Supramolecular Chemistry

Second Edition

Supramolecular Chemistry, 2nd edition J. W. Steed and J. L. Atwood© 2009 John Wiley & Sons, Ltd ISBN: 978-0-470-51233-3

Supramolecular Chemistry

Second Edition

Jonathan W. SteedDepartment of Chemistry, Durham University, UK

Jerry L. AtwoodDepartment of Chemistry, University of Missouri, Columbia, USA

This edition fi rst published 2009© 2009, John Wiley & Sons, Ltd.

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Library of Congress Cataloging-in-Publication DataSteed, 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)

Set in 10/12 pt Times by Thomson Digital, Noida, IndiaPrinted in the UK by Antony Rowe Ltd, Chippenham, Wiltshire

In loving memory of Joan Edwina Steed, 1922–2008

Contents

About the Authors xxi

Preface to the First Edition xxiii

Preface to the Second Edition xxv

Acknowledgements xxvii

1 Concepts 1

1.1 Defi nition and Development of Supramolecular Chemistry 2 1.1.1 What is Supramolecular Chemistry? 2 1.1.2 Host–Guest Chemistry 3 1.1.3 Development 4

1.2 Classifi cation of Supramolecular Host–Guest Compounds 6

1.3 Receptors, Coordination and the Lock and Key Analogy 6

1.4 Binding Constants 9 1.4.1 Defi nition and Use 9 1.4.2 Measurement of Binding Constants 11

1.5 Cooperativity and the Chelate Effect 17

1.6 Preorganisation and Complementarity 22

1.7 Thermodynamic and Kinetic Selectivity, and Discrimination 26

1.8 Nature of Supramolecular Interactions 27 1.8.1 Ion–ion Interactions 27 1.8.2 Ion–Dipole Interactions 27 1.8.3 Dipole–Dipole Interactions 28 1.8.4 Hydrogen Bonding 28 1.8.5 Cation–π Interactions 32 1.8.6 Anion-π Interactions 33 1.8.7 π–π Interactions 33 1.8.8 Van der Waals Forces and Crystal Close Packing 35 1.8.9 Closed Shell Interactions 36

1.9 Solvation and Hydrophobic Effects 38 1.9.1 Hydrophobic Effects 38 1.9.2 Solvation 39

1.10 Supramolecular Concepts and Design 41 1.10.1 Host Design 41 1.10.2 Informed and Emergent Complex Matter 42 1.10.3 Nanochemistry 44

Contentsviii

Summary 45

Study Problems 45

Suggested Further Reading 46

References 47

2 The Supramolecular Chemistry of Life 49

2.1 Biological Inspiration for Supramolecular Chemistry 50

2.2 Alkali Metal Cations in Biochemistry 50 2.2.1 Membrane Potentials 50 2.2.2 Membrane Transport 53 2.2.3 Rhodopsin: A Supramolecular Photonic Device 60

2.3 Porphyrins and Tetrapyrrole Macrocycles 61

2.4 Supramolecular Features of Plant Photosynthesis 63 2.4.1 The Role of Magnesium Tetrapyrrole Complexes 63 2.4.2 Manganese-Catalysed Oxidation of Water to Oxygen 68

2.5 Uptake and Transport of Oxygen by Haemoglobin 70

2.6 Enzymes and Coenzymes 74 2.6.1 Characteristics of Enzymes 74 2.6.2 Mechanism of Enzymatic Catalysis 77 2.6.3 Coenzymes 79 2.6.4 The Example of Coenzyme B12 80

2.7 Neurotransmitters and Hormones 83

2.8 Semiochemistry in the Natural World 85

2.9 DNA 86 2.9.1 DNA Structure and Function 86 2.9.2 Site-Directed Mutagenesis 91 2.9.3 The Polymerase Chain Reaction 92 2.9.4 Binding to DNA 93 2.9.5 DNA Polymerase: A Processive Molecular Machine 97

2.10 Biochemical Self-Assembly 99

Summary 102

Study Problems 102

References 103

3 Cation-Binding Hosts 105

3.1 Introduction to Coordination Chemistry 106 3.1.1 Supramolecular Cation Coordination Chemistry 106 3.1.2 Useful Concepts in Coordination Chemistry 106 3.1.3 EDTA – a Classical Supramolecular Host 112

ix

3.2 The Crown Ethers 114 3.2.1 Discovery and Scope 114 3.2.2 Synthesis 116

3.3 The Lariat Ethers and Podands 118 3.3.1 Podands 118 3.3.2 Lariat Ethers 120 3.3.3 Bibracchial Lariat Ethers 121

3.4 The Cryptands 122

3.5 The Spherands 125

3.6 Nomenclature of Cation-Binding Macrocycles 127

3.7 Selectivity of Cation Complexation 129 3.7.1 General Considerations 129 3.7.2 Conformational Characteristics of Crown Ethers 130 3.7.3 Donor Group Orientation and Chelate Ring Size Effects 132 3.7.4 Cation Binding by Crown Ethers 135 3.7.5 Cation Binding by Lariat Ethers 140 3.7.6 Cation Binding by Cryptands 142 3.7.7 Preorganisation: Thermodynamic Effects 144 3.7.8 Preorganisation: Kinetic and Dynamic Effects 147

3.8 Solution Behaviour 149 3.8.1 Solubility Properties 149 3.8.2 Solution Applications 149

3.9 Synthesis: The Template Effect and High Dilution 153 3.9.1 The Template Effect 153 3.9.2 High-Dilution Synthesis 157

3.10 Soft Ligands for Soft Metal Ions 160 3.10.1 Nitrogen and Sulfur Analogues of Crown Ethers 160 3.10.2 Nitrogen and Sulfur Analogues of Cryptands 163 3.10.3 Azamacrocycles: Basicity Effects and the Example of Cyclam 164 3.10.4 Phosphorus–Containing Macrocycles 167 3.10.5 Mixed Cryptates 168 3.10.6 Schiff Bases 170 3.10.7 Phthalocyanines 172 3.10.8 Torands 173

3.11 Proton Binding: The Simplest Cation 173 3.11.1 Oxonium Ion Binding by Macrocycles in the Solid State 174 3.11.2 Solution Chemistry of Proton Complexes 177

3.12 Complexation of Organic Cations 180 3.12.1 Binding of Ammonium Cations by Corands 181 3.12.2 Binding of Ammonium Cations by Three-Dimensional Hosts 183 3.12.3 Ditopic Receptors 184 3.12.4 Chiral Recognition 185 3.12.5 Amphiphilic Receptors 193 3.12.6 Case Study: Herbicide Receptors 194

Contents

Contentsx

3.13 Alkalides and Electrides 195

3.14 The Calixarenes 197 3.14.1 Cation Complexation by Calixarenes 198 3.14.2 Phase Transport Equilibria 204 3.14.3 Cation Complexation by Hybrid Calixarenes 206

3.15 Carbon Donor and π-acid Ligands 208 3.15.1 Mixed C-Heteroatom Hosts 209 3.15.2 Hydrocarbon Hosts 211

3.16 The Siderophores 213 3.16.1 Naturally Occurring Siderophores 213 3.16.2 Synthetic Siderophores 215

Summary 217

Study Problems 217

Thought Experiment 218

References 219

4 Anion Binding 223

4.1 Introduction 224 4.1.1 Scope 224 4.1.2 Challenges in Anion Receptor Chemistry 225

4.2 Biological Anion Receptors 227 4.2.1 Anion Binding Proteins 228 4.2.2 Arginine as an Anion Binding Site 229 4.2.3 Main Chain Anion Binding Sites in Proteins: Nests 230 4.2.4 Pyrrole-Based Biomolecules 231

4.3 Concepts in Anion Host Design 232 4.3.1 Preorganisation 232 4.3.2 Entropic Considerations 233 4.3.3 Considerations Particular to Anions 234

4.4 From Cation Hosts to Anion Hosts – a Simple Change in pH 236 4.4.1 Tetrahedral Receptors 236 4.4.2 Shape Selectivity 238 4.4.3 Ammonium-Based Podands 239 4.4.4 Two-Dimensional Hosts 240 4.4.5 Cyclophane Hosts 246

4.5 Guanidinium-Based Receptors 248

4.6 Neutral Receptors 251 4.6.1 Zwitterions 253 4.6.2 Amide-Based Receptors 253 4.6.3 Urea and Thiourea Derivatives 255 4.6.4 Pyrrole Derivatives 257 4.6.5 Peptide-Based Receptors 258

Contents xi

4.7 Inert Metal-Containing Receptors 259 4.7.1 General Considerations 259 4.7.2 Organometallic Receptors 261 4.7.3 Hydride Sponge and Other Lewis Acid Chelates 268 4.7.4 Anticrowns 271

4.8 Common Core Scaffolds 276 4.8.1 The Trialkylbenzene Motif 277 4.8.2 Cholapods 278

Summary 281

Study Problems 281

Thought Experiments 282

References 282

5 Ion Pair Receptors 285

5.1 Simultaneous Anion and Cation Binding 286 5.1.1 Concepts 286 5.1.2 Contact Ion Pairs 287 5.1.3 Cascade Complexes 289 5.1.4 Remote Anion and Cation Binding Sites 291 5.1.5 Symport and Metals Extraction 295 5.1.6 Dual-Host Salt Extraction 298

5.2 Labile Complexes as Anion Hosts 299

5.3 Receptors for Zwitterions 303

Summary 304

Study Problems 304

References 305

6 Molecular Guests in Solution 307

6.1 Molecular Hosts and Molecular Guests 308 6.1.1 Introduction 308 6.1.2 Some General Considerations 308

6.2 Intrinsic Curvature: Guest Binding by Cavitands 310 6.2.1 Building Blocks 310 6.2.2 Calixarenes and Resorcarenes 311 6.2.3 Dynamics of Guest Exchange in Cavitates 320 6.2.4 Glycoluril-Based Hosts 323 6.2.5 Kohnkene 326

6.3 Cyclodextrins 327 6.3.1 Introduction and Properties 327 6.3.2 Preparation 331 6.3.3 Inclusion Chemistry 331 6.3.4 Industrial Applications 335

Contentsxii

6.4 Molecular Clefts and Tweezers 336

6.5 Cyclophane Hosts 340 6.5.1 General Aspects 340 6.5.2 Cyclophane Nomenclature 341 6.5.3 Cyclophane Synthesis 342 6.5.4 Molecular ‘Iron Maidens’ 345 6.5.5 From Tweezers to Cyclophanes 346 6.5.6 The Diphenylmethane Moiety 347 6.5.7 Guest Inclusion by Hydrogen Bonding 353 6.5.8 Charge-Transfer Cyclophanes 357

6.6 Constructing a Solution Host from Clathrate-Forming Building Blocks: The Cryptophanes 358

6.6.1 Construction of Containers from a Curved Molecular Building Block 358 6.6.2 Complexation of Halocarbons 361 6.6.3 Competition with Solvent 363 6.6.4 Complexes with Alkyl Ammonium Ions and Metals 364 6.6.5 Methane and Xenon Complexation 365 6.6.6 An ‘Imploding’ Cryptophane 366 6.6.7 Hemicryptophanes 367

6.7 Covalent Cavities: Carcerands and Hemicarcerands 370 6.7.1 Defi nitions and Synthesis 370 6.7.2 Template Effects in Carcerand Synthesis 373 6.7.3 Complexation and Constrictive Binding 373 6.7.4 Carcerism 375 6.7.5 Inclusion Reactions 376 6.7.6 Giant Covalent Cavities 379

Summary 381

Study Problems 381

Thought Experiment 382

References 382

7 Solid-State Inclusion Compounds 385

7.1 Solid-State Host-Guest Compounds 386

7.2 Clathrate Hydrates 387 7.2.1 Formation 387 7.2.2 Structures and Properties 388 7.2.3 Problems and Applications 391

7.3 Urea and Thiourea Clathrates 393 7.3.1 Structure 393 7.3.2 Guest Order and Disorder 394 7.3.3 Applications of Urea Inclusion Compounds 398

Contents xiii

7.4 Other Channel Clathrates 399 7.4.1 Trimesic Acid 399 7.4.2 Helical Tubulands and Other Di-ols 401 7.4.3 Perhydrotriphenylene: Polarity Formation 403

7.5 Hydroquinone, Phenol, Dianin’s Compound and the Hexahost Strategy 406

7.6 Tri-o-thymotide 410 7.6.1 Inclusion Chemistry 410 7.6.2 Synthesis and Derivatives 412 7.6.3 Applications 413

7.7 Cyclotriveratrylene 414 7.7.1 Properties 414 7.7.2 Synthesis 414 7.7.3 Inclusion Chemistry 416 7.7.4 Network Structures 418

7.8 Inclusion Compounds of the Calixarenes 419 7.8.1 Organic-Soluble Calixarenes 419 7.8.2 Fullerene Complexation 423 7.8.3 Water-Soluble Calixarenes 426

7.9 Solid-Gas and Solid-Liquid Reactions in Molecular Crystals 429 7.9.1 The Importance of Gas Sorption 429 7.9.2 Gas Sorption by Calixarenes 431 7.9.3 Gas Sorption by Channel Hosts 434 7.9.4 Gas Sorption by Coordination Complex Hosts 435

Summary 437

Study Problems 438

References 438

8 Crystal Engineering 441

8.1 Concepts 442 8.1.1 Introduction 442 8.1.2 Tectons and Synthons 443 8.1.3 The Special Role of Hydrogen Bonding 447 8.1.4 Hydrogen Bond Acidity and Basicity 452

8.2 Crystal Nucleation and Growth 453 8.2.1 Theory of Crystal Nucleation and Growth 453 8.2.2 NMR Spectroscopy as a Tool to Probe Nucleation 455 8.2.3 Crystal Growth at Air–Liquid Interfaces 456 8.2.4 Chirality Induction: The Adam Effect 458 8.2.5 Dyeing Crystal Interfaces 462 8.2.6 Hourglass Inclusions 464 8.2.7 Epitaxy: Engineering Crystals 467 8.2.8 Crystals as Genes? 469 8.2.9 Mechanochemistry and Topochemistry 470

Contentsxiv

8.3 Understanding Crystal Structures 476 8.3.1 Graph Set Analysis 476 8.3.2 Etter’s Rules 478 8.3.3 Crystal Deconstruction 481 8.3.4 Crystal Engineering Design Strategies 482

8.4 The Cambridge Structural Database 484

8.5 Polymorphism 487 8.5.1 The Importance of Polymorphism 487 8.5.2 Types of Polymorphism 489 8.5.3 Controlling Polymorphism 492

8.6 Co-crystals 493 8.6.1 Scope and Nomenclature 493 8.6.2 Designer Co-crystals 494 8.6.3 Hydrates 497

8.7 Z′ > 1 498

8.8 Crystal Structure Prediction 500 8.8.1 Soft vs. Hard Predictions 500 8.8.2 Crystal Structure Calculation 501 8.8.3 The CCDC Blind Tests 504

8.9 Hydrogen Bond Synthons – Common and Exotic 505 8.9.1 Hydrogen Bonded Rings 505 8.9.2 Hydrogen Bonds to Halogens 510 8.9.3 Hydrogen Bonds to Cyanometallates 511 8.9.4 Hydrogen Bonds to Carbon Monoxide Ligands 512 8.9.5 Hydrogen Bonds to Metals and Metal Hydrides 514 8.9.6 CH Donor Hydrogen Bonds 517

8.10 Aromatic Rings 519 8.10.1 Edge-to-Face and Face-to-Face Interactions 519 8.10.2 Aryl Embraces 522 8.10.3 Metal-π Interactions 523

8.11 Halogen Bonding and Other Interactions 524

8.12 Crystal Engineering of Diamondoid Arrays 526

Summary 530

Study Problems 531

Thought Experiment 532

References 532

9 Network Solids 537

9.1 What Are Network Solids? 538 9.1.1 Concepts and Classifi cation 538 9.1.2 Network Topology 539 9.1.3 Porosity 542

Contents xv

9.2 Zeolites 543 9.2.1 Composition and Structure 543 9.2.2 Synthesis 547 9.2.3 MFI Zeolites in the Petroleum Industry 548

9.3 Layered Solids and Intercalates 550 9.3.1 General Characteristics 550 9.3.2 Graphite Intercalates 553 9.3.3 Controlling the Layers: Guanidinium Sulfonates 554

9.4 In the Beginning: Hoffman Inclusion Compounds and Werner Clathrates 556

9.5 Coordination Polymers 561 9.5.1 Coordination Polymers, MOFs and Other Terminology 561 9.5.2 0D Coordination Clusters 562 9.5.3 1D, 2D and 3D Structures 564 9.5.4 Magnetism 568 9.5.5 Negative Thermal Expansion 570 9.5.6 Interpenetrated Structures 571 9.5.7 Porous and Cavity-Containing Structures 575 9.5.8 Metal-Organic Frameworks 578 9.5.9 Catalysis by MOFs 583 9.5.10 Hydrogen Storage by MOFs 583

Summary 586

Study Problem 587

References 587

10 Self-Assembly 591

10.1 Introduction 592 10.1.1 Scope and Goals 592 10.1.2 Concepts and Classifi cation 594

10.2 Proteins and Foldamers: Single Molecule Self-Assembly 598 10.2.1 Protein Self-Assembly 598 10.2.2 Foldamers 599

10.3 Biochemical Self-Assembly 600 10.3.1 Strict Self-Assembly: The Tobacco Mosaic Virus and DNA 600 10.3.2 Self-Assembly with Covalent Modifi cation 602

10.4 Self-Assembly in Synthetic Systems: Kinetic and Thermodynamic Considerations 604

10.4.1 Template Effects in Synthesis 604 10.4.2 A Thermodynamic Model: Self-Assembly of Zinc Porphyrin Complexes 606 10.4.3 Cooperativity and the Extended Site Binding Model 610 10.4.4 Double Mutant Cycles – Quantifying Weak Interactions 615 10.4.5 Probability of Self-Assembly 616

Contentsxvi

10.5 Self-Assembling Coordination Compounds 620 10.5.1 Design and Notation 620 10.5.2 A Supramolecular Cube 621 10.5.3 Molecular Squares and Boxes 624 10.5.4 Self-Assembly of Metal Arrays 637

10.6 Self-Assembly of Closed Complexes by Hydrogen Bonding 641

10.6.1 Tennis Balls and Softballs: Self-Complementary Assemblies 641 10.6.2 Heterodimeric Capsules 646 10.6.3 Giant Self-Assembling Capsules 646 10.6.4 Rosettes 651

10.7 Catenanes and Rotaxanes 653 10.7.1 Overview 653 10.7.2 Statistical Approaches to Catenanes and Rotaxanes 655 10.7.3 Rotaxanes and Catenanes Involving π−π Stacking Interactions 656 10.7.4 Hydrogen Bonded Rotaxanes and Catenanes 666 10.7.5 Metal and Auxiliary Linkage Approaches to Catenanes and Rotaxanes 669 10.7.6 Molecular Necklaces 677

10.8 Helicates and Helical Assemblies 678 10.8.1 Introduction 678 10.8.2 Synthetic Considerations 681 10.8.3 [4 � 4] Helicates 682 10.8.4 [6 � 6] Helicates 683 10.8.5 Self-Recognition and Positive Cooperativity 684 10.8.6 Cyclic Helicates 686 10.8.7 Anion-Based Helices 687 10.8.8 Hydrogen-Bonded Helices 687

10.9 Molecular Knots 691 10.9.1 The Topology of Knots 691 10.9.2 Trefoil Knots 693 10.9.3 Other Knots 696 10.9.4 Borromean Rings 697

Summary 700

Study Problems 701

Thought Experiment 702

References 702

11 Molecular Devices 707

11.1 Introduction 708 11.1.1 Philosophy of Molecular Devices 708 11.1.2 When Is a Device Supramolecular? 708

Contents xvii

11.2 Supramolecular Photochemistry 710 11.2.1 Photophysical Fundamentals 710 11.2.2 Mechanisms of Energy and Electron Transfer 713 11.2.3 Bimetallic Systems and Mixed Valence 715 11.2.4 Bipyridine and Friends as Device Components 716 11.2.5 Bipyridyl-Type Light Harvesting Devices 718 11.2.6 Light-Conversion Devices 725 11.2.7 Non-Covalently Bonded Systems 726

11.3 Information and Signals: Semiochemistry and Sensing 730 11.3.1 Supramolecular Semiochemistry 730 11.3.2 Photophysical Sensing and Imaging 731 11.3.3 Colorimetric Sensors and the Indicator Displacement Assay 738 11.3.4 Electrochemical Sensors 742

11.4 Molecule-Based Electronics 746 11.4.1 Molecular Electronic Devices 746 11.4.2 Molecular Wires 746 11.4.3 Molecular Rectifi ers 750 11.4.4 Molecular Switches 752 11.4.5 Molecular Logic 756 11.4.6 Towards Addressable Molecular Devices 760

11.5 Molecular Analogues of Mechanical Machines 762

11.6 Nonlinear Optical Materials 765 11.6.1 Origins of Nonlinear Optical Effects 765 11.6.2 Second-Order Nonlinear Optical Materials 768 11.6.3 Third Harmonic Generation Nonlinear Optical Materials 771

Summary 771

Study Problems 771

References 772

12 Biological Mimics and Supramolecular Catalysis 777

12.1 Introduction 778 12.1.1 Understanding and Learning from Biochemistry 778 12.1.2 Characteristics of Biological Models 779

12.2 Cyclodextrins as Enzyme Mimics 780 12.2.1 Enzyme Modelling Using an Artifi cial Host Framework 780 12.2.2 Cyclodextrins as Esterase Mimics 782 12.2.3 Functionalised Cyclodextrins 783

12.3 Corands as ATPase Mimics 785

Contentsxviii

12.4 Cation-Binding Hosts as Transacylase Mimics 788 12.4.1 Chiral Corands 788 12.4.2 A Structure and Function Mimic 790

12.5 Metallobiosites 792 12.5.1 Haemocyanin Models 793 12.5.2 Zinc-Containing Enzymes 795

12.6 Haem Analogues 798 12.6.1 Models of Oxygen Uptake and Transport 798 12.6.2 Cytochrome P-450 Models 803 12.6.3 Cytochrome c Oxidase Models 807

12.7 Vitamin B12 Models 808

12.8 Ion Channel Mimics 809

12.9 Supramolecular Catalysis 813 12.9.1 Abiotic Supramolecular Catalysis 813 12.9.2 Dynamic Combinatorial Libraries 817 12.9.3 Self-Replicating Systems 819 12.9.4 Emergence of Life 823

Summary 825

Study Problems 825

Thought Experiment 826

References 826

13 Interfaces and Liquid Assemblies 829

13.1 Order in Liquids 830

13.2 Surfactants and Interfacial Ordering 831 13.2.1 Surfactants, Micelles and Vesicles 831 13.2.2 Surface Self-Assembled Monolayers 837

13.3 Liquid Crystals 839 13.3.1 Nature and Structure 839 13.3.2 Design of Liquid Crystalline Materials 846 13.3.3 Supramolecular Liquid Crystals 848 13.3.4 Liquid Crystal Displays 851

13.4 Ionic Liquids 852

13.5 Liquid Clathrates 854

Summary 858

Study Problems 858

References 859

Contents xix

14 Supramolecular Polymers, Gels and Fibres 861

14.1 Introduction 862

14.2 Dendrimers 862 14.2.1 Structure and Nomenclature 862 14.2.2 Preparation and Properties of Molecular Dendrimers 866 14.2.3 Dendrimer Host–Guest Chemistry 869 14.2.4 Supramolecular Dendrimer Assemblies 872 14.2.5 Dendritic Nanodevices 874

14.3 Covalent Polymers with Supramolecular Properties 876 14.3.1 Amphiphilic Block Copolymers 876 14.3.2 Molecular Imprinted Polymers 879

14.4 Self-Assembled Supramolecular Polymers 880

14.5 Polycatenanes and Polyrotaxanes 883

14.6 Biological Self-Assembled Fibres and Layers 885 14.6.1 Amyloids, Actins and Fibrin 885 14.6.2 Bacterial S-Layers 887

14.7 Supramolecular Gels 888

14.8 Polymeric Liquid Crystals 893

Summary 894

Study Problems 895

References 895

15 Nanochemistry 899

15.1 When Is Nano Really Nano? 900

15.2 Nanotechnology: The ‘Top Down’ and ‘Bottom Up’ Approaches 900

15.3 Templated and Biomimetic Morphosynthesis 902

15.4 Nanoscale Photonics 905

15.5 Microfabrication, Nanofabrication and Soft Lithography 907

15.6 Assembly and Manipulation on the Nanoscale 912 15.6.1 Chemistry with a Microscope Tip 912 15.6.2 Self-Assembly on Surfaces 914 15.6.3 Addressing Single Molecules 918 15.6.4 Atomic-Level Assembly of Materials 920

15.7 Nanoparticles 921 15.7.1 Nanoparticles and Colloids: Defi nition and Description 921 15.7.2 Gold Nanoparticles 922 15.7.3 Quantum Dots 925 15.7.4 Non-Spherical Nanoparticles 927

Contentsxx

15.8 Endohedral Fullerenes, Nanotubes and Graphene 927 15.8.1 Fullerenes as Hosts 928 15.8.2 Carbon Nanotubes 931 15.8.3 Graphene 935 15.8.4 Afterword – Damascus Steel 935

Summary 936

Thought Experiment 937

References 937

Index 941

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, work-ing 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 Springfi eld 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 scientifi c publications. His research interests revolve around a number of themes in supramolecular chemistry including gas storage and separation and the control of confi ned 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 fi ve-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 trans-lation 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 specifi c 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 defi nitions 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 defi ning that fi eld 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 fi eld, 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 respec-tive institutions and have found that there are a lot of people wanting to learn about the area. Unfortu-nately 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 excep-tion 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 fi nally 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 fi eld. We have not tried to offer any kind of compre-hensive literature review (for which purpose JLA has co-edited the 11 volumes of Comprehensive Supra-molecular Chemistry). What errors there are will be, in the main, ones of over-simplifi cation in an attempt to make accessible many very complicated, and often still rapidly evolving, topics. To the many fi ne work-ers whose insights we may have trivialised we offer humble apology. We hope that the overwhelming ad-vantages will be the excitement of the reader who can learn about any or all aspects of this hydra-like fi eld 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 fi rst edition of Supramolecular Chemistry in 2000 the fi eld 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 fi eld, including a two-volume encyclopaedia that we edited.

In this book we have tried to sample the entire fi eld, bringing together topical research and clear explanations of fundamentals and techniques in a way that is accessible to fi nal year undergraduates in the chemical sciences, all the way to experienced researchers. We have been very gratifi ed by the reception afforded the fi rst 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 ma-jor 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 fi eld 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 amelio-rating some of the uneven coverage and oversimplifi cations of which we may have been guilty.

The original intent of this book was to serve as a concise introduction to the fi eld of supramolecular chemistry. One of us (JWS) has since co-authored a short companion book Core Concepts in Supramo-lecular Chemistry and Nanochemistry that fulfi ls 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 fi eld. Undergraduates encountering Supramolecular Chem-istry for the fi rst time will fi nd 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 se-nior colleagues will fi nd 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 frame-works, 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 pub-lished 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 fi ne colleagues whose work we did not include. The objective of the book is to cover the scope of the fi eld with interesting and

xxvi Preface

representative examples of key systems but we cannot be comprehensive. We feel this second edition is more complete and balanced than the fi rst edition and we have really enjoyed putting it together. We hope you enjoy it too.

Jonathan W. Steed, Durham, UK Jerry L. Atwood, Columbia, Missouri, USA

Acknowledgements

Our thanks go to the many fi ne students, researchers and colleagues who have passed through our groups over the years, whose discussions have helped to both metaphorically and literally crys-tallize our thinking on this rapidly evolving fi eld. 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 fi rst edition. The second edition has benefi ted 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 fi ne 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 fi eld in supramolecular chemistry. (Images courtesy of the British Museum, London, UK).

Website

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