Supramolecular Chemistry (eBook)

Preface 5
Acknowledgements 6
Contents 7
1 An Introduction to Supramolecular Chemistry 12
1.1 Supramolecular Chemistry 12
1.2 Origins 14
1.3 Supramolecular Chemistry and Nanotechnology 16
1.4 Fundamental Supramolecular Interactions 18
1.4.1 Covalent Bonds 20
1.4.2 Reversible Covalent Bonds 20
1.4.2.1 Sulfur-Sulfur Bonds 21
1.4.2.2 Imine Formation 21
1.4.2.3 Metal-ligand Coordinate Bonds 21
1.4.3 Ionic Interactions 22
1.4.4 Ion-Dipole Interactions 22
1.4.5 Dipole-Dipole Interactions 23
1.4.6 Hydrogen Bonds 23
1.4.7 Cation-p Interactions 24
1.4.8 p–p Interactions 24
1.4.9 van der Waals Forces 24
1.4.10 Hydrophobic Effects 24
1.5 Supramolecular Components 25
1.5.1 Supramolecular Complexes from Simple Ligands 25
1.5.1.1 Pyridine Derivatives 26
1.5.1.2 Schiff Bases 27
1.5.1.3 Polyamines 28
1.5.1.4 Polyethers 28
1.5.1.5 Podands 29
1.5.2 Macrocycles 30
1.5.2.1 Calixarenes 31
1.5.2.2 Calixpyrroles and Resorcinarenes 34
1.5.2.3 Cyclotriveratrylene 34
1.5.2.4 Cyclophanes 35
1.5.2.5 Porphyrins and Phthalocyanines 36
1.5.2.6 Crown Ethers 37
1.5.2.7 Lariat Ethers 37
1.5.2.8 Cryptands, Sepulchrates and Sarcophagenes 38
1.5.2.9 Cyclodextrins 39
1.6 Supramolecular Entanglements 41
1.6.1 Catenanes and Rotaxanes 41
1.6.1.1 Maxwell's Demon 45
1.6.1.2 Borromean Rings 46
1.6.1.3 Natural Rotaxanes 47
1.6.2 Grids 48
1.6.3 Dynamic Combinatorial Libraries 48
1.7 Observing Supramolecules 50
1.7.1 Isolation 50
1.7.2 Detection 50
1.7.2.1 Mass Spectrometry 50
1.7.2.2 Infrared Spectroscopy 51
1.7.2.3 Ultraviolet/Visible Spectroscopy 51
1.7.2.4 Nuclear Magnetic Resonance Spectroscopy 51
1.7.2.5 X-Ray Crystallography 52
1.7.2.6 Solution Techniques 52
1.7.2.7 Electrochemical Techniques 53
1.7.2.8 Molecular Modelling 54
1.8 Summary 55
References 55
2 Supramolecular Chemistry and the Life Sciences 60
2.1 Life as a Supramolecular Phenomenon 60
2.2 Supramolecular Interactions in Biological Systems 61
2.2.1 Amino Acids 61
2.2.2 Proteins 65
2.2.3 Sugars 68
2.2.4 Glycoproteins 69
2.2.5 Lipids 70
2.2.6 RNA and DNA 71
2.2.7 Unusual Structural Forms of DNA 75
2.2.7.1 A-, B- and Z-DNA 75
2.2.7.2 Holliday Junctions and Other Features 76
2.3 Self-Replication as the Key to Life 77
2.3.1 Replicators 77
2.3.2 Replicator Evolution 79
2.3.3 Orthogonal Translation 80
2.4 Supramolecular Self-Replication 82
2.4.1 Self-Assembling and Self-Replicating Motifs 84
2.5 Supramolecular Chemistry and the Origin of Life 90
2.5.1 Compartmentalization: The Lipid World 91
2.5.2 Catalysis: The Iron-Sulfur World 94
2.5.3 Self-Replication: The RNA World 94
2.6 Supramolecular Biology and Synthetic Biology 97
2.7 Summary 98
References 98
3 Artificial Cells 101
3.1 Cells as Capsules 101
3.2 Natural Capsules 101
3.2.1 Clathrins 102
3.2.2 Viral Capsids 103
3.2.3 Coat Proteins 104
3.2.4 Vault Proteins 104
3.3 Unnatural Capsules 105
3.3.1 Self-Complementary Capsules 106
3.3.2 Boxes with Metal Hinges 107
3.3.3 Capsules as Reaction Flasks 110
3.3.4 More Complex Geometries 111
3.4 Synthetic Cells 112
3.4.1 Capsules with Mineral Walls 112
3.4.2 Polymer Based Capsules 114
3.4.3 Lipid Capsules 115
3.4.4 Capsid Virus Mimetics 117
3.5 Towards a Minimal Synthetic Cell 117
3.6 Cellular Aggregation 119
3.7 Summary 120
References 120
4 Supramolecular Enzyme Mimics 122
4.1 Enzymes 122
4.2 Metal Complexes as Enzyme Mimics 125
4.3 Enzymes and Their Supramolecular Analogues 127
4.3.1 Haemoglobin, Myoglobin and Their Models 128
4.3.2 Cytochromes 130
4.3.3 Protection from Radicals: Catalytic Pro- and Antioxidants 131
4.3.4 Copper-Containing Enzymes 136
4.3.5 Zinc-Containing Enzymes 141
4.3.6 Photosynthesis and Artificial Leaves 145
4.3.7 Cyclodextrins as Artificial Enzyme Supports 151
4.3.8 Model Enzymes that do not Require Metals 152
4.3.9 Molecularly Imprinted Polymers 153
4.3.10 Combinatorial Polymers 153
4.3.11 Dynamic Combinatorial Libraries 154
4.4 De novo Design and Evolutionary Development of Enzymes 154
4.5 Summary 157
References 157
5 Natural and Synthetic Transmembrane Channels 161
5.1 Cells and Their Membranes 161
5.1.1 Cell Membranes 161
5.1.2 Transmembrane Migration: Molecular Shuttles 163
5.1.2.1 Ionophore Mediated Transport 163
5.1.2.2 Siderophore Mediated Transport 164
5.1.2.3 Anion Transport 164
5.2 Transmembrane Channels: Selectivity and Gating Mechanisms 165
5.2.1 Voltage Gating 166
5.2.2 Ligand Gating 166
5.2.3 Gating by Aggregation 166
5.2.4 Gating by pH and Membrane Tension 167
5.2.5 Light Gating 168
5.3 Channel Architecture 169
5.3.1 Channels for Neutral Molecules 170
5.3.2 Anion Channels 171
5.3.3 Cation Channels 171
5.3.3.1 Na+ Channels and Transporters 172
5.3.3.2 K+ Channels 173
5.3.3.3 Cation Selectivity 175
5.4 Structural Determination 175
5.5 Measuring Channel Activity 177
5.5.1 Voltage Clamping 177
5.5.2 Patch Clamping 177
5.5.3 Bilayer Methods 178
5.5.4 Dye Release Methods 178
5.5.5 NMR Methods 178
5.6 Transmembrane Transport by Artificial Systems 179
5.6.1 Transporters 179
5.6.1.1 Synthetic Ionophores 179
5.6.1.2 Artificial Siderophores 180
5.6.1.3 Anion Transport 180
5.6.2 Channel-Forming Systems 180
5.6.2.1 Artificial Channel-Forming Peptides 181
5.6.2.2 Crown Ether Derivatives 183
5.6.2.3 Rigid Cavity Approaches 184
5.6.2.4 Acyclic Models 187
5.7 Summary 188
References 189
6 Diagnostic Applications 192
6.1 Applications of Supramolecular Chemistry in Medical Diagnostics 192
6.2 Design Principles 192
6.3 Supramolecular Sensors 195
6.3.1 Optical and Fluorescent Biosensors 195
6.3.1.1 Logic Gates 197
6.3.1.2 Detection of Critical Analytes 198
6.3.1.3 Displacement Assays 198
6.3.1.4 Squaraine Dyes 199
6.3.2 Electrochemical Sensors 202
6.3.2.1 Electrochemical Detection of Nitric Oxide 202
6.4 Macrocyclic Complexes for Imaging 204
6.5 In vivo Imaging: Magnetic Resonance Imaging Agents 206
6.6 Other Supramolecular Sensors 210
6.7 Summary 211
References 211
7 Supramolecular Therapeutics 214
7.1 Therapeutic Applications of Supramolecular Chemistry 214
7.2 Chelation Therapy 215
7.2.1 Desferrioxamine 216
7.2.2 Copper Imbalance: Wilson's Disease and Menke's Syndrome 217
7.3 Macrocyclic Complexes for Radiotherapy 218
7.4 Photodynamic Therapy 218
7.5 Texaphyrins 221
7.6 Targeting Cancer with Peptides 223
7.7 Drug Delivery and Controlled Release 223
7.8 Cyclams as Anti-HIV Agents 224
7.9 A Supramolecular Solution to Alzheimers Disease? 226
7.10 Calixarenes as Therapeutic Agents 229
7.11 Supramolecular Antibiotics 231
7.12 Summary 234
References 235
8 Bionanotechnology, Nanomedicine and the Future 237
8.1 Bionanotechnology 237
8.2 The Unnatural Chemistry of DNA 238
8.3 Molecular Muscles 241
8.4 Nanomedicine 244
8.4.1 Labelling with Nanoparticles 245
8.4.2 DNA Fingerprinting 246
8.4.3 Full Genome Sequencing 246
8.4.4 DNA Sequencing in Real Time 248
8.4.4.1 DNA Sequencing Through Natural Nanopores 248
8.4.4.2 DNA Sequencing Through Manufactured Nanopores 248
8.4.5 Therapeutic Multimodal Nanoparticles 250
8.5 Cell Mimics as Drug Delivery Vehicles 252
8.5.1 Polymer Encapsulated siRNA Delivery 252
8.5.2 Drug Delivery by Particle Disintegration 253
8.5.3 Minicells as Drug Delivery Systems 254
8.6 Supramolecular Protein Engineering 255
8.7 Antimicrobial Limpet Mines 255
8.8 Future Directions 257
8.8.1 Medicinal Nanodevices 257
8.8.2 Powering Nanodevices 258
8.8.3 Functional Nanodevices 258
8.8.4 Verification of Treatment 259
8.8.5 Nanodevice Control 260
8.9 Supramolecular Chemistry and Nanomedicine 260
References 260
Index 263