| | Contents | |
| |
| 1 | Some Reflections on Chemistry - Molecular, Supramolecular and Beyond | 1 |
| 1.1 | From Structure to Information. The Challenge of Instructed Chemistry | 1 |
| 1.2 | Steps Towards Complexity | 3 |
| 1.3 | Chemistry and Biology, Creativity and Art | 5 |
| 2 | Chemical Synthesis and Biological Studies of the Epothilones - Microtubule Stabilizing Agents with Enhanced Activity Against Multidrug-Resistant Cell Lines and Tumors | 8 |
| 2.1 | Introduction | 8 |
| 2.2 | Total Synthesis of Epothilones | 9 |
| 2.3 | First Generation Syntheses of Epothilones A and B | 9 |
| 2.4 | First Generation Synthesis of the Acyl Domain | 10 |
| 2.5 | Investigation of C9-C10 Bond Construction Through Ring Closing Metathesis | 12 |
| 2.6 | B-Alkyl Suzuki Strategy | 12 |
| 2.7 | Macrolactonization and Macroaldolization Approaches | 16 |
| 2.8 | A New and More Efficient Synthesis of Epothilone B | 18 |
| 2.9 | Dianion Equivalents Corresponding to the Polypropionate Domain of Epothilone B | 19 |
| 2.10 | B-Alkyl Suzuki Merger | 20 |
| 2.11 | Stereoselective Noyori Reduction | 21 |
| 2.12 | Discovery of a Remarkable Long-Range Effect on the Double Diastereoface Selectivity in an Aldol Condensation | 22 |
| 2.13 | Preparation of Other Epothilone Analogs | 25 |
| 2.14 | Biological Evaluation of Epothilones | 26 |
| 2.15 | SAR Analysis of Epothilones: The Zone Approach | 26 |
| 2.16 | In Vitro Analysis Comparison to Paclitaxel and Related Agents | 28 |
| 2.17 | In Vivo Analysis: Comparisons to Paclitaxe | l30 |
| 2.18 | Conclusions | 33 |
| 2.19 | Acknowledgements | 33 |
| 3 | The Spirotetrahydrofuran Motif: its Role in Enhancing Ligation in Belted Ionophores, Biasing Cyclohexane Conformation, and Restricting Nucleoside/Nucleotide Conformation | 37 |
| 3.1 | Introduction | 37 |
| 3.2 | syn-1,3,5-Orientation on a Cyclohexane Core | 40 |
| 3.3 | Maximally Substituted Hexa(spirotetrahydrofuranyl)-cyclohexanes | 43 |
| 3.4 | Spirocyclic Restriction of Nucleosides/Nucleotides | 49 |
| 3.5 | Acknowledgement | 51 |
| 4 | Heterogeneous Catalysis: from "Black Art" to Atomic Understanding | 54 |
| 4.1 | Introduction | 54 |
| 4.2 | A Case Study: Ammonia Synthesis | 55 |
| 4.3 | The Surface Science Approach | 57 |
| 4.4 | The Atomic Mechanism of a Catalytic Reaction: Oxidation of Carbon Monoxide | 62 |
| 4.5 | Further Aspects | 66 |
| 5 | Drugs for a New Millennium | 70 |
| 5.1 | Introduction | 70 |
| 5.2 | Cell Death | 70 |
| 5.3 | Stroke and Myocardial Infarct | 71 |
| 5.4 | Schizophrenia | 75 |
| 5.4.1 | Neuroleptic Drug Development | 76 |
| 5.4.2 | Drug Psychoses | 79 |
| 5.5 | Drugs of Abuse | 81 |
| 5.5.1 | Definitions and Varieties | 81 |
| 5.5.2 | Approaches to Treatment: Focus on Cocaine | 83 |
| 5.6 | Conclusions and New Directions | 85 |
| 5.7 | Acknowledgements | 87 |
| 6 | Protein Folding and Beyond | 89 |
| 6.1 | Introduction | 89 |
| 6.1.1 | Computational Protein Folding | 91 |
| 6.1.2 | All-atom Simulations of Protein Unfolding and Short Peptide Folding | 92 |
| 6.2 | All-Atom Simulations of Folding of Small Proteins | 93 |
| 6.2.1 | Concomitant Hydrophobic Collapse and Partial Helix Formation | 93 |
| 6.2.2 | A Marginally Stable Intermediate State | 94 |
| 6.3 | A Perspective View | 96 |
| 7 | The Enzymology of Biological Nitrogen Fixation | 102 |
| 7.1 | Early History | 102 |
| 7.2 | Practical Applications | 103 |
| 7.3 | Biochemistry of N2 Fixation | 104 |
| 7.4 | First Product of N2 Fixation | 105 |
| 7.5 | Studies with 15N as a Tracer | 105 |
| 7.6 | N2 Fixation with Cell-Free Preparations | 106 |
| 7.7 | Nitrogenase Consists of Two Proteins | 107 |
| 7.8 | ATP Furnishes Energy for Fixation | 108 |
| 7.9 | H2 an Obligatory Product of the Nitrogenase Reaction | 108 |
| 7.10 | N2 and HD Formation | 109 |
| 7.11 | Electron Transfer Sequence | 109 |
| 7.12 | Alternative Substrates | 110 |
| 7.13 | N2 Fixation in Non-Leguminous Plants | 110 |
| 7.14 | Control of Nitrogenase | 111 |
| 7.15 | Magnitude of Chemical and Biological N2 Fixation | 111 |
| 7.16 | Associative Biological N2 Fixation | 112 |
| 7.17 | Genetics of Biological N2 Fixation | 112 |
| 7.18 | Composition and Structure of Nitrogenases | 113 |
| 7.19 | Selection of N2 Fixers | 113 |
| 8 | The Chemistry of Nitrogen in Soils | 117 |
| 8.1 | Introduction | 117 |
| 8.2 | Nitrogen Fixation and Ensuing Reactions | 117 |
| 8.3 | Amino Acids, Amino Sugars, and Ammonia in Soils | 118 |
| 8.4 | Nucleic Acid Bases in Soils | 121 |
| 8.5 | Bioavailability of the NH-N Fraction | 121 |
| 8.6 | Chemistry of the UH-N Fraction | 122 |
| 8.7 | Chemistry of the NH-N Fraction | 122 |
| 8.8 | Pyrolysis-field ionization mass spectrometry (Py-FIMS) and Curie-point pyrolysis-gas chromatography/mass spectrometry (CpPy-GC/MS) of soils | 124 |
| 8.9 | Origins of Major N Compounds Identified | 125 |
| 8.10 | 15N MR analysis of soils | 126 |
| 8.11 | Distribution of N in Soils | 127 |
| 8.12 | Concluding Comments | 127 |
| 9 | Spherical Molecular Assemblies: A Class of Hosts for the Next Millennium | 130 |
| 9.1 | Introduction | 130 |
| 9.1.1 | Supramolecular Chemistry | 130 |
| 9.1.2 | Towards Supramolecular Synthesis | 131 |
| 9.1.3 | Self-Assembly | 131 |
| 9.2 | Overview | 132 |
| 9.3 | A Spherical Molecular Assembly Held Together by 60 Hydrogen Bonds | 132 |
| 9.3.1 | Polyhedron Model - Snub Cube | 133 |
| 9.4 | General Principles for Spherical Host Design | 134 |
| 9.4.1 | Spheroid Design | 134 |
| 9.4.2 | Self-Assembly | 134 |
| 9.4.3 | Subunits for Spheroid Design and Self-Assembly | 135 |
| 9.4.4 | Platonic Solids | 137 |
| 9.4.5 | Archimedean Solids | 138 |
| 9.4.6 | Models for Spheroid Design | 139 |
| 9.5 | Examples from the Laboratory and from Nature | 140 |
| 9.5.1 | Platonic Solids | 140 |
| 9.5.1.1 | Tetrahedral Systems (Td, Th, T) | 140 |
| 9.5.1.2 | Octahedral Systems (Oh, O) | 141 |
| 9.5.1.3 | Icosahedral Systems (Ih, I) | 142 |
| 9.5.2 | Archimedean Solids | 143 |
| 9.5.2.1 | Trunctated Tetrahedron (1) | 143 |
| 9.5.2.2 | Cuboctahedron (2) | 144 |
| 9.5.2.3 | Trunctated Octahedron (4) | 144 |
| 9.5.2.4 | Rhombicuboctahedron (5) | 145 |
| 9.5.2.5 | Snub Cube (6) | 145 |
| 9.5.2.6 | Trunctated Icosahedron (10) | 145 |
| 9.5.3 | Archimedean Duals and Irregular Polygons | 146 |
| 9.5.3.1 | Rhombic Dodecahedron (2) | 146 |
| 9.5.4 | Irregular Polygons | 147 |
| 9.6 | Why the Platonic and Archimedean Solids? | 147 |
| 9.7 | Conclusion | 148 |
| 10 | The Combinatorial Approach to Materials Discovery | 151 |
| 10.1 | Introduction | 151 |
| 10.2 | History of Rapid Synthesis Approaches in Materials Research | 152 |
| 10.2.1 | Early Work | 152 |
| 10.2.3 | Recent Innovations | 154 |
| 10.2.4 | The Continuous Compositional Spread (CCS) Approach | 156 |
| 10.3 | Systematized Search for a New High- Thin-film Material | 158 |
| 10.3.1 | General Considerations for Investigating New Materials Systems | 158 |
| 10.3.2 | The Problem: Finding New High Dielectric-Constant Materials | 159 |
| 10.3.3 | Measurement Strategy and Figure of Merit | 161 |
| 10.3.4 | Electrical and Compositional Evaluation | 162 |
| 10.4 | Identification of a Promising Candidate and Discussion of Trends | 164 |
| 10.4.1 | Initial Survey | 164 |
| 10.4.2 | The Zr-Sn-Ti-O System | 164 |
| 10.4.3 | Single-Target Synthesis and Detailed Electrical Characterization | 167 |
| 10.4.4 | HfTT Analog | 168 |
| 10.4.5 | Other Systems | 168 |
| 10.4.6 | Other Problems for Which a Combinatorial Approach is Well Suited | 171 |
| 10.4.7 | New Magnetic Materials | 171 |
| 10.4.8 | Superconductors | 172 |
| 10.4.9 | Thermoelectric materials | 172 |
| 10.4.10 | Piezoelectric materials | 172 |
| 10.4.11 | Ferroelectric Materials | 173 |
| 10.4.12 | Optical Materials | 173 |
| 10.4.13 | Catalysts | 173 |
| 10.5 | Concluding Comments | 173 |
| 11 | On One Hand But Not The Other: The Challenge of the Origin and Survival of Homochirality in Prebiotic Chemistry | 175 |
| 11.1 | Symmetry Breaking and Chiral Induction | 177 |
| 11.1.1 | Is it Intrinsic? | 177 |
| 11.1.2 | Is it Fluctuational? | 179 |
| 11.1.3 | Is it Extrinsic? | 181 |
| 11.2 | Experimental Studies of Chiral Induction | 181 |
| 11.2.1 | Intrinsic Mechanisms | 182 |
| 11.2.2 | Fluctuational Mechanisms | 183 |
| 11.2.3 | Extrinsic Mechanisms | 185 |
| 11.3 | Chiral Amplification and Takeover | 186 |
| 11.3.1 | Autoamplification by Polymerization/Depolymerization | 187 |
| 11.3.2 | Enantiomeric Amplification by Change of Phase | 189 |
| 11.3.3 | Metal-Assisted Enantiomeric Amplification | 189 |
| 11.3.4 | Amplification by Molecular Propagation from a Chiral Center | 191 |
| 11.3.5 | Amplification by CPL Photoinduction | 192 |
| 11.4 | The Sequestration of Chirality | 193 |
| 11.4.1 | Porous Minerals | 194 |
| 11.4.2 | Amphiphilic Vesicles | 195 |
| 11.5 | Setting the Scene for Life | 196 |
| 11.6 | The Rocky Road to Life? | 198 |
| 11.7 | Concluding Remarks | 202 |
| 11.8 | Acknowledgments | 202 |
| 12 | Chemical Reaction Dynamics Looks to the Understanding of Complex Systems | 209 |
| | Acknowledgement | 217 |
| 13 | The Past, Present, and Future of Quantum Chemistry | 219 |
| | Introduction | 219 |
| 13.2 | The History and Present Status of Quantum Chemistry | 221 |
| 13.2.1 | The Gaussian Programs | 221 |
| 13.2.2 | Coupled Cluster Theory | 222 |
| 13.2.3 | Multireference Approaches | 224 |
| 13.2.4 | Analytic Gradient Techniques | 226 |
| 13.2.5 | Density-Functional Theory | 228 |
| 13.2.6 | Integral-Direct Methods | 230 |
| 13.3 | The Future of Quantum Chemistry | 231 |
| 13.3.1 | Extensions to Large Systems | 232 |
| 13.3.2 | Pursuit of Spectroscopic Accuracy | 235 |
| 13.3.3 | Potential Energy Surfaces for Reaction Dynamics | 238 |
| 13.4 | Conclusions | 241 |
| 13.5 | Acknowledgements | 242 |
| 13.6 | Appendix: Nomenclature | 242 |
| 14 | Quantum Alchemy | 247 |
| 14.1 | From Alchemy to Quantum Theory | 247 |
| 14.2 | Applying Quantum Theory | 248 |
| 14.3 | Total Energy Calculations | 256 |
| 14.4 | Novel Materials | 262 |
| 14.5 | The Future | 266 |
| | Acknowledgements | 268 |
| 15 | Quantum Theory Project | 271 |
| 15.1 | Introduction | 271 |
| 15.2 | Background | 271 |
| 15.3 | Wave Function Theory | 274 |
| 15.4 | Density Functional Theory | 278 |
| 15.5 | Ab Initio Density Functional Theory | 281 |
| 15.5.1 | Exact Exchange | 281 |
| 15.5.2 | Exact Correlation | 283 |
| | Acknowledgements | 284 |
| | Index | 287 |