Language: English
Pages: 366
Part 2 Theory and Methods......Page 1
All rights reserved......Page 2
Who Should Read this Guide?......Page 17
Annotated Bibliography......Page 18
Practical Guide......Page 21
What is Computational Chemistry?......Page 23
Investigating the Reactivity of Molecules......Page 24
Evaluating Chemical Pathways and Mechanisms......Page 25
Studying the Dynamic Behavior of Molecules......Page 26
Exploring Potential Energy Surfaces......Page 27
Complexity of Potential Energy Surfaces......Page 30
Geometry Optimization......Page 32
Transition State Search......Page 33
Langevin Dynamics......Page 34
Monte Carlo Simulations......Page 35
Molecular Mechanics......Page 37
Bonds and Angles......Page 39
Torsions......Page 41
van der Waals Interactions and Hydrogen Bonding......Page 42
Electrostatic Potential......Page 43
United versus All Atom Force Fields......Page 44
Cutoffs......Page 45
Quantum Mechanics......Page 47
Calculating Electronic Potential Energy......Page 48
Exclusion Principle......Page 50
Simplified Wave Functions......Page 52
Configuration Interaction......Page 53
Møller-Plesset Perturbation Theory......Page 56
Orbital Occupancy......Page 57
Atomic Orbitals and Their Interactions......Page 58
SCF Technique......Page 59
RHF and UHF......Page 60
Multiplicity Considerations......Page 61
RHF Half-Electron Technique......Page 62
SCF Convergence......Page 63
Calculation Results......Page 64
Quantitative Results......Page 65
Single Point Calculations......Page 67
Total Spin Density......Page 68
Examples of Single Point Calculations......Page 69
Geometry Optimizations......Page 73
Steepest Descent......Page 74
Conjugate Gradient......Page 75
Setting Convergence Criteria......Page 76
Examples of Geometry Optimizations......Page 77
Solvation and Periodic Boundary Conditions......Page 78
2. Characterize a potential energy surface for a c.........Page 81
Eigenvector Following......Page 82
Synchronous Transit......Page 83
Molecular Dynamics......Page 85
Integration Algorithm......Page 86
Conservation of Energy......Page 87
Temperature Control......Page 88
Initial Conditions and Heating......Page 89
Equilibration and Data Collection......Page 90
Collecting Data......Page 91
Examples of Molecular Dynamics Simulations......Page 92
Constant Temperature versus Constant Energy......Page 93
Quenched Dynamics......Page 94
Randomization During Molecular Dynamics......Page 95
When is Conformational Space Adequately Sampled?......Page 96
Using Geometric Restraints......Page 97
Limiting Conformational Changes during High Temper.........Page 98
Freezing Part of a System......Page 99
Choice of Dielectric Constant......Page 100
Collecting Averages from Simulations......Page 101
9. Calculate the ratio.......Page 102
Conformational Searches......Page 103
Simulation or Run Time......Page 104
Step Size......Page 105
Bond Breaking......Page 106
Langevin Dynamics......Page 107
Integration Algorithm......Page 108
Time Step......Page 109
Friction coefficient......Page 110
Introduction......Page 111
Background and Method......Page 112
Temperature......Page 113
Equilibration and Statistical Averaging......Page 114
Heating and Cooling......Page 115
MM+......Page 117
Dielectric Function......Page 119
Nonbonded Cutoffs......Page 120
Restraints......Page 121
OPLS......Page 122
Obtaining a Starting Structure......Page 123
Calculating Part of a Molecular System......Page 124
Choosing a Basis Set......Page 125
Charge and Spin Multiplicity......Page 127
Convergence Acceleration......Page 128
Two-electron Integral Cutoff......Page 129
Raffenetti Two-Electron Integral Format......Page 130
Number of d Orbitals......Page 131
Ghost-Atoms......Page 132
Hückel Constant......Page 133
Convergence Criteria......Page 134
Configuration Interaction......Page 135
Types of Calculations......Page 136
Single Point Calculations and CI......Page 137
Transition State Search......Page 138
Energy Conservation in Molecular Dynamics Calculat.........Page 139
Vibrational Spectrum......Page 140
Extended Hückel Method......Page 141
Defining Electron-Electron Interactions......Page 142
CNDO, INDO, MINDO/3, ZINDO/1, and ZINDO/S Methods......Page 143
Parameterization......Page 144
Energies of Molecules......Page 146
Geometries of Molecules......Page 148
Energies of Transition States......Page 149
Dipole Moments......Page 150
Electrostatic Potential......Page 151
Atomic Charges......Page 153
Chemical Reactivity......Page 154
Atomic Charges and Reactivity......Page 156
Frontier Molecular Orbitals......Page 157
Vibrational Analysis and Infrared Spectroscopy......Page 159
Experimental Characteristic IR Fundamental Frequen.........Page 160
UV-visible Spectra......Page 163
Extended Hückel......Page 164
MINDO/3......Page 165
PM3......Page 166
ZINDO/S......Page 167
Further Reading......Page 168
Theory and Methods......Page 169
HyperChem Architecture......Page 171
The Back Ends......Page 172
HyperChem Philosophy......Page 173
Potential Energy Surfaces......Page 174
Single Point......Page 176
The Born-Oppenheimer Approximation......Page 177
The Hamiltonian of a Collection of Nuclei and Elec.........Page 178
The Nuclear Hamiltonian......Page 179
Molecular Mechanics versus Quantum Mechanics......Page 180
Classical Mechanics on a Potential Energy Surface......Page 181
Force-Energy Generators......Page 182
Molecular Mechanics......Page 183
Background......Page 184
Definition of Atom Type......Page 185
The Typing Rules......Page 186
Redefining or Adding Types......Page 188
Force Fields......Page 189
Energetic Terms in the Potential......Page 190
Dihedrals......Page 191
van der Waals......Page 192
Hydrogen Bonding......Page 195
Effective Dielectric Constants......Page 196
Cutoffs......Page 197
MM+......Page 198
Bond Stretching......Page 199
Bond Dipoles......Page 200
Angle Bending......Page 201
Out-of-Plane Bending......Page 202
van der Waals......Page 203
AMBER......Page 204
Dihedrals......Page 205
Electrostatic......Page 206
OPLS......Page 207
Electrostatic......Page 208
Bond Stretching......Page 209
Improper Dihedrals......Page 210
van der Waals......Page 211
Parameter Sets......Page 212
Modifying Existing Parameter Sets......Page 213
Creating New Parameter Sets......Page 214
Chem.ini or Registry Setup of Force Field Options......Page 215
Periodic Boundary Conditions and Solvent......Page 216
The Periodic Boundary Conditions......Page 217
Details of Solvation Methodology......Page 218
2. Use Restraints in the Setup menu to bring up th.........Page 219
The Default MM+ Force Field......Page 220
The Wild Card Approach......Page 221
The Default Force Field......Page 222
1. If the number of valence electrons is 0 or 8, t.........Page 223
12. If the number of electrons is 6 (O, S, etc.), .........Page 224
Bond Stretching......Page 225
Parameters for Butadiene and Related Molecules......Page 226
Torsions......Page 227
2. Aromatic bonds (as in benzene) have a two-fold .........Page 228
van der Waals......Page 229
Quantum Mechanics......Page 231
Background......Page 232
Approximate Solutions of the Schrödinger equation......Page 233
Charge and Multiplicity......Page 234
Molecular Orbitals......Page 235
Orbital Energy Diagrams......Page 236
The MO-LCAO Approximation......Page 237
The Matrix equations for the Molecular Orbitals......Page 238
Solving for the Molecular Orbitals......Page 239
1. Guess the position of each electron, that is, y.........Page 240
The Roothaan equations......Page 241
Spin Pairing......Page 242
Pople-Nesbet Unrestricted equations......Page 243
Convergence......Page 245
Spin Pairing—Restricted or Unrestricted?......Page 246
Electronic States......Page 248
4. Request configuration interaction, if you want .........Page 250
Configuration Interaction......Page 251
MP2 Correlation Energy......Page 252
The Neglect of Differential Overlap Approximation......Page 254
Contour Plots......Page 256
Total Electron Density......Page 257
Orbital Plots......Page 259
Electrostatic Potential......Page 260
Choosing the Classical–Quantum Boundary......Page 262
Capping Atoms and their Parameters......Page 264
Supported Methods......Page 266
Ab Initio Method......Page 267
Normalized Primitive Gaussian Functions......Page 269
Minimal Basis Sets: STO-3G......Page 270
Split-Valence Basis Sets......Page 273
Polarized Basis Sets......Page 276
Two-Electron Integrals......Page 278
Regular Integral Format......Page 279
Raffenetti Integral Format......Page 280
Direct SCF Calculation......Page 281
Projected CNDO/INDO......Page 282
Ghost-Atoms......Page 283
Basic Method......Page 284
Valence Atomic Orbitals......Page 285
Hamiltonian Matrix Elements......Page 286
Mixed Model......Page 288
The CNDO equations......Page 289
Mixed Model (CNDO and INDO)......Page 292
Exchange Phenomena......Page 293
Differences Between INDO and CNDO......Page 294
Spin Interactions in INDO......Page 295
MINDO/3......Page 296
One-Center One-Electron Integral Hmm......Page 297
One-Center Two-Electron Integral......Page 298
Mixed Model......Page 299
MNDO......Page 300
Two-Center Two-Electron Integrals......Page 302
One-Center One-Electron Integral Hmm......Page 305
One-Center Two-Electron Integrals......Page 306
Core-Core Repulsion Integrals......Page 307
AM1 and PM3......Page 308
ZINDO/1......Page 310
Mixed Model......Page 311
Mixed Model......Page 312
Single Points on a Potential Energy Surface......Page 315
Local Minima on a Potential Energy Surface......Page 317
Unconstrained Geometry Optimization......Page 318
Steepest Descent......Page 319
Conjugate Gradient Methods......Page 320
Fletcher-Reeves......Page 321
Block Diagonal Newton-Raphson......Page 322
Transition Structures on a Potential Energy Surfac.........Page 323
Eigenvector Following Method......Page 324
Synchronous Transit Method......Page 325
Temperature......Page 326
Leap-frog Algorithm......Page 327
Random Velocities or Restart Velocities......Page 328
The Basic Phases of a Trajectory......Page 329
Heating and Cooling......Page 330
Collecting Data......Page 332
Free Dynamics or Constant Temperature Dynamics......Page 333
The Snapshot Collection Period......Page 334
Averaging Energetic and Structural Data......Page 335
Averaging Energetic Values......Page 336
Deviations from the Average......Page 337
The CSV File......Page 338
Obtaining and Understanding MD Graphs......Page 339
Collecting Trajectory for Subsequent Playback......Page 340
Creating a Snapshot (SNP) file......Page 341
Reading a (HIN, SNP) File for Playback......Page 342
Simple Reactions on a Potential Energy Surface......Page 343
Trajectory Analysis......Page 344
Setting Initial Coordinates and Velocities......Page 345
RHF/UHF Considerations......Page 346
UV Visible Spectroscopy......Page 347
Vibrational Calculation......Page 348
Normal Coordinate Analysis......Page 349
Infrared Absorption......Page 352
Acknowledgments......Page 355
Index......Page 357
