Molecular Modeling of Inorganic Compounds

Contents 5
Preface to the Third Edition 13
Preface to the Second Edition 15
Preface to the First Edition 17
Part I: Theory 19
1 Introduction 21
1.1 Molecular Modeling 21
1.2 Historical Background 24
2 Molecular Modeling Methods in Brief 27
2.1 Molecular Mechanics 27
2.2 Quantum Mechanics 29
2.2.1 Hartree\u2013Fock Calculations 30
2.2.2 Semi-Empirical Approaches 31
2.2.3 Density Functional Theory 31
2.2.4 Methods and Basis Sets 32
2.3 Other Methods 33
2.3.1 Conformational Searching 33
2.3.1.1 Stochastic Methods 33
2.3.1.2 Molecular Dynamics 33
2.3.2 Database Searching 34
2.3.3 Cluster Analysis 34
2.3.4 Free Energy Perturbation 35
2.3.5 QSAR 35
3 Parameterization, Approximations and Limitations of Molecular Mechanics 37
3.1 Concepts 37
3.2 Potential Energy Functions 41
3.2.1 Bond Length Deformation 43
3.2.2 Valence Angle Deformation 45
3.2.3 Torsion Angle Deformation 49
3.2.4 Cross-Terms 51
3.2.5 van der Waals Interactions 51
3.2.6 Electrostatic Interactions 53
3.2.7 Hydrogen Bonding Interactions 55
3.2.8 Out-of-Plane Deformation 56
3.3 Force-Field Parameters 56
3.3.1 Bond Length Deformation 60
3.3.2 Valence Angle Deformation 61
3.3.3 Torsion Angle Deformation 63
3.3.4 Out-of-Plane Deformation 65
3.3.5 Non-Bonded Interactions 66
3.3.6 Electrostatic Interactions 67
3.3.7 Hydrogen-Bonding Interactions 68
3.4 Spectroscopic Force Fields 68
3.5 Model and Reality 70
3.6 Electronic Effects 71
3.7 The Environment 73
3.8 Entropy Effects 75
3.9 Summary 76
4 Computation 79
4.1 Input and Output 79
4.2 Energy Minimization 81
4.2.1 The Simplex Method 83
4.2.2 Gradient Methods 83
4.2.3 Conjugate-Gradient Methods 84
4.2.4 The Newton\u2013Raphson Method 84
4.2.5 Least-Squares Methods 85
4.3 Constraints and Restraints 85
5 The Multiple Minima Problem 87
5.1 Deterministic Methods 88
5.2 Stochastic Methods 88
5.3 Molecular Dynamics 89
5.4 Practical Considerations 90
5.5 Making Use of Experimental Data 91
6 Conclusions 93
Part II: Applications 95
7 Structural Aspects 97
7.1 Accuracy of Structure Prediction 97
7.2 Molecular Visualization 98
7.3 Isomer Analysis 100
7.4 Analysis of Structural Trends 101
7.5 Prediction of Complex Polymerization 102
7.6 Unraveling Crystallographic Disorder 102
7.7 Enhanced Structure Determination 104
7.8 Comparison with Solution Properties 106
8 Stereoselectivities 107
8.1 Conformational Analysis 107
8.2 Enantioselectivities 110
8.2.1 Racemate Separation 111
8.2.2 Stereoselective Synthesis 113
8.2.3 Prediction of Enantioinduction 116
8.3 Structure Evaluation 118
8.4 Mechanistic Information 123
9 Metal Ion Selectivity 129
9.1 Chelate Ring Size 130
9.2 Macrocycle Hole Size 134
9.3 Preorganization 138
9.4 Quantitative Correlations Between Strain and Stability Differences 141
9.5 Conclusions 143
10 Spectroscopy 145
10.1 Vibrational Spectroscopy 146
10.2 Electronic Spectroscopy 147
10.3 EPR Spectroscopy 159
10.4 NMR Spectroscopy 165
10.5 QM-Based Methods 166
11 Electron Transfer 167
11.1 Redox Potentials 169
11.2 Electron-Transfer Rates 172
12 Electronic Effects 177
12.1 d-Orbital Directionality 178
12.2 The trans Influence 181
12.3 Jahn\u2013Teller Distortions 182
13 Bioinorganic Chemistry 189
13.1 Complexes of Amino Acids and Peptides 189
13.2 Metalloproteins 190
13.3 Metalloporphyrins 193
13.4 Metal\u2013Nucleotide and Metal\u2013DNA Interactions 195
13.5 Other Systems 197
13.6 Conclusions 199
14 Organometallics 201
14.1 Metallocenes 202
14.2 Transition Metal\u2013Allyl Systems 206
14.3 Transition Metal\u2013Phosphine Compounds 206
14.4 Metal\u2013Metal Bonding 208
14.5 Carbonyl Cluster Compounds 210
15 Compounds with s-, p-, and f-Block Elements 213
15.1 Alkali and Alkaline Earth Metals 213
15.1.1 Crown Ethers 213
15.1.2 Cryptands 214
15.1.3 Spherands 215
15.1.4 Biologically Relevant Ligands 215
15.2 Main Group Elements 216
15.3 Lanthanoids and Actinoids 217
15.4 Conclusions 219
Part III: Practice of Molecular Mechanics 221
16 The Model, the Rules, and the Pitfalls 223
16.1 Introduction 223
16.2 The Starting Model 223
16.3 The Force Field 224
16.4 The Energy Minimization Procedure 225
16.5 Local and Global Energy Minima 228
16.6 Pitfalls, Interpretation, and Communication 229
17 Tutorial 233
17.1 Introduction to the Momec3 Program 234
17.1.1 Motivation and Rationale 234
17.1.2 The Program Setup and Philosophy 235
17.2 Building a Simple Metal Complex 238
17.2.1 Theory 238
17.2.2 Practice 239
17.3 Optimizing the Structure 240
17.3.1 Theory 240
17.3.2 Practice 244
17.4 Building a Set of Conformers 246
17.4.1 Theory 246
17.4.2 Practice 247
17.4.2.1 Building [Co(en)3]3+ 247
17.4.2.2 Changing Conformations 248
17.4.3 Exercise 249
17.5 Calculating the Strain Energies and Isomer Distribution of a Set of Conformers 249
17.5.1 Theory 249
17.5.2 Practice 250
17.5.3 Exercise 251
17.6 Constructing and Optimizing a Set of Isomers Automatically 251
17.6.1 Theory 251
17.6.2 Practice 252
17.6.3 Exercise 252
17.7 Building More Difficult Metal Complexes 253
17.7.1 Theory 253
17.7.2 Practice 253
17.7.2.1 Importing Structures from Other Sources 253
17.7.2.2 Building Fragments 254
17.7.3 Exercise 255
17.8 Analyzing Structures 255
17.8.1 Theory 255
17.8.2 Practice 255
17.8.3 Exercise 257
17.9 Potential Energy Functions I: Bond Length, Valence Angle, Torsion Angle, Twist Angle, and Out-of-Plane Deformation Functions 257
17.9.1 Theory 257
17.9.2 Practice 258
17.9.2.1 Bond Length Deformation 259
17.9.2.2 Valence Angle Deformation 260
17.9.2.3 Out-of-Plane Deviations 261
17.9.2.4 Torsion Angle or Dihedral Angle Functions 261
17.9.3 Exercise 264
17.10 Potential Energy Functions II: Non-Bonded Interactions 264
17.10.1 Theory 264
17.10.1.1 van der Waals Interactions 265
17.10.2 Practice 265
17.10.3 Theory 266
17.10.3.1 Hydrogen Bonds 266
17.10.4 Practice 267
17.10.5 Theory 267
17.10.5.1 Electrostatic Interactions 267
17.10.6 Practice 268
17.10.7 Exercise 269
17.11 Force-Field Parameters I: Developing a Force Field for Cobalt(III) Hexaamines \u2013 Normal Bond Distances 269
17.11.1 Theory 269
17.11.2 Practice 272
17.11.3 Exercise 273
17.12 Force-Field Parameters II: Refining the New Force Field \u2013 Very Short Bond Distances 274
17.12.1 Theory 274
17.12.2 Practice 275
17.12.3 Exercise 276
17.13 Force-Field Parameters III: Refining the New Force Field \u2013 Very Long Bond Distances 277
17.13.1 Theory 277
17.13.2 Practice 277
17.13.3 Exercise 279
17.13.4 Exercise 279
17.14 Force-Field Parameters IV: Comparison of Isomer Distributions Using Various Cobalt(III) Amine Force Fields 280
17.14.1 Theory 280
17.14.2 Practice 281
17.14.3 Exercise 284
17.15 Force-Field Parameters V: Parameterizing a New Potential \u2013 The Tetrahedral Twist of Four-Coordinate Compounds 284
17.15.1 Theory 284
17.15.2 Practice 286
17.15.3 Exercise 287
17.16 Using Constraints to Compute Energy Barriers 287
17.16.1 Theory 287
17.16.2 Practice 288
17.16.3 Exercise 290
17.17 Using Constraints to Compute Macrocyclic Ligand Hole Sizes 290
17.17.1 Theory 290
17.17.2 Practice 293
17.17.3 Exercise 297
17.18 Cavity Sizes of Unsymmetrical Ligands 298
17.18.1 Theory 298
17.18.2 Practice 299
17.18.3 Exercise 300
17.19 Using Strain Energies to Compute Reduction Potentials of Coordination Compounds 300
17.19.1 Theory 300
17.19.2 Practice 303
17.19.3 Exercise 305
17.20 Using Force-Field Calculations with NMR Data 306
17.20.1 Theory 306
17.20.2 Practice 306
17.20.3 Exercise 308
17.21 Optimizing Structures with Rigid Groups 308
17.21.1 Theory 308
17.21.2 Practice 309
17.21.3 Exercise 310
Appendix 1 Glossary 311
Appendix 2 Fundamental Constants, Units, and Conversion Factors 315
A2.1 Constants 315
A2.2 Basic SI Units 315
A2.3 Derived Units and Conversion Factors 316
A2.4 Energy Units in Molecular Mechanics Calculations 316
Appendix 3 Software and Force Fields 317
Appendix 4 Books on Molecular Modeling and Reviews on Inorganic Molecular Modeling 319
A4.1 List of Books on Molecular Modeling 319
A4.2 List of Reviews in the Field of Inorganic Molecular Modeling 320
A4.3 List of Publications on the Momec Force Field 322
References 323
Index 341