Supramolecular Chemistry - Jonathan W. Steed - ebook

Supramolecular Chemistry ebook

Jonathan W. Steed

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Supramolecular Chemistry is 'chemistry beyond the molecule' - the chemistry of molecular assemblies and intermolecular bonds. It is one of today's fastest growing disciplines, crossing a range of subjects from biological chemistry to materials science; and from synthesis to spectroscopy. Supramolecular Chemistry is an up-to-date, integrated textbook that tells the newcomer to the field everything they need to know to get started. Assuming little in the way of prior knowledge, the book covers the concepts behind the subject, its breadth, applications and the latest contemporary thinking in the area. It also includes coverage of the more important experimental and instrumental techniques needed by supramolecular chemists. The book has been thoroughly updated for this second edition. In addition to the strengths of the very popular first edition, this comprehensive new version expands coverage into a broad range of emerging areas. Clear explanations of both fundamental and nascent concepts are supplemented by up-to-date coverage of exciting emerging trends in the literature. Numerous examples and problems are included throughout the book. A system of "key references" allows rapid access to the secondary literature, and of course comprehensive primary literature citations are provided. A selection of the topics covered is listed below. * Cation, anion, ion-pair and molecular host-guest chemistry * Crystal engineering * Topological entanglement * Clathrates * Self-assembly * Molecular devices * Dendrimers * Supramolecular polymers * Microfabrication * Nanoparticles * Chemical emergence * Metal-organic frameworks * Gels * Ionic liquids * Supramolecular catalysis * Molecular electronics * Polymorphism * Gas sorption * Anion-pinteractions * Nanochemistry Supramolecular Chemistry is a must for both students new to the field and for experienced researchers wanting to explore the origins and wider context of their work. Review: "At just under 1000 pages, the second edition of Steed and Atwood's Supramolecular Chemistry is the most comprehensive overview of the area available in textbook form...highly recommended." --Chemistry World, August 2009

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Contents

About the Authors

Preface to the First Edition

Preface to the Second Edition

Acknowledgements

1 Concepts

1.1 Definition and Development of Supramolecular Chemistry

1.2 Classification of Supramolecular Host-Guest Compounds

1.3 Receptors, Coordination and the Lock and Key Analogy

1.4 Binding Constants

1.5 Cooperativity and the Chelate Effect

1.6 Preorganisation and Complementarity

1.7 Thermodynamic and Kinetic Selectivity, and Discrimination

1.8 Nature of Supramolecular Interactions

1.9 Solvation and Hydrophobic Effects

1.10 Supramolecular Concepts and Design

Summary

Study Problems

Suggested Further Reading

References

2 The Supramolecular Chemistry of Life

2.1 Biological Inspiration for Supramolecular Chemistry

2.2 Alkali Metal Cations in Biochemistry

2.3 Porphyrins and Tetrapyrrole Macrocycles

2.4 Supramolecular Features of Plant Photosynthesis

2.5 Uptake and Transport of Oxygen by Haemoglobin

2.6 Enzymes and Coenzymes

2.7 Neurotransmitters and Hormones

2.8 Semiochemistry in the Natural World

2.9 DNA

2.10 Biochemical Self-Assembly

Summary

Study Problems

References

3 Cation-Binding Hosts

3.1 Introduction to Coordination Chemistry

3.2 The Crown Ethers

3.3 The Lariat Ethers and Podands

3.4 The Cryptands

3.5 The Spherands

3.6 Nomenclature of Cation-Binding Macrocycles

3.7 Selectivity of Cation Complexation

3.8 Solution Behaviour

3.9 Synthesis: The Template Effect and High Dilution

3.10 Soft Ligands for Soft Metal Ions

3.11 Proton Binding: The Simplest Cation

3.12 Complexation of Organic Cations

3.13 Alkalides and Electrides

3.14 The Calixarenes

3.15 Carbon Donor and π-acid Ligands

3.16 The Siderophores

Summary

Study Problems

Thought Experiment

References

4 Anion Binding

4.1 Introduction

4.2 Biological Anion Receptors

4.3 Concepts in Anion Host Design

4.4 From Cation Hosts to Anion Hosts – a Simple Change in pH

4.5 Guanidinium-Based Receptors

4.6 Neutral Receptors

4.7 Inert Metal-Containing Receptors

4.8 Common Core Scaffolds

Summary

Study Problems

Thought Experiments

References

5 Ion Pair Receptors

5.1 Simultaneous Anion and Cation Binding

5.2 Labile Complexes as Anion Hosts

5.3 Receptors for Zwitterions

Summary

Study Problems

References

6 Molecular Guests in Solution

6.1 Molecular Hosts and Molecular Guests

6.2 Intrinsic Curvature: Guest Binding by Cavitands

6.3 Cyclodextrins

6.4 Molecular Clefts and Tweezers

6.5 Cyclophane Hosts

6.6 Constructing a Solution Host from Clathrate-Forming Building Blocks: The Cryptophanes

6.7 Covalent Cavities: Carcerands and Hemicarcerands

Summary

Study Problems

Thought Experiment

References

7 Solid-State Inclusion Compounds

7.1 Solid-State Host-Guest Compounds

7.2 Clathrate Hydrates

7.3 Urea and Thiourea Clathrates

7.4 Other Channel Clathrates

7.5 Hydroquinone, Phenol, Dianin’s Compound and the Hexahost Strategy

7.6 Tri-o-thymotide

7.7 Cyclotriveratrylene

7.8 Inclusion Compounds of the Calixarenes

7.9 Solid-Gas and Solid-Liquid Reactions in Molecular Crystals

Summary

Study Problems

References

8 Crystal Engineering

8.1 Concepts

8.2 Crystal Nucleation and Growth

8.3 Understanding Crystal Structures

8.4 The Cambridge Structural Database

8.5 Polymorphism

8.6 Co-crystals

8.7 Z′ > 1

8.8 Crystal Structure Prediction

8.9 Hydrogen Bond Synthons – Common and Exotic

8.10 Aromatic Rings

8.11 Halogen Bonding and Other Interactions

8.12 Crystal Engineering of Diamondoid Arrays

Summary

Study Problems

Thought Experiment

References

9 Network Solids

9.1 What Are Network Solids?

9.2 Zeolites

9.3 Layered Solids and Intercalates

9.4 In the Beginning: Hoffman Inclusion Compounds and Werner Clathrates

9.5 Coordination Polymers

Summary

Study Problem

References

10 Self-Assembly

10.1 Introduction

10.2 Proteins and Foldamers: Single Molecule Self-Assembly

10.3 Biochemical Self-Assembly

10.4 Self-Assembly in Synthetic Systems: Kinetic and Thermodynamic Considerations

10.5 Self-Assembling Coordination Compounds

10.6 Self-Assembly of Closed Complexes by Hydrogen Bonding

10.7 Catenanes and Rotaxanes

10.8 Helicates and Helical Assemblies

10.9 Molecular Knots

Summary

Study Problems

Thought Experiment

References

11 Molecular Devices

11.1 Introduction

11.2 Supramolecular Photochemistry

11.3 Information and Signals: Semiochemistry and Sensing

11.4 Molecule-Based Electronics

11.5 Molecular Analogues of Mechanical Machines

11.6 Nonlinear Optical Materials

Summary

Study Problems

References

12 Biological Mimics and Supramolecular Catalysis

12.1 Introduction

12.2 Cyclodextrins as Enzyme Mimics

12.3 Corands as ATPase Mimics

12.4 Cation-Binding Hosts as Transacylase Mimics

12.5 Metallobiosites

12.6 Haem Analogues

12.7 Vitamin B12 Models

12.8 Ion Channel Mimics

12.9 Supramolecular Catalysis

Summary

Study Problems

Thought Experiment

References

13 Interfaces and Liquid Assemblies

13.1 Order in Liquids

13.2 Surfactants and Interfacial Ordering

13.3 Liquid Crystals

13.4 Ionic Liquids

13.5 Liquid Clathrates

Summary

Study Problems

References

14 Supramolecular Polymers, Gels and Fibres

14.1 Introduction

14.2 Dendrimers

14.3 Covalent Polymers with Supramolecular Properties

14.4 Self-Assembled Supramolecular Polymers

14.5 Polycatenanes and Polyrotaxanes

14.6 Biological Self-Assembled Fibres and Layers

14.7 Supramolecular Gels

14.8 Polymeric Liquid Crystals

Summary

Study Problems

References

15 Nanochemistry

15.1 When Is Nano Really Nano?

15.2 Nanotechnology: The ‘Top Down’ and ‘Bottom Up’ Approaches

15.3 Templated and Biomimetic Morphosynthesis

15.4 Nanoscale Photonics

15.5 Microfabrication, Nanofabrication and Soft Lithography

15.6 Assembly and Manipulation on the Nanoscale

15.7 Nanoparticles

15.8 Endohedral Fullerenes, Nanotubes and Graphene

Summary

Thought Experiment

References

Index

This edition first published 2009

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Library of Congress Cataloging-in-Publication Data

Steed, Jonathan W., 1969-

Supramolecular chemistry / Jonathan W. Steed, Jerry L. Atwood. – 2nd ed.

p. cm.

Includes bibliographical references and index.

ISBN 978-0-470-51233-3 (cloth) – ISBN 978-0-470-51234-0 (pbk. :

alk. paper) 1. Supramolecular chemistry. I. Atwood, J. L. II. Title.

QD878.S74 2008

547’.1226--dc22

2008044379

A catalogue record for this book is available from the British Library.

ISBN: 978-0-470-51233-3 (Hbk)

ISBN: 978-0-470-51234-0 (Pbk)

In loving memory of Joan Edwina Steed, 1922–2008

About the Authors

Jonathan W. Steed was born in London, UK in 1969. He obtained his B.Sc. and Ph.D. degrees at University College London, working with Derek Tocher on coordination and organometallic chemistry directed towards inorganic drugs and new metal-mediated synthesis methodologies. He graduated in 1993, winning the Ramsay Medal for his Ph.D. work. Between 1993 and 1995 he was a NATO postdoctoral fellow at the University of Alabama and University of Missouri, working with Jerry Atwood. In 1995 he was appointed as a Lecturer at Kings College London and in 1998 he was awarded the Royal Society of Chemistry Meldola Medal. In 2004 he joined Durham University where he is currently Professor of Inorganic Chemistry. As well as Supramolecular Chemistry (2000) Professor Steed is co-author of the textbook Core Concepts in Supramolecular Chemistry and Nanochemistry (2007) and more than 200 research papers. He has published a large number of reviews, book chapters and popular articles as well as two major edited works, the Encyclopaedia of Supramolecular Chemistry (2004) and Organic Nanostructures (2008). He has been an Associate Editor of New Journal of Chemistry since 2001 and is the recipient of the Vice Chancellor’s Award for Excellence in Postgraduate Teaching (2006). His interests are in supramolecular sensing and molecular materials chemistry.

Jerry L. Atwood was born in Springfield MO, USA in 1942. He attended Southwest Missouri State University, where he obtained his B.S. degree in 1964. He carried out graduate research with Galen Stuckey at the University of Illinois, where he obtained his Ph.D. in 1968. He was immediately appointed as an Assistant Professor at the University of Alabama, where he rose through Associate Professor (1972) to full Professor in 1978. In 1994 he was appointed Professor and Chair at the University of Missouri – Columbia. Professor Atwood is the author of more than 600 scientific publications. His research interests revolve around a number of themes in supramolecular chemistry including gas storage and separation and the control of confined space. He has also worked on the self-assembly of non- covalent capsules, liquid clathrate chemistry, anion binding and fundamental solid state interactions, and is a world-renown crystal- lographer. He co-founded the journals Supramolecular Chemistry (1992) and Journal of Inclusion Phenomena (1983). He has edited an enormous range of seminal works in supramolecular chemistry including the five-volume series Inclusion Compounds (1984 and 1991) and the 11-volume Comprehensive Supramolecular Chemistry (1996). In 2000 he was awarded the Izatt-Christensen Prize in Supramolecular Chemistry

Preface to the First Edition

Supramolecular chemistry is one of the most popular and fastest growing areas of experimental chemistry and it seems set to remain that way for the foreseeable future. Everybody’s doing it! Part of the reason for this is that supramolecular science is aesthetically appealing, readily visualised and lends itself to the translation of everyday concepts to the molecular level. It might also be fair to say that supramolecular chemistry is a very greedy topic. It is highly interdisciplinary in nature and, as a result, attracts not just chemists but biochemists, biologists, environmental scientists, engineers, physicists, theoreticians, mathematicians and a whole host of other researchers. These supramolecular scientists are people who might be described as goal-orientated in that they cross the traditional boundaries of their discipline in order to address specific objectives. It is this breadth that gives supramolecular chemistry its wide allure, and sometimes leads to grumbling that ‘everything seems to be supramolecular these days’. This situation is aided and abetted by one of the appealing but casual definitions of supramolecular chemistry as ‘chemistry beyond the molecule’, which means that the chemist is at liberty to study pretty much any kind of interaction he or she pleases – except some covalent ones. The situation is rather reminiscent of the hubris of some inorganic chemists in jokingly defining that field as ‘the chemistry of all of the elements except for some of that of carbon’.

The funny thing about supramolecular chemistry is that despite all of this interest in doing it, there aren’t that many people who will actually teach it to you. Most of today’s practitioners in the field, including the present authors, come from backgrounds in other disciplines and are often self-taught. Indeed, some people seem as if they’re making it up as they go along! As university academics, we have both set up undergraduate and postgraduate courses in supramolecular chemistry in our respective institutions and have found that there are a lot of people wanting to learn about the area. Unfortunately there is rather little material from which to teach them, except for the highly extensive research literature with all its jargon and fashions. The original idea for this book came from a conversation between us in Missouri in the summer of 1995. Very few courses in ‘supramol,’ existed at the time, but it was clear that they would soon be increasingly common. It was equally clear that, with the exception of Fritz Vögtle’s 1991 research-level book, there was nothing by way of a teaching textbook of the subject out there. We drew up a contents list, but there the idea sat until 1997. Everybody we talked to said there was a real need for such a book; some had even been asked to write one. It finally took the persuasive powers of Andy Slade from Wiley to bring the book to fruition over the summers of 1998 and 1999. We hope that now we have written a general introductory text for supramolecular chemistry, many more courses at both undergraduate and postgraduate level will develop in the area and it will become a full member of the pantheon of chemical education. It is also delightful to note that Paul Beer, Phil Gale and David Smith have recently written a short primer on supramolecular chemistry, which we hope will be complementary to this work.

In writing this book we have been very mindful of the working title of this book, which contained the words ‘an introduction’. We have tried to mention all of the key systems and to explain in detail all of the jargon, nomenclature and concepts pertaining to the field. We have not tried to offer any kind of comprehensive literature review (for which purpose JLA has co-edited the 11 volumes of Comprehensive Supramolecular Chemistry). What errors there are will be, in the main, ones of over-simplification in an attempt to make accessible many very complicated, and often still rapidly evolving, topics. To the many fine workers whose insights we may have trivialised we offer humble apology. We hope that the overwhelming advantages will be the excitement of the reader who can learn about any or all aspects of this hydra-like field of chemistry either by a tobogganing plunge from cover to cover, or in convenient, bite-sized chunks.

Preface to the Second Edition

Since the publication of the first edition of Supramolecular Chemistry in 2000 the field has continued to grow at a tremendous pace both in depth of understanding and in the breadth of topics addressed by supramolecular chemists. These developments have been made possible by the creativity and technical skill of the international community and by continuing advances in instrumentation and in the range of techniques available. This tremendous activity has been accompanied by a number of very good books particularly at more advanced levels on various aspects of the field, including a two-volume encyclopaedia that we edited.

In this book we have tried to sample the entire field, bringing together topical research and clear explanations of fundamentals and techniques in a way that is accessible to final year undergraduates in the chemical sciences, all the way to experienced researchers. We have been very gratified by the reception afforded the first edition and it is particularly pleasing to see that the book is now available in Russian and Chinese language editions. For a short while we attempted to keep the book current by updating our system of key references on a web site; however it has become abundantly clear that a major overhaul of the book in the form of a refreshed and extended second edition is necessary. We see the strengths of the book as its broad coverage, the care we have tried to take to explain terms and concepts as they are encountered, and perhaps a little of our own personal interpretation and enthusiasm for the field that we see evolving through our own research and extensive contact with colleagues around the world. These strengths we have tried to build upon in this new edition while at the same time ameliorating some of the uneven coverage and oversimplifications of which we may have been guilty.

The original intent of this book was to serve as a concise introduction to the field of supramolecular chemistry. One of us (JWS) has since co-authored a short companion book Core Concepts in Supramolecular Chemistry and Nanochemistry that fulfils that role. We have therefore taken the opportunity to increase the depth and breadth of the coverage of this longer book to make it suitable for, and hopefully useful to, those involved at all stages in the field. Undergraduates encountering Supramolecular Chemistry for the first time will find that we have included careful explanations of core concepts building on the basics of synthetic, coordination and physical organic chemistry. At the same time we hope that senior colleagues will find the frontiers of the discipline well represented with plenty of recent literature. We have retained the system of key references based on the secondary literature that feedback indicates many people found useful, but we have also extended the scope of primary literature references for those wishing to undertake more in-depth reading around the subjects covered. In particular we have tried to take the long view both in temporal and length scales, showing how ‘chemistry beyond the molecule’ continues to evolve naturally and seamlessly into nanochemistry and molecular materials chemistry.

We have added a great deal to the book in this new edition including new chapters and subjects (e.g. supramolecular polymers, microfabrication, nanoparticles, chemical emergence, metal-organic frameworks, ion pairs, gels, ionic liquids, supramolecular catalysis, molecular electronics, polymorphism, gas sorption reactions, anion-π interactions… the list of exciting new science is formidable). We have also extensively updated stories and topics that are a part of ongoing research with new results published since 2000. The book retains some of the ‘classics’ which no less striking and informative for being a little long in the tooth these days. As before we apologise to the many fine colleagues whose work we did not include. The objective of the book is to cover the scope of the field with interesting and representative examples of key systems but we cannot be comprehensive. We feel this second edition is more complete and balanced than the first edition and we have really enjoyed putting it together. We hope you enjoy it too.

Jonathan W. Steed, Durham, UKJerry L. Atwood, Columbia, Missouri, USA

Acknowledgements

Our thanks go to the many fine students, researchers and colleagues who have passed through our groups over the years, whose discussions have helped to both metaphorically and literally crystallize our thinking on this rapidly evolving field. Many colleagues in both Europe and the USA have been enormously helpful in offering suggestions and providing information. In particular we are grateful to Jim Tucker, Mike Hannon, Jim Thomas and the late Fred Armitage for their help in getting the ball rolling and constructive comments on the first edition. The second edition has benefited tremendously from input by Kirsty Anderson and Len Barbour, and we are also very grateful to Len for the brilliant X-Seed which has made the crystallographic diagrams much easier to render. David Turner also provided some excellent diagrams. We thank Graeme Day for useful information on crystal structure calculation and a number of colleagues for providing artwork or additional data, particularly Sir Fraser Stoddart, John Ripmeester, Peter Tasker, Travis Holman and Bart Kahr. Beth Dufour, Rebecca Ralf and Hollie Budge, Andy Slade, Paul Deards, Richard Davies and Gemma Valler at Wiley have worked tirelessly to bring the book to the standard and accessibility it needs to have. JWS is very grateful to Durham University for providing a term of research leave which made this book so much easier to write, and we are both as ever indebted to the many fine co-workers who have passed through our labs over the years who make chemistry such an enjoyable subject to work in.

About the Front Cover

The front cover shows two views of the Lycurgus cup – a 4th century Roman chalice made of dichroic glass impregnated with nanoparticles made of gold-silver alloy. When viewed under normal lighting conditions the cup appears green but if light is shone through the glass the nanoparticles impart a gorgeous crimson colour. The chemistry of metallic nanoparticles remains a highly topical field in supramolecular chemistry. (Images courtesy of the British Museum, London, UK).

Website

Powerpoint slides of all figures from this book, along with the answers to the problems, can be found at http://www.wiley.com/go/steed

1

Concepts

‘Mankind is divisible into two great classes: hosts and guests.’

Max Beerbohm (b. 1872), Hosts and Guests

1.1 Definition and Development of Supramolecular Chemistry

Lehn, J.-M., ‘Supramolecular chemistry and self-assembly special feature: Toward complex matter: Supramolecular chemistry and self-organization’, Proc. Nat. Acad. Sci. USA, 2002, 99, 4763–4768.

1.1.1 What is Supramolecular Chemistry?

Supramolecular chemistry has been defined by one of its leading proponents, Jean-Marie Lehn, who won the Nobel Prize for his work in the area in 1987, as the ‘chemistry of molecular assemblies and of the intermolecular bond’. More colloquially this may be expressed as ‘chemistry beyond the molecule’. Other definitions include phrases such as ‘the chemistry of the non-covalent bond’ and ‘non-molecular chemistry’. Originally supramolecular chemistry was defined in terms of the non-covalent interaction between a ‘host’ and a ‘guest’ molecule as highlighted in Figure 1.1, which illustrates the relationship between molecular and supramolecular chemistry in terms of both structures and function.

These descriptions, while helpful, are by their nature noncomprehensive and there are many exceptions if such definitions are taken too literally. The problem may be linked to the definition of organometallic chemistry as ‘the chemistry of compounds with metal-to-carbon bonds’. This immediately rules out Wilkinson’s compound, RhCl(PPh3)3, for example, which is one of the most important industrial catalysts for organometallic transformations known in the field. Indeed, it is often the objectives and thought processes of the chemist undertaking the work, as much as the work itself, which determine its field. Work in modern supramolecular chemistry encompasses not just host-guest systems but also molecular devices and machines, molecular recognition, so called ‘self-processes’ such as self-assembly and self-organisation and has interfaces with the emergence of complex matter and nanochemistry (Section 1.10). The rapid expansion in supramolecular chemistry over the past 25 years has resulted in an enormous diversity of chemical systems, both designed and accidentally stumbled upon, which may lay some claim, either in concept, origin or nature, to being supramo-lecular. In particular, workers in the field of supramolecular photochemistry have chosen to adopt a rather different definition of a supramolecular compound as a group of molecular components that contribute properties that each component possesses individually to the whole assembly (covalent or non-covalent). Thus an entirely covalent molecule comprising, for example, a chromophore (light-absorbing moiety), spacer and redox centre might be thought of as supramolecular because the chromophore and redox centre are able to absorb light, or change oxidation state, whether they form part of the supermolecule or not (see Chapter 11). Similarly, much recent work has focused on the development of self-assembling synthetic pathways towards large molecules or molecular arrays. These systems often self-assemble using a variety of interactions, some of which are clearly non-covalent (e.g. hydrogen bonds) and some of which possess a significant covalent component (e.g. metal-ligand interactions, see Chapter 10). Ultimately these self-assembly reactions and the resulting self-organisation of the system rely solely on the intrinsic information contained in the structure of the molecular components and hence there is an increasing trend towards the study and manipulation of intrinsic ‘molecular information’. This shift in emphasis is nothing more than a healthy growth of the field from its roots in host-guest chemistry to encompass and inform a much broader range of concepts and activities.

Figure 1.1 Comparison between the scope of molecular and supramolecular chemistry according to Lehn.1

1.1.2 Host–Guest Chemistry

Kyba, E. P., Helgeson, R. C., Madan, K., Gokel, G. W., Tarnowski, T. L., Moore, S. S. and Cram, D. J., ‘Host-guest complexation. 1. Concept and illustration’, J. Am. Chem. Soc., 1977, 99, 2564–2571.

If we regard supramolecular chemistry in its simplest sense as involving some kind of (non-covalent) binding or complexation event, we must immediately define what is doing the binding. In this context we generally consider a molecule (a ‘host’) binding another molecule (a ‘guest’) to produce a ‘host-guest’ complex or supermolecule. Commonly the host is a large molecule or aggregate such as an enzyme or synthetic cyclic compound possessing a sizeable, central hole or cavity. The guest may be a monatomic cation, a simple inorganic anion, an ion pair or a more sophisticated molecule such as a hormone, pheromone or neurotransmitter. More formally, the host is defined as the molecular entity possessing binding sites (. Lewis basic donor atoms, hydrogen bond donors .). The guest possesses binding sites (. a spherical, Lewis acidic metal cation or hydrogen bond acceptor halide anion). In turn a binding site is defined as a region of the host or guest capable of taking part in a non-covalent interaction. The host–guest relationship has been defined by Donald Cram (another Supramolecular Chemistry Nobel Laureate) as follows:

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