Peter Comba, Trevor W. Hambley and Bodo Martin Molecular Modeling of Inorganic Compounds Third Completely Revised and Enlarged Edition WILEY- VCH WILEY-VCH Verlag GmbH & Co. KGaA
v Contents Preface to the Third Edition XIII Preface to the Second Edition XV Preface to the First Edition XVII I Theory 1 1 Introduction 3 1.1 Molecular Modeling 3 1.2 Historical Background 6 2 Molecular Modeling Methods in Brief 9 2.1 Molecular Mechanics 9 2.2 Quantum Mechanics 11 2.2.1 Hartree Fock Calculations 12 2.2.2 Semi-Empirical Approaches 13 2.2.3 Density Functional Theory 13 2.2.4 Methods and Basis Sets 14 2.3 Other Methods 15 2.3.1 Conformational Searching 15 2.3.1.1 Stochastic Methods 15 2.3.1.2 Molecular Dynamics 15 2.3.2 Database Searching 16 2.3.3 Cluster Analysis 16 2.3.4 Free Energy Perturbation 17 2.35 QSAR 17 3 Parameterization, Approximations and Limitations of Molecular Mechanics 19 3.1 Concepts 19 Molecular Modeling of Inorganic Compounds. Third Edition. Peter Comba, Trevor W. Hambley and Bodo Martin Copyright 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978.3-527-31799-8
VI Contents 3.2 Potential Energy Functions 23 3.2.1 Bond Length Deformation 25 3.2.2 Valence Angle Deformation 27 3.2.3 Torsion Angle Deformation 31 3.2.4 Cross-Terms 33 3.2.5 van der Waals Interactions 33 3.2.6 Electrostatic Interactions 35 3.2.7 Hydrogen Bonding Interactions 37 3.2.8 Out-of-Plane Deformation 38 3.3 Force-Field Parameters 38 3.3.1 Bond Length Deformation 42 3.3.2 Valence Angle Deformation 43 3.3.3 Torsion Angle Deformation 45 3.3.4 Out-of-Plane Deformation 47 3.3.5 Non-Bonded Interactions 48 3.3.6 Electrostatic Interactions 49 3.3.7 Hydrogen-Bonding Interactions 50 3.4 Spectroscopic Force Fields 50 3.5 Model and Reality 52 3.6 Electronic Effects 53 3.7 The Environment 55 3.8 Entropy Effects 57 3.9 Summary 58 4 Computation 61 4.1 Input and Output 61 4.2 Energy Minimization 63 4.2.1 The Simplex Method 65 4.2.2 Gradient Methods 65 4.2.3 Conjugate-Gradient Methods 66 4.2.4 The Newton Raphson Method 66 4.2.5 Least-Squares Methods 67 4.3 Constraints and Restraints 67 5 The Multiple Minima Problem 69 5.1 Deterministic Methods 70 5.2 Stochastic Methods 70 5.3 Molecular Dynamics 71 5.4 Practical Considerations 72 5.5 Malring Use of Experimental Data 73 6 Conclusions 75
Contents I VII II Applications 77 7 Structural Aspects 79 7.1 Accuracy of Structure Prediction 79 7.2 Molecular Visualization 80 7.3 Isomer Analysis 82 7.4 Analysis of Structural Trends 83 7.5 Prediction of Complex Polymerization 84 7.6 Unraveling Crystallographic Disorder 84 7.7 Enhanced Structure Determination 86 7.8 Comparison with Solution Properties 88 8 Stereoselectivities 89 8.1 Conformational Analysis 89 8.2 Enantioselectivities 92 8.2.1 Racemate Separation 93 8.2.2 Stereoselective Synthesis 95 8.2.3 Prediction of Enantioinduction 98 8.3 Structure Evaluation 100 8.4 Mechanistic Information 105 9 Metal Ion Selectivity 111 9.1 Chelate Ring Size 112 9.2 Macrocycle Hole Size 116 9.3 Preorganization 120 9.4 Quantitative Correlations Between Strain and Stability Differences 123 9.5 Condusions 125 10 Spectroscopy 127 10.1 Vibrational Spectroscopy 128 10.2 Electronic Spectroscopy 129 10.3 EPR Spectroscopy 141 10.4 NMR Spectroscopy 147 10.5 QM-Based Methods 148 11 Electron Transfer 149 11.1 Redox Potentials 151 11.2 Electron-Transfer Rates 154 12 Electronic Effects 159 12.1 d-orbital Directionality 160
VIII I Contents 12.2 The frans Influence 163 12.3 Jahn Teller Distortions 164 13 Bioinorganic Chemistry 171 13.1 Complexes of Amino Acids and Peptides 171 13.2 Metalloproteins 172 13.3 Metalloporphyrins 175 13.4 Metal Nucleotide and Metal DNA Interactions 177 13.5 Other Systems 179 13.6 Condusions 181 14 Organometallics 183 14.1 Metallocenes 184 14.2 Transition Metal Allyl Systems 188 14.3 Transition Metal Phosphine Compounds 188 14.4 Metal Metal Bonding 190 14.5 Carbonyl Cluster Compounds 192 15 Compounds with s-, p-, and f-block Elements 195 15.1 Alkali and Alkaline Earth Metals 195 15.1.1 Crown Ethers 195 15.1.2 Cryptands 196 15.1.3 Spherands 197 15.1.4 Biologically Relevant Ligands 197 15.2 Main Group Elements 198 15.3 Lanthanoids and Actinoids 199 15.4 Condusions 201 III Practice of Molecular Mechanics 203 16 The Model, the Rules, and the Pitfalls 205 16.1 Introduction 205 16.2 The Starting Model 205 16.3 The Force Field 206 16.4 The Energy Minimization Procedure 207 16.5 Local and Global Energy Minima 210 16.6 Pitfalls, Interpretation, and Communication 211 17 Tutorial 215 17.1 Introduction to the Momec3 Program 216 17.1.1 Motivation and Rationale 216 17.1.2 The Program Setup and Philosophy 217 17.2 Building a Simple Metal Complex 220 17.2.1 Theory 220
17.2.2 Practice 221 17.3 Optimizing the Structure 222 17.3.1 Theory 222 17.3.2 Practice 226 17.4 Building a Set of Conformers 228 17.4.1 Theory 228 17.4.2 Practice 229 17.4.2.1 Building [Co(en) 3]3+ 229 17.4.2.2 Changing Conformations 230 17.4.3 Exercise 231 17.5 Calculating the Strain Energies and Isomer Distribution of a Set of Conformers 231 17.5.1 Theory 231 17.5.2 Practice 232 17.5.3 Exercise 233 17.6 Constructing and Optimizing a Set of Isomers Automatically 233 17.6.1 Theory 233 17.6.2 Practice 234 17.6.3 Exercise 234 17.7 Building More Difficult Metal Complexes 235 17.7.1 Theory 235 17.7.2 Practice 235 17.7.2.1 Importring Structures from Other Sources 235 17.7.2.2 Building Fragments 236 17.7.3 Exercise 237 17.8 Analyzing Structures 237 17.8.1 Theory 237 17.8.2 Practice 237 17.8.3 Exercise 239 17.9 Potential Energy Functions I: Bond Length, Valence Angle, Torsion Angle, Twist Angle, and Out-of-Plane Deformation Functions 239 17.9.1 Theory 239 17.9.2 Practice 240 17.9.2.1. Bond Length Deformation 241 17.9.2.2 Valence Angle Deformation 242 17.9.2.3 Out-of-Plane Deviations 243 17.9.2.4 Torsion Angle or Dihedral Angle Functions 243 17.9.3 Exercise 246 17.10 Potential Energy Functions II: Non-Bonded Interactions 246 17.10.1 Theory 246 17.10.1.1 van der Waals Interactions 247 17.10.2 Practice 247 17.10.3 Theory 248 17.10.3.1 Hydrogen Bonds 248 17.10.4 Practice 249 Contents I IX
Contents 17.10.5 17.10.5.1 17.10.6 17.10.7 17.11 17.11.1 17.11.2 17.11.3 17.12 17.12.1 17.12.2 17.12.3 17.13 17.13.1 17.13.2 17.13.3 17.13.4 17.14 17.14.1 17.14.2 17.14.3 17.15 17.15.1 17.15.2 17.15.3 17.16 17.16.1 17.16.2 17.16.3 17.17 17.17.1 17.17.2 17.17.3 17.18 17.18.1 17.18.2 17.18.3 17.19 17.19.1 Theory 249 Electrostatic Interactions 249 Practice 250 Exercise 251 Force-Field Parameters I: Developing a Force Field for Cobalt(III) Hexaamines Normal Bond Distances 251 Theory 251 Practice 254 Exercise 255 Force-Field Parameters II: Refining the New Force Field Very Short Bond Distances 256 Theory 256 Practice 257 Exercise 258 Force-Field Parameters III: Refining the New Force Field Very Long Bond Distances 259 Theory 259 Practice 259 Exercise 261 Exercise 261 Force-Field Parameters IV: Comparison of Isomer Distributions Using Various Cobalt(III) Amine Force Fields 262 Theory 262 Practice 263 Exercise 266 Force-Field Parameters V: Parameterizing a New Potential The Tetrahedral Twist of Four-Coordinate Compounds 266 Theory 266 Practice 268 Exercise 269 Using Constraints to Compute Energy Barriers 269 Theory 269 Practice 270 Exercise 272 Using Constraints to Compute Macrocyclic Ligand Hole Sizes 272 Theory 272 Practice 275 Exercise 279 Cavity Sizes of Unsymmetrical Ligands 280 Theory 280 Practice 281 Exercise 282 Using Strain Energies to Compute Reduction Potentials of Coordination Compounds 282 Theory 282
Contents IXI 17.19.2 Practice 285 17.19.3 Exercise 287 17.20 Using Force-Field Calculations with NMR Data 288 17.20.1 Theory 288 17.20.2 Practice 288 17.20.3 Exercise 290 17.21 Optimizing Structures with Rigid Groups 290 17.21.1 Theory 290 17.21.2 Practice 291 17.21.3 Exercise 292 Appendix 1: Glossary 293 Appendix 2: Fundamental Constants, Units, and Conversion Factors 297 A2.1 Constants 297 A2.2 Basic SI Units 297 A2.3 Derived Units and Conversion Factors 298 A2.4 Energy Units in Molecular Mechanics Calculations 298 Appendix 3: Software and Force Fields 299 Appendix 4: Books on Molecular Modeling and Reviews on Inorganic Molecular Modeling 301 A4.1 List of Books an Molecular Modeling 301 A4.2 List of Reviews in the Field of Inorganic Molecular Modeling 302 A4.3 List of Publications an the Momec Force Field 304 References 305 Index 323