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
2.3.5 QSAR ......................................... 17
3 Parameterization, Approximations and Limitations
of Molecular Mechanics ..................................... 19
3.1 Concepts ............................................. 19
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 ................................................ 62
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 Making Use of Experimental Data ...................... 73
6 Conclusions ................................................ 75
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
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
12.2 The trans 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 Conclusions ......................................... 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 Conclusions ......................................... 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 МотесЗ 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 Importing 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
17.10.5 Theory ...................................... 249
17.10.5.1 Electrostatic Interactions ....... 249
17.10.6 Practice .................................... 250
17.10.7 Exercise .................................... 251
17.11 Force-Field Parameters I: Developing a Force Field
for Cobalt(III) Hexaamines - Normal Bond
Distances ........................................... 251
17.11.1 Theory ...................................... 251
17.11.2 Practice .................................... 254
17.11.3 Exercise .................................... 255
17.12 Force-Field Parameters II: Refining the New Force
Field - Very Short Bond Distances ................... 256
17.12.1 Theory ...................................... 256
17.12.2 Practice .................................... 257
17.12.3 Exercise .................................... 258
17.13 Force-Field Parameters III: Refining the New Force
Field - Very Long Bond Distances .................... 259
17.13.1 Theory ...................................... 259
17.13.2 Practice .................................... 259
17.13.3 Exercise .................................... 261
17.13.4 Exercise .................................... 261
17.14 Force-Field Parameters IV: Comparison of Isomer
Distributions Using Various Cobalt(III) Amine
Force Fields ........................................ 262
17.14.1 Theory ...................................... 262
17.14.2 Practice .................................... 263
17.14.3 Exercise .................................... 266
17.15 Force-Field Parameters V: Parameterizing a New
Potential - The Terrahedral Twist of Four-
Coordinate Compounds ................................ 266
17.15.1 Theory ...................................... 266
17.15.2 Practice .................................... 268
17.15.3 Exercise .................................... 269
17.16 Using Constraints to Compute Energy Barriers ........ 269
17.16.1 Theory ...................................... 269
17.16.2 Practice .................................... 270
17.16.3 Exercise .................................... 272
17.17 Using Constraints to Compute Macrocyclic Ligand
Hole Sizes .......................................... 272
17.17.1 Theory ...................................... 272
17.17.2 Practice .................................... 275
17.17.3 Exercise .................................... 279
17.18 Cavity Sizes of Unsymmetrical Ligands ............... 280
17.18.1 Theory ...................................... 280
17.18.2 Practice .................................... 281
17.18.3 Exercise .................................... 282
17.19 Using Strain Energies to Compute Reduction
Potentials of Coordination Compounds ................ 282
17.19.1 Theory ...................................... 282
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
norganic Molecular Modeling ............................... 301
A4.1 List of Books on Molecular Modeling ................. 301
A4.2 List of Reviews in the Field of Inorganic
Molecular Modeling .................................. 302
A4.3 List of Publications on the Momec Force Field ....... 304
References .................................................... 305
Index ......................................................... 323
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