REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 12 (1998)

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, 148, 235, 344
Absolute entropy functional, 50
Absolute free energy of binding, 39
Acetamide, 37
Acetaminophen, 352, 356, 357
Acetic acid, 335, 340, 348, 349, 352
Acetylene, 271
ACMM
, 344
Adaptive umbrella sampling, 28
Adiabatic switching, 58
Aggregates, 341
Alanine, 32
Alanine dipeptide, 29, 37
Alcohols, 335, 348
Alkanes, 75
Alloxan, 340
Alpha-helix, 30
Aluminum surface energy, 216
AMBER
, 284
AMBER force field, 315
Amidinoindanone guanylhydrazone, 353
Analytical method of constraint dynamics, 80, 84, 89, 98, 101
Analytical potential energy function characteristics, 211
Angle-bend constraints, 82, 118, 121, 123, 130, 133
Angular distributions, 182
Anharmonic effects, 290, 313
Antamanide, 29
Antibody, 39
Argon, 209
Aromatic hydrocarbons, 342
ASTERIX
, 373
Asymmetric unit, 331, 348
Atomic multipoles, 335
Atomic orbitals (AO), 213, 217, 220, 260
Atomic charges, 190, 292, 293, 301, 319, 334, 335, 347, 352, 357, 358
Atomistic simulations, 207
Avian pancreatic polypeptide (APP), 296, 321
Azurin, 36

Basis set dependence, 267
Basis sets, 210, 216, 265
Benzamidine, 32, 40
Benzene, 132, 331, 340, 342, 352, 357
Beta-sheets, 30
Bethe lattice, 229
Binding energy, 144, 217, 233
Bioactive molecules, 282
Biomolecular simulation, 281
Biomolecules, 313
Biphenyl, 254, 255
Boltzmann probability, 1, 4, 7, 12, 15, 20, 41, 43, 50, 56
Bond angle bending, 125, 284, 333
Bond angle constraint, 125
Bond distance, 211, 217, 230
Bond order, 228
Bond stretching, 118, 125, 284, 333
Bond stretching constraints, 77, 80, 83, 91, 92, 106, 115, 116, 118, 129, 130
Boundary conditions, 29, 176
Bovine pancreatic trypsin inhibitor (BPTI), 21, 28, 295, 296
Brillouin theorem, 371
Brownian dynamics, 165, 297, 314
Bulk adsorption energy, 190
Bulk materials, 242
Bulk modulus, 217, 219, 235
Bulk properties, 210
Bulk susceptibilities, 243
Bulk water, 141, 190, 195
Bulk water-semiconductor interface, 144
Butadiene, 273
Butane, 23, 79, 91

C4H6, 265
Caloric integration, 24
Cambridge Structural Database (CSD)
, 333, 340, 345, 347, 348, 353
Cancellation of errors, 318
Canonical (NVT) ensemble, 158, 163, 166
Carbon dioxide, 342
Carcinogenicity, 370
Car-Parrinello molecular dynamics, 144, 210
Cartesian coordinates, 77, 78, 84, 110, 155
CASTEP
, 333, 344
Cell parameters, 330, 338, 347
Centre de Mécanique Ondulatoire Appliquée (CMOA), 369
Centre Européen de Calculs Atomiques et Moléculaires (CECAM), 374
Centre National de la Recherche Scientifique (CNRS), 368
CFF force field, 347, 357
Chain attrition problem, 44
Charge groups, 336
Charge models, 334
Charge sensitivities, 292, 295, 311
Charge transfer, 258
Charged metal surfaces, 195, 197
Charges, 190, 292, 293, 301, 319, 334, 335, 347, 352, 357, 358
CHARMM
, 17, 284
CHELP
, 335
CHELPG
, 335
Chemical and Engineering News
, v, ix, xi
Chemical dynamics, 209
Chemical information retrieval, 374
Chemical literature, v
Chemical potential, 175
Chemical reactor, 282
Chemical stability, 327
Chemisorption, 139
Chiral compounds, 348, 352
Chromophores, 244, 309
Chymotrypsin, 32
CIPSI
, 373
Close contacts, 329
Close-packed metals, 233
Clustering, 338
Coherent anti-Stokes Raman spectroscopy, 244
Cohesive energy, 217, 227, 228, 235
Collective motions, 313
Complementary error function, 157
Computational chemistry, v, 241, 367
Computational Chemisty List (CCL), vi
Computer packages, 255
Computer simulation, 1, 137, 327
Computers, 374, 377
Condensed phase systems, 273
Configuration, 18
Configuration interaction (CI), 213, 257
Configuration space, 1, 12, 144, 173
Conformation, 18, 335
Conformational analysis, 347
Conformational search, 58
Conjugate momenta, 309
Constrained coordinates, 98, 103
Constrained degrees of freedom, 90
Constraint correction, 83, 99, 132
Constraint dynamics, 78, 111, 116
Constraint equations, 84
Constraint forces, 103
Constraints, 161, 165, 319, 350
Construction probability, 41, 45
Conventional cell, 331
Converged properties, 265
Convergence, 38, 47, 336
Convergence criteria, 256
Convergence of sensitivity coefficients, 294
Convergence rate, 123
Conversion factors, 251
Cooperative effects, 283, 291, 303
Cooperativity, 304, 306
Correlation energies, 213
Corrugated metal surfaces, 145, 146, 164, 176, 177, 180, 193, 194
Coulombic interactions, 155, 212
Coulomb's law, 146, 292, 310, 334
Coupled cluster methods, 248
Coupled-cluster equations-of-motion method, 264
Coupled holonomic constraints, 80, 89
Covariance matrices, 289, 312, 313
18-Crown-6, 307
CRYSCA
, 345
Crystal density, 331
Crystal packing, 336, 337
Crystal polymorphs, 327
Crystal structure prediction, 328, 339, 347, 353
Crystal surfaces, 332
Crystal95
, 333, 344
Crystalline solids, 216
Crystallization, 327, 332, 339
Crystals, 251, 273, 330
Cutoff radius, 29, 154, 300, 336, 342, 343, 346
Cytochrome P-450, 311

d orbitals, 226
D'Alembert's principle, 95
DARC system, 374
Database of physical properties, 208
de Broglie wavelength, 167
Decaglycine, 23, 48, 52
Defects, 138, 210, 218, 223, 225, 232, 234
Degenerate four-wave mixing, 246
Degrees of freedom, 76, 333
Deletions from an ensemble, 173
Density functional theory (DFT) calculations, 149, 150, 208, 209, 212, 214, 215, 219, 220, 232, 333
Density matrices, 261
Density of states, 222, 223
Density profiles, 166
Desktop mechanical calculator, 370
Detailed balance condition, 16, 56, 169, 173, 174
Diamond, 211, 219, 221, 230, 231
Diatomics, 216, 217
Dibenzoylmethane, 329
1,2-Dichloroethane, 29
DICVOL91
, 347
Dielectric constant, 337
Diffuse functions, 265, 268
Diffusion coefficient, 187, 189
Diffusional-influenced reaction rates, 314
Digital computers, 367
Dimethoxyethane, 342
Dipeptides, 311
Dipole moment, 141, 149, 191, 243, 250, 254, 256, 257, 266, 292, 294, 336
Dipole moment matrix, 261
Direct methods for computing entropy, 19, 49
Displacement correlation function, 288
Distributed multipoles, 344
Distribution function, 301
DMAREL
, 344
DNA, 21, 281
Docking, 334
Dodecane, 30
Domain of applicability, 123
Double excitation operators, 265
DREIDING force field, 355, 357, 358
Drug design, 209

ECEPP
, 17, 21, 48, 52
EEM method, 90
Effective medium theory, 208, 226, 231
Effective pair potential, 228
Einstein harmonic oscillator formula, 21
Elastic constants, 211, 236
Electric field, 195, 196, 242, 247, 254, 256, 259, 301
Electrical response property calculations, 266
Electrode, 191
Electron correlation, 213, 254, 272, 371
Electron density, 179, 212, 214, 232, 334
Electron dispersion, 334
Electron gas, 148, 150, 213, 215, 232
Electronic energy, 214
Electrooptic modulation, 244
Electrostatic interactions, 321, 333, 336, 342, 344, 346
Electrostatic potentials, 156, 192, 319
Electrostatically derived charges, 335, 347, 352, 357, 358
Embedded-atom method, 226, 231, 233, 234
Empirical bond order model, 208, 226
Empirical potential energy functions, 17
Endothiapepsin, 310
Energies, 211
Energy fluctuation, 34
Energy minimization, 333, 337
Energy surface, 337
Enrichment method, 48
Ensemble averages, 5, 12
Ensembles, 159
Entropy, 1, 2, 5, 9, 19, 20, 22, 23, 24, 36, 41, 55, 58, 300, 303, 306, 331
Entropy functional, 50, 52
Enzyme-ligand binding, 32
Equations of motion, 82, 85, 89, 160, 162, 164
Equilibration, 165
Equivalent alternative constraints, 109, 133
Ergotic process, 15
Error function, 157
Error propagation, 314
Errors, 89, 100, 101, 130, 132, 216
Essential dynamics approach, 312
Estrone, 350, 352, 355
Ethane, 31, 37
Ethylene, 273
Euler angles, 78, 151, 170, 173
Euler equations of rotational motion, 78
Ewald summation, 156, 336, 342, 344, 346
Exchange-correlation functional, 213, 214, 215
Exchange-correlation potential, 214
Excitation energies, 257, 265
Excited state, 247
Excluded volume, 42
Extended Hückel theory (EHT), 218, 219, 343
Extensive variables, 6

False energy minima, 346
Fermi energy, 222
FHI96MD
, 333, 344
Finite difference methods, 160
Finite field method, 252, 254
Finnis-Sinclair potential, 208, 220, 226, 229, 235
Fitting databases, 235
FlexCryst
, 340, 345
Flexibility in crystal structures, 211, 333
Fluctuations, 6, 12, 23, 166
Fluids, 17, 138
p
-Fluorobenzamidine, 32
Force fields, 2, 17, 22, 36, 37, 210, 281, 292, 315, 319, 333, 337, 347, 350
Forces of constraint, 89, 102
Fractional coordinates, 330
France, 367
Free energy, 1, 20, 32, 36, 41, 59, 295
Free energy difference calculations, 318
Free energy of binding, 32, 39, 40
Free energy of solvation, 34, 41
Free energy perturbation (FEP), 2, 39, 40
Frequency doubling, 244
Frequency upconversion lasing, 246
Frequency-dependent properties, 256, 257, 264
Friction term, 165
Friedel oscillations, 178
Fullerenes, 219

Galactose receptor, 40
GAMESS
, 266, 271, 335
Gasteiger atomic charges, 341
Gaussian
, 335
Gauss's principle of least constraint, 77, 95
GEOMO
, 374
Ghost molecule, 34
Gibbs free energy, 6, 41, 331, 332
Global minimum, 338
Glucocorticoid, 358
Glue model, 226
Glycine, 32
Glycine dipeptide, 29, 295, 296
Glycol, 29
GMP, 36
Gonadotropin-releasing hormone (GnRH), 52
Grain boundary, 211
Gramicidin A, 30
Grand canonical ensemble, 158
Grand canonical MC, 29, 173
Graphene sheets, 231
Green's function, 286, 287, 289, 290, 312, 313, 314, 322
GROMOS
, 284, 295
GROMOS force field, 284, 315
Ground state energy, 216

Hamiltonian, 10, 11, 22, 26, 30, 33, 38, 58, 77, 140, 147, 156, 212, 219, 221, 248, 254, 257, 264, 284, 309
Hamilton's principle, 95
Hardware companies, 374
Harmonic approximation, 20
Harmonic entropy, 20
Harmonic force constant, 300
Harris functional, 208, 215, 216, 220
Hartree potential, 212
Hartree-Fock calculations, 252, 255, 333, 347
Hartree-Fock equation, 213, 259
HCN, 266, 267, 268, 270
Helix bundle, 30
Helix-coil transition, 21, 38, 56
Hellmann-Feynman theorem, 248
Helmholtz free energy, 2, 5, 286, 311
Hessian, 20, 287, 289, 313
Hexatriene, 273
High pressure phases, 331
High pressure polymorph, 357
Histogram method, 59
Holonomic constraints, 75, 77, 82, 83, 106, 128, 133
Hückel calculations, 372
Hund's rule, 222
Hydration free energies, 311
Hydrazine, 371
Hydrocarbon interface, 191
Hydrogen bonds, 139, 166, 176, 186, 195, 300, 333, 340, 351, 357
Hydrogen fluoride, 371
Hydrophilic residue, 308
Hydrophobic contacts, 303, 308
Hydrophobic effects, 311, 321
Hyperpolarizability, 243, 247, 248, 249, 250, 252, 257, 258, 259, 264, 270, 271, 273
Hypothetical scanning method, 17, 49

Ice lattices, 195
ICE9
, 341, 342, 345
Ideal chain, 42
Image potentials, 146, 144, 148
Imaging enhancements, 246
Importance sampling, 13, 23, 26, 41, 47, 54, 167
Initial conditions, 159
Insertions in an ensemble, 173
Insulin, 21
Integration algorithm, 82, 84, 100, 132
Interatomic forces, 207
Interfaces, 137, 144, 207
Internal coordinate constraints, 75, 82, 110, 111, 115, 130
Internal coordinates, 77
Ionic solutions, 198
IR spectroscopy, 347
Ising model, 3, 6, 7, 24, 53, 54, 59

Jellium model, 140, 143, 148, 152, 178, 208, 232, 234, 235
Jellium potential, 150
Job cuts in industry, viii
Job opportunities for computational chemists, v, ix

Kerr effect, 249, 251
Kinetic energy operator, 212
Kirkwood equation, 10
Kirkwood factor, 294
Kleinman symmetry, 249
Kohn-Sham density functional theory, 149
Kohn-Sham orbitals, 214, 220

Lagrangian dynamics, 77, 78
Lagrangian multipliers, 78, 81, 82, 85, 89, 98, 102, 113, 161
Lasers, 244, 246
Lattice chain models, 56
Lattice constant, 217, 219, 235
Lattice coordinates, 155
Lattice models, 42, 58, 226, 228
Lattice spin models, 59
Lattice symmetry, 330, 339, 341
Lattice vectors, 330
Lattices, 195, 335, 338
Law of cosines, 124
Layering, 196
Leapfrog Verlet algorithm, 132
Leibniz rule, 86, 87
Lennard-Jones constants, 10, 17
Lennard-Jones energy, 298
Lennard-Jones fluids, 25, 31, 173
Lennard-Jones potential, 4, 144, 154, 192, 210
Leu-enkephalin, 21, 23, 52, 56
Ligand, 39, 334
Ligand binding, 30
Linear buildup procedures, 41
Linear constraints, 77
Linear response approximation (LRA), 39
Linear response theory, 310
Linear scaling algorithms, 218
Linearization, 104, 108
Liouville's theorem, 58
Lipids, 281
Liquid crystals, 251
Liquids, 273
Local density approximation (LDA), 150, 215, 219, 232
Local electronic bond energy, 227
Local energy minima, 337, 350
Local states (LS) method, 3, 17, 25, 51, 52
Localized microstates, 18
Lodge theory, 370
Low frequency modes, 76
Lysozyme, 39

M site, 142
Mach-Zender interferometer, 245
Magnetic susceptibility, 370
Many-body analytic potential energy function, 210
Marcus relationship, 39
Materials simulation, 207, 210
Matrix method, 83, 94, 103, 105, 111, 116, 118, 120
Matrix of constraint displacements, 113
Maxwell-Boltzmann distribution, 159
Maxwell's equations, 242
MDCP
, 341, 342, 345
Mean field approximation, 149
Melting points, 236
Mercury surfaces, 139, 176, 177, 181, 182, 186
Mercury-mercury potentials, 145
Mercury-water interface, 179, 185, 192
Metal clusters, 138, 139, 144, 197
Metal surfaces, 137, 138, 140, 147, 148, 152, 186, 196, 231
Metals, 230, 231, 233
Metal-water interfaces, 137, 143, 153, 175, 193, 194
Metastable structures, 350
Met-enkephalin, 21, 56, 58
Methanol, 31, 311, 317
Method of strides, 47
Method of undetermined multipliers, 102
Method of undetermined parameters, 81, 95, 101, 111, 126
Methyl chloride, 29
9-Methyladenine, 30
4-Methylpyridine, 329
1-Methylthymine, 30
Metropolis algorithm, 343
Metropolis Monte Carlo, 1, 13, 15, 52, 55, 56, 166, 175
Microcanonical ensemble, 158
Minimal basis sets, 272
Minimization, 350
Minimizers, 337
Minimum free energy principle, 6, 7, 45, 54
MISSYM
, 345
MM2, 341
MNDO, 254, 255
Mobility, 187
Modeling, 140
MOLDEN
, 335
Molecular conformations, 345, 347
Molecular design, 307
Molecular dynamics (MD), 1, 13, 15, 17, 41, 52, 75, 133, 140, 152, 159, 186, 196, 292, 298, 313, 322, 342, 346, 350, 373
Molecular dynamics trajectories, 289
Molecular electrostatic potential (MEP), 334
Molecular flexibility, 329, 344
Molecular mechanics (MM), 286, 333
Molecular orbital energies, 221
Molecular orbital (MO) basis, 262
Molecular packing analysis, 329
Molecular properties, 247
Molecular recognition, 306
Molecular vibrations, 110
Møller-Plesset (MP) perturbation theory, 264
MOLPAK
, 341, 342, 345, 346
Moments, 222, 223
Moments theorem, 224
Monolayers, 144
Monosaccharides, 329, 342, 353
Monte Carlo (MC) calculations, 1, 13, 15, 25, 31, 44, 55, 56, 140, 152, 166, 168, 174, 187, 196, 292, 341, 343, 349, 373
MOPAC
, 252, 335
Morphology, 327
Morse function, 235
MPA
, 341, 342, 345, 346
MSHAKE, 132
MSI PP
, 345
Mulliken charges, 334
Multicanonical algorithm, 3, 16, 56
Multicanonical probability, 56
Multiphoton pumping mechanisms, 246
Multipole expansion, 342
Multistage sampling method, 59
Myoglobin, 32

Naphthalene, 132
Native structure, 35
Newtonian mechanics, 78
NIST*LATTICE
, 344
p
-Nitroaniline, 271
NMR, 347, 353
Nonbonded cutoffs, 297, 303
Nonbonded interactions, 210
Nonbonded parameters, 307
Nonchiral compounds, 348
Nonholonomic constraints, 95
Nonlinear effects, 310
Nonlinear constraints, 107
Nonlinear optical (NLO) properties, 236, 241, 252, 256, 263
Nonlinear scaling relationships, 312
Nonlinearity, 99
Nonphysical transformations, 31, 32, 35
Non-self-consistent treatments, 149
Nonvariational methods, 248
Normal mode analysis, 20, 290, 313
Nosé-Hoover thermostats, 163
Numerical breakdown, 255
Numerical drift, 81
Numerical experiments, 367
Numerical integration, 89, 90, 160
NVT ensemble, 163

One-electron approximation, 212
OPLS force field, 315
Optical bistability, 245
Optical data storage, 246
Optical Kerr effect, 244
Optical rectification, 244
Optical signal processing, 245
Optical storage devices, 244
Order parameters, 182
OREMWA method, 337
Orientational potentials, 144

Packing energy, 331
Pair-additive interactions, 210
Paraffins, 333
Parameter optimization, 319
Partial atomic charges, 190, 292, 301
Partially constrained coordinates, 97, 101
Partially rigid models, 79
Particle mesh Ewald, 158
Partition function, 4, 9, 16, 18, 48, 59, 167, 169
PCILO, 373
PCK5
, 329
PCK83
, 344
PDM93
, 335
Peptide growth simulation, 38
Peptides, 56
Periodic boundary conditions, 154, 155
Periodic conditions, 335
Periodic interactions, 156
Perturbation potential, 287
Perturbation series expansion, 247
Perturbation theory, 248, 256, 264, 309
Pharmaceutical industry, x, 327, 375
Pharmaceutical Research and Manufacturers of America (PhRMA), viii
Phase conjugation, 246
Phase space, 5, 58, 77, 165, 309
Phase space volume, 58
Phonons, 145
Physical transformation, 40
Physisorption, 137, 139
Physisorption of water, 140, 143, 182
Pigment red, 353
pKa calculations, 31, 39, 309
Platinum-water potential, 146, 185
PLATON
, 344
Pöckels effect, 244
Point mutation, 307
Poisson-Boltzmann method, 29
Poisson's equation, 152
Polarizability, 243, 247, 248, 252, 258, 266, 292
Polarizable water model, 318
Polarization, 147, 149, 191, 242, 292
Polarization propagators, 263
Polarized continuum model (PCM), 273
Polyacetylene, 273
Polyalanine, 38
Polyenes, 265, 271, 272
Polymer films, 273
Polymers, 2, 42
Polymorph prediction process, 351
Polymorph Predictor
, 338, 343, 345, 346, 355
Polymorphs, 327, 350
Polypeptides, 30, 36
Polysaccharide structures, 329
Positional fluctuations, 313
Potential drop at interfaces, 180, 190, 192
Potential energy function, 36, 139, 142, 146, 207, 208, 211, 283, 329, 333
Potential energy function refinement, 318
Potential energy surface (PES), 2, 19, 209
Potential of mean force (PMF), 25, 26, 58, 60, 76, 198, 297
Powder diffraction, 328, 332, 338, 347, 350, 352, 353, 354
Predictor-corrector SHAKE algorithm, 132
Prednisolone t-butylacetate, 352, 358
Primitive cell, 331, 352
Principal component analysis (PCA), 283, 290, 312, 316, 317, 320
Probability density, 1
PROMET3
, 340, 345, 346
Propagators, 263
Protein engineering, 307
Protein environment, 35
Protein folding, 18, 30, 42, 56, 58, 303, 307, 308
Proteins, 2, 17, 22, 37, 39, 56, 75, 281
Pseudoenergy, 264
Pseudopotential, 210
Pyrimidine, 342

Quadrupole moments, 191
Quantum chemistry, 248, 370
Quantum mechanical bonding, 208
Quantum mechanical calculations, 144, 212, 265
Quantum mechanical entropy, 21
Quantum mechanics (QM), 333, 368
Quantum Monte Carlo calculations, 150
Quasi-harmonic approximation, 22, 312, 313
Quaternions, 78, 126, 173
Quinacridone, 352, 358

Racemates, 348
Radial distribution function, 26, 141, 143, 166, 180, 185, 300
Radius of gyration, 30
Random coil, 51
Random number generator, 174
Random phase approximation (RPA) methods, 261, 263
Random walk, 2, 42
Ras protein, 52
RATTLE, 82, 83, 128, 129, 132, 133
Reaction coordinates, 27, 30, 76
Reaction field model, 273
Receptor, 334
Reciprocal space, 336
Reduced cell, 331, 338, 344
Redundancy of constraints, 79, 109
Reference state, 39
Refractive index, 243, 245, 246
Research and development (R&D) expenditures, viii
Response functions, 264
Restraint potentials, 36, 38
Rietveld method, 347
Rigid body minimization, 337, 342
Rigid body translation, 288
Rigid bodies, 333, 343, 353
Rigid models, 78
Rigid water model, 116, 126
RNase T, 36
Rotamers, 352
Rotation matrix, 170
Runge-Kutta integration algorithm, 91

Sampling theory, 12
Scanning method, 3, 7, 44, 46, 51
Scanning probe microscope (SPM), 138, 197
Scanning transition probabilities, 49
Schrödinger equation, 212
Scoring functions, 334, 340
SCRIPT
, 375
Second harmonic generation (SHG), 243, 244, 245, 251
Second-moment approximation, 224, 225
Self-avoiding walks (SAWS), 42, 50
Self-consistent field (SCF), 260
Self-intersecting walks, 42, 50
Semiempirical molecular orbital approximations, 218, 271
Sensitivity analysis, 281, 290, 311
Sensitivity coefficients, 283, 284, 285, 307, 319
Sensitivity matrix, 287, 291, 316
Serine dipeptide, 315
SETTLE method, 82, 83, 132
SHAKE method, 82, 83, 106, 108, 110, 111, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 128, 129, 132, 133
Shear constants, 233
SIBFA force field, 374
Silver-water interfaces, 185
Simple fluids, 18
Simple sampling, 14, 42, 44
Simulated annealing, 337
Simulation box, 155
Singular value decomposition (SVD), 283, 290, 316
Slater determinant, 213
Slow growth thermodynamic integration, 29, 34, 37
Smooth surfaces, 176
Smooth truncation, 156
SN2 reaction, 29
Sodium chloride (NaCl), 29
Software, xiii, 225, 373
Solutes, 311
Solvation free energy, 31
Solvent effects, 289, 314
Solvent-accessible surface area (SASA), 40
Solvent-free polymorphs, 355
Solvochromatic method, 258
Somatostatin, 23
Space group constraints, 346
Space group symmetry, 331, 340, 342, 344, 348, 350
SPC water model, 141, 163, 292, 298, 299
SPC/E water model, 123, 124, 126, 141, 163
Specific heat, 6, 9, 11, 24
Spectral density, 189
Square lattice, 42, 48, 53, 225, 303, 308
State function, 32
Statistical mechanics, 4, 209, 373
Step-by-step buildup, 3
Sterically accessible regions, 192
Stochastic models method, 7, 53
Stochastic process, 15
Störmer algorithm, 101
Structural diversity, 339
Structural properties, 180
Structural response, 313, 314
Structure-binding relations, 209
Sum-over-states (SOS) methods, 252, 256, 263
Supercell, 350
Supercomputers, 375
Superlattice, 350
Surface area, 40, 311
Surface corrugation, 144
Surface effects, 340
Surface polarization, 139
Surface properties, 210, 223
Susceptibilities, 242, 248
Symmetry, 331, 340, 342, 344, 348, 350
Systematic search, 346

Target state, 39
Tautomeric forms, 355
Taylor series, 95, 100, 104, 107, 114, 243, 247
Teaching computational chemistry, 375
Temperature constraint, 95
Theoretical biochemistry, 369, 372
Theoretical chemistry, 368
Thermal expansion, 236
Thermodynamic cycle, 33, 34
Thermodynamic integration, 2, 9, 11, 24, 31, 33, 36, 37, 76
Thermodynamic perturbation, 36, 76
Thermodynamic properties, 286
Thermodynamics, 331
Third harmonic generation, 244
Three-dimensional grid, 340
Threonine, 335
Threonine dipeptide, 315
Tight binding method, 208, 218
Time scales, 75, 175, 176, 186
Time steps, 90, 133, 161, 162, 198
Time-dependent Hartree-Fock method, 258
Time-dependent response functions, 263
Time-dependent Schrödinger equation, 259
Tinfoil boundary conditions, 337
TIP3P, 292
TIP4P, 141, 163
TIP-4FP, 141, 163
Torsional constraints, 120, 130, 131
Torsional interactions, 333
Trajectory, 101, 209
Transferability, 211
Transformation paths, 37
Transition moments, 257, 258
Transition probabilities, 2, 41, 49, 51, 56
TREOR90
, 347
Trial crystal packings, 342
Trial structures, 340, 345
Triangulation procedure, 82, 109, 123
Tribochemistry, 231
Triphenylphosphine, 329
Triphenylverdazyl, 329
Trypsin, 32, 40
Tryptophan, 309
Two-dimensional bias function, 29
Two-electron integral calculations, 255
Two-photon upconverted emission, 247

Umbrella sampling, 14, 16, 23, 24, 25, 27, 30
Unconstrained coordinates, 102, 103
Undetermined parameters, 81, 82, 98, 100, 111
Unit cells, 329, 330, 331, 344
United atom model, 92, 342
Unrestricted Hartree-Fock (UHF) computations, 370
UPACK
, 341, 342, 345, 346

Valence bond calculation, 371
Valence electrons, 148
van der Waals energy, 336
van der Waals interactions, 333, 346
van der Waals surface, 319
Variational principle, 213, 233, 259
Velocity autocorrelation function, 188
Velocity Verlet integration algorithm, 83, 126
Verlet integration algorithm, 83, 101, 102, 111, 126, 127, 160, 164
Vibrational calculations, 273
Vibrational dynamics, 110, 113
Vibrational frequency, 217
Vibrational modes, 141
Visualization, 176
Volume, 40

Water, 17, 27, 29, 31, 80, 109, 139, 141, 142, 144, 148, 159, 160, 161, 162, 166, 173, 177, 181, 183, 184, 190, 193, 293, 298, 301, 318
Water density profile, 194
Water models, 292
Water-metal potentials, 144, 148
Water-water interactions, 37, 194
Wave equation, 242
Wavefunction, 212, 213
Weak coupling, 76
Wide microstates, 18
Wigner-Seitz radius, 148
Wilson G matrix, 113
Wilson vectors, 110, 112, 118, 119
Windows, 24
WMIN
, 329, 342
Work function, 149
World Wide Web, v, xiii

Xenon, 32
X-ray powder diffraction, 328, 332, 338, 347, 350, 352, 353, 354
X-ray scattering, 194

Zwanzig equation, 10

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