mixed type; the other has pairs of donor and acceptor moieties. Inﬁnite mixed stacks.

No

n n n

quinol/ﬂavin 3.49; ﬂavin/ﬂavin 3.72 3.4 in inﬁnite mixed stack; 3.26 and 3.52 in ‘‘paired’’ stack. 3.3

black

Not listed

P1

1

n n n

n n n

n n n

n n n

n n n

n n n

9. (Quinol)3 lumiﬂavinium bromide (Tillberg and Norrestam, 1972); LUMFHQ 10. (Naphthalene-2,7-diol)3 (10-methylisoalloxazinium bromide)22H2O (Langhoff and Fritchie, 1970); MAZNDO10 n n n

n n n

Charge transfer interaction suggested.

No

Yes Yes

1026 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

x

y

Fig. 15.18. Schematic diagram showing one sheet of the molecular packing in quinol lumiﬂavin chloride extended over two unit cells. The long and short full lines represent the lumiﬂavin and hydroquinone molecules respectively; the dashed lines are hydrogen bonds and the circles Cl ions. The four-moiety groups, in the sequence hydroquinone lumiﬂavin lumiﬂavin hydroquinone, lie approximately in the (301) planes. Similar DAAD groupings are found in the structure of (2,6diamino-9-ethylpurine lumiﬂavin)2C2H5OH.H2O (Scarborough et al., 1977). (Reproduced from Karlsson, 1972.) n n n

n n n

n n n

n n n

n n n

(Section 15.5.1). A much larger sample of ﬂavin complexes will have to be examined before drawing conclusions from the high frequency of interstitial donors among the complexes of Table 15.9. Judging from the colours of the complexes it appears that the ﬂavins act as quasiacceptors in the ﬁrst three complexes of Table 15.9 with essentially no charge transfer interaction with the donor; indeed adenine and 5 0 -bromo-5 0 -deoxyadenosine are both weak donors. The geometry of the -systems is rather variable and the ﬂavins appear to belong to that group of acceptors in which the strength of the -interaction varies little with the mutual lateral position of donor and acceptor molecules. This implies that any part of the ﬂavin nucleus can participate in charge transfer interaction and that the actual overlap that occurs in the crystals depends both on the nature of the partners and the requirements of the hydrogen bonding scheme. This may well be a requirement for a moiety so widely involved in biological and other oxidation-reduction reactions. The complexes containing riboﬂavin all crystallize in chiral space groups but this is just a consequence of the chirality of riboﬂavin itself. 15.7.3 15.7.3.1

Other crystals with both charge transfer and hydrogen bonding interactions Crystals without solvent of crystallization

In {1,5-diaminonaphthalene chloranil} (DAN CA) (Tamura and Ogawa, 1977; ˚ ), with CANANP) there are mixed stacks of DAN and CA molecules along [010] (7.95 A n n n

n n n

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1027

mixed donor–acceptor stacks with hydrogen bonding between adjacent stacks chloranil

2.749 1,5-diaminonaphthalene

Cl

N1

O1

N2

2.969 O2

y x

Fig. 15.19. Crystal structure of (DAN CA) projected down [001]. The N atoms are shown cross˚ . The two kinds of hydrogen bonds between amino groups and chloranil hatched. Distances in A oxygens are shown by broken lines. (Data from Tamura and Ogawa, 1977.) n n n

hydrogen bonding between carbonyl and amino groups of molecules in different stacks separated by [001]. Thus sheets of molecules, linked by both charge transfer interactions (there is carbonyl group–aromatic ring overlap) and hydrogen bonds, are formed in the (100) planes. These sheets are then stacked along [100] (Fig. 15.19). The component molecules are, of course, centrosymmetric and so is their arrangement within the sheets, at least to a very good approximation. However, the space group is Pn, which is noncentrosymmetric (see Table 15.4). It seems that most efﬁcient packing of the sheets is obtained when they are mutually offset along [010]. One may perhaps anticipate that both charge transfer interactions and hydrogen bonds will be found in {durendiamine chloranil} (Matsunaga, 1964) and in the two polymorphs of {1,6-diaminopyrene chloranil} (Matsunaga, 1966) but crystal structures have not been reported. Hydrogen bonding interactions have been used in an attempt to convert the herringbone arrangements of charge-transfer crystals into more planar arrangements, hopefully increasing the interaction between donor and acceptor moieties by reducing the interplanar distance and thus affording observable changes in moiety geometries (Bock, Seitz et al., 1996). Speciﬁcally the herring-bone structure of {perylene 1,2–4,5tetracyanobenzene} (P21/c, Z ¼ 4; REHMUM) was compared with that of {pyrene 2,3,5,6-tetracyanohydroquinone} (P 1, Z ¼ 1; TEXPOB10). Indeed, both planarization and (minor) shortening were achieved (Fig. 15.20), but there was no effect on moiety geometries. Perhaps more interesting is the way in which the formation of CN . . . HO hydrogen bonds gives a structure composed of pyrene and hydrogen-bonded tetracyanohydroqunone layers without removing the integrity of the donor–acceptor stacks. n n n

n n n

n n n

n n n

1028 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

NC

CN

NC

CN

345 pm

OH NC

CN

NC

CN

340 pm `

OH

277 162 191

`

(A) (B) 290 164° 204

(C)

197 156 172 159 256 299

299 `

`

Fig. 15.20. Comparison of the crystal structures of {perylene 1,2–4,5-tetracyanobenzene} (P21/c, Z ¼ 4) and {pyrene 2,3,5,6-tetracyanohydroquinone} (P1, Z ¼ 1). Both are viewed normal to the stack axes. Note the central layer of hydrogen-bonded tetracyanohydroquinone moieties. In the lower part of the ﬁgure the hydrogen-bonding patterns found with the 2,3,5,6-tetracyanohydroquinone molecular compounds with pyrene (left) and perylene þ 2H2O are shown. (Reproduced from Bock, Seitz et al., 1996.) n n n

n n n

When perylene is co-crystallized with 2,3,5,6-tetracyanohydroquinone, two molecules of water are incorporated in the crystals (TEXPUH10) and the dimerized hydrogen-bonding pattern found in {pyrene 2,3,5,6-tetracyanohydroquinone} is replaced by an interrupted pattern (Fig. 15.20 above). The donor–acceptor stacks remain. n n n

15.7.3.2 Crystals with solvent of crystallization For some donor–acceptor combinations, the combined occurrence of charge transfer interactions and hydrogen bonding allows formation of a more open arrangement of molecules, with interstices or channels which can be occupied by solvent. This occurs in the TCNQ compounds of benzidine (BD), toluidine (TL) and diaminobenzidine, where solvent-free and solvated types are found (Ohmasa et al., 1971). The BD/TCNQ system is the most thoroughly studied and three types of crystal have been obtained.

CHARGE TRANSFER AND HYDROGEN BONDING INTERACTIONS

1029

I – solvent-free BD TCNQ (crystal structure reported (Yakushi et al., 1974a; BZTCNQ); II – with aliphatic guests such as acetone, acetonitrile, CH2Cl2, CH2ClCH2Cl and CH2BrCH2Br. These crystals are all isostructural and the structure of BD TCNQ1.8CH2Cl2 has been determined in detail (Ikemoto, Chikaishi et al., 1972; BDTCQC10); III – with aromatic guests such as benzene and substituted benzenes (X ¼ CH3, Cl, Br, NO2, CN). The crystal structure of BD TCNQC6H6 has been determined (Yakushi, Ikemoto and Kuroda, 1974b; BDTCNB10). n n n

n n n

n n n

The crystal structures of {BD TCNQ1.8CH2Cl2} and {BD TCNQC6H6} are based on similar arrangements of hydrogen-bonded BD and TCNQ molecules in layers, as illustrated for {BD TCNQ1.8CH2Cl2} in Fig. 15.21. The stacking of these layers is rather different in the two types of inclusion complex. In the CH2Cl2 complex the layers are directly superimposed so that channel and stack axes coincide, while in the benzene complex a BD TCNQ pair forms the repeat unit in the stack and channel and stack axes are mutually inclined at an angle of 30 . The enthalpy of formation of crystalline {BD TCNQ1.8CH2Cl2} has been measured (Ohmasa, Kinoshita and Akamatsu, 1971), the reaction being: n n n

n n n

n n n

n n n

n n n

BD TCNQ(s) + 1.8CH2Cl2(g) ! BD n n n

n n n

TCNQ1.8CH2Cl2(s) + 83.6 kJ.

The reaction is thus exothermic and the inclusion complex is stable with respect to its components. The composition with 1.8 molecules of CH2Cl2 is the most stable, and the 10%

3.110 Å

C N Cl

Fig. 15.21. Projection of the {BD TCNQ1.8CH2Cl2} structure onto (001). The arrangement of BD and TCNQ molecules in a single layer of the benzene complex is very similar. (Reproduced from Ikemoto et al., 1972.) n n n

1030 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.10. Conductivities of benzidine/TCNQ inclusion complexes Type

Formula

Conductivity (ohm cm)1

Activation energy (eV)

I II III

{BD TCNQ} BD TCNQ1.8CH2Cl2 BD TCNQC6H6

109 104 106

0.54 0.11 0.28

n n n

n n n

n n n

of vacancies on solvent sites must contribute some entropy stabilization as well. All solvent sites are occupied in the benzene complex. It seems unlikely, however, that (in both types of complex) the solvent molecules are as ordered as depicted in the structure diagrams. Very different electrical conductivities and activation energies are found for the three types of crystal (Takahashi et al., 1976), the conductivities of the inclusion complexes being much larger than those of the solvent-free crystals (Table 15.10). The conductivity of {BD TCNQxCH2Cl2} is strongly dependent on the concentration of solvent vacancies; in the most stable crystals (x ¼ 1.8) there is extrinsic semiconduction due to the solvent vacancies. It is the presence of these vacancies that probably accounts for the larger conductivity and smaller activation energy of Type II as compared to Type III crystals. Polarized reﬂectance spectra of single crystals of {BD TCNQ} and {BD TCNQ1.8CH2Cl2} have been measured at 295 and 30K at ambient pressure and also at 295K, 56.7 kbar for {BD TCNQ}. The degree of charge transfer at 295K, 1 bar was estimated to be 0.3 and increased by 30% on cooling or application of pressure; however, the crystals retained their neutral ground states (Yakushi et al., 1985). n n n

n n n

n n n

n n n

N N

DPC N H

Monoclinic {[bis(dihydro-5,6-pyrimidino[5,4-c]carbazole)- TCNQ]-dihydro-5,6pyrimidino[5,4-c]carbazole dihydrate} (P21/c, Z ¼ 2; {[DPCTCNQDPC]DPC2H2O} for short; Dung et al., 1986; DULFAR) has mixed . . . DAD . . . stacks (shown within the ˚ ) linked by DPC and water molecules. Only the ﬁrstsquare brackets) along [100] (11.04 A mentioned DPC molecules are involved in donor–acceptor interactions. The mixed stacks retain their integrity despite the considerable perturbation of the structure. n n n

15.8

Mixed-stack crystals with both delocalized and localized charge transfer interactions

By analogy with the structures discussed in Section 15.7, one may anticipate mixed-stack structures in which the hydrogen bonding between stacks is replaced by localized charge transfer interactions, acting in addition to the delocalized charge transfer interactions

DEL OCALIZED AND LOCALIZED CHARGE TRANSFE R I NTERACTIONS

N(4)

a 3.15

N

N C

N(3) S(1)

3.37

C

1031

S(2) S(3)

3.54

N

0

N

S

c

S

N

N

N

C

C

N N(4)

bis(1,2,5-thiadiazolo) tetracyanoquinodimethane (BTDA-TCNQ)

3.15 S(2)

S(3) 3.58 S(1)

[b] – [101]

Fig. 15.22. Crystal structure of {TTF (BDTA-TCNQ)}, where the acceptor is bis(1,2,5-thiadiazolo)tetracyanoquinodimethane. (upper) ‘‘Sheet-like’’ network in the ac plane showing the secondary N S interactions between TTF and acceptor molecules and also between the acceptor molecules themselves; the TTF molecules are shaded. (lower) Arrangement of the corrugated sheets along the [010] (stack) axis, with -* interactions in the [010] direction. (Adapted from Susuki, Kabuto et al., 1987.) n n n

n n n

within the stacks. This is a striking feature of the structural arrangements in the Bechgaard salts, important as the ﬁrst organic superconductors (Williams et al., 1985) but outside the scope of this book. So far only one example is known among the mixed stack structures – {TTF (BTDA-TCNQ)}, where preparation of the acceptor (and of a number of its molecular compounds (Yamashita et al., 1985)), determination of the crystal structure of the acceptor (Kabuto et al., 1986; FARSOG6 ) and that of the TTF molecular compound (Suzuki, Kabuto et al., 1987; FUVYEA), have been described. The neat acceptor (formula in Fig. 15.22) forms a two-dimensional sheet-like network with strong n n n

6

For reinterpretation in space group C 2/m see FARSOG01 (Suzuki, Fujii et al., 1992).

1032 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

S . . . N C– interactions. The equimolar molecular compound is monoclinic (a ¼ ˚ , ¼ 91.312(1) , Z ¼ 2, space group P21/n) and 9.660(1), b ¼ 7.231(1), c ¼ 14.628(2) A has a neutral ground state. The interactions among the components are such that a threedimensional network is formed.

15.9

Donors and acceptors with special chemical features

We use the term ‘quasi-acceptor’ to describe the second component in binary systems where a donor and this component form mixed stack crystals but other evidence (generally spectroscopic) for a charge transfer interaction between the components is lacking. 15.9.1

Fluorinated aromatics as quasi-acceptors

Considerable effort has been devoted to the study of systems of aromatic hydrocarbons and polyﬂuorinated aromatics (Fenby, 1972; Swinton, 1974; Table 15.11); the spectroscopy and thermodynamics of solutions have been studied, phase diagrams have been reported and a number of crystal structures determined (Table 15.12; we include some other quasi-acceptors in this Table for convenience). Resurgence of interest in this area has been prompted by (expressed in currently fashionable terms) recognition of the areneperﬂuoroarene interaction as an important supramolecular synthon (Dai, Nguyan et al., 1999) with potential applications for solid-state chemistry, crystal engineering, molecular electronics, liquid crystals etc. Congruently melting 1 : 1 compounds have been found in the phase diagrams of C6F6 with benzene, toluene, p-xylene and mesitylene (Duncan and Swinton, 1966) and congruently melting 1 : 1 compounds in the phase diagrams of benzene and naphthalene with perﬂuoronaphthalene, and of benzene with perﬂuorobiphenyl, while the {biphenyl–C6F6} compound melts incongruently (McLaughlin and Messer, 1966). Equimolar molecular compounds have been found in most binary phase diagrams but not other compositions. No evidence of –* charge transfer interaction has been Table 15.11. Melting points of equimolar molecular compounds formed from various donors and hexafluorobenzene or octafluoronaphthalene Donor/hexaﬂuorobenzene

M.pt. (K)

Donor/ octaﬂuoronaphthalene

M.pt. (K)

Benzene (Patrick and Prosser, 1960) 1-methylnaphthalene (Grifﬁth et al., 1983) 2-methylnaphthalene (Jackson and Morecombe, 1986) 2-ethylnaphthalene (Dahl, 1988)

297

Anthracene (Collings, Roscoe Phenanthrene (Collings, Roscoe Pyrene (Collings, Roscoe Triphenylene (Collings, Roscoe

447

Tetralin (Dahl, 1988) Quinoline (Dahl, 1988) iso-quinoline (Dahl, 1988)

373 335.7 306.7 266.7 318.1 285.4

et al., 2001) 445 et al., 2001) 522 et al., 2001) 478 et al., 2001)

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

1033

found in solutions of aromatic hydrocarbons and ﬂuoroaromatics but there may be n–* charge transfer when nitrogen-containing heteroaromatics are used as donors (Beaumont and Davis, 1967); there is some crystallographic evidence for speciﬁc interactions between nitrogens of heteroaromatic donors and quasi-acceptors. Mixed stacks of donor and quasi-acceptor molecules have been found in almost all the crystal structures so far reported and thus these structures resemble those of -molecular compounds insofar as packing arrangements are concerned (Dahl, 1988). However, the absence of charge-transfer bands in the solution spectra, the colourless nature of the crystals, and the fact that lattice energy minimizations based on atom–atom potentials do not reproduce the observed crystal structures very well (Dahl, 1990) all indicate that directional forces of another kind must be invoked to account for the retained occurrence of mixed stacks despite replacement of true acceptors by quasi-acceptors. One possibility is localized dipole–dipole interaction between C-H and C-F bonds, expressed in terms of quadrupole interactions. The fact that both benzene and hexaﬂuorobenzene have large molecular quadrupole moments (MQM), of similar magnitude but of opposite sign7, led to the suggestion (Williams, 1993) that the stacking motif is dictated by electrostatic quadrupole-quadrupole interactions (see also Clyburne et al., 2001). The negative values for aromatic hydrocarbons indicate that the negative charge is clustered in the center and above the molecular plane, while that for perﬂuoroaromatics is located at the molecular perimeter and therefore there is a depletion of electron density at the center of the ring (Fig. 15.23). Illustrations, apparently based on Williams (1993), have been given by Dunitz (1996) and Collings, Roscoe et al. (2001). Many of the crystals show low temperature phase transitions; for example, the structures of four 1 : 1 benzene–hexaﬂuorobenzene phases have been determined (Table 15.13). The structural progression has been described as follows (Williams et al., 1992) ‘‘In phase I the molecules are rotating about the column axis, and the system behaves like parallel cylindrical rods. On lowering the temperature the molecules ﬁrst tilt with respect to the column axis, leading to a monoclinic phase, followed by a distortion to a triclinic phase due to the freezing out of the rotations of the heavier C6F6 molecules. At this stage the unfavorable interaction between the columns is compensated by the rotational freedom of

F– F–

F– + + F–

H H

+

+

–

+ + +

F–

– F–

H

+

+

H

–

+

– – – H H

+

+

Fig. 15.23. Schematic charge distributions in hexaﬂuorobenzene and benzene. 7

MQM of benzene 29.0, naphthalene 45, ferrocene 30 and hexaﬂuorobenzene þ31.7, all 1040 C m2.

Table 15.12. Summary of information available about mixed-stack crystal structures of molecular compounds formed between aromatic hydrocarbons and quasi-acceptors Aromatic hydrocarbon/reference/refcode

Quasi-acceptor

Space group

Z

Remarks

1. Anthracene (Boeyens and Herbstein, 1965a); ZZZGMW

C6F6

C2/m

2

Only cell dimensions and space groups (at 300K) reported for these three compounds.

2. 3. 4. 5. 6. 7.

Pyrene (Boeyens and Herbstein, 1965a); ZZZGKE Perylene (Boeyens and Herbstein, 1965a); ZZZLJY p-Xylene (Dahl, 1975a); PXYHFB Mesitylene (Dahl, 1971a); MTYHFB Durene (Dahl, 1975a); DURHFB C6(CH3)6; MBZFBZ

C6F6 C6F6 C6F6 C6F6 C6F6 C6F6

C2/m P21/a P 1 Pnma C2/m R 3m; P 1

8. N,N-dimethylaniline (Dahl, 1981b); BAPLEJ 9. N,N-dimethyl-p-toluidine (Dahl, 1981a); METOFB 10. TMPD (Dahl, 1979); MPAHFB 11. Trans-stilbene (Batsanov, Howard et al., 2001); TIJTUB 12. Perdeuterobenzene (Overell and Pawley, 1982); BICVUE 13. Cr(6-C6H6)2 (Aspley et al., 1999); FIBGUS

C6F6 C6F6 C6F6 C6F6

P 1 I2/m P 1 P21/c

2 2 1 4 2 3 1 1 2 1 2

14. o-diethynylbenzene dimer (Bunz and Enkelmann, 1999); JOCRIC 15. hexamethylmelamine (Aroney et al., 1987) 16. Naphthalene (Potenza and Mastropaolo, 1975); NFOFNP 17. anthracene (Collings, Roscoe et al., 2001); ECUTUR

triclinic below 223K at 298K (Dahl, 1971b); at 233K (Dahl, 1973)

Colourless plates

C6F6

m; or R3 R3m P 1

C6F6

P21/a

4

C6F6 octaﬂuoronaphthalene

C2/m P21/c

2 2

Poor, disordered crystals

octaﬂuoronaphthalene

P21/a

2

At 120K

C6F6

1 1

at 299K; phase transitions at lower temperatures (see Table 15.13) Red-pink blocks; there are also yellow plates of rather similar structure not described in detail. At 165K.

18. phenanthrene (Collings, Roscoe et al., 2001); ECUVED 19. pyrene (Collings, Roscoe et al., 2001); ECUVIH 20. triphenylene (Collings, Roscoe et al., 2001); ECUVON 21. TTF (Batsanov, Collings et al., 2001); TIJVAJ 22. Diphenylacetylene (Collings, Batsanov et al., 2001; at 100K); OCAYIA 23. 2,6-dimethylnaphthalene (Birtle and Naae, 1980); BPHFPC 24. 1,8-diaminonaphthalene (Batsanov, Collings, Howard and Marder, 2001); EDAWAH 25. ferrocene (Clyburne et al., 2001); YEBQOL 26. ferrocene (Burdenuic et al., 1997) 27. bis(decamethylferrocene) (Beck et al., 1998); SIBQOJ 28. bis(N-(2,6-dimethylphenyl)N’-(1,3,4,5,6,7,8heptaﬂuoro-naphth-2-yl)sulfurdiimide (Lork et al., 2001); NEMHOC 29. biphenyl (Lin and Naase, 1978); ZZZBRD 30. Biphenyl (Naae, 1979); BPPFBP 31. 4-bromobiphenyl (Birtle and Naase, 1980); BPHFBP 32. 4-methylbiphenyl (Birtle and Naase, 1980); BPHFPA 33. Naphthalene (Foss et al., 1984); CEKYUM 34. triphenylene (Weck et al., 1999); CUKXIP 35. Trans-stilbene (Bruce et al., 1987); SERQAH 36. Benzene (Hazell, 1978); DCLPYR 37. Diphenylbutadiyne (Coates et al., 1997). M.pt. 360K;

octaﬂuoronaphthalene

P21/a

2

Below 250K

octaﬂuoronaphthalene octaﬂuoronaphthalene

P1 P 1

1 2

At 120K At 120K

octaﬂuoronaphthalene octaﬂuoronaphthalene

P21/c P21/a

2 2

At 120K

octaﬂuoronaphthalene

P 1

octaﬂuoronaphthalene

P21

2

1.5(Octaﬂuoronaphthalene) Perﬂuorophenanthrene Perﬂuorophenanthrene

P 1 P 1 P21/c

2 2 4

Pseudo-isostructural with naphthaleneoctaﬂuoronaphthalene At 223K.

Octaﬂuoronaphthalene

P 1

1

2,3,4,5,6-pentaﬂuorobiphenyl decaﬂuorobiphenyl decaﬂuorobiphenyl

C*/c C2/c P21/c

4

decaﬂuorobiphenyl

P21/c

decaﬂuorobiphenyl Perﬂuorotriphenylene trans-decaﬂuoro-azobenzene decachloropyrene Decaﬂuorodiphenyl butadiyne. M.pt. 387K.

C2/c C2/c P 1 P21/c P 1

4 8 1 4 1

At 173K.

Orange crystals, m.pt. 428–430K. M.pt. 425K.

Table 15.12. (Continued ) Aromatic hydrocarbon/reference/refcode

Quasi-acceptor

38. Benzalazine (Vangala, Nangia and Lynch, 2002); EGAWEO 39. Pyrene (Damiani, De Santis et al., 1965) 40. Benzo[c]pyrene (Damiani, Giglio, Liquori and Ripamonti, 1967) 41. Coronene (Damiani, Giglio, Liquori, Puliti and Ripamonti, 1967) 42. Acridine (Yamaguchi and Ueda, 1984; Marsh, 1986); CEJTAM self complex

Bis(pentaﬂuorophenylmethylidene) hydrazone TMU (TMU)2

P 1

2

Pc P1

2 1

(TMU)2

P1

1

1,4-dithiintetra-carboxylicN,N 0 -dimethyldiimide 2,3,4,5,6-penta- ﬂuorobiphenyl (Brock et al., 1978); PFBIPH

P21/n

2

C2221

4

Notes: (1) TMU is 1,3,5,7-tetramethyluric acid. (2) There is no evidence for charge transfer interaction in compound #43. (3) Beck et al. (1999) note the preparation of {(ferrocene)4octaﬂuoronaphthalene} but a structure was not reported.

Space group

Z

Remarks

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

1037

˚ , deg.) for the four C6H6–C6F6 phases (angle values are given only if Table 15.13. Crystal data (A different from 90 ) Phase

T(K)

a/

b/

c/

V/formula ˚ 3) unit (A

Z

I (Overell and Pawley, 1982) II (Williams et al., 1992) III (Williams et al., 1992) IV (Williams et al., 1992)

279

11.952

11.952

7.238/120

299

3

R 3m

260

6.631

12.330/99.67

7.302

295

2

I2/m

215

6.380/93.99

12.338/96.37

7.395/91.85

284

2

P 1

30

9.516

7.429/95.60

7.537

265

2

P21/a

Space group

the C6H6 molecules. Reduction of their rotational energy leads to a realignment of the columns and the unusual transition from a triclinic to a monoclinic phase with decreasing temperature . . . The columnar nature of the structure[s] is a result of the strong attraction between the quadrupole moments of opposite phase of the benzene and hexaﬂuorobenzene molecules.’’ Shorter range electrostatic interactions determine the details of the packing. The structure determinations are noteworthy because they were carried out by combined use of X-ray (synchrotron) and neutron diffraction on polycrystalline samples. The electron afﬁnity of hexaﬂuorobenzene has been measured as 0.86(3) eV (Wentworth et al., 1987). The enthalpy of formation of crystalline {C6H6 C6F6} has been measured by a differential scanning calorimetric method as þ1.0(3) kJ/mol (Brennan et al., 1974). This implies that the entropy of formation must be positive and greater than 3.3 J/mol K (at 300K). In contrast to this situation, most -molecular compounds are enthalpy-stabilized (see Section 16.5). The enthalpy of formation of {p-xylene C6F6} has been reported to be –0.08 0.20 kJ/mol (Ott et al., 1976). The {triphenylene–perﬂuorotriphenylene} molecular compound, ﬁrst prepared by Smith and Massey (1969), has a melting point of 524K, compared with 472K for triphenylene and 382K for perﬂuorotriphenylene (structure by Hursthouse, Smith and Massey, 1977; Fdd2, Z ¼ 8; PPTRPH). The DSC trace of the molecular complex shows ﬁrst order transitions at 294 and 377K. The crystal structure reported (but the phase was not speciﬁed) is particularly interesting (Fig. 15.24; Weck et al., 1999; 7.390 20.987 ˚ , ¼ 95.26 , C2/c, Z ¼ 8; CUKXIP)) and has many features typical of the mixed16.998 A stack structures. There are mixed stacks of the two components, seen edge-on in the upper part of Fig. 15.24. This also shows the appreciable distortions from planarity of both components; Weck et al. summarize these as 33 and 16 tilts in the skeletons of perﬂuorotriphenylene and triphenylene in the cocrystal, to be compared with 40 and 2 tilts in the neat crystals. In the lower part of the ﬁgure one notes the almost ideal superpositioning of the component molecules, an unusual situation in crystal packing ˚ , while arrangements. The centroid to centroid distances for the central rings is 3.698 A ˚. the shortest intermolecular C . . . C distance is 3.369 A n n n

n n n

1038 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Most of the structures listed in Table 15.12 are of the mixed stack type (as illustrated in Figs. 15.24 and 15.25), some having particular features needing comment. The decaﬂuorobiphenyl (C12F10) molecule is not planar; the dihedral angles between the two rings are 59.5 in neat crystalline C12F10 (Gleason and Britton, 1976; DECFDP01) (and 64.4 in

B

mixed stacks (horizontal) triphenylene

perfluorotriphenylene

y

x

mixed stacks (vertical)

Fig. 15.24. The triphenylene . . . perﬂuorotriphenylene crystal structure viewed (above) edge-on to the stacks (ﬂuorines are large cross-hatched circles and hydrogens are open circles) and (below) normal to the mean molecular planes, showing the close-packed arrangement of the mixed stacks; perﬂuorotriphenylene has been removed from the central mixed stack. (Data from Weck et al., 1999.)

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

1039

z

y

Fig. 15.24. (Continued )

the gas phase (Bastiansen et al., 1989)), 55.3 in the naphthalene compound, 50.8 in the biphenyl compound and 52.9 in the analogous molecule 2,3,4,5,6-pentaﬂuorobiphenyl (C6H5–C6F5) (PFBIPH). In {C12H10 C12F10} (BPPFBP) the biphenyl molecule is also nonplanar (dihedral angle 36.6 ); however, mixed stacks are formed with an angle of 7.1 between juxtaposed halves of each molecule. A similar mixed stack arrangement is found in 2,3,4,5,6-pentaﬂuorobiphenyl with superpositioning of C6H5 and C6F5 portions of the molecule; this compound must therefore be classed as a self-complex. Stacks are not formed in {naphthalene-decaﬂuorobiphenyl}, where naphthalene is planar and decaﬂuorobiphenyl nonplanar; instead the naphthalene molecule is sandwiched between C6F5 halves of neighboring C12F10 molecules, with an interplanar angle of 6 . The naphthalene in the complex is phosphorescent, in contrast to its lack of phosphorescence in its neat crystals. The mixed-stack {naphthalene octaﬂuoronaphthalene} molecular compound has been studied by Raman spectroscopy at ambient pressure down to 10K, and at ambient temperature in the pressure range 1–80 kbar and found to be stable (i.e. no phase transitions or chemical reactions) under these conditions (Desgreniers et al., 1985). The unusual composition of {ferrocene1.5(octaﬂuoronaphthalene)} (Clyburne et al., 2001) is n n n

n n n

1040 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

ferrocence decafluorophenanthrene decamethylferrocence

Fig. 15.25. Comparison of the packing arrangements found in {ferrocene deca ﬂuorophenanthrene} (on the left : a 2 þ 2 supersandwich) and {decamethylferrocene deca ﬂuorophenanthrene} (SIBQOJ; Beck et al., 1998) (on the right : mixed stacks). (Adapted from Burdeniuc et al., 1997.) n n n

n n n

explained by noting that there are 1 : 1 mixed stacks of ferrocene and octaﬂuoronaphthalene separated by ‘‘octaﬂuoronaphthalene of crystallization’’, the molecules being located at centers of symmetry. The {ferrocene decaﬂuorophenanthrene} structure (Burdeniuc et al., 1997; no refcode) is unusual in that there is a 2 þ 2 supersandwich with the ferrocenes located between the wingtip arene rings of the decaﬂuorophenanthrene (Fig. 15.25). The {naphthalene (p-iodotetraﬂuorobenzene)2} (P1, Z ¼ 1) (Law and Prasad, 1982) molecular compound possibly belongs in this group. The crystal structure has not been reported but a Raman study shows that the crystals are ordered, with the components linked mainly by van der Waals interactions; no low-lying charge transfer band was found. Our inclusion of {benzene–decachloropyrene} in Table 15.12 is questionable; although mixed stacks are formed the material could be an inclusion complex of an unusual type. A spectroscopic study is needed to establish whether the orange color of {trans-stilbene trans-decaﬂuoroazobenzene} is due to charge transfer interaction. n n n

n n n

n n n

15.9.2

1,3,5,7-Tetramethyluric acid (TMU) as quasi-acceptor

TMU forms crystalline molecular compounds with a number of aromatic hydrocarbons and some crystal structures have been reported (Table 15.10). These are all mixed stack structures based on ---DQDQ--- and ---QDQ QDQ--- sequences (where Q represents the quasi-acceptor TMU). There is considerable disorder and low-temperature studies would appear to be necessary for understanding the interaction between the components. No charge transfer bands are found in the solution or solid state spectra.

15.9.3

Acceptor is a metal coordination complex

Examples of metal chelate complexes which act as electron acceptors have been brieﬂy noted in Chapter 13 and this material will now be expanded. The 1,2-ethylenebis (dithiolene)-M system (see Section 13.3.3, Table 13.4 for formula) forms many different

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

1041

salts and also molecular compounds with ionic and neutral ground states. For example, equimolar perylene and pyrene molecular compounds have been prepared with Ni dithiete (X ¼ CF3) as acceptor and found to have mixed stack structures with neutral ground states (Schmitt et al., 1969; PERNIT). The crystals are semiconductors with roomtemperature resistivities of 105 ohm cm; the activation energy for conduction in the perylene molecular compound is anisotropic with minimum activation energy along the stack axis. ,,,@-Tetraphenylporphyrinato-Zn(II) forms an equimolar neutral ground state molecular compound with Ni dithiete (from spectroscopy, crystal structure not known) but the analogous Co(II) porphyrin links to the Ni dithiete by a bridging Co–S bond to give a covalent molecule rather than a molecular compound (Shkolnik and Geiger, 1966). Ni dithiete is the anion in some ion-radical salts to be discussed later (Section 15.10.2). Bis(diﬂuoroboronbenzimidazole)Ni(II) (Ni(dmgBF2)2; formula in Table 13.4) forms equimolar molecular compounds with the donors anthracene (Stephens and Vagg, 1981; BADZOV) and benzimidazole (Stephens and Vagg, 1980; FBGLNJ). The acceptor exists in the solid state and in solution as a weakly bonded dimer, with –* interaction between the two halves of the dimer. It also occurs as a dimer in the mixed stack molecular compound with benzimidazole. However, in the anthracene molecular compound it is the monomer which acts as acceptor. Analogous examples of the effect of molecular compound formation on donor or acceptor structure have been found in the -dimerization of TCNQ in some ion-radical salts (Table 15.12 below). In both anthracene and benzimidazole molecular compounds donor and acceptor are mutually located so as to avoid interference with the protruding ﬂuorine atom of the BF2 groups. The metal atoms do not play a special role in any of these molecular compounds. In contrast to these nonconducting molecular compounds, {(perylene)2 MS4C4(CN)4} (M ¼ Ni, Cu, Pd) compounds have been found to be fairly good conductors (Alcacer and Maki, 1974); for example, the Pd molecular compound has a room temperature resisitivity of 50 ohm cm. Structures are not known but there are presumably stacks of (perylene)þ 2 moieties with the anions between the stacks (cf. Section 17.3). Molecular compounds are known with a 2 : 1 ratio of toluene to tetraphenylporphyrinato-M(II) [M ¼ Mn (Kirner et al., 1977); Cr (Scheidt and Reed, 1978); Zn (Scheidt et al., 1978)]. The Mn and Zn compounds are triclinic and isomorphous (P1, Z ¼ 1), while that with Cr is monoclinic (P21/c, Z ¼ 2). All three molecular compounds contain ˚ DAD sandwiches, with toluene and porphyrin planes approximately parallel and 3.5 A apart; the DAD triples are not stacked but are effectively isolated from one another (cf. Section 15.2). The bis(toluene)porphyrin arrangement is thought to be indicative of donor-acceptor interaction. We have discussed this group of molecular compounds in Chapter 8. The bis(arene)Fe(II) dication has been shown to act as an electron acceptor in the formation of mixed stack charge transfer crystals with the electron donor arenes ferrocene and durene, PF 6 acting as counterion. The structures of the carmine tetragonal crystals of [Cp2Fe, (durene)2Fe2þ, (PF 6 )2] (VIPJUZ) and of the red-orange triclinic crystals of [durene, (hexamethylbenzene)2Fe2þ, (PF 6 )2]acetone (VIPKAG) have been determined. There is spectroscopic evidence for the effectiveness of other arenes such as mesitylene, pentamethylbenzene, 1,4-dimethylnaphthalene and 9-methylanthracene (Lehmann and Kochi, 1991). n n n

1042 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

15.9.4

Donor is a metal coordination complex

15.9.4.1 Metal chelates as donors The structures of some seven metal oxinate acceptor molecular compounds have been determined (for references see Table 15.2), as well as those of a number of other metal chelate acceptor molecular compounds. The formulae of the metal chelates are shown in Fig. 15.26. These are all equimolar (or effectively equimolar) mixed-stack, neutral ground state molecular compounds, diamagnetic (except where the metal atom is paramagnetic) and with high resistivities. The interaction between metal atom and acceptor is weak and plays little, if any, role in determining the crystal structures. This is shown dramatically by the resemblances between the component arrangements in {Pd(II) oxinate chloranil} (Kamenar, Prout and Wright, 1965; CLAQPD) and in the metal-free {(8-hydroxyquinolinol)2 chloranil}.(Prout and Wheeler, 1967; HQUCLA). However, there is at least one exception (Matsumoto et al., 1979) to this generalization. Three members of this group show special features. Using bis(N-alkyl-2oxynaphthylidene-aminato)Cu(II) and Ni(II) chelates as donors, a series of 1 : 2 molecular compounds was prepared (Matsumoto et al., 1979) with TCNQ and chloranil as acceptors, and crystal structures were determined for Cu(L-i-pr)2 itself and for {Cu(L-ipr)2 (TCNQ)2}, (IPONTC) where L-i pr is the isopropyl substituted ligand. In Cu(L-ipr)2 itself the coordination at Cu is distorted tetrahedral, with a dihedral angle of 39 between the two intersecting Cu(NO) planes; this distortion from the expected square planar arrangement was ascribed to steric hindrance between the two bulky iso-propyl groups. In {Cu(L-i-pr)2 (TCNQ)2} there are two antiparallel sets of mixed stacks, with ‘‘naphthalene’’ portions of the chelate and TCNQ molecules in alternating array. The geometry of the metal chelate has changed to a centrosymmetric stepped structure with square planar coordination about Cu. It was suggested (Matsumoto et al., 1979) that the overall arrangement represents a compromise in which the favoured coordination about Cu, as indicated by the arrangement taken up in the neat compound, is distorted minimally in order to achieve the most favourable stacking of ‘‘naphthalene’’ and TCNQ moieties. This is one of the most striking examples known of the effect of molecular compound formation on donor (or acceptor) geometry. In {[Cu(salphen)2]2 TCNQ} (Cassoux and Gleizes, 1980; PSALTQ) there appear, at ﬁrst sight, to be segregated stacks of metal chelate and TCNQ molecules. However, the conductivity of powders is 108 S/cm and the moieties (especially TCNQ, as judged from bond lengths) appear to be neutral. The paradox is resolved by reference to the stereodiagram of the packing (Fig. 15.27). This shows that the two halves of the centrosymmetric TCNQ molecules interact with benzene rings of salicylaldiaminato groups of two different donors to form two separate ---DADA--- stacks, where A ¼ 1/2(TCNQ). The second salicylaldiaminato groups of each of these donors form a quasi-segregated stack, presumably without charge transfer interaction. In {Ni(gh)2 TCNQ} (Megnamisi-Belome and Endres, 1982; BEXZIN) there is an alternating arrangement of neutral moieties (as judged from the TCNQ bond lengths) but there is so little overlap between them that one can hardly refer to ‘‘mixed stacks.’’ Instead the black colour of the crystals is ascribed to Ni–NC interactions (d(Ni . . . N) ¼ 3.357(5) ˚ ) mediated through the conjugated system of the TCNQ molecules. A n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

N O

O

R

N

bis(8-hydroxyquinolato) M(II) metal chelates (M = Cu, Ni, Pd)

O N

H

R

O

M(II)

1043

M(II) N O

N

bis(N-alkyl-2-oxynaphthylideneaminato M(II) with M = Cu, Ni and R = CH3, C2H5, i-C3H7, n-C3H7, t-C4H9.

O S

N

S Pt

M N N OH O

S

bis(1,2-benzoquinondioximato)M(II) with M(II) = Ni, Pd. Abbreviated as M(BCD)2

O

S

bis(propene-3-thione1-thiolate)Pt(II)

O Cu

HC N

N

CH

N,N'-(1,2-phenylene)bis(salicylaldiaminato) Cu(II) Abbreviated as Cu(salphen). O

H

N

O

CH3

N N

Ni N

H3C

N

N M

N

N

O

O H3C CH3 H bis(ethanediol dioximato)Ni(II) tetramethylporphyrinato Ni(II) Ni(gh)2

Fig. 15.26. Formulae of metal chelate compounds which act as donors in various molecular compounds.

1044 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Fig. 15.27. Stereodiagram of [Cu(salphen)2]2 TCNQ structure viewed down [010]. The [100] axis is horizontal. (Reproduced from Cassoux and Gleizes, 1980.) n n n

15.9.4.2 Metal porphyrins as donors Some one hundred molecular compounds of various porphyrins with a variety of electron acceptors have been reported, most by Treibs (1929) and some by Hill et al. (1967). The molecular compounds are in the main coloured powders but some single crystals were obtained. The crystal structure of {(tetramethylporphyrinato)Ni(II) TCNQ} has been determined (Pace et al., 1982; BEGLUU); it has a mixed stack structure with a neutral ground state, is diamagnetic and has a needle axis conductivity of <105 S/cm. Inﬂuence of the metal atom on structure and properties appears to be minimal. The {Zn tetraphenylporphyrin Ni thiete} compound has been discussed previously and we have also noted that tetraphenylporphyrinatoM(II) (M ¼ Cr, Mn, Zn) appears to behave as an acceptor in its toluene molecular compounds (Chapter 8 and Section 15.9.3). n n n

n n n

15.9.4.3 Other metal compounds as donors The structures of {ferrocene TCNE} (Adman et al., 1967; FERTCE) and {tricarbonylchromium-anisole TNB} (Carter et al., 1966; CCATNB) have been reported. Both have mixed stack structures with neutral ground states and the donor molecules behave structurally as typical aromatic moieties. Indeed the two very different faces of the tricarbonylchromium-anisole molecule interact in much the same way with the TNB acceptor. Metallocenes and analogous molecules also form many molecular compounds with ionic ground states and these are discussed later. n n n

n n n

15.9.5

Donors based on phenazine

Donors based on phenazine provide a wide variety of interrelated systems in which both electron transfers and proton transfers among the various moieties are possible (Soos et al., 1977, 1978; Keller and Soos, 1986). The phenazine-based moieties appear in molecular compounds and salts as neutral molecules, neutral radicals and cation radicals; there are now sufﬁcient experimental results to allow comparison with the expected structures summarized in Fig. 15.28. (i)

Phenazine is a stable, diamagnetic molecule with 14 electrons; and has been found to be planar and aromatic in a number of structures, starting from phenazine itself

DONORS AND ACCEPTORS WITH SPECIAL CHEMICAL FEATURES

(two polymorphs PHENAZ04 (Wozniak et al., 1991) and PHENAZ11 (Jankowski and Gdaniec 2002) and including the neutral ground state mixed-stack -compound phenazine TCNQ (P TCNQ) (Goldberg and Shmueli, 1973c; TCQPEN10). Experiment and expectation coincide. 5,10-Dihydrophenazine is expected to be a stable, diamagnetic molecule with 12 electrons, folded about the N–N axis. In {5,10-dimethylphenazine TCNQ} (M2P TCNQ) (Goldberg and Shmueli, 1973a; TCQMHP) the M2P moiety is folded about the N–N axis with a dihedral angle of 165 . This ﬁts the expectation from Fig. 15.28, but the authors inferred a ‘‘markedly ionic (dative) state’’ so the matter remains to be resolved. It has been emphasized (Soos et al., 1977, 1978) that phenazine TCNQ compounds must be close to the neutral-ionic boundary for mixed stack charge transfer compounds. {N-methylphenazinium TCNQ} has segregated stacks and a high conductivity (Fritchie, 1966; MPHCQM); the 12- electron cation is diamagnetic, planar and aromatic, thus agreeing with Fig. 15.28. Butler et al., (1975) have suggested that a more accurate formulation would be NMPþ TCNQ, where ¼ 0.94. The cations in {bis(N-methylphenazinium) (-(TCNQ)2)} (Morosin, Plastas et al., 1978; EPZTCD) are slightly bowed with the least squares planes through the two sets of six C and two N atoms forming an angle of 2.1 . This deviation from planarity seems hardly large enough to be in contradiction to Fig. 15.28. The structures of a number of salts containing (variously) substituted N, N 0 dihydrophenaziniumyl cation radicals (HMPþ) (13 -electrons) have been determined. According to Fig. 15.28, this cation would be expected to be folded about the N . . . N axis. The cation radical is N-hydro-N 0 -methylphenaziniumyl (HMP)þ in two of these salts (Morosin, 1978). In (HMP)þClO 4 (HMPZPC10) the cation radical has a small twist (2 ) forming a ﬂattened propeller. In the mixed-stack ionic ground state {HMP TCNQ} molecular compound (MPHCQM12) the cation radical is folded about the N–N axis with a dihedral angle of 174 .8 Somewhat similar folding is found in 5,10-dihydro-5,10-dimethylphenazinium triiodide where the cation has a dihedral angle of 165.5 ; the ESR spectrum shows that this compound is paramagnetic as expected (Keller et al., 1978; HDMPZI; P21/n, Z ¼ 4). However, in 5,10-dihydro-5,10-dimethyl-phenaziniumþ TCNQF4 (Soos et al., 1981; BEXZOT) both components are planar (space group P1, Z ¼ 1); here the cation has a structure contradicting expectation. The cation in 5,10-dihydro-5,10-diethylphenazinium triiodide is centrosymmetric and planar (Keller, Moroni et al., 1978; HETPZI; P21/n, Z ¼ 2). while that in {5,10dihydro-5,10-diethylphenazinium TCNQ} (Dietz et al., 1982; BEWBUA) is somewhat twisted. Coordinates are not available for {5,10-dihydro-5,10-diethylphenazinium TCNQ}phenazine (Dietz et al., 1982; BEWCAH). In {5,10-dihydro-2,3,5,7,8,10-hexamethyl-phenaziniumyl TCNE} the M6Pþ cation radical is also planar (P21/n, Z ¼ 2); an ionic ground state for this mixed stack molecular compound was inferred from the occurrence of an ESR spectrum and from the length of the C-C bond in the TCNE moiety (Flandrois et al., 1983; n n n

(ii)

1045

n n n

n n n

n n n

n n n

(iii)

(iv)

(v)

n n n

n n n

n n n

n n n

(vi)

n n n

n n n

(vii)

n n n

8 Morosin (1978) has corrected his earlier report (1976) that the latter compound was a mixed–stack form of N-methylphenazinium TCNQ. n n n

1046 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

CEGYUI). According to the expectations of Fig. 15.28 these cations should be folded. The evidence from the geometrical structures of the phenazine (phenazinium) moieties in general favours the predictions as the deviations from planarity are small; one difﬁculty is that one does not know to what extent packing effects can affect the structures, nor does one know what ‘dihedral angles’ are to be expected. Physical evidence, as from ESR spectra, is helpful where it is available. {M2P TCNQ} appears to undergo a reversible neutral to ionic transition on heating to 390K; the high-temperature ionic form appears to be stabilized by spin contributions to n n n

H

N,N'-dihydrophenazinium: folded, paramagnetic, cation radical, 13␲ electrons. –e

+ •

N N

+H

H

+e

–H

H

H

N

N

N

N

H +H

N,N'-dihydrophenazine: folded, neutral, 12␲ electrons, diamagnetic.

+

–H

–H

+

N-hydrophenazinium: planar, aromatic, 12␲ electrons, diamagnetic cation.

+

–e +e

+H

N

N-hydrophenazine: folded, paramagnetic, neutral radical, 13␲ electrons.

•

N H +H

Phenazine: planar, aromatic, neutral, 14␲ electrons, diamagnetic.

–H

N N

Fig. 15.28. Relationships among different donor species based on phenazine. Hydrogen is used as the substituent for purposes of illustration but can be replaced by alkyl groups. It has been convenient to draw the formulae in terms of particular canonical forms but the actual structures are resonance hybrids. (Adapted from Soos et al., 1978.)

MIXED-STACK DONOR–ACCEPTOR MOLECULAR COMPOUNDS

1047

the entropy, accidental degeneracy of the energies of the neutral and ionic forms being inferred. This is an unusual situation as ionic states are generally energy-stabilized at low temperatures and/or high pressures (Chapter 17 and Section 15.10.1). The crystal structures of many of the ionic compounds with phenazine-based cations are discussed in Section 15.10. 15.10 Mixed-stack donor–acceptor molecular compounds with ionized ground states 15.10.1

Mixed-stack closed shell charge transfer salts

Many salts have been investigated where the components are closed-shell ions – the cations are based on pyridinium, quinolinium or pyrrylium while the anions (shown below) are derived from polycyanopropene acids. The crystal structures of 2,4,6-triphenylpyrrylium–1,1,3,3-tetracyanopropenide (Tamamura, Yamani et al., 1974; PYLTCP), bis(quinolinium)–2-dicyanomethylene1,1,3,3-tetracyanopropanediide (Sakanoue et al., 1971; QUPRCN10). and N,N 0 -dimethyl(Nakamura 4,4 0 -bipyridinium2-dicyanomethylene-1,1,3,3-tetracyanopropanediide et al., 1981; BELTER) have been determined. There are – Dþ A2 Dþ A – stacks in the ﬁrst of these salts but the relative positioning of cation and anion appears to depend more on ionic than on charge transfer interactions. In the second salt there are – Dþ A2 Dþ Dþ A2 Dþ – stacks with charge transfer interactions between the moieties in the Dþ A2 Dþ sandwiches. Occurrence of charge transfer interactions along the stack axes is conﬁrmed for both salts by single-crystal spectra using polarized radiation. The third salt has mixed stacks of alternating D2þ and A2 ions. R + N

H

H

pyridinium

NC

+

+

N

R

quinolinium

O

R

pyrrolinium

H

H

–H+

NC

CN–

CN

NC H

H NC

NC CN CN CN CN

NC H

CN

CN

1,1,3,3-tetracyanopropenide NC

CN

2–

–2H+ NC

CN NC

CN

2-dicyanomethylene-1,1,3,3-tetracyanopropenide

1048 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

15.10.2

Ion-radical salts

The crystal structures of some twenty mixed stack ion radical salts have been determined (Table 15.14). In overall structural arrangement there is little to distinguish these ionic materials from their neutral fellows; indeed neutral-to-ionic phase transformations are found in some on cooling or application of pressure (see Chapter 13). The ionic nature of the phase is generally demonstrated by magnetic measurements, spectroscopy (ESR, UV– visible, resonance Raman or infrared) or from bond lengths. The three latter types of measurement allow one to infer the degree of charge transfer (Z ) in the molecular compounds; in some compounds the degree of charge transfer is inferred to be nonintegral, in contradiction to earlier theoretical predictions (see Chapter 13). However, it has been shown, using valence-bond methods, that intermediate values of Z are possible (Soos et al., 1979) and that there is a useful limiting relationship between the charge on the moieties and the magnetic energy gap DEm. In a mixed stack compound with fully ionic ground state (Z ¼ 1) the material would be a regular Heisenberg antiferromagnet, with DEm ¼ 0. However, static magnetic susceptibility ((T)) measurements show that this is not so for molecular compounds such as {TMPD TCNQ} and {TMPD CA} where the following temperature dependence is found in the range 200 < T < 350K: n n n

n n n

TðTÞ / expðDEm =kTÞ: The magnetic gap DEm is found to be 0.1 eV, which is almost as large as the charge transfer integral t ¼ < Dþ AjHj D A > . Soos et al. (1979) have shown that in a regular charge transfer solid DEm > 0 when Z < 0.68 0.01. For example, DEm is measured as 0.07 eV in {TMPD TCNQ}, which corresponds to Z0.60 – 0.65, in good agreement with values obtained by other methods. The larger values of DEm 0.13 eV in TMPD CA and PD CA imply somewhat smaller values of Z. When Z > 0.68 then DEm is predicted to be zero and the solid becomes paramagnetic. The {TMPD CA} structure is unusual in that there is complete eclipsing of donor and acceptor ions in the quasi-hexagonally close-packed stacks; such eclipsing is found elsewhere only in the (neutral ground state) molecular compound between 2,4,6tris(dimethylamino)-s-triazine and TNB (Williams and Wallwork, 1966). Both X-ray diffraction and ESR measurements show that {TMPD CA} undergoes a phase change on cooling below 250K but the low-temperature structure has not been reported. Another unusual feature is -dimerization9 of TCNQ in the formation of molecular compounds with N-ethylphenazinium and bis(dipyridyl)Pt(II) (nos. 15–17 in Table 15.14). ˚, The two parts of the (TCNQ–TCNQ)2 ion are joined by a covalent bond of length 1.63 A ˚ 0.09 A longer than the standard C–C single bond length; the arrangement at the linked carbons is approximately tetrahedral. Each half of the (TCNQ–TCNQ)2 ion, represented as vertical lines in the diagram, participates in charge transfer interactions in separate stacks while the central portion of the dianion only links the stacks. n n n

n n n

n n n

n n n

n n n

NC

CN

NC

CN

9 -Dimerization is used here to indicate covalent bond formation between two moieties; -dimerization is used to describe pairing of moieties by HOMO–LUMO interation without formation of a covalent bond.

MIXED-STACK DONOR–ACCEPTOR MOLECULAR COMPOUNDS

1049

Table 15.14. Some mixed-stack ion radical salts for which crystal structures have been reported. (tfd)2 is sometimes called dithiete. Phenazine moieties are discussed earlier and, apart from one example, have been omitted Ion radical salt/Reference/refcode

Z

Remarks

1. Tropylium Ni(tfd)2 (Wing and Schlupp, 1970); TRFSNI

1

disorder of cations; Curie–Weiss magnetic behavior, i.e. two independent spins per D þ A pair.

2. Phenoxazinium Ni(tfd)2 (Singhabandu et al., 1975); FMENPX 3. TTF Pt(tfd)2 (Kasper and Interrante, 1976); FMEPTF 4. TMPD chloranil (Boer and Vos, 1968); TMABCA 5. TTF ﬂuoranil (Torrance, Vasquez et al., 1981); TTFFAN

1

n n n

n n n

n n n

n n n

1 0.60 Ionic form is stable at low temperatures or above 9 kBar at 300K

n n n

6. TTF chloranil (Torrance, Vasquez et al., 1981); TTFCAN 7. p-Phenylenediamine chloranil (Hughes and Soos, 1968) 8. Decamethylferroceniumþ DDQH (Gebert et al., 1982); MEFEQU10 9. TMPD TCNQ (Hanson, 1965b); QMEPHE 10. TMBTP TCNQ (Darocha et al., 1979); MBPTCR 11. Decamethylferrocenium TCNQ (Miller et al., 1987); MCFECT01 12. DBTSeF TCNQ (Emge, Bryden et al., 1982); BOWSUB 13. DBTTF 2,5-TCNQF2 (Emge, Wijgul et al., 1982); BITROL 14. OMTTF DBTCNQ (Akhtar et al., 1985) n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

-bonded TCNQ dimers 15. (N-ethylphenaziniumþ)2 (TCNQ–TCNQ)2 (Morosin et al., 1978) EPZTCD 16. [Bis(dipyridyl)Pt(II)]2þ (TCNQ–TCNQ)2 (Dong et al., 1977) TCQDPT; 17. [Bis(2,9-dimethyl-1,10-phenanthroline) Cu(I)] (TCNQ–TCNQ)2 (Hoffmann et al., 1983; CABKEV)

0.5 1

From Em; crystal structure known only in outline Both ions disordered

0.60 1 1 0.47 0.6 0.7 1

n n n

n n n

n n n

structure not stacked

structure not stacked

1050 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

The ESR spectrum of (NEPþ)2 (TCNQ–TCNQ)2 has been studied (Harms, Keller et al., 1981); in addition to a number of features that were not clearly understood, there are thermally activated triplet spin exciton (TSE) lines (line width 0.5 mT) which show an orientation-dependent ﬁne structure splitting that was identiﬁed with an S ¼ 1 excitation of the dianion, and was assigned to a transition to an excited state in which the long -bond was broken. The TSE is quasi-immobilized on the dianion, in contrast to TSEs in other TCNQ salts, which show extreme line narrowing because of the fast diffusional or hopping nature of the paramagnetic excitation along the TCNQ anion stack. In the {Pt(2,2 0 -dipy)2 (TCNQ-TCNQ)2} salt there is a phase transition at 87 C, accompanied by a color change and an enormous increase in paramagnetism (corresponding to two unpaired electrons per formula unit) which is ascribed to breaking of the long -bond. There are a number of molecular compounds where the components have ionic ground states and the stacks are mixed but where a simple alternation of moieties is not found. There are ﬁve examples of a –DþDþAADþDþAA– arrangement, which can be further subdivided in terms of the interactions between the moieties. The ﬁrst example is {phenothiazine Ni(tfd)2}, which is a cation radical, anion radical salt (Geiger and Maki, 1971; Singhabhandhu et al., 1975; FMENPZ). The cation is nonplanar, with a dihedral angle of ˚ ; the 172 and there is strong cation–anion interaction with an interplanar distance of 3.36 A ˚ ˚ anion–anion distance is 3.83 A and the cation–cation distance varies from 3.4–3.9 A because of cation folding. Thus the structure is based on individual cation . . . anion pairs, largely isolated from other such pairs, and could be represented schematically as n n n

n n n

n n n

----Dþ Dþ A A Dþ Dþ A A ----: The magnetic susceptibility is consistent with a spin-paired singlet ground state and a thermally populated triplet excited state; a detailed ESR study has not yet been reported. {Phenoxazine Ni(tfd)2}, which could be expected to be isostructural, has in fact a different stacking (–DþA DþA DþA) and very different physical properties (Singhabhandhu et al., 1975; FMENPX). n n n

X

S

S

X

S M

N

X

S

S

X

H Phenothiazine

M = Ni, X = CF3 Bis(cis-1,2-perfluoromethylethylene-1,2-dithiolato)Ni(II), abbreviated as Ni(tfd)2. M = Pt, X = CN Bis(dicyanoethylene-1,2dithiolato)Pt(II).

The three compounds of the second subset {5-(1-butylphenazinium) tetraﬂuoroTCNQ} (NBP TCNQF4) (Metzger et al., 1982; BISWAB10); {NBP TCNQ} (Gundel et al., 1983; BISWUU10); {N,N 0 -dimethylbenzimidazolinium TCNQ} (Chasseau et al., 1972; MBZTCQ) are all characterized by strong anion . . . anion interactions. Although {NBP TCNQF4} and {NBP TCNQ} are not isomorphous (space groups P21/c and P1, respectively) the structures of their stacks are very similar. The anion radicals interact ˚ ) and both have ring-external bond (R-EB) overlap strongly (interplanar spacings 3.15 A n n n

n n n

n n n

n n n

n n n

n n n

MIXED-STACK DONOR–ACCEPTOR MOLECULAR COMPOUNDS

1051

while the other interactions are much weaker. ESR studies show that there are ‘‘quasiimmobile’’ Frenkel excitons localized on the pairs of adjacent anion radicals. A similar cation-anion radical arrangement is found in {N,N 0 -dimethylbenzimidazolinium TCNQ}, where the interplanar spacing between adjacent anion radicals is remarkably ˚ , implying strong coupling. Physical properties have not been measured short at 3.07 A apart from conductivity which is very low at 1010 S/cm. These compounds with strongly bound TCNQ -dimers are also noted in Section 17.4.2. The brieﬂy-described {tetrakis(methylthio)TTF TCNQ}10 has a mixed stack ˚, –DDAADDAA– arrangement (Mori,Wu et al., 1987; FIJYEC) with d(D . . . D) ¼ 3.48 A ˚ ˚ d(A . . . A) ¼ 3.41 A, d(D . . . A) ¼ 3.58 A; thus -dimers do not appear to be formed. A similar stacking arrangement is found (Iwasaki, Hironaka, Yamazaki and Kobayashi, 1992) in {TTF 4,8-bis(dicyanomethylene)4,8-dihydrobenzo-[1,2-b : 4,5-b 0 ]dithiophene} ˚ , d(A . . . A) ¼ 3.49 A ˚ , d(D . . . A) ¼ 3.36 A ˚ , indicating that the with d(D . . . D) ¼ 3.62 A strongest interaction is between donor and acceptor units. The bond lengths in TTF suggest that the moieties are present as ions. There is a six-molecule periodicity along the stack axis in {4,4 0 ,5,5 0 -tetraethyltetrathiofulvalene (TCNQ)2} {(TETTF) (TCNQ)2} (Galigne´ et al., 1977; ETFTCQ). ˚ ). The arrangement The space group here is C2/c and the stack axis is [001] (¼22.61 A can be represented schematically as: n n n

n n n

n n n

n n n

1

TCNQ

TETTF C2

n n n

TCNQ

1

TCNQ

TETTF C2

TCNQ

1

TCNQ

TETTF C2

TCNQ

1

where 1 represents a crystallographic centre of symmetry and C2 a crystallographic two fold axis. The mixed stack arrangement explains the low conductivity. It was inferred, from the bond lengths in TCNQ, that 0.4 e had been transferred from donor to acceptor. ˚ and the angle between TETTF The interplanar distance between TCNQ moieties is 3.36 A and TCNQ planes is 9.3 . Thus a possible description is of weak TCNQ -dimers separated by TETTF moieties, with the -dimers having laterally displaced R/R overlap rather than the more usual R/EB overlap. Mixed stacks of neutral (TNF) and charged (TCVPDM) moieties are found in the crystal structure of {tetramethylammonium p-tricyanovinylphenyl-dicyanomethide 2,4,7trinitroﬂuorenone} {(CH3)4NþTCVPDMTNF} (Sandman et al., 1980; TCVPDA), with the tetramethylammonium acting as counterion. The charge transfer interaction is n n n

CN NO2

CN

NC

O2N

NC

CN

TCVPDM–

10

NO2 O TNF

{bis(tetrakis(methylthio)TTF) TCNQ}has also been studied(FIJYAY). n n n

1052 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

somewhat limited as there is an angle of 16 between the planes of the two moieties in the stacks; it was considered that TCVPDM behaved as a closed-shell mono-anion electron donor and TNF as a neutral closed-shell electron acceptor (which is its usual role in -molecular compounds).

15.11

Isomeric (polymorphic) molecular compounds

There are a number of examples of binary molecular compounds of the same overall chemical formula occurring in different crystal structures. This is the usual deﬁnition of polymorphism, which does not take into account that the nature of the chemical entity in two (or more) polymorphs can vary, without change of chemical formula, from ‘‘hardly different’’ to ‘‘very different’’ (Herbstein, 2001). The charge transfer molecular compounds provide many interesting examples of this range of possibilities, leading to ‘isomerism’ of the molecular compounds, where the state of the components may differ appreciably in the two polymorphs (or isomers), usually as a result of electron or proton transfer. This is evidence that different types of interaction between the components predominate as the crystals are formed under different (but not always well deﬁned) conditions. We call these ‘‘isomeric (polymorphic) molecular compounds’’, with ‘polymorphic’ usually being dropped for brevity. We restrict ourselves in this chapter to molecular compounds of the charge-transfer type, where three types of isomerism are known : Type 1 : If donor and acceptor can interact in different ways without appreciable change in their individual (chemical) structures, then different crystal structures can ensue, depending on which of the different types of intercomponent interaction (e.g. –*; n–*; hydrogen bonding) predominates in a particular isomeric molecular compound. Type 2 : Here the components differ chemically in the different isomers; among the examples are those where the components are neutral in the ground state of one isomeric molecular compound but ionic in the ground state of the other. Type 3 : Here the isomeric molecular compounds are distinguished by the occurrence of proton transfer from acceptor to donor in one isomer but not in the other, where electron transfer (usually virtual electron transfer, with the ground state neutral) takes place. A variety of isomeric molecular compounds is possible in principle in Type 1 but only pairs of isomers occur in Types 2 and 3. It is convenient to include here, as an extension of the discussion of Type 3 isomeric molecular compounds, a group of molecular compounds where both charge transfer and proton transfer occur; these CPT molecular compounds (Section 15.11.4) are not isomers. 15.11.1

Type 1 – isomerism due to different types of interaction without change of moiety structure

Two clearcut examples are currrently known : ﬁrstly, in {(9,10-diazaphenanthrene)2 TCNE} there is n–* interaction in the triclinic polymorph and –* in the monoclinic n n n

ISOMERIC (POLYMORPHIC) MOLECULAR COMPOUNDS

1053

polymorph (Shmueli and Mayorzik, 1980) (see also Section 12.4). Secondly, decamethylferrocene and TCNQ form two 1 : 1 salts (Miller, Zhang et al., 1987); the monoclinic salt (MCFETO01) is dark green, metamagnetic and has mixed . . . DADA . . . stacks, while the triclinic salt is purple, paramagnetic and has discrete stacks of DAAD dimeric units (MCFETO02; cf. Section 17.4.2). Formation of the mixed stack structure is kinetically controlled and that of the dimeric stacks thermodynamically.

Table 15.15. Cell dimensions at 120K for the high (red; HT) and low-temperature (black; LT) phases of biphenylene PMDA. The stack axis is [001] for both phases n n n

Phase Red (HT); DURZAR Black (LT); DURZAR01

˚) a(A

˚) b(A

(deg.)

˚) c(A

9.280(1)

11.869(2)

7.293(1)

98.68(2)

13.368(1)

5.809(1)

10.443(1)

102.30(1)

Volume/ formula unit

Calculated density g cm3

˚3 794.0 A

1.548

792.3

1.552

(a)

(b)

Fig. 15.29. ORTEP stereodiagrams of (a) donor–acceptor pair in red {biphenylenePMDA}; (b) donor–acceptor pair in black {biphenylene PMDA}. In both diagrams projection is onto the biphenylene plane. (Reproduced from Stezowski, Stigler and Karl, 1986.) n n n

1054 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

A more subtle example, essentially polymorphic in nature, is provided by {biphenylene PMDA}, which has a ﬁrst-order phase transition (with hysteresis) at 400K (Stezowski, Stigler and Karl, 1986). Cell dimensions (at 120K) for both phases are given in Table 15.15. The red phase has almost complete overlap of donor and acceptor molecules (Fig. 15.29(a)), with an interplanar angle of 4.1 and appears to be a –* donor–acceptor molecular compound of the standard type; there is typical overlapped disk packing. The black phase has donor and acceptor displaced along their long molecular axes, with an angle of 9.9 between molecular planes; this is typical slipped disk packing. Carbonyl groups of PMDA overlap benzene rings of biphenylene and it seems that both components behave as though composed of two virtually noninteracting halves. Thus one isomer has standard –* interaction whereas the second has more localized interaction between polar carbonyl and polarizable benzene ring. Typical slipped disk packing is also shown, for example, by {trans-stilbene PMDA} (Koduma and Kumakura, 1974a; PYMAST). n n n

n n n

15.11.2

Type 2 – isomerism due to electron transfer

There are two structural groups to be considered. In the ﬁrst group mixed stack -compounds undergo neutral , ionic polymorphic transitions at temperatures and pressures depending on the components involved, the mixed stack structure remaining largely unchanged through the transitions (see Section 13.2.1). The best studied example is {TTF chloranil} which has a mixed stack structure at room temperature and pressure (P21/n, Z ¼ 2) (Mayerle et al., 1979; TTFCAN) and undergoes a neutral , ionic polymorphic transition at 84K and atmospheric pressure (Batail et al., 1981). The conductivity of {TTF chloranil} at 300K is 8 104 S/cm, in conformity with its mixed stack structure (Torrance, Mayerle et al., 1979). An extended discussion is given in Section 16.9. The second group has pairs of isomers, one of which has a mixed stack structure and the other a segregated stack structure. There is a growing number of examples. In the TMTSF/ TCNQ system the red, semiconducting, and the black, conducting phases (1 : 1 compositions) were crystallized under rather similar conditions. The black form (Bechgaard, Kistenmacher, Bloch and Cowan, 1977; SEOTCR) has a segregated stack structure with ˚ 3, while the red form has charge transfer of 0.6 e and volume/formula unit of 272.0 A a mixed stack structure with a charge transfer of 0.2 e and volume/formula unit of ˚ 3 (Kistenmacher, Emge et al., 1982; SEOTCR01). The red form is obtained by 282.5 A recrystallization of either black or red forms from hot CH3CN (Bechgaard et al., 1977). The {bis(ethylenedithio)tetrathiafulvalene/TCNQ} {BEDT-TTF/TCNQ} system provides another example. One isomer has a mixed stack structure (space group P21/n, Z ¼ 2; ˚ 3), a resistivity of 106 ohm-cm and a sharp IR volume/formula unit of 610.9(5) A spectrum, charge transfer 0.2–0.3 e from TCNQ bond lengths (Mori and Inokuchi, 1987; FAHLEF01); the other has segregated stacks (space group P1, Z ¼ 1; volume/ ˚ 3), high conductivity, a broadened IR spectrum and a metal , formula unit of 598.5(2) A insulator transition at around room temperature (Mori and Inokuchi, 1986; FAHLEF). Similar polymorphism has been reported in {2,7-bis(methylthio)-1,6-dithiapyrene/ TCNQ} {MTDTPY/TCNQ}; Nakasuji et al., 1987). The black mixed-stack crystals n n n

n n n

ISOMERIC (POLYMORPHIC) MOLECULAR COMPOUNDS

1055

˚ 3 while that for (monoclinic; FUDTON01) have a volume per formula unit of 608.0(2) A 3 ˚ the segregated stack structure (triclinic; FUDTON) is 596.4(5) A . In all these examples the segregated stack phase has a lower volume/formula unit than the mixed stack phase, suggesting that the former has the lower enthalpy at 300K; it remains to be seen whether this is a general feature conﬁrmed for more examples and by direct measurement of the enthalpy differences. In {1,2-di(4-pyridyl)ethylene) TCNQ} there is a red, semiconducting form with a typical mixed stack, neutral ground state structure (BUKXOU) and a black, conducting form, the structure of which was not reported (Ashwell et al., 1983). Matsunaga (1978) has reported that {7-methylbenzo[a]phenazinium -TCNQ} is dark green when crystallized from ethanol and violet when crystallized from CH3CN. Recrystallization of the green form from CH3CN gave the violet form. Examination of the electronic, vibrational and ESR spectra suggested that the violet form is {NMBPþ TCNQ } and that the green form is non-ionic with a neutral ground state i.e. {NMBP TCNQ}. There was no N-H stretching vibration in the region of 3000– 3500 cm1 in the spectrum of either sample, thus eliminating the possibility that reduction of the diamagnetic NMBPþ cation to the HNMBPþ cation radical had occurred during preparation and that this was the cause of the apparent dimorphism (cf. Section 15.8.5). Thermodynamic results do not appear to be available for any of these systems. There are a number of actual or potential isomeric molecular compounds of the mixed stack/segregated stack type among the various TTF/haloanil binary systems. For example, {TTF ﬂuoranil} (Mayerle et al., 1979; Torrance, Mayerle et al., 1979; TTFFAN) has a structure similar to that of {TTF chloranil} although triclinic (P1,Z ¼ 1). {TTF ﬂuoranil} also appears as a micro-crystalline phase with RT ¼ 10 S/cm and, presumably, a segregated stack structure in analogy with that of {TMTTF bromanil} (RT ¼ 1 S/cm) (Mayerle and Torrance, 1981; TMFBRQ10). n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

15.11.3

Type 3 – isomerism due to proton transfer or to p–p* electron transfer

When the components of a binary system are acids and bases in both the Lowry-Brønsted (proton transfer from acid to base) and Lewis (electron transfer from base to acid) senses, then both types of interaction can occur. For the donor-acceptor combinations considered here the proton transfer will be actual for the ground state moieties but the electron transfer will be virtual, occurring only in the excited state. The comparative strengths of the Lowry–Brønsted and Lewis acid–base interactions will determine which structure occurs at a particular temperature, as the two interactions are temperature-dependent in the crystalline state, with the salt-like structure favoured at lower temperatures. Thus, 0 taking an amine–phenol pair as an example, the salt-like structure {RNHþ 3 – OR } will be favoured at lower temperatures but this may transform to a neutral -molecular compound form {[RNH2] [HOR 0 ]} on heating. The transition temperature can be anywhere between a very low temperature and the melting point, depending on the details of the system. In crystallographic terms the two isomers are polymorphs, the relationship being enantiotropic in most known examples but monotropic in some. Certain organic moieties function effectively as electron acceptors in both neutral and anionic states; for example, the picric acid–picrate anion pair (Matsunaga and Saito, 1972; Saito and Matsunaga, 1972; Saito and Matsunaga, 1973a, b). Thus both charge and n n n

1056 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

proton transfer can take place in the same crystalline species in many binary systems: these are the CPT complexes discussed in the next section. Early suggestions that ‘isomeric complexes’ could occur were elaborated in a series of experimental studies by Hertel and coworkers in the 1930s. Later Briegleb and coworkers used UV–visible and IR spectroscopy to identify the salt-like and molecular-compound forms of various isomeric complexes. This work has been summarized by Herbstein (1971). Many of the more recent developments are due to Matsunaga and his colleagues. It does not seem possible to give a clearcut relation between the type of molecular compound formed and the pKa values of acid and base (for summaries see Kortum et al., 1961 and Perrin (1965)). This is because of the competition between proton transfer and charge transfer and the temperature-dependence of these processes; also many pKa values are not known. In illustration we note that anilinium picrate and pyridinium picrates are salts (pKa of aniline, pyridine and picric acid are 4.51, 5.23 and 0.42 respectively). There are cations and anions in the crystal structure of pyridinium picrate; the original structure determination (Talukdar and Chaudhuri, 1976; PYRPIC) is wrong and has been corrected (Botoshansky et al., 1994; PYRPIC02). The picrates of o-chloroaniline (pKa ¼ 1.96), m-nitroaniline (pKa ¼ 2.46), 3-nitro-4-methyl-aniline (pKa ¼ 2.96) and N,N-dimethylamino-p-benzaldehyde (pKa ¼ 1.62) are yellow crystalline salts which give red solutions in benzene and red melts. Thus proton transfer occurs in the solid state but charge transfer interactions predominate in (nonpolar) solutions and in the melt (Saito and Matsunaga, 1971). Charge transfer molecular compounds are formed at room temperature when the bases involved are very weak, as in the picric acid compounds of carbazole, skatole and indole (Briegleb and Delle, 1960) and these are also found with bases such as o-nitroaniline (pKa ¼ 0.62) and p-nitroaniline (pKa ¼ 0.99); similarly p-dimethylaminobenzaldehyde (pKa ¼ 1.62) and o-nitroaniline give molecular compounds with 2,4,6-trinitrobenzoic acid

Table 15.16. Polymorphic transitions in crystals of some isomeric compounds. All transitions are from a salt-like structure at lower temperatures to a charge-transfer molecular compound stable above the transition temperature. pKa values are given in brackets Components

ttr( C)

Htr (kJ/mol)

A. Picric acid (0.42) as acceptor: 1. 2,5-dichloroaniline (1.57) (Matsunaga et al., 1974) 2. o-bromoaniline (2.55) (Komorowski et al., 1976) 3. o-iodoaniline (2.60) (Matsunaga et al., 1975) 4. 1-chloro-2-naphthylamine (Matsunaga et al., 1974) 5. 1-bromo-2-naphthylamine (Matsunaga et al., 1975) 6. 1,6-dibromo-2-naphthylamine (Matsunaga et al., 1975)

74 102 100–107 128–138 118–125 99–108

17.6 24.7 28.0 33.5 34.3 14.2

B. 2,4,6-trinitrobenzoic acid (0.65) as acceptor: 1. o-chloroaniline (2.65) (Matsunaga et al., 1974)

133

9.2

C. 2,6-dinitrophenol(3.57) as acceptor: 1. 4-bromo-1-naphthylamine (3.21) (Hertel and Frank, 1934) 2. 4-chloro-1-naphthylamine (Matsunaga et al., 1974)

monotropic 76

ISOMERIC (POLYMORPHIC) MOLECULAR COMPOUNDS

T (K)

1057

400 P+L

?

L+C

E1

c C

C+L

P1

b ?

d

S+L

350 P+C

P+?

S

P2

? D+L

S+? a

E2

S+D

300

BrA·(PiOH)2? BrA·PiOH (BrA)2·PiOH PiOH

D+B

50 mpc

BrA

Fig. 15.30. Phase diagram of the o-bromoaniline(BrA)–picric acid (PiOH or P) system. L = liquid; C = solid solution of charge transfer molecular compound type; S = solid solution of salt type; D = (BrA)2 PiOH; insert – the region of the solid state transition in expanded scale. (Reproduced from Komorowski et al., 1976.) n n n

(pKa ¼ 0.65) (Matsunaga and Osawa, 1974)). Results of studies of polymorphic transitions in isomeric compounds are summarized in Table 15.16. A complete study of a particular binary system that includes isomeric complexes does not appear to have been made, but some partial studies, extending beyond identiﬁcation by spectroscopic techniques, have been reported. For example, the phase diagram of the o-bromoaniline–picric acid system has been determined in some detail (Fig. 15.30) (Komorowski et al., 1976). Equimolar {o-bromoaniline picric acid} is an isomeric complex with a salt , molecular compound transition temperature at 102 C while the 2 : 1 compound is of the CPT type discussed in the next section. The appearance of solid solutions in both polymorphs of the equimolar material is quite unexpected and should be checked. Thermodynamic studies have been made of 4-bromo-1-naphthylamine 2,6-dinitrophenol (Hertel and Schneider, 1931), where the yellow (stable; m.pt. 91.5 ; measured density 1.654 g cm3 ) and red (metastable; m.pt. 84.5 ; measured density 1.56 g cm3) phases are monotropically related (Hertel and Frank, 1934). The enthalpies of formation of the yellow and red phases were determined calorimetrically (temperature not speciﬁed but presumably 300K) to be 13.4 and 0.4 kJ/mol respectively. The yellow phase has thus both lower enthalpy and higher density than the red phase, as would be expected from the stronger (Coulombic) binding between the components. The crystal structure of the (metastable) red phase has been determined at 298K (space group P21/a, Z ¼ 4, stack n n n

n n n

1058 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

axis [010]); the familiar mixed stacks were found and there is no hydrogen bonding between the components (Carsten-Oeser et al., 1968; PABRAN). 15.11.4

Isomerism stabilized by both charge (p–p*) and proton transfer (CPT compounds)

In these molecular compounds the charge and proton transfer can be carried out in a number of different ways and currently three types can be identiﬁed : (a)

CPT-A compounds: these are 1 : 1 (electron) donor–acceptor molecular compounds, where a proton is transferred from electron acceptor to donor, thus giving rise to the possibility of cation–anion and charge transfer interaction occurring in the same binary adduct; examples are tryptophan picrate (Matsunaga, 1973) and seretonin picrate (Thewalt and Bugg, 1972); see also Section 15.2. The red colours of both molecular compounds are due to charge transfer interactions between the cation donors and the picrate anions, acting as acceptors. This has been demonstrated directly for seretonin picrate by determination of the crystal structure of the monohydrate (P21/c, Z ¼ 4) that contains mixed stacks along [010] (cf. Section 15.2). H

H N

N O OH H2C

H 2C NH3+ Tryptophan cation

(b)

NH3+ Serotonin cation

CPT-B compounds: these are essentially 2 : 1 donor–acceptor molecular compounds, where one of the donor molecules acts as proton acceptor while the second participates in the charge transfer interaction with the anion, which acts both as an electron acceptor and a proton donor; examples are the black {(benzidine)2 picrate} (Saito and Matsunaga, 1973a), {(aniline)2–(2,4,6-trinitrobenzoic acid} (TNBA)) (Matsunaga, Osawa and Osawa, 1975) and the red {(o-aminobenzoic acid)2 picrate} (Matsunaga and Usui, 1980). More complicated compositions have been encountered in other systems (e.g. {(2,4,5-trimethylaniline)3(3,3 0 ,5,5 0 tetranitrobiphenyl-4,4 0 -diol (TNBP))2} (Matsunaga and Osawa, 1974) and the dark orange {(N,N-diethylaniline)5 (TNBP)3} (Saito and Matsunaga, 1973b; Lloyd and Sudborough, 1899); spectroscopic studies show that these are CPT compounds but crystal structure analyses are needed to show how the charge and proton transfers are distributed among the moieties. One can distinguish a subgroup in which these functions are combined in a single molecule but localized in different parts thereof; here one half of a monoprotonated (electron) donor acts as proton acceptor and the other half participates in chargetransfer interaction with the anion acceptor; examples are the picrates of o-dianisidine and of tetramethylbenzidine (Saito and Matsunaga, 1973a) and the 3 : 2

S ELF -C O MPLE XE S

1059

Fig. 15.31. ORTEP stereoview of pyridinium-1-naphthylamine–picrate crystal structure. The asymmetric unit has been marked. Only one orientation of the disordered 1-naphthylamine molecule is shown. (Reproduced from Bernstein et al., 1980.)

compound of benzidine (pKa ¼ 4.95) with 2,6-dinitrophenol (pKa ¼ 4.09) (Saito and Matsunaga, 1974). (c) CPT-C compounds : here the functions are localized in different molecules and thus a ternary composition can be expected. Ko¨ﬂer’s (1940) ternary complex {pyridine– 1-naphthylamine–picric acid} {PY-NA-PC} was shown, by spectroscopy, to be a CPT compound (Matsunaga and Saito, 1972). Crystal structure analysis (Bernstein et al., 1980; PYNPCR) showed that it was in fact {pyridinium–1-naphthylamine– picrate}, in which there was a herringbone arrangement of centrosymmetric planeto-plane stacks of composition PYþ NA PC ( 1) PC NA PYþ (Fig. 15.31). This arrangement has similarities to that found in {(acridine)2 . . . PMDA} (Fig. 15.3). Thus the proton transfer is from picric acid to pyridine while the principal charge transfer is from 1-naphthylamine to picrate anion. The 1-naphthylamine molecule was disordered over (at least) two orientations.

15.12 Self-complexes In a molecule that has regions with electron-donor properties and other regions with electron-acceptor properties, intramolecular and/or intermolecular charge transfer can occur. If nitrogen and/or oxygen is present, then there can be n–* interaction. Alternatively, with appropriate molecular conformation, –* interactions could occur. If these interactions are intramolecular, then charge-transfer bands would be expected in both solution and solid state spectra. If the charge transfer interactions are intermolecular then one would expect a charge-transfer band in the spectrum of the solid but not (or to a far lesser extent) in solution, and a pairwise or stacked arrangement in the solid, with propinquity of donor and acceptor regions of different molecules. Many examples have been studied and all the possibilities outlined above have been encountered (Table 15.17). Classiﬁcation can be conveniently made in terms of acceptor type and it will be noted that virtually all the well-known acceptor types are represented. The molecular arrangement in the red polymorph of 2-(4 0 -methoxyphenyl)-1,4-benzoquinone is shown in Fig.15.32 (Desiraju et al., 1977; PANQUO). Early and more recent work has been reviewed (Bleidelis, Shvets and Freimanis, 1976; Chitkina and Belskii, 2002).

1060 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

(a)

D

A

A

D

D

A

1– x, 1/2+y, 1/2–z

(b)

O1 C6

C1

C8

C2

C9 C10

C5

O3

C7 C4

C3

C12

C13

C11

1 – x, –1/2 + y, 1/2– z

O2 x, y, z

Fig. 15.32. –* Interactions in the red polymorph of 2-(4 0 -methoxyphenyl)-1,4-benzoquinone. (a) stereopair diagram of the alternating donor–acceptor interaction in a molecular stack with the schematic arrangement shown in the center; (b) Details of pairwise overlap. The molecules are projected onto the plane of the central benzoquinone ring (line shaded), with the molecule above darkened and that below shown with broken lines. (Reproduced from Desiraju et al., 1977.)

A few structures that do not ﬁt easily into the framework of Table 15.17 will be discussed separately. The crystal structure of 1-(2-indol-3-ylethyl)-3-carbamidopyridinium chloride monohydrate has been determined (tetragonal, space group P41) (Herriott et al., 1974; INYECP); it serves as an intramolecular model of the nicotinamide adenine dinucleotide – tryptophan charge transfer compound. In the crystal the molecules are in the fully extended transoid conformation, with the two planar portions (the donor and acceptor portions) of a particular molecule essentially mutually perpendicular. An indole ring of one molecule is stacked between nicotinamide rings of two other molecules, and conversely (Fig. 15.33; p. 1061). Thus there are two sets of mutually perpendicular donor–acceptor stacks in the crystal. Within a stack the donor and ˚. acceptor molecules are approximately parallel, with an interplanar distance of 3.7 A N

O Cl–· H2O

+ N Indole ring is donor portion H2C

CH2

NH2 Nicotinamide ring is acceptor portion.

S ELF -C O MPLE XE S

1061

Table 15.17. Self-complexes classified according to acceptor type (a) Polynitrobenzene acceptor portions NO2

NO2 H

O2N

N

CH2

O2N

N

NO2

CH3

N(Et)2

OCH3

1. Donor portion of one molecule overlaps with acceptor of adjacent molecule to form a stack (Shvets et al., 1974; NETPHN10).

R1

2. Donor and acceptor portions are approximately perpendicular, with hinge at tertiary nitrogen. ---DA DA DA--- stacks are formed (Shvets et al., 1975a). D

A

D

A

A

D

A

D

N R2 H

3. R1 = N(CH3)2; R2 = NO2. Dark brown crystals (Nakai et al., 1976; two polymorphs MABZNA (P1, Z = 4) and NBZMAA (P21/c, Z = 4)).

4. As for #3 but with R1 = NO2; R2 = N(CH3)2. Orange crystals. Stacking as for #3 (Shvets et al., 1974).

(b) p-Benzoquinone acceptor portions H3CO

O

O X

CH3 N

5.

O O

6.

R

5. Red crystals; stacks with overlap of donor and acceptor rings, with -* interaction between the rings. There is no overlap of carbonyl groups and aromatic rings (Desiraju, Paul and Curtin, 1977; PANQUO).

X = CH3, R = H. 6. Adjacent molecules are stacked antiparallel about two fold screw axes, thus allowing D---A interactions along the stack (Prout and Castellano, 1970).

7. As for #6 but with X = Cl, R = COOC2H5; orange crystals. Stacking as in #6 (Shvets et al., 1975b).

8. As for #6 but with X = Cl, R = CH3; orange crystals. Stacking as in #6, but with additional Cl...O interaction, ˚ (Shvets et al., 1979; d(Cl...O) = 3.29 A MAMNAQ).

1062 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Table 15.17. (Continued ) O

O Ph

C2H5

O O 9.

OCH3

N

N O H3C

N

O

10.

CH3

10. Molecule folded back on itself to allow intramolecular donor–acceptor interaction (Shvets et al., 1975c; AEPCNQ10).

9. Black crystals with metallic lustre. Molecules are grouped in isolated donor-acceptor pairs (Shvets et al., 1978).

11. 2,3-Dichloronaphthazarin (DCDHNQ01) – see Section 15.6. (c) TCNE type acceptor (for review see Chetkina and Bel’skii, 2002). CN NC CN

N(R1R2)

12. R1 = R2 = CH3. Violet crystals. Molecules are stacked antiparallel with donor–acceptor interactions between adjacent molecules (Chetkina et al., 1976; TCYVMA). 13. R1 = Ph, R2 = H. Dark-violet crystals. Partial overlap of donor and acceptor portions of the molecules (Popova et al., 1978). (d) TCNQ type acceptor NC

14, 15. NR2

NC CN

14. R = n-propyl; dark green crystals with metallic lustre. Pairwise interactions between TCNQ portions (Povot’eva et al., 1981; BAFGOE). 15. R = CH3; black crystals. Pairwise interactions between donor and acceptor portions of molecule (Povot’eva et al., 1981).

NC – NC

16. N+

CH3

H CN

16. Picolyl-tricyanoquinodimethan. Zwitterionic structure; diamagnetic. Angle of 30 between planes of benzene and pyridinium rings. The pyridinium nitrogen stacks above the dicyanomethide portion of the next molecule along the b axis (Popova, Chetkina and Bespalov, 1981).

(e) Hexaﬂuorobenzene type acceptor 17. Pentaﬂuorobiphenyl, see Section 15.9.1. 18. Two polymorphic forms, both of which have stacking arrangements similar to those shown for #3 and 4 earlier in this Table. (Lindeman et al., 1981; BANGOM).

S ELF -C O MPLE XE S

1063

Table 15.17. (Continued ) F

F HO

F

N F

F

(f) Various 19. 1,3-Indanedione (Bravic et al., 1976; INDDON). There are stacks of antiparallel molecules, thus allowing maximum interaction between donor and acceptor portions of the molecules and also maximum dipolar interaction. The crystals are tetragonal and the arrangement of the stacks resembles that found in {pyrene p-benzoquinone} (see Fig. 15.4). n n n

4.156

3.342

3.535

3.881

3.515

3.875

3.489

4.012

3.936

2.904

3.1 92

3.572

Carbon Nitrogen Oxygen Chlorine Hydrogen bond Intermolecular contact

94

2. 9

07

3.1

3.169

Fig. 15.33. Projection of part of crystal structure of 1-(2-indol-3-ylethyl)-3-carbamido-pyridinium chloride monohydrate onto (100); two mutually-perpendicular donor–acceptor stacks are shown. (Reproduced from Herriott et al., 1974.)

1064 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

The -orbital overlap between adjacent donor and acceptor portions appears nearly optimal, and the permanent dipoles are strongly coupled. It was suggested (Herriott et al., 1974) that unsymmetrical –* and dipole–dipole interactions could lead to a speciﬁc three-dimensional mutual orientation, provided that one of the faces of the molecule is blocked, and that such a mechanism could be important in enzyme-coenzyme interactions. The molecule of 2-(2-pyridylmethyldithio)benzoic acid has a hinged conformation in the solid, with pyridyl and phenyl rings approximately parallel and arranged in stacks ˚ ) (Karle et al., 1969; PYSBAC). Presumably the pyridyl ring acts as along [001] (¼7.37 A electron donor and the carboxyl-substituted phenyl ring as acceptor, and there are both intramolecular and intermolecular charge transfer interactions. The hinged conformation with parallel donor and acceptor portions is a feature that appears in many of the compounds discussed in this section. The compound 3,3 0 -diacetyl-5,5 0 -diethoxycarbonylglaucyrone gives black crystals from benzene, whose structure shows a stepwise arrangement of conjugated molecules connected by self charge transfer interactions (Baker et al., 1980; ETGLAU). The right hand side of the molecule in the diagram is considered to behave as the electron–donor portion and the left hand side as the electron–acceptor portion. These two portions are superposed in alternating fashion in the crystal. CO2Et

O

O

H3C

O

CH3

O H 3,3'-diacetyl-5,5'-diethoxycarbonylglaucyrone

15.13 15.13.1

O

CO2Et

O

Conclusions Structural variety in –* molecular compounds

One sees, from the survey above, that there is considerable structural variety in this family of molecular compounds. The simple picture of parallel mixed stacks of donors and acceptors in alternating array, although applicable to the majority of –* molecular compounds, and also to the quasi-acceptor molecular compounds, needs considerable emendation and extension. Stacks of limited size are found, stack axes are not necessarily parallel, and components with suitable functional groups can give rise to important lateral interactions. In particular, hydrogen bonding between like and/or unlike components, added to the primary stacking structural synthon, can provide possibilities for crystal engineering similar to those described in Chapter 14. Although the most usual donor : acceptor ratio is 1 : 1, other compositions are found. These generally maintain mixed stacks with the component in excess accommodated in various ways, often as ‘solvent of crystallization’ ﬁlling space but not playing any structural role.

CONCLUSIONS

15.13.2

1065

How should the packing arrangements in p–p* molecular compounds be described?

Despite the considerable structural variety in this family of molecular compounds, the essential feature appearing in virtually all structures is a plane-to-plane interaction between the two components. For most of the molecular compounds considered here, this is a donor–acceptor interaction leading to color changes on formation, and physical properties that stem from the anisotropic arrangement. However, the same feature appears also in the structures containing quasi-acceptors rather than true acceptors; as there is no sensible structural difference between these two groups, they can be treated together. A natural consequence is to describe the structures in terms of mixed stacks containing donors and acceptors (or quasi-acceptors) in alternating array. Some authors have, however, preferred a mixed-layer to a mixed-stack description. The matter could be settled if one could compare, for a particular structure, the one-dimensional interaction energy within mixed stacks to the two-dimensional interaction within layers but this information is not available. Description is a matter of choice, and we use three examples, from the extremes and the center, to illustrate the dilemmas. The interaction of a benzene ring (a polarizable donor group) with a polar acceptor group (e.g. a carbonyl group) often leads to a characteristic superposition (overlap diagram) within a mixed stack. An example is (monoclinic) {perylene ﬂuoranil} (Hanson, 1963; PERFAN; Section 15.6 and Fig. 15.10), which has a typical herring-bone structure also shown by (monoclinic) {perylene 1,2–4,5-tetracyanobenzene} (Fig. 15.20; Bock, Seitz et al., 1996; REHMUM). How could one visualize the growth of such a crystal in formal (not necessarily physical) terms? Perhaps as preformed quasi-cylindrical stacks, with a given mutual donor-acceptor disposition, that then aggregate into a quasi close-packed arrangement of the quasi-cylindrical stacks. The mutual orientation of the stacks is determined by secondary cross-stack interactions; in the particular example of {perylene . . . ﬂuoranil} these could be weak C–H . . . O¼C hydrogen bonds. At the other extreme one has a hydrogen-bonded layer such as that found in {hexamethylbenzene 1,3,5-tricyanobenzene} (LAGNAI) (Fig. 15.34; Reddy, Goud et al., 1993; Desiraju and Steiner, 1999; see p. 327 et seq.); each layer contains only a single component. Here the layers would be formed ﬁrst and then stacked one over the other to give optimal plane-to-plane overlap of hexamethylbenzene donor and tricyanobenzene acceptor. {Pyrene 1,2–4,5-tetracyanohydroquinone} (Fig. 15.20; Bock, Seitz et al., 1996; TEXPOB10) provides a similar example, again with the layers each containing a single component and the –OH . . . NC–C hydrogen bonding in the tetracyanohydroquinone layer providing the dominant structural interaction. What happens in the middle? One example is {dibenz[a,c]anthracene -1,3,5trinitrobenzene} ({DBA TNB}; Carrell and Glusker, 1997; RULLUF). Here the layers, which are somewhat corrugated, contain both components, with molecules of the smaller TNB acceptors surrounded by molecules of the larger DBA donors (Fig. 15.35). Carrell and Glusker provide a well-balanced description of the structure as having ‘‘. . . layers containing both DBA and TNB molecules, interconnected within a layer by C–H . . . O interactions. Layers stack on one another so that DBA molecules are sandwiched between TNB molecules and vice versa. The average distance between molecules in these sand˚ ’’ (italics added). Are the (relatively) many weak hydrogen bonds more wiches is 3.23 A n n n

n n n

n n n

n n n

n n n

n n n

1066 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

Fig. 15.34. The crystal structure of {hexamethylbenzene 1,3,5-tricyanobenzene} (15.207 8.839 ˚ , 110.48¯, Z = 4, C2/c; the HMB molecules are at inversion centers and the 1,3,5-tricyano14.460 A benzene molecules on two fold axes). The overlapped layers of hexamethylbenzene (darkened, below) and the hexagonal 1,3,5-tricyanobenzene network mediated by weak C–H . . . N hydrogen ˚) bonds (above) are shown. The weak C–H . . . NC–C hydrogen bonds (d(C . . . N) = 3.47, 3.52 A are indicated by dashed lines. The layers are parallel to (110). (Reproduced from Desiraju and Steiner, 1999.) n n n

important in determining the overall structure than the plane-to-plane interaction? At present there does not seem to be an answer to this question. However, stacking appears to be a feature occurring in all the structures of this family whereas layers can only be identiﬁed when there are appreciable lateral interactions. Thus, in our view, ‘stacking’ is the primary feature with ‘layering’ a possibly important secondary attribute. 15.13.3

Structural consequences of p–p* interactions

It is widely recognized that the donor–acceptor interactions in –* molecular compounds are too weak to cause changes in bond lengths that are measurable at current levels of precision. This applies even to measurements made at very low temperatures (e.g. {pyrene PMDA} at 19K (Herbstein, Marsh and Samson, 1994; PYRPMA04). n n n

CONCLUSIONS

1067

2.36 2.40

2.53 2.57

2.48

2.53 2.51 2.46

layer

TNB

DBA

Fig. 15.35. Structural features of the triclinic DBA TNB crystals (a ¼ 7.277(2), b ¼ 11.237(6), ˚ , = 104.13(4), = 96.04(3), = 95.15(2) , space group , Z = 2. (above) One layer c ¼ 13.902(5) A of the structure showing TNB surrounded by DBA molecules and linked by CH O interactions. (below) Stacking of layers showing that DBA and TNB are not entirely coplananr. (Reproduced from Desiraju and Steiner, 1999.) n n n

n n n

Charge density studies (Chap. 17.7), comparing neat components with such components in the molecular compounds, may provide evidence of interaction but this remains a task for the future. Deviations from planarity in ﬂexible molecules are more easily accessible. A clearly discernible effect has been found in {9,10-dihydroanthracene TNB}, where the DHA molecule is folded (dihedral angle 146 ) in its neat crystals (DITBOX) but planar in the molecular compound (ZZZAGS10) (Herbstein, Kapon and Reisner, 1986). Appreciable differences in the shapes of components in their neat crystals and in their molecular compounds has been found in {triphenylene–perﬂuorotriphenylene} (Weck et al., 1999; CUKXIP; Fig. 15.24) and, to a lesser extent, for (nonplanar) benzo[c] phenanthrene in its neat crystals (Lakshman et al., 2000; BZPHAN01) and its DDQ molecular compound (Bernstein, Herbstein and Regev, 1977; BZPCPQ). n n n

1068 CRYSTAL CHEMISTRY OF MIXE D-STACK –* MOLECULAR COMPOUNDS

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Chapter 16 Crystal (structural) physics of mixed stack –* molecular compounds

Be not curious in unnecessary matters for more things are shewed to you than men understand. Ecclesiaticus 3:23

Summary: Thermodynamic measurements for a limited sample of crystalline mixed-stack 1 : 1 -molecular compounds show that most are enthalpy-stabilized, some entropy-stabilized, and a few both enthalpy and entropy-stabilized. Correlation of these thermodynamic results with crystal structures remains a task for the future. Combination of optical spectroscopic methods at very low temperatures and electron spin resonance measurements have provided proof of Mulliken’s theory also for the solid state. The room temperature crystal structures of 1 : 1 -molecular compounds are not necessarily representative of the entire range of pressure–temperature behavior of these materials. There are often hints of disorder (usually of the donor) in the room temperature structures, and these have been correlated for a few systems with disorder-to-order transitions (thermodynamically second-order, following Ehrenfest) that occur on cooling; these have been studied by a combination of calorimetric, diffraction and resonance techniques. Despite overall similarities, each system surveyed has its own individual characteristics. A number of 1 : 1 -molecular compounds have been shown to transform to quasi-plastic phases on heating. A small number of mixed stack 1 : 1 -molecular compounds with neutral ground states have been shown to transform to ionic structures on cooling or application of pressure.

16.1 16.2 16.3 16.4

Introduction Thermodynamic parameters Spectroscopic measurements on the excited state Crystals with disorder ) order transformations on cooling – modern treatments of second order phase transitions 16.4.1 General introduction 16.4.2 The Ehrenfest order of a phase transition 16.4.3 Landau theory of phase transitions 16.4.4 The critical exponents 16.4.5 The permitted symmetries of a low symmetry phase derived from a particular high symmetry phase 16.4.6 Temperature dependence of the order parameter 16.4.7 Pressure dependence of the critical temperature for ordering 16.5 Thermodynamic, structural and kinetic investigations of various systems showing second order transitions on cooling

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16.5.1

The crystal structure of {Pyrene PMDA}(PYRPMA) and evidence for an order , disorder phase transition at 160K 16.5.2 The crystal structure of {Naphthalene TCNB} and evidence for an order , disorder phase transition around 72K 16.5.3 The crystal structure of {Anthracene TCNB} and evidence for an order , disorder phase transition at 213K 16.5.4 Other examples of second order transitions 16.6 Crystals with first order phase transformations on cooling 16.6.1 {Cycl[3.2.2]azine TNB} 16.6.2 Other examples 16.7 Physical nature of the disordered phase 16.8 Transformations to quasi-plastic phase(s) on heating 16.9 Transformation of the ground state from neutral ) ionic on cooling and/or application of pressure (NI transitions) 16.9.1 Introduction 16.9.2 {TTF chloranil} 16.9.3 {DMTTF chloranil} 16.9.4 Other examples 16.9.5 Concluding summary References n n n

1097

n n n

1105

n n n

n n n

n n n

n n n

16.1

1115 1119 1120 1120 1122 1122 1126 1128 1128 1129 1137 1139 1142 1142

Introduction

The mixed-stack model of crystalline -molecular compounds described in the preceding chapters requires ampliﬁcation in many respects for it to provide a full picture of current knowledge. In this chapter we shall concentrate on some aspects of the structural physics of mixed-stack 1 : 1 -molecular crystals; treatment is limited to the 1 : 1 composition and inﬁnite mixed stack arrangement because information is not available for other compositions and types of structure. We begin by considering the thermodynamic parameters reported for ambient temperature and pressure; this will give some overall feeling for the strengths of the interactions leading to the formation of the molecular compounds, and, in particular, whether these are enthalpy or entropy stabilized (or both) with respect to the individual components. In the next section we discuss low temperature spectroscopic studies that give information about the degree of charge transfer in the excited state and hence provide a test of the applicability of Mulliken’s theory to the solid state. The types of solid state transformation that occur on cooling are then discussed in some detail. Most of the transformations studied so far are of the second order, but there are also some ﬁrst-order transformations (‘order’ deﬁned below). This leads us to consideration of the nature of the structural disorder found in many crystalline -molecular compounds at room temperature. Then two types of solid state transformation pertinent to only a limited number of -molecular compounds are discussed – for some, to a quasi-plastic phase at high temperatures, and for some others to an ionic ground state on cooling or application of pressure. One aspect of the crystal physics of mixed-stack -molecular compounds has been entirely omitted – their electronic properties. This is not because of lack of importance but because it would move us too far from our essentially structural theme.

T HE R M O D Y N AM IC PA R A M E T E R S

1083

16.2 Thermodynamic parameters We note in Appendix 1 (section 1) that a crystalline binary adduct may be enthalpy and entropy stabilized with respect to its crystalline components (situation (i)), or entropy stabilized (situation (ii)), or enthalpy stabilized (situation (iii)). Values of Hc and Sc for three groups of -molecular compounds are plotted in Fig. 16.1. These values refer nominally to 298K and were determined by the electrochemical method (Appendix 1, Section 2.1.1), where Hc and Sc (assumed constant over the range 278–318K) are derived from the measured temperature dependence of Gc. The precision of the thermodynamic parameters is not high. Although the errors of the free energy values range from 0.01 to 0.18 kJ/mol, those of the derived Hc and Sc values range from 5% up to 40%. Fig. 16.1 shows that all three permitted quadrants of Hc – Sc space are populated, but not in equal measure. For the available sample, which is not necessarily randomly selected from the total population, most of the -molecular compounds are enthalpy stabilized, fewer are entropy stabilized and even fewer are both enthalpy and entropy stabilised. Abdel-Rehiem et al. (1975) pointed out that there is an approximately linear relationship between Hc and Sc for compound formation between a series of monosubstituted naphthalenes and picric acid; this is illustrated for a wider range 30 ✖ ✖

✖ ✖

20 Forbidden Region

✖

Entropy stabilized

✖✖✖✖ ✖

10 ∆Hc (kJ/mol)

✖

0

★ ● ✖ ● ★ ● ● ● ● ● ●★ ● ✖✖ ✖ ● ● ✖ ● ✖ ● ● ■■■ ● ● ■ ●■ ■■ ■■ ✖ ■ ■ ■ ■ ■■ ■■ ✖

–10 Enthalpy stabilized

–20 ■ ■

–30 –100

✖

Enthalpy and entropy stabilized

■ ■

■

–50

0

50

100

150

∆Sc (J/mol K)

Fig. 16.1. Plot of Hc against Sc for 60 -molecular compounds of the following groups: (a) crosses – Picric acid compounds of various aromatic hydrocarbons [19 values] (Shahidi and Farrell, 1980), denoted by diagonal crosses; (b) ﬁlled squares – Picric acid compounds of substituted naphthalenes [21 values] (Abdel-Reheim et al., 1975); (c) circles – Styphnic acid (1,3-dihydroxy2,4,6-trinitrobenzene) compounds of substituted naphthalenes [17 values] (Shahidi, Farrell and Westwood, 1980); (d) ﬁve-pointed stars – aromatic hydrocarbons with TNB (3 values). The detailed numerical values and identities of the compounds are given in the cited references.

CRYSTAL (STRUCTURAL) PHYSICS

1084

of compounds in Fig. 16.1. The values for the picric acid compounds of substituted naphthalenes and of aromatic hydrocarbons all fall on the same straight line; the ﬁrst of these groups is enthalpy stabilized all the latter either enthalpy and entropy stabilized or entropy stabilized. The line for the styphnic acid compounds (of much the same group of substituted naphthalenes) is parallel but displaced to higher Hc values; these are all enthalpy stabilized. The linear relationship between Hc and Sc follows from the form of the free energy equation recast as Hc ¼ TSc þ Gc A linear plot of Hc against Sc requires that the slope should be T ( ¼ 298K for the present set of data) and that Gc should be constant; using all the points in Fig. 16.1, we obtain Hc (kJ/mol) ¼ 250 (K) Sc (J/mol K)6.13 (kJ/mol). The derived slope (R2 ¼ 0.917) is reasonably close to the required value. The distribution of Gc is shown in Fig. 16.2, where the different groups of molecular compounds have not been distinguished. If this is done then one ﬁnds that the mean for the picric acid compounds of substituted naphthalenes is 6.54(2.4) kJ/mol), 1.1(0.7) kJ/ mol for the styphnic acid compounds of substituted naphthalenes and 10.5(2.7) kJ/mol for the picric acid compounds of aromatic hydrocarbons. The picric acid compounds of substituted naphthalenes and of aromatic hydrocarbons do not differ signiﬁcantly in terms of free energy values but are very different when enthalpies and entropies are compared; the least stable are the styphnic acid compounds of substituted naphthalenes. The deviations of individual points from the overall linear relationship must have a physical explanation, as must the location of particular types of compound in different quadrants of the diagram; for example (with the exceptions of indene and acenaphthylene) all the {aromatic hydrocarbon picric acid} compounds have large positive entropies of formation. Presumably the principal distinctions will have to be made among the compounds lying in the different quadrants, in terms of the different types of stabilization (enthalpy and/or entropy) that apply. Unfortunately there is not much overlap between the sample whose crystal structures have been determined and that for which thermodynamic n n n

20

Number of compounds

18 16 14 12 10 8 6 4 2 0 <3

[3,6)

[6,9) [9,12) [12,15) [15,18)

18

–∆Gc (kJ/mol)

Fig. 16.2. Distribution of Gc values for the whole sample. The values along the abscissa are for the limits of the bins, in kJ/mol.

T HE R M O D Y N AM IC PA R A M E T E R S

1085

parameters have been measured and thus attempts to ﬁnd such explanations now would appear to be premature. The linear relationship found between H and S in a wide range of experimental solution studies is called ‘enthalpy–entropy compensation’. There are some thousands of references under this heading in Chemical Abstracts, starting from 1925 (Liu and Guo, 2001a). Brieﬂy stated, ‘‘Entropy–enthalpy (SH) compensation occurs when a small change in G is caused by large, and nearly compensatory, changes in H and S. It is considered a ubiquitous property of reactions in water’’ (Beasely, Doyle et al., 2002). Nevertheless, ‘‘Enthalpy–entropy compensation remains a mystery in chemistry and biophysics’’ (Liu and Guo, 2001b). Dunitz (1995) has used a simple thermodynamic argument applied to hydrogen bonding of a water molecule to a very large molecule in solution and concluded that enthalpy–entropy compensation is a general property of weak intermolecular interactions and not limited to reactions in water. The relationship does not appear to have been widely studied in solid state interactions; the pioneering contribution of Abdel-Rehiem et al., (1975) was not set in the context of enthalpy–entropy compensation. We present Figs. 16.1 and 16.2 as empirical ﬁndings without attempting to assess their signiﬁcance. In addition to the information summarized in Fig. 16.1, individual thermodynamic parameters have been measured for a number of molecular compounds and it is sometimes possible to combine Gc and Hc values from different sources to give Sc; for example Gc has been measured electrochemically for {naphthalene TNB} and {anthracene TNB} (and also for other arene TNB and TNT compounds) (Hammick and Hutchinson, 1955) while Hc has been measured by a dissolution method (Suzuki and Seki, 1955). Some of the available values are listed in Table 16.1. n n n

n n n

n n n

Table 16.1. Thermodynamic parameters (at 298K) for some mixed stack –* molecular compounds. Gc and Hc in kJ/mol and Sc in J/mol K. The errors (bracketed) have been taken from the original publications Molecular compound Donor 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12.

Naphthalene [2H8]-naphthalene Anthracene Naphthalene Anthracene Benzene Phenanthrene 0.65 (Phenanthrene)/ 0.35 (anthracene) Anthracene Naphthalene Naphthalene [2H8]-naphthalene

Acceptor

Gc

Hc

Sc

Reference

picric picric picric TNB TNB TNB picric picric

acid acid acid

8.60(4) 8.85(2) 2.05 8.66 3.52

1.9(4) 8.1(5) 24.3 13.4 7.1

acid acid

8.59(7) 6.99

8.03(15) 6.44(15) 9.25 4.69 1.43 2.93 0.1(1.89)

SF80 SF80 H71 H71 H71 H71 SF80

TNT TNT styphnic acid styphnic acid

0.59 5.98 2.66(2) 2.74(2)

6.10(45) 6.60(35)

28.5(6.1)

11.5(1.4) 13.0(1.1)

HH55 HH55 SF78 SF78

References: H71 – Herbstein (1971), Tables 10 and 11 where references to earlier work are given; HH55 – Hammick and Hutchison, 1955; SF78 – Shahidi and Farrell, 1978; SF80 – Shahidi and Farrell, 1980.

CRYSTAL (STRUCTURAL) PHYSICS

1086

Some individual Hc values are of special interest. Thus a combustion method has been used to measure enthalpies of formation at 298K for the 1:1 TCNQ -molecular compounds of naphthalene, anthracene and TMPD, giving values of 30.0 7.6, 30.3 5.3 and 82.1 4.3 kJ/mol (Metzger and Arafat, 1983). The ﬁrst two values are at the lower end of the range of values included in Fig. 16.1, and indicate appreciable enthalpy stabilization, although the ground state is neutral for both compounds. The much more negative value for {TMPD TCNQ} presumably indicates that an even greater degree of enthalpy stabilization is achieved when the ground state is ionic (see Section 15.10). n n n

16.3

Spectroscopic measurements on the excited state1

The originally colorless solutions of the individual donor and acceptor compounds give, on mixing, a vividly colored solution; similarly, highly colored crystals of the molecular compound appear on crystallization from a mixture of the colorless components. In quantitative terms, a new broad, structureless absorption band appears in the UV – visible region of the spectrum which is otherwise, to a good approximation, made up of the sum of the spectra of the individual components. The Mulliken theory of the spectra and stabilization of charge transfer compounds postulates an essentially neutral ground state and an essentially ionic (or dative) ﬁrst excited state. Light absorption in the charge transfer band leads to electron transfer from the HOMO of the donor to the LUMO of the acceptor (for references see Section 13.1). A possible arrangement of energy levels is shown schematically in Fig. 16.3. The various possible situations according to the relative energies of CT and locally excited states (based on Iwata et al., 1967) are summarized as follows (for brevity the energy of a state is given, for example, by 1(D þ A )): Situation I

(a) (b) Situation II (a) (b) Situation III (a) (b) Situation IV

(DA) < (DA) < 1 (DA) < 1 (DA) < 1 (DA) < 1 (DA) < 1 (DþA) 1

1

(DþA) 3(DA*), 3(D*A) (DþA) 3(DA*), 3(D*A) 3 (DA*) < 3(DþA) 1(DþA) 3 (D*A) < 3(DþA) 1(DþA) 3 (DþA) 3(DA*) 3 (DþA) 3(D*A) 3(DþA) < 1(DA) 1

3

In the ﬁrst three of these ‘Situations’ the no-bond singlet is the ground state of the molecular compound (molecular compounds of this type are discussed in Section 15.3); the ﬁrst excited state is shown as a charge transfer singlet 1(DþA) in I(a) and a charge transfer triplet 3(DþA) in I(b), which are the usual situations. Situation II(b) with a locally excited donor triplet state is also found, but the locally excited triplet state of the acceptor is usually at much higher energies. III(a) and (b) are limiting cases of I(b). In Situation IV the ionic state is the ground state, and the triplet state may be thermally accessible (molecular compounds of this type are discussed in Section 15.10). There are very few experimental demonstrations of the nature of the excited state. The degree of charge transfer in the 1(DþA) state (Zs) has been measured for hexamethylbenzene TCPA in solution (Czekalla and Meyer, 1961); values of m, the change in dipole moment following the creation of the excited charge transfer state, of n n n

1

This section draws heavily on the reviews of Ponte Goncalves (1980) and Krzystek and von Schutz (1993).

SPECTROSCOPIC MEASUREMENTS ON THE EXCIT ED STATE 3

1087

(D*A) 1W

3(D+A–) 1

(D+A–)

3W

phosphore scence

absorption

fluorescence

1(DA) 1W

0

Fig. 16.3. Schematic diagram of a possible arrangement of the energy levels of a charge transfer compound. The zero-order (unmixed) charge transfer states are shown in the center of the diagram, and the effects of mixing on the left (3W is the lowest triplet CT state) and right (1W is the lowest singlet CT state), together with the transitions involved in phosphorescence, absorption and ﬂuorescence. The arrangement of energy levels corresponds to Case II(b) below. (Adapted from Iwata et al., 1967.)

10 D were obtained, corresponding to Zs 1. The ﬁrst demonstration of the occurrence of charge transfer triplet states followed the ﬁnding that the phosphorescence spectra of several 1 : 1 aromatic hydrocarbon-acceptor combinations in glassy media at 77K were considerably red-shifted with respect to the phosphorescence spectra of the individual components (the aromatic donors were benzene, toluene, mesitylene, durene, hexamethylbenzene, phenanthrene and triphenylene; the acceptors were 1,2,4,5tetracyanobenzene (TCNB), phthalic anhydride and pyromellitic dianhydride (PMDA)). Analogous measurements for singlet excited states of crystalline CT compounds (discussed in a general context by Ponte Goncalves (1980)) have been made, only for {anthracene PMDA}, but there are many investigations involving triplet states. The triclinic crystal structure of {anthracene PMDA} (deep red crystals, P1, Z ¼ 1, at T ¼ 153K, Robertson and Stezowski, 1978; Table 15.2; ANTPML) consists of sheets of stacks (Fig. 16.4). The molecules of the two components are at crystallographic centers of ˚ and the normal symmetry and related by translations; the interplanar distance is 3.33 A to the plane of the central ring of anthracene makes an angle of 20.7 with [001], which is the stack axis. All donor molecules are mutually parallel, as are all acceptor molecules. Donor and acceptor molecules are almost parallel, with an angle of 3.0 between their planes, and of 4.2 between their long axes. As there is no evidence for a phase change between 300 and 2K, we may assume that the spectroscopic studies, carried out at 2K (Haarer, 1977) are of this structure. The emission (ﬂuorescence) and absorption spectra associated with the lowest CT transition of crystalline {anthracene PMDA} at 2K are shown in Fig. 16.5 (Haarer, 1977). There is a phonon continuum, and sharp lines that correspond to vibrations of the donor and acceptor moieties. The zero-phonon electronic transition centred at ˚ ) (identiﬁed as such from the mirror image relation of the vibronic 18320 cm1 (5459 A structure in emission and absorption) was shown to be strongly polarized along the [001] stack axis. A zero-phonon line is intense when the coupling between electronic transition and lattice vibrations is small (S 9 1; S is the average number of phonons coupled to the electronic transition); when the coupling strength increases (S 10 is strong electron–phonon coupling) the intensity is redistributed into a broad phonon wing n n n

n n n

n n n

CRYSTAL (STRUCTURAL) PHYSICS

1088

Fig. 16.4. Stereodiagram of the molecular arrangement in {anthracene PMDA}, viewed normal to the moiety planes, i.e. approximately along c*; the a axis points to the right and the b axis points upwards, both being in the plane of the page. The reduced cell can be obtained from that in the diagram by the transformation (001/100/111). (Reproduced from Robertson and Stezowski, 1978.) n n n

Optical density

Fluorescence intensity

PMDA

Zero-phonon transition

Absorption

Emission

5900

5700

5500

5300

5100

Wavelength Å

Fig. 16.5. Emission and absorption spectra of crystalline {anthracene PMDA} at 2K. The sharp lines correspond to anthracene and PMDA vibrations as determined by Raman spectroscopy. (Reproduced from Haarer, 1977.) n n n

and the zero-phonon transition cannot be detected under normal experimental conditions. The intensity of the zero-phonon line from {anthracene PMDA} is strongly temperature dependent and the line is not detectable above 20K (Haarer, 1974). S was estimated from the temperature dependence as 6.0 0.3 and is thus in the intermediate regime. The electric ﬁeld dependence of the frequency of the zero-phonon line (the Stark effect) has been measured and gives an approximate value for the change in dipole moment which characterizes the creation of the ionic charge transfer state as m ¼ 11 1 D (Haarer, 1975; Haarer et al., 1975). Thus Zs 1, and Mulliken’s theory receives experimental conﬁrmation also for the solid state. n n n

SPECTROSCOPIC MEASUREMENTS ON THE EXCIT ED STATE

1089

The broadened (and hence structureless) nature of the charge transfer band of -molecular compounds in solution is ascribed to the variety of geometrical approaches, in terms of both intermolecular distances and orientations, that occur between the donor ˚ can lead to energy ﬂuctuations of and acceptor moieties. Variations of 0.01 A 1 100 cm (Czekalla et al., 1957). However, the broadening due to such geometrical inhomogeneities is small or negligible in crystals. Here Haarer (1975) has suggested that the additional Coulombic attraction that occurs in the polar excited state leads to a contraction of the interplanar distance between adjacent donor and acceptor molecules by ˚ ; this gives rise to the observed broadening of the CT band, and also to the observed 0.1 A Stokes shift between absorption and emission spectra. The nature of the excited triplet state in single crystals of donor–acceptor molecular compounds has been extensively investigated by electron paramagnetic resonance, which leads to determination of Zt, the fraction of charge transferred in the triplet state. This brief account of the theory closely follows Ponte Goncalves (1980). The dipole–dipole interaction between two unpaired spins in a molecular triplet state is given by Hss ¼ STS ¼ D(Sz2–1/3S2) þ E(Sx2 – Sy2). For the planar molecules considered here we choose x, y, z (the principal axes of the interaction tensor T) with z normal to the molecular plane, and x and y determined by the in-plane symmetry (if any) of the molecule (these axes correspond to the L, M, N axes deﬁned in Section 15.1). The dipole-dipole interaction results in the splitting (even in the absence of an external ﬁeld) of the three spin sublevels of the triplet state into levels at (2D/3) and (D/3 E), where D and E are the zero-ﬁeld splitting parameters. Their values are given by 2 2 5 3 – 3z12 ) r12 j i D ¼ (3g2b 2/4) h3 j (r12 2 2 3 2 2 5 3 E ¼ (3g b /4) h j (y12 – x12 ) r12 j i

D and E can be measured by optical detection of magnetic resonance (ODMR), which involves monitoring the changes induced in phosphoresence intensity by application of resonant microwaves to induce transitions between the zero-ﬁeld spin sublevels. Because in-plane delocalization of spin is generally larger than that normal to the molecular plane, the ﬁrst term in the equation for D is usually much larger than the second, leading to fairly facile estimation of D. E, however, is given by the difference between two terms of similar magnitude and hence is more difﬁcult to calculate. We now turn to estimation of Zt. Assuming Situation III(b) above to apply, we write the wave function for the triplet state in terms of conﬁguration mixing between the donor triplet state and the charge transfer triplet state: 3

¼ (1 – Zt)1/2

3

(D*A) þ (Zt)1/2

3

(DþA)

The value of D is then, assuming a common magnetic axis system for donor and compound, given by D ¼ (1 – Zt) Dd þ Zt Dct þ [Zt (1 – Zt)]1/2 Dd,ct where Dd refers to the individual donor molecule, Dct refers to the fully charge transferred state, and Dd,ct is a hybrid contribution (zero if the two-center approximation applies). Thus, if it is found that D Dd, then one may conclude that Zt 0 and that the triplet state is localized on the donor molecule. This situation occurs in the triplet state of crystals of highly

CRYSTAL (STRUCTURAL) PHYSICS

1090

Table 16.2. Values of D and E measured for anthracene in various environments compared with those found in vapour-grown crystals of {anthracene PMDA} n n n

Host

phenazine

diphenyl

anthracene-d10

{anthracence PMDA}

D (cm1) E (cm1)

0.07055 0.00791

0.07156 0.00844

0.06945 0.00836

0.0695(3) 0.0079(3)

n n n

puriﬁed {anthracene PMDA} (Haarer and Karl, 1973) grown by sublimation; these crystals show (at 1.6K) an EPR spectrum on irradiation and a phosphorescence spectrum (crystals grown by the Bridgman method show only very weak phosphorescence and EPR signals). Comparison of values of D and E for anthracene in various environments (Table 16.2) shows that the triplet state in {anthracene PMDA} is localized on the donor molecule. More sophisticated methods must be used for determination of Zt when this is not small. EPR methods have given valuable information about D and E parameters, triplet states immobilized at low temperatures, kinetics of spin state migration and hyperﬁne interactions. We shall consider below particularly those measurements relevant to the study of phase transitions in charge transfer molecular compounds. n n n

n n n

16.4

16.4.1

Crystals with disorder ) order transformations on cooling – modern treatments of second order phase transitions General introduction

Room temperature x-ray diffraction photographs of crystalline -charge transfer molecular compounds are generally (but not always) characterized by a strong reduction in reﬂection intensity with increasing scattering angle; this has been interpreted (see Herbstein (1971) for summary) to mean that donor and/or acceptor molecules are dynamically or statically disordered. This in turn suggests that disorder ) order transformations may occur on cooling, as been demonstrated experimentally by diffraction and other physical techniques for a number of systems; these transitions are (generally) second order (as deﬁned below) and can be related to the classical treatments of Bragg and Williams (1935) and Landau (1937). We plan to integrate experiment and theory (at its simpler levels) for the systems that have been studied, ﬁrst introducing concepts encountered in modern discussions. The various experimental techniques are complementary while the various systems maintain a similar overall behavior with individual quirks. Speciﬁc heat–temperature curves provide a concise qualitative and quantitative picture of thermal behaviour showing whether phase transformations occur and allowing some deductions about their nature; they also provide values of the thermodynamic functions over the temperature range of measurement (see Appendix 1). The relatively few Cp–T measurements reported for -molecular compounds show a diversity of effects. The yellow polymorph of {naphthalene PMDA} shows no transition over the range 0–300K (BoerioGoates and Westrum, 1979; Appendix 1); {pyrene PMDA} shows a second-order transition at 155K (Boerio-Goates and Westrum, 1980b; Dunn et al., 1978); {naphthalene TCNB} shows a broad second-order transition over the range 40–75K (Boerio-Goates n n n

n n n

n n n

DISORDER ) ORDER TRANSFORMATIONS

1091

and Westrum, 1979); {naphthalene TCNE} (Boerio-Goates and Westrum, 1980a) shows a combination of a broad second-order transition over the range 150–210K and a sharp transition over the range 155–163K, with the added complication that the sharp peak is split; these detailed and intricate results for {naphthalene TCNE} should be useful in guiding diffraction studies of this substance beyond the room temperature results currently available. Although our approach is quite standard, it is perhaps desirable to clarify certain concepts and set out our treatment in a general context. The term ‘order’ is an abbreviation for ‘long range order’ and has its origins in studies of metallic alloys; a general account is given by Ziman (1964). Here we assume that A and B in a binary (metallic) crystal AB are completely segregated onto two different sublattices in a state of perfect long range order at T ¼ 0K (A, B are different types of atom). A classic example is b-brass (ideally CuZn) with the B2 CsCl structure, in which Cu atoms have only Zn nearest neighbors and conversely. As the temperature increases, some B atoms are found on the A sublattice (i.e. in the wrong positions) and the degree of long range order is reduced, due to the interplay of enthalpy (favoring order) and entropy (favoring disorder) contributions to the overall Gibbs free energy. The degree of long range order Q is deﬁned as the fraction of atoms in their right positions minus the fraction of atoms in their wrong positions; here Q ¼ j1 – 2pj, where p is the probability of ﬁnding an A atom on the A sublattice. When p ¼ 1, then Q ¼ 1 and the long range order is complete; when p ¼ 1/2, then Q ¼ 0 and the long range order disappears. The temperature of disappearance is Tc, the critical temperature. Long range order gives rise to superlattice reﬂections in the diffraction pattern, with intensities proportional to Q. Although it is not taken into account in the simple theory, short range order can exist above Tc, i.e. the probability of ﬁnding a B atom as nearest neighbor to an A atom is greater than statistical; short range order gives rise to diffuse scattering in the diffraction pattern, generally centered at the superlattice reciprocal lattice points. Although we have used chemical ordering as the basis for our description above, the concepts are general and can refer, for example, to ordering of spins in magnetic systems, or to ordering of orientations in mixed stack -molecular compounds, which is the context relevant here2. We shall ﬁnd that, in the systems discussed below, the donor molecule can take up two orientations on its sublattice sites; at 0K these orientations are arranged in completely ordered fashion but wrong orientations begin to appear as the temperature is increased until the long range order (together with the accompanying superlattice reﬂections) disappears at Tc. Thus the transitions (on heating from 0K) to be discussed are from orientational order to orientational disorder. n n n

n n n

16.4.2 The Ehrenfest order of a phase transition The order of a phase transition was ﬁrst deﬁned by Ehrenfest (1933): in an nth order phase transition the nth and higher derivatives of G (Gibbs free energy) with respect to T and P show discontinuities. Examples relevant here are: First order – discontinuities in V ( ¼ (@G/@P)T), S ( ¼ (@G/@T)P), H, U, etc. Second order – discontinuities in ( ¼ (1/V)(@V/@T)p ¼ {(1/V)[@/@T(@G/@P)T)]P}) and CP ( ¼ [T(@S/@T)P] ¼ [–T(@ 2G/@T2)P]. 2 Chemical ordering does not occur in these structures except perhaps of mixed donors or acceptors in the ternary systems noted in Section 13.5.

CRYSTAL (STRUCTURAL) PHYSICS

1092

P ordered phase K disordered phase

T (K) Fig. 16.6. The line representing the transition between two polymorphic phases of a one-component system, drawn in the P–T plane. The continuous line represents a ﬁrst order transition and the broken line a second order transition. The point K is the tricritical point. (Adapted from Fig. 66 of Lifshitz and Pitaevskii (1980).)

Higher order phase transitions can be deﬁned similarly but it is not clear whether they exist as other than mathematical concepts. We give a brief deﬁnition of ﬁrst order transitions for completeness. The two phases (A and B) have different structures and the transition shows hysteresis (i.e. superheating and supercooling are possible). Because of the structural difference, the transition mechanism is generally of the nucleation and growth type and one would expect a single crystal of phase A to transform into a polycrystal of phase B on heating, and conversely on cooling; twinning often occurs. In another nomenclature, these are called discontinuous transitions. In a second order transition the two phases have structures that merge into one another and the transition does not show hysteresis. Because of the structural similarity, the transition mechanism is generally from a single crystal of the A phase to a single crystal of the B phase, with preservation of component orientations; these are often called continuous transitions. Transitions between phases of similar structure can be either ﬁrst or second order depending on external conditions (here T and P); this is illustrated by a diagram adapted from Lifshitz and Pitaevskii (1980, Chapter 10, Fig. 66, p. 493) (Fig. 16.6). 16.4.3

Landau theory of phase transitions

Phase transitions are often described in terms of a theoretical approach originally developed by Landau (1937) and, at a deeper level that takes ﬂuctuations into account, in terms of renormalization groups (Wilson, 1971). We shall restrict ourselves to Landau theory, which is a mean ﬁeld theory and has been detailed in a number of texts (Lifshitz and Pitaevskii, 1980; Salje, 1990; Stanley, 1971; Stokes and Hatch, 1988; Tole´dano and Tole´dano, 1987) and many articles. Our brief description is primarily based on Salje and

DISORDER ) ORDER TRANSFORMATIONS

1093

Stokes and Hatch, and we consider only those aspects relevant to the present chapter. Landau theory is generally considered to apply only to second order (continuous) changes but its extension to discontinuous (ﬁrst order) changes has been discussed (see Stokes and Hatch (1988), pp. 2–3 for references). The excess Gibbs free energy G (T) is the difference in Gibbs free energy between high symmetry and low symmetry phases of the crystalline compound under consideration. Assuming that the excess enthalpies (H) and entropies (S) are not temperature dependent, G(T) can be written as G(T) ¼ 1/2A (T – Tc)Q2 þ 1/4BQ4 þ 1/6CQ6

(16.1)

where the parameters A, B, C are not temperature dependent; Tc is the temperature of the phase transition (the critical temperature) and Q is the order parameter deﬁned above in Section 16.4.1. G (T) as given above is called a 2-4-6 potential; when B ¼ 0 (the 2-6 potential), the transition is tricritical, representing the intermediate stage between continuous (B > 0) and discontinuous (B < 0) transitions (see Fig. 16.6). The condition for thermodynamic equilibrium is determined by the minima of the potentials, i.e. for @G/ @Q ¼ 0. The solutions for second order (2-4) and tricritical (2-6) potentials are 2-4: Q2 ¼ A/B (Tc.– T) and 2-4-6: Q4 ¼ A/C (Tc – T), T < Tc. In Landau’s original work the implicit assumption was made that the polynomial expansion of the potential was only valid in the vicinity of Tc, and hence for small values of Q, but Salje (1990) has proposed that ‘‘the polynomial expansion of G is a good approximation over an extended temperature interval and that the approximation also holds for larger values of the order parameter.’’ We consider in the next section how the results summarised here can be used to determine whether there is justiﬁcation for applying Salje’s extension of Landau theory to binary molecular compounds. 16.4.4 The critical exponents In a more general approach, the behaviour of the system is described in terms of critical exponents , the values of which depend on the physical property under investigation and the nature of the transition (Berry, Rice and Ross, 1980, p. 863–864; Lifshitz and Pitaevskii, 1980; Stanley, 1971; Tole´dano and Tole´dano, 1987). Very general relationships among the various critical exponents can be derived that do not depend on the physical system. A physically measurable quantity such as spontaneous strain (deﬁned below), intensity of a superlattice reﬂection (for these two quantities the symbol b is generally used for the exponent) or the excess speciﬁc heat Cp (here is generally used for the exponent) can be given as f(–") ¼ A(–") {1 þ B(– ")xþ }

(x > 0), where " ¼ (T – Tc)/Tc.

The correction terms drop out on taking the limit in order to obtain the critical exponent, which is deﬁned as ¼ lim ½lnf ð"Þ=lnð"Þ : "!0

CRYSTAL (STRUCTURAL) PHYSICS

1094

is expressed as a function of temperature in the form f(1–T/Tc), which is given (to a ﬁrst approximation) as f ð1 T=Tc Þ ¼ Að1 T=Tc Þ

ð16:2Þ

or, recast in log-log form, as log½ f ð1 T=Tc Þ ¼ log A þ log½ð1 T=Tc Þ :

ð16:3Þ

The critical exponents have generally been obtained from measurements made very close to Tc (perhaps within 0.5–1 ) because then the effect of ﬂuctuations can be investigated. Ignoring the correction terms, one has f(– ") ¼ A(–"). We have used this power law form to ﬁt various order parameters and obtain accompanying values for the exponents. The Salje extension implies that data over the whole available temperature range can be used; thus equation (16.3) should give a linear plot with slope . We shall ﬁnd that this holds well for {pyrene PMDA} (PYRPMA), but that there are problems, discussed below, with {naphthalene TCNB} (NAPTCB) and {anthracene TCNB} (ANTCYB); however, these are hardly critical exponents in the sense of the theory, particularly because experimental values sufﬁciently close to Tc are usually lacking. We consider them convenient for description but their physical signiﬁcance has still to be established. n n n

n n n

16.4.5

n n n

The permitted symmetries of a low symmetry phase derived from a particular high symmetry phase

The permissible space groups of the low temperature phase derived from a particular high temperature phase after a second order phase transition were ﬁrst obtained by Landau and Lifshitz in 1937–1939 (see Lifshitz and Pitaevski, 1980, XIV x145) and, more extensively, by Lyubarski (1960) and Koci 0 nski (1983). The latter authors have treated some tetragonal and hexagonal space groups in detail. However, space groups of mixed stack -molecular compounds are usually monoclinic and, to the best of our knowledge, those relevant to second order phase transitions have been treated only by Bernstein (1967). We quote a limited set of Bernstein’s results, assuming that the high temperature phase has space group C2/m or P21/a, that the moieties are located at crystallographic centers, and that the transition occurs with preservation of axial directions. I. High temperature phase has space group C2/m. The conditions and possible space groups for the low temperature phase are: 1. Unit cell remains centered and cell volume remains unchanged (a) Cm, (b) C2, (c) C 1. 2. Unit cell becomes primitive but cell volume remains unchanged (a) P2/m, (b) P21/a, (c) P2/a, (d) P21/m. Examples of I.2(b) are {naphthalene TCNB}, {anthracene TCNB}, {pyrene C6F6}, and (perhaps) {anthracene TCNQ}. 3. Unit cell remains C-centered, cell volume is doubled and lattice becomes triclinic (P). The axial directions are not preserved in the reduced cell. 4. Unit cell becomes body centered monoclinic, c axis and cell volume are doubled. The axial directions are not preserved in the reduced cell. (a) I2/m, (b) I2/c. Example of I.4(b) is {anthracene C6F6}. 5. Unit cell remains C-centered monoclinic, c axis and cell volume are doubled. (a) C2/m, (b) C2/c. n n n

n n n

n n n

n n n

n n n

DISORDER ) ORDER TRANSFORMATIONS

1095

II. High temperature phase has space group P21/a. The conditions and possible space groups for the low temperature phase are: 1. Unit cell remains primitive monoclinic, but center of symmetry disappears (a) P21, (b) Pa. The C-polymorph of naphthazarin (of course, not a -molecular compound) belongs to II.1(b) (Herbstein et al., 1985), as does (TTF-CA} (x16.9.2). 2. Unit cell becomes primitive triclinic, without change of volume (a) P 1 A possible example of II.2(a) is {naphthalene TCNE}. 3. Unit cell remains primitive monoclinic, c axis and cell volume are doubled. (a) P21/a, (b) P21/n. Example of II.3(b) is {pyrene PMDA}. 4. Unit cell becomes pseudo-centered monoclinic, but the actual space group is P 1. The axial directions are not preserved in the reduced cell. (a) pseudo-C-centered (b) pseudo-I-centered. n n n

n n n

The piecemeal contributions described above, important as they were, have now been consolidated into the tables of Stokes and Hatch (1988). The parent (high symmetry) polymorphic phase with space group G0 transforms, with a physical generalized distortion (r), to a low symmetry phase with space group G, where G is a subgroup of G0. Stokes and Hatch (1988) have derived the G space groups for all the 230 G0 space groups. The G0 space groups of interest here are C2/m and P21/c and we excerpt in Table 16.3 the relevant information from the Stokes and Hatch tables; this is discussed together with phase transitions of the various compounds. The label ‘Spec(ies)’ in Table 16.3 refers to the ferroic species of the transition. For the three examples of interest here, this label is ‘nf’ nonferroic. A ‘nonferroic’ or ‘co-elastic’ crystal has ‘‘elastic and strain anomalies . . . correlated with the structural phase transition’’ (Salje, 1990). The Bernstein and Stokes and Hatch prescriptions can be reconciled when one remembers that in Bernstein the transition occurs with preservation of axial directions

Table 16.3. Information from the Stokes and Hatch (1988) tables for the G0 space groups C2/m and P21/c. The definitions of the various column headings are given by Stokes and Hatch. The columns relevant in the present context have been emphasized Space group G0

Parent Irrep.

Image

Lan

Lif

Subgroup G

Spec.

Dir

Size

Basis

Origin

C2/m

Yþ 2

A2a

0

0

14 P21/c

nf

P1**

2

(000)

Aþ 2

A2a

0

0

15 C2/c

nf

P1**

2

Yþ 2

A2a

0

0

14 P21/c

nf

P1**

2

(001); ð0 10Þ; (100) (100); (010); (002) (001); (010); ð 20 1Þ

P21/c

(000)

(000)

1096

CRYSTAL (STRUCTURAL) PHYSICS

while the space group can change (as we have done here for {pyrene PMDA}, whereas Stokes and Hatch maintain space group and allow axial directions to change. n n n

16.4.6

Temperature dependence of the order parameter

We now deﬁne ‘‘spontaneous strain’’ and show how it is measured, basing ourselves extensively on Salje (1990; see Chapter 4). In a ferroelastic (not relevant here) or co-elastic transition the shape of the crystal is changed and this creates a macroscopic spontaneous strain. Ignoring microstructures (justiﬁed by the absence of transitioninduced twinning in the crystals considered here), the macroscopic spontaneous strain can be replaced by the structural spontaneous strain, usually called the spontaneous strain, which is measured as the volume average of the deformation of the unit cell. Originally introduced for ferroelastic systems by Aizu (1970), this deﬁnition has been expanded to include all structural phase transitions that lead to variation of the shape of the crystallographic unit cell, especially for co-elastic systems. In order to measure the spontaneous strain the lattice parameters of the high-symmetry phase have to be extrapolated into the temperature regime of the low-symmetry phase, i.e. the high symmetry phase is the reference phase. This extrapolation represents that part of the thermal expansion that is not related to the structural phase transition and therefore does not contribute to the excess spontaneous strain. The numerical values of the spontaneous strain are now deﬁned by the strain tensor that relates the low-symmetry unit cell to the high-symmetry unit cell when extrapolated to the same temperature. The spontaneous strain in the (low-symmetry) ordered phase is conveniently given in terms of the Vogt coefﬁcients ej, calculable as a function of temperature from the measured cell dimensions of the ordered phase (not subscripted) and the extrapolated cell dimensions of the disordered phase (subscripted) using e1 ¼ a/a0 – 1, e2 ¼ b/b0 – 1, e3 ¼ (c sin b*/c0 sin b0*) – 1, e5 ¼ (a cos b*/a0 sin b0*) – (c cos b*/c0 sin b0*).

(16.4)

We give the equations only for monoclinic crystals as the three present examples are all monoclinic; Salje (1990) gives the equations for all the crystal families. The (scalar) spontaneous strain in the ordered phase is es ¼ (ej2)1/2. The long range order parameter Q refers to the crystal structure averaged over many unit cells; it can be determined from measurements on the intensities of superlattice reﬂections, from the spontaneous strain and from the ESR spectrum. Spontaneous strain in the ordered phase, and intensities of the superlattice reﬂections are both proportional to Q2. There is also a (structural) short range order parameter referring to the crystal structure averaged over a few unit cells, which will be only brieﬂy considered in what follows; it can be determined from measurements on the intensities of the diffuse scattering of x-rays (or neutrons). The diffraction aspects of these parameters are clearly discussed by Warren (1969; see Chapter 12). The physical interpretation (i.e. at the molecular level) of the measured values is often controversial. The disordered state above Tc is usually described in terms of one or other of two extremes, statistical ‘static’ disorder where the potential energy diagram for a molecule in the ﬁeld of its neighbors is a double-well potential with

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1097

the barrier height appreciably higher than kT, or as ‘dynamic’ disorder where the potential energy diagram is a ﬂat-bottomed well (deﬁnitions adapted from Lefebvre et al., 1989). One is able to build up a fairly satisfactory picture of the ideally ordered structures below the transition temperature but it is much more difﬁcult to deﬁne the nature of the high temperature, disordered structure, and particularly to decide whether the disorder is dynamic or static. Some progress has been made by use of rigid-group reﬁnement of diffraction data and solid state NMR methods, and by model calculations. These results are described in the ﬁnal parts of this section. One important concept, mentioned here only in passing, is that of the ‘antiphase domain’ (Warren, 1990; pp. 216–227). These are well-ordered regions of the crystal separated by ‘change step’ boundaries. As the name suggests, neighbouring domains are mutually out-of-phase. The concept has been applied mostly to metallic alloys (e.g. Cu3Au) and hardly to organic systems. 16.4.7 Pressure dependence of critical temperature for ordering Applying Fig. 16.6 to PYRPMA, the point K has the coordinates P ¼ 1 atm. (1 bar), Tc 165K, the line separating ordered and disordered phases has a positive slope and, following Fig. 16.6, one would expect increase of pressure to favour ordering. The pressure dependence of Tc. can be calculated from Ehrenfest’s second order analog to the ﬁrst order Clapeyron equation given by Pippard’s (1964), equations (8.19) and (9.1.) Ehrenfest’s equation can be written as dTc/dP ¼ Tc[(@V/@T)2 – (@V/@T)1]/[(CP)2 – (CP)1]

(16.5)

where the subscripts 1 and 2 refer to the state of the system just below and just above Tc. A value of [(@V/@T)2 – (@V/@T)1] is obtained from Fig. 16.10 and a value of [(CP)2 – (CP)1,] from Fig. 16.7; using these values we calculate that dTc/dP þ17 K/kbar, if the speciﬁc heat values given by Boerio-Goates and Westrum (1980) are used, and about half this amount using those of Dunn et al. (1978). Thus application of a pressure of a few kbar should produce the ordered phase of PYRPMA at room temperature. Anticipating later discussion we note that [(@V/@T)2 – (@V/@T)1] is negative for PYRPMA and ANTCYB and positive for NAPTCB. As [(CP)2 – (CP)1] is negative, application of pressure should increase Tc for PYRPMA and ANTCYB, and reduce it for NAPTCB. The only experimental test is for ANTCYB (Ecolivet et al., 1988; see x16.5.3(d)).

16.5 Thermodynamic, structural and kinetic investigations of various systems showing second order transitions on cooling3 16.5.1 The crystal structure of {Pyrene PMDA} (PYRPMA) and evidence for an order , disorder phase transition at 160K n n n

(a) Introduction. The melting point diagram (Herbstein and Snyman, 1969; HS69) shows three molecular compounds, the equimolar compound being by far the most stable of the three. The 160K phase transition in PYRPMA was ﬁrst demonstrated by x-ray 3

This treatment is largely based on Herbstein (1996).

CRYSTAL (STRUCTURAL) PHYSICS

1098

35

∆Cp (J/mol K)

30 25 20 15 10 5 0 120

130

140 T (K)

150

120

140

160

∆Cp (J/mol K)

260

210

160 100

160

180

200

T (K)

Fig. 16.7. Part of the Cp – T curve for {pyrene PMDA}, showing the broad transition centred about 155K which corresponds to the second-order transition studied by x-ray diffraction. The ﬁlled circles show the results from Boerio-Goates and Westrum (1980) and the open circles those from Dunn et al., (1978). The speciﬁc heat is a smooth function of temperature outside the range shown. The enlarged inset shows CP after subtraction of background. The values of Cp1, and Cp2, the speciﬁc heats just below and above Tc, are 272 and 245 J/mol K. The curves are guides to the eye. (Adapted from HS93.) n n n

diffraction (HS69) but many of its parameters were established by two independent sets of calorimetric measurements (Dunn, Rahman and Staveley, 1978; Boerio-Goates and Westrum, 1980; Fig. 16.7), These showed a small -type anomaly at 155K, with the enthalpy and entropy of the transition calculated as 222 J/mol and 1.34 J/molK by BoerioGoates and Westrum. There is another transition at 353K about which very little is known. In a much more detailed study (Herbstein, Marsh and Samson, 1993; HMS93; Herbstein and Samson, 1993; HS93) the earlier structural results were conﬁrmed, the structure of PYRPMA at 19K was determined and cell dimensions measured as a function of temperature, as well as intensities of some superlattice reﬂections. No hysteresis of intensities or cell dimensions was encountered. The experimental measurements were analysed using Ehrenfest’s criteria for determining the order of a transition and then, more quantitatively, in terms of Landau theory, using the temperature dependence of

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1099

spontaneous strain and superlattice intensities to determine the nature of the transition. The excellent agreement obtained for these two parameters between theory and experiment was then checked against the excess speciﬁc heat, but here agreement was incomplete. Detailed studies by resonance techniques and measurements of elastic constants as functions of temperature are lacking for PYRPMA. (b) Crystal structure of PYRPMA in ordered and disordered phases. The earlier x-ray studies on PYRPMA (HS69) showed that there were mixed stacks (stack axis [001]) of alternating pyrene and PMDA molecules; in the 295K structure, both moieties were located at crystallographic centres (space group P21/a, Z ¼ 2). The c axis was found to have doubled on cooling to 110K and the space group changed to P21/n. There were now two pairs of pyrenes at independent centres, with the four PMDA molecules in the cell at general positions, but only slightly displaced from their 295K positions. The transition was single crystal to single crystal, with conservation of axial directions. The crystal structure of PYRPMA at 295K has been redetermined by Allen, Boeyens and Levendis (1989) and described in terms of a model in which the pyrenes are statically disordered over three orientations. (c) Experimental study of the order–disorder transition. The most striking feature of the cell dimension–T curves (Fig. 16.9) is the expansion of b on cooling from 300 to 165K, followed by the more usual contraction on further cooling. b – T and b–T curve have a cusps at 165K; a–T and c–T curves show only changes of slope in this region. As V ¼ abc sin b, the V–T curve must also show a cusp at Tc. The cell dimensions given in Fig. 16.9 for the disordered phase were extrapolated (‘‘by eye’’) into the region of stability of the ordered phase for use in the calculation of the spontaneous strain. Superlattice reﬂections, corresponding to a doubling of the c axis (i.e. those with l odd in the ordered structure), appear below 165K (Fig. 16.11). A smooth increase of relative superlattice intensities (IT/I0)hkl from zero at Tc to unity at T ¼ 0K, all (IT/I0)hkl showing the same behavior, is characteristic of the occurrence of a second order phase transformation (Cowley, 1980). The behavior of the superlattice intensities on cooling is quite different from the usual temperature dependence of Bragg reﬂections; these may increase or decrease as the crystal is cooled, in accord with small changes in atomic positions, but uniform behavior is not found (the different behavior of fundamental and superlattice intensities is illustrated below for ANTCYB (Fig. 16.25)). (d) The Ehrenfest order of the transition. The following items of evidence taken together indicate that the transition is of the second order as deﬁned by Ehrenfest. The V–T curve (Figs. 16.9 and 16.10) is continuous but has a change in slope at Tc ¼ 160K; all three thermal expansion coefﬁcients (not shown) have discontinuities at 165K; there are no superheating or supercooling effects (i.e. no hysteresis); the speciﬁc heat CP has a peak (Fig. 16.7) but not a discontinuity. The detailed behaviour of the cell dimensions (Fig. 16.9) suggests that the real physical situation is more complicated than that implied by the formal deﬁnition. (e) Application of Landau theory. Analysis following Stokes and Hatch (1988; see p. 1–10) gives many possible subgroups G when the high-symmetry space group (G0)

CRYSTAL (STRUCTURAL) PHYSICS

1100

(i) sin

b

(ii)

sin

b

5Å carbon oxygen

Fig. 16.8. Crystal structure of {pyrene PMDA}, showing the projections down [001] in (i) the low-temperature ordered structure (ii) the room-temperature disordered structure. In (i) the atoms of the PMDA molecules near c/4 are represented by shaded circles and those near 3c/4 by open circles; ˚ (at 19K). The length of [001] is 7.3 A ˚ (at 300K). For clarity two the length of [001] is 14.4 A molecules at each corner of the projection have been omitted in (i) while in (ii) one pyrene and one PMDA molecule have been omitted; hydrogens omitted throughout for clarity. (Reproduced from Herbstein and Snyman, 1969.) n n n

is P21/c (Table 16.3). The description used here has maintained analogous cell axes for both phases with consequent differences in the space groups, whereas Stokes and Hatch follow the converse path. On our basis one of the possibilities for the space group of the low temperature ordered phase is P21/n with one axis doubled as reported by HS69 and HS93. The physically irreducible representations for this transition is Y2þ and

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1101

13.9

TC a (Å)

13.8 13.7

9.34 7.31

9.32

b (Å)

9.30

c (Å)

7.27

9.28 93.5 7.23 93.1 (deg)

950

92.7 92.3

940

V (Å3)

91.9

930 920

TC 0

300

100 200 T (K)

Fig. 16.9. a(T ) plotted against T(K); there is a change of slope in the region of Tc (165K) but no cusp. b(T ) plotted against T(K); there is a cusp at Tc. c(T) and c(T)/2 plotted against T(K). The ordinate values below Tc must be doubled. There are indications of a change of slope at Tc (167K). b(T) plotted against T(K). There is a cusp at Tc. V(T) (or V(T)/2) plotted against T(K). There is a cusp at Tc (160K). (Reproduced from HS93.)

Volume per formula unit (cubic Å)

466 Disordered phase (dV/dT )P = 0.065 Å3/K

465 Tc Ordered phase (dV/dT)P = 0.111 Å3/K 464 150

155

160 T (K)

165

170

Fig. 16.10. The variation in (volume/formula unit) of the ordered and disordered phases in the vicinity of Tc (¼160K), as calculated from quadratic expressions ﬁtted to the cell dimension curves. (Adapted from HS93.)

CRYSTAL (STRUCTURAL) PHYSICS

1102

1.2 –441 –521 –131

1.0

IT I0

0.016 0.014

0.6 0.4

0.012 0.2

es

0.010 0.008

0.0

Normalized intensity

Spontaneous strain

0.8

0.006 0.004 0.002 0.000

Tc 0

50

100 T (K)

150

200

Fig. 16.11. Upper graph – variation of the normalized intensities (IT/I0) of superlattice reﬂections as a function of temperature (I0 was estimated for each reﬂection from a smooth extrapolation of the I–T curve to T ¼ 0K). Lower graph – the spontaneous strain in the ordered phase of PYRPMA plotted against temperature. The curves shown are guides to the eye. (Reproduced from HS93.)

a continuous change is permitted by both Landau and Lifshitz conditions and also under renormalization group analysis. The relationship between the space groups was discussed in HS69. The usual method of deriving the critical exponents depends on ﬁtting a power law equation of the type given above with experimental values measured as close as possible to the critical temperature. As the measurements for PYRPMA covered a wide temperature range but were sparse close to Tc, the Salje extension of classical Landau theory to large values of the order parameter was used. The (scalar) spontaneous strain es ¼ (ej2)1/2 in the ordered phase calculated from the Vogt coefﬁcients ej as a function of temperature is proportional to Q2, as is the superlattice intensity. Both curves have similar shapes (Fig. 16.11). If the phase transition is tricritical (the intermediate stage between continuous and discontinuous transitions), then it follows from Landau theory that the fourth power of the order parameter is linearly proportional to T; this is indeed found in the plot of (es)2 against T (Fig. 16.12). A further test of the tricritical nature of the transition can be made using the intensities of the superlattice reﬂections. The squares of the normalized intensities against T give a linear plot (Fig. 16.12). Finally dependence of the excess speciﬁc heat on temperature (Fig. 16.7 (insert)) was tested for compatibility with a tricritical transition by plotting log (CP) against log (Tc– T ), where Tc ¼ 155K. The log–log plot (Fig. 16.13) shows that CP as a function of (1 – T/ Tc) is not well represented by the power law equation CP ¼ A[1–(T/Tc)]. A forced linear ﬁt gives ¼ 0.77, whereas ¼ 0.5 for a tricritical transition (Salje (1990, p. 120)).

1.2

– I 2N (44 1) – I 2N (521) –– I 2N (1 3 1)

2.0

1.0 0.8 0.6

1.5

0.4 0.2

1.0

0.0

–104e 2S

(Normalized intensity)2

(Spontaneous strain)2

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1103

0.5

0.0

0

50

100 T (K)

150

200

Fig. 16.12. Upper graph – the square of the normalised intensity (IT/I0)2 plotted against temperature for three superlattice reﬂections of the ordered phase of PYRPMA. The origin has been moved up for clarity. Lower graph – the square of the spontaneous strain (es)2 in the ordered phase of PYRPMA plotted against temperature. (Reproduced from HS93.)

1.6

log (∆Cp (J/mol K))

1.4 1.2 1 0.8 0.6 0.4 0.2 0 –0.2 –1 –0.5

0 0.5 1 log (Tc–T (K))

1.5

2

Fig. 16.13. Log–log plot of the excess heat capacity (Cp in Fig. 16.7) against deviation from critical temperature in the vicinity of the phase transition. (Reproduced from HS93.)

A problem with this calculation is that the two independent sets of CP measurements agree well over the range 0–300K except in the region of the peak. A standard calculation of the entropy of transition gives 2.87 J/molK (as there are two orientations, but for only one of the components, a speciﬁc heat anomaly of 1/2R ln 2 would be predicted); this is about twice the measured entropy of transition of 1.34 J/molK.

1104

CRYSTAL (STRUCTURAL) PHYSICS

The theory of an almost tricritical phase transition with a simple one-component order parameter indicates that the power-law exponents b, obtained from the temperature dependence of the spontaneous strain and the intensities of the superlattice reﬂections, should be 0.25 and , obtained from (CP), should be 0.5 (Salje, 1990). Good agreement with experiment was found for the ﬁrst of these predictions but not for the second. There is a physical difference in that the diffraction measurements cover the whole temperature range below Tc while (Cp) is restricted to between Tc–35 and Tc. (f) Crystal structures of disordered and ordered phases. One way of describing the process in which the long range order of the ordered phase is decreased is by comparing ordered and disordered unit cells through their cell dimensions and molecular arrangements. Perhaps a natural approach is to note that the stack axis ([001]) doubles at Tc and to infer that one is dealing with a Peierls phenomenon,4 due to some change in the -electron HOMO–LUMO interaction between donor pyrene and acceptor PMDA molecules. However, this would appear to be ruled out by the fact that the [001] axial length changes smoothly with temperature. The most striking change in cell dimension behaviour at Tc is that in [010], where (abnormal) expansion on cooling (of the disordered phase) changes to (normal) contraction (of the ordered phase). This could imply that the interaction between adjacent stacks in the direction of [010] is normal from 0–165K, and then becomes (in some unspeciﬁed way) abnormal when the long range order along the stack axis disappears. Expansion on cooling is unusual but not unprecedented; however, neither NAPTCB nor ANTCYB behave in this way. More deﬁnite, but still tentative, indications were inferred from an analysis of the molecular arrangement at 19K (Herbstein, 1996, which should be consulted for details). There is as yet no consensus about the nature of the driving force for ordering. Wideline NMR studies have been made of {pyrene PMDA} (Fyfe, 1974a, b). Line width and (H)2 begin to fall at 195K, about 30 above Tc but there is no sign of any change in line width or (H)2 at Tc itself nor at 353K where there is a ﬁrst-order transition to a phase of unknown structure. The measured value of (H)2 is 4.9 G2 at 77K, which is about 20% smaller than the calculated value for a rigid lattice based on the crystal structure, suggesting that there is still appreciable reorientational motion below Tc. A similar lack of correlation between wide-line NMR results and studies of solid-state transitions appears also for other systems discussed here. The explanation (Darmon and Brot, 1967) is that the proportion of molecules jumping from one orientation to another at any given instant is very small and the contribution of these molecules to the thermodynamic functions is essentially negligible. The values of (H)2 at high temperatures (2.0–2.4 G2 at 300–420K) are explicable (but still not entirely) only if reorientation of the pyrene molecules takes place by both small angle (20 ) and large angle (160 ) in-plane jumps. Measurements of spin-lattice relaxation times (Fyfe et al., 1976) give an activation energy of 57 kJ/mol for the large angle process; Ea could not be measured for the small angle jumps. n n n

4 The Peierls phenomenon (Peierls, 1954, see Chapter 5) refers to the doubling of the periodicity of an . . . ABABAB . . . stack at low temperatures because the ‘dimerized’ arrangement . . . AB AB AB . . . has lower energy.

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1105

16.5.2 The crystal structure of {Naphthalene TCNB} and evidence for an order , disorder phase transition around 72K n n n

(a) Introduction. The order-disorder transitions in the -molecular compounds {naphthalene TCNB} (NAPTCB) and {anthracene TCNB} (ANTCYB) are rather similar (Lefebvre, Odou, Muller, Mierzejewski and Luty, 1989 (LOMML89); Ripmeester, (1995)). We ﬁrst discuss NAPTCB and then ANTCYB; comparisons are also made with the (somewhat different) behavior of PYRPMA. The order–disorder behavior in NAPTCB and ANTCYB is similar in the sense that the same space group changes occur, but Tc values are appreciably different at 76 and 212K (Fig. 16.14). n n n

n n n

CP (J/mol K)

(b) Crystallographic background and x-ray diffraction measurements of temperature dependence of degree of long range order. Cell dimensions have been measured by XRD at 294, 95 and 65K (LOMML89) and by neutron diffraction over the range 300–15K

125 75 K 100

NAPTCB

75 40

50

60 T (K)

70

80

CP (J/mol K)

350

300 ANTCYB 250 150

170

190 T (K)

210

230

Fig. 16.14. (Upper panel) the calorimetrically measured speciﬁc heat of NAPTCB in the region of the order–disorder transition. The CP–T curve is smooth over the rest of the temperature range 0–300K. (Lower panel) the speciﬁc heat of ANTCYB in the region of the order–disorder transition, measured by differential scanning calorimetry (DSC). Ecolivet et al. (1988) suggest that there may be a double peak (shown by arrows) in the DSC curve, corresponding to two events, but this remains to be proved. (Reproduced from Ecolivet, Leme´e, Delugeard, Girard, Bertault, Collet and Mierzejewski, 1988.)

1106

CRYSTAL (STRUCTURAL) PHYSICS

(Czarniecka et al., 1985) (Fig. 16.15). There are systematic differences between XRD and ND values and closer temperature intervals are required before deﬁnite inferences can be drawn about the order of the transition; the indications are that there is no discontinuity in cell volume at Tc, in accordance with a second order character for the transition. Calculation of the temperature dependence of the spontaneous strain requires a better set of cell dimensions. The NAPTCB and ANTCYB molecular compounds have closely related structures but are not isomorphous. An early room temperature structure analysis on a twinned crystal of NAPTCB (Kumakura, Iwasaki and Saito, 1967) showed that the components were arranged in the usual donor–acceptor mixed stacks, with stack axes along [001] (Fig. 16.16). These results were conﬁrmed (and extended) in a later single crystal study of the structures at 300, 95 and 65K (LOMML89). The same formal description applies to NAPTCB and ANTCYB although the arrangement of the molecules, and their relationship to the cell axes, is different for the two compounds; one structural difference is that in NAPTCB the molecules lie very nearly in (102) planes, but in ANTCYB in ð102Þ planes (Fig. 16.17). NAPTCB TC

9.4 9.3 a (Å) 9.2

12.7 12.6 b (Å) 12.5 6.9 6.8 c (Å)

6.7

(deg)

108.0 107.5

780

V (Å3)

770 760 750 740 TC 0

100

200 T (K)

300

Fig. 16.15. NAPTCB – cell dimensions as a function of temperature, measured by XRD (centered circles, LOMML89) and ND (solid circles, Czarniecka et al., 1985).

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1107

At 300K the naphthalene molecules are disordered in equal measure over two orientations separated by 36 , while the TCNB molecules are completely ordered. On cooling, the space group changes from C2/m in the disordered phase to P21/a in the ordered phase, without appreciable change in unit cell dimensions. In the C2/m, Z ¼ 2 structure, the naphthalene centres are at Wyckoff positions (a) (000, 1/2 1/2 0) and TCNB centres at Wyckoff positions (c) (00 1/2, 1/2 1/2 1/2); the site symmetry of (a) and (c) positions is 2/m. In the P21/a, Z ¼ 2 structure, the naphthalene centres are at Wyckoff positions (a) (000, 1/2 1/2 0) and the TCNB centres at Wyckoff positions (b) (001/2, 1/2 1/2 1/2); the site symmetry of (a) and (b) positions is 1. The donor molecules take up one (averaged) orientation above Tc and two below; the TCNBs do not change. Above Tc the two stacks

N

N

N

N

a sin

O

N

N

N

N

b

N

N

N

N

N

N

N

N

N

N

N

N

Fig. 16.16. The ordered structure of NAPTCB, space group P21/a (hydrogens omitted for clarity). In the diagram the centers of symmetry at cell corners, centers of cell edges and at cell center have been omitted. The site symmetry is for both components. The naphthalenes are centred at Wyckoff positions (a) [000; 1/2,1/2,0] and the TCNB’s at Wyckoff positions (b) [00,1/2; 1/2,1/2,1/2]. The molecules lie nearly in ð102Þ planes. The disordered structure (space group C2/m) has essentially the same cell dimensions, but the units at cell corners and center are now identical (i.e. related by translations). The naphthalene molecule is disordered over the orientation shown and its mirror image, with equal occupancies. The site symmetry is 2/m for both components, the two fold axis running along [010] and the mirror plane lying in (010). (Adapted from Kumakura et al., 1967.)

CRYSTAL (STRUCTURAL) PHYSICS

1108 (a)

III

(b) II I

I II III D

c

A

c a

D

A b down a Stack axis Stack axis NAPTCB

ANTCYB

˚, Fig. 16.17. Comparison of the stack arrangements in NAPTCB (at 300K: 9.420 12.684 7.31A ˚ 107.4 , Z ¼ 2, C2/m) and ANTCYB (at 300K: 9.526 12.780 7.440 A, 92.36 , Z ¼ 2, C2/m), with the donor molecules (respectively naphthalene and anthracene) labelled as D and denoted by thick lines, while the acceptor molecules (TCNB) are labelled A and denoted by hatched rectangles. Stacks I and III are translationally equivalent, while stack II is shifted by b/2 behind the plane of the page and is related to I by the a-glide. (Adapted from LOMML89.)

(stack axis [001]) in the unit cell are related by the C-centering operation while below Tc the two stacks are related by the a-glide. The structure can be described as a close packed arrangement of stacks of elliptical cross section, with the packing of the stacks shown in Fig. 16.16. Within a particular stack, all donor molecules are translationally equivalent, as are all acceptor molecules; this applies to both disordered and ordered structures. In the disordered structure the arrangement of components along a stack is . . . ..hDi A hDi A hDi A hDi . . . where hDi represents the averaged orientation of the donor molecules in a stack. In the fully ordered structure the arrangement of components along stack I (Fig. 16.16) is . . . ..D1 A D1 A D1 A D1 . . . and that in stack II is . . . D2 A D2 A D2 A D2 . . . where D1 and D2 are the two orientations of the donor molecules, related by the a-glide; the TCNBs have the same orientations in both stacks but this is not required by the crystal symmetry. Thus the disordering process, viewed from ‘‘within stack I’’, is to produce sections of . . . D1 A D2 A D1 A D1 . . . and analogously for stack II. Analysis following Stokes and Hatch (1988; see p. 1.8–9) gives many possibilities for a contiuous transition from the high symmetry (G0) space group C2/m; one of these is to P21/a, without change of cell dimensions or shift of origin, the physically irreducible

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1109

I(323) (arbitary units)

10

1

0.1 0.0010

0.0100

0.1000

1.0000

(1–T/73.5)

Fig. 16.18. I(323) against (1 – T/73.5) for NAPTCB, both on a logarithmic scale; the intensity measurements (in arbitary units) extend over the range 60–75K. Apart from the two points closest to Tc, the measurements are well ﬁtted by I(323) 1 (1 – T/73.5)0.334.

representation being Y2þ and a continuous change being permitted by both Landau and Lifshitz conditions and also under renormalization group analysis. The relationship between the space groups is discussed above. The critical exponent can be determined from the temperature dependence of the intensities of the superlattice reﬂections; the necessary measurements (by LOMML89) are available only for reﬂection (323). We have noted above (equation (16.2)) that Q2 Isuperlattice ¼ A(1–T/Tc)2b The log/log plot (Fig. 16.18) shows that the exponent 2b ¼ 0.334 except in the region closest to Tc, where a higher value could be appropriate. b ¼ 0.33 is generally considered to indicate an order–disorder transition so that there is a considerable discrepancy here, perhaps due to the fact that I(323) was measured over a range of only 13.5K (compared to ranges of 145K for the analogous measurements for PYRPMA and ANTCYB). The values of the order parameter Q at 65K from various sources can be compared as follows: an extrapolated value of I(323) ¼ 9 at 0K is obtained from Fig. 16.18, with I(323) ¼ 4.3 at 65K (from Fig. 6 of LOMML89). Thus Q(65K) ¼ (4.3/9)1/2 ¼ 0.7, which is not in good agreement with the NMR value (essentially unity) or that of LOMML89 from XRD (Q(65K) ¼ 0.90). The diffraction measurements of superlattice intensities at different temperatures for ANTCYB are more extensive than those for NAPTCB and we discuss extraction of order parameters and critical exponents below.

1110

CRYSTAL (STRUCTURAL) PHYSICS

(c) Other physical measurements. Speciﬁc heat measurements (Boerio-Goates, Westrum and Fyfe, 1978) (Fig. 16.14(a)) show that there is a gradual transition over the range 40–75K (Htrans ¼ 192 21 J/mol, Strans ¼ 3 0.3 J/mol K); Htrans is not very different from the value found for the transition in PYRPMA (222 J/mol) but the Strans values differ by a factor of 2 because of the difference in Tc values. On the basis of the structural results given above, we note that ordering of the molecules below Tc would give a speciﬁc heat anomaly of 1/2R ln 2, because there are two orientations, but only for one of the components. This prediction (2.87 J/molK) is in excellent agreement with the measured entropy of transition. Unfortunately the same argument applied to PYRPMA resulted in a discrepancy of 100%! The anomalous regions in the CP–T curves of NAPTCB and ANTCYB have strikingly similar shapes that differ from the classical shape found in PYRPMA. The signiﬁcance of these differences is not clear. The occurrence of a phase transition was conﬁrmed by Raman spectroscopy which placed Tc at 69K and 62K for the C10H8 and C10D8 molecular compounds respectively (Bernstein, Dalal, Murphy, Reddoch, Sunder and Williams, 1978). The donor molecule (labelled D in Fig. 16.17) at 000 (for NAPTCB) or 100 (for ANTCYB) impinges on the TCNB molecule at 1,0,1/2 (labelled A in Fig. 16.17); the H . . . N interactions between these two components are responsible for the ordering. This is illustrated for NAPTCB at 65K in Fig. 16.19. There are three N . . . H–(C) interactions at the ¼ 0 equilibrium position while there are only two such interactions if the naphthalene is rotated in its own plane to ¼ 36 . At both these positions the N . . . H nonbonded distances are close to the sum of the van der Waals radii. If the naphthalene molecule took up an intermediate orientation at ¼ 18 , ˚ less than the sum of the van the closest N . . . H nonbonded distances would be 0.2–0.3 A der Waals distances. This suggests that the transition is driven by intermolecular interactions (‘‘packing effects’’), in accordance with the lowering of Tc when hydrogen is replaced by deuterium (Bernstein, Dalal, Murphy, Reddoch, Sunder and Williams, 1978; Dalal, Ripmeester et al., 1978). These qualitative considerations can be rendered quantitative by theoretical calculations and the results of measurements by various resonance techniques. A double well potential energy curve for naphthalene in the ﬁeld of the surrounding TCNB molecules was calculated by Shmueli and Goldberg (1973) with barrier height about 12kJ/mol and minima separated by 36 , in accordance with the 300K crystal structure; naphthalene to TCNB interactions were found to be the most important.

2.

68

A

2.

99

5

A

2

2.774 A

) plane of {naphthalene TCNB} (almost the plane Fig. 16.19. Two adjacent molecules in the (102 of the molecules), showing the closer N . . . H distances in the ordered crystal structure. (Reproduced from Lefebvre et al., 1989.) n n n

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1111

A converse, quasi-experimental, analysis was carried out by LOMML89. They calculated structure factors for the disordered structure at 294 and 95K in terms of an orientational probability function for the disordered molecule. For NAPTCB the best ﬁt between observed and calculated structure factors was obtained when the orientational probability function had two maxima at 16 (at 294K) or 18.5 (at 95K). An angle of 36 between the energy minima was measured by 2H NMR spectroscopy (Ripmeester, 1982). Thus these three approaches agree in describing the disordered structure as statically disordered, with the two orientations separated by a barrier height of 12kJ/mol. Earlier wide line (Fyfe, 1974a, b) and pulsed NMR measurements (Fyfe, Harold-Smith and Ripmeester, 1976) have since been extended to lower temperatures, and supplemented by ESR measurements (Ripmeester, Reddoch and Dalal, 1981). We consider all these results together. Pulsed NMR measurements of relaxation times (Fig. 16.20; T1, the spin– lattice relaxation time, and T1 the spin–lattice relaxation time in the rotating frame) were used to obtain activation energies of 9.4 (Ea) and 42.6 kJ/mol (Eb) for small and large angle reorientations respectively, to be compared with calculated values of 8 and 46 kJ/mol (Fyfe, Harold-Smith and Ripmeester, 1976); only T1 changes noticeably at Tc. The spin–lattice relaxation times (Fig. 16.20) were also used to estimate E (the energy difference between sites 1 and 2) as a function of temperature (Ripmeester, Ratcliffe et al., 102 Naphthalene – TCNB Tc

101 TI 10 MHz TI 25.3 MHz TIr 25.3 MHz HI = 22 G

TI 25.3 MHz 100 TI/sec TIr /sec 10–1 TIr 25.3 MHz H1 = 10 G 10–2

1000K /T 10–3 2

4

6

8

10

12

14

16

18

Fig. 16.20. Static (T1) and rotating frame (T1) 1H spin-lattice relaxation times measured for NAPTCB. (Spin–lattice relaxation times vs. 1000/T.) Dashed lines represent measurements from Fyfe, Harold-Smith and Ripmeester, 1976. (Reproduced from Ripmeester, Dalal and Reddoch, 1981.)

CRYSTAL (STRUCTURAL) PHYSICS

1112

1995). These values increase from 1.5 kJ/mol to 7.15 kJ/mol over the range 71.5–63K, and can be ﬁtted to E ¼ 6.72T þ 49.54 (R2 ¼ 0.99) (Fig. 16.20). Extrapolation gives Tc ¼ 73.7K (E ¼ 0), in good agreement with the value obtained from temperature of disappearance of the 323 superlattice reﬂection (Fig. 16.18; 73.5K; LOMML89). The anomalous increase of the speciﬁc heat occurs (on cooling) at 75K (Fig. 16.14(a)). Linear extrapolation, which seems inherently unlikely, would give E ¼ 49.5 kJ/mol at T ¼ 0K. The ratio of the occupancies of the two sites 1 and 2 is given by p2/p1 ¼ exp(E/RT) and can be calculated from the E–T dependence. At 71.4K, p1 ¼ 7.2%, falling to 0.2% at 68.6K and is essentially zero (i.e. complete ordering) at lower temperatures. LOMML89 measured p1 ¼ 4.8% from their 65K crystal structure analysis, using the heights of residual (difference) electron density peaks in the alternative orientation; possibly their temperature was slightly underestimated. A diagram of potential energy as a function of orientation of the naphthalene molecule in the unit cell is shown in Fig. 16.22 for the ordered and disordered phases. The correlation times (average time between instantaneous 36 jumps) have been measured by NMR (Ripmeester, Dalal and Reddoch, 1981), ESR (Grupp, Wolf and Schmid, 1982) and incoherent quasi-elastic neutron scattering (QNS) (Czarniecka et al., 1985). The values obtained by the different methods for the disordered structure all fall on the same straight line in a plot of log against 1000/T (Fig. 16.23). However, a distinct break occurs at Tc. The QNS measurements give an average residence time at room temperature of 8 ps. Density of states curves for the components and the molecular compound have been obtained by incoherent inelastic neutron scattering. The 15K ESR measurements of Erdle and Mo¨hwald (1979) showed that the triplet state was largely localized on naphthalene (Zt0.25 0.05) and that the normal to

8 ∆E

7

∆E (kJ/mol)

6 5 4 3 2 1 0 60

62

64

66

68

70

72

T (K)

Fig. 16.21. E (the energy difference between favorable and unfavorable orientations of naphthalene (sites 1 and 2) in the ordered phase) as a function of temperature for NAPTCB; these values were redrawn from those given by Ripmeester, Ratcliffe et al. (1995).

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1113

50 Energy (kJ/mol)

40

L

30

50

20

40

10 Ea

30 20

Disordered phase M

Eb

Ordered phase (~63 K) 1

2

10 –60

0

60 120 180 240 300 Clockwise angle of rotation of M axis from a sin direction (deg.)

360

Fig. 16.22. Potential for the reorientation of the naphthalene molecule in the disordered and ordered phases of NAPTCB; Ea, Eb and E are deﬁned in the text. is 36 . In the disordered phase, a particular naphthalene molecule is located in the isoenergetic (and hence equally populated) minima about 0 (and 180 ) and separated by . In the ordered phase these two minima no longer have equal energies (energy difference as function of temperature shown in Fig. 16.21) and one is favored and the other disfavored. (Adapted from Ripmeester, Ratcliffe et al. (1995).)

1 × 10–6 QNS ESR NMR

1 × 10–7 1 × 10–8 tau (sec) 1 × 10–9 1 × 10–10 1 × 10–11 1 × 10–12

2

4

6

8

10 12

14

16

1000/T (K–1)

Fig. 16.23. Correlation time as a function of temperature for NAPTCB. NMR measurements from Ripmeester, Dalal and Reddoch, 1981; ESR from Grupp, Wolf and Schmid, 1982; QNS from Czarniecka et al., 1985. The latter authors note . . . ‘‘we conclude that the correlation times determined by NMR and QNS methods corroborate each other, and we are inclined not to consider the difference in slopes of the NMR and QNS results as real..’’ Arrow marks Tc. (Adapted from Czarniecka et al., 1985.)

1114

CRYSTAL (STRUCTURAL) PHYSICS

the plane of the triplet state naphthalene molecules was tilted by 10 with respect to [001]. However, this tilt angle was less than 2 in the 65K structure. This indicates that formation of the excited state leads to a geometrical change, a phenomenon for which there is considerable evidence from other sources (Ponte Goncalves, 1977). (d) The phase transition in summary. A rather complete picture emerges when the results from the various experimental methods are concatenated. The transition can be inferred to be second order (in agreement with LOMML89) from the form of the speciﬁc heat curve (Fig. 16.14(a)) and from the absence of a discontinuity in cell volume at Tc (¼73.5K) (Fig. 16.15). At very low temperatures the naphthalene and TCNB molecules are completely ordered in space group P21/a, each moiety being located at a crystallographic centre of symmetry. The long axes of the two naphthalenes are 36 apart and their mean molecular planes are mutually tilted by 2 . The TCNB molecules are so located that they are all parallel, although this is not required by the space group. The temperature dependence of the intensity of a superlattice reﬂection indicates that the long range order begins to fall below its 0K value of unity as the crystal is heated. There is some disagreement about the temperature at which this becomes appreciable, one interpretation of the XRD measurements suggesting fairly low temperatures, while another suggests 65K, while NMR relaxation times indicate that this process occurs even closer to the critical temperature of 73K. The average energy difference between a naphthalene molecule favorably and unfavorably oriented at an inversion centre is 7kJ/mol at 63K, falling to zero at Tc and rising to some tens of kJ/mol at 0K. There is a second-order ‘order to disorder’ transition at 73K, accompanied by an anomalous additional speciﬁc heat corresponding to a measured entropy of transition of 3 0.3 J/mol K, which is very close to the expected value of 1/2R ln 2. As the temperature approaches Tc from below, the probability of ﬁnding an unfavorably oriented naphthalene molecule increases. Unfavorably oriented molecules lead to a decrease in the energy difference between sites with correctly and unfavorably oriented molecules, and this cooperative effect leads to complete loss of long range order as Tc is reached. The driving force for disordering on heating is the small energy difference between correctly and unfavourably oriented molecules in a particular lattice site, which decreases as the temperature approaches Tc from below. Above Tc the space group changes to C2/m, without change in cell dimensions. The site symmetry of the sites occupied by naphthalene and TCNB molecules increases to 2/m. This is achieved for naphthalene by statistical occupation of a particular site by the molecule in two orientations separated by 36 , while the orientation of the TCNB molecule (which hardly changes from that in the ordered structure) is now ﬁxed by the 2/m symmetry of its site. Above Tc the potential barrier between the two naphthalene orientations, which are of equal energy, is 8.0 kJ/mol. Nothing seems to be known about possible existence of short range order above Tc – in other words, the diffuse scattering in the diffraction pattern requires investigation. One anomaly awaits explanation – the pressure dependence of Tc. One can make an approximate calculation using the results given in Figs. 16.14(a) and 16.15 (‘approximate’ because of the nature of the experimental evidence) similar to that carried out for PYRPMA and this gives dTc/dP ¼ 31 K/kbar, contrary to the expectations from Fig. 16.6. No explanation has been offered.

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1115

16.5.3 The crystal structure of {Anthracene TCNB} and evidence for an order , disorder phase transition at 213K n n n

(a) Introduction. The molecular compound {anthracene TCNB} (ANTCYB) has been extensively studied. The speciﬁc heat has been measured by DSC (Fig. 16.14(b); Ecolivet, Bertault, Mierzejewski and Collet, 1987) and the anomalous region is remarkably similar in shape to that found for NAPTCB and shown in Fig. 16.14(a); Htrans ¼ 150 J/mol and Strans ¼ 0.7 J/mol K. The enthalpy of transition is similar to that found for NAPTCB (192 21 J/mol) but the entropy of transition is smaller by a factor of 4, again (as in PYRPMA) a reﬂection of the higher transition temperature. A Brillouin scattering study of the elastic anomalies at the phase transition conﬁrms that Tc ¼ 212 0.5K. This study also allowed determination, in the ordered phase, of the order parameter relaxation time as [5 1011/(Tc T)] s K1 (Ecolivet and Mierzejewski, 1990). n n n

(b) Crystallographic background. The crystal structure at 300K was ﬁrst determined by Tsuchiya, Marumo and Saito (1972) and structures above and below Tc ﬁrst by Stezowski (1980; crystal structures at 297, 234, 226, 202, 170, 138 and 119K), and then by LOMML89 (crystal structures at 294, 225 and 65K). There is a comprehensive series of cell dimension – temperature measurements for ANTCYB that show very weak cusps at Tc but no discontinuities (Fig. 16.24). These results show that the spontaneous strain in the ordered phase is almost entirely in the [100] direction. The disordered structure is isostructural with that of NAPTCB but the two ordered structures differ in the gross sense (as noted above) that the naphthalene molecules are in (102) planes but the anthracene molecules in ( 102) planes, and in a subtle sense in that the TCNBs in ANTCYB change their orientations slightly (by 2 ) on ordering but not in NAPTCB. Stezowski used his intensity measurements to calculate molecular libration amplitudes using the rigid body model. Electron density plots at the different temperatures were also calculated, from which the angles between various axes of symmetry-related molecules were obtained; these angles are in good agreement with values deduced from ESR measurements by Mo¨hwald, Erdle and Thaer (1978). However, this approach seems to ignore the essential order-disorder features of the system, as pointed out by Park and Reddoch (1981); in particular, the electron density plots and the (inferred) libration amplitudes will contain contributions from both thermal vibrations and disorder. The LOMML89 and Stezowski measurements of the superlattice (h þ k odd) reﬂection (140) and the fundamental reﬂection (240) are in excellent agreement; the different modes of temperature dependence of these different reﬂection types are shown in Fig, 16.25. A check on whether the superlattice reﬂections all show the same dependence of Fobs on T, as required by theory, shows a considerable spread and more closely spaced measurements like those made for (140) appear to be required. (c) ESR measurements of the order parameter as a function of temperature. The temperature dependence of the order parameter has also been determined by ESR and can be compared with the diffraction measurements. Measurements on the ESR spectra of the triplet excitons produced by optical irradiation of ANTCYB in its charge transfer band give the temperature dependence of the long range order parameter. Below Tc, for a

CRYSTAL (STRUCTURAL) PHYSICS

1116

ANTCYB TC a (Å)

9.50

12.75 7.45

b (Å) 12.70

7.40 12.65

c (Å) 7.35 7.30

93.0 (deg)

92.5

900 V (Å)

890

TC

880 870 50

100 150 200 250 300 T (K)

Fig. 16.24. ANTCYB – cell dimensions as a function of temperature, including 65K values (centered circles), are from LOMML89. The cell dimensions given by Stezowski (1980) at 297, 234, ˚ , 0.2 ) with those of 226, 202, 170, 138 and 119K are in satisfactory agreement (to within 0.01 A LOMML89. The curves are guides to the eye. 350 300 (240) fundamental

10 F (obs)

250 200

(140) superlattice

150 100 50 0 0

50

100

150 200 T (K)

250

300

Fig. 16.25. ANTCYB: Dependence of Fobs of the 140 superlattice and 240 fundamental reﬂections on temperature. The measured values are from LOMML89 and Stezowski (1980). The curves are guides to the eye.

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1117

general orientation, the ESR spectrum for each of the ms ¼ 1 transitions consists of two lines, corresponding to the ﬁne structure tensors of the two sublattices (which are related, as noted earlier, by the a glide plane). As the temperature is raised, these two lines approach and broaden, coalescing near Tc into a single line that becomes narrower at higher temperatures. The separation between the two lines gives the long range order parameter S ¼ S0(1 – 2p), where S0 would be the separation for a perfectly ordered crystal, and p is the fraction of sites occupied by unfavorably oriented molecules. This experiment was ﬁrst done for ANTCYB by Mo¨hwald, Erdle and Thaer (1978), who identiﬁed their order parameter with the angle between the long axes of the anthracene molecules. Park and Reddoch (1981) pointed out that this approach suffers from the same deﬁciencies as that of Stezowski. We quote from Park and Reddoch ‘‘An exciton moving rapidly along a chain [stack in our nomenclature] will then sample this disorder [of the orientations of the anthracene molecules along the stack]. In the fast limit the position of its resonance line will be the average of the lines for the two orientations, weighted by the relative populations within a given chain. Such a fast-limit resonance can thus shift with temperature, but need not broaden. If this fast moving exciton now jumps at a slow rate to a neighboring chain which is predominantly of opposite orientation, line broadening may be expected . . . One way to treat this problem is to consider a four-site exchange model with two rate constants and four sites, consisting of the two orientations in each of the two sublattices . . . The separation [of the lines] S is . . . a statistical average weighted by the number of correctly [xA] and incorrectly [xB] oriented anthracenes in the chain [(xA þ xB) ¼ 1]. Thus S ¼ S0 (xA – xB) ¼ S0(1 – 2xB) where S0 would be the separation for a perfectly ordered crystal.’’ Park and Reddoch derived xB (our p) from their experimental measurements as a function of 1/T and their values have been replotted as Q (¼S/S0) against T, to which we have added the XRD values of Q derived from reﬂection 140 (see Fig. 16.26, which should be compared with Fig. 16.25). There is excellent agreement between Q(ESR) and Q(XRD) (from 140) showing that both have the same functional dependence on T/Tc. We next plot log(IT/I0) against log(1 – T/Tc) (a form that allows direct comparison with the NAPTCB analog in Fig. 16.18) to test whether the power law equation (16.2) is applicable; Fig. 16.27 shows that a linear relation is not obtained. Park and Reddoch reported b ¼ 0.34 for the range 198–208.3K and made a comprehensive comparison of their experimental results with various theoretical treatments and came to the conclusion that the renormalization group calculation gave best agreement with their value for b. This is not surprising as there is evidence for the occurrence of ﬂuctuations in the temperature region for which their value was derived. Park and Reddoch determined the rate constant for interchain hopping as !12 ¼ [1.6 107 þ 1 1011 exp(Ea/kT)] s1, where Ea ¼ 1051 cm1 ( ¼ 12.6 kJ/mol). The second term was tentatively interpreted as due to scattering of triplet excitons by anthracene molecules undergoing large amplitude vibrations. Ea is the barrier between A and B orientations. The corresponding activation energy in NAPTCB was given as 9.4 kJ/mol. (d) The phase transition in summary. The weight of the evidence suggests that the driving force for the phase transition comes from intermolecular packing interactions, and

CRYSTAL (STRUCTURAL) PHYSICS

1118

1.00 Long range order parameter

0.90 0.80 0.70 0.60 0.50 0.40 0.30 0.20 0.10 0.00 0

50

100

150

200

250

T(K)

Fig. 16.26. ANTCYB – long range order parameter Q as a function of temperature. The open circles show values derived from the splitting of ESR lines and are replotted from Fig. 1 of Park Reddoch (1981); the dots show XRD values for Q(140) and are transferred from Fig. 16.25.

Q2

1.000

0.100

0.010 0.001

0.010

0.100

1.000

(1–T/215)

Fig. 16.27. ANTCYB – ESR and XRD values of Q2 plotted against (1T/Tc) (Tc ¼ 215K); the scales are logarithmic. The data are replotted from Fig. 16.26.

not from orientation dependence of charge transfer interactions. One important indication comes from the lowering of Tc in ANTCYB with increasing deuteration of anthracene (h10 – 214.5 ( 0.5) K; b-d4 – 202.5; -d4 – 201.5; d10 – 198.5), that has been ascribed (Dalal, Haley, Northcott, Park, Reddoch, Ripmeester, Williams and Charlton, 1980) to reduction in intermolecular repulsions on deuteration (d(CD) < d(CH)). A similar effect found for NAPTCB has already been noted. There are resemblances between the NAPTCB and ANTCYB situations but details differ. At the two equilibrium positions separated by an in-plane rotation angle of 16 () the average N . . . H distance is close to the

C R Y S T AL S WI T H S E C OND OR DE R P HAS E T R ANSFOR MATI ONS I N C OOLING 1119

sum of the van der Waals radii (in NAPTCB ¼ 36 , the average N . . . H distance again being close to the sum of the van der Waals radii). If the anthracene molecule took up an intermediate orientation at ¼ 8 , the closest N . . . .H non-bonded distances would be ˚ less than the sum of the van der Waals distances (0.28 A ˚ in NAPTCB). The 0.18 A ˚ difference of 0.1 A could lead one to expect dynamic disorder in ANTCYB instead of the static disorder found in NAPTCB. The potential energy curves calculated for an anthracene molecule librating in the ﬁeld of its nearest neighbours have been found to show a broad single-well minimum rather than the double potential well noted above for NAPTCB. The orientational probability function determined by LOMML89 shows a single maximum at ¼ 0 . The differences between the two structures have led LOMML89 to suggest that the phase transition at 213K has elements of both a ‘displacive’ and a ‘disorder to order’ transition. In this sense ‘displacive’ means that the molecules (here only anthracenes) undergo a continuous change in orientation as the temperature is lowered below Tc (this is similar to the points of view expressed by Mo¨hwald and Stezowski) while ‘disorder to order’ means that the fraction of molecules in the correct orientation for a particular sub-lattice increases as T falls below Tc. The matter is not yet settled. A semiquantitative analysis of the pressure dependence of Tc can be carried out using equation (16.4). From Figs. 16.14(b) and 16.24, we calculate dTc/dP ¼ 80 K/kbar; a measured value of 32 K/kbar has been reported (Ecolivet, Leme´e, Delugeard, Girard, Bertault, Collet and Mierzejewski, 1988). The agreement seems reasonable considering the difﬁculties of interpreting the speciﬁc heat curve (Fig. 16.14(b)) and of inferring values of @V/@T from Fig. 16.24, where the slopes must be measured close to Tc and not averaged over the whole 0–300K temperature interval, which would give zero slope difference. We shall not discuss the many preliminary theoretical calculations made on ANTCYB but give two leading references (Brose, Luty and Eckhardt, 1990; Kuchta, Luty and Etters, 1990). 16.5.4 Other examples of second order transitions There is clear evidence for two orientations for anthracene in {anthracene TCNQ} at 300K (Williams and Wallwork, 1968). These crystals are isomorphous with those of the disordered structure of {naphthalene TCNB}, with [001] stack axis in both examples. It seems reasonable to infer that {anthracene TCNQ} will show a disorder-to-order transition on cooling, perhaps also to space group P21/a without appreciable change of cell dimensions. Heat capacity measurements on {pyrene TCNB} showed an approximately symmetrical anomaly in the range 220–250K; the details were difﬁcult to reproduce even with samples of the same thermal history and there was facile supercooling of the 290K crystals down to at least 150K (Clayton et al., 1976). Thermal hysteresis of 40 has been reported and shattering of the crystals, on cooling through a transition at 183 3K. The crystal structures at 290 and 178K were found to be similar (Prout, Morley et al., 1973) and it is possible that supercooled crystals were used for the 178K diffraction measurements. The structure analysis showed the pyrene molecules to be azimuthally disordered and the TCNB molecules ordered; the available NMR measurements (Fyfe, 1974a, b) are not detailed enough for comparisons to be made n n n

n n n

n n n

n n n

1120

CRYSTAL (STRUCTURAL) PHYSICS

with the x-ray diffraction and Cp results. Further study is needed before conclusions can be drawn. There are also indications of pyrene disorder in {pyrene TCNQ} (Prout, Tickle and Wright, 1973). Low temperature phase transformations without change of crystal system have been demonstrated in {anthracene C6F6} and {pyrene C6F6} (see Bernstein (1967)) – these are probably disorder to order transitions. Measurements of reorientational motion of both components have been made in {pyrene C6F6}, using 19F in addition to proton resonance. The two molecules behave rather similarly. A decrease in the second moment of the 19 F line above 130K was attributed to onset of reorientation about the hexad axes of hexaﬂuorobenzene, which would not be detectable by x-ray diffraction or Cp measurements; such reorientation has been detected by NMR in {benzene C6F6} (Gilson and McDowell, 1966). The crystal structures of two polymorphs (yellow and orange) of {naphthalene PMDA}, which are presumably monotropically related, have been reported (LeBarsCombe et al., 1979). The crystal structure shows that the yellow polymorph is ordered at 293K; speciﬁc heat and Raman scattering measurements (Macfarlane and Ushioda, 1977) show that there are no transitions in the range 2–300K. Donor and acceptor molecules have their long axes parallel over the whole temperature range; such an eclipsed mutual orientation is unusual. In the orange polymorph, for which only crystallographic results are available, two orientations (separated by 42 ) are found for the naphthalene molecules at a particular site, with unequal populations of 72 and 28%. Although one might expect a disorder to order transition on cooling (perhaps analogous to that in {pyrene PMDA), none has been found in the range 300–148K. n n n

n n n

n n n

n n n

n n n

n n n

n n n

16.6 16.6.1

Crystals with ﬁrst order phase transformations on cooling {Cycl[3.2.2]azine TNB} n n n

The ﬁrst order transformation in {cycl[3.2.2]azine TNB} (orange needles elongated along [001]) is monoclinic to monoclinic (Table 16.4), with clear discontinuities in the cell dimensions at T ¼ 143 3K (Fig. 16.28) (Hanson, 1978). The transition was n n n

˚, Table 16.4. {Cycl[3.3.2]azine TNB} – unit cell dimensions (A deg.) at 293 and 91K. Describing the 91K structure in terms of a non-standard B-centered cell shows that the a and c dimensions have approximately doubled as a result of the transformation n n n

a b c b ˚ 3) V(A Z Space group

B 293K

A 91K

14.37(1) 15.99(1) 6.682(4) 92.17(5) 1534.3 4 P21/n

centered 28.474(15) 15.636(8) 13.102(6) 91.39(4) 5831.5 16 B21/d

primitive 15.528(8) 15.636(8) 13.102(6) 113.56(5) 2915.9 8 P21/c

CRYSTALS WITH FIRST ORDER PHASE T RANSFORMATIONS ON COOL ING 1121

cycl[3.2.2]azine N

92.5 A 1.01

a sin beta

A

B

B

92 beta

2a sin beta

beta

1.00 91.5 1.02

1.01

1.05 b

b

4V V

1.00

1.00

1.02 2 1.01

– 1(202)

– 1(404)

c sin beta

2c sin beta

1 – 1(505)

1.00

– 1(2.5 0 2.5)

0 100

200 T(K)

300

100

200 T(K)

300

Fig. 16.28 {Cycl[3.2.2]azine TNB} – variation of some crystal properties with temperature. B refers to the P21/n disordered structure and A to the B21/d ordered structure given in Table 16.4. Cell lengths and volume are expressed as multiples of the values at 91K; the temperature dependence of one fundamental reﬂection and one ‘‘superlattice’’ reﬂection is illustrated. (Adapted from Hanson, 1978.) n n n

reversible but there was a small hysteresis between the transition temperature on cooling (140K) and heating (146K); the transition was single crystal to single crystal. The 293K structure has mixed stacks of alternating cycl[3.2.2]azine and TNB molecules along [001]; the former take up three (or more) orientations in disordered fashion, and calculations suggest that there is no steric reason why the cycl[3.2.2]azine molecule should not rotate (presumably in hindered fashion) in its own plane. In the ordered structure the stack axis periodicity has doubled and the two TNB molecules differ in orientation by 12 ; the two cycl[3.2.2]azine molecules also take up (to a good approximation) two orientations. The two TNB molecules change their orientations slightly as the ordered form is heated, and become indistinguishable above 143K; at the same time the constraints on the orientations of the cycl[3.2.2]azine molecules are relaxed and these molecules rotate, at random, into their high temperature orientations. Some of these rotations are through angles as large as 134 . There are resemblances to the {pyrene PMDA} system. n n n

CRYSTAL (STRUCTURAL) PHYSICS

1122

100

CP /calth K–1 mol–1

80

4

60

40 2 20 0 0

100

10 200

20

0 300

T/K

Fig. 16.29. Measured heat capacity for {naphthalene TCNE}; the dashed line shows the lattice heat capacity. The splitting of the peak at 155K is shown at top left, and the (very) lowtemperature speciﬁc heat at lower right. (Reproduced from Boerio-Goates and Westrum, 1980a) n n n

16.6.2

Other examples

There are transformations from monoclinic room temperature structures to triclinic low temperature structures in {TMPD chloranil} (Boer and Vos, 1968), {naphthalene TCNE} (Bernstein, 1967) and {TDT5 TNB} (Williams and Wallwork, 1966). These are ﬁrst order transformations but may also have disorder–order features; low temperature crystal structures are not known. 14N NQR measurements show that there are two independent N atoms in {naphthalene TCNE} at 77K (Onda et al., 1973), which is compatible with the triclinic symmetry found by x-ray diffraction at a somewhat higher temperature. However, NMR measurements (Fyfe, 1974b) do not give any indication of the complicated phase behavior revealed by Cp measurements (Fig. 16.29; Boerio-Goates and Westrum, 1980a). n n n

n n n

n n n

n n n

16.7

Physical nature of the disordered phase

Disorder of one or other of the components is a not-unusual feature of mixed stack -molecular compounds. A key question is whether such disorder is static or dynamic. A condition of static disorder at low temperature may well change to one of dynamic disorder at higher temperature. It is perhaps worth emphasizing that it is much more difﬁcult to describe a disordered than an ordered state. The experimental methods available can be divided into three groups: (a)

Those sensitive to the presence of disorder, but not to reorientational motions. The principal methods are x-ray and neutron diffraction (as employed for crystal structure analysis by use of Bragg reﬂections). (b) Those sensitive to reorientational motions but not to the presence of disorder. NMR line width and spin–lattice relaxation time measurements come into this category. 5

2,4,6-tris(dimethylamino)-1,3,5-triazine

PHYSICAL NATURE OF THE DISORDERED PHASE

1123

(c) Those sensitive both to disorder and to reorientational motion. Raman scattering and the behavior of triplet excitons are suitable methods. Elastic and inelastic scattering of neutrons are also powerful techniques in the study of phase transformations (Axe, 1971) but have hardly been applied as yet to the study of -molecular compounds. The most direct method of demonstrating the occurrence of disorder is via x-ray (or neutron) crystal structure analysis, particularly if the molecular compound has been studied at only one temperature, the most common current situation. Under these circumstances the disorder is revealed by the atoms of one or other of the components having abnormally large displacement factors. The room temperature structure of {naphthalene TCNE} (P21/a, Z ¼ 2, both components at centers of symmetry) provides a convenient example (Williams and Wallwork, 1966), which has been much discussed. The atomic displacement factors are much larger for naphthalene than for TCNE (Fig. 16.30) and the difference increases for atoms at the periphery of the molecule, suggesting large librational motions, or static disorder. These results can be shown in another way through electron density and difference electron density syntheses; the electron density synthesis is essentially independent of any postulated model. A comparison is made for the disordered naphthalene and ordered TCNE molecules in Fig. 16.31. Two models can be postulated at this stage: n n n

(a) large in-plane librations of naphthalene about the normal to the molecular plane, corresponding to the dynamic disorder deﬁned above, (Fig. 16.32(a)); or (b) static disorder of naphthalene in two orientations (Fig. 16.32(b)).

Individual Debye–Woller factors (Å2)

16 C5

14 Naphthalene (300 K)

12 10 8

C4

6

C3

4 C1 2

C2

N TCNE (300 K)

0

1 2 3 Distance from mol. center (Å)

4

Fig. 16.30. The equivalent isotropic atomic displacement factors for the individual atoms in {naphthalene TCNE} at room temperature, plotted against the distance of the atom from the molecular centre. Separate curves are shown for the two molecules (naphthalene – C3 to C5; TCNE – C1 to N). (Reproduced from Herbstein and Snyman, 1969.) n n n

1124

CRYSTAL (STRUCTURAL) PHYSICS

0

0

1Å

1Å

Fig. 16.31. Electron density and difference syntheses in the planes of (a) naphthalene and (b) TCNE molecules in the crystals of {naphthalene TCNE} at room temperature. The contours of electron ˚ 3 and start at 0 eA ˚ 3, while the contours of difference density are at density are at intervals of 1 eA 3 ˚ intervals of 0.5 eA (thick lines zero and positive contours, thin lines negative contors). Two naphthalenes, mutually rotated by 12 , give a reasonable ﬁt to the electron density and difference density contours. (Reproduced from Herbstein and Snyman, 1969.) n n n

A distinction can be made between the two models by calculating the potential energy (PE) curves for libration of the naphthalene molecule in the {naphthalene TCNE} structure (Shmueli and Goldberg, 1974). The complete PE calculations show minima at two orientations separated by 90 in-plane rotation (the N atoms of TCNE lie nearly at the n n n

PHYSICAL NATURE OF THE DISORDERED PHASE

(a)

1125

(b)

Fig. 16.32. {Naphthalene TCNE} – ORTEP diagrams illustrating (a) dynamic disorder (b) static disorder. (Reproduced from Shmueli and Goldberg, 1974.) n n n

corners of a square). The ﬁrst orientation has a double well, indicating model (b). The second orientation is 8 kJ/mol higher in energy and is not populated in {naphthalene TCNE}. However, in {[3,3]paracyclophane TCNE} these two positions are occupied in 3 : 1 ratio (Bernstein and Trueblood, 1971) and in {(d8-pyrene) TCNE} at 105K in 93 : 7 ratio (Larsen et al., 1975), corresponding to at least 2.3 kJ/mol energy difference between the potential minima. Supporting evidence for static disorder in {naphthalene TCNE} came from the results of a constrained reﬁnement of the x-ray diffraction data, in which the molecules were treated as rigid bodies of standard dimensions whose translational and librational motions were reﬁned. The constrained reﬁnement gave an R-factor of 9.0%, compared to 12.8% for a conventional reﬁnement, in which positions and anisotropic displacement factors of the individual atoms were reﬁned. The physical reason for favoring static disorder is that N. . . . H contacts are more repulsive for model (a) than (b), a situation similar to that illustrated above for {naphthalene TCNB} (Fig. 16.16). Two points should be noted about the calculations of librational potential energy. Firstly changes in charge transfer energy as a function of libration angle have been neglected; quantum mechanical calculations (Kuroda, Amano et al., 1967) indicate that the charge transfer interaction energy between naphthalene and TCNE increases by only 0.4 kJ/mol when naphthalene is rotated in-plane by 12 from the model (a) structure. Secondly, as Shmueli and Goldberg (1974) point out, the possible relaxation of the surroundings of a molecule during its libration was not taken into account in their PE calculations. Such correlation of molecular motions was included in later calculations by Allen, Boeyens and Levendis (1989). The disorder discussed above is a thermodynamic disorder characteristic of the equilibrium state of the crystal and thus temperature dependent. However, there are also some examples of nonequilibrium disorder, presumably frozen-in during growth of the crystals, and thus dependent on their history and not alterable by changes in temperature. One could expect two orientations, widely separated in azimuth, for one (or both) of the components, possibly unequally populated and perhaps not interconvertible by in-plane rotation. This type of disorder has been postulated for {azulene TNB} (structure determined at 300K (Brown and Wallwork, 1965) and 178K (Hanson, 1965)) and for {indole TNB} at 133K. However, the evidence does not seem to be conclusive – in {azulene TNB} there are indications of a phase change at lower temperatures, while in {indole TNB} the existence of the disorder depends on a distinction made between C and NH groups. A more established example is provide by depends on a distinction made between C and NH groups. A more established example is provide by {benzo[c] n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

n n n

CRYSTAL (STRUCTURAL) PHYSICS

1126

phenanthrene DDQ} where there is disorder of the Cl and CN groups in the acceptor (Bernstein et al., 1977). Orientational disorder must certainly occur in the quasi-plastic phases of charge transfer molecular compounds (Section 16.8) and substitutional disorder in the solid solutions discussed earlier (Section 13.4) but detailed studies have not yet been reported in either of these areas. n n n

16.8

Transformations to quasi-plastic phase(s) on heating

The occurrence of disorder to order transformation on cooling in many charge transfer molecular compounds has been noted above. Conversely, it has been found that many charge transfer molecular compounds transform on heating to a quasi-plastic phase stable at temperatures close to their melting points (Inabe et al., 1981; see also Section 13.4). The systems investigated and the results obtained are summarized in Fig. 16.33(a). Three donors (pyrene, ﬂuoranthene and phenanthrene) have been studied in combination with (a) A D Py

DNF

DNC

DNP

DNT

TNB

TNC

TNP

TNT

NPA

PMDA NBF

DNBF

BTF

st

st

st

st

st

st

st

st

st

st

st

st

st

st

st

st

st

st

st

mst

st

st

st

mst

mst

st

Fl

st

Ph F

Cl

OH

Py

NO2

DNF

DNC

DNP

TNB

O

TNC

CO O CO

OC OC

N

O2N

PMDA

NBF

O

O2N

N N

O DNBF

CO O CO

O2N

TNT NO2

N

CH3 NO2 NO2

TNP

O Ph

O2N

NO2

NO2 F1

NO2

O2N

NO2

O2N

DNT

OH NO2

O2N

NO2

NO2

Cl

NO2

CH3 NO2

NO2

NO2

NO2 NO2

st

NPA O NO N N

O

O

N N O NO

O

BTF

Fig. 16.33. (a) The -molecular compounds that give isomorphous quasi-plastic phases on heating, and the structural formulae of the compounds; ‘st’ refers to stable and ‘mst’ to metastable molecular compounds. (b) The structure proposed for the quasi-plastic phases. The molecules located at 000 and 2/3,1/3, 1/3 are different from those at 00,1/2; 2/3, 1/3, 5/6 and 1/3, 2/3, 1/6. (Reproduced from Inabe et al., 1981.)

TRANSFORMATIONS TO QUASI-PLASTIC PHASE(S) ON HE AT ING

1127

(b)

Fig. 16.33. (Continued )

6 4 2

a

b

c

d

e

f

g h

i

0 6 Second moment/G2

4 2 0 6 4 2 0 6 4 2 0 –50

50

150

–50

50

150

t/°C

Fig. 16.34. Second moments of the proton resonance for the ﬂuoranthene compounds with (a) DNP; (b) TNB; (c) TNC; (d) TNP; (e) TNT; (f) NPA; (g) PMDA; (h) DNBF and (i) BTF. The vertical arrows indicate the transition temperatures to the quasi-plastic phases. (Reproduced from Inabe et al., 1981.)

13 different acceptors; of the 39 possible combinations, 28 transform to quasi-plastic phases characterized by very simple Debye–Scherrer x-ray diffraction patterns, of the type illustrated in Fig.13.9(b) (P and I@ ). The crystal structure proposed for the isomorphous quasi-plastic phases is shown in Fig. 16.33(b); the donor–acceptor stacks continue to exist

CRYSTAL (STRUCTURAL) PHYSICS

1128

but both donor and acceptor molecules are supposed to be azimuthally disordered so that the differences between the various donors, on the one hand, and the various acceptors, on the other, are eliminated by the rotational disorder. Such rotational disorder is feasible because of the disk-like shapes of the donor and acceptor molecules. The proton NMR spectra (Fig. 16.34) indicate that the disorder is dynamic rather than static; the second moments at lower temperatures (4 G2) are consistent with those crystal structures that are known, while the much reduced values of 1 G2 above the temperatures of transition to the quasi-plastic phases are consistent with rotation of the donor molecules in their own planes (there are too few protons in the acceptors for conclusions to be drawn about their state of motion). Another indication of the quasi-plastic nature of the high-temperature phases comes from the values measured for the entropies of transformation to these phases, which range up to 57 J/K mol and are comparable with the entropies of fusion of many of the compounds (46–67 J/K mol). Similar results have been obtained in a high-temperature infrared study of {pyrene 4nitrophthalic anhydride} (Swamy et al., 1983). n n n

16.9

16.9.1

Transformation of the ground state from neutral ) ionic on cooling and/or application of pressure (NI transitions) Introduction

We have already noted in Chapter 13, following McConnell, Soos and Torrance and their coworkers, that crystalline 1 : 1 mixed stack -molecular compounds are quite sharply divided into those with nominally neutral and those with nominally ionic ground states. However, some of the nominally neutral group are close to the neutral–ionic border (Fig. 13.2) and ten of the compounds in Table 13.1 (those with values of Pc appended) have been shown to transform reversibly to an ionic state on the application of pressure (pressure-induced NIT or PINIT; Torrance, Vasquez et al., 1981), as could well be expected on the basis of McConnell’s original ideas.6 The transformation pressure was determined as the onset of a distinct colour change from yellow or green (neutral) to red or brown (ionic). This phenomenon of a neutral , ionic transformation in the solid state has received considerable attention. Originally {TTF chloranil} was the only example of a transition induced on cooling (temperature-induced NIT or TINIT) but others have since been added, most having 1:1 ratios and being composed of TTF and chloranil derivatives or analogs. Transition temperatures are mostly below 100K, while transition pressures are a few kbar; the ionic states achieved by cooling or pressure may well differ in detail. Spectroscopic techniques are usually employed to show that a transition does occur and permit inferences about its nature. Diffraction studies appear mandatory for a proper understanding of the system but are still quite rare. The transition can also be photo-induced (Tanimura and Koshihara, 2001) but this will not be discussed here. Experiment shows that both ﬁrst-order and second-order NITs are found. Most n n n

6 Girlando, Painelli et al. (1993) state that investigations carried out on members of the original series have not conﬁrmed the occurrence of transitions. Discontinuous NI transitions have been found only for TTF-CA, TTF – ﬂuoranil and tetramethylbenzidine – TCNQ.

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1129

information is available for {TTF chloranil} (summarized by Le Cointe, Lemee´Cailleau, Cailleau and Toudic, 1996; see also Bernstein (2002), pp. 195–197); this is one of the few organic crystals to have been studied over a range of temperatures and pressures and by a variety of experimental techniques. We shall ﬁnd that there are two primary parameters describing (perhaps determining) the occurrence of a transition and its nature. The ﬁrst is the charge transfer from neutral to ionic state, leading to a difference in ionicity between the two states. The N state has an ionicity of about 0.3 (quasi-neutral could be a preferable descriptor) and that in the I state is larger. The second parameter is the degree of dimerization – donor and acceptor molecules are equally spaced along the stack axis in the N state but unequally spaced in ˚ or less, dimerization is an the I state. As the difference between the two distances is 0.2 A unfortunate term but too well-established to be dislodged; some schematic diagrams should be viewed with caution. The ionicity is best determined spectroscopically and the degree of dimerization from comparison of N and I crystal structures. n n n

16.9.2 {TTF

n n n

chloranil}

The ﬁrst study of the molecular compound (needles crystallized from acetonitrile) showed a mixed stack, neutral ground state crystal structure at 300K (a ¼ 7.411, b ¼ 7.621, ˚ , b ¼ 99.20 , P21/n, Z ¼ 2; stack axis [100]; degree of charge transfer c ¼ 14.571 A 9 20%; Mayerle et al., 1979; TTFCAN). In parallel studies, powder patterns (temperature range 10–300K at 1 bar) were indexed in terms of the same unit cell throughout; no additional reﬂections appeared on cooling to 4K nor was there evidence for a triclinic distortion. There were also cell dimension measurements, from single crystals at 300K, over the pressure range 0–20 kbar. Distinct changes of slope were seen at 84K and 1 bar, which was identiﬁed as the 1 bar neutral , ionic transformation temperature, and at 11 kbar and 300K, identiﬁed as the 300K neutral , ionic transformation pressure.7 This work was followed by a detailed neutron diffraction study using co-sublimed crystals (Le Cointe, 19948; Le Cointe, Lemee´-Cailleau, Cailleau, Toudic, Toupet et al., 1995; TTFCAN); other techniques (CP–T, 35Cl NQR, IR and Raman spectroscopy) were also used. The cell dimensions at various temperatures and pressures (up to 5 kbar) are shown in Fig. 16.35 (Le Cointe, 1994); at atmospheric pressure there are abrupt changes in [010] and [001] around 81K, and to a lesser extent in b and V, while [100] is continuous. The P–T phase diagram derived from these (and other) measurements (Leme´e-Cailleau, Le Cointe et al., 1997) is shown in Fig. 16.36. The space group below 84K is determined by the behaviour of the 030 reﬂection which is systematically absent above 84K.9 The intensity of this reﬂection increases 7 Some of the earlier results must be treated with caution. We give a few examples. Batail et al. (1981) give a curve of cell volume against T with a cusp at 84K, i.e. V ¼ 0 (their Fig. 1). This suggests that the NI transition is second order, contrary to all later views. Unfortunately the later neutron diffraction measurements are not complete enough to allow calculation of V–T curves. Kagoshima et al. (1985) give a (heating) curve (their Fig. 2) of I (31 1) against T with an abrupt fall to zero at 78.5 (5)K; it is not clear how this can be reconciled with the known structures. 8 I am grateful to Dr Marylise Buron-Le Cointe for a copy of her doctoral thesis (University of Rennes I). 9 Le Cointe, Lemee´-Cailleau, Cailleau, Toudic, Toupet et al., 1995; (see III B#2, Ionic phase; p. 3378) remark that ‘‘only the (070) superstructure reﬂection was clearly extracted from the background’’; however, it is the temperature dependence at 1 bar of I(030) that is shown in Fig. 2(a) of this reference. The temperature and pressure dependence of I(030) is shown in Fig. 3 of Le Cointe (1994), from which our Fig. 16.37 has been adapted.

CRYSTAL (STRUCTURAL) PHYSICS

1130

7.4 1 kbar

7.35 7.3

2.55 kbar 1 bar

a (Å)

7.25

5 kbar

7.2 7.15 7.1 7.05 – 7.62 7.6

1 kbar

7.58

2.55 kbar

b (Å)

7.56

5 kbar

1 bar

7.54 7.52 7.5 7.48 7.46

0

50

100

150 200 T(K)

250 300

14.51

c(Å)

14.5 14.49 14.48 14.47 79

80

81

82 83 T (K)

84

85

8

Fig. 16.35. The temperature and pressure dependence of the cell dimensions of TTF-CA (values for [001] were given only for the temperature range shown; b is 99.1 at 300K and 98.6 at 50K (both at 1 bar). From Le Cointe (1994).

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1131

1500 TTF-CA 1000 P(MPa)

Ipara Iferro C

500

Npara

0 100

200

300

T (K)

Fig. 16.36. TTF-CA pressure-temperature phase diagram – circles ND, squares NQR, diamonds vibrational spectroscopy. The subscripts para and ferro are abbreviations for paraelectric and ferroelectric. C is the estimated critical point. Lines are guides to the eye. (Reproduced from Leme´eCailleau, Le Cointe et al., 1997.)

Integrated intensity of (030) reflection (arbitrary units)

6 5 4 3 1 bar 2.55 1 kbar kbar

2

5 kbar

1 0 0

50

100

150

200

250

300

T(K)

Fig, 16.37. Neutron diffraction intensity of TTF-CA (030) reﬂection as a function of temperature and pressure. (Adapted from Le Cointe (1994).)

monotonically with falling temperature; similar behaviour is found over the range 0 to 5 kbar (Fig. 16.37). Thus the transition involves a change of space group from P21/n, Z ¼ 2 (N phase) to Pn, Z ¼ 2 (I phase). In the N phase the D and A molecules are located at centres of symmetry but this requirement is relaxed in the I phase. Conﬁrmation of the loss of centrosymmetry comes from the 35Cl NQR spectra – two independent resonances in the N phase and four in the I phase (Gallier et al., 1993; Gourdji et al., 1991; Le Cointe, Gallier et al., 1995). The shape of the curves of I(030) against T (Fig. 16.37) requires some comment. These start out as though the transition was second order (cf. Fig. 16.25) and then fall abruptly to

1132

CRYSTAL (STRUCTURAL) PHYSICS

Table 16.5. Calorimetric measurements on TTF-CA Reference

H J/mol

S J/mol K

Kawamura et al. (1997) Leme´e-Cailleau et al. (1997)

504(5) 461(32)

6.12(6) 5.49(9)

Note: S measured on 0.2 mg samples was given as 4 J/mol K (Wolfe, 1982).

TTF-CA T≈70 K b I

N

a 100 µm

Fig. 16.38. TTF-CA – coexistence of the N and I phases at 70K observed by optical microscopy with unpolarized light. (Reproduced from Buron-Le Cointe et al. (2003; Fig. 6).)

zero, as one would expect for a ﬁrst order transition. The overall shape, which appears to be qualitatively the same up to at least 5 kbar, is reminiscent of that found for long range order in Cu3Au (see Fig. 12.4 of Warren (1969)). There are a number of measurements of speciﬁc heat for TTF-CA; Kawamura et al. (1997) found a single peak while Leme´e-Cailleau, Le Cointe et al. (1997) found a split peak in the same temperature region; nevertheless, the transition enthalpy and entropy values are in reasonably good agreement (Table 16.5) and the thermodynamic parameters are in the expected range for a ﬁrst order transition. The Clapeyron equation (dP/dT ¼ H/TcV, where dP/dT is the slope at Tc) provides a test of various interrelated quantities. A precise value of dP/dT ( ¼ 4.17 Mpa/K) is obtained from Fig. 16.36 and Tc is precise at 81K. However, neither H nor V is that precisely deﬁned. We have estimated V from the cell dimensions above ˚ 3 (Leme´e-Cailleau, Le Cointe et al. and below Tc (Fig. 16.35) and obtain V ¼ 7.2 A 3 ˚ ). Using a mean value for H (Table 16.5) we obtain (dP/dT) calc ¼ (1997) give 4–5 A 1.37 Mpa/K, some 40% of the phase diagram value. Leme´e-Cailleau, Le Cointe et al. (1997) give a phase diagram value of 3.1 Mpa/K (3.6 Mpa/K from Fig. 8 of Le Cointe (1994)) and a derived value of 3.2 0.4 Mpa/K. The source of the discrepancies is not known. Buron-Le Cointe, Leme´e-Cailleau et al. (2003) show a micrograph of a TTF-CA needle crystal in which the interface ((010) plane) between the N and I phases can be clearly seen in Fig. 16.38. This is an example of Mnyukh’s (2001; see pp. 121–143 and Figs. 2.34 and 2.43) category of epitaxial growth when the two phases resemble one another. The hysteresis and related phenomena can all be described in terms of Mnyukh’s treatment of ﬁrst-order enantiotropic phase transitions (see his Fig. 2.30) and have no direct connection with the neutral-to-ionic nature of the phase transformation.

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1133

The details of the crystal structures of the N and I phases of TTF-CA (Le Cointe, Lemee´-Cailleau, Cailleau, Toudic, Toupet et al., 1995) require some comment. The N phase structure was determined by neutron diffraction at 300 and 90K; we consider only the 90K results (1223 independent reﬂections, R ¼ 3.4%, 118 parameters, goodness of ﬁt 1.40, all nonhydrogen atoms reﬁned anisotropically). Both component molecules have D2h–mmm symmetry within the precision of the measurements; bond lengths and angles have standard values. The I phase structure was determined by neutron diffraction at 40K (1636 independent reﬂections, R ¼ 5.0%, 105 parameters, goodness of ﬁt 1.48, all atoms reﬁned isotropically). There are large differences between chemically equivalent bonds; for example, the (intraring) C ¼ C bond lengths in ˚ , with / ¼ 29. Thus either there is a TTF are given as 1.323(1) and 1.364(1) A remarkable (and unprecedented) polarization effect in the I structure or the standard uncertainties have been underestimated by a factor of about 10;10 the second alternative seems more likely. Le Cointe, Lemee´-Cailleau, Cailleau, Toudic, Toupet et al. (1995) give considerable attention to differences in some intermolecular distances between N and I structures. They also assign NQR frequencies to speciﬁc Cl atoms in the I phase ˚ , all with s.u.s on the basis of C–Cl bond lengths (d(C–Cl) ¼ 1.724, 1.705,1.711,1.714 A of 0.001 A). These differences are less impressive if the true standard uncertainties are ˚. 0.01 A The main difference between N and I structures lies in the separation of the TTF and CA molecules along the [100] stack axis; these (center to center, not plane to plane) ˚ (at 90K, ¼ a/2) but unequal at 3.50 and distances are equal in the N structure at 3.61 A ˚ 3.69 A in the I structure at 40K. This alternation is called ‘dimerization’. Batail et al. (1981) pointed out that there was C–H . . . O hydrogen bonding along the [001] direction, at a time when such bonding was controversial. However, it seems disputable that the transformation is due to changes in C–H . . . O hydrogen bonding because hydrogenated and deuterated molecular compounds transform in essentially the same way (Ayache and Torrance, 1983), On the other hand, Oison et al. (2001) contend that charge transfer produces a strengthening of these hydrogen bonds. Lack of precision prevents the use of component dimensions to estimate the degree of charge transfer (ionicity) in the I phase, and this must be done by spectroscopic techniques (see below). The temperature (Girlando et al., 1983) and pressure (Tokura et al., 1986; Girlando et al., 1986) induced neutral to ionic phase transitions in {TTF chloranil} have been studied by IR spectroscopy (Fig. 16.39). The differences between the spectra of the neutral and ionic phases are shown by comparing the upper spectrum with those in the centre and lower positions. The resemblances between temperatureinduced and pressure-induced ionic phases is shown by a comparison of centre and lower parts – the low-temperature and high-pressure ionic phases are, at least, very similar in nature. The Le Cointe 300K ND measurements (Fig. 16.35, up to 5 kbar) indicate a ﬁrst order transition but one that deviates somewhat from classic expectations. These measurements show a linear dependence of a and b cell dimensions on pressure in both phases; the values n n n

10 Le Cointe et al. (1995) remark ‘‘ . . . the standard deviations have particularly small values at 40K, which can be explained as an effect of the isotropic reﬁnement.’’ It does not seem reasonable that a structure reﬁned isotropically (even at lower temperature) will be more precise than one reﬁned anisotropically, conditions of measurement being essentially the same.

CRYSTAL (STRUCTURAL) PHYSICS

1134

TTFCAN–neutral phase at 1 bar, 300K

Absorbance

PINI at 11 Kbar, 300 K

TINI 1 bar, 15 K

1800

1400

1000 – –1 v/cm

600

Fig. 16.39. IR spectra of {TTF chloranil}. (top), the neutral phase at room temperature and pressure; (center) the ionic phase at 300K and 11 kbar; (bottom) the ionic phase at 15K, 1 bar (Girlando et al., 1986). The spectra shown in the centre and lower panels were obtained with polarized IR – full line, electric vector parallel to stack axis; dashed line, perpendicular to it). The resemblance between the central and lower spectra implies that the same ionic phase is obtained by cooling to 15K at 1 bar and by compression to 11 kbar at 300K. (Reproduced from Girlando et al. (1986).) n n n

˚ /kbar in the N and I phases, and the corresponding of da/dP are 0.041 and0.025 A values for the b dimension are 0.013 and 0.012 respectively. At 1 bar the (020) reﬂection shows deﬁnite hysteresis between heating and cooling curves (Fig. 16.40; this is also found by other techniques such as 35Cl NQR and speciﬁc heat measurements), in

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1135

7.58 7.57

b(Å)

7.56 7.55

1 bar: Hysteresis

TTF-CA (URennes) EFFECT OF PRESSURE ON HYSTERESIS

7.54 7.53 7.52 7.51 75

77

79

81

83

85

T(K) 7.6

1 kbar

7.58

2.55 kbar

b(Å)

7.56

5 kbar

1 bar

7.54 7.52 7.5 7.48 7.46 0

50 100 150 200 250 300 T(K) 7.54

b(Å)

7.53

5 Kbar: No hysteresis

7.52 7.51 7.5 195

200

205 T(K)

210

215

Fig. 16.40. The effect of pressure on the TINI in TTF-CA. The central panel is taken from Fig. 16.35, while the upper and lower panels are from the Le Cointe (1994) thesis (Figs. 7 and 16). The ﬁlled circles are for the heating regimen and the open circles for cooling.

contrast to what is found at 5 kbar (Fig. 16 from Le Cointe (1994)), where there is no hysteresis. This conﬁrms the ﬁrst order nature of the transition at 1 bar and suggests that the transition at 5 kbar is second order. If so, the tricritical point in the phase diagram (Fig. 16.36) must be shifted.

CRYSTAL (STRUCTURAL) PHYSICS

1136

7.5 7.4

Neutral

a (300K) (Å)

7.3 7.2 Intermediate region

7.1 7

Ionic

6.9

11 kbar 6.8 0

5

10

1700

15 P (kbar)

20

25

CA° 0.0 0.2

Wavenumber (cm–1)

N

0.4

I1

0.6 1600 TTF-CA

0.8

I2 1.0 K 1500

0

10

+

CA–

20 Pressure (kbar)

30

Fig, 16.41. Upper panel: Diffraction study of PINI transition in TTF-CA at 300K; the diagram has been redrawn from Metzger and Torrance (1985) who quote results (‘‘to be submitted’’) of King et al. The King results do not appear to have been submitted. Lower panel: frequencies of the C¼O stretch band at 290K as a function of hydrostatic pressure; the pressure dependences for neutral chloranil and for KþCA were used for calibration purposes. Approximate values deduced for the ionicity are shown by the right-hand ordinate (Tokura et al., 1986). (Adapted from Metzger and Torrance (1985) and Tokura et al., (1986).)

The PINI transition at 300K, 11 kbar is shown by diffraction (the variation of the [100] cell dimension with pressure; upper panel of Fig. 16.40) and by IR spectroscopy (lower panel of Fig. 16.41; Tokura et al., 1986); the transition is essentially ﬁrst order but neither diffraction nor spectroscopy shows an ideally sharp transition. Some care is needed in the preparation of {TTF chloranil} as it crystallizes from solution as plates or needles, and, by co-sublimation, as parallelepipeds of up to 20 mm3 in n n n

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1137

volume (Kawamura et al., 1997). It is the structure of the co-sublimed form (also obtainable from solution) that is discussed above. Two other phases of {TTF chloranil}, named as I and II, have been reported; I and II both appeared as black needles, with phase II shown to have a 1 : 1 composition, and this was presumed to hold also for phase I (Matsuzaki et al., 1983). The analogous black ‘‘snowﬂakes’’ (Girlando et al., 1983) appear, from comparison of 300K IR spectra, to be essentially II, perhaps with a small contamination of I. Kawamura et al. (1997) noted that their speciﬁc heat measurements required correction for the presence of more than one phase. It was inferred (Girlando et al., 1986) that phase I was a mixed valence ionic solid but detail is lacking. Phase II is a fully ionic solid containing (TTFþ)2 and (CA)2 self dimers, present either in distorted stacks or as discrete units (e.g. as in TTF.Br) (Girlando et al., 1986; Matsuzaki et al., 1983); IR and Raman spectra show that there is no phase transition between 300 and 15K (Matsuzaki et al., 1983). Electronic spectra for {TTF bromanil} suggest that phases I and II are also found in this system. No crystallographic information is available for these phases. n n n

n n n

16.9.3 {DMTTF chloranil} n n n

A TINI transition at 65 5K in {2,6-dimethyltetrathiafulvalene chloranil} was ﬁrst proposed by Aoki et al. (1993) on the basis of studies of polarized visible reﬂection and IR spectra; a ‘‘most striking feature’’ was the appearance of a coexisting neutral-ionic phase at lower temperatures. Deﬁnitive structure determinations at 300, 75 and 45K by x-ray diffraction (Collet et al., 2001) clariﬁed earlier confusions (Nogami et al., 1995) about the low temperature structure. Cell dimensions are given in Table 16.6; there is excellent agreement among the three independent 300K measurements and this applies also to the two crystal structure determinations. Nogami et al. have reported unusual behaviour of the cell dimensions at low temperatures (their Fig. 2, reproduced here as Fig. 16.42); the Collet values at 75 and 40K agree well with those Nogami, thus suggesting that the full set of Nogami cell dimensions can be relied upon to give valuable information about the nature of the transition. Information about the nature of the transition is also obtained from spectroscopy. The optical conductivity spectra for the C ¼ O stretch mode are shown in Fig. 16.43(left), while the wave numbers of the peaks of the spectra at different temperatures are shown in Fig. 16.43(right). The transition is not abrupt but is spread over some 50K, suggesting that it is second order. Similar conclusions can be drawn from the temperature dependence of the IR spectra of DMTTF-CA (Fig. 16.44) and from the cell dimension–T curves (Fig. 16.41), The low temperature phase has a unit cell doubled along [001] with noncentrosymmetric space group P1; thus there are two crystallographically independent molecules of each component in the unit cell. Detailed crystal structures have been reported by Collet et al. at 300, 75 and 40K. We compare the 75K (2395 independent reﬂections, R ¼ 2.82%, 125 parameters, goodness of ﬁt 1.04, all nonhydrogen atoms reﬁned anisotropically) and 40K (4693 independent reﬂections,11 R ¼ 3.44%, 485 parameters, n n n

11 2777 with F20 > 2(F20); 2362 of the 4693 were superstructure reﬂections, 765 with F20 > 2(F20). In the 40K determination the coordinates of one atom should have been ﬁxed and the Friedel parameter should have been included in the reﬁnement. The low internal R value for Friedel opposites (2.16%) suggests the possibility of polysynthetic twinning.

CRYSTAL (STRUCTURAL) PHYSICS

1138

˚ , , A ˚ 3) for DMTTF-CA from various sources and at Table 16.6. Cell dimensions (reduced cell; A different temperatures. The space group is P1, Z ¼ 1 at all temperatures except for 40K, where it is P1, Z ¼ 2 T(K)

a

b

c

V

Reference

300 300

7.272 7.285

7.666 7.678

8.512 8.521

95.91 95.90

103.89 103.89

91.89 91.91

457.4 459.4

300 75 75 40# 40

7.269 7.121 7.118 7.099 7.090

7.673 7.586 7.581 7.563 7.556

8.514 8.476 8.464 16.937 8.450 X2

95.87 95.87 96.00 95.77 95.83

103.91 104.07 104.02 104.21 104.17

91.87 90.92 90.83 91.02 90.98

457.2 441.4

Aoki et al. (1993) Horiuchi et al. (2001); UDEQUP01 Collet et al. (2001) Collet et al. (2001). Nogami et al. (1995)* Collet et al. (2001). Nogami et al. (1995)*

876.2

* Values read off Fig.2 of Nogami et al.; volumes deliberately omitted. ˚ , 83.78 79.84 88.99 . # Reduced cell 7.100 7.564 16.680 A

b

0 Lattice parameter increment [%]

c 0 a –1 b

d

–2 a

0

100

–1

200

Temperature [K]

300

0

100

200

300

Temperature [K]

Fig. 16.42. Cell dimension decrements for DMTTF–CA as a function of temperature. The space group is P1 above 65K and P1 below. (Reproduced from Nogami et al., 1995.)

goodness of ﬁt 0.93, all nonhydrogen atoms reﬁned anisotropically) structures. At 75K ˚ there is a . . . DMTTF..CA . . . stack along [100], the components being separated by 3.56 A ( ¼ a/2). At 40K there are two crystallographically independent . . . DMTTF–CA . . . ˚ in one stack, and 3.46 stacks, with the pairs of components separated by 3.49 and 3.61 A ˚ in the second. Collet et al. describe these as neutral and ionic stacks and 3.64 A respectively but critical scrutiny suggests that the component dimensions are not precise enough for such an identiﬁcation. Although it was reported (Nogami et al., 1995) that structures had been determined at 293, 109, 48 and 29K, details do not appear to have been published.

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

(a)

1139

(b) DMTTFQCI4

Peak of optical conductivity spectra, C=O stretch mode, E perpendicular to DA stack (Horiuchi et al., 2001)

C=O stretch mode 10K

47 55 60 63.5 65 70 200 S cm–1 90 1600 1650 Wave number (reciprocal cm)

Wave number (reciprocal cm)

35

1635 1630 1625 1620 1615 1605 1605 1600 0 10 20 30 40 50 60 70 80 90 100 T (K)

Fig. 16.43. (left) The optical conductivity spectra of DMTTF-CA (E perpendicular to DA stack; C¼O stretch mode) over a range of temperatures. The dashed line is a guide to the eye. (right) Wave numbers of spectral peaks (from the dashed line in the left diagram) plotted against temperature. These values can be compared with the values given for CA0 (1685 cm1) and CA1 (in K CA) (1520 cm1) in Fig. 16.40 (lower panel). (Reproduced from Horiuchi et al., 2001.)

Aoki et al. (1995) report that the N phase transforms into a fully ionized I phase above 12 kbar at 300K. Thus there may be a difference in pressure and temperature induced transitions in this system. The NI transition in TTF-CA is essentially ﬁrst order in nature while that in DMTTF– CA appears to be essentially second order. 16.9.4 Other examples (a) TTF – 2,5-dichloro-p-benzoquinone. This molecular compound (TTF–2,5-Cl2BQ) ˚ , 106.94 97.58 93.66 , crystallizes as dark green triclinic needles (7.935 7.216 6.844 A Z ¼ 1, space group P 1) (Girlando, Painelli et al., 1993). There are resemblances to the TTF-CA crystal structure. Raman and polarized IR spectra allowed the evaluation of many microscopic parameters involved in the contrasting behaviour of TTF-CA and TTF–2,5-Cl2BQ. However, we shall not dwell on these as study over a wide range of temperatures and pressures is lacking. A putative lower-symmetry structure was studied theoretically by Katan and Koenig (1999). (b) 2-chloro-5-methyl-p-phenylenediamine–2,5-dimethyldicyanoquinone-diimine. This molecular compound (abbreviated as ClMePD–DMeDCNQI) shows unique features not yet encountered in other molecular compounds that show neutral-to-ionic transitions. IR

CRYSTAL (STRUCTURAL) PHYSICS

1140

Ionicity

0.5 DMTTF-CA from C=0 stretch mode of CA

0.4

Mode Intensity L

67 K

1 DMTTF a(g) mode

0.5

0

50

150 100 Temperature (K)

200

Fig. 16.44. Upper curve – ionicity estimated from frequency of C¼O stretch mode versus temperature. Note that the ionicity extrapolates to 0.5 at 0K. Lower curve–mode intensity from DMTTF mode. (Adapted from Horiuchi et al. (2001).)

and visible spectra of powdered crystals over the range 50–350K led to the conclusion that a continuous change in molecular ionicity over a range of 200K is accompanied by dynamic distortions of the stacks at low temperatures (Aoki and Nakayama, 1997). The ˚ , 91.23 112.19 crystals (from dichloromethane) are triclinic needles, 7.463 7.504 7.191 A 96.91 , Z ¼ 1 (presumably at 300K). The space group was given as P1, although ‘‘to obtain suitable values of thermal factors in the analysis, 2- and 5-substitutional sites [in ClMePD] were assumed to be occupied by Cl atoms and methyl groups with equal probability.’’ The ClMePD and DMeDCNQI molecules formed mixed-stack columns in a direction parallel to the b axes. This description suggests that the space group could be P 1; however, no structural details have been published so this remains a speculation. These spectroscopic results were conﬁrmed by a Raman and polarized IR study over the range 80–400K (Masino et al., 2001). Spectroscopic studies at various pressures have been carried out by Masino et al., (2003). A low temperature diffraction study seems essential. (c) 3,3’,5,5’-Tetramethylbenzidine–TCNQ. A TINI transition was found in this mixedstack molecular compound at around 205K. At 300K the golden-yellow cosublimed ˚ , 100.19 , Z ¼ 2, space group P21/n crystals are monoclinic, 6.722 21.873 8.108 A (Iwasa et al., 1990; details of the structure not reported). Polarized visible and IR spectra show a ﬁrst-order transition on cooling at 200K and on heating at 228K; thus there is appreciable hysteresis. The ionicity is 0.59 in the high temperature N phase and

NEUTRAL TO IONIC TRANSFORMATION OF THE GROUND STATE

1141

1550

0.5

1500

Degree of Ionicity

Wav number/cm–1

0

1 1450

0

1 2 Pressure/GPa

3

Fig. 16.45. Pressure dependence of the C¼N stretching IR peak frequency at 300K (left hand scale) of JIXWES and ionicity (right hand scale). Note the hint of phase coexistence around 1 Gpa. (Reproduced from Aumu¨ller et al. (1991).)

0.69 in the low temperature I phase; we retain the N/I nomenclature despite its limitations here. Details of the spectra suggest that there are two types of TCNQ molecule in the I phase. A micrograph at 180K shows that the I phase has a striated appearance. ‘‘Narrow diagonal I domains appear in (a, c) planes whose number increases as the temperature decreases. Such coexistence is observed over several [tens of] degrees Kelvin. However, when large parts of the crystal are transformed,.. the transition is always accompanied by a sharp breaking of the crystal along the a and c axes.’’ (Buron-Le Cointe et al., 2003). It is difﬁcult to obtain diffraction-quality crystals for further studies. There are two PINI transitions at 300K, one at 6 and the other at 20 kbar. (Iwasa et al.,1993). The 6 kbar transition is to an equal mixture of ‘‘ionic’’ and ‘‘neutral’’ molecules, while there are only ionic entities above 20 kbar. (d) TTF–N,N 0 -dicyano-2,5-dimethyl-1,4-benzoquinone-di-imine. NC N CH3 N,N⬘-dicyano-2,5-dimethyl-1,4-benzoquinone-di-imine H3 C N CN

The 300K crystal structure of this mixed-stack neutral molecular compound was reported ˚ , 101.41 , Z ¼ 2, P21/c; JIXWES). The by Aumu¨ller et al. (1991) ( 6.172 7.831 17.998 A high-pressure FT-IR and electronic spectra of powdered samples (300K, up to 3.5 GPa;

CRYSTAL (STRUCTURAL) PHYSICS

1142

Fig. 16.45) were measured, and also the electronic conductivity along the needle axis of a single crystal. There is a sharp PINI transition at 1.0 GPa from an essentially neutral state to an almost completely ionic state. The electrical conductivity increases by ﬁve orders of magnitude above about 1.5 GPa. One could anticipate a ﬁrst order transition to an ionic state on cooling but this has not been investigated. JIXWES appears to resemble TTF-CA more closely than any of the other examples discussed above. 16.9.5

Concluding summary

What started off as a rather limited enterprise, exempliﬁed only by TTF-CA, has blossomed into a multifacetted study with a growing number of subjects, each differing from TTF-CA in one or more aspects. The experimental work summarized above has been accompanied by many theoretical studies, mostly employing the twin concepts of ‘ionicity’ and ‘dimerization’ and neglected here for reasons of space.

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Chapter 17 Segregated stack -molecular complexes

7,7,8,8-Tetracyanoquinodimethane (TCNQ) is a strong -acid which forms stable crystalline radical salts of type MþTCNQ and a new class of complex salts represented by MþTCNQ TCNQ which contain formally neutral TCNQ. The complex anion-radical salts have the highest electrical conductivities known for organic compounds, exhibiting volume electrical resistivities as low as 0.01 ohm cm at room temperature. Both the conductivity and electron paramagnetic absorption are anisotropic as determined by measurements along major crystal axes. Melby, Harder, Hertler, Mahler, Benson and Mochel, 1962 The term ‘organic metal’ is a misnomer because these solids are neither ductile nor malleable; they are frail organic crystals or relatively brittle polymers. The only properties reminiscent of metals are high reﬂectivity and relatively low room temperature resistivity, which decreases with decreasing temperature over a certain temperature range. F. Wudl, 1984

Summary: The unexpected phenomenon of high electrical conductivity in some organic crystals appears to be associated with stacked arrangements of radical ions of electron donors and/or acceptors. A variety of chemical types has been developed, principally based on the parent donor tetrathiafulvalene (TTF) and the parent acceptor tetracycanoquinodimethane (TCNQ). TTF cation radical salts and TCNQ anion radical salts have stacked structures with marked anisotropy of arrangement and physical properties and hence are termed ‘quasi-one dimensional’. However, lateral interactions between stacks lead to a measure of two-dimensional character in some of these salts, and this aspect is taking on increasing importance with the development of some of the newer types of donor and acceptor. The degree of stacking ranges from -dimeric pairs to stacks of inﬁnite length; the longer stacks often contain dimeric or tetradic subgroupings, particularly in the TCNQ radical anion salts. In the cation radical-anion radical salts, of which the most famous example is {[TTF][TCNQ]}, there are segregated stacks of cation and anion radicals. {[TTF][TCNQ]} itself has monad stacks in its averaged structure, but there are also examples of diad stacks. The phase transitions in {[TTF][TCNQ]} below 54K are of an unusual type, the drastic drop in stack axis conductivity on cooling below 54K not being accompanied by appreciable changes in average moiety arrangement. Studies of the very weak diffuse scattering above 54K and the weak satellite reﬂections below 54K lead to a model in which the high resistivity below 54K is accounted for in terms of pinned charge density waves (CDW), which become mobile above the phase transitions. In the temperature region from 54K up to 300K the conductivity can be explained semiquantitatively by a combination of CDW and single phonon scattering.

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17.1 17.2

Introduction Chemistry of donors and acceptors that participate in segregated stacks 17.2.1 Introduction 17.2.2 Donors 17.2.3 Acceptors 17.2.4 Preparation of crystals 17.3 Structures of cation-radical salts 17.3.1 Introduction 17.3.2 Cations are polycyclic aromatic hydrocarbons 17.3.3 TTF and related compounds as cations 17.3.4 TMPD salts containing -dimerized cation radicals 17.4 Structure of TCNQ anion-radical salts 17.4.1 Mutual arrangements of approximately plane-parallel TCNQ moieties 17.4.2 Structures with stacks of limited length 17.4.3 TCNQ anion-radical salts in which the cations are metals 17.4.4 Stacked structures with e average charge on the TCNQ moieties 17.4.5 Stacked structures with 0.8e average charge on the TCNQ moieties 17.4.6 Stacked structures with 2/3e average charge on the TCNQ moieties 17.4.7 Stacked structures with 0.5e average charge on the TCNQ moieties 17.4.8 Stacked structures with 0.4e average charge on the TCNQ moieties 17.4.9 Systems studied over a wide range of temperatures 17.4.10 Conclusions drawn from a survey of the structural results for TCNQ anion-radical salts 17.5 Other anion-radical salts 17.5.1 Alkali-metal chloranil salts 17.5.2 M(dmit)2 and M(mnt)2 as anion radicals in various guises 17.6 Structures of cation-radical anion-radical salts 17.6.1 General survey 17.6.2 Cation : anion ratio 1 : 1; monad stacks 17.6.3 Cation : anion ratio 1 : 1; diad stacks 17.6.4 Cation : anion ratio 2 : 1 or 1 : 2; monad stacks 17.6.5 Cation : anion ratio 2 : 1 or 1 : 2; diad stacks 17.7 Electron density studies of some segregated stack complexes 17.8 Theoretical studies of some segregated stack complexes 17.9 Studies of {[TTF][TCNQ]} and some related materials 17.10 Concluding summary References

17.1

1148 1151 1151 1152 1157 1161 1162 1162 1163 1167 1175 1177 1177 1180 1187 1189 1192 1193 1196 1202 1205 1211 1214 1214 1215 1220 1220 1220 1227 1229 1230 1232 1234 1235 1252 1253

Introduction

Many, many studies have been stimulated by the discovery (Ferraris et al., 1973; Coleman et al., 1973) of a large, temperature-dependent electrical conductivity in {[TTF][TCNQ]} (nomenclature is discussed below) and the association of this striking physical property with the (then-novel) segregated (and not mixed-stack) arrangement of donor and acceptor moieties in the crystal. TTF (tetrathiafulvalene) was indexed in Chemical Abstracts under 0 ‘‘2,2 -Bi-1,3-dithiole’’ until 1972 and thereafter as ‘‘1,3-Dithiole, 2-(1,3-dithiol-2ylidene)’’; registry number 31366–25–3) and TCNQ (7,7,8,8-tetracyanoquinodimethane;

I NT RO D UC T I O N

1149

0

ﬁrst under ‘‘2,5-Cyclohexadiene-1,a:4,a -dimalonitrile’’ and then as ‘‘Propanedinitrile, 2,2 0 -(2,5-cyclohexadiene-1,4-diylidene)bis’’; registry number 1518-16-7); the twocomponent complex has registry number 51159-15-0. Considerable effort has been invested in chemical modiﬁcation of TTF and TCNQ and in the study of analogous systems in the hope of ﬁnding materials with new or better physical properties. The many new materials synthesized can be classiﬁed as cation-radical salts (i.e. with closed shell anions), as anion-radical salts (i.e. with closed shell cations) and as cation-radical anionradical salts. Crystal structures have been determined for many of these new materials and their physical properties (especially electronic properties such as conductivity, thermoelectric power and magnetic susceptibility) have been measured over a wide range of temperatures and (sometimes) pressures. The donors and acceptors that form cation and anion radicals and give segregated stack crystal structures can also participate as neutral or ionic moieties in mixed-stack crystals, and also sometimes present crystal structures of new, albeit related, types. The behaviour of individual moieties in a binary system depends on the properties and interactions of both components. As noted in Chapter 1, the structure determining inﬂuences in segregated-stack binary molecular complexes are A . . . A and B . . . B and not A . . . B – hence ‘complexes’ and not ‘compounds’. A different symbolism is also needed. Thus we emphasize the segregation by replacing the inappropriate {TTF TCNQ} by {[TTF][TCNQ]}, in more general terms {[donor][acceptor]}; in some instances only one of the components is stacked and only it is placed in the square brackets. Problems arise with known structures that do not ﬁt into the simple mixed stack/segregated stack framework and with unknown structures: then we replace ‘complexes’ and/or ‘compounds’ by the noncommittal ‘adduct’ and use a {donor–acceptor} symbolism. The sequence of events leading to the discovery of high conductivity in {[TTF][TCNQ]} seems to have been as follows. The synthesis of TCNQ and its ability to form highly-conducting organic salts (conductivities of 102 S/cm) had been reported in 1962 (Melby et al., 1962); rapid progress was made during the next decade in determining and relating crystal structures (Shibaeva and Atovmyan, 1972) and physical properties of relevant materials. Dibenzo-TTF (then called 2,2 0 -bis-1,3-benzdithiolene) had been prepared in 1926 (Hurtley and Smiles, 1926). TTF itself was reported by a number of groups towards the end of the 1960s (Prinzbach et al., 1965; Wudl et al., 1970). TTFþCl was prepared by Wudl and coworkers in 1970, its conductivity at 25 C being reported as 0.2 S/cm in 1972 (Wudl et al., 1972). The crucial step of combining TTF and TCNQ was taken very soon thereafter, essentially simultaneously, by research groups at Monsanto, Johns Hopkins and the University of Pennsylvania (who published their results (Miles et al., 1972; Ferraris et al., 1973; Coleman et al., 1973) and at SUNY-Buffalo (who did not). To quote from Wudl’s lively account: (Wudl, 1984) n n n

‘‘Having established that TTF salts are highly conducting, it did not take long before the marriage of the young donor with the old acceptor took place. The exact location of the ceremony is somewhat obscure. It is clear it was a fertile coupling as judged from the number of papers it generated between 1973 and the present. The sudden interest (1973–1975) in this solid was caused by two, almost simultaneous, events: the discovery of metal-like conductivity between room temperature and 56K and the report of ‘superconductivity’ just above 56K. Of these only the former survived scrutiny.’’

1150

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8000

6 5

6000 4

{[TTF ] [ TCNQ]}

Conductivity {[TTF] [TCNQ]} 4000 [010] S/cm

3

Conductivity Lead MS/cm

2

2000 1 Pb 0

0 0

100

200 T(K)

300

400

Fig. 17.1. Schematic representations of the conductivities of Pb (Onnes and Tuyn, 1929) (righthand scale; the superconductivity of Pb below 7.2K has been omitted from the ﬁgure) and {[TTF][TCNQ]} (along the stack axis; left-hand scale) as functions of absolute temperature; note that Pb is about 1000 times more conductive than {[TTF][TCNQ]}Pb has been chosen for comparison because its Debye temperature is not very different from that of {[TTF][TCNQ]}, which is considered to have metallic behaviour down to 60K because its –T curve follows the same course as that of Pb and other metals.

While much interesting physics and chemistry has been developed in this area since 1973, it is perhaps fair to state that no system has yet been found with properties more striking than those of the classical {[TTF][TCNQ]} molecular complex, although the discovery of superconductivity in the Bechgaard salts (TMTSF)2X (Friedel and Jerome, 1982) may require some modiﬁcation of this judgment. Our primary concern in this chapter is with the structures of segregated stack molecular complexes and related ion radical salts and the properties that derive from these structures rather than with the phenomenon of high conductivity as such, which has been the main interest of most investigators in this ﬁeld (Howard, 1988). Thus we do not discuss many important high conductivity materials, such as the essentially inorganic materials reviewed elsewhere (Miller and Epstein, 1976). However, we have considered the TTF and TCNQ salts with closed shell counterions (and analogs) to come within our boundaries, both because of their intrinsic structural interest in the context of stacked arrangements and because of their relevance to {[TTF][TCNQ]} and related molecular complexes; similar latitude has been extended to some other ion radical salts. A rough picture of the changing interest in TCNQ, TTF and {[TTF][TCNQ]} can be obtained from Fig. 17.2, where the total number of entries under each of these three headings (in practice using the Registry Numbers) in the quinquennial indexes of Chemical Abstracts has been plotted against the end-year of the quinquennium. The interest in TCNQ and TTF appears to have peaked in the early 1990’s, as other donors (many based on TCNQ and TTF) and other types of ion radical salt have taken over part of the stage. {[TTF][TCNQ]} seems to have disappeared from the area of active research but surely it is not yet completely understood.

CHEMISTRY OF DONORS AND ACCEPTORS

1151

600 TCNQ

Number of publications

500

TTF 400 TTF–TCNQ 300 200 100 0 1977

1982

1987

1992

1997

1992

1997

2002

End of quinquennium

Fig. 17.2. The numbers of references to TCNQ, TTF and {[TTF][TCNQ]} in Chemical Abstracts for 5-year periods are plotted against the end-year of the quinquennium. The numbers of references have been obtained from the Registry Numbers for the three materials using Sciﬁnder ScholarTM but no attempt has been made to check their relevance or eliminate duplication.

17.2 Chemistry of donors and acceptors that participate in segregated stacks 17.2.1 Introduction The donors and acceptors of interest here are oxidized or reduced by multistage electron transfers without the formation or rupture of electron pair single bonds. Such reactions have been summarized in terms of three equations by Deuchert and Hu¨nig (1978), whose treatment we follow closely. Their structural principle is stated as follows: ‘‘Reversible redox reactions with transfer of two electrons in two separate steps are to be expected with compounds in which the end groups X and Y of the reduced form 1. have free electron pairs or -systems available, and 2. are connected by vinylene groups (n ¼ 0, 1, 2 . . . ).’’ The various stages are represented by the reduced (RED), radical (‘semiquinone’ or SEM) and oxidized (OX) forms. The systems A and B differ only by two charges; otherwise they are iso--electronic. The SEM radical appears as a cation in A and an anion in B. System C, where the SEM stage is a neutral radical, is less relevant in the present context. All three redox systems are capable of many variations. Deuchert and Hu¨nig (1978) deﬁne two particular types of redox system which contain most of the examples of donors and acceptors to be considered below: Two-stage Wu¨rster-type redox systems: two-stage redox systems are said to be of the Wu¨rster type if their end groups are located outside a cyclic -system that has aromatic character in the reduced form.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1152

E1 –e $ þe

REDa

E2 –e $ þe

SEMaþ1

OXaþ2

Equation A X–(–CH¼CH–)n–X

–e $ þe

{X–(–CH¼CH–)n–X þ $ þX–(–CH¼CH–)n–X}

–e $

þ

X–(–CH¼CH–)n–Xþ

þe

Equation B –

Y–(–CH¼CH–)n–Y–

–e $ þe

{–Y–(–CH¼CH–)n–Y $ Y–(–CH¼CH–)n–Y–}

–e $

Y–(–CH¼CH–)n–Y

þe

Equation C X–(–CH¼CH–)n–Y

–e $ þe

{X–(–CH¼CH–)n–Y $ þX–(–CH¼CH–)n–Y–}

–e $

þ

X–(–CH¼CH–)n–Y

þe

Notes: 1. (electron loss (oxidation) occurs for the forward directions of the arrows, and conversely). 2. SEM is shown as a resonance hybrid.

Two-stage Weitz-type redox systems: two-stage redox systems are said to be of the Weitz type if their end groups form part of a cyclic -system that has aromatic character in the oxidized form. In the discussion that follows the chemical formulae of the donors and acceptors are given together with partial reference to the appropriate equations and values of n.

17.2.2

Donors

By the early 1970s it had become clear that the following donors had a high tendency to appear as cation radicals in appropriate systems (ionization potentials are given in Table 13.5): TMPD TTF TTT

N,N,N 0 ,N 0 -tetramethylphenylenediamine tetrathiafulvalene tetrathiotetracene.

Some effort has also been invested in the synthesis of related systems, especially those based on pyranylpyrans. An extensive review, especially of newer examples, is given by Yamashita and Tomura (1998). TMPD forms stacks in some of its cation-radical salts (see Section 17.3.4) but mixed rather than segregated stacks in most molecular compounds with acceptors. It has a Wu¨rster type redox system.

CHEMISTRY OF DONORS AND ACCEPTORS

1153

Equation A: H

H N

H N

N

H

H reduced form

H +

N

H

+

H oxidised form

The major synthetic efforts applied to TTF, and to many other donors, have been in two directions: (i) replacement of S by its congeners Se and Te; for example, in the TTF and TTT systems the Se and Te congeners have been synthesized. Three important trends to be expected upon replacement of S or Se by Te have been noted (McCullough et al., 1987). We quote: The more diffuse p and d orbitals centred on tellurium should give larger conduction bandwidths due to increased interstack interactions and result in materials with reduced electron scattering and enhanced metallic electrical conductivity. In addition this increase in orbital spatial extension ought to increase the interchain interactions giving rise to more two- or three-dimensional character. This extended dimensionality should help suppress the various instabilities which often lead to insulating ground states in quasi-one-dimensional organic conductors. Finally, the greater polarizability of tellurium should reduce the on-site Coulombic repulsion and help support doubly-charged species. Unless the molecular component can support doubly-charged species, only a correlated type of conductivity is possible.

(ii) preparation of substituted TTFs and congeners; in particular, alkylthio substituents could alter the dimensionality of the crystals by increasing interstack interactions. The relevant complexes are shown below, together with notes and references; synthetic details are in the original papers. Most synthetic studies have been accompanied by the preparation of donor – TCNQ molecular complexes of various compositions and measurements of electrical conductivities on compacted powders or single crystals; a wide range of conductivities is often found (a list of over 400 crystalline conducting organic quasi-one-dimensional molecular complexes has been compiled by Howard (1988)). Other acceptors have sometimes also been used. Structural information for correlation with physical properties is slowly being accumulated. (i) 1,2,4,5-Tetrakis(dimethylamino)benzene is a powerful donor of the Wu¨rster type (Eqn. A, n ¼ 0) (Elbl et al., 1986). 1,6-Diaminopyrene – TCNQ has a conductivity of 2 S/cm (Scott et al., 1965); its structure is not known. 2,7-Bis(dimethylamino)tetrahydropyrene – TCNQ has a conductivity of 0.4 S/cm and has been estimated from the CN stretching frequency to have a charge transfer of 0.57; its structure is not known. A number of related molecular complexes of low conductivity have been prepared (Ueda et al., 1983). Fully aromatic 2,7-bis(dimethylamino)- and 1,3,6,8-tetrakis-(dimethylamino)-pyrene and partially-reduced 2,7-bis(dimethylamino)pyrene have been shown to be good electron donors (Sakata et al., 1984).

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1154

(ii) Dithiapyrenes (Tilak, 1951) (Eqn. A, n ¼ 2) and dithiaperylenes (Eqn. A, n ¼ 3). These are Weitz type systems. S

R2 R1 S

S S R1 R2

1,6-dithiapyrene (DTPY; R1 ¼ R2 ¼ H). When R1 ¼ SCH3, R2 ¼ H the complex is 2,7-bis(methylthio)-1,6-dithiapyrene and when R1 ¼ H, R2 ¼ SCH3 it is 3,8-bis(methylthio)-1,6-dithiapyrene.

3,10-dithiaperylene (DTPR)

{[DTPY][TCNQ]} has a segregated stack crystal structure (see Table 17.10 ) (Thorup et al., 1985; DAKTIS); the structures of some salts of 2,11-diphenyl-DTPR have been reported (Nakasuji et al., 1986) and also of some molecular complexes of substituted DTPYs (see Table 17.10). 3,4:3 0 ,4 0 -Bibenzo[b]thiophene (BBT), the thiophene analog of DTPR (i.e. with the S atoms in ﬁve-membered rings) has been prepared (Wudl et al., 1978) and is isoelectronic in its neutral state with perylene. Structures of molecular complexes have not been reported. S S

S

S

S

S

S

S S

4,5:9,10-bis(ethanediylthio)1,6-dithiapyrene (Nakasuji et al., 1986)

S S S

2,3:7,8-bis(ethanediylthio)-1,6-dithiapyrene (ETDTPY) (Nakasuji et al., 1986)

CHEMISTRY OF DONORS AND ACCEPTORS

1155

The crystal structures of the TCNQ (FUDTON) and chloranil (FUDTUT) adducts of 3,8-bis(methylthio)-1,6-dithiapyrene have been reported (Nakasuji et al., 1987). (iii) Benzotrichalcophenes (Cowan et al., 1982): X

X

X

X ¼ S (BTT) (Hart and Sasaoka, 1978), Se (BTS), Te (BTTe)

BTT forms intensely coloured, moisture-stable crystalline 1 : 1 charge transfer adducts with TCNE, DDQ, TCNQ and chloranil. Structures and physical properties do not appear to have been reported. (iv) Systems based on TTF and congeners (Eqn. A, n ¼ 1; these are Weitz type systems); syntheses have been extensively reviewed (Narita and Pitman, 1976; Krief, 1986; Schukat et al., 1987); Nielsen et al., 2000; Yamada and Sugimoto, 2004). The basic structure (below left) has been substituted in many ways, some of which are illustrated and others referenced (Fangha¨ngel et al., 1983). R

Ch

R

Ch

Ch

Ch

Ch

Ch

R

R R

Ch

Ch

R

TTF : Ch ¼ S, R ¼ H; TSF (or TSeF) : Ch ¼ Se, R ¼ H TTeF : Ch ¼ Te, R ¼ H (Narita and Pitman, 1976) Tetrakis(alkylthio)TTF (Mizuno et al., 1978): Ch ¼ S, R ¼ SCH3; TMTTF : Ch ¼ S, R ¼ CH3; TMTSF : Ch ¼ Se, Te, R ¼ CH3 (Iwasawa et al., 1987)

HMTSF (Berg et al., 1976) : Ch ¼ Se, R ¼ CH21; HMTTeF (Saito et al., 1983) : Ch ¼ Te, R ¼ CH2 DTTSF (Elbl et al., 1986): Ch ¼ Se, R ¼ S

H3C

CH3 S

S NR

RN S H3C

S CH3

Bis(2,5-dimethylpyrrolo[3,4-d]tetrathiafulvalene: R ¼ H (BP-TTF); Ph (BPP-TTF) (Chen etal., 1988) 1

2, 2 0 -bis(2,4-diselenabicyclo[3.3.0]octylidene).

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1156

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

Ch

DBTTF : Ch ¼ S (Spencer et al., 1977) (Unsymmetrical versions with only one benzene ring have been prepared, and also symmetrically (E) and unsymmetrically (Z) substituted dimethyl complexes) (Shibaeva and Yarochkina, 1975; Tanaka et al., 1983; Nakano et al., 1989) DBTSF : Ch ¼ Se

Bis(ethylenedithiolo)TTF (BEDT-TTF) Ch ¼ S (Saito et al., 1982); Ch ¼ Se (Lee et al., 1983).

(iii) Systems based on pyran derivatives: R

R S X

X

S S

R

R

X ¼ O, S, Se, Te; (Alizon et al., 1976; Detty et al., 1983); X ¼ S, R ¼ H or CH3 (Sandman, Epstein et al., 1977). See also Sandman, Fisher et al., 1977. 4,4 0 -Bithiopyranylidene (BTP, X ¼ S, R ¼ H) is isoelectronic with TTF. Note: when X ¼ O and R ¼ C6H4C12H25, then charge transfer salts (counterions BF4, ClO4, TCNQ) with appreciable mesophase (liquid crystalline) temperature ranges are found (Saeva et al., 1982).

(iv) Systems based on p-quinobis(1,3-dithiole): R

S

S

R

R

S

S

R

R ¼ CH3, TMCHDT (Bis(4,5-dimethyl-2H-1,3-dithiolylidene-2)-1,4-cyclohexa-2,5-diene) (Fabre et al., 1978).

R

S

S

R

R

S

S

R

R ¼ H (Sato et al., 1978), H, CH3 (Ueno et al., 1978). Also analogues based on the anthracenediylidene system (Bryce et al., 1990). Dithiadiazafulvalenes have been shown to be strong electron acceptors (Tormos et al., 1995).

CHEMISTRY OF DONORS AND ACCEPTORS

1157

(v) Systems based on tetrathiotetracene: X

X

X

X

X ¼ S TTN (dehydrotetrathianaphthazarin). Se TSN (naphtho[1,8-cd:4,5-c 0 d 0 ]bis(1,2-diselenole)

TTN was shown electrochemically to be a much poorer donor than TTF; however, {[TTN] [TCNQ]} crystallizes as black needles with a single crystal conductivity of 40 S/cm between 200–300K, which is higher than that of {[TTT][TCNQ]} (1 S/cm) and the same as the microwave conductivity of {[TTT][(TCNQ)2]} (Wudl et al., 1976). Crystal structures are discussed later. X

X

X

X

Equation A, n ¼ 2,3. Se TSA (tetraseleno-anthracene; anthra[9,1-cd:10,5-c 0 d 0 ]bis(1,2-diselenole)) (Endres et al., 1982)

X

X

X

X

X ¼ S TTT (naphthacene[5,6-cd: 11,12-c 0 d 0 ]bis(1,2-dithiole)) Se TSeT (Khidekel and Zhilyaeve, 1981) Te TTeT (Sandman et al., 1982)

(vi) Systems with both N and S atoms: S N R

.

S

R ¼ H, CH3 Benzo-1,3,2-dithiazol-2-yl and derivatives (Wo¨lmerhauser et al., 1984).

17.2.3 Acceptors The synthesis of TCNQ (Acker and Hertler, 1962) was accompanied by a thorough investigation of its ion radical salts (Melby et al., 1962) (the abstract of this paper is quoted at the head of this chapter); there are examples (Yamaguchi et al., 1989) of alternative syntheses. A number of substituted TCNQs have been synthesized as well as

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1158

analogs of various kinds. A new family of segregated stack crystals is based on TTF with tetrahalo-p-benzoquinones as acceptors (Torrance et al., 1979). Bis(dithiolene)metal complexes behave as acceptors with many cations (Interrante et al., 1975); the crystal structures are rather different from those of TCNQ molecular complexes and the materials have interesting physical properties. The various acceptors are compiled below; structures and properties are discussed at appropriate places later in this chapter. (i) TCNQ and related complexes: Equation B: NC

NC

CN C–

C–

NC

CN C

NC

CN

CN oxidized form

reduced form

7,7,8,8-tetracyanoquinodimethane (TCNQ) (Equation B, n ¼ 3; these are Wu¨rster type systems). Among the derivatives synthesized are monoﬂuoroTCNQ (Ferraris and Saito, 1979), 2,5diﬂuoro-TCNQ (Saito and Ferraris, 1979), tetraﬂuoro-TCNQ (TCNQF4) (Wheland and Martin, 1975), and methyl-, ethyl- and 2,5dimethyl-TCNQ (Andersen and Jorgensen, 1979).

C

N N N N

11,11,12,12-tetracyanonaphthoquinodimethane (TNAP) (Diekman et al., 1963) (Equation B, n ¼ 4)

Some three-dimensionally modiﬁed TCNQ derivatives such as dihydro- and tetrahydrobarreleno-TCNQ, monobenzo- and dibenzobarrelleno-TCNQ have been NC

CN

NC

CN

Tetracyanodiphenoquinodimethane (Aharon-Shalom et al., 1979) (Equation B, n ¼ 7)

NC

CN

NC

CN

13,13,14,14-Tetracyano-4,5,9,10-tetrahydropyrenequinodimethane (TCNTP) (Aharon-Shalom et al., 1979; Maxﬁeld et al., 1979) (Equation B, n ¼ 5); see also Suguira et al., 2000.

CHEMISTRY OF DONORS AND ACCEPTORS

1159

prepared and shown to form molecular complexes of varying degrees of ionicity with TTF derivatives (Nakasuji et al., 1986). 11,11,12,12,13,13,14,14-octacyano-1,4:5,8-anthradiquinotetramethane{OCNAQ;1,4:5,8tetrakis-(dicyanomethylene)anthracene} has been prepared (Mitsuhasi et al., 1988) and shown to form molecular complexes with TTF, pyrene, phenothiazine, TMTTF and TTT. Structures (Inabe et al., 1988) are discussed later. The acceptor is somewhat nonplanar because of steric hindrance between adjacent C(CN)2 groups. (ii) Other polycyano complexes:

CN

NC

NC

N

N

N

N

CN

CN NC

NC NC

CN

H

Hexacyanobutadiene (HCBD), also called tetracyanomuconitrile (Webster, 1964).

NC

CN

NC

CN

CN

H

Tetracyanobi-imidazole (Rasmussen et al., 1982).

O2N

NO2

NC

CN

O2N

Tetracyanoethylene (TCNE) (Equation B, n ¼ 1)

2,4,5-Trinitro-9-(dicyanomethylene)ﬂuorene (Dupuis and Neel, 1969)

(iii) S-heteroquinoid acceptors: The tetracyanothieno[3,2-b]thiophene system, where the tetracyano groups bracket a heteroquinoid nucleus, has been used as a basis for acceptors (Yui et al., 1989). The corresponding dicyano complexes (2,5-bis(cyanoimino)-2,5-dihydrothieno[3,2b]thiophenes (DCNTTs)) are also good acceptors in charge transfer complexes and, especially, in highly conductive salts (Aumu¨ller et al., 1988). R1 NC

R1 S

CN

NC

CN

S R2

CN

S N NC

N S DCNTT

R1 and R2 are various combinations of H, CH3, Cl, Br.

R2

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1160

(iv) Other acceptors containing S and N atoms: N

N S

S N

N BDTA

Bis([1,2,5]thiadiazolo)[3,4-b;3 0 ,4 0 -e]pyrazine (BDTA; the formula is drawn to indicate that the molecule is best represented as a resonance hybrid) is a 14 electron heterocycle (Yamashita et al., 1988), with a higher electron afﬁnity than that of BDTA-TCNQ below. Its crystal structure has been determined but formation of molecular complexes and radical ion salts has not been reported in detail. NC

CN

N

N

N

N

NC

CN

NC

CN

N S

S

NC

S N

CN

BDTA-TCNQ

TDA-TCNNQ

Two related acceptors are (bis[1,2,5]thiadiazolo)TCNQ (BDTA-TCNQ) (Se and S, Se analogs have also been reported (Suzuki et al., 1987)) and [1,2,5]thiadiazolo)tetracyanonaphtho-quinodimethane (TDA-TCNNQ). The electron donors TTF, TMTTF and TMTSF gave very low conductivity (109 S/cm) adducts with BDTA-TCNQ and these are probably mixed stack compounds; however, the TTN molecular compound had a conductivity of 1 S/cm and could have segregated stacks (Yamashita et al., 1985). Structures have not been reported. (v) Tetrahalo-p-benzoquinones and analogs: O X

Y

X

Y O

X ¼ Y F, Cl, Br, I X ¼ CN, Y ¼ Cl 2,3-Dichloro-5,6-dicyano-pbenzoquinone (DDQ)

NC

Various substituents CN

N,N 0 -dicyanoquinone diimines (Aumu¨ller and Hu¨nig, 1986a,b)

CHEMISTRY OF DONORS AND ACCEPTORS

1161

(vi) Aromatic anhydrides: 1,4,5,8-naphthalenetetracarboxylic anhydride (NDTA) forms conducting salts with various cations. The salt (5,6-dihydro4a,6a-phenanthrolinium)2(NDTA)5 has a stacked structure (Heywang et al., 1989; VARKEE, P 1, Z ¼ 1; Born and Heywang, 1991; VARKEE10; see Section 17.4.5). (vii) 1,2-Ethylenebis(dithiolene)metal complexes (see Section 17.5.2): X

S

S

X

n– n– S

M

Rn+ X

S

S

X

n ¼ 0, 1, 2. X ¼ H, CH3, CN (abbreviated as mnt which is maleonitrile dithiolate or cis-2,3dimercapto-2-butenedinitrile), CF3 (abbreviated as tfd), C6H5 etc. M ¼ Ni, Pd, Pt, Fe, Co, Cu, Au etc.

S

Rn+ S

S

S

M S

S

S S

S

n ¼ 0.5, 1, 2. Abbreviated as dmit. H2(dmit) ¼ 4,5-dimercapto-1,3-dithiole2-thione.

17.2.4 Preparation of crystals A feature of most synthetic papers is that some charge transfer radical ion salts crystallize without difﬁculty, generally as needles of intense colour (deep green, blue or black) showing metallic reﬂectivity; on the other hand, some products are obtained only as microcrystalline powders. The reason for such behaviour is generally not understood. Standard methods are used for growth of crystals or recrystallization of powders – slow cooling of saturated solutions, slow evaporation, interdiffusion of components in U-tubes (Kaplan, 1976), simultaneous sublimation of components on to cold surfaces (Andersen, Engler and Bechgaard, 1978). However, many beautiful crystals show disappointing diffraction patterns, the apparent external perfection being accompanied by appreciable disorder at the unit cell level. Electrocrystallization (Chiang et al., 1971; Ristagro and Shine, 1971; Rosseinsky and Kathirgamanathan, 1982) is a technique of increasing popularity for growing crystals of highly conductive materials. It was ﬁrst used for the perchlorates of pyrene, perylene and azulene and later extended to {[perylene][Ni dithiolate]} (Alcacer and Maki, 1974) and various salts of TCNQ and analogs (Kathirgamanathan et al., 1979, 1980, 1982). Both potentiostatic and galvanostatic arrangements have been used (Fig. 17.3), and it has been shown that the crystals growing on the anode function directly as electrodes (Enkelmann, Morra et al., 1982). The nature of the solvent can also be important (Anzai et al., 1982). The highly conductive materials considered here are usually very anisotropic, with the metallic conductivity generally restricted to the stack axis. Thus chemical impurities and lattice imperfections would be expected to strongly inﬂuence the one-dimensional electron transport, and more so than in three-dimensional metals. This anticipation is reinforced by the many reports that the conductivity of {[TTF][TCNQ]} is sample dependent (Fig. 17.46). The matter is somewhat controversial. One group (McGhie et al., 1974, 1978) claims that extreme precautions (gradient sublimation under argon, use of quartz

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1162

– –

+

70~80

100~125

+

15

50 30

Fig. 17.3. Example of a crystal growth cell used for growing highly conductive crystals in a nitrogen atmosphere. Concentrations of 104 M were used, with voltages in the range 1–5 V and currents in the range 1–10 mA. Dimensions in mm. (Reproduced from Anzai et al., 1982.)

apparatus) are essential while another (Gemmer et al., 1975) suggests that the simple standard techniques of recrystallization and sublimation are adequate to yield TTF and TCNQ of excellent chemical purity (impurities at the ppm level as judged by the use of high performance liquid chromotography (HPLC)). Gemmer et al. (1975) conclude that the variations in the conductivity of different {[TTF][TCNQ]} samples are due to lattice defects. McGhie et al. (1974, 1978) emphasize that large well formed crystals of {[TTF][TCNQ]} are obtained only when high purity components are used and that the physical perfection of the crystals depends both on the chemical purity of the components and the growth conditions.

17.3 17.3.1

Structures of cation-radical salts Introduction

The structures of a fairly large number of cation-radical salts have been determined in the last few years and many of these are important in the context of high conductivity (Shchegolev and Yagubskii, 1982; Shibaeva, 1982)), or even superconducting (Williams, Beno et al., 1985) materials. Space limits us to considering here only the cation-radical salts derived from polycyclic aromatic hydrocarbons because of their fundamental position in the crystal chemistry of charge transfer molecular complexes, and the salts of TTF, which illustrate some of the principles found also in other cation radical salts, and where the cation participates in the much-studied {[TTF][TCNQ]}.

STRUCTURES OF CATION-RADICAL SALTS

1163

17.3.2 Cations are polycyclic aromatic hydrocarbons We shall treat these as one structural group with subdivisions; however, there are already enough structural types to suggest that the true picture may well be more complicated. Three structural subdivisions can be discerned – those in which all the radical cations are in stacks, those in which some are stacked and others not, and a non-stacked group.

17.3.2.1 Stacked radical cations {(Naphthalene)þ PF6} forms dark red-violet conducting ( ¼ 0.12 S/cm) crystals 2 ˚ , space group P42/n, (grown by electrocrystallization; tetragonal, a ¼ 11.56, c ¼ 6.40 A Z ¼ 2) that are stable at low temperature but decompose on warming to room temperature (Fritz et al., 1978; NAPHFP10); the AsF6 salt (ZZZBTG) is isomorphous. The structure consists of segregated stacks of (C10H8)2þ cations and PF6 anions along [001]. The

0

A hexafluorophosphate

B x y Fig. 17.4. Crystal structure of {(naphthalene)þ 2 PF6 } at 223K projected down [001]. The diagram shows the mutual arrangement of nearly coplanar cations and anions. The 1-9 and 2-3 bonds in the naphthalene cation are signiﬁcantly shorter than those in neutral naphthalene at 90K (Brock and ˚ and 1.386(6) as against 1.415(2) A ˚ ). (Data from Fritz Dunitz, 1982) (1.408(6) as against 1.423(2) A et al., 1978.)

1164

SEGREGAT ED STACK -MOLECULAR COMPLEXES

cations lie in (002) planes and are separated by the remarkably small interplanar distance ˚ , successive cations along the 42 axis of a stack being mutually rotated by of 3.20 A 90 ; presumably there is a random arrangement of neutral molecules and cations in each stack and this accounts for the conductivity. The packing arrangement (Fig. 17.4) is similar to those of bis(diphenylglyoximato)Ni(II) iodide and Ni(phthalocyanine) iodide (Marks, 1978). The preparation of some of the above and related salts [e.g. (triphenylene)2X, X ¼ PF6 or AsF6; (perylene)2BF4] has been reported (Kro¨hnke et al., 1980). Conductivities ranged from 103 to 101 S/cm. The salts (ﬂuoranthene) þ 2 X (X ¼ PF6 (FANTHP10), AsF6 (BOSJUO), SbF6 (BUNCAO)) are isomorphous (a ¼ 6.50, b ¼ 12.49, c ¼ ˚ , ¼ 104.0 , P21/c, Z ¼ 2 for hexaﬂuoroarsenate at 120K) and, judging 14.75 A from the curves of cell dimensions versus T, all show second (or perhaps higher) order phase transitions at 200K (Enkelmann, Morra et al., 1982). The small differences between high and low temperature structures derive from small rotations of cations and anions; adjacent stacked ﬂuoranthenium cation radicals are separated ˚ . The dimensions found for the ﬂuoranthenium cation radical are by 3.22 and 3.28 A not precise enough for comparison with those of the neutral molecule. The salts are quasi-metallic above 200K and semiconducting below. In both (naphthalene) þ 2 X and (ﬂuoranthene) þ X the cation planes are exactly or nearly normal to the 2 stack axes. Three isomorphous bis(perylenium) salts [(pe)2(X)x(Y)y, with X ¼ PF6 (CUWBAX01), AsF6 (PITDOL), x ¼ 0.8 1.5; Y ¼ CH2Cl2, C4H8O, y ¼ 0.5, 0.8] have been studied (Keller, No¨the et al., 1980); the black needles were grown by electrocrystallization. These have structures (orthorhombic, a ¼ 4.285, b ¼ 12.915, c ¼ ˚ , space group Pnmn, Z ¼ 1) different in many respects from that of 14.033 A (naphthalene) þ PF6. The translationally equivalent perylenium cation radicals are 2 ˚ and an inclination of 38 to stacked along [100] with an interplanar spacing of 3.40 A (100) and are mutually shifted along their long axes. The channels between the cation stacks are ﬁlled with an ill-deﬁned melange of anions and solvent molecules. The stack axis DC conductivities are in the range 102–103 S/cm at room temperature, follow a metallic regime down to 200K and then diminish rapidly. Keller, No¨the et al. (1980) suggest that the rather high conductivities are due to enhancement of the mixed valence state of the cation radical stacks by non-stoichiometry arising from replacement of some anions by neutral solvent molecules. Other perylene charge transfer salts are discussed in Section 17.5.2. 17.3.2.2

Structures in which not all cations are stacked

There is a second conducting form of (pe)2(PF6)2/3(THF) ( 102 S/cm; CUWBAX) that has inﬁnite stacks of perylene moieties, with a slight tendency to the formation of tetrads (Endres et al., 1985). However, only half the perylene moieties are in stacks, while the others ﬂank the stacks on all four sides, the planes of the ﬂanking perylenes being virtually perpendicular to the planes of those in the stacks (Fig. 17.5). Endres et al. (1985) note that ‘‘intuition would suggest that the charges are distributed in the stacks but there are some physical arguments against this idea.’’ Thus we shall not venture an explanation for the conductivity.

STRUCTURES OF CATION-RADICAL SALTS

1165

Bis(perylenium) hexafluorophosphate. THF stack of perylenes

flanking perylenes with anions and solvent molecules

y x

Fig. 17.5. Crystal structure of (pe)2(PF6)2/3(THF) viewed down [001] (a ¼ 13.076, b ¼ 14.159, ˚ , ¼ 110.87 , space group P2/m, Z ¼ 3). (Data from Burggraf et al., 1995.) c ¼ 13.796 A

Fig. 17.6. Stereoview of the (pe)3ClO4 structure viewed along [001], showing the stacked but jogged tetrad and the ﬂanking perylene moieties. The ClO4 anions are ordered. (Reproduced from Endres et al., 1985.)

1166

SEGREGAT ED STACK -MOLECULAR COMPLEXES

(Perylene)3ClO4 is a semiconductor in which there are two offset pairs (-dimers) of perylene moieties per triclinic unit cell, thus forming jogged stacks (Endres et al., 1985; CUWBEB); the interplanar distances within and between the -dimers are not sensibly ˚ . Adjacent stacks are separated by ﬂanking perylenes (Fig. 17.6), different at 3.37(5) A very much as in (pe)2(PF6)2/3(THF). It was not possible to infer moiety charges from bond lengths because of disorder problems. In {(perylene)4[Co(mnt)2]3} there are three perylenes stacked as trimers, a trinuclear [Co(mnt)2]3 moiety and a ﬂanking perylene approximately normal to the perylenes (Gama et al., 1993; see Section 17.5.2). Thus there are a number of examples of ﬂanking perylenes and analogs have been encountered in other structures; (TTF)2-[Ni(S4C4H4)] (see Section 17.3.7) is a possibly relevant example for comparison. The overlap of the perylene pairs or triads, whether stacked or not, has been described as ‘graphite-like’ but ‘ring-over-bond’ is more appropriate. The structure of (quaterphenyl)12(quaterphenyl)4(SbF6)10 has been brieﬂy reported (Enkelmann, Go¨ckelmann et al., 1985). The structure consists of stacks of quaterphenyl cations (the ﬁrst group) separated by layers of anions, in which the second group of cations is incorporated. Thus there appear to be resemblances to (pe)2(PF6)2/3(THF) but a detailed comparison is not possible.

17.3.2.3 Structures in which the cations are not stacked (Pe)6ClO4 has three independent -dimers arranged about centers of symmetry of the triclinic unit cell; the overlap diagrams are very similar and the interplanar spacings ˚ (Fig. 17.7). This material is a semiconductor are 3.38(2), 3.44(2) and 3.46(3) A ( 102 S/cm (Endres et al., 1985; CUWBIF).

Fig. 17.7. (Pe)6ClO4, stereoview along [100], showing the herring-bone arrangement of -dimers. The disordered anions (at symmetry centres) have been omitted for clarity. (Reproduced from Endres et al., 1985.)

STRUCTURES OF CATION-RADICAL SALTS

1167

17.3.2.4 Various The crystal structure of (pyrene)þ has not been reported. In (pheno2 (ClO4) þ thiazine)2 SbCl6 (BUFZEH) the cation radicals are isolated in the crystals and do not interact (Uchida et al., 1983). 17.3.2.5 Conclusions The structures of the aromatic hydrocarbon cation-radical salts show some interesting resemblances to the cation-radical salts of TTF discussed below. There are non-stacked and stacked -dimers and inﬁnite monad and diad stacks. Formation of a cation-radical anion-radical salt analogous to {[TTF][TCNQ]}, in which the cation radical is an aromatic hydrocarbon and the anion radical is a suitable open shell acceptor and the stacks are segregated, has so far been achieved only for perylene–M(mnt)2 derivatives (see Section 17.5.2). 17.3.3 TTF and related compounds as cations TTF forms salts with many closed shell anions. Quite complex relations were found early on (Scott, La Placa et al., 1977) for the TTF halides (Fig. 17.8) and the situation becomes even more complicated when TTF salts of polyatomic anions are considered. Our classiﬁcation is based on the overall structural arrangement, and we make a major distinction between nonstacked and stacked arrangements of the TTF moieties. Type A: Non-stacked arrangements of TTF moieties. Group 1: Salts of type (TTF2þ)(X)2 are isostructural for X ¼ Cl (TTFDCL), Br ˚ (for X ¼ Cl), space group (TTFDBR). These are tetragonal with a ¼ 13.56, c ¼ 10.10 A

4b

Chloride

Bromide 4b

Iodide

0.6

0.8 1.0 Effective Charge (y)

2.0

Fig. 17.8. Phases observed in the TTF-halide systems, indicated by vertical lines. The abscissa y is the halogen content deﬁning the effective or average charge per cation site, thus the compositions are given as TTFXy. The rectangles show the composition ranges found for some salts. (Adapted from Scott et al., 1977.)

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1168

I41/acd, Z ¼ 8 (Scott, La Placa et al., 1977). (TTF2þ)(ClO4)2 is monoclinic (Ashton et al., 1999, who give references to other (TTF2þ) structure determinations). In both instances, the cations are nonplanar with the two halves of the moiety mutually rotated by 60 about the central C–C bond. Ashton et al. comment ‘‘We believe, in all probability, that the conformation of (TTF2þ) is determined by the multiple interactions that determine its supramolecular order.’’ TTF(OCN)2 has been reported as a microcrystalline insulating powder (Kathirgamanathan and Rosseinsky, 1980). Group 2: Salts of type TTFX, where X ¼ Cl (TTFMCL), Br (TTFMBR). The iso˚ (for morphous halide salts are orthorhombic, with a ¼ 11.073, b ¼ 11.218, c ¼ 13.95 A X ¼ Cl), space group Pbca, Z ¼ 8 (Scott et al., 1977). There are centrosymmetric pairs ˚ (-dimers), and ordered anions of eclipsed cations with interplanar spacing 3.34 A (Fig. 17.9). Their importance in the present context is to suggest that adjacent neutral TTF molecules and TTFþ cation radicals can be present in a stack without seriously perturbing the stack. Other examples are TTFI3, (Teitelbaum et al., 1980; TTFIOD), TTF3Sn(CH3)2Cl3 (Matsubayashi et al., 1980) and TTFDDQ (Mayerle and Torrance, 1981b). The TTFI3 structure has pairs of cations (TTFþ)2 surrounded by noninteracting triiodide ions, while TTF3Sn(CH3)2Cl3 has similar (TTFþ)2 dimers in a matrix of centrosymmetric 2 chlorine-bridged dimeric [Cl2(CH3)2Sn(Cl)2Sn(CH3)2Cl2] moieties. TTFDDQ (dark red ˚ , ¼ 77.51(2), ¼ triclinic crystals, a ¼ 10.272(4), b ¼ 12.195(5), c ¼ 6.609(2) A 81.93(2), ¼ 87.30(4) , P1, Z ¼ 2; Fig. 17.10) has eclipsed TTF -dimers (interplanar ˚ ) and also stacks of DDQ -dimers with very short interplanar spacings of spacing 3.4 A ˚ ˚ between them. The axes of the two kinds of stacks 2.97 A within the -dimers and 3.56 A

c H

H C

C

S C

S

C

C

S

H

S C

H

Br

S

C H b

Fig. 17.9. Bounded a axis projection of the orthorhombic crystal structure of TTFBr; TTF moieties viewed edge-on. The chloride is isostructural. (Reproduced from Scott et al., 1977.)

STRUCTURES OF CATION-RADICAL SALTS

b pair of ~ DDQ dimers

1169

TTF dimer

Å

4Å

2.97

3.

a ~

3.5

c ~ Cl

6Å

TTF dimer

C≡N DDQ

b ~

Fig. 17.10. Two projections of the crystal structure of TTFDDQ. The interplanar spacing between ˚ . (Reproduced from Mayerle and Torrance, 1981b.) the DDQ moieties is 2.97 A

are considerably inclined to one another. In these salts the moieties are fully ionized and the conductivities are correspondingly low ( 108 S/cm). TTF.DDQ is probably better described as a DDQ anion-radical salt, with the DDQ moieties arranged in jogged tetrad stacks and the (TTFþ)2 -dimers acting as (possibly spin paired) cations. TTFClO4 (ZZZBWA10) has a rather complicated structure (a ¼ 16.762(1), b ¼ ˚ , Z ¼ 16, space group Pbca) (Yakushi et al., 1980) in which 20.906(2), c ¼ 12.538(1) A ˚) there are pairs of essentially eclipsed cations (-dimers with interplanar spacing of 3.41 A arranged in tetrads. The structure is not stacked. TTF(OSO2CH3), TTF(SCN)1.4 and TTF(HSO4)1.2 have also been reported (Kathirgamanathan and Rosseinsky, 1980). but structures are not known. -Dimers are characteristic of many structures of this group but (TTF)32þ triads arranged 2 (Fig. 17.11) (Kondo et al., between (SnCl6)2 anions are found in (TTF)2þ 3 (SnCl6) 2þ 2 1984; CELREQ); (TTF)3 (PtCl6) (DERKAM) is isomorphous. Salts with [SnCl4R2]2 anions (R ¼ methyl, ethyl) are isostructural (Matsubayashi et al., 1985; ethyl is DERJUF). As the dimensions of the two independent TTF moieties of the triad do not differ signiﬁcantly, delocalization of the charge across the triad was inferred. Powder conductivity of 2.4 103 S/cm was ascribed to in-layer transport through sulfur–sulfur contacts. Type B: Stacked arrangements. Group 3: (stacks with the long axes of the TTF moieties mutually perpendicular): This group comprises the salts TTFXy, where X ¼ Cl, NO3, SCN (disordered anions), Br, I (ordered anions). The values of y vary from 0.55 to 0.7 and depend on the nature and degree of ordering of the anion. The overall gross structural pattern common to all these salts is rather simple but there are many complications of detail. The basic structural pattern has stacks of eclipsed TTF cation moieties (with average charge Z < 1) arranged as shown in Fig. 17.12 (broken-line cell in the centre of the diagram). The alignment of TTF moieties in adjacent stacks is mutually perpendicular. The channels between the stacks of Fig. 17.12 contain the anions; as Johnson and

1170

SEGREGAT ED STACK -MOLECULAR COMPLEXES

S(12) TTF triad

2– (SnCl6)

S(4) S(2)

S(11)

S(3) S(1) Sn b a

Fig. 17.11. The non-stacked structure of (TTF)3SnCl6 showing the layers of (TTF)32þ triads ˚ , P4/mbm, Z ¼ 2. The interspersed among the anions. The crystals are tetragonal, 11.801, 11.861 A ˚ . (Reproduced from Kondo et al., 1984.) interplanar spacing in the triad is 3.49 A

Watson (1976) originally pointed out, anions in these channels with ionic radii greater ˚ will distort the arrangement of the TTF stacks. The prototype structure is than 1.8 A ˚, TTFCl0.7 (MTTFCL), which has a tetragonal unit cell with a ¼ 11.12, c ¼ 3.595 A Z ¼ 2, space group P42/mnm (we use the highest symmetry space group among the possibilities, unless there is good reason to the contrary). The salts TTFBr0.59 (ZZZBGJ), TTFI0.69 (Scott et al., 1977) and TTF(SCN)0.570.03 (Kobayashi and Kobayashi, 1977) have essentially the same structure, while there is a small monoclinic distortion in TTF(NO3)0.55. Two different modes of distortion come into play when the halide content increases slightly. In TTFCl0.7 the unit cell distorts to orthorhombic (see Fig. 17.12) while in TTFBr0.740.77 (LaPlaca et al., 1975) and TTFI0.700.72 (ZZZBGD) the TTF and halide subcells become incommensurable (Table 17.1). The discussion of the mutual interaction of TTF and I sublattices in TTFI0.70, as inferred by Johnson and Watson (1976) from the details of the very complicated x-ray diffraction patterns, is remarkable for its thoroughness but too complex for summary here. Measurements of the peak shapes of the S 2p peaks in the x-ray photoelectron spectra (Ikemoto, Yamada et al., 1980) indicate that the fraction of cations in TTFBr0.7 is 0.71(5) but 0.52(5) in TTFI0.7, suggesting that some larger polyiodide anions may be present in the latter; both salts contain TTF cations and neutral molecules but in different amounts. The system TTFCly (0.67 y 0.70) has been investigated in some detail over a range of temperature (Williams, Lowe Ma et al., 1980). All crystals in this composition range show the same temperature dependence of conductivity; however, x-ray diffraction (oscillation) photographs from crystals at the two extremes of composition show slightly different diffuse layer lines. These have their origins in the disordered Cl

STRUCTURES OF CATION-RADICAL SALTS

1171

arrangements; the TTF and Cl sublattices are commensurable for y ¼ 0.67 (ZZZBGG) and incommensurable for y ¼ 0.70 (indeed the composition range was inferred from the detailed spacings of the diffuse layers). There is a phase change at 250K for TTFCl0.67 (cf. the conductivity behaviour in Fig. 17.13) and the diffuse lines sharpen and resolve into individual Bragg reﬂections indicating ordering of the Cl sublattice. The ordered monoclinic phase has composition (TTF)3(Cl)2 and commensurable TTF and Cl sublattices. Orientation relations between the monoclinic and tetragonal phases can be

Table 17.1. The TTF and halide sub-cells for TTFBr0.76 and TTFI0.72. These phases, shown as 4b in Fig. 17.9, have small ranges of composition and the values of c and vary with composition Subcell parameter

˚) a (A b c (deg)

TTFBr0.76 MTTFBR

TTFI0.72 MTTFID

TTF

Br

TTF

I

15.617 15.627 3.573 91.23

17.368 15.623 4.538 116.01

15.998 16.114 3.558 90.96

8.19 16.11 4.871 102.82

2b

2a sin b

Fig. 17.12. Projection down [001] of the structures of all the TTFXy (y < 1) phases, with the exception of TTFCl0.92. The broken-line cell in the center of the diagram is for the disordered ˚ ). The full broken-line rectangle shows tetragonal salts of Group 4a such as TTFCl0.68 (a ¼ 11.12 A ˚ ), while the TTF sublattices of the orthorhombic cell of TTFCl0.77 (a ¼ 10.77, b ¼ 22.10 A TTFBr0.76 and TTFI0.72 are shown in the top left quarter of the overall diagram. Minor distortions ˚ . (Adapted from Scott et al., 1977.) are not shown in the diagram. For all the cells c 3.6 A

1172

SEGREGAT ED STACK -MOLECULAR COMPLEXES

300 0

250

T(K)

200

0 –1 –1 260K 3.5

–2 260K

4.5 1000/T (K)–1

–3 167K –4 126K 2

4

6 8 1000/T (K)–1

10

12

Fig. 17.13. Temperature dependence of the conductivity of TTFCl0.67. The ordinate (/RT) is on a logarithmic scale, and the approximate temperatures of the breaks have been inserted into the diagram. (Adapted fromWilliams et al., 1980.)

summarized as follows: p amono ¼ bmono ¼ 2atetr ; cmono 3ctetr ; mono 92 (temperature dependent). Because the four h110i directions of the tetragonal cell are equivalent, four equally probable orientations will be obtained for the monoclinic cell. Thus the low temperature phase is a quintuple twin, consisting of the domains of the four monoclinic orientations and of unchanged tetragonal phase (twinning often accompanies ﬁrst-order phase changes). Overlap of diffraction patterns prevented determination of the details of the low temperature structure. When TTFCl0.70 is cooled, it forms two types of low temperature phase with compositions (TTF)3(Cl)2 and (TTF)7(Cl)5 respectively; the TTF and Cl sublattices are commensurable in both. The ordered structure of (TSeF)3(ClO4)2 is a monoclinic distortion of the tetragonal subhalide structure, in which the (TSeF) moieties are arranged in triads with their long axes approximately mutually perpendicular (Shibaeva, 1983; CENBIG). Group 4: (stacks with the long axes of the TTF moieties mutually parallel): This group comprises the salts (TTF)3(BF4)2 (Legros et al., 1983; CELVIJ) and (TTF)3(I3)2 (Teitelbaum et al., 1980). The ﬁrst of these (Fig. 17.14) has slightly jogged stacks of TTF moieties and orientationally disordered anions; bond lengths are said to differentiate between TTF cations and neutral molecules, and XPS measurements of the shape of sulphur 2p peak indicate that 2/3rds of the TTF moieties are cations (Ikemoto et al., 1980). The powder conductivity is 2 105 S/cm. Only a gross structure has been reported for (TTF)3(I3)2 (Johnson et al., 1975).

STRUCTURES OF CATION-RADICAL SALTS

1173

TTFHgCl3 has a remarkable structure that combines in one crystal features encountered above in separate structures (Kistenmacher, Rossi et al., 1980; FTFHGC10). There are two types of layer (Fig. 17.15); in the layer about y ¼ 0 there is an inorganic polymer of composition HgCl3 and a stack of TTF cation radicals with an interplanar spacing ˚ , while in that about y ¼ 1/2 there are isolated (Hg2Cl6)2 ions and (TTFþ)2 of 3.6 A ˚ . The resonance Raman spectrum shows a -dimers, with an interplanar spacing of 3.43 A splitting of the TTF 3 mode, indicating the presence of two types of TTF cation; the difference between their charges was estimated to be <0.2e. The subhalide phases show high conductivities at room temperature (1–5 102 S/cm) while both (TTF)3(I3)2 and TTFI3 have conductivities of 103 S/cm (Warmack et al., 1975; Teitelbaum et al., 1980), (TTF)(N3)0.74 and TTF(CH3COO)0.70 have been reported as fairly highly conductive phases ( 1 S/cm) but their structures are not known.

– [001] [110] [010]

TTF+ 3.40Å TTF+ 3.40Å TTF •

Fig. 17.14. Crystal structure of triclinic P1, (Z ¼ 1) (TTF)3(BF4)2 (a) perspective view of the structure showing the stacks of TTF moieties (hydrogen atoms omitted) with their long axes parallel. The disordered anion is shown in its major (30%) orientation. (b) Side view of stacking along [110] of TTF moieties (tilted by 15 with respect to the page normal). (Reproduced from Legros et al., 1983.)

1174

SEGREGAT ED STACK -MOLECULAR COMPLEXES

X S22 Cl11 Cl13

Z

Cl12

S21

Hg1

S31 8

3.2

S32

y = 0.0

X Z Cl21 Hg2

3.29

Cl23 S2

S4

Cl22 S1 S3

y = 0.5

˚ , 98.69, 95.73, Fig. 17.15. (a) The structure of TTFHgCl3 (P1, Z ¼ 1; 12.661, 15.969, 7.416 A 120.01 , cell not reduced). The section about y ¼ 0 shows the polymeric HgCl3 species and the TTF stacks, which are ring-over-bond, while the section about y ¼ 0.5 shows the Hg2Cl6 anions and the eclipsed TTF -dimers. (Reproduced from Kistenmacher et al., 1978.)

Bis(tetrathiafulvalene)-tetracyanomuconitrile2 ((TTF)2-TCM) crystallizes in long blue needles with a conductivity of 103 S/cm at 298K (Wudl and Southwick, 1974), similar to that of {[TTF] [TCNQ]}. The structure has not been reported. The free energies and entropies of formation of the various TTF iodides have been measured by determining the voltages of suitable solid state electrochemical cells over the temperature range 20–40 C (Euler et al., 1982). The reaction is: TTF(s) þ (x/2)I2(s) ¼ TTFIx(s); x ¼ 0.71, 2, 3 for the phases discussed earlier. 2

Also known as ‘hexacyanobutadiene’.

STRUCTURES OF CATION-RADICAL SALTS

1175

Table 17.2. Thermodynamic formation quantities at 298K for the TTF iodides. ‘‘Uncertainties’’ are given as G 0.4 kJ/mol, S 1.2 J/mol K, H 0.8 kJ/mol. Data from Euler et al., 1982 Phase

G (kJ/mol)

S (J/mol)

298S (kJ/mol)

H (kJ/mol)

TTFI0.71 (TTF)3(I3)2 TTFI3

7.9 16.3 21.7

20.9 74.9 106.6

6.2 22.3 31.8

14.2 38.5 53.5

The results are summarized in Table 17.2. The experimental results show that the TTF iodides are enthalpy-stabilized but entropydestabilized (see Appendix I); the two stacked phases (TTFI0.71 and (TTF)3(I3)2) are less stable than the non-stacked TTFI3 phase. The enthalpy of formation of {[TTF] [TCNQ]} has been measured as 37.4kJ/mol (see Section 16.7), which is not very different from the values for the TTF iodides. In mixed stack -molecular compounds enthalpy of formation values range from 29 to 25 kJ/mol (see Section 16.5). The negative entropies of formation of the TTF iodides are presumably due to reduced thermal vibration consequent on the stronger ionic interactions in the iodides as compared to those between the neutral moieties in TTF and I2. 17.3.4 TMPD salts containing -dimerized cation radicals The TMPD moiety is the prototype Wu¨rster type redox system (Section 17.2.1). Discrete (TMPDþ)2 -dimers are found in TMPDClO4 (Wu¨rster’s blue perchlorate), where the dimers are stacked, and in (TMPD)2 {bis(maleonitriledithiolato)Ni(II)} [(TMPD)2 {Ni(mnt)2}], where the -dimers are not stacked. There is a ﬁrst-order phase change in TMPDClO4 at 186K (Fig.17.16); above this temperature the crystals are orthorhombic (TMPDPC) and the cations are arranged in regular stacks with EB/EB overlap and ˚ (Boer and Vos, 1972a), similar to the arrangement found an interplanar spacing of 3.55 A in TMPD iodide (Boer et al., 1968; TMDABI). Below 186K the cations are arranged in ˚ between planes of successive cations (Boer stacks, but with distances of 3.10 and 3.67 A and Vos, 1972b; TMPDPC01). -Dimerization has occurred, with coupling of the unpaired electrons of the pairs of closer cations. The variation of paramagnetic susceptibility with temperature (Fig. 17.17) can be explained in terms of a theory due to Soos (1965) in which the stacks are treated as linear alternating Heisenberg antiferromagnets. The agreement of theory and measurements in the low-temperature region can be improved by allowing the exchange integral J to increase as the temperature is reduced; evidence for such an increase is provided by the increased intensity of the CT band at 12 kK on cooling (Fig. 17.16(c)). The experimental singlet-triplet separation (Thomas, Keller et al., 1963) is 246 20 cm1. In (TMPD)2[Ni(mnt)2] (space group P 1, Z ¼ 1) (Hove et al., 1972; TMDNMI) the ˚ ; the distance cations are arranged as -dimers with an interplanar spacing of 3.25 A ˚ . The interaction between between neighbouring ions of two different -dimers is 6.57 A -dimers is small because of the large distance between them but is not zero, as is shown by the absence of hyperﬁne splitting in the ESR spectrum. The (TMPD)2 moieties form a strongly alternating chain, that could be called a ‘jogged stack.’

SEGREGAT ED STACK -MOLECULAR COMPLEXES

(a)

4.8

4.4

Dielectric constant

1176

7.0

DSC

Endo

Exo

(b)

150

200 250 Temperature (K)

300

(c)

Optical density

2

// a

(5) 1

// b (1) (3) 10

20

30

Wave number/103cm–1

Fig. 17.16. (a) Temperature dependence of the dielectric constant of TMPDClO4. An approximate scale of the dielectric constant is shown on the right hand side of the upper part of the diagram. (b) The reversible differential scanning calorimetry (DSC) heating and cooling curves are shown in the lower part of the diagram. (c) Temperature dependence of the crystal spectra of TMPDClO4 at 285K (1) and 83K (3). Spectra at intermediate temperatures are not much different. The different absorption spectra obtained when the electric vector of the plane polarized light is parallel to a and b axes respectively are shown. (Reproduced from Ishii et al., 1976.)

TMPD dimensions have been determined in crystals of different types. Neutral TMPD has a benzenoid structure with a slightly pyramidal arrangement of bonds about N (sum of bond angles at N, ¼ 352 ) (Ikemoto et al., 1979). However, in TMPDþ the quinoid form is the major contributor to the resonance hybrid, with a planar disposition of bonds about N ( ¼ 359.3 ). PPP calculations of bond lengths in TMPD and its singly- and doubly-charged cations show excellent agreement with experiment, the degree of quinoid

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1177

16

12 I

II

χ 8

6

0

100

200 T (K)

300

Fig. 17.17. The dashed lines show two independent measurements of the paramagnetic susceptibility (in units of 104 e.m.u./mol) of TMPDClO4 as a function of temperature, while the full line shows calculated values due to Soos (1965). (Reproduced from Boer and Vos, 1972b.)

character increasing with increasing charge on the cation (Kracht, quoted in Boer and Vos (1972a), p. 835).

17.4 Structure of TCNQ anion-radical salts 17.4.1 Mutual arrangements of approximately plane-parallel TCNQ moieties We shall devote most of our attention to TCNQ anion-radical salts, which currently constitute the major part of the larger family of anion-radical salts; hopefully it will be possible to generalize many of the broad features of structures and properties of the TCNQ salts to other members of the family, although the details are bound to differ. The relatively few salts of other anion radicals (such as the haloanils and Ni(dmit)2) are discussed later; the stacked arrangements there emphasize that stacking is not a prerogative of TCNQ alone. Future studies are likely to furnish many other examples. The closed shell counter ions of TCNQ anion-radical salts include alkali-metal and many organic cations. TCNQ moieties not interacting with other TCNQ moieties have been found only in two examples of composition A2(TCNQ)3 and will be discussed separately below. Otherwise the invariant feature of TCNQ anion-radical salt structures seems to be the appearance of face-to-face arrangements of pairs or larger numbers of TCNQ moieties. Such paired (or larger) aggregates form stacks of limited or unlimited length. Thus the TCNQ salts generally have quasi-one-dimensional structures, and this is reﬂected in many of their physical properties. However, there are a growing number of examples where interstack interactions are also important and this quasi-two dimensional group is likely to be more important in the future, especially in systems other than TCNQ.

1178

SEGREGAT ED STACK -MOLECULAR COMPLEXES

We distinguish between groups with stacks of limited or unlimited length. In both groups we classify the various structures ﬁrstly on the basis of the average charge per TCNQ moiety. This parameter depends on the cation charge (which is unequivocally deﬁned for closed shell cations), and on the composition (i.e. the cation/TCNQ ratio) for stacks of limited length. Here a monad unit will contain one TCNQ moiety, a diad unit two, and so on. Further distinctions can be made on the basis of the type of TCNQ overlap within the diad, etc. It is often convenient to describe stacks of limited length as isolated (to a greater or lesser extent) diads, triads, tetrads, etc. When the stacks are of unlimited length the stack periodicity (i.e. the number of TCNQ moieties in a crystallographic repeat along the stack axis) must also be considered. A monad stack has one TCNQ per period, a diad stack two TCNQs per period, and so on; triad, tetrad, pentad and heptad stacks have also been reported and it would seem that an upper limit to the periodicity depends only on cation shape, size and charge. The composition and cation charge are chemical invariants for a particular compound while the stack periodicity is a physical feature which depends (at least in principle) on external conditions such as temperature and pressure. The 1 : 2 composition with singly-charged closed-shell cations can be taken as an example. A stack ˚ implies monad stacks, with translationally equivalent axis periodicity of 4 A 1/2 ions, presumably better described as a (dynamically or statically) disordered TCNQ array of TCNQ0 and TCNQ moieties. If there are diad stacks (stack periodicity now ˚ ) then the TCNQ1/2 moieties are no longer crystallographically equivalent, 7–8 A but it is not always possible to distinguish them as TCNQ0 and TCNQ. Tetrad stacks ˚ ) are also found for the 1 : 2 composition; there may be (stack periodicity now 14 A pairs of -dimers. Again it may not be possible to differentiate between TCNQ0 and TCNQ. The relations between physical properties and temperature have been explored for many TCNQ systems, but only a few parallel structural studies have been made. Some examples of the cations used in preparing TCNQ anion radical salts are shown below: +

NHR3 + PHPh3

R = methyl, ethyl, etc. triphenyphosphonium

N+

O

R' substituted morpholiniums

R

R N R'

substituted benzamidazoliums

N+ R" S

S CH

N+ CH3

N H3C

3,3'-dimethylcyanine and related compounds

STRUCTURE OF TCNQ ANION-RADICAL SALTS

R'

N+

N+ R'

R

N+ R

R'

1179

N+

R'

R = (CH2)3 or CH2C6H4CH2 are examples. Many cations of these types have been used by the Nottingham group in a long series of systematic studies.

[Ph3P=N=PPh3]+

The mutual arrangement of approximately parallel TCNQ moieties can be succinctly described in terms of the overlap parameters of adjacent moieties, in much the same way as has been done for mixed stacks (Section 15.1); we describe the situation for stacks of unlimited length but the same principles apply when the stacks are of limited length. Consider a pair of TCNQ moieties; idealized types of overlap are deﬁned below in terms of displacements with respect to the orthogonal molecular axes L, M and N: M

NC

NC

CN

CN L

NC

NC

CN

CN

The axial system is centred at the centre of the lower molecule, with N upwards out of the page. Ring-external bond overlap (R/EB) is illustrated, with L ¼ 2.0, M ¼ 0, ˚ (the interplanar distance). In ring–ring (R/R) overlap L ¼ M ¼ 0, N ¼ 3.3 A ˚ N ¼ 3.3 A, i.e. the rings are eclipsed; in displaced R/R overlap L ¼ 0, M ¼ 1.4, ˚ . The absolute values of the signs of the displacements are arbitrary in the usual N ¼ 3.3 A situation of centrosymmetric crystals; however, the correct relative values must be used in the description of the stacks. This is exempliﬁed for the two arrangements shown below, both with R/EB overlap. Stack axis Stack axis TCNQ

TCNQ ∆L ∆M ∆N

N M down

2.0 0

3.3

2.0

0

3.3

2.0

0

3.3

L

∆L ∆M ∆N

2.0 0

3.3

–2.0 0

3.3

2.0 0

3.3

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1180

The TCNQ molecules are represented by the thick horizontal lines and the values of L, etc. are given with respect to each successive molecule as one progresses upwards along the stack axes, starting from the bottom molecule in each part of the diagram. In the example on the left the stack is monad and linear, while a jogged or zigzag diad stack is shown on the right. Jogged diad and tetrad stacks are fairly common. Unfortunately, most authors only report the overall type of overlap and the interplanar spacing, i.e. N but not L or M. One should also note that the TCNQ moieties are usually slightly bow-shaped, with the ¼C(CN)2 groups both displaced (in the same direction) out of the plane of the central quinoid ring, and there is also sometimes a slight twisting of these groups. The structural signiﬁcance of these distortions is not clear at present. We shall ﬁnd it useful to show the moiety arrangement in a stack or elsewhere in the following abbreviated fashion, illustrated for a triad: – 1 B⬘---------A----------B 3.15 R/EB

– 1 B⬘---------A⬘----------B 3.45 R/EB

Here A (at a crystallographic centre) and B (at a general position) are crystallographically independent TCNQ moieties, with A 0 and B 0 their congeners related as shown by the crystallographic centres of symmetry ( 1) and translations. The type of overlap is shown as ˚ ); the three moieties of the triad are shown as linked. well as the interplanar spacing (A Obviously much more information is conveyed by suitable stereodiagrams or even projections of a crystal structure. The crystal structure found for a particular TCNQ salt will be that for which the free energy is lowest (ignoring metastable polymorphs). This free energy will be composed of contributions from three sources: 1. 2. 3.

the free energy of the anion arrangement, which will depend on the type of stacking of TCNQ moieties and the degree of overlap in the stacks; the free energy of the cation arrangement; and the free energy derived from cation–anion interactions.

In organic crystals the differences between the free energies of different polymorphs are small – up to a few kJ/mol; the TCNQ salts are expected to behave similarly. Thus the crystal structure (which determines such properties as lattice speciﬁc heat and thermal expansion) will depend on all three contributions, and it is unlikely that any one will be decisive. However, physical properties such as electrical conductivity, thermoelectric power and magnetic susceptibility depend to a good approximation only on the anion arrangement.

17.4.2

Structures with stacks of limited length

17.4.2.1 Salts in which each TCNQ moiety bears an average charge of e (i) Isolated diad structures: here -bonded pairs of TCNQ moieties are found, isolated to a greater or lesser extent from other such pairs. We use the term ‘‘–dimer’’ (well entrenched in the literature) to distinguish these pairs from the covalently-bonded -dimer

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1181

anions described earlier (Section 15.9.2). The isolated -dimers found in {1,2,3-trimethylbenzimidazolium TCNQ} (Fig. 17.18) (Chasseau et al., 1972; MBITCQ) provide an illustrative if extreme example, the TCNQ -dimers being enclosed in channels between stacks of cations. A similar example of isolated -dimers comes from {(2,4,4,6,8,8hexamethyl-3,4,7,8-tetrahydroanthracene-1,5-dione)TCNQCH3CN} (Brook and Koch, 1997; PULWAU), although here the overlap is displaced R/R despite an interplanar ˚ . Other examples are {3,3 0 -diethylthiacyanine TCNQ} (Saakyan et al., distance of 3.14 A 1972; ECYTCN10), where there is R/EB overlap in -dimers with interplanar spacing ˚ and{[Fe2(5-C5Me5)2(-SEt)2(CO)2]þ}2(TCNQ2)2} (Bu¨chner et al., 1997; 3.23 A NEHSEY) where there are isolated units of composition Dþ(A2)2 Dþ. and the TCNQ ˚ . Weaker -dimers (displaced dimers have R/EB overlap and interplanar spacing of 3.26 A ˚ R/EB overlap, interplanar spacing 3.40 A) are found in S-methylthiouronium TCNQ (COFRIY10) and its isomorphous Se analog (Abashev et al., 1987; COFROE10). Isolated -dimers bounded on both sides by cations are found in the paramagnetic decamethylferrrocenium TCNQ salt formulated as {[Fe(C5Me5)2þ]}2–(TCNQ)22 (Reis et al., 1979; Miller, Zhang et al., 1987); MCFETC), in {N,N 0 -dimethylbenzimidazolinium TCNQ} (Chasseau et al., 1972; MBZTCQ) and also in {[(MeCp)5V5S6](TCNQ)2} (Bollinger et al., 1986; no refcode). The ﬁrst of these contains isolated units of composition [Fe(C5Me5)2](TCNQ)(TCNQ)[Fe(C5Me5)2]. (Fig. 17.19); bond lengths suggest that the TCNQ moieties have charge 1. There is strong antiferromagnetic coupling within the -dimer, with b2g–b2g interactions giving a ﬁlled au bonding orbital. There is

TCNQ π-dimer

y

0

x

Fig. 17.18. {1,2,3-Trimethylbenzimidazolium TCNQ} (MBITCQ), projection down [100]. The TCNQ anions are associated in pairs across centers of symmetry, with R/EB overlap and interplanar ˚ ; these pairs are the -dimers. (Reproduced from Chasseau et al., 1972.) spacings of 3.12 A

1182

SEGREGAT ED STACK -MOLECULAR COMPLEXES

2 Fig. 17.19. Crystal structure of {[Fe(C5Me5)þ represented schematically; each 2 ]}2(TCNQ)2 cylinder depicts an A : B : B : A formula unit. (Reproduced from Reis et al., 1979.)

slightly displaced R/R overlap of the moieties of the -dimer, with an interplanar spacing ˚ . Mo¨ssbauer studies show that the cations contain Fe(III). The third salt appears of 3.15 A to have R/R overlap (described as ‘‘cofacial pairs’’) with an interplanar spacing of ˚. 3.37(1) A In the TCNQ salt of tris[(di--chloro)(hexamethylbenzene)niobium] of composition {[Nb3(-Cl)6(C6Me6)3]2þ(TCNQ)2} there are zigzag chains of alternating trimer cations ˚ ). The odd electron is and TCNQ -dimers (R/EB overlap, interplanar spacing 3.10 A assigned to the cation cluster, while the -dimer has strong coupling of the TCNQ moieties, with two electrons in an ag bonding orbital (Goldberg, Spivak et al., 1977; HMBNBQ). The ferrocenium salt {[Fe(C5H5)2]2[(TCNQF4)]3} contains isolated TCNQF4 -dimers ˚ interplanar spacing enclosed in a matrix of ferwith displaced R/R overlap and 3.16 A rocenium cations and neutral TCNQF4 molecules (Miller et al., 1987; FETBEL). The presence of the latter as ‘‘TCNQF4 of crystallization’’ is unusual but not unprecedented (cf. Section 15.5.1). Thus, in summary, a variety of situations is encountered – more examples are known of R/EB overlap than R/R overlap but the latter group are present; interplanar spacings range from 3.1 A upwards. 17.4.2.2 Average charge of –2/3e on TCNQ moieties There are a number of structures containing isolated triads. In {[(5-propylphenazinium)þ]2 (TCNQ)3} {(NPP)2 (TCNQ)3} (Harms et al., 1982; BIXHUL) the mixed stacks contain an alternating arrangement of pairs of NPP moieties and triads of TCNQ (Fig. 17.20). There is strong interaction within the TCNQ triads and weak interaction between the NPP moieties. Charge balance requires that two of the TCNQ’s are anion radicals and one is neutral; however, the distribution of charge over the triad is not known.

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1183

c NPP

Triad of TCNQ’s

b

0

Fig. 17.20. Projection of the crystal structure of {(5-propylphenazinium)2(TCNQ)3} down the [100] axis of the triclinic cell, showing the arrangement of a pair of NPP moieties and a triad of TCNQ moieties in a mixed stack. The TCNQ triad is centrosymmetric and there is R/EB overlap. The precision of the analysis is too low to allow assignment of charges to the TCNQ moieties through bond lengths. The NPP pair is also centrosymmetric. (Reproduced from Harms et al., 1982.)

Parenthetically we note that {DBTTFþ I 3 } (Shibaeva, Rozenberg, Aldoshina et al., 1979) (Fig.17.21), which should be included among the cation radical salts, can be considered, insofar as the stacks are concerned, as an anti-structure of (NPP)2 (TCNQ)3. There are mixed stacks, consisting of sequences of three DBTTFþ cation radicals and then two I3 anions; additional, non-interacting I3 anions are located between the stacks. The conductivity is fairly low [293 (powder) 2 102 S/cm] and not at all anisotropic. There is a very similar . . . D D A A A D D A A A D D . . . arrangement of moieties in (4,4 0 -bithiopyranylidene)2(TCNQ)3} {(BTP)2(TCNQ3} (Sandman et al., 1980; TCNBTP). Bond lengths in the TCNQ moieties suggest that the charge distribution is A AA, the mutual arrangement being analogous to that in Cs2TCNQ3 (see below).

S

S

4,4'-bithiopyranylidene (BTP)

Perhaps the most unusual of the structures of nominal composition A2TCNQ3 is {(trimethylammonium)22þ (TCNQ)32 } (Fig. 17.22(a)), where there are discrete pairs of strongly-interacting TCNQ anions (R/R overlap with an interplanar spacing of ˚ ; -dimers) as well as single molecules of neutral TCNQ (Kobayashi, Danno 3.26 A and Saito, 1973; TATCNQ). A given -dimer interacts neither with other -dimers nor with neutral TCNQ. The only other example known to us of an analogous structure is {(quinuclidinium)2(TCNQ)3}, where there is a very similar sheet arrangement of

1184

SEGREGAT ED STACK -MOLECULAR COMPLEXES

I

1/4

II

I

1/4

1/4

1/4

a

1/4

1/4

b

Fig. 17.21. {DBTTF I3}: projection of crystal structure down [001] (a ¼ 19.89, b ¼ 14.55, ˚ , ß ¼ 90.03(3) , Z ¼ 6, space group B21/m). The three DBTTF moieties are c ¼ 9.29A labelled I (symmetry m), II (symmetry 2/m). I and II are seen edge-on; they have an eclipsed ˚ . The moieties of stacks separated by c overlap and the interplanar spacing is 3.5–3.6 A (normal to the page) are differentiated by open and ﬁlled circles. (Reproduced from Shibaeva et al., 1979.)

TCNQ -dimers and TCNQ0 moieties (Bandrauk, Truong et al., 1985) (Fig.17.22(b)). The type of overlap and the interplanar spacing differ from what has been found in most other -dimers. The IR spectrum of {(QND)2(TCNQ)3} shows the presence of TCNQ and TCNQ0; despite their different structures, the IR spectra of (QND)2(TCNQ)3 and Cs2(TCNQ)3 (see Section 17.4.6 below for discussion of this structure) are very similar (Truong et al., 1985). Here we note a resemblance between the structures of {[(TMA)2]2þ [(TCNQ)3]2} and {[TTF]þ.[{Pt(dmit)2}3]} (Bousseau et al., 1986; DOPMUG) despite the difference in formal charges on the anions. The latter contains Pt(dmit)2 monomers and [Pt(dmit)2]2 ˚ . These dimers dimers, in which the moieties are linked by a Pt–Pt bond of length 2.935 A ˚ resemble analogous dimers (d(Pt–Pt) ¼ 2.748 A) found in the neutral PtS4C4H4 complex (Browall et al., 1978; PTETOL10); dimerization of acceptors has previously been noted in bis(diﬂuoroboron-benzimidazole)Ni(II) (Section 15.9.3). The TTF moieties are located

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1185

c

a

c

b

QND cation layer

TCNQ mixed layer

Fig. 17.22. (a), above): Projection on (010) of the {(TMA)22þ(TCNQ)32} structure (26.662, 9.767, ˚ , 93.98 , C2/m, Z ¼ 2) showing the segregation of cations and anions in sheets parallel 7.725 A to (100). There are sheets of TCNQ moieties in both structures. In {(TMA)22þ(TCNQ)32} there are pairs of eclipsed (i.e. R/R overlap) TCNQ moieties at 0,1/3,1/2 and 0,2/3,1/2, with an ˚ . The bond lengths indicate that these are anions; they constitute the interplanar distance of 3.26 A -dimers. The TCNQ centred at the origin appears to be a neutral molecule and does not make close contacts to other TCNQ moieties. The dashed lines indicate cation . . . anion hydrogen bonds. (Reproduced from Kobayashi et al., 1973.) (b), below): Projection on (100) of the 2 ˚ fðQNDÞ2þ 2 ðTCNQÞ3 g structure (9.906 28.562 7.791 A, 92.75 , Z ¼ 2, P21 =n). The TCNQ moieties are in sheets normal to [010], separated by sheets of QND cations. There are no stacks in the TCNQ sheets. The monomers at the centres of symmetry (shaded rings) are essentially neutral ˚ interplanar spacing), about the centers, have while the -dimers (with R/R overlap and 3.26 A charge 1. (Reproduced from Bandrauk, Ishii et al., 1985.)

interstitially between the stacks (Fig. 17.23); the charge distribution is uncertain. The compound has a room temperature conductivity of 20 S/cm, which Bousseau et al. (1986) describe as ‘‘surprisingly high’’ in view of the structure; lateral interactions between stacks may be an important factor.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1186

y

Pt(dmit)2 dimers

z Pt(dmit)2 monomers

˚ , 84.50 89.60 81.90 , Z ¼ 1, P Fig. 17.23. Stereodiagram of the unit cell (6.314 11.660 16.810 A 1) of TTF.[Pt(dmit)2]3 viewed in a direction close to [100]. This diagram should be rotated by 90 clockwise for comparison with Fig. 17.22. (Reproduced from Bousseau et al., 1986.)

17.4.2.3 Average charge of –4/7e on TCNQ moieties One of the most striking examples of a stack of limited length is found in {{N(nbutyl)pyridinium}44þ (TCNQ)74} where there are isolated heptads of TCNQ moieties (Fig. 17.24) (Konno and Saito, 1981; PYTCNB10). This is the largest isolated grouping of TCNQ moieties so far reported. The authors suggest, on the basis of bond lengths, that TCNQ A and C carry more negative charge than B and D. The n-butyl groups of the two crystallographically-independent cations are extended, and disordered, in different ways. This may be important in the ﬁrst-order insulatorto-insulator (I ! I) phase transformation that occurs above room temperature (Murakami and Yoshimura, 1980). The high temperature structure has not yet been reported. 17.4.2.4

Average charge of 0.5e on TCNQ moieties

A -tetrad of TCNQs, bounded at each end by planar cations, has been found in the triclinic polymorph of {3,3 0 -diethylthiacarbocyanine (TCNQ)2} (Kaminski et al., 1973; DTCTCQ11) and in {1-methyl-3,3-dimethyl-2-( p-N,N-methyl--chloroethylstyryl)indole-(TCNQ)2}(Shibaeva, Rozenberg and Atovmyan, 1973; MSTYTQ10). There are some structures in which -dimers are arranged in stacks, but with virtually no overlap between successive -dimers. These are discussed below. ˚, Two independent sets of isolated -dimers of TCNQF4 (interplanar spacing 3.18 A displaced R/R overlap) are found in the complex salt {[(10-methyl-5,10-dihydrophenarsazine-10-oxide)2H]þ[(TCNQF4)2](10-methyl-5,10-dihydrophenarsazine-10-oxide) (acetonitrile)}{[(C13H12AsNO)2H]þ[(C12N4F4)2](C13H12-AsNO)CH3CN} (Dietz, Endres, Keller and Moroni, 1984; CELYUN). The structure is ionic and contains slightly folded

STRUCTURE OF TCNQ ANION-RADICAL SALTS

Seven TCNQs in a limited stack

1187

A9

B9 C9 D csinα C B9

B

B

A asinγ

A

O

4 Fig. 17.24. Projection of the structure of (NBPþ y )4(TCNQ)7 along b. Disordered butyl groups of NBPyþ are shown by dotted lines. The stack of seven TCNQ moieties has the following arrangement, running diagonally down from top left hand corner. (Reproduced from Konno and Saito, 1981.)

1

½A B C D 3:22 3:33 3:36 R=EB R=EB R=EB

C0

B0

A0

[(C13H12AsNO)2H]þ cations and -dimeric [(C12N4F4)2] anions. The spaces between the large ions are ﬁlled with neutral (C13H12AsNO)2 dimers and a molecule of acetonitrile. H3C

O As

C13H12AsNO N H

The cation consists of two C13H12AsNO moieties syn linked by a very strong ˚ ), while the neutral dimer has the O . . . Hþ . . . O hydrogen bond (d(O . . . O) ¼ 2.39(2) A two C13H12AsNO moieties anti-overlapped, which would add a dipole–dipole component to any –* interaction. 17.4.3 TCNQ anion-radical salts in which the cations are metals The so-called ‘simple’ salts Mþ(TCNQ) (M ¼ Li, Na, K, Rb, NH4) are discussed here while the so-called ‘complex’ (Mþ)2(TCNQ)32 salts are discussed later with other triad stacked salts in Section 17.4.6. Although free energies of formation have been determined for the Li, Na, K, Ba, Ag, Cu, Ni and Pb TCNQ salts (Aronson and Mitelman, 1981) and ˚ between 10–300K) have been studied for electronic absorption spectra (3100–24000 A the K, Cs and Ba salts of TCNQ (Michaud et al., 1979), the crystallographic information

1188

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Fig. 17.25. Projection of the crystal structures of two polymorphs of Rb(TCNQ). The unit cell of ˚ at 113K) is outlined by broken lines and that of phase III phase I (projection on (100); a ¼ 7.19 A ˚ at 298K) by full lines. The Rb ions are denoted by small squares. This (projection on (001); c ¼ 3.86 A diagram should be compared with Fig. 17.12. (Adapted from Bodegom, de Boer and Vos, 1977.)

(Table 17.3) is more limited. Two groups can be distinguished – the ﬁrst group is antistructural to TTFCly, with cations and anions interchanged. This group contains all except one of the known structures. There are two sets of TCNQ stacks, the stack axes being parallel while the long axes of the TCNQs are mutually perpendicular (Fig. 17.25). Salts of different cations differ in their coordination and in the details of TCNQ stacking. In Na(TCNQ) the sodium ions are enclosed by a nearly octahedral arrangement of six nitrogens from different TCNQ moieties, while the larger potassium ions of K(TCNQ) (in both low and high temperature polymorphs) are at the centre of a distorted cube of nitrogens from surrounding TCNQs. The crystal structure analyses were complicated by problems of twinning and disorder (in particular in the phases of NH4(TCNQ)). Most of the salts show phase transitions on cooling, which are generally associated with changes from monad to diad stacking; there are accompanying changes in magnetic (Fig. 17.28) (Kommandeur, 1980) and other properties. In K(TCNQ) the structural changes have been correlated with the temperature-dependent magnetic susceptibility using the Heisenberg model. However, more work is needed to complete the correlations between physical properties and crystal structures, particularly for Rb(TCNQ). The triclinic phase II of

STRUCTURE OF TCNQ ANION-RADICAL SALTS

2.40

1189

2.40

NH4TCNQ

2.00

2.00

1.20

1.60

C3TCNQ

1.20

0.80

RbTCNQ II

0.80

KTCNQ

0.40

0.40

0 140

x in 10–4 e.m.u.

1.60

x in 10–4 e.m.u.

RbTCNQ

0

T(°K) 220

300

380

NaTCNQ

T(°K) 140

400

220

300

380

400

Fig. 17.26. Variation with temperature of the spin susceptibility (shown on the ordinate in units of 104 emu) for a number of crystalline M(TCNQ) salts. A Curie-type ‘impurity’ contribution has been subtracted from each curve. (Adapted from Kommandeur, 1980.)

Rb(TCNQ) constitutes, at present, the second structural group; here all the TCNQ stacks are translationally equivalent and hence parallel. Rb(TCNQ)-I has a room-temperature conductivity of 105 S/cm while that of Rb(TCNQ)-II is 102 S/cm. 17.4.4 Stacked structures with e average charge on the TCNQ moieties 17.4.4.1 Monad stacks The blue-black crystals of (oxamide oximato) (oxamide oxime)Pt(II)TCNQ {[Pt(oaoH2)(oaoH2)]þ(TCNQ)}, where ‘oaoH2’ is oxamide oxime HON ¼ C(NH2)C(NH2) ¼ NOH ˚ ) (Endres, 1982 BIWWAF) contain segregated stacks of cations (P 1, Z ¼ 1, c ¼ 3.797 A ˚ respectively and an and anions along [001], with interplanar spacings of 3.41 and 3.20 A angle of 36 between cation and anion planes. The TCNQs show R/EB overlap. There is hydrogen bonding between the stacks. The powder conductivity is low at 103 S/cm, which is compatible with integral charges on the anions. H2N

OH

O

N

N

NH2 2+

Pt H2N

N

N

O

HO

NH2

N-methylphenazinium TCNQ attracted early attention because of its high conductivity (1.5 102 S/cm) along the needle axis (Melby, 1965). The crystal structure contains stacks

1190

SEGREGAT ED STACK -MOLECULAR COMPLEXES

˚ , deg., A ˚ 3) for the 1:1 alkali-metal salts of TCNQ. The stacking axis is Table 17.3. Crystal data (A in bold Salt

a/

b/

TTFCl0.77

10.77

22.10

to TTFCl0.77 6.99 23.71 90.1 98.6

Group I: Antistructures Na TCNQ at 296K (Konno and Saito, 1974); NATCNQ Na TCNQ at 353K (Konno and Saito, 1975); NATCNQ01 K TCNQ at 298K (Konno, Ishii and Saito, 1977)*; KTCYQM01 K TCNQ at 413 (Kobayashi et al., 1973); KTCYQM02 Rb TCNQ-I at 113K (Hoekstra et al., 1972); RBTCNQ Rb TCNQ-III at 298K # (Bodegom et al., 1977); RBTCNQ02 NH4 TCNQ-I at 293Kx NH4 TCNQ at 311Kx NH4 TCNQ-II at 298K; AMTCNQx Group II Rb TCNQ-II# (Shirotani and Kobayashi, 1973); RBTCNQ01

c/

Vol.

Z

Space group

3.56

847.3

4

12.47 90.8

2044

8

C 1

Interplanar spacings

3.21/3.49 Displaced R/R

3.51

11.87 98.2

12.47

514

2

P21/n

3.39 Displaced R/R

7.08

17.77 95.0

17.86

2240

8

P21/n

3.24/3.57 Displaced R/R

3.59

12.68 96.4

12.61

570

2

P21/c

3.48 Displaced R/R

7.19

12.35 98.9

13.08

1147

4

P21/n

3.16 (R/R) 3.48 (R/EB)

17.65

17.65

3.86

1203

4

P4/n

3.33(R/EB)

18.19 18.23 12.50

17.75 17.80 12.50

7.19 3.61 3.82

2321 1171 5972

8 4 2

orthorhombic orthorhombic P4/mbm average structure

no structure no structure (R/EB )

9.91 92.7

7.20 86.2

3.39 97.7

275

1

P 1

3.43(R/EB)

Notes: ˚ , has been reported (Richard et al., 1978; * A very similar structure at 298K, differing only in that a ¼ 3.54 A ˚. KTCYQM). The interplanar spacing is 3.44 A # Region of temperature stability not stated. x NH4 TCNQ polymorphs studied by Kobayashi (1978).

˚ ), the interplanar spacing being 3.26(1) A ˚ . As there of TCNQ ions along [100] (¼3.868 A is one formula unit in space group P 1, the planar but noncentrosymmmetric cations must be disordered over two orientations. The high conductivity is difﬁcult to reconcile with the apparently integral charge on the anions. Thus it seems probable that the crystal structure reported by Fritchie (1966; MPHCQM) is only an average structure and disorder must be taken into account in any explanation of the physical properties (Kobayashi, 1975). This does not yet seem to have been worked out in detail.

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1191

17.4.4.2 Isolated diad stacking {[Pt(NH3)4]2þ (TCNQ)22} contains centrosymmetric -dimers with an interplanar ˚ and displaced R/R overlap (L ¼ 0, M ¼ 1.1 A ˚ ) (Endres et al., spacing of 3.14 A 1978a; TCQMPT). Limited precision prevented assignment of charges to TCNQ moieties via bond lengths. The ESR spectra show one exchange-narrowed line of about 5G width without ﬁne structure; the paramagnetism increases with temperature. If it is assumed that a thermally activated triplet state becomes occupied, then the activation (or exchange) energy is 0.05 eV (400 cm1); this is similar to the singlet-triplet separation of 246(20) cm1 in TMPD.ClO4 (Section 17.3.4). {Dibenzenechromium TCNQ} appears to have a similar structure with isolated diads ˚ ) stacked along [001] (Shibaeva, Shvets (displaced R/R overlap, interplanar spacing 3.28 A and Atovmyan, 1971; BCRLQM). 17.4.4.3 Diad stacks Four examples have been reported. In {4-oxo-6-iodoquinolinium TCNQ} there are stacks ˚ ), with TCNQ interplanar spacings of 3.09 and 3.32 A ˚ (Keller, along the a axis (7.16 A Steiger and Werner, 1981; BARTIX). In {ditoluenechromium TCNQ} (Shibaeva, ˚ ), Atovmyan and Rozenberg, 1975; DTCRCQ10) there are diad stacks along [100] (7.00 A with incipient -dimerization in the following sense. There is R/R overlap of two cen˚ ; such pairs are trosymmetrically related TCNQs, the interplanar spacing being 3.33 A ˚ with themselves related by centres of symmetry, the interplanar spacing here being 3.42 A some sideways displacement from an eclipsed arrangement. The conductivity is low (4 102 S/cm), in agreement with integral charges on the cations and anions. There is more deﬁnite -dimerization in {morpholinium TCNQ} (Sundaresan and Wallwork, 1972e; MORTCD), where the almost eclipsed TCNQs of the centrosymmetric -dimer ˚ , while adjacent -dimers in a stack hardly overlap (R/R overlap) are separated by 3.28 A ˚ . Each morpholinium across centres of symmetry, with an interplanar spacing of 3.61 A cation forms two pairs of weak bifurcated N . . . N hydrogen bonds (d(N . . . N) ranges from ˚ ) to four TCNQ anions. There is a phase change at 424K, with 2.92 to 3.11 A H ¼ 2.1(1) kJ/mol; ESR studies suggest there is only a minor structural change and essentially no change in the spin state of the anions (Bailey and Chesnut, 1969). Rather similar -dimerization is found in {[Fe(C5H5)2][(TCNQF4)]} (FETBEL) where TCNQF4s ˚ , while adjacent -dimers in of the -dimer (displaced R/R overlap) are separated by 3.22 A a stack overlap somewhat less (but also in displaced R/R fashion) with an interplanar ˚. spacing of 3.68 A 17.4.4.4 Tetrad stacks These have been brieﬂy reported in {chlorpromazine TCNQ} (Metzger et al., 1974). More detail is available for {(1,1 0 -ethylene-2,2 0 -bipyridylium)2þ(TCNQ)2} (Sundaresan and Wallwork, 1972d; EBPTCQ), where the TCNQ stack contains two crystallographicallyindependent -dimers well separated from one another (Fig. 17.27). In {diethylmorpholinium (2,5-dichloro-TCNQ)} (DEMTCNQCl2) (Bryce and ˚ ) and Howard, 1982; BIPJAL10); P21/n, Z ¼ 8) there is a sequence of R/EB (3.38 A ˚ displaced R/R (3.28 A) overlaps, the latter being across a crystallographic centre of symmetry. Thus -dimers can hardly be identiﬁed.

1192

SEGREGAT ED STACK -MOLECULAR COMPLEXES

row of cations c sin β

A⬘ little overlap B⬘ R/EB overlap

B

A

0

b sin γ

Fig. 17.27. The moiety arrangement in (1,1 0 -ethylene-2,2 0 -bipyridylium)2þ(TCNQ)2 viewed ˚ ) and the two anions denoted as A and B are along [100]. The stack axis is [001] (14.625 A crystallographically independent. The interplanar distances A 0 A and B 0 B (shaded pair) are ˚ and the overlap is R/EB. The A and B anions hardly overlap, the respectively 3.22 and 3.26 A ˚ . The dihedral angle between the two pyridinium rings of nominal interplanar spacing being 3.59 A the cation is 22 . (Reproduced from Sundaresan and Wallwork, 1972d.)

17.4.5

Stacked structures with 0.8e average charge on the TCNQ moieties

The cation is 1,2-di(N-ethyl-4-pyridinium)ethane (DEPA) in the only TCNQ example, {(DEPA2þ)2(TCNQ)54},(Ashwell, Eley, Wallwork, Willis, Welch and Woodward, 1977; EPETCR). The crystals are triclinic, P 1, Z ¼ 1. There are pentad stacks along [001] ˚ ). Although the interplanar spacings between adjacent TCNQs are essentially the (16.24 A ˚ ), there are different kinds of overlap, as shown below: same (3.24(5) A |←⎯⎯⎯⎯⎯⎯⎯16.24 Å⎯⎯⎯⎯→| – 1 TCNQ moiety Type of overlap

C⬘

C R/EB

– 1 A

B R/R

– 1 B⬘

C⬘

C

R/EB

The stack can thus be considered as made up of a -dimer (CC 0 ) and a centrosymmetric triad (BAB 0 ). The CSD formulation as {(DEPA2þ)2 (TCNQ)(TCNQ)4} does not seem to be justiﬁed, The conductivities along the three crystallographic axes are 6.7 104, 5.6 102 and 4 102 S/cm respectively. As the bond lengths in the various TCNQ moieties were not signiﬁcantly different (but precision was not high), it was inferred that the four electrons are delocalized over the ﬁve TCNQ moieties. The ESR spectra were complex and not completely interpretable. The modest conductivity along the stack axis presumably is a consequence of the R/R overlap separating the -dimer and the triad in the stack. 1,4,5,8-Naphthalenetetracarboxylic anhydride and diimide analogs have been shown to form semiconducting anion radical salts with various cations (Heywang et al., 1989).

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1193

Line of cations Stack of anions C

A A/A⬘; 0°; 3.206 A; graphite-like overlap A⬘ A⬘/B⬘; 5°; 3.188–3.643 A; carbonyl/ring overlap B⬘ B⬘/D⬘; 1°; 3.194–3.288 A; carbonyl/ring overlap D, at centre

A z B y

Fig. 17.28. Projection of {[(5,6-dihydro-4a,6a-phenanthrolinium)2][(1,4,5,8-naphthalenetetracarboxylic anhydride)5]} structure down [100]. The reduced cell (used in the structure analysis) is 8.935 ˚ , 112.38 92.03 93.68 . Z ¼ 1)). The molecules are denoted A, B . . . following Born 12.785 15.995 A and Heywang (1991), and interplanar spacings, angles between successive pairs of molecular planes and modes of overlap are shown in the diagram. (Data from Born and Heywang, 1991.)

Pentad stacking is found in the centrosymmetric triclinic crystals of {[(5,6-dihydro-4a,6aphenanthrolinium)2][(1,4,5,8-naphthalenetetracarboxylic anhydride)5]} (Born and Heywang, 1991; VARKEE10) (Fig. 17.28). Conductivity measurements suggest a phase change at 150K; only the 300K structure has been determined. The carbonyl ˚ , with a mean of 1.206 A ˚ . This suggests bond lengths vary between 1.202 and 1.210 A delocalization of charges. The carbonyl bond length in neat 1,4,5,8-naphthalene˚ (Born and Heywang, 1990; KENDEM). tetracarboxylic anhydride is 1.186 A The importance of this structure lies in the demonstration that radical anions other than TCNQ and some others can form stacks. It is not clear whether attempts were made to prepare cation radical anion radical salts. Does a crystal chemistry analogous to that of TCNQ exist for 1,4,5,8-naphthalenetetracarboxylic anhydride, and perhaps other acceptors? 17.4.6 Stacked structures with –2/3e average charge on the TCNQ moieties Nine examples are discussed, six as {(Mþ)2(TCNQ)32} and three as {M2þ(TCNQ)32}. The arrangements of the TCNQ moieties in the triads are summarized in Table 17.4; these triads can be isolated (three examples) or stacked (six examples). The formation of triads

1194

SEGREGAT ED STACK -MOLECULAR COMPLEXES

is characteristic of a Peierls distortion of a uniform stack when 2n excess electrons are shared by 3n moieties (Su and Schrieffer, 1981; Gammell and Krumhansl, 1983). IR spectroscopy has potential usefulness for demonstrating the presence of TCNQ0 and TCNQ; two distinct absorptions, at 1453 cm1 (TCNQ0) and 1386 cm1 (TCNQ), have been found for {(morpholinium)2(TCNQ)3} (Sundaresan and Wallwork, 1972a; MORTCQ) and Cs2(TCNQ)3 (Fritchie and Arthur, 1966; CSSCNM10). The more isolated triads can be described as (TCNQ TCNQ0 TCNQ) but the interplanar distances in Rb2TCNQ3 and Cs2TCNQ3 suggest the alternative description of -dimers separated by neutral TCNQs in the pseudomonad stacks of these salts: : . . . ðTCNQ TCNQ Þ TCNQ0

ðTCNQ TCNQ Þ: . . .

Perhaps there is a gradual transition from one arrangement to the other. The -dimer – TCNQ0 – -dimer description is compatible with the zero-splitting parameters in Cs2TCNQ3 (D ¼ 280.4(6), E ¼ 45.3(1.4) Mc/sec), which indicate that the two electrons of the TCNQ triad are present as a tightly bound or Frenkel exciton, probably located on the triad itself (Chesnut and Arthur, 1962). Very similar values have been obtained for the zero-splitting parameters in {(morpholinium)2TCNQ3} (Bailey and Chesnut, 1969). Considerable attention has been paid to Cs2TCNQ3. This salt is a semiconductor with 103 S/cm at room temperature, only slightly higher than that of K(TCNQ). There are two CT transitions, one at 3900 cm1 between the neutral molecule and anions of a triad, and one at 10000 cm1 between anions of different triads. The electronic charge along a stack is described as a ‘‘pinned charge density wave,’’ presumably induced by the Coulomb potential of the cations. The IR and Raman spectra in the region of the intramolecular modes have been reinterpreted, taking interactions between electronic and molecular vibrations into account (Painelli et al., 1986). On this basis a charge of 0.1e has been assigned to the formally neutral TCNQ moiety at centres of symmetry and of 0.9e to the anions in general positions. The crystal structure of {3-( p-methoxyphenyl-1,2-dithiolylium)2(TCNQ)3}, which has not been included in Table 17.4, has been brieﬂy (Amzil et al., 1986) and more extensively reported (Mathieu, 1986; DUXRET). The interplanar distance within the triad ˚ (R/EB overlap, L ¼ 2.03, M ¼ 0.03 A ˚ ) and that between triads is 3.43 A ˚ is 3.17 A ˚ ). Bond lengths suggest that the charge (displaced R/R overlap, L ¼ 0.51, M ¼ 1.69 A is equally distributed over all three TCNQ moieties. H3C O

S

S

+

3-(p-methoxyphenyl-1,2-dithiolylium)

Triads are also found in the 2 : 3 charge-transfer salt of tetraethylammonium and 4,8-bis(dicyanomethylene)-4,8-dihydrobenzo[1,2-b:4,5-b 0 ]dithiophene (P21/n, Z ¼ 2) (Yasui et al., 1992; PANVOX). The salt shows the relatively high conductivity of 0.46 S/cm. One of the anions (A) is at a centre of symmetry and the other (B) at a general position. Bond lengths suggest that A is neutral and B singly charged. The A . . . B

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1195

Table 17.4. Arrangement of TCNQ moieties in M2(TCNQ)3 anion radical salts. The structures were ˚ ) are not strictly determined at room temperature unless stated otherwise; the interplanar distances (A comparable because the various authors do not use a standard method of calculation Compound

Stacking arrangement

1. (N-methylphenazinium)2 (TCNQ)3 (Sanz and Daly, 1975); MPZTCQ

B0

2. [1,4-di(N-quinoliniummethyl)benzene](TCNQ)3 (Ashwell, Eley, Wallwork, Willis, Peachy and Wilkos, 1977); AMBTCQ 3. [Bis(triphenylphosphoranediyl) (TCNQ)32CH3CN (Halfpenny, 1985); COVMIJ 4. 1,1 0 -bi-cobaltocene[CoIIICoIII](TCNQ)3 (Lau et al., 1982); BEHGEA 5. [Fe2(-C5H5)2(-CO)2 {-Ph2PN-(Et)PPh2}] (TCNQ)3CH3CN (Bell et al., 1991); KIRDUK 6. Bis(2,2 0 -bipyridyl)-Pt(II) (TCNQ)3 (Endres et al., 1978b); PYPTCR 7. Rb2(TCNQ)3 at 294K (Wal and Bodegom, 1978); RBTCNR 8. Rb2(TCNQ)3 at 113K (Wal and Bodegom, 1979); RBTCNR01 9. Cs2(TCNQ)3 at 294K (Fritchie and Arthur, 1966); CSSCNM10 10. (Morpholinium)2 (TCNQ)3; (Sundaresan and Wallwork, 1972d); MORTCQ

B0

B

0

Remarks

1

1 A (3.15)B(3.26)B 0 R/EB 1

1 A(3.12)B R/EB

B0

A0

A0

1 A(3.30)B R/EB

1 1 B 0 (3.15)A(3.15)B(3.45) B 0 R/EB mixed B 0 (3.24)A (3.24)B(3.39)B 0 R/EB displaced R/R

B

0

B0 B0 B0 B0

1 1 (3.23)A (3.23)B(3.33)B 0 R/EB displaced R/R 1 1 A (3.28)B(3.12)B 0 R/EB displaced R/R 1 1 A (3.23)B(3.07)B 0 R/EB displaced R/R 1 1 A (3.27)B(3.12)B 0 R/EB displaced R/R 1 1 A (3.25)B(3.24)B 0 R/EB displaced R/R

No B/B 0 overlap, thus isolated triads; A, B charges not assignable. No B/B 0 overlap, thus isolated triads; A, B charges not assignable. Triads widely separated; A assigned as TCNQ0, B as TCNQ. Triad stacks; A, B charges not assignable. Triad stacks; A, B charges not assignable. Triad stacks; A, B charges not assignable. Triads arranged in pseudo-monad stacks. Triads arranged in pseudo-monad stacks. Triads arranged in pseudo-monad stacks. Triads arranged in pseudo-monad stacks.

Notes: Rb2(TCNQ)3 and Cs2(TCNQ)3 are isomorphous; in # 7, 8, 9, 10 A ¼ TCNQ0 and B ¼ TCNQ, from bond lengths and IR spectra.

˚ , with R/EB overlap, and the B . . . B separation 3.39 A ˚ , with separation in a stack is 3.47 A displaced R/R overlap. The interpretation of these intrastack separations is ambiguous because of the presence of the bulky S atoms in the anions, and of side-by-side linkages ˚. between stacks by short S . . . S contacts of 3.570(3) and 3.529(3) A

1196

SEGREGAT ED STACK -MOLECULAR COMPLEXES

(Triethylenediammonium)2(TCNQ)3 [(TEDA)2(TCNQ)3] (also not in Table 17.4) requires special mention. The IR spectrum shows only one absorption, at 1416 cm1, leading to the inference that this triad is delocalized. The crystal structure (Bandrauk, Ishii et al., 1985) has irregular stacks of TCNQ moieties arranged in centrosymmetric triads ˚ ) and a more with displaced R/R overlap within a triad (interplanar spacing 3.22 A ˚ accentuated R/R overlap (3.45 A) between triads). The bond lengths suggest that the central TCNQ bears a charge of 0.8e and that the ﬂanking TCNQs each have a charge of 0.6e; this is quite different from the approximately e, 0, e distributions of some of the M2TCNQ3 structures listed in Table 17.4. The difference was ascribed to the much weaker interaction between cations and anions in (TEDA)2(TCNQ)3 than in, say, Cs2TCNQ3. 17.4.7

Stacked structures with 0.5e average charge on the TCNQ moieties

Two major groups can be distinguished. In the ﬁrst group TCNQ diads (-dimers) or tetrads are arranged in stacks but with virtually no overlap between successive diads or tetrads. We call these isolated diad or tetrad stacks. In the second group the diads or tetrads, although distinguishable to a greater or lesser extent, quite clearly overlap and interact. 17.4.7.1 Isolated diad or isolated tetrad stacking The following salts have been reported with isolated-diad stacking at room temperature (for #1–10 only cations are listed, the anions all being (TCNQ) 2 ). 1. 3,3 0 -diethylthiacarbocyanine (monoclinic polymorph) (Kaminskii et al., 1973a); ECYTCN10 2. tetraphenylphosphonium (Goldstein et al., 1968); PPHTCQ 3. 5,5 0 -dimethylphosphonium (Ashwell, Allen et al., 1982); BINREV 4. tetraethylammonium (Shibaeva, Kaminskii and Simonov, 1980) 5. N-(n-propyl)pyridinium (Konno and Saito, 1981); PYTCNA10 6. N-methyl-N-ethylmorpholinium(at113K)(Bosch andBodegom,1987); MEMTCQ10 7. 1,2,4-trimethylpyridinium (at 300K; Rizkallah et al., 1983; BOHNOB. At 173K Graja et al., 1983) 8. 4,4 0 -diethylmorpholinium (Morssink and Bodegom, 1981); DEMTCN 9. 1-methyl-1,4-dithianium (Bryce et al., 1988); JACPUY 10. N2-methylcinnalinium (Daoben et al., 1985); CUMHAT10 11. N1-methylcinnalinium (Daoben et al., 1985); CUMHEXT10 12. (1,1 0 -tetramethylene-dipyridinium)2þ (TCNQ)42 (cation is also called ‘dipyridylbutene’ DBP) (Waclawek et al., 1983); PYBUTQ10 13. (N,N,N,N 0 ,N 0 ,N 0 -hexamethylhexa-methylenediammonium)2þ (TCNQ)42 (Flandrois et al., 1979); HMACQM The arrangement of the anions is remarkably similar in all these salts – the -dimers are centrosymmetric (although not necessarily located at a crystallographic centre of symmetry e.g. entries #4 and 6), and have interplanar spacings lying between 3.17 and ˚ , with R/EB overlap between the two moieties. In some of the examples it was not 3.23 A possible to distinguish between the two TCNQ moieties of the -dimer on the basis of

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1197

bond lengths, while in others the two TCNQ moieties were crystallographically equivalent; the usual inference was that there was real electron delocalization. The conductivities were found to be intermediate, i.e. 103 S/cm. At room temperature #5 has two independent dimers in the unit cell, with an angle of 17.5 between their planes. The bond lengths in the TCNQ moieties are identical so both are described as TCNQ1/2. There is a ﬁrst-order insulator-metal transition at 388K; the high-temperature phase has a uniform zigzag stacking of TCNQ moieties. #6 has been studied over a wide range of temperatures and is discussed in more detail in Section 17.4.8. (DEM)(TCNQ)2 (#8) requires special mention because there are two kinds of TCNQ arrangement in sheets parallel to (010), separated by disordered cations (Fig. 17.29(upper)); there are both isolated -dimers (A 0 A) and isolated tetrads (BB00 B00 B), the angle between the normals to the planes of A and B being 57.4(5) . Such a marked difference between the arrangements of two sets of TCNQ moieties in the same crystal is most unusual. The so-called AA 0 ˚ being typical ‘-dimer’ is rather weakly bound, with the interplanar spacing of 3.41 A of R/R overlap; the planes of these TCNQ moieties are approximately parallel to (001). The B moieties have their planes approximately parallel to (111). The ‘isolated tetrad’ is probably better described as consisting of two poorly-overlapping -dimers, which have ˚ typical of strongly bound moieties with R/EB overlap. The the internal spacing of 3.14 A types of overlap are shown in Fig. 17.29(lower) and are described by the displacements given in the caption to this ﬁgure. Various morpholinium derivatives have the formula shown below; thiomorpholinium has O replaced by S. (thio)morpholinium formulae R1 O

N R2

+

R1 = R2 = methyl: DMM , 4,4⬘-dimethylmorpholinium; R1 = methyl, R2 = ethyl: MEM; R1 = R2 = ethyl: DEM; R1 = methyl, R2 = H: HMM.

An arrangement similar to that in {DEM(TCNQ)2} is found in N-methylmorpholinium (TCNQ)2 {HMM(TCNQ)2} (space group P41, Z ¼ 4); the successive TCNQ stacks along [001], interleaved by cations, are equivalent but mutually rotated by 90 (Visser et al., 1990; DESGIR11). Indeed {HMM(TCNQ)2} and {pyrene p-benzoquinone} (Section 15.2) have structural resemblances. There is another remarkable structure (Endres, 1984; CURTIS) with a resemblance to (DEM)(TCNQ)2 in the sense of having non-parallel stacks. This is bis[(oxamide oximato)(oxamide oxime)Pt(II)] [tris(tetracyanoquinodimethane)diide] or {[Pt(oaoH)(oaoH2)]þ}2(TCNQ)32 (for formula see Section 17.4.4(a)). The triclinic crystals (space group P1 Z ¼ 1) have two sets of mutually-perpendicular stacks. One is a diad stack containing crystallographicallyequivalent TCNQ moieties with average charge of 0.5e arranged in zigzag fashion with ˚ . The second stack is mixed and alternating interplanar spacings of 3.08 and 3.27 A contains a n n n

: . . . D D A D D A D D: . . . arrangement. The DC conductivity is 12 S/cm at 300K. This is the only structure known (to me) in which there are both segregated and mixed stacks.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1198

TCNQ stack B

TCNQ cations

B

stack A A

cations cp

bp

O

A

AA0

A9

A

A

B0

B B

B9 B B

B-

B9

Fig. 17.29. (upper) The crystal structure of (DEM)(TCNQ)2 projected down [100]. The A and B stacks are inclined at an angle of 57.4(5) ; (lower) the types of overlap. The A00 and A000 moieties are diagonally displaced above A, as are B00 and B000 with respect to B; the BB 0 overlap is that of a standard -dimer. The mutual displacements of various pairs of moieties are given below: Pair of moieties 0

AA B 0 B -dimer’ BB00

˚) L(A

˚) M(A

˚) N(A

Type of overlap

0.14 2.02 1.17

0.76 0.07 2.08

3.41 3.14 3.36

Shifted R/R R/EB Diagonal shift between R/R and R/EB

(Adapted from Morssink and Bodegom, 1981)

(ii) Isolated-tetrad stacking: the known structures are listed in Table 17.5; two groups can be distinguished. In the ﬁrst of these (Type I) the tetrads can be separated into two -dimers, with displaced R/R overlap between them, while in the second group (Type II) the four TCNQ moieties of a tetrad are separated by essentially identical interplanar spacings and have R/EB overlap. The salts [1,3-di(N-pyridinium)propane](TCNQ)4 (Ashwell, Bartlett et al., 1977; PYPTCQ) and [N, N 0 -diethyl-4,4 0 -bipyridylium](TCNQ)4 (Ashwell, Eley et al., 1975;

STRUCTURE OF TCNQ ANION-RADICAL SALTS TCNQ anions

TCNQ anions

TCNQ anions cations

C

1199 TCNQ anions

cations

A

B

D9 A

B z

B

A

D9 y

D

O

y x

Fig. 17.30. Left: Crystal structure of [1,3-di(N-pyridinium)propane](TCNQ)4 projected down [100]. The crystals are monoclinic, space group P21; this is a rare example of a TCNQ salt crystallizing in a Sohncke space group. Note the eight molecules of TCNQ in a stack period, and the sinusoidal proﬁle of the stack, conforming to the conformation of the cation. Right: analogous projection (down [001]) for [N, N 0 -diethyl-4,4 0 -bipyridylium](TCNQ)4; the crystals are monoclinic, space group P21/c. (Data from Ashwell, Bartlett et al., 1977 and Ashwell, Eley et al., 1975.)

EPMTCQ) require special mention because they have the largest (room temperature) ˚ ) yet encountered. These are octad stacks with two tetrads stack periodicities (both 25.3 A ˚ period, each tetrad consisting of two -dimers. The sinusoidal proﬁles of the in the 25.3 A stacks (Fig. 17.30) suggest that there is a strong mutual interaction between the detailed arrangements of the cation and anion stacks, but it is not clear which of these has the predominating inﬂuence. The conductivities along the stack axes have intermediate values, consistent with the jogs in the stacks. 17.4.7.2 Fully stacked arrangements (i) Monad or pseudomonad stacking: There are a number of examples in this category ˚ along the stack (Table 17.6); we note that a monad stack will have a periodicity of 3.6 A ˚ but the overlaps are axis, while in a pseudomonad stack the periodicity is 7.2 A crystallographically equivalent. (ii) Diad or pseudo-diad stacking: The examples reported are summarized in Table 17.7. Presumably the distinction between this group and those classiﬁed earlier as isolated diads is gradual rather than sharp. -Dimers can be identiﬁed in most of the present group and the entries in Table 17.7 have been arranged so as to proceed from salts with greater separation (isolation) between -dimers to those in which this separation tends towards that in the -dimer itself.

1200

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Table 17.5. Salts with isolated-tetrad stacking (all measurements at room temperature, unless stated otherwise) Salt TYPE I: 1. [1-methyl-3,3-dimethyl-2( p-N-methyl-N--chloroethylstyryl)indole]þ(TCNQ)2 (Shibaeva, Rozenberg and Atovmyan, 1973) 2. [1,2-di(N-methyl-4pyridinium)ethane]2þ(TCNQ)42 (Ashwell, Eley et al., 1977); MPETCQ 3. [1,3-di(N-pyridinium)propane]2þ(TCNQ)42 (Ashwell, Bartlett et al., 1977); PYPTCQ 4. [N, N 0 diethyl-4,4 0 bipyridylium)]2þ-(TCNQ)42 (Ashwell, Eley et al., 1975); EPMTCQ TYPE II: 1. [3,3 0 -diethylthio-carbocyanine]þ (TCNQ)2 (Kaminskii et al., 1973b) 2. [N, N 0 -dibenzyl- 4,4 0 bipyridylium)]2þ- (TCNQ)42 (Sundaresan and Wallwork, 1972c); BPYTCQ

3. [1,2-Di(N-ethyl-4-pyridinium)ethylene]2þ(TCNQ)42 (Ashwell, Eley, Fleming et al., 1976); EPETCQ 4. [1,1 0 -bis(p-cyano-phenyl4,4 0 -bipyridylium)]2þ (TCNQ)42 (Ashwell, Cross et al., 1983); CAVJIS 5. [Pd(NCCH3)4]2þ(TCNQ)22CH3CN (Goldberg, Eisenberg et al., 1976); ICPTCQ 6. [1,4-di(diphenyl-methylphosphonium)benzene]2þ(TCNQ)42 (Batail et al., 1985); DOZPAJ

Stacking arrangement

Remarks

A(3.12)B(3.45)B 0 A 0 R/EB displ R/R

A(3.20)B(3.39)B 0 R/EB displ R/R

A(3.20)B(3.25)C (3.18) D R/EB displR/EB R/R B(3.19)A(3.16)A 0 R/EB R/EB

A(3.28)B(3.28) B 0 R/EB R/EB B(3.16) A(3.24) A 0 B 0 R/EB R/EB

B(3.32) A(3.15) A 0 displ R/EB R/EB B(3.36) A(3.28) A 0 displ R/EB R/R B(3.29)A(3.32) A 0 B 0 displR/EB R/EB 7.4 dihedral angle A(3.25)B(3.33) B 0 A 0 R/EB R/EB

Two such tetrads per period along stack axis. Two such tetrads per period along stack axis.

The tetrads are separated by BB 0 overlap of displaced EB/EB type and interplanar spacing ˚. of 3.62A The tetrads do not overlap directly.

No overlap between adjacent tetrads. A is neutral (0.3e) and B is anion (0.7e) from bond lengths. Solvate molecules poorly deﬁned. No overlap between adjacent tetrads. Overlap of tetrads not described.

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1201

Table 17.6 TCNQ arrangements in M(TCNQ)2 ion radical salts with monad or pseudomonad ˚ ) is the interplanar spacing, and (S/cm) is the conductivity, both along the stack stacks. D(A direction Salt

TCNQ stack arrangement

1. N-methylphthalazinium (TCNQ)2 at 130K (Yan and Coppens, 1987); FOVZUL

A... ...A R/EB

2. Quinolinium (TCNQ)2 (Kobayashi, Marumo and Saito, 1971); QUTCNQ 3. Ditoluene-chromium (TCNQ)2 at 153K (Shibaeva, Atovmyan and Ponomarev, t 1975). 4. Acridinium (TCNQ)2 (Kobayashi, 1974); ARDTCQ 5. 5-t -butyl-3-methylthio1,2-dithiolyl- (TCNQ)2 (Amzil et al., 1986); 6. [5-Cyclo-pentadienyl-6hexamethylbenzene-Fe(II)] (TCNQ)2 (Lequon et al., 1985); 7. (Diphenylphosphoniumcyclohexadiene)2þ (TCNQ)2 4 (Batail et al., 1985); DOZPEN

1 A . . . . . . A0 R/EB 1 1 A . . . . . . A0 R/EB

˚) D(A A

1

3.178(2)

Remarks (S/cm) 120

3.22(1)

100

3.16(1)

2

A 1 A

x1 and x2 isomorphous, C2/c, Z ¼ 4. Monad stack with TCNQs translationally equivalent. ˚ x1 has [010] ¼ 3.77 A and x2 has ˚. [010] ¼ 3.838 A TCNQs at independent centres of symmetry.

1 1 A . . . . . . A0 A R/EB A . . . . . . A0 . . . . . . A R/EB R/EB

3.246

3.24, 3.24

4

Zigzag pseudomonad stack.

A . . . . . . A0 . . . . . . A R/EB R/EB

3.34, 3.34

4

Zigzag pseudomonad stack.

A . . . . . . A0 . . . . . . A . . . . . . A0 R/EB R/EB R/EB

3.20, 3.27

>> 1

Zigzag pseudomonad stack. Phase change at 205K.

Possible 2nd order transition at 180K.

(iii) Tetrad or pseudotetrad stacking: this group (Table 17.8) follows on gradually from the structures summarized in Table 17.7. The structures and physical properties of the {(thio)morpholinium (TCNQ)2} complexes have been reviewed (Visser, de Boer and Vos, 1993) and the abstract bears quotation in full: Crystal structures of the title compounds are compared. Classes I, II and II’ with 2, 4 and 8 TCNQ moieties per translation period, respectively, are distinguished. For class I a subclassiﬁcation is made according to: the number of inequivalent stacks (1 or 2); cation disorder [dynamic (d) or static (s)]; and chain directions [parallel (p) or crossed (c)]. Crystals of classes II and II’ appear to be (1, d, p). Disorder of the cations is a frequent phenomenon. Generally, changes in the ordering of the cations play an important role in the phase transitions. Magnetic susceptibility curves (T) turn out to be different for the various (sub)classes. Within each (sub)class the electrical conductivity decreases with increasing calculated band gap. A quantitative interpretation of the electrical transport properties is considered impossible because of the interaction between charge carriers and the dynamic

1202

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Table 17.7. Salts with diad or pseudo-diad stackings. All structures determined at room temperature ˚ unless stated otherwise. Interplanar spacings are in A Salt

Stacking arrangement

1. Trimethyleneferrocenium (TCNQ)2 (Willi et al., 1980) 2. (3,3 0 -dimethylthiacyanine)(TCNQ)2 (Shibaeva et al., 1974)

A . . . (3.14) . . . A 0

3. (N-ethyl-ophenanthrolinium) (TCNQ)2 (Chasseau et al., 1976); EOPTCO 4. (4,4 0 -dimethylmorpholinium) (TCNQ)2 (DMM)(TCNQ)2 (Kamminga and Bodegom, 1981); DMMTCN 5. (1-N-methylcinnalinium) (TCNQ)2 (Daoben et al., 1985); CUMHEX10

A . . . (3.25) . . . B displR/EB

(3.54)

Remarks A . . . A0

(3.38) A 0 . . . .B 0 displR/R

A00 . . . (3.17) . . . A (3.40) A 0 R/EB displR/EB

A00 . . . (3.25) . . . A (3.29) A 0 displR/R displR/EB

A00 . . . (3.27) . . . A R/EB

(3.24) R/EB

Formally a cation-radical anion- radical salt. Zigzag stack; A, B crystallographically independent; A, A 0 and B, B 0 related by 21 axis. Cations disordered across centre of symmetry.

Cations disordered across mirror plane. Little overlap between -dimers.

A0

Notes: 1. N,N 0 -dimethylthiomorpholinium (TCNQ)2 (DMTM)(TCNQ)2; Visser, de Boer and Vos, 1990b; DAWVOM02) is isomorphous with DMM(TCNQ)2. 2. Diad stacks are also found in N-methyl-N-ethylthiomorpholinium (TCNQ)2 (DESFOW03) and N-methyl-Nbutylthiomorpholinium (TCNQ)2(VEJPIJ) (Visser, Bouwmeester, de Boer and Vos, 1990a). 3. Diad stacks are also found in N-methyl-N-propylmorpholinium (TCNQ)2 (DESFUC02) and N-methyl-Nbutylmorpholinium (TCNQ)2 (VEJFEV) (Visser, de Boer and Vos, 1990a). 4. Diad stacks are also found in N-butylthiomorpholinium (TCNQ)2 (DESFUC02) and N-methyl-Nbutylmorpholinium (TCNQ)2 (SEMZUF) (Visser, Smaalen, de Boer and Vos, 1990).

lattice as a whole. Large unpredictable variations in crystal structure are observed for chemically small modiﬁcations of the cations. Therefore, crystals with a priori desired properties cannot be designed in a systematic way.

The descriptions and conclusions can be carried over without much change to the wider variety of cations considered in the various parts of this chapter. 17.4.8

Stacked structures with 0.4e average charge on the TCNQ moieties

Two examples, of formula A2þ(TCNQ)2 5 , are known; the cations are respectively [1,2di(N-benzyl-4-pyridinium)ethylene] (Ashwell, Eley, Harper et al., 1977; BPETCQ) and

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1203

2þ 2 Table 17.8. Mþ(TCNQ) 2 and M (TCNQ) 4 salts with tetrad or pseudotetrad stacking. All structures determined at room temperature unless stated otherwise

Salt 1. Methyltriphenylphosphonium (TCNQ)2 (at 326K) (Konno and Saito, 1973; MPPTCQ01) 2. Methyltriphenylphosphonium (TCNQ)2 (at 298K) (Konno and Saito, 1973; MPPTCQ02); McPhail et al., 1971; MPPTCQ) 3. [N-(n-propyl)phosphonium (TCNQ)2 (Sundaresan and Wallwork, 1972b); PQTCNQ 4. 4-Ethylmorpholinium (TCNQ)2 (Bodegom and Boer, 1981); HEMTCN 5. [N-ethyl-2-methylthiazolinium (TCNQ)2 (Shibaeva and Ponomarev, 1975); 6. Triethylammonium (TCNQ)2 (Filhol, Zeyen et al., 1980); TCQETA02; ND at 40K. 7. [1-Methyl-3ethylbenzimidazolinium](TCNQ)2 CH3CN (Chasseau et al., 1973a); TCQMIM 8. [N,2-Dimethyl-N 0 ethylbenzimidazolinium] (TCNQ)2CH3CN (Chasseau et al., 1973b); TCQMEJ 9. [8-Hydroxyethoxy-5chloro-1-methylquinolinium] (TCNQ)2CH3CN (Bunzel et al., 1984); CINKEP 10. (C24H23N2O)þ (TCNQ)2 Malatesta et al., 1995 ZAGCEP

Stacking arrangement 1 1 B 0 (3.32) A 0 (3.26) A (3.32) B (3.55) B 0 R/EB R/EB displR/R 1 1 B (3.20) A (3.20) A (3.20) B (3.58) B 0 R/EB R/EB displR/R 0

0

Remarks First order transformation at 316K; H 2 kJ/mol. 2 105 S/cm. Isomorphous with arsonium analogue (MPATCQ)

1 1 B 0 (3.24) A 0 (3.28) A (3.24) B (3.43) B 0 R/EB R/EB displR/R 1 1 0 0 B (3.24) A (3.42) A (3.24) B (3.31) B 0 R/EB R/EB displR/R 1 1 B (3.30) A (3.30) A (3.30) B (3.30) B 0 R/EB R/EB displR/EB 0

0

1 1 B (3.24) A (3.30) A (3.24) B (3.32) B 0 R/EB R/EB R/EB 0

0

1 1 B (3.28) A (3.32) A (3.28) B (3.28) B 0 R/EB R/EB R/EB 0

0

1 1 B 0 (3.21) A 0 (3.27) A (3.21) B (3.38) B 0 R/EB R/EB R/EB 1 1 B (3.18) A (3.18) A (3.18) B (3.41) B 0 R/EB R/EB displR/R 0

0

1 1 A 0 (3.20) B (3.28) B00 (3.20) A00 R/EB R/EB R/EB

See text for detailed discussion (#17.4.9). x7 TCQMIM and x8 TCQMEJ are isostructural by comparison of reduced cells. Zigzag pseudomonad stack.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1204

Table 17.5. (Continued ) Salt 11. [1,4-Di(N-pyridinium methyl)benzene]2þ (TCNQ)2 4 (Ashwell, Wallwork et al., 1975); PYMBTQ 12. (Diethyl-morpholinium) (TCNQBr2)2 (Bryce and Howard, 1982); BIPJAL10

Stacking Arrangement

Remarks

1 1 B 0 (3.21) A 0 (3.31) A (3.21) B (3.48) B 0 R/EB displR/R displR/EB

A is anion, B is neutral, from bond lengths.

1 1 B (3.29) A (3.42) A (3.32) B (3.55) B 0 R/EB R/EB displR/R 0

0

Twisted; isomorphous with dichloro analogue.

Note: 1. Tetrad stacks are also found in N-ethyl-N-butylmorpholinium (TCNQ)2 (DESFUC02) and N-ethyl-Nbutylthiomorpholinium (TCNQ)2 (VEJFEV) (Visser, Bouwmeester, de Boer and Vos, 1990b).

TCNQ anions

TCNQ anions cations

TCNQ anions B

TCNQ anions

C9 C9 C

C

B

B O

A

A

y z

A

y

x

cations

cations cations

centro-symmetric pentad matching shape of cation

centro-symmetric pentad matching shape of cation

Fig. 17.31. BPETCQ – conformation of the pentad stacks to the shape of the cation. (Data from Ashwell, Eley, Harper et al., 1977.)

[1,2-di(N-benzyl-4-pyridinium)-ethane] (Ashwell, Eley, Drew et al., 1978; BPYETC). ˚ , 110.17 95.04 Comparison of the reduced cells3 (BPETCQ: 8.043 14.558 16.103 A ˚ 101.75 ; BPYETC: 8.109 14.607 16.165 A, 109.04 95.19 101.92 ; both P1, Z ¼ 2) shows that these two salts are isomorphous and thus can be discussed together. Within the 3

the cells in the original reports were not reduced.

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1205

pentads there is R/EB overlap between adjacent moieties, with the same direction of ˚ ; between pentads there is R/EB overlap staggering and interplanar spacings of 3.23(2) A ˚ but with the direction of staggering reversed and the interplanar spacing now 3.40 A (Fig. 17.31). The pentads of TCNQ conform to the disposition of the cation, as has been found in other examples (Fig. 17.30).

17.4.9 Systems studied over a wide range of temperatures The structural results summarized and classiﬁed in the previous sections generally refer to measurements made at room temperature. Physical measurements have often been made over a wide range of temperatures. However, very few systems have been studied both structurally and in terms of physical properties over a wide range of temperatures. The few results available illustrate the complexities of individual systems and how important it is to base interpretations of properties on detailed structural studies of well deﬁned chemical systems. Two obvious but often neglected points are emphasized ﬁrst and we then discuss four systems that have been studied extensively. (a) ordered systems are easier to describe and understand than disordered systems. Thus, where possible, we ﬁrst discuss the most ordered state of the system and then extrapolate towards the disordered situation. (b) the state of the crystal at any particular temperature is determined by interactions between cation and anion partial structures4 as well as by interactions within these partial structures. These are coupled systems; while the three types of interaction can be described separately, it is not easy to ascribe causes – for example, is ordering of the cations or an electronic transition in the anion partial structure responsible for a particular phase transition? (i) Triethylammonium (TCNQ)2 {[(TEA)(TCNQ)2]} The crystal structure has been determined at 345, 295, 234, 173, 110 (all by XRD) and 40K (neutron diffraction; TCQETA02) and the results, including earlier work, have been summarized by Filhol and Thomas (1984), whom we follow quite closely. The crystals are triclinic, P1, with Z ¼ 2 and a TEA cation and two TCNQs, A and B, in the asymmetric unit; the mean charge per TCNQ is 0.5e. The planar TCNQ moieties are stacked face to face with the repeat sequence BA( 1)AB leading to three independent spacing distances (dAA, dBB, dAB) and three independent overlapping modes (see Table 17.8). The packing may thus be described as a set of stacks of tetrads parallel to c and spaced in the a direction by chains of disordered TEA cations; the overlap within and between the tetrads is R/EB, but there is a jog between one tetrad and the next. There are no abrupt changes in cell dimensions as a function of temperature (Fig. 17.32(a)), but there are discontinuities in the principal coefﬁcients of expansion. Thus the transition that occurs around 200K appears to be one of higher order, without change of space group. The structure at 40K is shown in 4 We avoid the term ‘sublattice’ because ‘lattice’ is a precisely deﬁned mathematical concept; we avoid the term ‘substructure’ because of its use in studies of crystal texture and mosaicity.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1206

(a)

70 69.5

14.4

α (°) β (°)

a (Å) 83.5

14.3 14.2

82.5

7.85 b (Å) 7.75 13.8 c (Å)

73.5

γ (°)

72.5 13.6

Vol (Å3) 1400

13.4 1350 13.2 1300 100

200

300 T(K)

(b)

100

200

300 T(K)

(c) d (Å)

345K

295K

173K

110K

3.40

3.30

BB

3.20

AA AB

3.10

234K

40K

0

100 B A A B B A A B

200

300

T(K) B A

tetrads

diads

A B B A A B

Fig. 17.32. (a) Cell parameters of (TEA)(TCNQ)2 as a function of temperature; results from a number of sources; the lines are guides to the eye. (b) ORTEP diagrams (50% probabilities) of the asymmetric unit at 300K viewed in projection on the ac plane. The two fold disorder of the TEA cation has been partially resolved at 173 and 110K and fully at 40K, where the two orientations are shown separately to left and right. (c) Temperature dependence of the interplanar spacing between adjacent TCNQ molecules in the stacks. The transition from tetrads to diads is shown. (Reproduced from Filhol and Thomas (1984).)

Fig. 17.32(b). The details of the overlap mode, but not its general form, change with temperature. At 0K (by extrapolation) the tetrad stacks have equally spaced TCNQ moieties, with an ˚ ; these tetrads are separated by a BB 0 jog with a spacing of interplanar spacing of 3.11 A

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1207

˚ (the tetrads are represented schematically by the sequence 3.25 A 1Þ A B ð 1Þ B0 . . . ; . . . B0 A0 ð as shown in Entry #6 in Table 17.8)). The tetrads separate into -dimers as the tem˚ at 300K, and separated perature rises, with an internal (AB) interplanar spacing of 3.22 A ˚ and a between-diad (BB 0 ) spacing of 3.31 A ˚ . The by an intra-diad AA 0 overlap of 3.29 A ˚ at 0K to 0.45 A ˚ mutual M displacement of adjacent A moieties increases from 0.25 A at 300K (Fig. 17.32 (c)). This has led Farges (1985a) to describe the change in structure with temperature as a transverse shift of -dimers within a jogged tetrad stack. It is not clear whether the TCNQ moieties are ordered into anions and neutral molecules at low temperatures, as suggested by Farges (1985b), or disordered (with respect to charge) over the whole temperature range, as preferred by Filhol and Thomas (1984). There is two fold orientational disorder of the TEA cations, which is reported to be static below 200K and dynamic above this temperature; the corresponding species (TEA 0 and TEA00 ) have different structural roles. Two half-populated hydrogen bonds link molecules TCNQ(A) to TEA 0 and TCNQ(B) to TEA00 respectively. Thus there is coupling between cation and anion partial structures but the cations do not couple adjacent TCNQ stacks. Extensive measurements (Farges, 1980) have been made of electrical conductivity along three perpendicular directions: axis 1 is parallel to the TCNQ stack axis (i.e. along c), 2 is in the TCNQ layers perpendicular to the stacks and 3 is perpendicular to the alternate layers of TEA and TCNQ ions. At room temperature 1 ¼ 7.4 S/cm, 1/2 ¼ 164 and 1/3 ¼ 2850; thus there is a remarkable anisotropy at 300K which decreases with decreasing temperature. This can be explained in terms of the structural changes described above. (ii) {N-ethyl-N-methylmorpholinium (TCNQ)2} [(MEM)(TCNQ)2]. Three phases have been found from studies of structure and physical properties over a wide range of temperatures: IA

19 K

340 K

IB , II , 2nd order 1st order large change in increases by 103 magnetic properties

It has also been suggested (Kobayashi, 1982) that there is a second order transition at 315K; this has not been included as the structural change appears to be very small. The structure of phase IA at 6K has been determined by neutron diffraction; the c-axis is doubled with respect to IB (Visser, Oostra et al., 1983) and there are small changes in the stacking arrangement. However, this requires clariﬁcation as the doubling of c was not conﬁrmed in an XRD study at 10K (Figgis et al., 2001); radiation damage to the crystal used or insufﬁcient measurement sensitivity were invoked as possible reasons for the discrepancy. The crystal structure of phase IB at 113K (Bosch and Bodegom, 1977; MEMTCQ10) is shown in Fig. 17.33 (see Section 17.4.7.1, #6). There are AB -dimers (R/EB overlap) in tetrad stacks, with little overlap between successive -dimers. The values of L, M and N (at 113K) change

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1208

˚ at 323K, slightly decreasing the AB overlap and increasing the AB 0 only by 0.05 A overlap.

AB BB 0

L

M

N

Overlap type

1.97 2.57

0.12 2.21

3.15 3.27

R/EB displR/EB

B⬘

A 3.15 Å (b) B (a)

3.27 Å A⬘

B⬙

Fig. 17.33. [(MEM)(TCNQ)2] at 113K (Phase IB). The triclinic (not reduced) cell is 7.824 15.426 ˚ 113.59 73.27 112.71 , Z ¼ 1. As the crystals are piezoelectric, the space group is P1. 6.896 A (a) Projection of the structure on the plane perpendicular to [100]. The TCNQ stacks are separated by lines of cations. (b) TCNQ molecules seen along the average direction of the longest axis. The ˚ , on the left) overlap diagrams are shown. (Adapted from AB (3,15 A, on the right) and B 0 A (3.27 A Bosch and Bodegom, 1977.)

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1209

The principal change between 19 and 340K is an increasing disorder of the MEM cation. To a ﬁrst approximation there are two preferred orientations with occupancies x and (1 – x); x decreases from 1.0 at 113K through 0.84 at 294K to 0.63 at 323K. Above the ﬁrst order transition at 340K, an approximately monad stack is found with ˚ ) (Bodegom and Bosch, 1981): the following overlap shifts (in A

AB AB 0

L

M

N

Overlap type

1.96 2.02

0.10 0.40

3.28 3.30

R/EB R/EB

The transformation occurs with change of space group from P1 (in phases IA and IB) to P1 in phase II; there are small and abrupt changes in the axial lengths and angles and a ˚ , b þ0.4 A ˚ , c 0.4 A ˚ , 6 , small volume contraction (a 0.1 A þ5.5 , þ1 ; V 0.3%); a and b do not change their mutual orientation but the tilt of c to these axes does change. Thus phases IB and II differ in two ways: (i) the cation in II is disordered over two orientations (i.e. x ¼ 1/2) whereas in phase IB x decreases from 1.0 at 113K to 0.6 just below 340K; (ii) the change in TCNQ stacking pattern from offset -dimers in IB (right up to 340K) to essentially monad stacks in II. Similar changes in TCNQ stacking patterns occur in the ﬁrst order phase changes in Na(TCNQ) at 345 K (Konno and Saito, 1974, 1975), K(TCNQ) at 395K (Konno, Ishii and Saito, 1977) and {methyltriphenyl-phosphonium (TCNQ)2}at 326K (Konno and Saito, 1973; MPPTCQ02). However, the changes in conductivity which occur at Tc in these salts are much smaller than the thousand-fold increase found in {(MEM)(TCNQ)2}, for which a detailed explanation has still to be given. (iii) N, N-dimethylmorpholinium (TCNQ)2 {(DMM)(TCNQ)2} This salt provides a (so-far) rare opportunity to study phase changes in two polymorphs. The ﬁrst crystals obtained from acetonitrile were monoclinic but only one such batch has so far been prepared (Kamminga and Bodegom, 1981; DMMTCN); nevertheless, they have been studied extensively and show phase transformations on cooling (Middeldorp et al., 1985). Later crystallizations gave only triclinic crystals. The smaller volume per ˚ 3) than for the monoclinic phase formula unit at 100K for the triclinic phase (1288 A 3 ˚ ) suggests that the former is more stable than the latter; presumably the two (1299 A phases are monotropically related. The 300K monoclinic phase changes to another monoclinic phase at 120K, but with 4 formula units in a P21/c cell and there is a further change to another monoclinic phase at 95K with 8 formula units in a P21/c cell. At 300K there are stacks of -dimers with R/R overlap and an interplanar spacing of ˚ ; adjacent -dimers overlap only to a small extent. The DMM cation, in chair 3.25 A conformation, is disordered across the mirror plane. The structure has also been determined at 95K and the principal change is an ordering of the DMM cations, which is considered to be the major driving force for the transition. Minor changes in TCNQ ˚. positions lead to reduction of the -dimer spacing to 3.19 A

1210

SEGREGAT ED STACK -MOLECULAR COMPLEXES

˚, Table 17.9. Cell dimensions (A {(DMM) (TCNQ)2} Phase/refcode/ T(K)

a/

Monoclinic phases DMMTCN; 300 RT phase DMMTCN02; 120 beta phase DMMTCN01; 95 alpha phase

7.730 13.280

16.487 103.24 16.452 103.18

DMMTCN03; 95

) for the various phases of the two polymorphs of

b/

7.792

Triclinic phases DMMTCN04; 294

c/

26.814 58.44 26.500 120.90 26.497 92.35 12.909 99.60 12.838 98.79

Z

Volume of formula unit

Space group

7.594

2

1352

P21/m

14.780

4

1299

P21/c

14.782)

8

1299

P21/c

2

1333

P 1

2

1288

6.783 102.95 6.783 103.52

superspace 1. group PP

Unit cells of the three phases of monoclinic {DMM (TCNQ)2] viewed down [010]

a(alpha)

c(alpha) c(beta)

c(RT) a(RT) a(beta)

z

origin x

Fig. 17.34. Relations between the unit cells of the three phases of monoclinic {DMM(TCNQ)2} viewed down their common [010]. Small dimensional differences have been ignored. The following vectorial relationships hold between the axes of the three monoclinic cells (axes without subscripts refer to 300K cell): (Adapted from data given for DMMTCN and companion structures.) and RT : and RT : and :

a ¼ a; a ¼ a þ c; a ¼ 2a c;

b ¼ b; c ¼ 2½c a : b ¼ b; c ¼ 2½c a : b ¼ b; c ¼ c:

STRUCTURE OF TCNQ ANION-RADICAL SALTS

1211

Crystallization from acetonitrile also gave triclinic crystals (cell dimensions in Table 17.9). In the 300K structure the TCNQ moieties are arranged in diad stacks along ˚ ) with R/EB overlap while the randomly (and dynamically) disordered [001] ( 6.6 A DMM cations are located between the anion stacks (Visser et al., 1994; DMMTCN04). The marked differences in the dimensions of the two crystallograpically independent TCNQ moieties have been ascribed to a difference of 0.7e between the charges on the moieties, i.e. one is neutral and the other an anion. At 207K satellite reﬂections appear in the diffraction patterns, showing incipient formation of an incommensurately modulated phase whose structure has been determined at 99K. The driving force for modulation is the need to accommodate the ordered DMM cations within the conﬁnes of the TCNQ ‘partial structure’ (see footnote on p. 1203). The overall structure is considered to be of an intergrowth type whose elastic energy is minimized by incommensurate modulation (Steurer et al. (1987)). (iv) Trimethylammonium TCNQ Iodine (TMA-TCNQ-I). Perhaps the most complicated TCNQ structure yet studied is that of the ternary salt [(CH3)3NHþ]3(3TCNQ)2(I3), which is a representative of a wider family of isostructural ternary anion radical salts of general formula [R(CH3)2NHþ]3(3TCNQ)2(I 3 ) (Dupuis et al., 1978). A comprehensive study (Gallois et al., 1985) is remarkable for its integration of x-ray and neutron diffraction techniques with the ﬁrst use of high voltage (2000 kV, ˚ ) electron microdiffraction in the study of TCNQ salts. There are three phase ¼ 0.0054 A transitions, at 150, 95 and 65K, associated with different modulations of the lattice. The structural relationships are too complex for detailed discussion here and the reader is referred to Gallois et al. (1985), who also give references to earlier work (MATCQI to MATCQI09). 17.4.10

Conclusions drawn from a survey of structural results for TCNQ anion-radical salts

Crystal structures have been reported for more than one hundred TCNQ anion radical salts, mostly at room temperature. The fundamental feature common to all these structures is plane-to-plane stacking of TCNQ moieties in segregated stacks of limited or unlimited length. We focus our attention in this section on the -dimers, whose arrangement in the crystals ranges from isolated to stacked, and distinguish between -dimers carrying single and double charges. The overlap of the two TCNQ moieties can, to a good approximation, be classiﬁed as either R/R (eclipsed) or R/EB (slipped), with deviations from the ideal overlaps being ascribed to packing effects rather than to electronic interactions within the dimers. The available results are summarized in Table 17.10. Stacks with mean charges of 4/7 and 2/3 per TCNQ moiety have also been found but there are not enough examples for conclusions to be drawn. R/R overlap seems to be about twice as frequent as R/EB when the -dimer is doubly charged, but only R/EB overlap is found when the -dimer is singly charged. No trends ˚ , apart from a few are discernible in the interplanar spacings that lie in the range 3.1–3.3 A ˚ less than that found in neutral outliers. The interplanar distance is thus about 0.5–0.3 A TCNQ. From this we infer that there is an attractive interaction operating between anions in stacks additional to that operating between neutral molecules. Furthermore, this additional attraction does not appear to depend (at least to a ﬁrst approximation) on the

1212

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Table 17.10. TCNQ -dimers classified according to overlap type and mean charge. References ˚ have been given in previous tables. The interplanar spacings (D) are in A Group I. Average charge of –e on each TCNQ moiety (doubly charged -dimer). R/EB Overlap

D

R/R Overlap

D

1. (1,2,3-trimethylbenzimidazolinium) (TCNQ)2 2. [Nb3(m-Cl)6(C6Me6)3] (TCNQ)2 3. (1,1 0 -ethylene-2,2 0 bipyridylium) (TCNQ)2 4. N,N 0 -dimethylbenzimidazolinium) (TCNQ)

3.12

1. (TMA)2(TCNQ)3

3.26

3.10

1a. (quinuclidinium)2 (TCNQ)3 2. [Fe(C5Me5)2]2 (TCNQ)2 3. Na(TCNQ) at 300K

3.26

4. 5. 6. 7. 8.

3.24 3.16 3.14 3.28 3.37

3.22 3.26 3.07

K(TCNQ) at 300K Rb(TCNQ) at 113K [Pt(NH3)4]2þ(TCNQ)2 {Morpholinium (TCNQ)} [(MeCp)5V5S6] (TCNQ)2

3.15 3.22 3.20

Group II. Average charge on each TCNQ moiety 0.5e (singly charged dimers). All these examples have R/EB overlap and have been listed as follows: ˚. Section 17.4.7, Group I (i) 11 examples, interplanar spacings in the range 3.15–3.24 A ˚. Table 17.5, Type I: 4 examples, interplanar spacings within the -dimer in the range 3.12–3.20 A ˚. Table 17.7: 3 examples, interplanar spacings within the -dimer in the range 3.14–3.25 A

mean charge of the TCNQ moiety. The Coulomb repulsion energy between two planar ˚ apart would be about 400 kJ/mol. Theoretical approaches singly-charged anions 3.3 A to the preferred overlap modes of various donors and acceptors are discussed later (Section 17.7). TCNQ salts with different donors show a wide variety of physical properties despite the essential structural resemblance that results from the stacked arrangement of the TCNQ moieties. A broad classiﬁcation into four types (Fig. 17.35) has been proposed (Torrance, 1978) on the basis of stoichiometry and physical properties. Classes I and II are ‘simple’ TCNQ salts with cation : TCNQ ratio 1 : 1 but differing in conductivity by a factor of 106. Class II salts are also discussed in more detail below under the heading of ‘Cationradical Anion-radical salts.’ Classes III and IV are ‘complex’ TCNQ salts with cation:TCNQ ratio 1 : r (where r is the ratio of two small integers and r > 1)), the two classes differing in conductivity by a factor of 102–106, the value depending on the temperature at which the comparison is made. Taking the overall segregated stack structure as given, Torrance (1978) considered that there were two factors primarily responsible for determining details of structure and two others for determining physical properties. The ﬁrst of the structure-determining factors is the cation–anion interaction, which we consider to be of predominant importance in the salts containing closed-shell cations. An example of the way in which the stacking of

STRUCTURE OF TCNQ ANION-RADICAL SALTS

(a) 4

1213

HMTSeF Class II TTF

log s (S/cm)

BTP

0

106 Rb(II)

NMP

Cs K Class I Na

–4 Morph.(~10–9) NMQn 0

100

200

300

400

T(K)

(b) 104 III 102

Ad Class IV

s (Ω–1cm–1)

Qn NPQn

100

TEA CNNMQn

10–2

Class III

Mf3 As Cs (2: 3)

11–4 1 : 2 TCNQ Salts 10–6

100

200 300 T (°k)

400

500

Fig. 17.35. (a) The temperature dependence of the conductivity for a number of simple TCNQ salts (1 : 1), showing how they fall into two distinct classes I and II; (b) the temperature dependence of the conductivity for a number of complex TCNQ salts (1 : r, where r is the ratio of two small numbers and r > 1), showing how they fall into two distinct classes III and IV. Some acronyms are: BTP 4,4 0 -bithiopyranium; NMP N-methylphenazinium; NMQn N-methyl-quinolinium; Ad acridinium; TEA triethylammonium; CNNMQn 4-cyano-N-methylquinolinium, TTT tetrathiotetracene. (Reproduced from Torrance, 1978.)

1214

SEGREGAT ED STACK -MOLECULAR COMPLEXES

-dimers depends on the nature of the cation is shown rather vividly in Figs. 17.30 and 17.31 where long cations are threaded through the channels between TCNQ stacks, that conform themselves to the overall cation shape. Cations can play an important role in the overall structure in two other ways – ﬁrstly, there is often hydrogen bonding between cation and nitrogens of the TCNQ anion, and, secondly, the degree of disorder of the cations affects physical properties. Torrance’s second structure-determining factor is the bandwidth, 4t, associated with overlap of -orbitals of adjacent TCNQ moieties in the stacks. A variety of types of overlap is found, and hence 4t is structure sensitive. Torrance suggests that a reasonable average value for 4t is 0.5 ev ( 50 kJ/mol). The other two factors relate more to physical properties and particularly to the conductivity. The ﬁrst of these is the effective Coulomb repulsive energy U ¼ U0 – V1, where U0 is the Coulomb repulsion energy between two electrons on the same molecule (here the TCNQ anion) and V1 is the Coulomb repulsion energy between two electrons on neighbouring molecules. Although U0 and V1 may both depend on the nature of molecule and environment, their difference appears to be reasonably constant and Torrance has suggested that U 1 ev ( 100 kJ/mol). The key parameter affecting conductivity is Z, the degree of charge transfer or the average number of unpaired electrons per TCNQ moiety (see Section 14.3.6). The conductivity is very low in those simple salts where Z ¼ 1 because the energy required to activate conduction is the effective Coulomb repulsion energy U; this is the situation in the alkali metal TCNQ salts. However, as we shall see below, Z ¼ 0.59 in {[TTF][TCNQ]}, and an electron can travel from anion radical to adjacent neutral molecule in the same stack (the pair then exchanging roles) without an activation energy, thus accounting, in principle, for the high conductivity. The details are, of course, more complicated (see Section 17.9).

17.5 17.5.1

Other anion-radical salts Alkali-metal chloranil salts

Physical properties of these salts were ﬁrst extensively investigated around 1970 (Ishii et al., 1976). There appear to be two groups (chloranil is abbreviated as CA). LiþCA and NaþCA show a strong intermolecular CT band in the near IR, whereas KþCA and RbþCA each show a weak CT band and a band corresponding to monomeric radical anion absorption. Only the crystallography of KþCA has been studied (Konno, Kobayashi, Marumo and Saito, 1973). There are several polymorphs, two of which have rather similar cell dimensions and are unusual in that they crystallize in the Sohncke space groups P212121 () and P21212 () although the components are centrosymmetric. The structure of the -polymorph has been studied (but only roughly because of poor quality crystals, R ¼ 0.13 for 146 reﬂections); there are stacks of chloranils with interspersed Kþ ions. There is little overlap between successive anions in a stack, thus accounting in broad terms for the room temperature electronic spectra. Dielectric constant and spectroscopic studies over a range of temperature show a phase transition at 210K (presumably ﬁrst order because of the appreciable hysteresis). The striking

OTHER ANION-RADICAL SALTS

1215

increase in the intensity of the CT band on cooling has been interpreted in terms of -dimerization (pairing) of the anions in the low temperature phase, and a similar explanation (augmentation of electronic polarization consequent on pairing) has been proposed for the increase in dielectric constant on cooling; however, the structure of the low temperature phase has not been reported. There are resemblances to the behaviour of TMPDClO4. 17.5.2 M(dmit)2 and M(mnt)2 as anion radicals in various guises The increasing number of structures available for the M(dmit)2 and M(mnt)2 (M ¼ Co, Ni, Pd, Pt, Au; see Section 17.2.3 for formulae of (dmit)) and (mnt)5) anion radical salts (and also one example for a 1,4,5,8-naphthalenetetracarboxylate salt) suggest that their stacking arrangements are analogous to those found in TCNQ anion radical salts. This encourages one to believe that TCNQ is only the ﬁrst of a number of acceptors that behave similarly. However, we emphasize that each acceptor is likely to show its own special features in addition to ﬁtting into a general pattern. There are also some examples of cation radical anion radical salts containing M(mnt)2, and it is convenient, breaking our usual pattern, to consider all these examples together even though some clearly belong in the next section. The anion radical salts of M(dmit)2 There are diad stacks along the [010] axis of ˚; 1, Z ¼ 2), with interplanar distances of 3.44 and 3.76 A triclinic (Et4N)0.5[Ni(dmit)2]6 (P there are also many interstack S . . . S distances somewhat less than the van der Waals ˚ (Kato, Mori et al., 1984; CEVFIS). The cations are disordered and distance of 3.6 A located between the stacks. The anions bear charges of 0.5e and the material is a semiconductor with a maximum conductivity of 4 102 S/cm along [010]. In (AsPh4)[Ni(dmit)2]4 (Valade, Legros, Cassoux and Kubel, 1986; DIBNAD20) there are tetrad stacks with displaced-eclipsed overlap within the tetrads and metal-over-ring ˚ ) that suggest overlap between them, and also lateral S . . . S approaches (closest is 3.55 A weak interactions. The conductivity along the stack axis is 15 S/cm at room temperature. The crystals show appreciable diffuse scattering so ﬂuctuations from this average structure are large. A more complicated arrangement of anions in stacks is found in (n-Bu4N)2 [Ni(dmit)2]7.2CH3CN (Valade, Legros, Bousseau et al., 1985; DEWKOF) (crystal ˚ , ¼ 108.49(1), structure at 118K; triclinic, a ¼ 13.425(2), b ¼ 22.791(3), c ¼ 24.183(4) A ˚ 3, Z ¼ 2, space group P1). The stacks contain ¼ 103.02(1), ¼ 89.82(1) , V ¼ 6818 A alternating tetrads and triads of Ni(dmit)2 moieties (Fig. 17.36) and are located in thick layers parallel to (001), which are separated by sheets of cations and solvent molecules. ˚ . Relations between There are also some interstack S . . . S distances of less than 3.6 A physical properties and the rather complicated crystal structure are discussed by Valade et al. (1985). The structures of [NBu4]2[Ni(dmit)2] and of [Nbu4][Ni(dmit)2] have been studied (Lindqvist, Sjo¨lin et al., 1979; DBNTNI10); Lindqvist, Andersen et al., 1982; ITTNBU01) 5 6

H2(dmit) is 4,5-dimercapto-1,3-dithiole-2-thione and (mnt) is maleonitriledithiolate. tetraethylammonium bis(bis(trithionedithiolato))Ni(II).

1216

SEGREGAT ED STACK -MOLECULAR COMPLEXES

20.2° [110] Triad 3.48 Å 3.53 3.55 Tetrad 3.57

21.4°

Fig. 17.36. Part of the crystal structure of (Bu4N)2 [Ni(dmit)2]72CH3CN showing one of the two crystallographically independent stacks of planar Ni(dmit)2 moieties along [110]. Both triads and tetrads are centrosymmetric and have their stack axes equally inclined to [110]; there is little variation in the interplanar spacings. (Reproduced fromValade et al., 1985.)

but do not appear to have any features noteworthy in the present context, presumably because the [Ni(dmit)2] moieties do not have fractional charges. The structure of (Et4N)[Ni(dmit)2] is highly one-dimensional (Kramer et al., 1987; FEMNIU10). The cation radical anion radical salts of perylene with M(mnt)2 The cation radicals are perylenium or modiﬁed perylenium. Thus perylene is the ﬁrst aromatic hydrocarbon to function as a cation radical in cation radical anion radical salts. Crystallographic data are summarized in Table 17.11. The {(per)2[M(mnt)2]} salts (per ¼ perylene, M ¼ Pd, Pt, Au) are closely isomorphous and have segregated monad stack structures (Fig. 17.37). Unfortunately, coordinates are not available for any of these and so detailed comparisons are not possible. PAJWUS was solved as an averaged structure, so again some detail is lacking. The perylenes in a ˚ and have ring-bond overlap similar to that found in other stack are separated by 3.36 A perylene stacks of this group. Mo¨ssbauer spectroscopy (295, 80 and 15K) of {(per)2[Fe(mnt)2]} gave spectra very similar to those obtained for alkylammonium salts of [Fe(mnt)2]} and it was inferred that there were actually ([Fe(mnt)2]2) dimers in all these materials. {(per)[Co(mnt)2]} has been prepared but the structure is not known; the dichloromethane solvate (Gama, Henriques, Bonfait, Almeida et al., 1992; SUCCOI) has segregated stacks with perylenes in general positions; however, the two independent interplanar ˚ ; these are pseudo-monad stacks. The anions are distance are essentially the same at 3.27 A arranged in polymeric chains along [100].

OTHER ANION-RADICAL SALTS

1217

Table 17.11. The cation radical anion radical salts of perylene with [M(mnt)2]. Measurements at 295K unless stated otherwise Metal

a/

b/

c/

V

Z

Space group

Group of three Pd

16.469

4.1891 95.07 4.1891 94.54 4.194 94.58

26.640

3846

2

P21/n

26.583

1846

2

P21/n

26.546

1841

2

P21/n

4.176 91.57 4.17

25.18

1833

2

P21/n

25.5

1856

2

P21/n

25.88

3778

4

P21/n

17.726

7354

8

C2/c (averaged as P21/n)

13.3297 87.785 16.633

1543.7

1

P1

4194.5

2

P21/n

16.481 94.62

1251

2

P 1

Pt (Alcacer et al., 1980) PRLNPT Au Group of four Ni

16.612 16.602

17.44

Cu (Alcacer, 1985; Gama, Almeida et al., 1991)

17.6

Co (PAJXAZ)

17.75

Fe (Gama, Henriques, Bonfait, Pereira et al., 1992; PAJWUS)

50.571

{(pet)3[Ni(mnt)2]2} (3) SOHMAD {(per)4[Co(mnt)2]3} (4) HAKJEI {(per)[Co(mnt)2]} CH2Cl2 (5) SUCCOI

10.2972 78.320 12.093 6.551 92.08

91.4 8.22 92.0 8.212 92.43 11.5037 87.096 20.912 94.290 11.732 95.30

Notes: 1. The Fe compound (PAJWUS) has been indexed in the standard space group C2/c; interchange of a and c axes (space group A2/a) makes the comparison of cell dimensions for the ﬁrst four compounds more obvious. 2. the ‘group of three’ and the ‘group of four’ are isostructural, not isomorphous; however, taken together they constitute the phase. There is also a poorly-deﬁned semi-conducting phase 3. pet ¼ perilo[1,12-b,c,d]thiophene 4. per ¼ perylene 5. there is a modulated structure with wave vector 0.22a*, 0.13b*, 0.36c*. This has not been taken into account in the structure solution which thus refers to an averaged structure.

Some physical properties of these compounds have been measured (Henriques, Alca˚cer et al., 1984; Henriques, Almeida et al., 1987). Perylene also forms a 4 : 3 complex (Gama, Henriques, Almeida et al., 1993; HAKJEI) with [Co(mnt)2] that has perylene trimers, perylene of crystallization (almost perpendicular to the perylene trimers) and trimeric [Co(mnt)2]3 moieties in a complicated

1218

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Fig. 17.37. Projection down [010] for the {(per)2[M(mnt)2] (per ¼ perylene, M ¼ Pd, Pt, Au) structures. This diagram provides an approximate representation of the M ¼ Ni, Cu, Co and Fe structures but does not take into account possible ordering along the stack axis or in lateral directions. (Reproduced from Gama, Almeida et al., 1991.)

Fig. 17.38. Projection down [100] for the {(per)4[Co(mnt)2]3} structure. The perylene trimer is seen edge-on and the perylene of crystallization plane-on. The centrosymmetric {[Co(mnt)2]3} trimer is at the corners of the unit cell. (Reproduced from Gama et al., 1993.)

OTHER ANION-RADICAL SALTS

1219

a

b

Fig. 17.39. Projection of the SOHMAD structure down [100]. The dashed lines show short S . . . S distances between the two components. (Reproduced from Morgado et al., 1997.)

a

pet B pet A Ni(1) pet C

Ni(2) c 0

b

Fig. 17.40. SOHMAD: Side view of the [Ni(mnt)2]2 stacks locked between the pet stacks. The pet trimers and pseudo-monad [Ni(mnt)2]2 stacks are clearly visible. (Reproduced from Morgado et al., 1997.)

1220

SEGREGAT ED STACK -MOLECULAR COMPLEXES

arrangement (Fig. 17.38) that has structural features encountered previously. There is one perylene in a general position, one (half) at a center of symmetry, the three molecules constituting the trimer, while the (half) perylene of crystallization is at an independent ˚ ), all perylene moieties center of symmetry. Within experimental uncertainty ( 0.01 A are planar and have identical bond lengths. Perilo[1,12-b,c,d]thiophene (pet) is the perylene derivative in which two hydrogens of one bay region are replaced by a sulfur atom. This forms a triclinic non-centrosymmetric 3 : 2 complex with [Ni(mnt)2] in which there are jogged segregated stacks of (pet) trimers and [Ni(mnt)2] dimers (Fig. 17.39; Morgado et al., 1997; SOHMAD). ˚ The interplanar spacings within a pet trimer are 3.37 (petA–petB) and 3.23 A ˚ (petA–petC) and between them (petC*–petB) 3.47 A; the overlap modes also differ (Fig. 17.40).

17.6 17.6.1

Structures of cation-radical anion-radical salts General survey

The criterion for inclusion in this group is that both the cation radicals and the anion radicals should form (separate) segregated stacks. Salts of this kind, typiﬁed by {[TTF][TCNQ], appear to be fairly rare, although many different chemical types have been observed. There is some, but not much, crystallographic similarity among the various salts (Table 17.12). Our classiﬁcation, as elsewhere, is based on structural rather than chemical resemblances and we distinguish between salts with different cation: anion ratios and between monad and diad stack periodicities. We start with 1:1 cation : anion ratios, where both monad and diad stacks are found. 17.6.2

Cation : anion ratio 1 : 1; monad stacks

This group of monad-stack structures shows considerable overall uniformity in the arrangement of the moieties within the stacks, with the radical cations and radical anions both being located face-to-face in separate segregated homologous stacks. Overlap of unsubstituted TTF and TCNQ moieties is invariably ring-double bond (R/DB) and ring-external bond (R/EB) respectively; however, substitution can lead to changes in the type of overlap. The values of DC and DA differ and hence (because both stacks have the same periodicity) the angles of inclination of the moiety planes to the stack axis also differ. The resemblances and differences among the various structures arise from the relationships between the stacks. We ﬁrst consider the group of triclinic structures. These structures all crystallize in space group P1 with one formula unit in the unit cell; thus both moieties are located at crystallographic centres of symmetry but there are otherwise no symmetry restrictions on their arrangement. In our descriptions we give priority to the concept of approximately close-packed stacks but modiﬁcation of this approach is necessary when there are strong interstack interactions. The stacks have elliptical cross-sections because of the elongated shapes of the

˚ , deg., A ˚ 3) for cation-radical anion-radical salts with monad-stack structures and 1 : 1 compositions. The triclinic cells have Table 17.12. Crystal data (A been reduced so that interaxial angles are all either acute (Type I) or obtuse (Type II). Stack axis is in bold. Standard uncertainties of cell parameters are ˚ ) in cation-radical and anion-radical stacks respectively given in the original publications. DC and DA are interplanar spacings (A Salt

a/

b/

c/

V

Remarks

7.645 87.78

18.85 85.37

547

3.76 85.54

8.100 83.98

16.568 88.00

500 588

3.93 91.57 3.872 81.45

7.598 88.22 7.362 89.87

19.76 94.45 18.643 87.60

Black conducting polymorph. Metal to insulator transition at 59K. DC ¼ 3.60; DA ¼ 3.27.(see Fig. 17.36.) Two-dimensional analysis. Poor quality crystals. Crystals twinned (R ¼ 0.15); DC ¼ 3.59, DA ¼ 3.35. Metal to insulator transition at 45K.

3.76 91.13

7.867 93.28

20.09 91.46

593

3.94 97.3

8.085 98.12

18.96 91.37

592

3.859 83.75

10.094 85.91

13.654 83.00

524

(i) Triclinic (all examples have space group P1; Z ¼ 1) 3.88 1. {[TMTSeF][TCNQ]} 79.18 (Bechgaard et al., 1977); SEOTCR

2. {[TTF][TNAP]} (Berger et al., 1975); TTFNAP 3. {[DEDMTSeF][TCNQ]}* (Andersen et al., 1982); 4. {[BMDT-TTF][TCNQ]} (Kobayashi et al., 1986); FERCAG 5. {[DBTTF][2,5-dichloro-TCNQ]} (Soling, Rindorf and Thorup, 1981); BABCIQ 6. {[TMTSeF] [2,5-dimethyl-TCNQ]} (Andersen et al., 1979); SEFTCQ

7. {[TTF][2,5-diethyl-TCNQ]} (Schultz, Stucky, Blessing and Coppens, 1976); TFETCQ * not reduced

525

At 295 and 115K; no phase change. DC ¼ 3.51; DA ¼ 3.41. Metal to insulator transition at 42K (Pouget et al., 1980; Pouget, 1981). DC ¼ 3.64; DA ¼ 3.31. Metal to insulator transition at 111K. DC ¼ 3.60; DA ¼ 3.26.

Table 17.12. (Continued) Salt

a/

b/

c/

V

8. {[ß-MTDTPY]@ [TCNQ]} (Nakasuji, Sasaki et al., 1987); FUDTON 9. {[1,6-dithiapyrene] [TCNQ]} (Thorup et al., 1985); DAKTIS 10. {[1,6-pyrenediamine] [TCNQ]} at 118 K (Inabe, Okinawa et al., 1993). WEMHEB 11. {[ß-MTDTPY]@ [chloranil]} (Nakasuji, Sasaki et al., 1987); FUDTUT 12. {[DBTTF][Ni(dmit)2]} (Kato, Kobayashi et al., 1985); CUWCIG

4.370 92.80

8.286 90.12

16.957 103.48

596

3.83 89.77

8.106 83.96

15.61 84.77

480

DC ¼ 3.39; DA ¼ 3.27.

3.851 82.76

7.923 88.60

16.363 85.93

494

DC ¼ 3.23; DA ¼ 3.19. #9 and 10 are isostructural

3.797 85.24

9.994 89.32

14.585 80.60

536

3.830 73.74

12.256 89.84

14.29 89.97

644

Salt (ii) Monoclinic 1. {[TTF][TCNQ]} (Kistenmacher et al., 1974; TTFTCQ01) (for neutron study of fully deuterated salt at 10–1 MPa and 460 MPa see Filhol, Bravic et al., 1981; TTFTCQ05 and 06).

Remarks

Crystals twinned, data collected as monoclinic.

a

b/

c

V

S. G.

Z

Remarks

12.30

3.82 104.4

18.47

840

P21/c

2

DC ¼ 3.47; DA ¼ 3.17. Three transitions at 38, 48 and 54K.

2. {[DSeTDTF#][TCNQ]} (Etemad et al., 1975) 3. {[TSeF][TCNQ]} (Etemad et al., 1975; Corﬁeld and LaPlaca, 1996) ZUGRUO 4. {[TMTF][TCNQ]} (Phillips et al., 1977); THOTCQ 5. {[TTTF][TCNQ]} (Chasseau, Gaultier, Hauw, Fabre et al., 1978); MYFLTC 6. {[TMTF][bromanil]} (Mayerle and Torrance, 1981a); TMFBRQ10 7. {TTMTTF][HCBD]} (Katayama, Honda et al., 1985); DATNIV10 8. {TMTTF][HCBD]} (Katayama, Honda et al., 1985); DATNER10 9. {[TMTSeF]Ni(dmit)2]} (Kobayashi et al., 1985); DALPUB 10. {[HMTSeF][TCNQ]} (Phillips et al., 1976); SEOTCQ

12.41 12.505

3.85 104.3 3.872 104.13

18.49

855

P21/c

2

Tc ¼ 64K.

18.504

869

P21/c

2

Tc ¼ 40K; crystals 1, 2 and 3 are isomorphous.

18.82

3.85 103.7

15.08

1062

P2/c

2

DC ¼ 3.53; DA ¼ 3.27.

40.88

3.82 100.9

12.28

1883

C2

4

31.32

3.95 121.2

19.30

2042

C2/c

4

DC ¼ 3.58; DA ¼ 3.20; d(S . . . .N) ¼ 3.11, 3.21. Sohncke space group. DC ¼ 3.60; DA ¼ 3.37.

30.16

4.04 117.5

23.41

2535

C2/c

4

DC ¼ 3.63; TTMTTF planar.

12.80

21.62 108.1

4.02

1058

C2/m

2

Components ionic. DC ¼ 3.61; DA ¼ 3.43.

15.23

34.6 105.7

25.46

P21/n

18

22.00

12.57 90.29

3.89

1076

C2/m

2

Transverse sinusoidal modulation of b, fundamental ˚. period 3.84 A Disorder along [100]. DC ¼ 3.6(1); DA ¼ 3.2(1).

Table 17.12. (Continued) Salt (iii) Orthorhombic 1. {[HMTTF][TCNQ]} (Silverman and LaPlaca, 1978; Chasseau et al.,1978); HMTFCQ 2. {[HMTSeF][TCNQF4]} (Torrance et al., 1980) @ #

a

b/

c

V

S. G.

Z

Remarks

12.47

3.91

21.60

1053

Pmna

2

DC ¼ 3.57; DA ¼ 3.25.

12.61

4.07

21.40

1098

Pmna

2

DC ¼ 3.62; DA ¼ 3.27.

2,7-bis(methylithio)-1,6-dithiapyrene. There is an isomeric mixed stack (chloranil) compound (Table 15.3) cis/trans-diselenadithiafulvalene.

STRUCTURES OF CATION-RADICAL ANION-RADICAL SAL TS

1225

moieties. In the triclinic structures an anion radical stack (for example) will have four cation radical stacks and two anion radical stacks as nearest neighbours, and conversely for the cation radical stacks. The stacks in the group of four are identical as they are related by translations, and this also holds for the group of two. The tilts of the moieties to the stack axes are independent in the two types of stack; for most of the present structures the tilts have opposite signs. In {[TMTSeF][2,5-dimethyl-TCNQ]} the long axes of the two moieties are roughly perpendicular (Fig. 17.41) while in {[DBTTF][TCNQCl2]} (Soling et al., 1981) they are approximately parallel. In {[DBTTF][TCNQCl2]} the interstack approach distances are larger than the sums of the van der Waals distances and both structures are described as ‘one-dimensional’. In some structures there are interstack distances (usually chalcogen . . . N) shorter than ˚ ; Se . . . N 3.45 A ˚ ) leading the sum of the van der Waals distances (S . . . N 3.35 A to ‘two-dimensional character’. In {[DAP][TCNQ]} (DAP is 1,6-pyrenediamine; WEMHEB) there is hydrogen bonding between amino groups of the cation-radical and cyano groups of the anion-radical. In isostructural {[1,6-dithiapyrene][TCNQ]} (DAKTIS) a S . . . NC approach presumably ﬁlls the same function. Both TCNQ bond lengths and IR spectroscopy indicate that WEMHEB is a simple salt rather than a cation-radical anion-radical salt. Similar descriptions can be used for the monoclinic and orthorhombic structures, care being necessary to take the symmetries of the various space groups into account. The monoclinic structures can be divided into two subgroups, the larger having the stack axis along monoclinic b, and the smaller having c as stack axis. The only two examples in the orthorhombic group are isomorphous. The structures of {[TTF][TCNQ]} (Fig. 17.48) and some related salts will be described in more detail later. Resemblances in structure do not mean that there are necessarily resemblances in electrical conductivity and related physical properties, and in their dependence on temperature and pressure. A partial classiﬁcation, based on conductivities, of cation radicalanion radical salts (where the cation radicals are TChF (Ch ¼ chalcogen) and substituted TChF’s and the anion radicals are TCNQ and substituted TCNQ’s) has been given by Bechgaard and Andersen (1980); we use their classiﬁcation and note how the salts chosen for illustration (ambient pressure behaviour only) ﬁt into Table 17.9 (crystal type and number given in brackets): Class I. Semiconductors. The presence of strong acceptors causes full charge transfer, leading to Mott insulators with RT 1 S/cm. An example is {[HMTTF][TCNQF4]} (ortho-#2){[DAP][TCNQ]} (tri-#10) ﬁts into this category from a structural viewpoint but the transport properties are discordant. Class II. Intermediate semiconductors. Metal–insulator transition occurs at relatively high temperatures. Examples are {[TTF][DETCNQ]} (tri-#8), {[TTF][TNAP]} (tri-#3), {[DBTTF][TCNQCl2]} (tri-#5). Class III. Metals/insulators, with transitions occurring at relatively low temperatures; RT 200–1500 S/cm, TC < 100K. Examples are {[TTF][TCNQ]} (mono-#1), {[TMTSeF][DMTCNQ]} (tri-#7), {[HMTTF][TCNQ]} (ortho-#1), {[TMTSeF] [TCNQ]} (mono-#2).

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1226

sheet of 2,5-dimethylTCNQ stacks

C

A N

Se sheet of tetramethyltetraselenofulvalene stacks

B

z y

2,5dimethylTCNQ stack

tetramethyltetraselenofulvalene stack

2,5dimethylTCNQ stack

A

B

C x z

Fig. 17.41. Projections down [100] (upper) and [010] (lower) of the structure of {[TMTSeF][2,5-dimethyl-TCNQ]} (SEFTCQ). (Data from Andersen, Bechgaard et al., 1978.)

STRUCTURES OF CATION-RADICAL ANION-RADICAL SAL TS

1227

Class IV. Metals/semimetals, still highly conducting below TC. One example is {[HMTSeF][TCNQ]} (mono-#7) and {[DEDMTSeF][TCNQ]} (tri-#4) appears to be another. The structures of {[HMTSeF][TCNQ]}, {[HMTTF][TCNQ]} and {[HMTTF][TCNQF4]} require some comment. All three compounds have very similar cell dimensions (Table 17.10) and {[HMTTF][TCNQ]} and {[HMTTF][TCNQF4]} are isomorphous, while {[HMTSeF][TCNQ]}, with a different space group, is not isomorphous with the other two. It has a parallel arrangement of stacks when viewed along [100] while the two isomorphous structures have a herring-bone arrangement. The room temperature conductivities of {[HMTSeF][TCNQ]}, and {[HMTTF][TCNQ]} are about 106 times as large as that of {[HMTTF][TCNQF4]}. The conductivity difference is ascribed (Torrance et al., 1980) to partial charge transfer in {[HMTSeF][TCNQ]}, (Z 0.72) and also in {[HMTTF][TCNQ]} leading to high conductivity, while the much lower conductivity of {[HMTTF][TCNQF4]} is a consequence of complete ionization in the ground state due to the greater electronegativity of ﬂuorine compared to hydrogen. {[HMTSeF][TCNQ]} is classiﬁed as ‘two-dimensional’ because of the short interstack Se . . . N distance of ˚. 3.10(3) A In some structures lateral interactions between stacks appear to be more important than those within stacks. Thus in {[TTF][[Ni(dmit)2]2]} (Bousseau et al., 1986) the monoclinic ˚ , ¼ 119.3 , C2/c, Z ¼ 4) have segregated crystals (a ¼ 46.22, b ¼ 3.73, c ¼ 22.86 A stacks of TTF (at centres of symmetry) and Ni(dmit)2 moieties (at general positions) leading to an arrangement of alternating sheets of the moieties in the (100) planes (Fig. 17.42). The interplanar spacings within the stacks are much larger than usual ˚ respectively) while there are sixteen crystallographically independent (3.65 and 3.55 A ˚ , which are less than the standard S . . . S approaches, ranging from 3.68–3.38 A ˚ on the basis of the intermolecular van der Waals diameter of sulphur (taken as 3.70 A contacts in orthorhombic sulphur (Abrahams, 1955). These results, taken together, suggest that the crystal structure is determined by a quasi-three dimensional network of intermolecular S . . . S interactions. However, no conclusions could be drawn about the charges on the donor and acceptor moieties. The compound has metallic conductivity down to 4K, with RT 300 S/cm and 4K 105 S/cm. The isomorphous Pd compound has RT 750 S/cm but shows a metal-to-semiconductor transition at 220K. 17.6.3 Cation : anion ratio 1 : 1; diad stacks Four examples are discussed. The ﬁrst of these, {[TTF] [2,5-TCNQF2]} (Emge, Wijgul ˚ , ¼ 87.94, et al., 1981; BERYOM) is triclinic (a ¼ 7.082, b ¼ 8.761, c ¼ 14.447 A 1, Z ¼ 2; the crystals were twinned and measurements were made ¼ 81.74, ¼ 84.54 , P ˚, on one individual of the twin). There are stacks along [001] with DC ¼ 3.34 and 3.60 A ˚ , showing clear dimerization within both types of stack. There and DA ¼ 3.23 and 3.55 A is nearly eclipsed overlap within the dimerized pairs; moiety dimensions suggest full charge transfer. The second example, {[DBTTF][TCNQF4]} (Emge, Bryde et al., 1982; BOMGIT) is ˚ , ¼ 63.47, ¼ 77.11, ¼ 74.02 , P1, also triclinic (a ¼ 7.533, b ¼ 10.094, c ¼ 13.703 A

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1228

z

x [010]

Ni(dmit)2

TTF

Fig. 17.42. (a) Projection of the crystal structure of {[TTF][[Ni(dmit)2]2]} onto (010), showing ˚ as thin lines and the sheets of TTF stacks (shaded); (b) view in the S . . . S distances less than 3.70 A plane of the TTF moieties showing the stacking arrangement and the lateral interactions. (Reproduced from Bousseau et al., 1986.)

˚ (eclipsed overlap) and 3.68 A ˚ Z ¼ 2). There are stacks along [001] with DC ¼ 3.35 A ˚ ˚ (R/DB overlap), and DA ¼ 3.18 A (displaced R/EB overlap) and 3.54 A (displaced R/R overlap), showing even clearer dimerization within both types of stack. Moiety dimensions suggest full charge transfer, providing an explanation for the insulating qualities of the salt. The third example, {[BEDT.TTF][TCNQ]}, is polymorphic, one structure having mixed stacks (see Section 15.11.2) and the other segregated stacks (Mori and Inokuchi, 1986; FAHLEF). The latter crystals are triclinic (a ¼ 6.650, b ¼ 7.817, ˚ , ¼ 89.18, ¼ 85.67, ¼ 74.90 , P1, Z ¼ 2) and have the unusual c ¼ 23.915 A feature that there are stacking motifs with approximately-perpendicular stacking axes. The TCNQ moieties are stacked along [001] in a diad arrangement with ˚ (displaced R/EB overlap) and 3.24 A ˚ (displaced R/R interplanar spacings of 3.34 A overlap); this stack is one-dimensional in character. The cations are stacked along ˚ (R/DB overlap) and 3.87 A ˚ (sideways [010] with interplanar spacings of 3.63 A displaced R/EB overlap). However, lateral interactions appear to be more important than those within the stacks. Thus it seems that the crystal has a structure that is a compromise between the conﬂicting requirements of the one-dimensional interactions characteristic of TCNQ and the two-dimensional interactions characteristic of BEDTTTF.

STRUCTURES OF CATION-RADICAL ANION-RADICAL SAL TS

1229

Br S S N N NC NC

CN N

S Br

Dibromo-DCNTT

˚, The fourth example is {[TTF][dibromo-DCNTT]} (a ¼ 13.82, b ¼ 19.19, c ¼ 6.97 A Pccn, Z ¼ 4), which has segregated stacks of planar donors and acceptors, with equidistant ˚ in both stacks. The stack axes are parallel to [001], the interplanar separations of 3.48 A TTF moieties are almost exactly eclipsed while the unsymmetrical acceptors alternate in orientation along the stack. The single crystal conductivity (presumably along the stack axis) is 2 102 S/cm (Gunther et al., 1990; SETWOD). 17.6.4 Cation : anion ratio 2 : 1 and 1 : 2; monad stacks We treat these two cation : anion ratios together because, in a formal sense, many of the structures are related as structure and anti-structure (i.e. roles of cation and anion are interchanged). Relatively few examples are known. {[(Perylene)2][Pt(mnt)2]}, which could have been discussed in Section 17.5.2, is monoclinic with space group P21/c, Z ¼ 2 ˚ ) (Alcacer, Novais et al., 1980; PRLNTP; Alcacer, 1985); (stack axis [010] ¼ 4.194(1) A thus the perylenes are at general positions and the Pt(mnt)2 moieties at centers of symmetry. Six perylene stacks surround a Pt(mnt)2 stack. The (perylene)þ moieties overlap ˚ ; bond lengths were not in graphite-like fashion with an interplanar spacing of 3.32 A ˚ . The reported. The Pt(mnt)2 moieties have a metal-over-ring overlap, separated by 3.65 A room temperature conductivity is 50 S/cm, rising to 1250 S/cm at 20K, where there is a metal-to-insulator transition to a very high resistivity material. The positive thermopower ( 28 mV/K) shows that the predominant charge carriers are holes on the perylene stacks, the electrons on the [Pt(mnt)2]2 moieties being localized. (TTF)2 HCBD, the crystal structure of which has not been reported, possibly has an analogous structure; RT 103 S/cm. There are two analogous anti-structures. {[(TMTTF)1.3][(TCNQ)2]} is monoclinic, space group P21/n, with TMTTF moieties at centres of symmetry and TCNQs at general positions (Kistenmacher et al., 1976; MDTTCQ); the additional TMTTFs are located in channels between the stacks and do not appear to play any part in determining the electronic properties of the crystals. The material is a semiconductor with RT 10 S/cm. The ˚ and the TMTTF TCNQ stacks have R/EB overlap with an interplanar spacing of 3.24 A ˚ . The second example is stacks have R/DB overlap with an interplanar spacing of 3.59 A ˚ , space group P1, {[TTT]) [(TCNQ)2]}; the stacking was reported as monad (c ¼ 3.754 A Z ¼ 1), with TTT cations at centers of symmetry and TCNQ moieties at general positions but translationally equivalent. The TCNQ stacks have R/EB overlap with an interplanar ˚ and the TTT stacks have graphite-like overlap with an interplanar spacing of 3.18 A n n n

n n n

1230

SEGREGAT ED STACK -MOLECULAR COMPLEXES

˚ . The material shows metallic behaviour down to 90K, below which the spacing of 3.52 A conductivity decreases rapidly; RT 10 S/cm. Studies of its physical properties appear to be complicated by presence of solvent (perhaps 1/2 molecule of nitrobenzene per formula unit) and poor crystal quality (Shchegolev and Yagubskii, 1982). 17.6.5

Cation : anion ratio 2 : 1 and 1 : 2; diad stacks

The crystals of {[(TTF)2][OCNAQ7]} are triclinic, space group P1, Z ¼ 1.(Inabe et al., ˚ , with weak 1988; SAJNIA). The interplanar spacings in the cation stack are 3.42 A dimerization and little overlap between dimers while there is R/EB overlap (spacing ˚ ) between halves of the anions. There is metallic conductivity of 10 S/cm down to 3.30 A 43K and then a marked reduction in conductivity. The crystals of {[(TTT)2] [OCNAQ]}DMF are also triclinic, space group P 1, Z ¼ 1. (Inabe et al., 1988; GAXCUD10). The TTT moieties are weakly dimerized in stacks along [001] (interplanar ˚ ) while there is limited overlap of the OCNAQ moieties, whose spacings 3.26 and 3.38 A mean planes are steeply inclined to those of the cations. There is metallic conductivity down to 250K below which the material is a semiconductor; RT 60 S/cm. {[(TMTTF)2][HCBD]}, although monoclinic, has a rather similar structure with the anions in channels between the stacked (and weakly dimerized) cations (Katayama, 1985); the anion planes are parallel to the axis of the cation stacks. This material is a semiconductor with RT 3 104 S/cm. A similar structure is found for {[(TMTSeF)2][(2,5-TCNQBr2)]} (Stokes et al., 1982; BEVHUF), where there is considerable disorder of the anions located between the TMTSeF diad (but nearly monad) ˚ . The nitrile stretching frestacks, whose mean interplanar spacing is given as 3.6 A quency corresponds to unit charge on the anions and hence to an average half-unit charge on the cation moieties. The DC conductivity at room temperature is 100 S/cm and is ascribed to phonon-assisted hopping. {[TMPD][(TCNQ)2]} has a DA2 anti-structure compared to the above group of D2A ˚ ) (Hanson, structures; the crystals are triclinic (space group P 1, Z ¼ 1; stack axis c ¼ 6.488 A 1968; TCQPDA) with the TCNQ moieties forming a zigzag pseudomonad stack while the TMPD’s are inclined at a large angle to the TCNQ planes (Fig. 17.43(a)). Measurements of conductivity and other properties as a function of temperature on powder samples conﬁrm that only the TCNQ stacks contribute to the transport properties (Somoano et al., 1975). There is evidence for structural transitions at 200 and 70K but parallel crystallographic studies have not been reported. {[E2P][(TCNQ)2]} (E2P is 5,10-dihydro-5,10diethylphenazine (Section 15.9.5)) provides an analogous example. The crystals are tri˚ ) with diad stacks; there are weakly overlapping -dimers clinic (stack axis a ¼ 6.843 A ˚ ) separated by 3.54 A ˚ (Fig. 17.43(b)) (Dietz et al., (R/EB overlap, interplanar spacing 3.25 A 1981). Thus, in structural terms, both {[TMPD][(TCNQ)2]} and {[E2P][(TCNQ)2]} could be better described as anion radical salts, as could some of the other examples included for convenience in this section. Because of differences in the TCNQ stacking patterns, differences are to be anticipated in appropriate physical properties. We conclude this section by noting another structure in which lateral interactions appear to determine the overall crystal structure; this should be compared with the situation in 7

OCNAQ is 11, 11, 12, 12, 13, 13, 14, 14-octacyano-1,4,5,8-anthradiquinotetramethane.

STRUCTURES OF CATION-RADICAL ANION-RADICAL SAL TS

1231

(a)

c

(b)

E2P cation

A

TCNQ Stack C x

O B

z

Fig. 17.43. (a) {[TMPD][(TCNQ)2]} viewed normal to the stack axis, showing the zigzag pseudomonad stackof TCNQ anions seen edge-on, and the cations steeply inclined to the stack. (Reproduced from Hanson, 1968.) (b) {[E2P][(TCNQ)2]} viewed normal to the stack axis, showing the stacked TCNQ -dimers (within the conﬁnes of the unit cell) and the cations steeply inclined to the stack. (Data from Dietz et al., 1981.)

the stacked structures of the M(dmit)2 salts discussed in Section 17.5.2. In ˚, 1, Z ¼ 2, a ¼ 15.47, b ¼ 13.53, c ¼ 10.59 A {[HMTTeF)2][(Pt(dmit)2)2]}8 (triclinic, P ¼ 92.85, ¼ 102.50, ¼ 75.91 ) the HMTTeF moieties form nonstacked tetrads, which are linked diagonally to other tetrads by Te . . . Te contacts (Kobayashi, Sasaki et al., 1986; FIFRUH). These form a framework enclosing two Pt(dmit)2 moieties (Fig. 17.44) and the salt has strong structural resemblances to the channel inclusion complexes. The temperature dependence of the conductivity ( 20 S/cm at room temperature) suggests that the material is a semiconductor. Thus we have travelled a long way from our 8 This notation is hardly applicable here. Also, there is a monoclinic crystal FIFRUH01, the structure of which has not been reported.

1232

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Fig. 17.44. Partial view of the crystal structure of (HMTTeF)2 Pt(dmit)2 showing the tetrad of HMTTeF moieties in the centre of the cell and individual Pt(dmit)2 moieties on the ﬂanks; the planes of the two components are approximately mutually perpendicular and the view direction is approximately along the long axis of the Pt(dmit)2 moiety. The shorter Te . . . Te distances range from 3.33 to 3.9. (Reproduced from Kobayashi et al., 1986.) n n n

starting point – structures based on segregated stacks of donors and acceptors, arranged with stack axes parallel.

17.7

Electron density studies of some segregated stack complexes

The ﬁrst attempt at investigating the interaction between the components of an ion radical salt through the medium of electron density studies was for {[TMSF]2AsF6} at 300K (Wudl, Nalawajek et al., 1983). This was at an early stage in the development of these techniques and it is perhaps no surprise that the criticism was made that the conclusions drawn were not supported by the experimental measurements (Dunitz, 1985). The only other study of this kind is by Espinosa et al. (1997) on the {[bis(thiodimethylene)TTF)][TCNQ]} complex ({[BTDMTTF][TCNQ]}) using measurements made at 130K and the more recently-developed computational techniques. Crystal data are in Table 17.9. X

X

Y

Y X

X

BTDMTTF X = Y = S; HMTSF X = Se, Y = CH2 HMTTF X = S, Y = CH2

ELECTRON DENSITY ST UDIES

1233

Table 17.13. Crystal data for three related structures. The first two crystals are isomorphous while the third is isostructural. Z ¼ 2 for the three structures

Space group a b c Vol Mol. Wt. Refcode/ reference

{[BTDMTTF][TCNQ]}

{[HMTSF][TCNQ]}

{[HMTTF][TCNQ]}

298K

130K

RT

RT

C2/m

C2/m

C2/m

Pmna (no. 53)*

21.296 15.567 3.928 92.74 1050 524.7 Rovira et al. (1995).

21.205 12.530 3.859 93.30 1023.6 524.7 Espinosa et al. (1997).

21.999 12.573 3.980 90.29 1076 676.3 SEOTCQ; Philips et al. (1976).

12.462 3.901 21.597 1050 488.7 HMTFCQ; Chasseau et al. (1978).

* The space group was misprinted as Pmma (no. 51) in the paper by Rovira et al. (1995).

We shall introduce this area by ﬁrst considering three related structures for which crystal data are given in Table 17.13. In the C2/m structures the cations (symmetry 2/m at 0, 0, 0) and anions (symmetry 2/m at 0, 1/2, 1/2) are located in segregated stacks along [001], with each donor stack surrounded by four acceptor stacks, and conversely; both types of molecule have ‘ringover-bond’ overlap; the Pmna structure is analogous. The BTDMTTF cations are ˚ and the TCNQ anions by 3.194 A ˚ at 130K. The structures are separated by 3.521 A ˚ shown in projection down the short 4 A axes (Fig. 17.45). There are distances shorter ˚ ) and between than the sum of van der Waals radii between ‘internal’ S and N (3.24 A ˚ ‘external’ S and C (of cyano) at 3.44 A. There are similar short ‘internal’ S(Se) . . . N distances in the other two structures but the CH2 that replaces ‘external’ S does not make short contacts. The similarities and differences between the two structure types are shown in the two parts of Fig. 17.45. More detail emerges from the 130K structure analysis of {[BTDMTTF][TCNQ]}. Bond lengths in the two components, x-ray diffuse scattering and Raman and IR frequency measurements all agree that there is transfer of 0.56e from BTDMTTF to TCNQ. Multipolar reﬁnement of the electron density showed a transfer of 0.34e from each of the two external S atoms (almost entirely) to the four N of TCNQ. The concentration of electron density was found to be appreciably higher in TCNQ than in BTDMTTF. Detailed analysis showed that ‘external’ S interacted not with cyano N or C but with the –CN triple bond itself, with the interaction having features similar to those of weak hydrogen bonds. It was concluded that this was the mechanism that controlled the electronic properties – the conductivity and the charge density waves. These very interesting results pose the question ‘what happens when ‘external’ S is replaced by CH2?’ Study at low temperatures of {[HMTTF][TCNQ]} and of the isostructural pair {[1,6-dithiapyrene][TCNQ]} (DAKTIS) and {[1,6-diaminopyrene][TCNQ]} (WEMHEB) (see Table 17.10) should prove illuminating.

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1234

(a)

{[[BTDMTTF][TCNQ]} (b)

x

S N

z {[HMTTF][TCNQ]}

Fig. 17.45. Comparison of the short-axis projections of {[BTDMTTF][TCNQ]} (C2/m) and {[HMTTF][TCNQ]} (Pmna). S is denoted by ﬁlled circles in the upper diagram and by open circles in the lower diagram. (Adapted from Rovira et al. (1995) and Chasseau et al. (1978).)

17.8

Theoretical studies of some segregated stack complexes

Theoretical studies of the molecular complexes discussed in this chapter have been directed to two ends: the ﬁrst is to provide an explanation for the overwhelming predominance of stacked structures; the second is to provide an explanation for the physical properties of the complexes, ﬁrst and foremost the electrical conductivity. Structural ends are usually expressed in the standard terminology of quantum chemistry, physical properties in terms of band structure. In accord with the structural bias of this book, we shall not discuss the theoretical approaches to the physical properties but concentrate on the quantum chemistry, essentially restricting ourselves to TTF, TCNQ and the [TTF][TCNQ] system. We start with some experimental facts. TCNQ dimerizes in aqueous solution to give (TCNQ)2 (Boyd and Philips, 1965) with an equilibrium constant (at 298K) of 2.5 103 litre/mol and H ¼ 43.5 kJ/mol dimer. The authors comment ‘‘The solution dimer is presumably related to the structure of some of the ion radical salts of TCNQ, where paired electrons are found in a singlet state with an ESR-detectable population of a triplet state.’’

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1235

Neutral TCNQ has a herringbone packing of planar molecules with an interplanar spacing ˚ at room temperature (Long, Sparks and Trueblood, 1965, see their Fig. 3; of 3.45 A TCYQME); polymorphs have not been reported. There are two polymorphs of neutral TTF – monoclinic (Cooper et al., 1974) and triclinic (Weidenborner et al., 1977; Ellern et al., 1994). Only the (apparently more stable) monoclinic polymorph is relevant in the ˚ present context. It also has a herringbone crystal structure, with a spacing of 3.63 A between planar, parallel molecules. As we have seen, the interplanar spacings between ˚ less than these values, adjacent TTF cations and between TCNQ anions can be 0.2–0.3 A suggesting attractive interactions additional to those due to van der Waals interactions. The tasks of theory are to provide an explanation for the reduced spacings and then to indicate the relative stabilities of various mutual moiety arrangements. The ﬁrst of these does not appear to have been met at all as authors generally ﬁx the ˚ for TCNQ, 3.47 A ˚ for TTF), and then interplanar spacing at experimental values (3.17 A investigate interaction energy as a function of slip along the long molecular axis. Calculations up to 1980 by extended Hu¨ckel MO (EHMO) methods have been reviewed by Lowe (1980); minima are found for the appropriate degrees of slip for the neutral and singly and doubly charged entities; however, it would not be unfair to say that the point has been illustrated rather than demonstrated. Shifts other than along the long molecular axes do not appear to have been considered. There have been a number of attempts to calculate the stable overlap modes for TCNQ -dimers and the results have been summarized critically (Silverman, 1981). The available results do not seem to be easily comparable with experiment. The essential problem is that the molecular orbital programmes in current use, despite their wide range, were designed primarily for calculating interactions between atoms at or around covalent bonding distances and do not perform well when interactions at van der Waals distances are involved. Silverman (1981) applied a procedure due to Gordon and Kim (1972) to the calculation of interaction energies for TTF neutral dimers but this does not yet seem to have been done for TCNQ anions. A bridge between the quantum chemical and energy band approaches is provided (Starikov, 1998) by a three-dimensional HF crystal orbital calculation using CRYSTALS92 (Dovesi, Saunders and Roetti, 1992); we discuss only the results for {[TTF][TCNQ]}. As the calculation was based on the experimental crystal structure, no insight is provided about stacking or mutual arrangement of moieties but the component charge distributions were obtained (for TTF positive charges on S and negative charges on C, for TCNQ negative charges on N) and there is charge transfer of 0.5–0.9 e (depending on details of the calculation) from TTF to TCNQ, which ﬁlls the conduction band in the [010]* direction. The mobile charge density is carried on the TCNQ stack while the rest of the charge density residing on the TTF stack is essentially localized and immobile. This corresponds to the experimental ﬁnding that the TCNQ stacks carry most of the conductivity and the TTF stacks most of the magnetic susceptibility.

17.9 Studies of {[TTF][TCNQ]} and some related materials In the previous section we described the structural chemistry of cation radical–anion radical salts in general terms, with most of the results referring to room temperature. Here

1236

SEGREGAT ED STACK -MOLECULAR COMPLEXES

we give more detail about the most famous member of this class {[TTF][TCNQ]}, whose physical and structural properties have been studied over a wide range of temperature and pressure; some closely related materials are included in the discussion. Above 54K crystalline {[TTF][TCNQ]}, is disordered in subtle fashion, crucial for explanation of its unusual physical properties. Three phase transitions (of somewhat unusual type) occur around 50K, below which temperature ordering occurs. We start by considering physical properties and room temperature crystal structure and then discuss the dependence of structure on temperature, ﬁnally relating structural features to physical properties on the basis of current theoretical treatments. A number of comprehensive reviews have been published (Garito and Heeger, 1974; Berlinsky, 1976; Friend and Jerome, 1979; Schulz, 1980; Conwell, 1988a, b), and the structural physics of {[TTF][TCNQ]}, and related compounds has been discussed in particular detail by Pouget (1988). As mentioned at the beginning of this chapter, interest in {[TTF][TCNQ]}, rocketed when it was found to have a large metallic-type conductivity along the [010] axis over the range 300–56K (cf. the conductivity of Pb shown in Fig. 17.1), followed by a drastic drop as the temperature was lowered further (Figs. 17.1 and 17.46). The three crystalline compounds {[TTF][TCNQ]}, {[DSeDTF][TCNQ]} and {[TSeF][TCNQ]} are isomorphous (Table 17.10) and their conductivities along [010] show very similar types of temperature dependence (Fig. 17.46); such similarity may well be expected to extend to 14.0 13.0 12.0 11.0 10.0 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0

0

50 100 150 200 250 300 T(°K)

Fig. 17.46. The ordinate shows the normalized conductivity s/s295 along [010] as a function of temperature for {[TTF][TCNQ]} (highest values), {[DSeDTF][TCNQ]} (lowest) and {[TSeF] [TCNQ]} (intermediate). The conductivity of {[TTF][TCNQ]} at 5K is about 5106 S/cm (Cohen and Heeger, 1977). (Reproduced from Etemad et al., 1975.)

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1237

other physical properties. Microwave measurements (9400 Mhz 0.3 cm) (Miane et al., 1986) give the following room temperature values (units of S/cm) along the principal axes of the (markedly anisotropic) conductivity ellipsoid : a ¼ 1.00 0.16, b ¼ 325, c* ¼ 0.0115 (anisotropy b/a 330; b /c* 28000; a /c* 100). These values are essentially DC conductivities. The conductivity of {[TTF][TCNQ]} has been studied more intensively than that of any related material not only because of its intrinsic interest but also because comparatively large, high quality crystals can be grown. Results for the b-axis conductivity of some 600 crystals studied in 16 laboratories are summarized in Fig. 17.47 (Thomas et al., 1976). There is some evidence for an increase in conductivity with time as crystal quality has improved. An average value of max/RT would be about 20. Values of max/RT 500 were reported (Coleman et al., 1973) for three crystals out of 70 studied by the University of Pennsylvania group but are not generally accepted (Thomas et al., 1976; Cohen et al., 1976). Clearly there was, some 25 years ago, no such thing as a standard and reproducible value for the conductivity of {[TTF][TCNQ]} at a given temperature comparable to the values available for copper and other substances. Despite these reservations, the general dependence of conductivity on temperature is well established as well as the overall anisotropy of the conductivity. The crystal structure of {[TTF][TCNQ]} is shown in Fig. 17.48. Interplanar distances ˚ in the TTF stack (ring over double bond overlap) and 3.17 A ˚ in the TCNQ are 3.47 A

log conductivity (s/cm) 2

3

4

5

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 300 K values

maximum values

1Å

100 Å I≈b

I ≈10b

Fig. 17.47. Diagram summarizing the values of the room temperature and maximum conductivities along [010] (stack axis) for {[TTF][TCNQ]}, as reported by different laboratories: 1. Johns Hopkins U.; 2. U. Pennnsylvania; 3. Stanford U. and IBM, San Jose; 4. Bell Labs.; 5. Dupont; 6. IBM, Yorktown Heights; IBM, San Jose; 8. U. Illinois; 9. NBS; 10. Monsanto; 11. U. Chicago; 12. U. British Columbia; 13. Hughes; 14. Clemson; 15. Tennessee; 16. Tokyo. The effective mean free path is shown below the frame of the diagram. (Adapted from Thomas et al., 1976.)

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1238

stack (R/EB overlap). The angles between molecular plane normal and [010] are not very different (24.5 for the TTF stack and 34.0 for the TCNQ stack) but have opposite signs, giving rise to the overall herringbone arrangement of the stacks. Each TCNQ stack has six nearest-neighbor stacks, four TTF and two TCNQ. Alternatively the overall arrangement y

S(1) N(1)

S(2) N(2)

z

x z

C(3) S(1) C(1)

C(7) C(8)

S(2) C(2) N(1)

C(9)

C(6) C(4) C(5)

N(2)

Fig. 17.48. Crystal structure of {[TTF][TCNQ]} viewed in projection down [100] (above) and [010] (below) axes. There is a herring-bone arrangement of segregated TTF and TCNQ stacks that are located in alternate (100) planes. (Reproduced from Kistenmacher et al., 1974.)

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1239

can be described in terms of sheets of like stacks, with TTF and TCNQ moieties arranged in alternate (200) planes. Some approaches between S atoms of the cation and N atoms of ˚ ; for the anion are closer than the sum of the van der Waals radii 1.85 þ 1.75 ¼ 3.60 A ˚ example, in {[TTF][TCNQ]} there are two S . . . N distances of 3.20 and 3.25 A directed roughly normal to the sheets of like stacks. Such approaches, which are roughly along [100], suggest that the intrastack interactions are supplemented by interactions between them, thus giving rise, in some of these materials, to what has been termed a quasi-two dimensional character. The molecular dimensions measured at room temperature by XRD (Kistenmacher et al., 1974) and neutron diffraction (Filhol, Bravic et al., 1981) are in good agreement, and were interpreted to imply a charge transfer Z of between 0.5 to 1.0 electron from TTF to TCNQ (Kistenmacher et al., 1974). We draw a similar conclusion about the imprecision of the determination of the amount of charge transfer from our discussion of the moiety dimensions in {[TTF][TCNQ]} over a range of temperature (#13.3.6). A much more precise value of Z is obtained from the diffuse scattering measurements to be discussed below. There are similar moiety arrangements in {[TMTTF][TCNQ]}, {[TMTSeF] [DMTCNQ]}, and {[TMTTF][HCBD]} but the herring-bone pattern is less marked in {[TTF][DETCNQ]} and {[DBTTF][TCNQCl2]}. Description in terms of ‘sheets of stacks’ can also be applied to the other examples in Table 17.10. The long axes of the moieties are parallel in projection in all these examples except for {[TMTSeF][DMTCNQ]} and {[TTF][DETCNQ]}. Some fundamental thermodynamic quantities for {[TTF][TCNQ]} and its components are summarized in Table 17.14. The standard enthalpy of formation of the salt from its components Hc is 37.4 kJ/mol, in good agreement with determination of the enthalpy of sublimation of the salt as 38 kJ/mol more endothermic than the sum of the values for the components. The entropies of salt and components do not appear to have been measured. The value of Vc is 8.1%, which is considerably larger than, for example, the

Table 17.14. Fundamental thermodynamic quantities for {[TTF][TCNQ]} and its components at room temperature and pressure Parameter

TTF

TCNQ

{[TTF][TCNQ]}

X*

m.pt. (K) ˚ 3) Volume (A Hf (kJ/mol) (Metzger, 1977) Hsubl(kJ/mol) (Kruif and Govers, 1980)

567–9 202.1 290.8 1.7

464 254.9 664.9 0.7

483(dec.) 419.9 918.4 2.1

– 37.1 37.4

97.1 7.1

131.8 5.4

266.9 18.4

38

Notes: 1. X ¼ [X{[TTF][TCNQ]}–{X(TTF) þ X(TCNQ)}]. This follows from the deﬁnition of the measured standard thermodynamic quantities of formation as Xc ¼ X[DA]c – {X(Dc) þ X(Ac)}, where the reaction is Dc þ Ac ) [DA]c. The temperature is usually taken as 298K and the subscript c denotes that all substances are in the crystalline state. This deﬁnition applies to a 1 : 1 composition and has been specialised from the more general deﬁnition given in Appendix I. 2. The volume per moiety in the crystal is calculated from measured cell dimensions. 3. The measured values, at various temperatures, have been corrected to 298K by Govers (1978).

1240

SEGREGAT ED STACK -MOLECULAR COMPLEXES

value of 4.8% found for the ionic mixed stack -molecular compound {TMPD TCNQ}. The cohesion of the crystal attracted early interest. The crystal consists of segregated stacks of TTFZþ and TCNQZ moieties; the electrostatic energy is repulsive within the stacks and between like stacks but attractive between unlike stacks. The ionization energy of TTF is 672.5 kJ/mol and the electron afﬁnity of TCNQ is 272.1 kJ/mol; if one assumes (as discussed below) that the charge transfer Z is 0.59, then the energy needed to stabilize the crystal is at least 236.2 kJ/mol. The Madelung energy, calculated on the basis of various quantum-mechanical models of the charge distributions in the TTF and TCNQ moieties, ranged from 71.4 to 91.7 kJ/mol (Metzger and Bloch, 1975). Later calculations, summarized by Govers (1978), give a mean value of 72.9 and a range of 57.5 to 83.7 kJ/mol for Z ¼ 0.59. Thus the Madelung energy is not enough to stabilize the crystal. This was termed ‘‘the electrostatic binding energy defect’’ by Metzger and Bloch (1975), and much effort has been devoted to reﬁnement of its calculation and ﬁnding routes to its elimination (Metzger, 1981). One possibility is to include polarization, dispersion and charge-dipole contributions in the cohesive energy; this has been done by Govers (1978), using the atom-atom approximation of Kitaigorodskii. The sum of the van der Waals and repulsive energies calculated for {[TTF][TCNQ]} amounts to 196 kJ/ mol, thus giving an overall cohesive energy of 269 kJ/mol, which is enough to stabilize a crystal containing partially ionized moieties. These results suggest that it is essential to include both dispersion and Madelung contributions in any calculation of the cohesive energy of {[TTF][TCNQ]}, but there are so many uncertainties in the numerical values that it does not appear justiﬁed to give them in detail. The elastic properties (thermal expansion and compressibility) are summarized in Fig. 17.49 and have been discussed in some detail (Filhol et al., 1981). The thermal expansion coefﬁcient along [010] for {[TTF][TCNQ]} has also been measured by a microwave technique in the range 80–300K (Krause et al., 1983) and agrees well with the analogous diffraction results. The temperature region of the phase transitions was not covered in these sets of measurements. The anisotropy of elastic properties is much less than the anisotropy of conductivities. The maximum compressibility kb and thermal expansion 2 are both directed along [010] while the other two, much smaller values, have very similar directions with respect to the packing of the molecules; there is a minor dependence of the orientations of the two ellipsoids in the ac plane on pressure and temperature respectively. The ‘‘softest’’ direction is along the stack axis, roughly normal to the molecular planes, while the ‘‘harder’’ directions are between stacks. A similar situation is found in mixed stack molecular compounds (Chapter 15). The speciﬁc heat of {[TTF][TCNQ]} has been measured in the region of the phase transitions (Craven et al., 1974; Djurek et al., 1977). The effects are very small (Fig. 17.50). It is now accepted that there are three transitions at ambient pressure (TL at 38, TM at 48 and TH at 54K), in accordance with the results of Djurek et al. (1977). The entropy change in the transition around 52K has been estimated to be 0.03 R, with similar values for the other transitions. The low-temperature ( 1.5–4K) speciﬁc heat can be ﬁtted by a T 3 equation, without any linear term arising from electronic or magnetic excitations. The Debye temperature was estimated as 89.5K and the material characterized as a small band gap nonmagnetic semiconductor (Wei et al., 1973). n n n

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

k (x10–4 MPa–1)

k1

0.6

kb

S(2)

a

S(1)

N(1) N(2)

kb

0.5

1241

0.4 0.3 P = 4.6 x 102 MPa

k1

0.2

k3

0.1

P = 10–1 MPa

c

k3

P × 102 MPa–1 0

1

2

3

4

a × 104 (K–1) a1 ab

1.5

a

ab 1.0 T = 64 K a3 T = 293 K c

0.5 a1 a3 0

T (K) 100

200

300

Fig. 17.49. (Top) The principal compressibilities (ki ¼ (1/li)((dli/dp)) at 293K of {[TTF][TCNQ]} and their directions at two representative pressures (101 MPa on left and 4.6 102 MPa on the right); (bottom) principal thermal expansion coefﬁcients i ¼ (1/li)((dli/dT)) as functions of temperature and their directions at two representative temperatures. kb and 2 are along [010] because of the monoclinic symmetry of the crystals. (Reproduced from Filhol, Bravic et al., 1981.)

1242

SEGREGAT ED STACK -MOLECULAR COMPLEXES

0.25

Specific heat Cp /R

0.20 0.15 0.10 0.05 Craven 0.00 –0.05

45

50 55 Temperature (K)

60

Cp Re

1st run = a/T/ + ∆Cp

3rd run

a/T/

Specific heat ∆Cp(R)

1.0 Djurek

.5

0 40

temperature (K) 45

50

55

Fig. 17.50. Speciﬁc heat of {[TTF][TCNQ]} in the range 36–62K; the values of Craven et al. (1974) (background subtracted) and Djurek et al. (1977) (background not subtracted) are in qualitative agreement over part of the range but the latter show two (or perhaps three) additional transitions. (Adapted from Craven et al. (1974) and Djurek et al. (1977).)

The low temperature maximum in the conductivity naturally encouraged investigation of diffraction patterns over a range of temperatures and we shall distinguish here between evidence obtained from Bragg diffraction and diffuse scattering (x-rays and neutrons have been used in both types of study). Bragg diffraction gives information about the average structure while the diffuse scattering gives information about deviations from this average. We start with some of the results obtained from Bragg diffraction. Soon after the ﬁrst studies of {[TTF][TCNQ]}, it was reported (Skelton et al., 1974) that (x-ray) oscillation photographs at 294, 77 and 10K showed that there was no doubling of the b axis below the metal–insulator transition at about 50K. A full set of cell dimensions was measured somewhat later (single crystal diffractometer, Mo K radiation) over the range 40–295K and crystal structures determined at 60, 53 and 45K (Schultz et al., 1976). The cell dimensions in the range 40–295K (the diagrams in Schultz et al. (1976) include data ˚ and points at 5 and 25K of unstated provenance) showed some irregularities (of 0.02 A 0.2 ) in the values of a, c and in the temperature region of the transitions. These have

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1243

not been conﬁrmed in later work. One should note that cell dimensions, especially if measured using Mo K radiation, are susceptible to larger errors (perhaps by a factor of 5 for cell lengths and 2.5 for cell angles (Taylor and Kennard, 1986; Herbstein, 2000) than may appear from an internal statistical analysis. The lack of irregularity along the stacking direction b was conﬁrmed by a capacitance dilatometric study (Schafer et al., 12.30 FBGCV81 12.28

PSSGH79

12.26

a (Å)

12.24 12.22 T (K) 12.20 FBGCV81

3.82

PSSGH79 3.80 b (Å)

3.78 3.76 3.74

T (K)

3.72 FBGCV81 18.42 c (Å)

18.40 18.38 18.36

T (K) 18.34 0

100

200

300

Fig. 17.51. Cell dimensions of {[TTF][TCNQ]} as a function of temperature. The values labelled FBGCV81 (Filhol et al., 1981) were measured by neutron diffraction using 17–26 centered reﬂections and have been reported (perhaps optimistically) to have standard uncertainties of 0.002– ˚ . The value of is 104.51(2) at 293K and is essentially constant at 104.40(1) in the region 0.004 A 90–60K. The values labelled PSSGH79 were measured by neutron diffraction (Pouget et al., 1979) ˚ (a was using the 300 and 020 reﬂections and have reported standard uncertainties of 0.008 A calculated here from a sin by using the values of noted above).

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1244

1975), while a later and more comprehensive study by the same method showed that there were no anomalous length changes (L/L) greater than about 2105 in all three crystallographic directions (Ehrenfreund et al., 1981). The available cell dimensions are summarized in Fig. 17.51. Lattice parameters and transition temperatures (see below) of hydrogenated (used mainly for x-ray diffraction studies) and deuterated (used mainly for neutron diffraction studies) samples do not differ appreciably, implying that the hydrogens do not have more than a minor role, if any, in the structural chemistry of {[TTF][TCNQ]}. Parenthetically we note here two other crystals for which the variation of cell dimensions with temperature has been measured. The back-reﬂection Weissenberg method (Cu K Bragg > 80 ; estimated precision of 3 in 104) has been applied to {[TMTSeF][DMTCNQ]} (Guy et al., 1982) (triclinic, Table 17.10) over the range 300– 10K; there is a metal-to-insulator transition at 40K. There were no indications of anomalies in lattice parameters at the Peierls transition within the precision of the experiment, in agreement with what was found for {[TTF][TCNQ]}. Single crystal diffractometer measurements (Mo K radiation) have been made for {[TTF][2,5-diethyl-TCNQ]}; Fig. 17.52; Schultz and Stucky, 1977). Irregularities in cell dimensions in the region of the transition are similar to those reported for (but not conﬁrmed) in {[TTF][TCNQ]}. Only the irregularities in a would appear to be signiﬁcant. This salt has a transition at 111K as inferred from the speciﬁc heat, which shows a fairly sharp anomaly (Fig. 17.53(a)) corresponding to S 0.17(2) R, about six times larger than that found for {[TTF][TCNQ]}. The conductivity of {[TTF][DETCNQ]} shows a quite different temperature dependence (Fig. 17.53(b)) from that of {[TTF][TCNQ]} and there is no peak in the -T curve. We now return to {[TTF][TCNQ]} and its structure analysis using Bragg reﬂections. Intensities of the fundamental reﬂections have been used for crystal structure

10.64 10.60

a-Axis

10.56

97.4 DEG. 97.0

10.52 10.48

b

96.4 DEG. 96.2

Å b-Axis

3.84

86.0 DEG. 85.6

3.80 3.76 c-Axis

10.10 10.06

a

0

80

160 T (K)

g 80

160 T (K)

240

240

Fig. 17.52. Plot of unit cell dimensions vs. T for {[TTF][DETCNQ]}. (Reproduced from Schultz and Stucky, 1977.)

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1245

Conductivity (ohm–cm–1)

27.25 26.50 CP/R

25.75 25.50 24.25 23.50 22.75 22.00 96 99 102 105 108 111 114 117 120 123 126 T (K)

42

1.5

36

1

30

0.5

24

0

Log conductivity

2

28.00

18

–0.5

12

–1

6

–15

0 70

90 110 130 150 170 190 T (K)

–2

Fig. 17.53. (a) The speciﬁc heat {[TTF][DETCNQ]} in the vicinity of the transition; (b) variation of conductivity with temperature. (Reproduced from Schulz, Stucky, Craven et al., 1976.)

determinations at 60, 53 and 45K (i.e. above and in the region of the phase transitions) and the differences found to be very small Schultz, Stucky, Blessing and Coppens, 1976). ˚, Thus the averaged structure (i.e. of the subcell, a ¼ 12.30, b ¼ 3.82, c ¼ 18.47 A ¼ 104.4 , P21/c, Z ¼ 2) (Table 17.10)) is essentially unchanged over the whole temperature range from 300K downwards. We conclude, from the evidence summarized above, that the drastic changes in conductivity are not accompanied by appreciable changes in average crystal structure. Whatever structural changes occur in {[TTF] [TCNQ]} during the phase transformations must be very different from the appreciable structural changes that occur in ﬁrst-order transformations (for example, those illustrated for the urea-parafﬁn channel inclusion complexes discussed in Chapter 7) or even in second-order transitions like that in {pyrene PMDA} at 160K (see Chapter 16). Furthermore, the transitions in {[TTF][TCNQ]},and {[TTF][DETCNQ]} would appear to be different in nature, although it is difﬁcult at this stage to deﬁne these differences. We now consider the deviations from the average structure of {[TTF][TCNQ]} described above. x-ray and neutron diffraction patterns show, in addition to the Bragg reﬂections and thermal diffuse scattering, an additional type of diffuse scattering (found to sharpen to discrete satellite reﬂections at the very lowest temperatures), that provides vital evidence for the explanation of the electronic and other physical properties. The extreme weakness of this type of scattering, and the low temperatures involved, has greatly complicated the experimental investigations. We summarize some of the experimental results for {[TTF][TCNQ]}, (Kagoshima et al., 1976; Khanna et al., 1977; Kagoshima, 1982) before considering the physical implications of such scattering. The diffuse scattering considered here is analogous to the ‘‘ghost’’ spectra obtained, in addition to the diffraction pattern of the averaged grating, from optical diffraction gratings with periodic errors of ruling (Wood, 1946). Similar effects are obtained in the diffraction of x-rays or slow neutrons from appropriately distorted crystals; the basic theory has been set out by James (1950). A periodic lattice distortion (PLD) [also sometimes called a periodic structural distortion (PSD)] will give satellite reﬂections displaced by wave vectors q from the parent reciprocal lattice point Gi. For small amplitude distortions the ﬁrst order intensity of such satellites is given by n n n

IðqÞ ¼ NIc ½FðGi Þ 2 ½Sj hu2q j iðS eq jk ÞðSq jk0 Þ=ðmr mr0 Þ1=2 :

1246

SEGREGAT ED STACK -MOLECULAR COMPLEXES

In this equation F(Gi) is the structure factor of Bragg reﬂection Gi, juqj is the distortion amplitude with wave vector q, S is the diffraction vector (S ¼ Gi þ q), N is the number of unit cells in the crystal, Ic is the electron scattering intensity, mr denotes the mass of the rth atom and j denotes the mode of lattice modulation. The mean square amplitude of modulation of the jth branch with wave vector q is given by hu2q jk i and eq jk is the corresponding polarization vector. When S and eq jk are parallel the scalar product (Seq jk) will be unity, while it will be zero when S and eqjk are mutually perpendicular. This allows distinction to be made between modulations of different polarizations. The modulation may be either static, when measurement of the intensities of the satellites will give, after suitable analysis, the modulation amplitudes in various directions, or dynamic. Dynamic lattice modulations are due to phonons, and hu2q j i is proportional to hEq ji/wq j2, where hEq ji and wq j are the average energy and angular frequency of the (q j) phonon. The diffuseness of the ghosts from an optical grating depends on the degree of correlation of the errors of ruling; the greater the correlation, the sharper the ghosts. Similar considerations apply to distorted crystals. The ﬁrst studies of the {[TTF][TCNQ]} satellites used photographic methods for surveying regions of reciprocal space, and the dependence of the scattering on temperature. Counter methods were introduced later for more quantitative investigation of limited regions of the reciprocal lattice; presumably the next step will be to employ area detector diffractometers. We shall attempt to put the available results in perspective, starting with the structure of the insulating phase as it is generally easier to proceed from ordered to disordered structures. The sharp satellite reﬂections at the lowest temperatures show that the structure tends towards complete order in this region. Below 38K, the incommensurate superstructure has dimensions a 0 ¼ 4a, b 0 ¼ 3.4b, c 0 ¼ c (unprimed values refer to the subcell) and the unit cell has the ﬁve-dimensional superspace group P : P21/c : cmm. (Bak and Janssen, 1978) The situation in {[TTF][TCNQ]} is complicated by the fact that satellites due to static and dynamic modulations have similar q wave vectors. The following quotation (Bouveret and Metgert, 1989) is illuminating: The structure of the low temperature modulated phases was only slightly touched even if the available data were of ﬁrst importance for the community. This state came from the fact that there was no sample big enough to perform exhaustive inelastic scattering studies and because the weakness of the satellite intensities (typically 103–104 of the main Bragg reﬂections) rendered x-ray data collection time prohibitive. Nowadays new intense light sources like rotating anodes or synchrotron radiation facilities became customary and make almost possible what was unrealistic before.

Two independent measurements have been made of the intensities of the 2kF group of satellite reﬂections of the insulating phase. Coppens et al. (1987) used synchrotron radiation to measure the intensities of 437 satellite reﬂections from a crystal at 15K. Bouveret and Metgert (1989) measured the intensities of 137 unique satellite reﬂections from a crystal at 13K, using Cu K from a rotating anode tube, The occurrence of the satellites was ascribed to displacements of the molecules by translational and librational modulation waves, whose parameters were determined by least squares analysis (Petricek et al., 1985); the Coppens group treated the molecules as rigid bodies while Bouveret and Megtert allowed for their segmentation into a number of separate rigid parts (e.g. the fulvalene rings, the quinoid ring, the C(CN)2 groups). The largest modulation was a slip of

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1247

˚ ; the TTF in the direction of the long axis of the molecule with an amplitude of 0.02 A TTF molecules are rigid. The TCNQ translational modulations are of similar nature but of even smaller magnitude, and there are also rotations of 0.1–0.6 about its long axis; the TCNQ molecules undergo intramolecular distortions involving displacement of the quinoid ring normal to the mean molecular plane. While it is difﬁcult to generalize about modulation amplitudes, the {[TTF][TCNQ]} values would appear to be at the lower end of the range; in -bis(1,2-benzoquinone dioximato)Pd(II) at 19.5K, for example, the commensurate superlattice has a transverse modulation wave with a maximum dis˚ (Kistenmacher and Destro, 1983; BZQXPD04, 12, 13). The zeroplacement of 0.84 A point translational amplitude of thermal vibration in an organic crystal would be expected ˚ at these temperatures, while librational amplitudes could lie in the range to be about 0.1 A 0.5 to 3 . Thus the structural effects in {[TTF][TCNQ]} are remarkably subtle. Even these exacting analyses are incomplete as the much weaker group of 4kF satellites was not included. We now consider the changes in the diffraction pattern of {[TTF][TCNQ]} on heating from 20K. The behavior of {[TTF][TCNQ]}, in the temperature range between 20 and 54K is intricate with changes in both positions and intensities of superlattice reﬂections (Fig. 17.54); it is clear that gradual disordering is taking place and the superlattice structure (incommensurate along [010]) changes from a 0 ¼ 4a, b 0 ¼ 3.4b, c 0 ¼ c below 38K to a 0 ¼ 2a, b 0 ¼ 3.4b, c 0 ¼ c just below 54K. We shall not attempt to discuss the theoretical treatments proposed (Bak and Emery, 1976). The satellite reﬂections are diffuse above 54K and typical diffractometer scattering curves obtained (at various temperatures) in two of the many zones investigated are shown in Figs. 17.55. There are diffuse peaks at ¼ 0.29, 0.41 and 0.59b*. The latter pair are

Intensity counts/250 secs

j

0.4

0.6

0.3

0.7

7500

(j, 2.29, 1)

1–j

15 000

(j, 0.29, 12)

5000

10 000

2500 (1– j, 2.29, 0)

5000

20

30

40

50

T (K)

Fig. 17.54. In the upper portion of this ﬁgure the variation of the positions of the satellite reﬂections along the a* axis with temperature is shown for the satellites at 0.29b* in the (021), (00,12) and (020) zones. The corresponding intensity dependence is shown in the lower part of the ﬁgure. The index x represents the wave number of the lattice modulation along a* in units of a*. (Reproduced from Kagoshima et al., 1976.)

SEGREGAT ED STACK -MOLECULAR COMPLEXES

1248

5000

4000

Intensity (Counts/1000 Sec.)

(0, 2 + h, 0)

(0, 2 + h, 1)

3500

4500 200 K R.T.Z. R.T

3000

150 K 70 K 120 K

2500 60 K

2000 0

150 K

4000

120 K 70 K 55 K 36 K

41.5 K 36 K 0.1 0.2 0.3 0.4 0.5 0.6 h

0.1 0.2 0.3 0.4 0.5 h

Fig. 17.55. Observed intensity in the (020) (left) and (021) (right) zones at several temperatures. The right hand scale is for the RT measurements and the left hand scale for all the other temperatures. The anomaly appearing at 0.41b* below 150K moves toward 0.45b* with increasing temperature. The sharp peak at T ¼ 36K is an example of the satellites used in the determination of the modulation amplitudes. Note the absence of a diffuse peak at 0.29b* in the left portion of the diagram, where the scattering vector S is parallel to b. (Reproduced from Kagoshima et al., 1976.)

considered equivalent in the reduced zone scheme (0.59 ¼ 1 0.41) and the two remaining peaks are considered to be related by a factor of 2; that at ¼ 0.29b* is the 2kF anomaly and that at 0.59b* is the 4kF anomaly. The average charge density on the moieties is estimated from Z ¼ 2(2kF/b*) ¼ 0.59 (electrons for TCNQ and holes for TTF).9 However, their different temperature dependences suggest that 4kF is not a simple second harmonic of 2kF, nor is it clear that the change in 4kF from 0.59 at 50K to 0.55 at 300K implies a parallel change in . From the dependence of diffuse peak intensity on zone of measurement it appears that the 2kF anomaly is mainly polarized along c* (transverse polarization) and the 4kF anomaly along b* (longitudinal polarization). Kagoshima (1982) has noted that ‘‘Naively speaking the periodic lattice distortion should be a longitudinal mode.’’ Thus the polarization of the 4kF anomaly ﬁts in well with a modulation of the stacks of TTF and TCNQ moieties along b (b and b* are parallel in a monoclinic crystal) while that of the 2kF anomaly could be related to displacements of the stacks in the direction of the long molecular axes, which is close to c*. However, the more generally accepted explanation is that tilting of the molecules in the stacks leads to perturbation of the longitudinal (along [010]) electron transport by the transverse (along c*) mode and thus it is the 2kF anomaly that demonstrates the existence of charge density waves 9 Other similar values come from XPS and Raman scattering measurements. Pouget (1988) gives a comprehensive collection of Z values for twelve radical cation : radical anion salts; all lie within the range 0.5 to 0.75.

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

24

TTF-TCNQ

20

x × 105 emu/mole

1249

xT

16

xF

12

8

xQ

4 0 30

35

40

45 T (K)

50

55

60

Fig. 17.56. The total susceptibility T of {[TTF][TCNQ]} and the susceptibilities of the TTF (F) and TCNQ (Q) stacks as a function of temperature. (Reproduced from Tomkiewicz, 1980.)

along b and these, as described below, account for the high conductivity in this direction above 54K. There is independent experimental evidence from ESR measurements indicating that the TTF and TCNQ stacks behave differently in this temperature range (Tomkiewicz, 1980). The susceptibility of the crystal can be decomposed into contributions from the separate stacks (Fig. 17.56). The metal–insulator transition at 54K is ascribed to ordering of the TCNQ stack, where the greatest change in susceptibility occurs in this temperature region, while the transition at 38K is ascribed to changes in the TTF stack; there do not appear to be clear magnetic effects of the 48K transition. The complicated phase transition behavior of {[TTF][TCNQ]} suggests that there is much to be said for investigating an analogous but simpler material; {[TSeF][TCNQ]} is a good candidate because there appears to be only a single (metal-insulator) transition, at 29K, but it has been studied (Kagoshima et al., 1978; Yamaji et al., 1981) less extensively than {[TTF][TCNQ]}. Below 29K an incommensurate superlattice is formed with a 0 ¼ 2a, b 0 ¼ 3.17b, c 0 ¼ c (a, b, c are the lattice parameters of the subcell). A photographic study (Yamaji et al., 1981) of a twinned crystal at 55K showed diffuse sheets of weak scattering normal to [010]* that derive from a 2kF anomaly transversely polarized along c*, as in {[TTF][TCNQ]}. The analysis was based solely on the TSeF molecules as, according to the authors, the contribution of the TCNQ molecules to the diffuse scattering is two orders of magnitude less and can thus be neglected. The TSeF molecules are found to slide along their long axes, as in {[TTF][TCNQ]}; translations of TSeF molecules are weakly correlated, being in-phase along [001] and out-of-phase along [010]. A 4kF anomaly was not observed and thus does not appear to be required for the explanation of the high conductivity peak at low temperatures (Fig. 17.46). The next stage is to relate the physical properties (we shall consider only the conductivity) of {[TTF][TCNQ]} and its analogs to the diffraction phenomena (Gill, 1986).

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The electronic structure of {[TTF][TCNQ]} is derived from the one-dimensional stacking of TTF and TCNQ moieties along the b axis; there are two bands, an electron band on the TCNQ stack and a hole band on the TTF stack. These are ﬁlled to the 2kF level; this value is measured as 0.59 electron (hole) from the diffuse scattering. Thus the stacks are composed of disordered arrays of molecules and ions (in the ratio 41 : 59) and a qualitative, chemically oriented explanation of the high conductivity along the stacks follows from the assumption of facile electron (hole) transfer between adjacent molecules and ions. A more physically oriented explanation is generally given in terms of charge density waves. Diffuse scattering shows there is a periodic structural distortion (PSD) along b. The PSD is accompanied by a corresponding redistribution of the conduction electrons in order to restore electrical neutrality along the stack (Fig. 17.57); the new distribution is the charge density wave. When the CDW is incommensurate with respect to the average lattice, it can slide along the stack in a coherent manner giving rise to a contribution to the b-axis conductivity which, according to Je´rome (1980), can be as large as 80% of the total conductivity at T 60K. This contribution drops to zero at 300K and also below the phase transitions where the CDW is pinned to the lattice. A quantitative explanation of the temperature dependence of the conductivity along the stack axis is much more controversial, and perhaps a dozen models (or mechanisms for scattering of the electrons) have been proposed, of which only some will be noted here. The temperature dependence of the conductivity of {[TTF][TCNQ]} (above the region of the phase transitions) has been explained in terms of single-phonon scattering of electrons (Conwell, 1980), by two-phonon scattering (the libron model) (Weger, 1980), and by a combination of single-phonon scattering and charge-density wave (CDW) conductivity (Je´rome, 1980; Je´rome and Schultz, 1982). Weger (1980) has remarked: ‘‘Different materials display different mechanisms, and even the same material may change from one region to another when the temperature, pressure, doping or other conditions are varied. There is not yet complete consensus as to where {[TTF][TCNQ]} at 100K (say) is.’’ The resistivity ( ¼ 1) of normal three-dimensional metals is not zero because the electron waves are scattered by phonons; as the phonon amplitudes decrease with temperature the conductivity increases with decreasing temperature (e.g. Fig. 17.1). On

PSD (a) Concentration of conduction electrons modulated by r

CDW

(b)

Fig. 17.57. The periodic structural distortion of a previously regular one-dimensional lattice is represented in (a); the regions of compression are shaded. The associated charge density wave (CDW) is shown in (b). Both diagrams are much exaggerated. (Reproduced from Gill, 1986.)

STUDIES OF {[TTF][TCNQ]} AND SOME RELATED MATE RIALS

1251

14 000

4000

12 000

3000 80K 2000

10 000

8000

1000

300K

Conductivity (S/cm) at 300K

Conductivity (S/cm) at 80K

the simple Bloch model the resistivity is proportional to T, for T > D (the Debye temperature). For {[TTF][TCNQ]} it is found that ¼ BT n, in the range 60–300 K, with n 2.3 and B strongly pressure dependent; thus there appear to be differences between the behaviour of one and three dimensional metals (the basic physics of one-dimensional systems has been summarized by Schulz (1980). A most comprehensive discussion has been given by Conwell (1988a, b). The room temperature conductivity of {[TTF][TCNQ]} is linearly dependent on pressure (Fig. 17.58; other TCNQ salts behave analogously) and this indicates that a signiﬁcant portion of the temperature dependence of is actually due to volume dependence. When correction is made for this effect, then the resistivity at constant volume is found to have a nearly linear temperature dependence; thus the behaviour becomes more metal-like. Calculation, using a simpliﬁed model with one molecule per unit cell and neglect of mode mixing, shows that two-phonon scattering, and other sources of scattering, are negligible compared with acoustic one-phonon scattering, which dominates the resistivity at least above 200K, and that the TCNQ stacks contribute about four times as much to the conductivity as the TTF stacks. At lower temperatures there is a distinct dip in the –P curve at 20 kbar, the 80K behaviour being shown in Fig. 17.58. When this is coupled with diffraction evidence for the occurrence of commensurability at 20 kbar and 80K, then the conclusion is that charge density wave conductivity makes an appreciable contribution to the overall conductivity at lower temperatures; the charge density waves can slide at lower pressures and higher temperatures but are pinned to the lattice at higher pressures and lower temperatures. The transverse conductivity, lower than the longitudinal conductivity by a factor of 100 to 1000, is ascribed to hopping. This brief account has neglected many important physical properties which can also be accounted for in terms of the above general picture; some references are given for completeness (Jacobsen, 1988; Scott, 1988).

0

6000 0

10

20

30

P (kbar)

Fig. 17.58. Dependence of conductivity of {[TTF][TCNQ]} on pressure (Andrieux et al., 1979). The room temperature dependence is approximately linear ( ¼ 118P þ 470) but the 80K values show a distinct dip at P 20 kbar.

1252

17.10

SEGREGAT ED STACK -MOLECULAR COMPLEXES

Concluding summary

Such a tortuous path has been followed in this chapter that it is perhaps desirable to retrace the way in which we have developed the material; for convenience we include references to ﬁgures and chapter sections in which the various aspects are described in greater detail. Our major goal has been to describe the structures and physical properties of segregated stack -molecular complexes, as we have done for other classes of molecular complexes and compounds in previous chapters. In order to keep the treatment within reasonable bounds, we concentrate on {[TTF][TCNQ]}, which is the most famous and widely studied example of such molecular complexes because of its unusually high electrical conductivity (Fig. 17.1). We begin in a wider context by introducing the current range of electron donors (Section 17.2.2) and acceptors (Section 17.2.3) used for formation of segregated stack -molecular compounds. We then describe structures of cation and anion radical salts (i.e. those with closed shell counterions), emphasizing those of the TTF (Section 17.3.3) and (the much more numerous) TCNQ salts (Section 17.4). The principal structural feature common to these salts is the stacking of the cation (anion) radicals, and thus they are described as essentially one-dimensional. The TCNQ salts show considerable structural variety, with stacks extending in length from isolated -dimers (Fig. 17.18) to unlimited. The structures of the stacks show considerable variety, with periodicities (the number of TCNQ moieties in a crystallographic repeat unit) ranging from diads through octads (Fig. 17.31). Indeed it seems reasonable to anticipate that the periodicity of TCNQ stacks will be limited only by the size of the counterions, with the ﬁne structure within the periods determined by the mutual interaction between cation arrangement and anion stacking; for example, the octad stacks shown in Fig. 17.31 consist of two tetrads, each made up of two -dimers. The stack axis conductivities of the crystals depend critically on the ﬁne structure of the TCNQ stacks. The overall phase behaviour (and hence some of physical properties) of TCNQ salts are often strongly inﬂuenced by the cation arrangement, whether this is ordered or disordered and whether there is cation–cation hydrogen bonding and/or cation–anion hydrogen bonding; examples such as DMM (TCNQ)2 and MEM (TCNQ)2 are discussed in Section 17.4.9. The limited available evidence suggests that these conclusions can be generalised to other anions (e.g. chloranil and M(dmit)2 (Section 17.4)) and cations (e.g. TTF and, to a lesser extent, TMPD (Section 17.3.4)). Thus stacking appears to be the essential structural feature of one dimensional cation and anion radical salts. The group of cation radical, anion radical salts discussed here all have their cations and anions arranged in separate homologous (hence ‘‘segregated’’) stacks, and the molecular complexes of greatest current interest, exempliﬁed here by {[TTF][TCNQ]} (Section 17.7), have average structures with monad stacks. However, {[TTF][TCNQ]} is not entirely typical because it crystallizes in the monoclinic system whereas most of the segregated stack -molecular compounds are triclinic, and a very few orthorhombic (Table 17.10). These crystallographic differences imply different mutual arrangements of symmetry-related stacks. The average structure of {[TTF][TCNQ]} does not change appreciably with temperature but the detailed structure, as revealed by the diffuse scattering in the diffraction pattern, is dependent on temperature (and also on pressure, although this aspect has not been considered at any length here). In thermodynamic terms

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the temperature dependence is shown by the occurrence of three phase changes at 54, 48 and 38K at ambient pressure (Fig. 17.50). However, these phase changes are very different in nature from the ﬁrst or second order changes encountered in other crystalline molecular complexes and compounds; there are no appreciable changes of average structure and the changes in enthalpy ( 5 J/mol) and entropy ( 0.03 R) are very small. The diffuse scattering shows an incommensurate modulation of the structure along [010], the stack axis, and commensurate modulations in the other directions. The incommensurate modulation indicates that the average charges on the moieties are Z ¼ 0.59 (holes for the TTF stack and electrons for the TCNQ stack); in chemical terms one can say that each stack has a disordered array of molecules and ions in ratio 0.41:0.59 and that the facile exchange of charge between the moieties leads to the high conductivity. The parallel description due to physicists is couched in terms of partially ﬁlled energy bands. The key to the conductivity is provided by the existence of a disordered array of molecules and ions or, alternatively, a partially ﬁlled band. {[TTF][TCNQ]} becomes ordered as the temperature is reduced below 38K (Fig. 17.47) and measurement (at 15K) and analysis of the intensities of the satellite reﬂections (no longer diffuse) suggests ˚ ) and librational ( 0.1–0.6 ) modulations very small and subtle translational ( 0.02 A in the TTF and TCNQ arrangement. None of its analogs has been studied to the same extent as {[TTF][TCNQ]} itself, and so it is not yet clear what generalizations are permissible. One other caveat is needed. The remarks above apply to ‘‘essentially one-dimensional’’ structures but it is clear that many donor-acceptor -compounds have structures appreciably different from the mixed and segregated stack prototypes. Sometimes there are clear indications of two- (Fig. 17.42), and even three-dimensional interactions, while in other examples the structures are quite unexpected (Fig. 17.44). It seems inevitable that further work will present us with a landscape even more variegated than that which we have today.

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Appendix 1 Thermodynamic measurements on binary adducts

A.1

Introduction

Treatments of the thermodynamics of solids (Westrum and McCullough, 1963; Swalin, 1987; Gaskell, 1995) will not be duplicated here. Instead, we intend only to summarise the speciﬁc features of the various methods that have been used to determine thermodynamic parameters for crystalline binary adducts (molecular compounds and complexes). Quantitative results for the different types of binary adduct, and consequent structural implications, are discussed in the body of the text. We principally consider the thermodynamic parameters of the reaction in which a crystalline binary adduct is formed from its crystalline components, i.e. mDc þ nAc , ½Dm An c Xc ¼ X (DmAn)c { mX(Dc) þ nX(Ac)} Here Xc represents Gibbs free energy (G), enthalpy (H ), entropy (S) or volume (V ) of formation of the crystalline molecular compound, [DmAn]c, from its components, Dc and Ac; the subscripts denote that the substances are in the crystalline state. In most of the following we shall set m ¼ n ¼ 1 for simplicity. If the components and/or the binary adduct are polymorphic, then care must be taken to deﬁne the polymorphs involved in the reaction. The Xc values refer to the temperatures at which the measurements were made. We shall, in general, restrict ourselves to atmospheric pressure, although pressure provides another variable that has hardly been explored. Use of thermodynamic functions for the crystalline substances implies that we hope to extract from the values of Xc information about the factors which lead to the formation of the binary adduct; in general such hopes will be best realized when the nature of the components changes minimally on formation of the binary adduct (cf. our original definition in Chapter 1). Thus the thermodynamic functions of packing complexes are expected to be easier to interpret than those of, say, molecular compounds of metal salts. Formation of a binary adduct means that Gc must be negative, its magnitude giving a measure of the stability of the binary adduct. However, the individual values of Hc and Sc are more informative from a structural point of view. As holds in general, three different situations are possible at a particular temperature: (i) when Hc is negative and Sc positive, then the binary adduct will be both enthalpy and entropy stabilized; (ii) when Hc and Sc are both positive, then Gc will be negative if TSc > Hc and the binary adduct will be entropy stabilized; (iii) when Hc and Sc are both negative, then Gc will be negative if TjScj < jHcj and the binary adduct will be enthalpy stabilized.

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All three situations are realised in practice and a detailed illustration is given in Chapter 16 where values (at 298K) of Hc are plotted against Sc for some -molecular compounds (see Fig. 16.1).

A.2

Experimental methods Methods that permit determination of all three thermodynamic parameters

A.2.1 A.2.1.1

Electrochemical method

This method was ﬁrst used by Brønsted (1911), extended by Bell and Fendley (1949) and described in detail by Abdel-Rehiem et al. (1974). The EMF difference is measured between the two cells shown, a picric acid molecular compound being used for illustration. .. saturated picric HgI picrate Hg(I) E1 : glass electrode acid solution solution saturated with .. HgI picrate Hg(I) E2 : glass electrode both picric acid molecular compound and donor It is assumed that the complexed picric acid does not ionize; the results do not depend on the solvent (water or mixed solvents such as 9 : 1 CH3CN-H2O have been used). The free energies are obtained from the EMF measurements as follows: Gc ¼ F(E2–E1) where F is the Faraday. The entropy of formation Sc is obtained from the temperature dependence of the EMF difference, i.e. Sc ¼ (@[Gc] / @T )p The enthalpy of formation values Hc(298) are then obtained from the Gibbs-Helmholtz equation {H ¼ G T(@[G] / @T )p}. A typical set of experimental measurements is shown in Fig. A1.1. This method appears to have been applied only to -molecular compounds and the results are discussed in Chapter 16.2.

A.2.1.2

Solubility method

If c1 is the solubility of component A in a suitable solvent and c2 its solubility in the solvent saturated with respect to both the other component and the binary adduct, then Gc ¼ RT ln(c2/c1). The assumption is made that the solutions are sufﬁciently dilute for activities to be proportional to concentrations. Repetition of the measurements at a number of temperatures allows calculation of Sc and Hc. The method was used to determine the Gc values at 298K for a number of TNB and TNT -molecular compounds of various aromatic donors (Hammick and Hutchison, 1955), water being used as solvent for these systems; values of Sc and Hc were not obtained.

EXPERIMENT AL METHODS

1269

94

92

90

∆E/mV

88 32

30

28

26

278

288 Temp./K

298

308

Fig. A1.1. Temperature variation of the e.m.f. differences for molecular compound formation. The curves are (in order, from the top) for {naphthalene picric acid}; {[2H8]-naphthalene picric acid}; {naphthalene styphnic acid}; {[2H8]-naphthalene styphnic acid}. (Reproduced from Shahidi and Farrell (1976).) n n n

n n n

n n n

n n n

A.2.1.3 Dissociation pressure method We illustrate using results obtained (Choi and Brown, 1966) for the thermal decomposition of {C6H6 . . . Al2Br6} according to the equation: {C6H6 . . . Al2Br6}(s) ) Al2Br6(s) þ C6H6(g). The equilibrium constant Kp ¼ P and the free energy of the dissociation reaction is given by G ¼ RT ln Kp. If the dissociation pressure is measured at a number of temperatures, then the enthalpy of dissociation is obtained from the van’t Hoff equation d(ln Kp)/dT ¼ H/RT2. The dissociation pressures were measured as 11.5 mm at 273K, 0.650 mm at 237.3K and 0.223 mm at 229.5K; we calculate H ¼ 42.5 kJ/mol, with G ¼ 9.5 kJ/mol and S ¼ 121 J/mol K (all at 273K), in agreement with the Choi–Brown values (H ¼ 44.4 kJ/mol; S ¼ 125.5 J/mol K). However, the reaction relevant in the present context is Al2Br6 (s) þ C6H6 (s) ) {C6H6 Al2Br6}(s). n n n

and so the above values must be corrected for the enthalpy and entropy of sublimation of benzene, where, as an approximation, we use the values appropriate to the melting point of benzene (278K), which are H(sublimation) ¼ 44.0 kJ/mol and S(sublimation) ¼ 44.0/278 ¼ 158 J/mol K. Thus Hc ¼ 42.5 (44.0) ¼ þ1.5 kJ/mol and Sc ¼ 121 (158) ¼ þ37 J/mol K. The molecular compound is entropy stabilized with respect to its crystalline components.

T H E R M OD Y N A M I C M E A S UR E M E NT S O N B I NA R Y A D D U C T S

1270

A.2.1.4 Speciﬁc heat measurements The thermodynamic functions of a crystal over a range of temperatures can be obtained from measurements of the speciﬁc heat cp as a function of temperature: Z Enthalpy funtion

T

HðTÞHð0Þ ¼

cp dT 0

Z SðTÞ Sð0Þ ¼

entropy

T

cp dð ln TÞ 0

free energy function ½GðTÞ Hð0Þ =T ¼ ½GðTÞ Hð0Þ =T ½SðTÞ Sð0Þ : H(0) is a constant characteristic of the substance, while S(0) is set equal to zero for perfect crystalline materials, in accordance with the third law of thermodynamics; thus care must be taken when there is reason to believe that a material has residual zero-point entropy. Speciﬁc heat measurements on a binary adduct and its crystalline components will give as functions of temperature the enthalpy of formation of the adduct Hc, (apart from the contribution of the three H(0) values), the entropy of formation Sc (subject to the applicability of the third law), and the free energy of formation function, (apart from the contribution of the three H(0) values). These functions all represent integrals (of different kinds) over the speciﬁc heats. This is the only method that will give values for the thermodynamic parameters at low temperatures. It has been suggested that cp ¼ {cp (binary adduct) [cp(component 1) þ cp(component 2)]} could give useful information (Dunn, Rahman and Staveley, 1978) but it seems preferable to work with the enthalpy function and the entropy. We illustrate the calculations for the yellow polymorph of {naphthalene PMDA}, where the results are simpliﬁed by the absence of phase transformations in molecular compound and components; the sources of the thermodynamic data are: naphthalene (McCullogh, Finke, Messerly, Todd, Kincheloe and Waddington 1955); PMDA (Dunn, Rahman and Staveley, 1978); {naphthalene PMDA} (Boerio-Goates and Westrum, 1980). For convenience in plotting we show values for H and TS. The values of H in Fig. A1.2 do not include the contributions of the three H(0) values and thus the position of the curve along the ordinate is not known; this could be ﬁxed by an independent measurement of Hc but such is not available for (naphthalene PMDA) nor, indeed, for any of the other -molecular compounds for which speciﬁc heats have been measured. The requirement of negative Gc means that {H(0)(naphthalene PMDA) [H(0)(naphthalene) þ H(0)(PMDA)]} must be less than 1100 J/mol at 300K. Application of the third law gives S equal to Sc. The temperature dependence of Cp is qualitatively similar to that of Sc. At this stage we cannot say whether {naphthalene PMDA} is only entropy stabilized or enthropy and enthalpy stabilised. Both H and TS are strongly temperature dependent. n n n

n n n

n n n

n n n

n n n

A.2.2

Determination of Gc only

Measurement of the depression of the freezing point gives Gc at a particular temperature (Brown, 1925); thus Sc and Hc cannot be determined.

EXPERIMENT AL METHODS

1271

2500

■ ■

2000

■ ■ ■ ■

1500 J/mol

■ ■ ■

T∆S

1000

500 ■

■

■

■

■

■

■ ● ●● ■ ●● ■■● ●● ● ■■ ●● ●● ●■ ●■ ●■ 0■ ●■ ●■

0

50

100

150 T(K)

■

■

●●

■

●

■

■

●●

200

●●

●

●

●

●

● ● ●

∆H

250

300

Fig. A1.2. The temperature dependence of H and TS (see text for deﬁnitions) for {naphthalene PMDA}. n n n

A.2.3

Determination of Hc only

A.2.3.1 Combustion method This method will give absolute enthalpies and is illustrated here for quinhydrone (Suzuki and Seki, 1953). The enthalpies of combustion (kJ/mol) of crystalline quinhydrone and its components were measured and their difference gives Hc(quinhydrone). A.2.3.2 Dissolution method This method was introduced by Suzuki and Seki (1953) for the study of quinhydrone; further applications have been made to other quinhydrones (Artiga, Gaultier, Haget and Chanh, 1978) and to some -molecular compounds (Suzuki and Seki, 1955). The difference is measured between the enthalpies of solution (under the same conditions) of the same quantities of binary adduct and a mechanical mixture of the two components. The results obtained for quinhydrone from measurement of enthalpies of combustion are compared in Table A1.1 with those obtained by the enthalpy of dissolution method at 24 , using acetone as solvent. A.2.3.3

Phase diagram method

The enthalpy of formation of a binary adduct at its melting point (Tm) from the liquid components (reaction below) can be calculated from the detailed form of the

1272

T H E R M OD Y N A M I C M E A S UR E M E NT S O N B I NA R Y A D D U C T S

Table A1.1. Measurement of enthalpy of formation of quinhydrone by various methods. All values are in kJ/mol Method

Hydroquinone

p-Benzoquinone

Quinhydrone

Hc(Quinhydrone)

Enthalpy of combustion Enthalpy of dissolution

2863.0 1.7 1.54

2746.3 2.5 17.27

5575.4 4.6 38.25

33.9 5.5 22.52 0.18

Table A1.2. Calculation of enthalpy of formation for a binary adduct by the method of BoerioGoates, Goates, Ott, and Goates, (1987) Reactants (state, T(K))

Products (state, T(K))

H (kJ/mol)

C6H6(l, 239.12) þ CCl4(l, 239.12) C6H6(s, 278.66) C6H6(l, 278.66) CCl4(s, 250.41) CCl4(l, 250.41) C6H6(s, 239.12) þ CCl4(s, 239.12)

{C6H6 . . . CCl4}(s, 239.12) C6H6(l, 278.66) C6H6(l, 239.12) CCl4(l, 250.41) CCl4(l, 239.12) {C6H6 . . . CCl4}(s, 239.12)

15.05 þ9.87 0.50* þ2.52 0.08* 3.24

liquidus (solid–liquid equilibrium) curves (Boerio–Goates, Goates, Ott, and Goates, 1985). mA(l) þ nB(l) ¼ [AmBn](s) at Tm. A thermodynamic cycle was then used to allow for the enthalpies of fusion of A and B and their speciﬁc heats in order to calculate Hc(Tm) for the reaction mAc(Tm) þ nBc(Tm) ¼ [AmBn]c(Tm). We illustrate for {C6H6 CCl4} (Tm ¼ 239.12K), using data from Boerio-Goates, Goates, Ott, and Goates, (1987) (Table A1.2). Enthalpies of fusion are more generally available than speciﬁc heats and thus approximate values of Hc can be obtained if the generally small speciﬁc heat contributions (asterisked) can be neglected. These methods have been applied to a number of binary adducts (Goates, Boerio-Goates, Goates and Ott, 1987); the uncertainties in the enthalpies were conservatively estimated to be 0.50 kJ/mol. n n n

References Abdel-Rehiem, A.G., Farrell, P. G. and Westwood, J. V. (1974). J. Chem. Soc. Faraday I, 70, 1762–1771. Artiga, A., Gaultier, J., Haget, Y. and Chanh, N. B. (1978). J. Chim. Phys., 75, 378–383. Bell, R. P. and Fendley, J. A. (1949). Trans. Farad. Soc., 45, 121–122. Boerio-Goates, J. and Westrum, E. F., Jr. (1980). Mol. Cryst. Liq. Cryst., 60, 249–266. Boerio-Goates, J., Goates, S. R., Ott, J. B. and Goates, J. R. (1985). J. Chem. Thermodynam., 17, 665–670. Brønsted, J. H. (1911). Z. phys. Chem., 78, 284–292.

REFERENCES

1273

Brown, F. S. (1925). J. Chem. Soc., pp. 345–348. Choi, S. U. and Brown, H. C. (1966). J. Amer. Chem. Soc., 88, 903–909. Dunn, A. G., Rahman, A. and Staveley, L. A. K. (1978). J. Chem. Thermodynamics, 10, 787–796. Gaskell, D. R. (1995). ‘‘Introduction to the Thermodynamics of Materials,’’ Third Edition, Taylor and Francis, Washington, D. C. Goates, J. R., Boerio-Goates, J., Goates, S. R. and Ott, J. B. (1987). J. Chem. Thermodynamics, 19, 103–107. Hammick, D. Ll. and Hutchison, H. P. (1955). J. Chem. Soc., pp. 89–91. McCullogh, J. P., Finke, H. L., Messerly, J. F., Todd, S. S., Kincheloe, T. C. and Waddington, G. (1957). J. Phys. Chem., 61, 1105–1161. Shahidi, F. and Farrell, P. G. (1978). J. Chem. Soc. Chem. Comm., pp. 455–456. Suzuki, K. and Seki, S. (1953). Bull. Chem. Soc. Jpn., 26, 372–380. Suzuki, K. and Seki, S. (1955). Bull. Chem. Soc. Jpn., 28, 417–421. Swalin, R. A. (1987). ‘‘Thermodynamics of Solids.’’ 2nd edition. 400 pp. Wiley–VCH, Berlin. Westrum, E.F.,Jr. and McCullough, J.D. (1963). ‘‘Thermodynamics of crystals’’ in Physics and Chemistry of the Organic Solid State, edited by D. Fox, M.M. Labes, and A. Weissberger, Interscience, New York and London.

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Book Index Some notes: 1. Although there is no separate Author Index, names of prominent personalities are indexed together with some leading references. 2. Many, but not all, crystal structures mentioned in the text are indexed. CSD Refcodes are given where possible. 3. Information given in the overall and chapter Tables of Contents is only partially duplicated here.

Acceptors Chelates as acceptors 937 Pure 685 Self-interacting 685 Ag(I) salts 686, 765–784 HgX2 739–761 MX3 (M ¼ Bi, Sb; X ¼ Cl, Br) 686, 788–822 Acronyms in common use 933 Anion radical salts TCNQ anion radical salts 1177–1214 Chloranil as anion radical 1214 M(dmit)2 and M(mnt)2 as anion radicals 1215 o-Benzyne 65 Binary adducts Deﬁnition 4 How many? 11 Other classiﬁcations 10 Structural classiﬁcation 5, 7 Catenanes and catenation 33, 325, 447 Cation radical salts 1162–1177 Cations are aromatic hydrocarbons 1163–1167 TMPD dimer as cation radical 1175–1177 TTF as cation radical 1167–1175 Cell dimensions as a function of temperature Anthracene . . . TCNB (ANTCYB) 1116 CS-I ethylene oxide hydrate 375 Cycl[3.2.2]azine . . . TNB 1121 d(CGCGAATTCGCG)2 184 DMTTF . . . CA 1138 Naphthalene . . . TCNB (NAPTCB) 1106 Pyrene . . . PMDA (PYRPMA) 1101 (TEA)(TCNQ)2 1206 thiourea.(cyclohexane 240 [TTF][CA] 1130 [TTF][DETCNQ] 1244

[TTF][TCNQ] 1243 urea.(n-hexadecane) 221 Chemical formulae 9-Aminoacridine-4-carboxamide 154 Bikhaconine derivatives 614 Bipyridinium 32 Bishop-Dance hosts 252–264 Budesonide 591 Cholic acid and derivatives 273 Cis--camphanic acid 570 Cyclophanes 960 Cyclotriphosphazenes 292–297 Daunomycin (daunorubicin), adriamycin (doxorubicin), idarubicin 146 Dehydroeriolanin 614 Dianin’s compound 399 Diquat 32 Glaucolide-D 615 Gossypol 460 Heilbron host (DHDK) 456 Inosine 165 Minor groove binders 168–171 N-(p-tolyl)tetrachlorophthalimide (TTP) 307 Nogalomycin 151 Paraquat 32 Perhydrotriphenylene (PHTP) 299 Pyridine-2-carbaldehyde oxime 443 Pipitzol 591 Spermine, spermidine 158 TADRIZ (formula 10.25) 592 1,2,3,4-tetrahydroxybutane-1,1-dicarboxylic acid 445 Tri-o-thymotide 423 Tris(5-acetyl-3-thienyl)methane (TATM) 470 Zeyloxanthonone 291 Chiral recognition Tri-o-thymotide complexes 429 Clathrasils 363–370

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

INDEX

[2] Clathrates Dianin’s compound and analogs as hosts 399–406 Hexahosts 408–410 Phenol and analogs as hosts 396–399 Polyhedral clathrates 348 Quinol 323–345 Tetraphenylene as host 406–408 Constitutional isomers and stereoisomers 565 Crystal chemistry comparison of cyclodextrin, oligonucleotide and TPP complexes 142 Crystal data and structures (Acridine)2 . . . PMDA (BIWVUY) 991 Anthracene . . . PMDA (ANTPML) 1088 Anthracene . . . TCNB (ANTCYB) 1108 {benzene . . . AgAlCl4} (SALBEN) 775 {benzene . . . AgClO4} (AGPCGE) 768 benzene . . . Br2 (BENZBR) 727 Benzene . . . CuAlCl4 (BZCACT) 776 Biﬂuorenylidene . . . perylene (CUNZAK) 632 Biﬂuorenylidene . . . pyrene (CUNWUD) 632 Br2.8.6H2O 381 Caviplexes 49 Coronene . . . I2 (DUPCIA) 730 18-crown-6.[nitromethane] (DIZTIP) 31 {[(5,6-Dihydro-4a,6a-phenanthrolinium)2] [(1,4,5,8-napthalenetetracarboxylic anhydride]} (VARKEE10) 1193 {1,4-Dithiane.2I2} (DTHINI) 696 {3(Dioxane) . . . AgClO4} (AGPDOX) 687 Diphenyl . . . 2SbBr3 (PYRSBB) 791 Diphenyl . . . 2SbCl3 (BIPHSB) 791 (Fluorene)3 . . . (TNB)4 (ZZZAGP02) 1006 Layered cyclophanes (BUZROD, BICFAU, CECTIN, DALTOZ, DALVER, DAVHAI, DEBZEP) 967–982 Naphthalene . . . 2SbCl3 (NAPSBC) 803 Naphthalene . . . TCNB (NAPTCB) 1107 (Perylene) 3.Bi4Br12 (ZUVTAL) 816–819 Phenanthrene . . . 2SbBr3 (DEJYEW) 802 Phenazine . . . I2 (PHNAZI01) 689 Pyrene . . . 2SbBr3 (PYRABR) 794 {Quinuclidine . . . CBr4} (FEGYEV) 696 {S8 . . . SbCl3} 763 {3S8 . . . CHI3} (IFOSUL) 702 (tolane . . . 4SbCl3) ZOQWUX 807 bis-p-phenylene-34-crown-10 BPP(3n þ 4) Cn crown ethers 34 neat compound (FIKVEA) 32 neat compound (KOLMAZ) 33 paraquat complexes 33 Pyrene-benzoquinone (PYRBZQ) 994 Pyrene . . . PMDA at 19K (PYRPMA) 1100 Spectroscopy 1087

Tetraaza[3.3.3.3]paracyclophane 2,11,20,29tetramethyl-2,11,20,29- tetraaza[3.3.3.3] paracyclophane complexes 41 (TMA.TCNQ.I} (MATCQI) 1211 Triphenylene–perﬂuorotriphenylene (CUKXIP) 1037 Urea.[hexadecane] 217, 221, 225, 229 Crystal structure analysis Views of Cram and Maverick 24 Applied to DNA oligomers 140 Applied to intercalation complexes 517 Diffraction patterns from tunnel inclusion complexes 213 Reduced cells, value for comparisons 461, 1204 Cyclobutadiene 64 Cyclodextrins, 74 Aqueous solubilities 74 Chemically-modiﬁed hosts 90–94 Formation of complexes 76 Head and tail (deﬁnition) 79 Larger cyclodextrins 123 Oligosaccharide analogs 123 Preparation (schematic) 75 Solution thermodynamics 79 Statistics of types of complex 78 Use of polycrystalline samples for identiﬁcation and structure solution 78 –Cyclodextrins chemically-modiﬁeds, as hosts in clathrate complexes 80–84 hydrates 81–82 tunnel complexes 84–90 –Cyclodextrins chemically-modiﬁeds, as hosts 114 clathrate complexes 97 hydrates 96 pyrene-octanol complex 110 tunnel complexes 100 dimer formation 100 overall structural description 111 unusual structures 114 –Cyclodextrins chemically-modiﬁeds, as hosts 122 clathrate complexes 118 hydrates 118 tunnel complexes 119 Cyclophanes, doubly-bridged, as hosts 30 Cyclophanes, layered Circular dichroism spectra 978 Charge-transfer bands in layered cyclophanes 959–961, 983–984 Meta-para 976–980 Meta 980–984 Multi-layered para 974–976 Para 959–974

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

I N DE X Deﬁnitions A-, B- and Z-DNA conformations 136, 138 Adaptability 200 Anti-isomorphous 90 Anti structures 1184, 1229 Binary adducts 4 Binding site pre-organization 28 Carcerands 59 Catenanes 33 Clathrates 8 Conglomerates 567, 569 Container molecules 48, 58 Dimensionality 7 Enantiomers 566 Enantiotropic and monotropic 931 Enclosure species 28 Cavitands 48 Cleft molecules as hosts 44 Crown ethers 32 Cryptophanes as hosts 54 Cyclophanes as hosts 30 General formulation 52 Hemicarcerands 61 Heteromorphism 143 Heterosoric, homosoric and nonsoric 925 Host-guest complementarity 28 Hydration numbers (neutral structures) 357 Hydration numbers (charged structures) 383 Inclusion complexes 6, 28 Interallogon complexes 603 Intercalation complexes (GICs) 518 Ionic and neutral ground states, factors determining 928–931 Isomorphic and isostructural 143 Long range order 1091 Moieties within molecules 9 Molecular complexes 6 Molecular compounds 10 Oligonucleotide-drug complexes Intercalation complexes 134 Minor-groove complexes 135 Order of phase transition (Ehrenfest) 1091 Packing complexes 10 Polyfunctionality 200 Polymorphism 142, 265 Pseudo-rotaxanes 33 Racemate and racemic 567 Rotaxanes 33, 40 Self complexes 931, 1059–1064 Sohncke space groups 446 Spherands 59 Stacks (monad, diad etc) 1176 Staging (intercalation complexes) 516 Structural parsimony 824 Supermolecule, supramolecular 23

Tubulates, helical and cylindrical 205 Types of triclinic unit cells 481 Versatility 200 Weber-Josel nomenclature 11 DNA structures and fundamentals 136, 140 Books 135 Conformations of A, B, Z forms 138 Low-temperature structures down to 12K 184 Minor and major grooves 139 Mixed A- and B-DNA conformations 187 Necessary to include effect of solvent 135 Nucleic acids database 135, 141 Phase rule relationships 143 Polymorphs or intermediate phases? 142, 178 Watson-Crick base pairing 136 Donors-acceptor interactions Aromatics to halogens 727–733 Aromatics to Ag(I) salts 765–777 Benzene-AgClO4 (AGPCBE) 768 Aromatics to MX3 (M ¼ Sb, Bi, X ¼ Cl, Br) 788–822 Aromatics to np3 metal ions 822–836 N, O, S ligands to HgCl2 and HgBr2 739–761 Six coordinate Hg(II) 740–750 Five coordinate Hg(II) 750–754 Four coordinate Hg(II) 754–761 Oleﬁns to Ag(I) salts 777–783 Electron afﬁnities of acceptors 940–943 Chelates as acceptors 939 Electron donors–chemical types 934–935 Coordination complexes 1042–1044 Ionization potentials (ﬁrst) 940–942 Phenazine based 1044–1047 Polarization energy 933 Enantiomorph-racemate pairs, Comparing stability 571–574 Non-mimetic 574 Mimetic 575 Fullerene packing complexes 634–667 C60 and calix[n]arenas 650–655 C76–(S8)6 642 (Ferrocene)2–C60 639 (Ferrocene)2–C76 639 Fullerenes and porphyrins 663–667 Gas hydrates Bromine hydrate structure 381 CSI structure type 357 CSII structure type 359 HSIII structure type 358 Low temperature structures 379 Packing of pentagonal dodecahedra 355

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

[3]

INDEX

[4] Gas hydrates (cont.) Potential fuel reserves 349 Siberian pillar 350 Stoichiometry and thermodynamics 372–379 Gossypol complexes 459–469 Polymorphism 460 Graphite intercalation complexes (GIC) 515–539 Degree of charge transfer 528 Dense alkali-metal GICs 533 Electron spectroscopy 529 Halogens as guests 533–539 Preparation 520 Staging (classical and ‘‘non-classical’’) 525 Structures of 1bar alkali-metal GICs 520–525 Thermodynamics 526 Heat capacity as function of temperature Anthracene . . . TCNB 1105 Naphthalene . . . TCNB 1105 Naphthalene . . . TCNE 1122 Pyrene . . . .PMDA 1098 [TTF][DETCNQ] 1245 Heilbron complexes 456–459 Hexahosts 408–410 Highly oriented pyrolytic graphite (HOPG) 518 Hilfsgassen 364 Historical background to binary adducts General 15, 18 GICs 517 Hosts not found unsolvated DCA 273 TATM 469 DHDK 456 Hydrogen bonding Accounting for formation of pair 904 Appendage structures 864–866 Formic acid–HF 864 Books on 853 Charged components give salts 868, 908–911 Crystal engineering with, an example 905–908 Deﬁnition of n-centered 854–855 Directionality of acceptor lone pairs 858–860 Discrete D . . . A . . . D triples 877–881 Donors and acceptors 853 Early examples in binary adducts 853 Graph theory applied to 861 Mixed framework type 866, 876, 882, 890 Molecular recognition 871–875 Rebek’s diacid 874 Neutral components give molecular compounds 868, 908–911 Phase relations 861, 891, 899 Ribbons and tapes 884–886, 894–896 Statistical surveys of H-bonded binary adducts 857–860

Three-dimensional frameworks 901–904 Use in enantiomer separation 875–877 Types of ring formed 863 Weak H-bonds 860–861 Inclusion complexes 199–202 Interrupted hydrogen bonding In 1,1’-binaphthyl-2,2’-dicarboxylic acid and other complexes 886–888 In urea complexes 229 In TMA complexes 441 Intramolecular -complexes 929 Melanophlogite 364 Metalloid structures of the gas hydrate type 360–363 Mimetic complexes 723 Mixed stack -* molecular compounds First order neutral to ionic phase transformation on cooling 1129 Second order disorder to order phase transformations on cooling 1090–1126 Thermodynamics 1083–1086 Transformation to quasi-plastic phases on heating 1124–1126 Moiety ﬁlling two structural roles 500, 627 Pentachlorophenol 870 Perylene 1162 Pyrazine 872–873 TCNQF4 1182 [TMTTF]1.3 [TCNQ] 1229 Molecular complexes (isomeric, polymorphic) 724, 1052 Molecular compounds 10 Charge transfer in , estimating degree of 944–948 Families of 1:1 mixed stack 996–1000 Doubled stack periodicity 1001–1002 Molecular mechanics 66 Molecular recognition 23 Molecular tweezers 44–47 Mo¨ssbauer effect 129 I 708, 710, 729, 730 Nuclear quadrupole resonance 127 I 708, 729 35 Cl of HgCl2 molecular compounds 760 35 Cl and 121Sb and 123Sb of MX3 (M ¼ Sb, Bi; X ¼ Cl, Br) molecular compounds 819 Nucleic acids database (NDB) 141 Organic racemates, statistical survey 567 Packing complexes 10 Of fullerenes 634

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

I N DE X Parallel intercalators in DNA oligomers Anthracyclines 145 Nogalamycins 151 9-aminoacridines 154 Personalities and some leading references Amma, E. L. 765, 823 Atwood, J. L. 19 Cram, D. J. 9, 10 Cramer, F. 17 Crick, F. H. C. 134 Davidson, D. W. 371 Davy, H. 15 Desiraju, G. R. 12, 17 Dickerson, R. E. 140, 171, 183, 184 Dyadin, Yu A. 334, 350 Faraday, M. 15 Harata, K. 75, 86, 95 Harris, K. D. M. 4, 8, 206 Hassel, O. 17, 688, 741 Herbstein, F. H. 795, 819, 1097 Jeffrey, G. A. 349 Kennard, O. 149, 164 Kitaigorodskii, A. I. 740 Kochi, J. K. 723, 728, 736, 738 Lehn, J. M. 9, 11, 17 Mavridis, I. M. 93, 113 Menshutkin, B. N. 761, 788 Mootz, D. 789 Mulliken, R. S. 16, 685 Nassimbeni, L. R. 67 Neidle, S. 136 Pedersen, C. J. 9, 19, 23, 24 Pfeiffer, P. 16 Powell, H. M. 8, 17, 823 Priestley, Joseph 15 Rich, A. 149 Ripmeester, J. A. 381, 474, 1112 Saenger, W. 30, 86 Schlenk, W. Jr. 206 Schmidtbaur, H. 686, 736, 773, 777, 804, 823 Shakked, Z. 162 Shibaeva, R. P. 1184 Stackelberg, M. von 7 Steiner, T. 98 Stezowski, J. J. 1053, 1088 Stoddart, J. F. 32, 44 Strouse, C. E. 478 Sundaralingam, M. 156, 166, 178 Tsoucaris, G. 90 Torrance, J. B. 928 Vos, A. 1188, 1201 Waals, J. H. van der 334 Wallwork, S. C. 1192, 1204 Wang, A.H.-J. 149, 162 Watson, J. D. 134

[5]

Wo¨hler, F. 17 Wudl, F. 1148, 1149, 1232 Phase diagrams ACA (apocholic acid)–montanic acid 275 Anthracene–2,3-dimethylnaphthalene 620 o-Bromoaniline–picric acid 1057 Carbazole–trinitroﬂuorenone 948 ()-Carvoxime 581 ()-Cis--camphanic acid 570 Dibenzyl–trans-stilbene 612 (þ) and () 2,4-Dioxo-3,3-diethyl-5methylpiperidine 587 Diphenyl sulphoxide–diphenyl sulphone 615 Diphenylamine–SbCl3 795 Enantiomers 568 Fluoranthene–(TNB/TNF) 950 (Phenanthrene/anthracene)–picric acid 949 PHTP–n-heptane 300 PHTP–trans-stilbene 300 Pyrene–(TNB/TNF) 950 Pyrene-(various mixed acceptors) 951 SO2 H2O 378 Sym-tetrabromobenzene–hexabromobenzene 629 Sym-tetrachlorobenzene–symtetrabromobenzene 618 Urea-n-heptane 251 Phase rule concepts Applied to DNA oligomers, and comparison with cyclodextrin and TPP complexes 144 Phase transitions Anthracene . . . TCNB 1119 ESR study 1117 [Cycl[3.2.2]azine . . . TNB (1st order) 1120 Critical exponents 1093 Effect of pressure on Tc Ehrenfest relations 1097 Landau theory 1094–1096 Naphthalene . . . TCNB 1114 Neutral to ionic phase transitions DMTTF . . . chloranil 1137 TTF . . . chloranil 1129 Peierls phenomenon 1104 Permitted symmetries 1094 Pyrene . . . PMDA 1097 Spontaneous strain and Vogt coefﬁcients 1096 Tricritical point 1104 3(thiourea).ferrocene 237 3(thiourea).cyclohexane 240 3(urea).trioxane 243 Pi molecular compounds Component ratios 952 Delocalized and localized interactions 1030–1032 Donor also in interstitial positions 1005–1007 Flavins 1022–1026 Inﬁnite stacks 994–1002

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

INDEX

[6] Pi molecular compounds (cont.) Interactions between polar and polarizable groups 1011–1013 Limited stacks 993–994 Ternary 953 Which structural description is preferred? 1065 Polyhedral clathrates-overview 348 Alkylamine hydrates 389–392 Peralkylonium hydrate structures 383–389 Pre-organization 28 Crown ethers 33, 45 Quasi-acceptors 939–940 Polyﬂuoro-aromatics 1032–1040 Quinhydrones 1013–1022 Thermodynamics 1020–1022 Quinol clathrates -phase 324 -phase (three types) 325–329 C60 complex 329 C70 complex 330 Statistical thermodynamics 333–345

Segregated stack molecular complexes 9 Acceptors 1157–1161 Cation radical–anion radical salts 1216–1232 Bechgaard–Andersen classiﬁcation 1225 Donors 1152–1157 Electrochemical preparation 1161–1162 Electron density studies 1230–1232 Nomenclature 1149 Perylene as cation, M(mnt)2 as anion 1216–1220 Weitz type donors 1152 Wu¨rster type donors 1151 Self-complexes Localized interactions (N, O to halogen) 713–717 Localized and delocalized interactions 1059–1064 Solid solutions Conditions for formation 605–607 Enantiomers 585 Inhomogeneity 620 Interblock 622 Interstitial 622 Substitutional 605 Trans-azobenzene/trans-stilbene 608 Spectroscopy Charge-transfer bands 697 In layered cyclophanes 961–963 Excited triplet state in -* molecular compounds 1089 Spontaneous resolution on crystallization Tri-o-thymotide complexes 428 Stacking Crown ether complexes 36

in Mixed-stack -molecular compounds 991–993 Staging (intercalation complexes) 516, 525 Statistics of organic racemates 567 Superdense GICs 530 Systems Anthrone-anthraquinone 613 Phenazine–N-oxyphenazine 613 Tantalum sulﬁde intercalation complexes 540–545 Tautomers, cocrystallization of 600 TCNQ anion radical salts 1177–1214 Average charge on TCNQ moiety 1177 Background 1177–1180 Cations are metals 1187–1189 Cations are organic moieties 1178–1196 Diad stacks 1202 E/B and R/R overlap modes 1180 Inﬁnite stacks 1189–1205 Pentad stacks 1204 Stacks of limited length 1180–1187 Studies over wide range of temperatures 1203–1209 Survey of structural results 1211–1214 Temperature dependence of conductivity 1212–1214 Tetrad stacks 1201 Theoretical studies of TCNQ stacking 1232–1233 Tetraphenylmetalloporphyrins (TPP-M2 þ ) as hosts 478–508 Contrasting coordination and inclusion complexes 480 Polymorphism of {(TPP-Zn2 þ )(toluene)2} 505 Use of ‘lattice sections’ 480, 506 Varieties of metals 479 Varieties of ligands/guests 479 Thermodynamics (Aromatic hydrocarbons . . . AlBr3} 734 {Benzene . . . AgClO4} 768 {Benzene . . . CBr4} 733 Crown ether complexes, in solution 30 Enthalpy-entropy compensation in -* molecular compounds 1085 of alkali metal GICs 526 Methods see Appendix -* mixed stack molecular compounds 1083 Urea and thiourea complexes 247–251 Trimesic acid and analogs as hosts 437 Catenated hexagonal networks 446, 451 Quasi-hexagonal non-catenated networks 437–446 Tri-o-thymotide complexes Crossed tunnel inclusion 433 Hexagonal tunnel inclusion 429 Miscellaneous 435

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

I N DE X Spontaneous resolution on crystallization 428 Trigonal clathrates 425 Tunnel type with organometallic guests 431 Tris(5-acetyl-3-thienyl)methane (TATM) complexes 470 TATM conformations 473 Mechanism of formation of complexes 476 [TTF][TCNQ] 1235–1253 Cell dimensions as function of temperature 1243 Charge density wave 1250 Cohesion 1240 Conductivity Comparison of values from different laboratories 1237 Comparison with that of Pb 1150 Pressure dependence 1251 Temperature dependence 1236 Crystal structure (300K) 1238 Debye temperature 1240 Historical background 1148–1151 Principal compressibilities 1241 Principal thermal expansion coefﬁcients 1241 Satellite reﬂections in diffraction pattern 1247–1248 Speciﬁc heat 35–60K 1242 Susceptibility as function of temperature 1249 The electrostatic binding energy defect 1240 Thermodynamic parameters 1234 Tunnel hydrates 271 Tunnel inclusion complexes 269–272 Arrangements of urea spirals 211 Comparison of structure types 310 Hydrogen bonded hosts

[7]

Bishop-Dance compounds 251–268: Tetragonal complexes 264–267; Trigonal complexes 251–264 Urea, thiourea and selenourea 204–251: Absolute conﬁguration of urea sublattice in hexagonal complexes 218; Guests giving hexagonal urea complexes 207; Guests giving rhombohedral thiourea complexes 209; Guests giving rhombohedral urea complexes 208; Guests giving rhombohedral selenourea complexes 209; Hermann’s comprehensive Model 210; Polar guest sequence in rhombohedral thiourea complexes 209; Prototype n-hexadecane complex 219 Van der Waals bonded hosts Cholic acid 281–289 Deoxycholic acid 272–281 N-(p-tolyl)tetrachlorophthalimide 307–310 Perhydrotriphenylene (PHTP) 298–307 Polar guest sequencesin tunnels 306 Modelling diffuse scattering 304 Spirocyclophosphazenes 281–297 UPS, XPS and SXS of GICs 529 Vegard’s rule and Zen’s rule 606 Wallach’s rule 571 Zr phosphate and phosphonate intercalation complexes 546–551

Pages 1–678 appear in Volume 1; Pages 679–1274 appear in Volume 2.

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