"**" atom type, 178
10-12 potential, 24
1-4 electrostatic interactions, 86
1-4 interactions, 154, 168
1-4 van der Waals interactions, 86
6-12 function, 24
6-12 potential, 148

A

absolute energy, 20
absorption, infrared, 283
acceleration, convergence, 45, 203
accuracy
atomic charges, 109
dipole moments, 106
heats of formation, 102
proton affinities, 104
rotational barriers, 105
UV-visible spectra, 119
vibrational frequencies, 115
activation energy, 105
affinities, proton, 104
All Atom force fields, 26
all atoms, 142, 161, 166
alpha electrons, 35
alpha spins, 42
AM1, 92, 99, 122, 209, 244 to 246
AMBER, 83, 88, 140, 161
angle bending, 146, 157, 162, 166, 184
angle bending, sextic, 157
anharmonicity, 115
annealing time, molecular dynamics, 81
annealing, simulated, 71, 276
annealing, trajectory, 262
anti-parallel spins, 228
architecture, HyperChem, 127
atom types, 140, 141
atom types, new or changed, 144
atom velocities, 65
atomic charges, 109, 156
atomic mass, 142
atoms, fixed, 75
atoms, unknown type, 178
Aufbau principle, 38, 41
Austin Model 1 See AM1
averages, molecular dynamics results, 77
averaging, dynamics data, 268
averaging, dynamics, deviations, 271

B

back end, 127
barrier, rotational, 105
barriers, potential, 74
barriers, reaction, 30
basis set, 40
bath relaxation constant, 64
Beer-Lambert Law, 286
beta electrons, 35
beta spins, 42
bibliography, computational chemistry, 2
binding energy, 102
BIO+, 83, 140, 165
biradicals, 43
black box - not, 129
block diagonal method, 56
block diagonal Newton-Raphson optimization, 258
Boltzmann distribution, 260
bond angle bending, 147
bond angles, 21
bond breaking, 45
bond breaking/formation, simulation, 82
bond dipoles, 85, 156
bond dissociation, 35
bond formation and breaking, 20
bond stretch, 146
bond stretching, 147, 155, 161, 166, 181
bonded neighbors, 141
bonding interactions, 146
bonds, 21
Born-Oppenheimer approximation, 11, 30, 133
boundary conditions, periodic, theory, 174
breaking bonds, simulation, 82
Brillouin's Theorem, 37
butadiene, modeling, 183

C

calculation types, 16
calculations, mixed mode, 215
canonical ensemble, 64
capping atoms, 216, 217 to 219
charge density, 106
charge, formal, 141
charge-charge interaction, 165
charges, atomic, 109, 156
charges, point, 85
CHARMM, 83, 88, 165
chem.rul, 142
chemical environment, 141
chemical equilibrium, 103
chemical reactions, 30, 277 to 280
chemical reactivity, 110
CI, 206
clamped-nuclei approximation, 133
classical mechanics, 137
classical trajectory analysis, 277
closed-shell singlet ground states, 36
CNDO, 92, 99, 120, 209, 212, 224 to 228
CNDO mixed model, 227
comma-separated values file, 271
Complete Neglect of Differential Overlap (CNDO), 209
computational modules, 127
Configuration Interaction (CI), 36, 206
conformational searching, 70, 79
conjugate gradient, 55
conjugate gradient optimization, 94, 256
conservation, energy, 63, 95
constant energy, 78
constant temperature, 64, 79
constant temperature/energy, 69
contour plots, 213
convergence, 202
convergence acceleration, 45
convergence criteria, 56
convergence, SCF, 45
cooling time, molecular dynamics, 81
cooling, dynamics, 65
cooling, trajectory, 262
core orbitals, 40
correlation energy, 36
coulomb field, external, 215
covalent radii, 182
CSV file, 271
cubic stretch, 140, 155
cutoffs, nonbonded, 59, 86, 153
cutoffs, nonbonded potential, 27
cycles, optimization, 56

D

d Orbitals, H|ckel method, 91
DBF files, parameters, 169
default force field, 179
default MM+ force field, 177
default orbital exponents, table, 221
default scheme, 154
degenerate state, 37
density, charge, 106
density, electron, 48
density, spin, 48
dielectric constant, 25, 76, 152
dielectric constant, distance dependent, 152
dielectric functions, 85
dielectric permittivity, 152
dihedral angle, 159, 162, 166
dihedral angle rotation, 146
dihedral angles, 147, 184
dihedral potential, 23
dihedrals, improper, 148
DIIS convergence accelerator, 203
dipole moment, 48, 106, 209, 227
dipole, oscillating electric, 283
dipole, transition, 283
dipole-dipole interactions, 151
dipoles, bond, 85, 156
Direct Inversion in the Iterative Subspace (DIIS), 45, 203
dispersion forces, 146
dissociation, bond, 35, 45
docking molecules, 75
doublet, 192, 205
doublet open-shell ground states, 36
Dreiding force field, 179
dynamics data, averages, 266
dynamics results file, 271
dynamics sampling interval, 72
dynamics, molecular, 61
dynamics, periods, 65
dynamics, quenched, 70

E

EHT, 119, 219 to 224
electron density, 48, 211
electron lone pairs, 164
electron spin resonance (ESR), 213
electronic density, 94
electronic spectra, 37
electronic spectrum, 96
electronic states, 205
electrons, alpha and beta, 35
electrostatic interactions, 85, 146, 151, 163, 165, 168, 185
electrostatic potential, 25, 48, 94, 107, 214 to 215
energy barriers, 74
energy conservation, 63, 95
energy, activation, 105
energy, binding, 102
energy, constant, 69, 78
ensemble averaging, dynamics, 260
ensemble, isokinetic vs. isothermal, 64
enthalpies, 20
enthalpy of formation, 102
environment, chemical, 141
equilibration time, molecular dynamics, 80
equilibration, molecular dynamics, 66
equilibration, trajectory, 262
equilibrium, chemical, 103
Ergodic Hypothesis, 260
ESR, 213
exchange integrals, one-center, 229
exchange phenomena, 228
exchange repulsion, 35, 146
excited singlet states, 36
excited state, 205
Exclusion Principle, Pauli, 32
Extend to sp3, 216
Extended H|ckel method, 32, 97
Extended H|ckel method, options, 90
Extended H|ckel Theory (EHT), 119, 192, 219 to 224
external coulomb field, 215

F

file, CSV, 271
file, dynamics results, 271
files, snapshot, 274 to 276
fixed atoms, 75
Fletcher-Reeves, 55
Fletcher-Reeves optimization, 257
force constants, units, 155
force field options, set up, 171
force field parameters, 140
force field selection, 83
force fields, 19
force fields, distinguishing features, 83
force fields, limitations, 139
formal charge, 141
formation, heat of, 102
forming bonds, simulation, 82
free radicals, 205
frequency, dynamics sampling, 72
front end, 127
Frontier molecular orbitals, 112
Frontier Orbital theory, 112
Frontier orbitals, 39
frozen atoms, 75

G

geminal interactions, 146
geometric restraints, 73
geometry optimizations, 16, 53, 104
geometry, molecular, 38
global minima, 276
global minimum, 253
gradient, RMS, 56
graphical user interface, 127
ground state, 205

H

half-electron excited singlet states, 36
half-electron method, 206
half-electron technique, 44
Hamiltonian, 134, 190
electronic, 135
exact, 134
nuclear, 135
Hamiltonian matrix elements, 222
hard nucleophiles and electrophiles, 112
harmonic approximation, 115
harmonic frequencies, 95
harmonic oscillator, 19
harmonic potential, 22
Hartree-Fock, 35, 197
Hartree-Fock approximation, 98
heat of formation, 102
heating time, molecular dynamics, 80
heating, dynamics, 65
heating, trajectory, 262
Hessian matrix, 95
HOMO, 113, 194
Hooke's law, 19
H|ckel constant, 90, 223
hybridization, 141, 179
hydrogen bond potential, 24
hydrogen bonding, 146, 152, 163
hydrogen bonding term, 169
HyperChem architecture, 127
hyperconjugation, mixed mode calculations, 218
HyperMM+, HyperNewton, HyperEHT, HyperNDO, HyperGauss, 128

I

improper dihedrals, 148, 162, 167
independent-electron approximation, 192
independent-electron method, 220
INDO, 92, 99, 121, 209, 212, 228 to 231
INDO mixed model, 227
infrared absorption, 283
Infrared frequencies, characteristic, 116
infrared spectroscopy, 115
infrared spectrum, negative frequencies, 115
initial conditions, dynamics, 260
interactions, bonding, 146
interactions, electrostatic, 146
interactions, nonbonding, 146
Intermediate Neglect of Differential Overlap (INDO), 209
intermediates, 30
intermediates, potential, 103
interval, dynamics sampling, 72
ionic reactivity, 112
ionization energy, 106
ionization potential, 38
isokinetic energy ensemble, 64
isosurfaces, 213
isothermal ensemble, 64

K

Klopman-Salem equation, 111
Koopmans' theorem, 106

L

LCAO, 195
LCAO-MO, 39
leap-frog algorithm, 62, 261
Lennard-Jones function, 24
Lennard-Jones potential, 148, 160
Linear Combination of Atomic Orbitals-Molecular Orbital, 39
local minima, 253
London dispersion forces, 37
lone pairs, 164
lowest state, 205
LUMO, 113, 194

M

mass, atomic, 142
mechanisms, reaction, 103
microcanonical ensemble, 64
Microstate CI Method, 37
microstates, 207
MINDO/3, 92, 99, 121, 209, 212, 231 to 236
minima, global, 276
minima, local, 253
minimizations, geometry, 53
minimum, global, 253
mixed mode calculations, 215
mixed model, CNDO and INDO, 227
mixed model, MINDO/3, 235
mixed model, MNDO, AM1, and PM3, 244
MM+, 84, 140, 154
MM2, 88, 154
MM2(1977), 84
MNDO, 92, 99, 121, 209, 236 to 244
Modified Intermediate Neglect of Differential Overlap See MINDO/3
modifying parameters, 170
MO-LCAO approximation, 195
molecular dynamics, 17, 61, 95, 259 to 276
Molecular dynamics calculations, 77
molecular dynamics equilibration, 66
molecular geometry, 38
molecular mechanics, 19, 139
molecular mechanics, type selection, 83
Morse function, 22
Mulliken approximation, 223
Mulliken atomic charges, 109
multiplicity, 192, 205
multiplicity, spin, 42

N

NDDO, 99, 209
NDO, 32, 208 to 209
NDO methods, 98
NDO methods, options, 91
negative frequencies, 115
Neglect of Diatomic Differential Overlap (NDDO), 99, 209
Neglect of Differential Overlap (NDO), 32, 98, 208 to 209
neighbors, bonded, 141
Newton-Raphson, 56
Newton-Raphson optimization, 258
next lowest state, 205
NOE data, 74
nonbonded cutoffs, 59, 86
non-bonded interactions, 24
nonbonded interactions, 146
nonbonded potential, 27
Normal Coordinate Analysis, 280
normal modes, vibration, 95
Nuclear Overhauser Effect (NOE), 74

O

occupancy, orbital, 38
one-center exchange integrals, 229
OPLS, 83, 88, 140, 164
optimization cycles, 56
optimization methods, 255 to 259
optimization termination, 56
optimizations, structural, 53, 104
options, force field, set up, 171
Orbital Criterion, 37
orbital energy diagrams, 194
orbital exponents, default, table, 221
orbital occupancy, 38
orbital plots, 213
oscillating electric dipole, 283
out-of-plane bending, 159
out-of-plane bends, 184
overlap weighting factors, ZINDO, 247

P

parallel spins, 228
parameter sets, 169
parameter sets, compiling, 171
parameter sets, new, 171
parameters, changed molecular mechanics, 145
parameters, default, 154
parameters, force field, 140
parameters, missing, 178
parameters, modifying, 170
parameters, wild-card approach, 178
Pauli Exclusion Principle, 32
period, dynamics averaging, 268
period, dynamics data collection, 267
period, dynamics sampling, 72
period, dynamics screen refresh, 268
period, dynamics snapshot, 268
periodic boundary conditions, 58, 173
periodic boundary conditions, theory, 174
permittivity, dielectric, 152
phases, trajectory, 262
planar molecules, 254
PM3, 92, 99, 122, 209, 244 to 246
point charges, 85, 215
Polak-Ribiere, 55
Polak-Ribiere optimization, 258
polarizability, 151
Pople-Nesbet equations, 200
potential
angle, 21
electrostatic, 25, 48
harmonic, 22
Morse, 22
non-bonded, 24
nonbonded, 27
torsional, 23
potential energy surfaces, 11, 12, 130
potential intermediates, 103
potential switching function, 27
potential, electrostatic, 107
potential, shifting, 28
products, reaction, 110
proton affinities, 104
pseudo-halogens, 217 to 219

Q

quadratic stretch, 140, 155
quantum mechanics
semi-empirical, 29
quartet, 205
quenched dynamics, 70

R

radicals, free, 205
random velocities, 262
reaction barriers, 30
reaction coordinate, 14, 30, 111
reaction mechanisms, 103
reaction products, 110
reactions, chemical, 277 to 280
reactivity, chemical, 110
reactivity, ionic, 112
relaxation constant, bath, 64
repulsion, exchange, 146
resonance integrals, 247
restart velocities, 262
restraints, 87
restraints, structural, 73
restraints, theory, 175
Restricted Hartree-Fock (RHF), 35, 203 to 207
RHF, 35, 42, 200, 203 to 207
RHF half-electron technique, 44
RMS Gradient, 252
RMS gradient, 56
Roothaan equations, 198
root-mean-square gradient, 56
rotational barriers, 105
rules, atom typing, 142
running, trajectory, 262

S

saddle points, 30
sampling interval, 72
SCF, 36, 197
SCF convergence, 45
SCF Technique, 40
Schrvdinger equation, 11, 136, 190
second order optimizer, 56
Self-Consistent Field (SCF), 36, 197
semi-empirical method, selection, 100, 119
semi-empirical quantum mechanics, 29
sextic angle bending, 157
shifted function, 86
shifting function, 153
shifting potential, 28
simulated annealing, 71, 276
single point calculation, 16, 47, 251
single point calculations, 94
singlet, 192, 205
singlet ground states, 36
singlet molecules, 35
singlet-triplet splittings, 37
Slater Type Orbitals (STO), 39
Slater-Condon parameters, 230
snapshot files, 274 to 276
snapshot, dynamics period, 268
soft electrophiles and nucleophiles, 112
solute temperature, 67
solute-solute interactions, 58
solvation, 58
solvent effects, 58, 173
solvent temperature, 67
spin couplings, 37
spin density, 48, 94, 212
spin interactions, 230
spin multiplicity, 42
spin pairing, 199
spin state, 192, 205
spins, parallel or anti-parallel, 228
spins, unpaired, 35
splittings, singlet-triplet, 37
state, excited, 205
state, lowest, 205
static field, classical, 215
statistical mechanical averages, dynamics, 261
steepest descent, 54
steepest descent optimization, 94, 255
step size, molecular dynamics, 81
STO, 39
stretch-bend cross term, 84
stretch-bend interactions, 158, 184
structural optimizations, 104
structural restraints, 73
switching function, 86, 153
switching function, potential, 27
symmetrical systems, 37

T

temperature regulation, 63
temperature, constant, 64, 69, 79
temperature, constant dynamics, 264, 266
temperature, dynamics, 259
temperature, reaction simulation, 279
temperature, solvent, 67
termination condition, optimization, 56
time step, trajectory, 263
TIP3P water model, 58
torsional angle rotation, 146
torsional angles, 147
torsional energy, 159, 162, 166, 184
torsional potential, 23
torsions, improper, 148
total electron density, 48
total spin density, 48
trajectory phases, 262
trajectory, classical, 277
transition dipole, 283
transition states, 30, 105
triplet, 192, 205
triplet ground states, 43
triplet open-shell ground states, 36
txt files, parameters, 169
types, atom, 140, 141
typing rules, atom, 142

U

UHF, 35, 42, 200, 203 to 207
United Atom force fields, 26
united atoms, 142, 161, 164, 165
units, force constants, 155
unpaired spins, 35
Unrestricted Hartree-Fock (UHF), 35, 203 to 207
Urey-Bradley term, 84
user interface, 127
UV-visible spectra, 37, 96
computing, 285
theory, 285 to 286
UV-visible spectra, characteristic, 119

V

valence atomic orbitals, 220
Valence state ionization energy (VSIE), 222
van der Waals, 146, 148, 160, 162, 165, 167, 185
van der Waals interactions, 24
velocities, distribution of atom, 65
velocities, random distribution, 262
velocities, rescaling, 264
velocities, restart, 262
vibrational analysis, 95, 115
and IR spectroscopy, 280 to 285
vicinal interactions, 146, 154
virtual orbitals, 38, 40
VSIE, 222
VSIE values, table, 222

W

Walsh's rules, 38
water box, 175
water model, TIP3P, 58
wave function, 34
wild-card approach, parameters, 178
Woodward-Hoffmann rules, 38

Z

ZDO, 224
zero differential overlap (ZDO), 224
ZINDO/1, 92, 99, 122, 209, 212, 246 to 248
ZINDO/S, 92, 99, 123, 209, 212, 247 to 249