REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 1 (1990)

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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A

4-Amino-1,2,4-triazin-5-ones, 360
4-Amino-3-methyl-6-phenyl-1,2,4-triazin-5(4H)-one, 361
Ab initio
, 1, 45, 328, 355
Abstract factors, 175
Accessible region, 215
Accessible surface, 234
Activation energies, 357
ADAPT, 193, 200
Additive-constitutive models, 223
Additivity assumption, 137
Adrenaline, 248
Agrochemical industry, 357, 362
Agrokinetic optimization, 122
AHn compounds, 11, 12
ALADDIN, 243, 244, 246, 255
AlBmHn, 12
ALCHEM, 222
Alcohols, 65
Aldehydes, 65
All-atom model, 297
All-valence-electron methods, 46
Alpha-helix, 250
Aluminum, 32
AM1, 57, 58, 62, 63, 69, 70, 71, 72, 73, 75, 336, 337, 338
AMBER, 389
AMPAC, 73, 336
Analgesic activity, 238
Angiotensin converting enzyme inhibitors, 240
Animal health products, 357
Anions, 69
Anti-ischemic agents, 366
Antisickling agents, 366
Approximations, 326
Argon, 33
Aromatic hydrocarbons, 65
Artificial intelligence, 253, 345
Association energies, 357
Atom-centered basis sets, 30
Atomic natural orbitals (ANOs), 27, 28, 29
Atomic orbital basis set, 5
Atomic orbitals (AOs), 4, 99, 375
Atomic surface, 268
Atomic trajectories, 76
Aufbau principle, 327
Austin Model 1 (AM1), 57, 58, 62, 63, 69, 70, 71, 72, 73, 75, 336, 337, 338


B

B atom, 23
Backbone atoms, 236
Balanced basis set, 34
Ballast positions, 121
Basis set incompleteness error, 30
Basis set superposition error (BSSE), 30, 35, 36
Basis sets, 1, 332
3-21++G, 33
3-21+G, 33
3-21G*, 14
6-31G**, 15, 18, 19, 20, 29, 31, 337
6-31G*, 7, 12, 14, 15, 17, 30, 334, 337, 341
6-311++G(3df,3pd), 20
Double zeta (DZ) basis sets, 6, 7, 10, 26, 28, 29, 35
MAXI-i, 26
MIDI split valence contracted basis, 13, 15
MIDI-i, 26, 27
MINI-i, 26
Slater-type orbitals (STOs), 4, 5, 49, 54, 329, 332
STO-3G, 10, 11, 12, 14, 16, 17, 18, 19, 27, 35, 333, 337, 341
STO-nG, 333
Basis set superposition error (BSSE), 9, 10, 12, 13, 14, 34
Benzene, 191, 231
Berlin diagrams, 273
Beryllium, 31
Beta-strand, 250
Bicyclobutane, 64
Binding sites in macromolecules, 357
Bioactive conformation, 214, 246, 247
Bioevaluation, 131
BIOGRAF, 388
Bioisosteric analogs, 122
Biological activity, 356
BIPED, 236, 255
Bit map, 221, 239
Bit string, 221
BMDP1R, 158
BMDP2M, 144
BMDP4M, 129
Boat conformations, 231
Boltzmann probability function, 309, 310
Bond angles, 357
Bond lengths, 357
Bond-centered functions, 30
Born-Oppenheimer approximation, 100, 326
Boron, 23, 31
Bromine pentafluoride, 68
Bromobutide, 361, 362
Brookhaven Protein Data Bank, 235, 236, 342, 344
Brownian dynamics, 308
Broyden-Fletcher-Goldfarb-Shanno (BFGS), 74, 338
Bulrush, 362
Bump checking, 244
Butadiene, 274, 275


C

C atom, 23
CAChe, 386
CADPAC, 391
Calibration, 178
Cambridge Structural Database, 214, 224, 234, 235, 236, 237, 239, 214, 249, 252, 253, 255, 256, 341
Camp-King converger, 61
Camphor monooxygenase, 363
CAMSEQ/M, 386
Canonical ensemble, 309
Canonical form, 220
Carbon, 11, 16, 23, 31, 199
Carbon monoxide, 65
Carbon sulfide, 66
Carbon tetraiodide, 66, 67
Carbonic anhydrase, 238
Cartesian gaussian, 7, 93
CAS Online, 224
Cations, 69
CAVEAT, 241, 255
Central nervous system, 240
Chair conformations, 231
Chance correlation, 157
Charge density, 269, 277
Charge distributions, 357
CHEM-X, 388
Chem3D Plus, 385
ChemCad+, 385
Chemical Abstracts System Chemical Registry Service, 220, 224, 365
Chemical accuracy, 336
Chemical shielding tensor, 86
Chemical shift, 202
CHEMLAB-II, 389
Chemometrics, 169, 170, 182, 355
Chlorine, 33
Chloroplasts, 361
Chromatographic optimization function, 173
Chromatographic response functions (CRF), 172
Chromatographic retention, 188
Classical least-squares (CLS), 179
Classification, 182
Clique, 228
Clique algorithms, 237
Clique-detection, 228
Cluster analysis, 145, 146, 147, 185, 234, 237
Clustering, 182, 184, 228
CNDO, 47, 49, 50, 51, 52, 58
CNDO/2, 50, 51, 52, 88, 337
CO, 9, 17, 18, 24
CO2, 17, 18, 25
Cofactor NADH, 227
COFCl, 67
Colinearity, 147
COLUMBUS, 392
Complete basis set, 8
Complete neglect of differential overlap (CNDO), 47, 49, 50, 51, 52, 58
Composite design, 170
Compressed matrix connection table, 218
Computational chemistry, 1, 356
Computational expense, 3
Computer graphics, 348, 355
Computer programs, 364
Computer program 3DSEARCH, 240
Computer program ADAPT, 193, 200
Computer program ALADDIN, 243, 244, 246, 255
Computer program AMBER, 389
Computer program AMPAC, 73, 336
Computer program BIOGRAF, 388
Computer program BIPED, 236, 255
Computer program BMDP1R, 158
Computer program BMDP2M, 144
Computer program BMDP4M, 129
Computer program CAChe, 386
Computer program CADPAC, 391
Computer program CAMSEQ/M, 386
Computer program CAVEAT, 241, 255
Computer program CHEM-X, 388
Computer program Chem3D Plus, 385
Computer program ChemCad+, 385
Computer program CHEMLAB-II, 389
Computer program COLUMBUS, 392
Computer program CONCORD, 214, 235, 247, 253, 255, 345, 388, 392
Computer program COUSIN, 224
Computer program DAYMENUS, 392
Computer program DelPhi, 389
Computer program DMol, 389
Computer program GAMESS, 10, 391
Computer program GAUSSIAN, 10, 345, 390
Computer program GRADSCF, 391
Computer program GRID, 390
Computer program GROMOS, 390
Computer program GSTAT, 236, 237
Computer program HONDO, 10, 391
Computer program HYPERCHEM, 389
Computer program INSIGHT/DISCOVER, 389
Computer program MACCS-3D, 235, 240, 256, 389
Computer program MACCS-II, 224, 235, 240
Computer program MacroModel, 341, 387
Computer program MM2/MMP2, 200, 389, 338
Computer program MNDOC, 61, 75
Computer program MOLIDEA, 385
Computer program MOLPAT, 238, 248
Computer program MOPAC, 56, 57, 70, 73, 74, 75, 336, 345, 363, 387
Computer program NITRO, 385
Computer program ORTEP, 389
Computer program OWL, 236, 255
Computer program PCMODEL, 385
Computer program POLYGRAF, 388
Computer program Prometheus, 390
Computer program PROPHET, 389
Computer program QUANTA/CHARMm, 388
Computer program Quantum Chemistry Program Exchange (QCPE), 384, 387
Computer program SAS CLUS, 144, 147
Computer program SAS CROSS, 129
Computer program SAS REGRESS, 158
Computer program SHAKE, 301
Computer program SYBYL, 341, 388
Computer program VDWSG, 289
Computer program ZINDO, 75
Computer representation, 218
Computer-assisted molecular design (CAMD), 355
CONCORD, 214, 235, 247, 253, 255, 345, 388, 392
Configuration interaction (CI), 14, 15, 17, 18, 19, 20, 22, 30, 31, 88, 91, 335
Conformational populations, 357
Connection table, 218, 234, 241
Connectivity indices, 200
Constraining potentials, 305
Continuum models, 308
Contour surfaces, 265, 270, 277
Contracted basis, 7, 21
Contracted functions, 5, 27, 104
Contracted gaussians, 4, 8, 9, 34
Contracted primitives, 12
Contraction coefficients, 6, 10, 14, 20, 26
Contraction error, 28
Contraction scheme, 27
Contractions, 333
Copper, 8
Correlated wavefunctions, 8, 35
Correlation coefficient r, 159, 195
Correlation consistent series of basis sets, 28, 29, 30
Correlation effects, 110
Correlation energy, 34, 334
Correlation matrix, 146, 176
Correlation recovery, 14, 16, 30
Counterpoise method, 9, 35, 36
Coupled cluster (CC) theory, 91
Coupled-perturbed Hartree-Fock (CPHF), 90
Coupling parameter, 309
COUSIN, 224
Covariance matrix, 176, 183
Critical point, 285
Cross-correlation matrix, 129
Cross-validation, 177, 182, 195, 234
Crystallographic data, 213, 225, 341
Cubane, 64
Cyanide radical, 65
Cyclohexane, 231
Cyclopropyl cation, 66
Cytochrome P-450, 363


D

2-(2,4-Dichlorophenyl)-1-(1-imidazolyl)hexane, 363
2D-NMR data, 250, 348
3DSEARCH, 240
D-2 pharmacophore, 245
DARC, 224
Database management, 355
Databases, 213
Davidon-Fletcher-Powell (DFP), 55, 74, 338
Davidson correction, 19
DAYMENUS, 392
Debye-Waller factors, 306
Del Re sigma-charge, 193, 200
Delocalized orbitals, 277
DelPhi, 389
Density domain approach (DDA), 271, 273
Density function, 269
Derivative Fock operator matrices, 98
Derivative Hamiltonians, 93
Derivative Hartree-Fock (DHF) method, 90, 99
Derivative Numerov-Cooley (DNC), 92, 100
Derivative properties, 301
Derivative SCF equations, 98
Derivative Schrödinger equations, 93, 100
Derivative vibrational wavefunctions, 101
Descriptors, 189, 358
Desktop Molecular Modeller, 386
Diacetylene, 64
Difference distance matrix, 228
Differentiation, 95
Diffuse functions, 28
Dihydrofolate reductase (DHFR), 227, 368
Dipole hyperpolarizability, 92, 103
Dipole moments, 3, 8, 10, 36, 72, 86
Dipole polarizability, 86, 101, 104
Dipole, 12
Directed search techniques, 171
Disconnected atoms, 241
Discriminant analysis, 152, 183
Dispersion force, 35
Dissociation energy De, 30
Distance geometry, 230, 241, 256, 281, 307, 321, 345, 349
Distance screens, 241, 247
Distance search, 239, 240
DMol, 389
DNA structures, 213
Dopamine, 245
Dopaminergic compound, 246
Dot surface, 244
Double zeta (DZ) basis sets, 6, 7
Double zeta quality basis sets, 26, 29, 35
Double-wide sampling, 311
Double-zeta plus polarization (DZP) basis sets, 7, 10, 28
Drug design, 147, 161, 164, 355
Drug discovery, 357
Dummy atoms, 244
Dunning double zeta contracted basis, 13, 15
Dunning-Hay split valence contracted basis, 13, 15
Dynamic reaction coordinate (DRC), 76


E

Electric dipole, 36
Electric field, 36, 84, 102
Electric potential, 84
Electrical properties, 103, 225, 357
Electron affinities, 357
Electron correlation, 15
Electron density contour surfaces, 269
Electron density, 273, 326
Electron pairs, 377
Electronic descriptors, 198
Electronic parameters, 142, 363
Electronic properties, 127, 243, 248
Electrostatic potential, 231, 357
Ellipsoidal gaussians, 5
Empirical force field, 321, 325
Empirical potential energy functions, 296, 314
Endo-5-methyl-endo-2-norbornanol, 206
Energies, 357
Energy derivatives, 84
Energy minimization, 298, 323, 349
Energy-optimized basis sets, 33
Ensemble averages, 299, 301
Entropy, 357
Envelope surface, 268, 280, 281
Environmental safety, 358
Ergodic hypothesis, 301
Ergosterol biosynthesis, 363
Error-correction feedback linear learning machines, 183
Es steric parameter, 30, 362
ESCA, 57
Ethane, 11
Ethers, 65, 66
Ethylene, 330
Even-tempered Gaussians, 21, 22, 26, 28
Evolutionary factor analysis, 177
Exponential functions, 4
Extended even-tempered Gaussian basis set, 24
Extended floating spherical Gaussian basis, 29
Extended Hückel theory (EHT), 46, 88, 337
Extinction coefficients, 357


F

6-Fluoroquinolones, 360
F (field) parameter, 123, 130
F atom, 23
Factor analysis (FA), 129, 175, 176
Factorial designs, 147, 155, 161, 170
Field gradient tensor, 85
Filter function, 175
Floating basis function, 30
Floating orbital geometry optimization (FOGO), 29
Floating spherical gaussian, 5, 28, 29
Flow chart of modeling, 350
Fluorine, 323, 2
Fock matrix, 49, 51, 53, 54, 55, 327
Forbidden region, 215
Force constants, 16, 63, 75, 86, 89, 109, 296
Force field, 322
Free energy perturbation (FEP) method, 295, 306, 308
Free-Wilson analysis, 135, 137, 140, 143
Full counterpoise method, 35
Fungicide, 362
Fused spheres van der Waals surface, 269, 271, 278, 281, 283
Fused spherical guided homotopy method (FSGH), 289


G

3-21++G, 33
3-21+G, 33
3-21G*, 14
3-21G, 8, 10, 12, 14, 17, 18, 19, 333, 337, 341
4-21G, 14
4-31G, 14
5-31G, 14
6-31G**, 18, 19, 20, 29, 31, 337
6-31G*, 7, 12, 14, 15, 17, 30, 334, 337, 341
6-31G*/3-21G, 334
6-31G, 14, 30
6-311++G(3df,3pd), 20
6-311G*, 8, 12
GAMESS, 10, 391
Gas chromatographic retention indices, 192
Gauge invariant atomic orbitals (GIAO), 108
Gaussian basis functions, 1, 2, 4, 5, 7, 93
Gaussian functions, 58
Gaussian primitive basis set, 7, 8, 14, 20, 21, 26, 28
GAUSSIAN, 10, 345, 390
Gaussian-1 method, 336
Gaussian-type orbitals (GTOs), 4, 329, 332
Generalized valence bond (GVB), 377
GENIE Control language, 222, 223, 243, 244
GENSAL, 222
Geometric data, 357
Geometric properties, 226, 249
Geometric search, 239, 240, 251
Geometrical basis sets, 22
Geometries, 69
Geometry optimization, 323
Global minimum energy structure, 214
GRADSCF, 391
Gram-negative organisms, 359
Grape diseases, 364
Graph theoretical treatment, 190, 237, 252
Greek key, 253
GRID, 390
GROMOS, 390
GSTAT, 236, 237
GVB, 377


H

(H2)2, 35
H2COH, 25
Hammett sigma constant, 189
Hansch-Fujita QSAR approach, 358
Hard spheres, 267
Harmonic approximation, 16
Harmonic dynamics, 298
Hartree, 8
Hartree-Fock ab initio methods (HF), 2, 10, 11, 16, 26, 28
Hartree-Fock energy, 21
Hartree-Fock level, 3, 5, 17
Hartree-Fock limit, 8, 15, 17, 18, 20, 29
Hartree-Fock wavefunction, 8
Hartree-Fock-Roothaan equation, 97, 327
Hashing function, 220
Hashing methods, 186
HCl, 331, 332
HCN, 15
Heat bath, 303
Heats of formation, 357
Helices, 253
Helium, 31, 34
Hellmann-Feynman force, 29
Helmholtz free energy, 309
Heme, 238
Herbicidal activity, 360, 361
Hessian matrix, 285
Heuristic, 221
HF/3-21G, 15, 20
HF/4-31G, 15
HF/6-31G**, 15
HF/6-31G*, 15, 20
HF/6-311G**, 15
HF/STO, 20
HF/STO-3G, 15
Hierarchical clustering methods, 185
Hierarchical trees, 186
HONDO, 10, 391
Hückel theory, 46, 49, 87
Hydrocarbons, 64
Hydrogen, 31, 34, 35
Hydrogen bonding, 34, 35, 36, 57, 58, 70, 214, 236, 237, 230, 243, 250, 342
Hydrogen bonding potential, 232
Hydrogen fluoride (HF), 24, 36
Hydrophobic properties, 121, 225
HYPERCHEM, 389
Hyperpolarizabilities, 57, 84, 103
Hysteresis, 312, 313


I

Independent variable, 359
Indicator variable, 359
INDO, 51, 52, 54, 89, 337
Information theory, 175
Infrared and Raman intensities, 357
Input, 329
Insect development disrupters (IDDs), 121, 163
INSIGHT/DISCOVER, 389
Interatomic distances, 357
Interatomic screens, 251
Intermediate neglect of differential overlap (INDO), 51, 52, 54, 89, 337
Intermolecular interactions, 1, 34
Internal coordinates, 330
Interpenetration of molecular contour surfaces, 281
Intrinsic reaction coordinates (IRC), 77
Inverse least-squares method, 180
Inverted (sorted) files, 186
Inverted bit map, 221, 239, 241
Iodine heptafluoride, 67, 68
Ionization potentials, 12, 71, 357
Isodata (Iterative self-organizing data), 185
Isodensity contour surface, 270, 272, 273, 281
Isomorphism, 251
Isomorphism algorithms, 218
Iterative least-squares methods, 183


J

Jelly roll, 253


K

K-matrix method, 179
K-means, 185
Kabsch-Sander algorithm, 250
Kalman filter, 174
Kappa indices, 191, 193
Ketones, 65
Koopmans' theorem, 70
Kovats retention index scale, 189, 192


L

Labeled graph, 239
Langevin equation of motion, 308
Langevin forces, 303
Lanosterol, 363
LCAO approximation, 5, 48, 327
Least-median of squares approach, 179
Lesk algorithm, 251
Levels of success, 355
LHRH, 247
Library searching, 186
Linear discriminant analysis, 183
Linear parametric equations, 192
Linear regression analysis, 138, 158, 178
Lipophilic parameters, 363
Lipophilicity potentials, 231
Lipophilicity, 123, 127, 132, 142, 190, 357, 358, 361, 362
Lithium, 31
Local canonical curvatures, 285
Local CI, 99
Local curvature properties, 283
Local space approximation (LSA), 99
Localized orbitals, 273, 277
Log P, 123, 132, 190
LSD, 238


M

MACCS, 224
MACCS-3D, 235, 240, 256, 389
MACCS-II, 235, 240
Macintosh, 384
MacroModel, 341, 387
Magnesium, 32
Magnetic dipole moment, 86
Magnetic properties, 107
Magnetic susceptibility, 86
Magnetizability, 86, 107
Many-body perturbation theory (MBPT), 91
Marine neurotoxins, 230
Markush structures, 222
MAXI-i, 26
Maximal common subgraph (MCS), 228
Maximum common substructure algorithm, 255
Maximum entropy, 175
MCSCF, 18, 28, 34
MENTHOR, 235, 243
Metamitron, 360
Methane, 330
Methotrexate, 227, 368
Methylene cyclobutane, 64
Metric matrix, 346
Metropolis Monte Carlo technique, 299
Microcanonical ensemble, 301
MicroChem, 386
MIDI split valence contracted basis, 13, 15
MIDI-i, 26, 27
Millihartree, 8
MINDO/3, 53, 54, 55, 56, 58, 62, 69, 75, 89, 336, 337, 338
MINI-i, 26
Minimal basis set, 5, 6, 17, 26, 88, 333
Minimization algorithms, 298
Minimum energy path, 77
Mixture analysis, 178
MM2', 362
MM2, 336, 349
MM2/MMP2, 200, 389, 338
MNDO, 2, 46, 57, 58, 62, 63, 69, 70, 71, 72, 73, 75, 88, 336, 337, 338, 363
MNDOC, 61, 75
Modified neglect of diatomic overlap (MNDO), 55
Molar refractivity (MR), 123, 359
Molecular body, 266
Molecular connectivity indices, 190, 193
Molecular descriptors, 358
Molecular dynamics, 295, 300, 321, 349, 355
Molecular electrostatic potential surfaces, 234, 274
Molecular electrostatic potential, 231, 274
Molecular energies, 357
Molecular flexibility, 238
Molecular geometries, 11
Molecular graphs, 218, 226
Molecular identification number (MID), 193
Molecular interactions, 357
Molecular mechanics, 1, 2, 3, 45, 70, 77, 138, 223, 233, 321, 324, 325, 336, 355, 362, 363
Molecular modeling, 321, 322, 265, 363
Molecular orbitals, 276, 332
Molecular orbital (MO) calculations, 1, 336
Molecular properties, 225, 355, 357
Molecular property surfaces, 234
Molecular quadrupole moment, 103
Molecular shape, 226, 265, 269, 274
Molecular similarity, 266, 288
Molecular simulations, 321
Molecular structure, 323
Molecular surface, 266, 268, 283
Molecular surface area, 357
Molecular topology, 190
Molecular volume, 357
MOLIDEA, 385
MOLPAT, 238, 248
Monte Carlo, 299, 300, 301, 313, 349
MOPAC, 56, 57, 70, 73, 74, 75, 336, 345, 363, 387
Morgan algorithm, 220
Morse potentials, 297
MP2, 16, 17, 18, 19, 30, 335, 337
MP2/6-31G*, 15
MP3, 30, 335, 337
MP3/6-31G**, 15
MP3/6-311G**, 15
MP4, 17, 18, 20, 35, 36, 335, 337
MP4/6-311G**, 15
MR SDQ-CIs, 18, 34
MSD, 226
MTD, 226
Multiple linear regression analysis, 138, 179, 192, 196, 358
Multiple three-dimensional pharmacophoric patterns, 248
Multipole polarizabilities, 103
Multivariate analysis, 169
Multivariate classification, 183
Multivariate curve resolution procedure, 177
Multivariate data, 175, 182
Myclobutanil, 362, 363
Myoglobin, 238
Møller-Plesset perturbation theory, 14, 17, 19, 335


N

N atom, 23, 31
N[+] atom, 23
N-(1-Methyl-1-phenylethyl-2-bromo-3,3-dimethylbutanamide), 362
N2 CO, 35
N2, 20
Nalidixic acid 1, 359, 360
Neglect of diatomic differential overlap (NDDO), 52, 53, 55, 62, 70, 71, 72
Neon, 32
Newtonian mechanics, 300
Newtonian trajectories, 303
NH3, 20, 25
NITRO, 385
Nitroethanol, 66
Nobel prizes, 379
Nonhierarchical clustering, 185
Nonparametric linear discriminant development methods, 183
Norbornan-2-ols, 198
Norfloxacin, 359
Normal mode analysis, 298
Nuclear magnetic resonance, 198
Numerical sensitivity, 337
Numerov-Cooley method, 101


O

O atom, 9, 23
O[-] atom , 23
OCOH, 18
Octanol/water system, 358
Octuple moment, 86
OH, 18, 24
Omega technique, 50
One-electron properties, 3
Operator, 325
Optical properties, 110
Orbital exponents, 4, 31, 32, 33, 329, 333
Organocarbon compounds, 213
ORTEP, 389
Output, 331
OWL, 236, 255
Oxacephalosporins, 368
Oxygen, 32


P

P-450 enzyme, 363
P-matrix method, 180
Papain, 238
Parameter focusing, 152
Parametric discriminant development methods, 183
Pariser-Parr-Pople method, 49, 87
Partial least-squares (PLS), 181, 233
Partition coefficient, 190, 358, 360
Patentability, 358
Pattern recognition, 152, 184, 248
Patterns of atoms, 249
PC software, 384
PCA, 176
PCILO (perturbative configuration interaction using localized orbitals), 88, 337
PCMODEL, 385
Perchloryl fluoride, 67
Perennial weeds, 362
Periodic boundary conditions, 302
Perturbation theory, 15, 19, 29, 30, 84, 87, 90, 110, 309, 376
Pharmaceutical industry, 357
Pharmacophore, 214, 215, 244, 246
Pharmacophore searching, 238
Pharmacophore target, 240
Pharmacophoric atoms, 227, 238, 244
Pharmacophoric conformations, 357
Pharmacophoric patterns, 239, 248, 254
Phenanthrene, 65
Phosphorus, 33
Photosystem II (PSII), 143, 361
Pi parameter, 123, 130, 142, 358
Pi-molecular orbital theory, 87
pKa's, 357
Plant growth regulators, 215
PM3, 58, 62, 63, 69, 70, 71, 72, 73, 75, 89, 336, 337
PMO theory, 46
Polarizability, 36, 57, 59, 84, 91, 103, 189, 191, 357
Polarization basis sets, 19, 334
Polarization counterpoise method, 35
Polarization functions, 7, 8, 16, 20, 22, 26, 28, 29, 30, 35
Polyenes, 3
Population analyses, 276
Post Hartree-Fock methods, 3, 334
Potential energy functions, 296, 297
Potential energy surfaces, 357
Prealbumin, 238
Predictions, 355, 374
Primitive functions, 5
Primitive gaussians, 6, 329
Principal components analysis, 175, 181
Principal components regression (PCR), 176, 181
Probability density, 305
Probability-based matching (PBM), 188
Programming languages, 222, 223, 224, 243, 244, 253
PROLOG, 253
Prometheus, 390
Propane, 11
Properties, 357
PROPHET, 389
Protein Data Bank (PDB), 214, 224, 234-237, 239, 249, 252, 253, 255, 256, 341, 342, 344
Protein structures, 213, 215, 251
Proton affinities, 357
Pseudomonas, 360
Pulay's method, 60, 61
Pyridazine, 65


Q

Quadrupole moment, 86
QUANTA/CHARMm, 388
Quantitative evaluation library searching (QELS), 187
Quantitative reliability metric (QRM), 187
Quantitative structure-activity relationship (QSAR), 119, 121, 125, 135, 143, 223, 225, 231, 254, 355, 358, 359, 361, 362
Quantitative structure-efficacy optimization (QSEO), 125
Quantitative structure-retention relationships (QSRR), 188, 192, 198
Quantum Chemistry Literature Data Base, 79, 365, 380, 381
Quantum Chemistry Program Exchange (QCPE), 256, 384, 387
Quantum chemistry, 1, 373
Quantum mechanics, 323, 324, 355
Query pattern, 251, 252, 254


R

R parameter, 123
r correlation coefficient, 159
Radicals, 69
Random phase approximation, 111
Rational design, 355
Reaction coordinate, 305
Reaction intermediates, 357
Reaction path, 75, 76, 357
Reaction topology, 286
Receptor mapping, 215, 232, 233, 237
Regression analysis, 361
Relativistic effects, 326
Relativistic Hartree-Fock wavefunctions, 91
Residuals, 178
Response surfaces, 170
Retention index (RI), 196
RMS, 228
Rydberg excited states, 3, 33, 34
Rydberg levels, 376


S

s standard deviation, 160
Saddle technique, 76
Sampling theory, 170
SAS CLUS, 144, 147
SAS CROSS, 129
SAS REGRESS, 158
Saxitoxin, 230
SCF, 18
Schrödinger equation, 325, 375
Screen search, 221, 238, 239
Screen similarity data, 255
SD-CI, 18, 22, 27, 28, 31, 35
SDQ-CI, 18
Searching structural fragments, 217, 219, 220
Second order hyperpolarizability, 36
Secondary binding sites, 121
Secondary structural elements, 249
Secondary structure motifs, 252, 253
Segmented contractions, 27
Semiempirical methods, 2, 47, 61, 87, 99, 328, 355
Semiempirical MO theory, 1, 2, 45, 328, 329
Sequential search, 186
Sequential simplex optimization (SSO), 161, 171
SHAKE, 301
Shape analysis, 282
Shape codes, 282, 288
Shape comparisons, 281
Shape graph, 285, 287
Shape group method (SGM), 283
Shape matrix, 284, 285, 286
Shape properties, 225, 237, 266, 270, 277
Shift technique, 59
Sickle cell disease, 366
Sigma parameters, 123, 142, 359
Signal processing, 173
Silicon, 33
SIMCA (Soft Independent Modeling by Class Analogy), 183, 184
Similarity matrix, 185
Similarity search, 218, 221, 222, 235
Similarity, 186, 225, 234, 282
Simple linear regression, 179
Simple mixing scheme, 59
Simplex method, 138, 164, 171, 183
SIMPLEX, 55, 74
Simulated annealing, 307
SINDO1, 75
Single-zeta basis set, 7
Size consistent, 19, 335
Slater determinant, 327, 331, 335
Slater-type orbitals (STOs), 4, 5, 49, 54, 329, 332
Slow growth technique, 312
Small molecules, 217
SMILES, 218, 220, 224, 235, 243
Smoothing function, 174, 304
Sodium, 32
Software, 255, 288, 364, 383
Solvation energies, 357
Solvent accessible surfaces, 265, 278, 282, 288
Somatostatin, 365
Space-filling models, 214
Spacers, 121
Spectroscopic properties, 357
Spherical gaussians, 57
Spherical harmonic, 4
Spin densities/ESR constants, 357
Spin-spin coupling constant, 86
Split valence polarization (SVP), 7, 14, 29
Split-valence basis set, 6, 333
Standard geometries, 345
Stationary points, 74
Statistical mechanics, 308
Stereochemically extended Morgan algorithm (SEMA), 220
Steric bulk, 357
Steric hindrance, 225
Steric parameters, 359, 363
Steric properties, 127, 226, 231, 243
Steric test, 244
STERIMOL parameters, 123, 144, 157
STO-3G, 10, 11, 12, 14, 16, 17, 18, 19, 27, 35, 333, 337, 341
STO-nG, 333
Stochastic boundary conditions, 304
Strand secondary structure elements (SSEs), 252
Strands, 253
Structural similarity, 254
Structure search, 217
Structure-activity relationships (SARs), 122, 135, 138, 214, 215, 282, 358, 361
Structure-property relationship (SPR), 188, 214
Structure-property space, 359
Structure-reactivity relationships, 225
Student's t test, 137, 158
Subgraph isomorphism, 220, 240, 249
Substituent set, 128, 143
Substructural environment, 243
Substructure search, 217, 220, 235
Successes, 355
Sugar beets, 361
Sulfur, 33, 63
Supercomputers, 367, 368, 392
Superstructure search, 217, 221, 235
SYBYL, 341, 388
Synthetic pathways, 225


T

Taft Es value, 359
Target transformation factor analysis method, 177
Templates, 223
Terminology, 4
Tetrodotoxin, 230
Thermodynamic cycles, 313
Thermodynamic integration method, 311, 312
Thermodynamic state function, 314
Thermodynamics, 357
THOR, 224
Three-dimensional molecular structures, 213, 215, 217, 218, 223, 228, 234, 236, 241, 295, 307, 321, 325, 345
Three-dimensional patterns, 253
Three-dimensional pharmacophoric patterns, 238
Three-dimensional properties, 231, 234, 236
Three-dimensional screen, 241
Three-dimensional similarity, 225, 227, 231, 234
Three-dimensional structure, 238, 249, 252, 357, 362
Three-dimensional substructure searching, 239, 242
Thymidylate synthase, 369
Thyroxine, 238
Time-dependent Hartree-Fock (TDHF) theory, 111
Topliss strategy, 125, 132, 133, 141, 142
Topological description, 253
Topological descriptors, 200
Topological indices, 189, 226
Topological shape, 191, 288
Torsional angles, 357
Toxophore, 121
Trajectory, 301
Transition probabilities, 110
Transition state theory, 305
Transition states, 18, 63, 75, 357
Transport properties, 357
Tree search, 251
Tree-searching algorithm, 240
Trimethoprim, 368
Triple zeta contracted functions, 27
Triple-zeta polarization functions, 7
Turn secondary structural elements, 250
Two dimensional screen, 241
Two-dimensional chemical structures, 217, 219, 225
Two-dimensional connection table, 242
Two-dimensional connectivity, 345
Two-dimensional similarity searching, 254
Two-dimensional substructure searching, 239, 241, 243, 254
Two-dimensional topological descriptors, 226


U

Ullman subgraph isomorphism algorithm, 240, 251, 253
Umbrella sampling, 305, 309, 314
Uncontracted even-tempered Gaussian, 34
Union, 215
Union surfaces, 231, 238, 244, 279, 288
United-atom model, 297
Universal basis sets, 22
Urinary tract infections, 359
UV excitation coefficients, 357


V

Valence-electron method, 53
Value-added compounds, 358
Van der Waals complexes, 34
Van der Waals distances, 57
Van der Waals energy, 200, 202
Van der Waals surfaces, 231, 244, 265, 267, 269
Van der Waals volume, 231
Variance-covariance matrix, 175
VAX computers, 250, 387
VDWSG, 289
Verlet algorithm, 300
Verloop length and width, 359, 362
Vertical ionization potentials, 13
Vibrational frequencies, 357
Vibrational frequency calculations, 56
Vibrational Schrödinger equation, 92, 100
Vibrational spectral properties, 306
Vibrational wave functions, 101
Vibrational-rotational Hamiltonian, 102
Virtual orbitals, 327


W

Warburganal, 228
Water, 8, 24, 36
Wavefunctions, 2, 374
Weighted paths, 200
Weiner number, 193
Well-tempered gaussians, 22, 26
Window method, 313
Woodward-Hoffmann orbital symmetry rules, 331, 357


Z

Z matrix, 329, 330
Zero-lag adaptive Kalman filter methods, 179
ZINDO, 75

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