REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 14 (2000)

The numbers following each term refer to the pages on which it is mentioned. Computer programs are denoted in boldface; databases and journals are in italics. (This document does not contain the minor corrections that were made to the proofs.)

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Ab initio calculations, 226
Ab initio charge distributions, 269
Ab initio molecular dynamics, 296
Absorption line shape, 181
Accuracy of distributed multipole electrostatic energies, 261
ACES II
, 110, 111
Acetamide, 4, 22, 24, 274
N
-Acetyl N'-methylamide, 279
N
-Acetyl N'-methylamine diglycine, 277
N
-Acetylalanine N'-methylamide, 261
Acetylene, 256, 264
N
-Acetyl-L-alanylamide, 8
N
-Acetyl-L-serinylamide, 8
Acidity, 144
Acrolein, 279
Active site, 183
Additive approximation, 234
Adsorption, 147, 186, 211
Adsorption sites, 140, 141, 147
Alanine, 122
Alanine dipeptide, 22, 24
Alanyl dipeptide, 13
Alkanes, 256, 363
Aluminophosphates, 157, 161
Aluminosilicates, 137, 157, 161, 162, 163
AMBER force field, 245, 443, 444
AMBER* (MacroModel) force field, 448
American Theory Conferences, 401
Amino acids, 8
Ammonia, 253, 262
Analytic derivatives, 34, 115
Angular momentum theory, 231
Anisotropic atom-atom potentials, 227, 234, 256, 264, 268, 270, 271, 272, 280
Anisotropic multipole moments, 269
Annihilation operators, 39, 48, 55, 60, 78
[10]Annulene, 123
Anticommutation relation, 40, 48, 55, 76
Antisymmetrization, 35, 37, 247
Argon, 226, 228, 238, 318
Aromatic compounds, 259
Aromatic heterocycles, 252
Aromatic pi-pi interactions, 251
Atlas of Protein Side-Chain Interactions, 250
Atlas of Zeolite Structure Types
, 138, 165, 175
Atom electronegativity, 153
Atom hardness, 153
Atom-atom potential method, 244
Atom-centered point charges, 2, 3, 4
Atomic charge distribution, 273
Atomic charges, 1, 2, 154, 163, 182
Atomic point charge model, 263
Atoms-in-Molecules partitioning scheme, 258
Augmented triples correction, 106
Autocorrelation functions, 376
Automobile exhaust, 150
Axilrod-Teller term, 239, 242
Axis system, 228
Azabenzene molecules, 274

Bader partitioning, 275
Bader population analyses, 3
Baker-Campbell-Hausdorff theorem, 340
Barostat, 305, 318, 323
Basis functions, 263
Basis set selection, 15
Basis set superposition errors (BSSE), 152, 208, 240, 246, 247
Basis sets, 114, 152
3-21G, 26
3-21G*, 5, 23, 162
6-31G*, 277
6-31G**, 11, 248, 261
double-zeta, 162
Bending potential, 159
Benzene, 148, 149, 251, 253, 271, 274
Beta-turns, 277
Biased thermostating, 378
BIGSTRN force field, 453
BIGSTRN3 force field, 455
BIOGRAF force field, 448
Biomolecular simulations, 245
Biorthonormality, 53
BIOSYM Technologies, Inc., 443
Biradicals, 124
Boltzmann-weighted charges, 279
Bond breaking, 123
Bond moments, 460
Bond polarizabilities, 182
Bond polarizability tensor, 183
Born-Oppenheimer approximation, 151, 189
Boundary conditions, 355, 365
Box dynamics method, 358
BOYD, R. H., Force Field, 448
Bra-state excitation operators, 52
Brenner potential, 387
Brillouin zone, 183
Brillouin's theorem, 51, 64, 68, 96, 106
Brønsted acid site, 149
Brønsted acidity, 144
Brueckner condition, 119
Brueckner coupled cluster doubles (B-CCD), 120
Brueckner determinant, 121
Brueckner methods, 34
Brueckner orbitals, 113, 119
Bulk behavior, 294
Bulk fluids, 365, 368
Bulk homogeneous conditions, 387
Bulk properties, 293, 355
Bulk transport coefficient, 369
Buried atoms, 20
Butane, 139, 271, 363
Butanol, 28
tert
-Butoxide, 22, 24, 26

C60, 389
CADPAC
, 258, 272
Calculus, v.
Cambridge Structural Database
, 250, 442
CAMM electrostatic models, 268
Canadian Symposia on Theoretical Chemistry, 401
Canonical distribution function, 383
Canonical (NVT) ensemble, 180, 302, 310, 316, 344
Carbohydrates, 273
Carbonyl bond, 4
Car-Parrinello molecular dynamics, 187, 210, 211, 214
Cartesian coordinates, 165
Catalysts, 137
Catalytic activity, 200
Catechol, 139
Cation mobility, 196
CCSD amplitude equations, 70, 88
CCSD energy equation, 67, 82
Center of mass (CoM), 176
Central cell, 166
Central force field, 156
Central multipole expansion, 257
CFF and CVFF force field, 449
CFF Rasmussen force field, 448
CFF91, 443
CFF93, 443
CFF95, 443
Chabazite, 209, 212
Characteristic relaxation time, 373
Charge density, 277
Charge density difference maps, 258
Charge distribution, 1, 2, 3, 4, 7, 8, 11, 13, 22, 154, 155, 163, 182, 227, 233, 237, 259, 269, 273, 274, 280, 460
Charge equilibration method (QEq), 155
Charge sensitivity, 12
Charge sensitivity analysis (CSA), 155, 164
Charge transfer, 228, 240, 246, 247, 249, 252, 266
Charge variability, 14
Charge-compensating cations, 148, 195
CHARMm force field, 443, 450
CHARMM force field, 245, 443, 450
CHEAT95, 450
CHELP
, 6, 7, 8, 9, 22, 23, 25, 27
CHELP-BOW
, 27, 29
CHELPG
, 7, 11, 27
CHELP-SVD
, 7, 25
Chemical bonds, 37
Chemical design, 251
Chemical intuition, 2, 14, 158, 273
Chemical potential, 152, 302
Chlorine molecule, 226, 252, 265
Class III charges, 8, 13, 22
Classical mechanics, 140
Classical properties, 299
Closed-shell atoms, 226
Cluster amplitudes, 45, 47, 53, 55, 70, 107, 111
Cluster approach, 150, 165
Cluster function, 35, 36, 38
Cluster operator diagrams, 82
Cluster operator expansion, 53
Cluster operators, 41, 47, 49, 52, 63, 78, 84, 99, 100, 116, 119
Clusters, 144, 203, 208
Colloids, 379
Combining rules, 244, 269
Commutation relations, 41
Competition effects, 253
Complementary error function, 168
Composite set of charges, 13
Computational chemistry, 401, 404
Computational problems, 116
Computer code, 343, 346, 349, 351, 353, 354, 356
Computer implementation of coupled cluster theory, 107
Computers and Chemistry
, 403
Configuration interaction (CI), 35, 42, 152
Configuration interaction with singles and doubles (CISD), 43, 44
Configurational space, 142, 147
Configuration-biased Monte Carlo, 186, 363
Configurations, 303
Confined fluids, 364, 365, 368, 371, 389
Conformation, 176, 275, 276
Conformational energies, 441
Conformational instability, 8
Conformation-dependent charge distributions, 13, 276, 278
Conformation-dependent potential, 276
Conjugate gradient method, 171
Connected cluster, 67, 92
Conservation of energy, 179, 367
Conservation of total momenta, 377
Consistent implementation of the electronegativity equalization method (CIEEM), 163, 173
Constant energy hypersurface, 298, 303
Constrained internal coordinates, 189
Constrained minimization, 172
Constrained reaction coordinate dynamics, 149
Constraint matrix, 27
Continuity, 307
Contraction theorem, 59
Contractions between operator pairs, 57
Coordinate systems, 228
Coordinates, 297
Core orbitals, 37
Correlated wavefunctions, 115
Correlation operators, 63
Couette flow, 331, 336, 337, 344, 349, 357, 358, 379
Coulombic energy, 153, 364
Coulombic interaction, 236, 255
Coulombic potentials, 158
Counterpoise procedure, 246
Coupled-cluster amplitude equation, 96
Coupled-cluster analytic second derivative, 112
Coupled-cluster (CC) methods, 33, 35, 45
Coupled-cluster diagrams, 77, 78
Coupled-cluster doubles (CCD), 33
Coupled-cluster energy, 49, 95, 97
Coupled-cluster Hamiltonian, 53, 63, 100
Coupled-cluster singles and doubles (CCSD), 34, 44
Coupled-cluster theory, 98, 115, 152
Coupled-cluster wavefunction, 70
Crack branching, 387
Crack propagation, 384
Crack simulation, 385
Creation operator strings, 78
Creation operators, 39, 48, 55, 60
Creation-annihilation operator pairs, 40
Crystal engineering, 250
Crystal field, 157
Crystal structure modeling, 245
Crystal structures, 245, 250, 251, 269
Crystallographic data, 245
Crystals, 240
Cu-exchanged zeolites, 150
Cumulative atomic multipole moments (CAMM), 258, 272
Cutoff distance, 359
Cutoff radius, 167, 168, 169, 177
Cutoff region, 169
CVFF force field, 443
Cyclophane host, 271
L-Cysteine, 22, 24

Damping, 240, 266
Database searches, 251
Davidson correction, 97
Decane, 335, 363
De-excitation operators, 50, 52
Degrees of freedom, 176
Densities of alkanes, 245
Density functional theory (DFT), 152, 209, 210
Density matrix element, 4
Design of new materials, 225
Detergents, 138
Diagrammatic techniques, 55, 77, 82, 88, 110, 119
Diatomics, 256, 260
trans
-Diazabutene, 273
Di(cyclohexylmethyl)dimethylammonium ion, 146
N
,N-Diethyl-3,5-diethylpiperidinum ions, 197
Diffusion coefficients, 148, 149, 183, 292
Diffusion constant, 364
Diffusion of adsorbates, 140, 143
Diffusion in zeolites, 148
Diffusion process, 183, 296
N,N
-Dimethylacetamide, 279
Dimethylamide, 273
Dimethylphosphate, 22, 24, 25
Dipole, 237
Dipole moment, 2, 7, 15, 116, 161, 181, 261
Dipole tensor autocorrelation function, 181
Dipole-dipole polarizability, 238
Dirac's dictum, vi
Dirac's notation, 62, 86
Direct product decomposition (DPD), 112
Disconnected wavefunction contributions, 43
Discover force field, 443, 450
Disilicic acid, 161
Dispersion, 167, 242, 244, 263, 266
Dispersion damping, 256
Dispersion energy, 238, 239, 246
Dissipative flux, 329, 334, 368
Distributed dispersion, 256
Distributed multipole analysis (DMA), 249, 258, 260, 276, 277
Distributed multipoles, 251, 255, 256
Distributed polarizabilities, 256, 263
Distributed sites, 259
Distribution function, 143, 300
Division of Computers in Chemistry of the American Chemical Society (COMP), 403
DL_POLY
, 271
DMAREL
, 271
Docking, 145, 175
DOLL's algorithm, 293
Dopamine, 13
Doubly excited states, 123
DREIDING force field, 452
Drift velocity, 368
Drug design, 250
Dynamic friction coefficient, 313
Dynamical operators, 78

ECEPP force field, 452
Effective viscosity, 362
Einstein relationship, 183
Elastic moduli, 161
Elastic scattering amplitudes, 180
Electric field, 292, 323
Electron correlation, 35, 37, 152, 263
Electron density, 152
Electron density distribution, 2
Electron fluctuations, 246
Electronegativity, 154, 173
Electronegativity equalization method (EEM), 153, 154, 163
Electron-electron interaction energy, 153
Electronic Hamiltonian, 38, 47, 53, 55, 71, 78, 88, 99, 100, 117
Electrons, 2
Electrostatic damping, 266
Electrostatic energy, 236, 249, 262
Electrostatic interactions, 154, 167, 169, 226, 255, 269, 277, 319
Electrostatic parameters, 273
Electrostatic potential derived charges, 155
Electrostatic potentials, 1, 210, 275
Embedding, 165
Empirical fitting, 244
Empirical force fields (EFF), 269, 292, 441
Empirical parameterization, 244
Energy, 266
Energy of interaction, 236
Energy minimization, 141, 142, 147, 166, 171, 212, 405
Ensemble, 300
Enthalpies of vaporization, 245
Entropy, 292, 308
EOMEA-CC method, 54 EOMIP-CC method, 54 EPEN/2 force field, 452
Equation of constraint, 173
Equation-of-motion coupled cluster (EOM-CC), 54, 107, 123
Equations of motion, 174, 175, 179, 293
Equilibration, 177
Equilibrium distribution function, 308
Equilibrium ensemble, 302
Equilibrium fluctuations, 379
Equilibrium geometry, 172, 266
Equilibrium molecular dynamics, 292, 346, 380
Equilibrium state, 308, 367
Equilibrium statistical mechanics, 296
Equilibrium time correlation function, 303, 331
Equipartition principle, 177
Ergodic trajectory, 303, 312, 315
Ergodicity principle, 174
Error in charges, 15
Ethane, 148
Ethanol, 279
Euler angles, 176, 228, 230
Evans-Morriss PUT equation, 374
Ewald summation, 167, 271, 319, 360, 364
Exact wavefunction, 43, 46
Exchange energy, 247
Exchange-correlation energy, 153
Exchange-repulsion energy, 266, 273, 240
Excimer, 239
Excitation operators, 42, 81
Excited determinants, 71
Excited states, 34, 53, 54, 123, 187
Excluded determinant, 46
Expectation value coupled cluster (XCC) method, 50
Exponential ansatz, 38, 46
Exponentiated cluster operators, 42, 46
Exposed atoms, 10
Extended coupled cluster method (ECCM), 50
Extended Lagrangian, 177, 188
External field, 292, 305, 323, 325, 355, 358, 368, 380
External heat reservoir, 177
Extra-framework cations, 157, 195

Factorization, 109
FAU zeolite, 138
Faujasite, 149, 194
Fermi resonance, 207
Fermi vacuum, 60
Fermions, 35
Feynman diagrams, 33, 54
Field-driven dynamics, 365
Fine chemical processes, 143
Finite difference, 175, 179
Fixed charge approximation, 163, 182
Fixed electrostatic model, 279
Flexible molecules, 225, 279
Flexible zeolite lattice, 148, 178
Fluctuation dissipation relations, 331
Fluctuation potential, 99
Fluorine molecule, 265
Fluid catalyst cracking, 139
Fluid density, 295
Fluid flow, 364
Fluid-fluid interactions, 369
Fluids, 292
Fluid-wall interactions, 369, 370
Fock matrix element, 71
Fock operator, 64, 117
Fock-space multireference coupled cluster theory
(FS-MRCC), 54
Force constants, 160, 161, 243, 272
Force field parameters, 161, 441
Force fields, 13, 139, 140, 142, 156, 157, 166, 174, 187, 189, 225, 241, 252, 278, 340, 405
Formamide, 11, 12, 22, 27, 230, 272, 274, 278
FORTRAN
, 356
Four-body term, 234
Fractional coordinates, 165
Fracture, 387
Framework structure, 142
Framework topologies, 137, 165
Free energy of hydration, 275
Friction, 389
Friction coefficient, 365, 366, 369, 370, 386
Frictional force, 369, 372
Fructopyranose, 8
Full coupled cluster, 43
Full configuration interaction, 43
Full-matrix second-derivative minimizer, 171
Functional group interactions, 250
Functional group replacement, 252
Furan, 252

GAMESS
, 9
Gas flows, 365
Gauche effect, 464
Gaussian
, 2, 9
Gaussian isokinetic thermostats, 373
Gaussian multipoles, 256, 262
Gaussian-type basis functions, 124
Generalized equations of motion, 323
Generalized Liouville equation, 390
Generalized valence force field (GVFF), 158
Generalized Wick's theorem, 59
Generic repulsion-dispersion parameters, 273
Geometric mean combining rule, 244
Geometry-dependent charges, 162, 163, 173
Gibb's ensemble Monte Carlo, 363
Gibb's entropy, 308
Global molecular electronegativity, 154
Global properties, 15
Global thermostat, 373
Glucose, 26
Glycerylphosphorylcholine (GPC), 13, 14, 16, 22, 24
Golub's algorithm, 21
Gordon Research Conference on Computational Chemistry, 399, 406
Gordon Research Conference on Quantitative Structure-Activity Relationships in Biology, 403
Gordon Research Conferences (GRCs), 399
Grand-canonical Monte Carlo method, 186
Grand-canonical (uVT) ensemble, 302
Green-Kubo relations, 329 331, 335, 361, 379
Grid sampling, 11
GROMOS
, 245, 452
GSLLOD equations, 336, 338

Hamiltonian diagrams, 84
Hamiltonian dynamics, 297, 344
Hamiltonian systems, 313
Hamiltonians, 38, 47, 48, 51, 53, 55, 61, 71, 78, 79, 80, 88, 99, 100, 103, 117, 151, 179, 246, 328
Hamilton's equations of motion, 297, 340
Hard-sphere repulsion, 249
Harmonic approximation, 158
Harmonic frequencies, 266
Harmonic oscillator, 298, 299, 315, 316, 317, 370
Harmonic spring, 156
Harmonic vibrational frequencies, 116
Hartree-Fock energy, 62
Hartree-Fock (HF) theory, 151
Hartree-Fock self-consistent field (SCF) procedure, 35
Hausdorff expansion, 34, 47, 48, 63, 74, 87, 100
Heat bath, 294, 305
Heat capacity, 296, 311, 312
Heat gradient, 292
Heat transfer, 295
Heats of sublimation, 245
Helium, 226
Hellmann-Feynman theorem, 189
Hermitian operators, 50
Herringbone crystal structure, 252
Hessian matrix, 162, 172
Heteroaromatics, 458
High accuracy methods, 124
High strength materials, 384
High temperature molecular dynamics, 145
Hirshfeld partitioning, 258
Histidine, 262
Hole lines, 78, 83
Hole states, 60, 78
Homogeneous flows, 362
Homogeneous methods, 293
Homo-parameters, 244
Hopping processes, 148
Host-guest interactions, 145, 186
Hybrid models, 141, 164
Hybridization state, 273
Hydrated molecules, 279
Hydration effects, 268
Hydrazine clusters, 268
Hydrodynamic boundary conditions, 364, 365
Hydrodynamics, 365, 369
Hydrogen bonding, 248, 249, 250, 252, 253, 254
Hydrogen cyanide, 249
Hydrogen fluoride, 44, 226, 249, 255
Hydrogen fluoride dimer, 259, 264, 268
Hydrogen molecule, 44
Hydrogen peroxide radical cation, 121
Hydrogen sulfide, 256, 265
Hydrogen-bonding potentials, 252
Hydroquinone, 139

Imaginary frequency, 172, 239
Importance sampling, 185
Imprinting, 145
IMPT charge transfer, 256
Incoherent scattering function, 181
Independent-particle approximation, 36
Induction, 263, 266
Induction energy, 237, 247
Industrial lubricant design, 364
Inelastic neutron scattering experiments, 181
Infrared intensities, 116, 182
Infrared spectra, 159, 181, 190, 198
Inhomogeneous differential equation, 348
Inhomogeneous environment, 387
Inhomogeneous methods, 293
Initial conditions, 184
Instantaneous dipolar fluctuations, 238
Instantaneous secondary flows, 374
Interatomic potentials, 140, 385
Intermolecular forces, 226, 242, 262, 268, 280
Intermolecular pair potential, 227, 235, 241, 243, 256
Intermolecular perturbation theory (IMPT), 247, 249, 251, 252, 266
Intermolecular potentials, 225, 241, 272, 280
Intermolecular synthons, 250
Internal coordinates, 159, 160, 166, 172, 176
Internal fractures, 385
Internal hydrogen bonds, 277
Internal pressure, 350
Internal pressure tensor, 321
International Zeolite Association (IZA), 138
Intrafragment excitations, 43
Intramolecular hydrogen bond, 279
Intrinsic errors, 273
Irreducible representations, 111
Ionic solids, 156
Irving-Kirkwood procedure, 338
Isobaric-isoenthalpic ensemble, 177
Isobaric-isothermic (NPT) ensemble, 177, 302, 317, 349, 351
Isomorphic substitution, 138, 177, 200
Isomorphous framework substitution, 143
Isomorphous substitution, 143
ISOSTAR
library, 250, 252
Isotropic atom-atom model, 233, 252
Isotropic atom-atom potentials, 227, 268, 270, 280
Isotropic cell fluctuations, 350

Jacobian, 301, 307
Journal of Computational Chemistry
, 403
Journal of Molecular Graphics
, 403
Journal of Molecular Structure
, 403

Kohn-Sham orbitals, 153
Kronecker delta functions, 40, 48, 55, 57, 62

Laboratory velocity, 334
Lactose, 27
Lagrange multipliers, 7, 27
Lagrangian, 188
Large molecules, 122
Lattice, 165, 202, 204, 205
Lattice dynamics, 171
Lattice energy, 234, 264, 269, 271
Lattice vibrations, 166
Lees-Edwards boundary condition, 360
Leibniz, G. W., v
Lennard-Jones potential, 158, 167, 241, 319, 376, 385
Levi-Civita tensor, 391
Ligand binding, 252
Linear combination of atomic orbitals molecular orbital (LCAO-MO), 3, 35, 152
Linear combination of excited determinants, 99
Linear combination of Slater determinants, 37
Linear least squares (LLS), 16, 17, 22, 23
Linear molecules, 231
Linear response coupled cluster (LR-CC), 54
Linear response theory, 323, 324, 361, 368
Linear velocity profile, 333
Link atom, 164
Liouville equation, 301, 307, 325
Liouville operator, 300, 339
Liouville's theorem, 302
Liquid flow, 364
Local correlation, 123
Local density approximation (LDA), 153
Local energy minimum, 142, 147
Local streaming velocity, 373
Localization schemes, 264
Long chain molecules, 186
Longitudinal polarizability, 183
Long-range energy terms, 239
Long-range interactions, 166
Long-time-scale studies, 385
Lookup tables, 170
LTA zeolite, 138
Lubricants, 292, 294, 361, 363, 388

Macroscopic observables, 296
Madelung sum, 167
Magic angle spinning (MAS) NMR, 209
Magnetic interactions, 239
Many-body effects, 235, 268
Many-body perturbation theory (MBPT), 34, 35, 55, 77, 85, 98
Many-electron wavefunction, 151
Martyna-Tuckerman-Klein (MTK) thermostat, 317
Material failure, 384
Matrix-based storage, 110
Maxwellian velocity distribution, 334
Mechanical piston, 305
Metals, 458
Methane, 148, 228, 265
Methanol, 9, 10, 11, 208, 211, 212, 231, 248, 251, 268, 273
Methanol-to-gasoline (MTG) process, 149, 206
Methoxonium ion, 149, 207
Methylacetate, 27
Methyl cyanide, 262, 273
N
-Methylacetamide, 13, 272, 274, 279
N
-Methylformamide, 274
Metropolis Monte Carlo method, 142, 185
MFI zeolite, 138, 199, 200, 201, 203
MFL zeolite, 199, 201, 202
Mica, 389
Microcanonical (NVE) ensemble, 176, 302
Microcanonical partition function, 303
Micropores, 137, 145
Microscopic motion, 296
Microstates, 367
Migration path, 148
Millot-Stone potential, 267
Minimal image convention, 168
Minimization, 171
Minimum imaging, 355, 356, 360
MMI force field, 443
MM2 force field, 453, 458
MM2 force field, 461
MM2+ force field, 456, 459
MM2*
(MacroModel) force field, 461
MM2AE force field, 456
MM2CARB force field, 461
MM2ERW force field, 461
MM2X force field, 461
MM3 force field, 463
MM3*
(MacroModel) force field,, 465
MM3-GE force field, 464
MM4 force field, 465
MMFF force field, 465
MMP2 force field, 459
MMX force field, 465
MOBY force field, 465
Modeling schemes, 150
Molecular crystal structures, 280
Molecular dynamics (MD), 139, 141, 168, 174, 268, 271, 291, 296, 363, 441
Molecular electrostatic potential (MEP), 1, 3, 15, 22
Molecular geometries, 116
Molecular graphics, 139
Molecular mechanics, 402, 441
Molecular mechanics force fields, 2, 157, 263
Molecular modeling, 140
Molecular orbital theory, 2, 35
Molecular properties, 33, 103
Molecular reactivity, 2
Molecular sieve, 137, 157
Molecular Simulations Inc. (MSI), 443
Molecular structure, 1
Molecular surface, 7
Molecule centered expansions, 232
Møller--Plesset (MP) perturbation theory, 100, 106, 152, 162
MOLPRO
, 110, 111
MOMEC force field, 466
Momenta, 297
Momentum transfer, 365
MOMO
, 271
Monopole charges, 4
Monopole potentials, 3
Monosaccharides, 8
Monte Carlo (MC) methods, 147, 174, 185
Monte Carlo simulations, 141, 268, 271, 441
MOR zeolite, 138
Mori-Zwanzig formalism, 369
Morse potential, 158, 252, 386
Mulliken population analysis, 2, 3, 11, 154, 258, 275
Multiconfigurational SCF (MCSCF), 123
Multipolar interactions, 167
Multipolar moments, 257
Multipole expansion, 237
Multiple minima, 172
Multireference coupled cluster (MRCC), 123
Myoglobin, 27

Navier-Stokes equation, 364
NaY zeolite, 198
Nearest-neighbor atoms, 274
NEMO method, 268
Neopentane, 22, 24, 26
Nested commutators, 47, 63
Net atomic charges, 11
Newton, I., v
Newton's equations of motion, 175, 179
Nitrate radical, 121, 122
Nitrobenzene, 257
Nitrogen dimer, 264
Nitrogen molecule, 228, 255, 256, 265
NO, 150
NO2, 121, 122
Nonadditivity, 234, 244
Nonbonded atoms, 158
Nonbonded interactions, 166
Nonbonded parameters, 245, 273
Nonbonded potential, 225
Noncentral forces, 270
Nonequilibrium ensemble, 330
Nonequilibrium field, 379
Nonequilibrium molecular dynamics (NEMD), 291, 292, 324
Nonequilibrium properties, 363
Nonequilibrium response, 379
Nonequilibrium statistical mechanics, 308, 329
Nonequilibrium steady states, 293
Nonergodicity, 315
Non-Hamiltonian dynamics, 293, 304, 305, 325
Non-Hamiltonian equations of motion, 297, 305
Non-Hamiltonian systems, 313
Normal mode analysis (NMA), 159, 172, 190
Normal modes, 191
Normal ordering, 55, 60
Normal-ordered dynamical operators, 77
Normal-ordered electron Hamiltonian, 61, 62, 78
Normal-ordered operators, 82
Normal-ordered second-quantized operators, 55
Nosé thermostat, 310
Nosé-Hoover chain (NHC), 315, 370
Nosé-Hoover equations of motion, 313, 370
Nosé-Hoover thermostat, 315, 333, 338, 344, 370, 372, 373, 375, 382
No-slip, 364
NPT ensemble, 302, 317, 322, 349, 357
Nuclear magnetic resonance (NMR), 207, 210
Nucleic acid bases, 262
Nucleic acids, 273
Numerically integrating SLLOD equations, 339
NVT dynamics, 344
NVT ensemble, 310, 330

O3, 106
O4[+] ion, 121
Observable, 155, 185
Occupation-number formalism, 34
Occupied orbitals, 36, 40, 48
Octopole, 237
One-electron wavefunctions, 35, 152, 187
One-particle excitation operators, 46
Onsager regression hypothesis, 331
Open-shell methods, 34
Open-shell molecules, 116
Open-shell perturbation theory, 107
Operator, 151, 340
Operator identities, 326
Operator products, 77
Operator strings, 58
OPLS force field, 467
Optimized potential for liquid simulation (OPLS), 13
Orbital exponent, 155
Organic molecules, 225, 241, 243, 245, 249, 256, 269, 272, 280
ORIENT
, 259, 268, 271
ORIENT3
, 271
Orientational dependence, 228, 249
Orthonormality, 53
Oscillator strength, 239
Overlap model, 256
Oxygen molecule, 120, 239

Packing motifs, 251
Pair distribution function, 180
Pairwise additive approximation, 234
Pairwise additivity, 158
Parallel computing, 385
Parameters for potential functions, 161
Particle lines, 78, 83
Particle states, 60, 78
Particle-hole formalism, 60, 77
Partition function, 311, 312, 313, 318
Path integral molecular dynamics, 316
Pauli exclusion principle, 240
PCFF force field, 443
PDQC
(Potential Derived Quantities Charge), 9, 11
Peculiar frame, 334
Peculiar momentum, 334, 357, 368, 374
PEF91L force field, 449
PEFIM force field, 449
Penetration energy, 262, 266
Penetration model, 256
Peptide charge distribution, 277
Peptide conformations, 252
Peptides, 273
Periodic boundary conditions (PBC), 166, 183, 318, 337, 355, 378
Periodicity, 151, 154, 165
Permutation operators, 76, 95, 104
Perturbation operator, 99
Perturbation theory, 235, 242, 247, 256
Petrochemical industry, 137, 149
Petrochemistry, 139, 143
Phase space, 174, 180, 184, 297, 298, 305, 306, 307, 346
Phase space compressibility, 301, 314, 319, 324
Phase space distribution function, 301, 367
Phase space probability density, 301
Phase transition, 142, 177
Phenol, 22, 24, 26, 139
Phenyl rings, 251
Phenylalanine dipeptide, 253
Physical data, 442
Physical observables, 49
Planar Couette flow, 337, 344, 349, 358, 360, 372, 379
Planar Couette geometry, 365
Plane waves basis, 209
Poincaré section, 316
Point charge approximation, 2, 155, 277
Point distribution schemes, 8
Point group symmetry, 111
Poisson bracket, 298
Polar fluids, 364
Polarizability, 161, 182, 264
Polarizability tensor autocorrelation function, 181
Polarization, 157, 244
Polarization energy, 237
Polygen, 443
Polymer, 388
Polymer flows, 365
Polymorphism, 142, 269
Polypeptide charge distribution, 275
Polypeptides, 272
Population analysis, 2
Pore-opening vibrations, 193
Post-Hartree-Fock models, 152, 246
Potential derived atomic charges, 275
Potential derived charges (PDC), 210
Potential energy function, 229
Potential energy surfaces, 123, 155, 161, 171, 172, 246, 255
Potential functions, 174
Potential model, 156, 163
Power series expansion, 50
Power spectra, 181, 192, 197
Pressure, 302
Pressure tensor, 296, 334, 368
Principal components analysis (PCA), 15
Profile-biased thermostat (PBT), 373
Profile-unbiased thermostat (PUT), 372, 373
Propagator, 326, 327, 352
Propane, 148
Protein backbone atoms, 253, 277
Protein binding energies, 252
Protein Data Bank (PDB)
, 250
Protein structure predictions, 251
Protein structures, 251
Protein-ligand binding, 268
Proteins, 271, 316
Proton affinities, 145
Proton-catalyzed reactions, 149
Proton-exchange, 212
PSI
, 110, 111
Pyrazine, 257
Pyridazine, 248, 274
Pyridine, 231, 252, 273, 274
Pyrimidine, 262, 274

q-annihilation operators, 60, 78
QCFF force field, 468
q-creation operators, 60, 78
QDGROMOS force field, 453
QMFF force field, 449
q-particle construction operators, 60
Quadrupole, 237
Quadrupolar polarizability, 238
Quantum chemistry, 33
Quantum mechanical models, 151
Quantum mechanical observable, 1, 3
Quantum mechanical region, 164
Quantum mechanics, 49, 139, 140
Quartz, 161, 167
Quasiparticle contruction operators, 60
Quasi-restricted Hartree-Fock (QRHF) orbitals, 113
Quaternions, 176

Radical cation, 116
Raman spectra, 159, 181, 190
Random point distribution, 8
Rank, 19
Rank deficiency, 17, 22, 27
Rank estimates, 24
Rank-deficient problem, 22
Rate constants, 149
RATTLE method, 176
Rayleigh-Schrödinger perturbation theory, 99, 235
Reactions, 296
Reactive bond order potential, 387
Reactive center, 164
Reciprocal space sum, 360
Redistribution of energy, 178
Reduced normal-ordered strings, 59
Redundant internal coordinates, 160
Reentrant solid phase, 378
Reference determinant, 95
Reference state, 60
Reference wavefunction, 78, 84
Repulsion-dispersion parameters, 273
Resistance to shear, 362
Resonance interactions, 239
RESP method, 24, 27
Response operators, 54
Reversible integration, 339
Reversible profile-unbiased thermostat (RPUT), 376
Rheological properties, 388
Riemannian manifold, 390
Rigid framework approach, 166
Rigid ion potential model, 156
Rigid molecule approximation, 176
Rigid zeolite framework approximation, 176
Rotation-vibration microwave spectrum, 241
Rules for diagrammatic representation, 83

Saddle point, 172
Sampling of microstates, 141
Sanibel Symposia, 401
Scattering calculations, 232
Schrödinger equation, 33, 45, 47, 95, 141, 151, 246
Scoring functions, 250
Second quantization, 33, 34, 39, 55
Second virial coefficients, 242, 266
Secondary flows, 373
Second-quantized equations, 75
Second-quantized operator strings, 119
Second-quantized operators, 40, 48, 55, 58, 60, 71
Self-consistent field (SCF), 152
Self-diffusion coefficient, 331
Semicanonical molecular orbital basis, 117
Semiempirical models, 153
SHAKE method, 176, 189
Shape selectivity, 148
SHAPES force field, 468
Shear, 364, 368, 378
Shear field, 333
Shear flow, 323, 361
Shear induced collisions, 362
Shear induced microstructure, 377
Shear motion, 294
Shear rates, 296, 324, 377
Shear thinning, 362
Shear viscosity, 292, 324, 331, 335, 369
Shell model, 156, 161, 162
Shielded Coulomb potential, 169
Shift operator, 342
Shifted-force Coulomb potential, 169
Shifted-force method, 168
Shifted-force potential, 177
Short-range terms, 264
SIBFA (sum of interaction between fragments ab-initio-computed) approach, 268, 272
Sign sequence, 88
Silica faujasite, 179, 182, 184, 192, 193, 195
Silica polymorphs, 161
Silicate structures, 159
Silicates, 157, 161, 162
Siliceous zeolites, 158
Similarity-transformed equation of motion coupled cluster (STEOM-CC), 54
Similarity-transformed Hamiltonian, 67
Similarity-transformed normal-ordered Hamiltonian, 63
Simulated annealing, 142, 147
Simulation noise, 380
Simulations, 225
Single-determinant reference, 120
Single-determinant wavefunction, 36, 78
Single-orbital cluster operators, 40
Singular value decomposition (SVD), 18, 28
Size consistency, 42, 44, 95
Size extensivity, 34, 45, 95
Size extensivity error, 97
Slater determinant, 35, 39, 151
Slater orbitals, 155
Slater-Kirkwood approximation, 239
Slater's rules, 70, 95
Slip, 364
SLLOD algorithm, 293, 362
SLLOD dynamics, 296, 339, 364, 365, 382
SLLOD equations of motion, 316, 330, 331, 335, 336, 344, 366, 379
Small-field methods, 379
Small-field nonequilibrium simulations, 380
Sodalite, 191, 209, 212
Sodalite cage, 161
Sorption of molecules, 177
Spartan
, 2
SPASIBA force field, 468
Spatial inhomogeneities, 293
Spatial symmetry, 111
SPC/E water, 332, 364
Spherical cutoff, 360
Spherical harmonic function, 231
Spherical molecules, 228, 242
Spherical tensor distributed multipoles, 272
Spherical tensor theory, 227
Spin contamination, 116
Spin factorization, 112
Spin-adapted open-shell coupled cluster wavefunctions, 117
Spin-orbital Fock operators, 62
Spin-restricted Hartree-Fock orbitals, 113
Spin-restricted open-shell B-CC theory (RB-CC), 121
Spin-restricted open-shell Hartree-Fock (ROHF), 116
Spin-restricted open-shell Hartree-Fock (ROHF) orbitals, 113
Spin-restricted open-shell Hartree-Fock (ROHF) reference functions, 99
Spin-restricted reference determinants, 116
Spin-restricted reference wavefunction, 107
Spin-restricted triple-excitation corrections, 117
Spin-unrestricted Hartree-Fock (UHF) orbitals, 113
Squalane, 363
Stacked geometries, 254
Static equilibrium properties, 304
Statistical ensembles, 297
Statistical mechanics, 185
Steady state, 292, 293
Steam, 266
Steric energy, 157, 163
Strain, 324
Strain rate tensor, 358
Streaming velocities, 377
Stress autocorrelation function, 363
Stress tensor, 324
Stress-stress autocorrelation function, 332
String phase orientations, 378
String phases, 372, 377
Structural properties, 296
Structural transformations, 296
Structure directing agents, 145
Subtraction method, 379, 380
Supermolecule calculations, 246, 247
Supermolecules, 247
Supramolecular complexes, 254
Surface area, 23
Surface force apparatus (SFA), 389
Surfaces, 294, 460
Symmetric spin orbital basis, 118
Symmetry orbital (SO), 114
Symmetry-adapted cluster configuration interaction (SAC-CI), 54
Symmetry-adapted perturbation theories, 247
Symmetry-breaking orbital instabilities, 120
Symposium on Molecular Mechanics, 402
Synthetic fuels, 143
Systematic potential approach, 255, 266

(T) correction, 34, 103, 117
Taper functions, 169, 170, 177
Taylor series expansion, 153, 156, 163, 171, 182, 342
Teflon, 388
Temperature, 178, 296, 302
Templates in zeolites, 145
Tensor properties, 231
Test particle model, 256, 265
Tetrabutylammonium (TBA) ions, 197, 200, 201, 202
Tetracosane, 363
Tetrahydrofuran, 252
Tetrapropylammonium (TPA) ions, 197, 200
Tetrazine, 244, 274
Thermal bath, 177
Thermal fluctuations, 373
Thermal velocity, 334
Thermodynamic quantities, 296
Thermostats, 295, 305, 318, 323, 334
Three-body term, 234, 242
Three-orbital cluster functions, 38
Through-space polarization, 276
Time correlation functions, 183, 296, 304, 329
Time dependence, 340
Time scale, 181, 293, 313, 318, 319, 377
Time-dependent boundary conditions, 337
Time-dependent external field, 308
Time-dependent Liouvillian, 325
Time-dependent phase space compressibility, 308
Time-independent boundary conditions, 367
Time-reversal symmetry, 340
Time-step procedure, 348
Toluene, 389
Topologically partitioned dispersion energies, 256
Topologically partitioned electric properties, 256
Topologically partitioned polarizabilities, 256
Torques, 270
Trajectory, 174, 298, 312
Trajectory average, 304
Transferability, 227, 275, 277
Transferability of potentials, 272
Transient time correlation functions (TTCF), 381
Transition state theory, 148
Transition states, 460
Transport coefficients, 183, 304, 324, 329, 331, 365, 368
Transport properties, 141, 361
Triacontane, 363
Trial configurations, 185
Triazine, 274
Triply excited determinants, 123
TRIPOS force field, 468
Trotter factorizations, 340, 345, 352, 376
Truncated Hausdorff expansion, 49
T-sites, 203, 205
Two-electron cluster function, 39
Two-electron integral, 85
Two-particle operators, 46
Two-phase coexistence, 377

UFF force field, 469
UNI force field, 245
Uniform shear viscosity, 365
University of Rhode Island, 400
Unlinked diagrams, 98
Unstable system, 175
Uracil, 230, 246, 262
Urey-Bradley potential, 158

Vacuum state, 56, 58
VALBOND force field, 469
Valence electrons, 153, 187, 233
Valence orbitals, 37
van der Waals clusters, 271
van der Waals complexes, 226, 240, 242, 249, 252, 253, 262, 263, 280
van der Waals surface, 9, 23, 277
Vapor pressures, 245
Variable charges, 20
Variation in atomic charge with conformation, 13
Variational approaches, 34
Variational principle, 152
Velocity, 334, 373
Velocity autocorrelation function, 181
Velocity distribution functions, 322
Velocity gradient, 293
Velocity Verlet algorithm, 343
Velocity Verlet operator, 351
Velocity-velocity autocorrelation function, 332
Verlet algorithm, 175
Verlet integrator, 344
Vibrational frequencies, 172, 181, 209
Vibrational modes, 271
Vibrational spectra, 158, 162, 191, 304
Vibrational spectroscopy, 143, 181
Virial coefficients, 241
Virtual orbitals, 36, 40, 48
Viscosity, 296, 361, 363
Viscous damping, 386
Viscous heating, 294, 379
Volume, 302
Volume distribution functions, 322

Wall atoms, 295
Water, 226, 228, 230, 253, 256, 262, 274
Water dimer, 246, 266, 267
Water potential, 266
Water-accessible surface, 277
Wavefunction separability, 42
Wavefunctions, 1
Weeks-Chandler-Andersen fluid, 377
Weeks-Chandler-Andersen (WCA) potential, 295
Well-conditioned data set, 19
Wick's theorem, 55, 56, 59, 64, 72, 75, 87, 88, 95, 100, 119
Wigner 3-j symbol, 231
Wigner rotation matrices, 231, 246
Wobbly charges, 8

Xenon, 148
X-ray charge densities, 275
X-ray diffraction, 142, 180

YETI force field, 468

Z-averaged perturbation theory (ZAPT), 118
Zeolite A, 191, 196
Zeolite acidity, 144
Zeolite aperture dimensions, 142
Zeolite aperture dynamics, 159, 193
Zeolite beta, 146
Zeolite channels, 175
Zeolite framework flexibilty, 141
Zeolite framework local modes 190
Zeolite frameworks, 138, 156, 171, 189
Zeolite modeling, 137
Zeolite reactivity, 206
Zeolite structures, 142
Zeolite vibrational spectra, 159
Zeolite window diameters, 183
Zeolite-catalyzed chemical reactions, 140, 149
Zeolite-template interactions, 197
Zeolites, 137, 161, 186

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