REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 2 (1991)

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* algorithm, 17
AAMOM, 320
Ab initio, 84, 101, 102, 117, 119, 121, 144, 156, 165, 192, 219, 222, 313, 346, 358
Abscisic acid, 454
Accessible surface area, 63
Acetaldehyde, 231, 260, 261
Acetamide, 231, 247, 260, 290, 292
Acetic acid, 231, 260
Acetone, 231, 260
Acetonitrile, 246
Acetyl fluoride, 290, 291
Acetylene, 181, 231, 240, 260
Adaptive importance sampling Monte Carlo, 28
Additive atomic multipole moments (AAMM), 233
Adenine, 234, 279
ALADDIN, 492
Alchemy-II, 486
Alcohols, 383
Aliphatic Amines, 93
Alkanes, 109, 382
Alkylation, 279
Alloxan, 294
Alpha-helix, 67, 69
Alpha-modified kappa values, 402
AM1, 195, 285, 315, 339, 343-347, 355, 356, 466
AMBER, 38, 73, 114, 466, 489
Ambergris odor, 447
Amides, 247, 290
Amino acid residues, 11, 12
Aminoribofuranosides, 18
Ammonia, 231, 245, 260, 295
Ammonia dimer, 197, 200, 220
AMPAC, 347, 357, 495
Androstanedione, 37
Anesthetics, 386
Angiotensin converting enzyme (ACE), 11
Angle bending, 86
Anharmonicities, 26, 109, 125, 205, 207
Anilines, 388
Anisotropic van der Waals potential, 254
Anisotropy, 171, 178, 180, 182, 186, 209
Annealed molecular dynamics, 46
Annealing, 43
Anthraquinone, 282
Antibody hypervariable loops, 10, 24
Antiinflammatory activity, 406
Antisarcoma activity, 429
Antisymmetrization, 169
Antiviral activity, 388
Apo-alcohol dehydrogenase, 19
Arachidonic acid, 29
Arcs, 5
Artificial intelligence (AI), 8, 16, 427
Artificial potential function, 68
Aryl hydrocarbon hydroxylase, 281
Atom identity, 400
Atom-centered basis set, 177
Atomic charge model, 249, 256, 259
Atomic charges, 100, 293, 438
Atomic dipole model, 259
Atomic dipoles, 234
Atomic monopoles, 234
Atomic multipolar models, 234
Atomic multipoles, 147
Atomic polar tensor, 149, 150, 152
Atomic units, 228
Austin Model 1, 195, 285, 315, 339, 343-347, 355, 356
Avian pancreatic peptide, 17
Azabenzenes, 250, 251
Azimuthal angles, 131


B2H6, 248
Backbone conformations, 9, 10, 72
Backtracking, 5
Balaban J index, 380
Barbituric acid, 291
Basis functions, 171
Basis set dependence, 182
Basis set extension effects, 178, 179
Basis set superposition error (BSSE), 172, 173, 178, 179, 191, 207, 209
Basis sets, 166, 170, 205, 313, 338
Basis set 3-21G, 177, 179, 183, 185, 205, 209, 224
Basis set 3-21G*, 248
Basis set 4-21G, 95
Basis set 4-31G, 205, 209, 224
Basis set 4-31G*, 198
Basis set 4-31G**, 248
Basis set 6-31G, 205, 209, 224, 225, 249
Basis set 6-31G(d), 183
Basis set 6-31G(d,p), 183
Basis set 6-31G*, 95, 124, 126, 183, 185, 198, 205, 284, 286, 288
Basis set 6-31G**, 145, 151, 175, 198, 200, 225, 228, 234, 238, 239, 243, 244, 255-257
Basis set 6-31+G(d), 183
Basis set 6-31+G(d,p), 183
Basis set 6-31+G**, 193
Basis set 6-31++G(d), 183
Basis set 6-311+G(d,p), 183
Basis set 6-311+G(2df, 2p), 197
Basis set 6-311++G(2d,2p), 183
Basis set 6-311++G(3df,3pd), 177, 183
Basis set 6-311G**, 224
Basis set Double-zeta STOs, 223
Basis set DZP, 183, 206
Basis set Gaussian basis set, 287
Basis set MINI-1, 175, 179, 209
Basis set n-31G, 224
Basis set Slater-type atomic orbital (STO), 223, 330
Basis set STO-3G, 174, 175, 179, 183, 185, 205, 224, 240, 245, 276, 285, 296, 347
Basis set STO-4G, 224
Basis set STO-5G, 279, 283, 285, 291, 292, 296, 298, 299
Basis set STO-6G, 224
Basis set STO-nG 174, 209, 223
Beads-on-a-string model, 72
Bent bond, 303
Benzene, 153, 154, 234, 240, 259, 279
Benzene dimer, 220
Benzimidazoles, 388
Beta-barrel, 69
Beta-sheets, 66
Beta-strand, 67
BH3NH3, 238
Bicyclobutane, 302
Bicyclo[1.1.1]pentane, 86
Bicyclo[3.3.0]octane, 92
Bifurcated geometries, 192, 195
Bifurcated hydrogen bonds, 60
Bioconcentration factor (BCF), 389
BIOGRAF, 490
BIO-GROMOS, 490
Bioreceptor, 439
Biphenyls, 83, 282, 389
Black box, 358
Boat conformation, 15
Boiling point, 390
Boltzmann, 25, 28
Boltzmann-weighted trajectory, 61
Bond charge models, 254
Bond dipole models, 245, 259, 261
Bond dipole moments, 89, 100, 262
Bond energy, 91
Bond path concept, 302
Bond stretch, 59, 85, 107
Born-Oppenheimer approximation, 82, 102, 106, 112, 121, 328
Boundary effects, 62
Boundary groups, 434
Boundary surfaces, 391
Bovine pancreatic trypsin inhibitor (BPTI), 14, 26, 61, 63, 72
Branch index, 370
BrH, 207
Bromo substituent, 445
Brookhaven Protein Data Bank (PDB), 18, 19, 63, 64, 73, 483
Brownian motion, 26
Broyden-Fletcher-Goldfarb-Shanno procedure, 337
Buckingham potential, 88
Buckingham-Fowler model, 180
Build-up approach, 13
Build-up procedures, 65
Butane, 16, 95, 126
2-Butanone, 95
t-Butyl group, 445


C2H2, 179
C6F6, 241
CAChe, 486
CADPAC, 490
Cahn-Ingold-Prelog system, 34
Cambridge Structural Database (CSD), 18, 23
CAMSEQ/M, 486
Canonical structures, 66
Carbon atom, 321
Carbon dioxide, 221, 231, 244
Carboxypeptidase A, 60
Cartesian coordinate, 20
Cartesian derivatives, 120
Cartesian stochastic search, 20
CCSD-T technique, 190
CEPA-1, 206
CERIUS, 490
C-H bond lengths, 114
CH2O, 242
CH2=C=O, 242
(CH3)2CO, 242
(CH3)2O, 242
(CH3)2NH, 245
(CH3)3N, 245
CH3CHO, 242
CH3CN, 245
CH3CONH2, 246
CH3CONHMe, 246
CH3COOCH3, 243
CH3COOH, 242
CH3F, 241
CH3NH2, 245
(CH3)NH3+, 167
CH3OH, 242
CH4, 220
Chain folding, 63
Chair conformation, 15
Charge, 345
Charge controlled interaction, 428
Charge density, 273
Charge flux, 148, 150
Charge polarization, 257
Charge screening, 63
Charge transfer, 170
CHARMM force field, 114
Chem3D Plus, 487
ChemCad+, 487
Chemical Design Automation News, 470
Chemical graph theory, 369, 394
Chemical reactivity, 273
CHEMLAB-II, 494
CHEM-X, 491
Chi indexes, 367, 368, 376, 378, 386
Chiral constraints, 34, 37
Chiral volume, 34
Chromatographic retention, 380
Chymotrypsin, 436, 448, 451, 452
CISD, 184
Citation classic, 469
ClF, 181
CLOGP, 492
Closed shell, 165
Cluster, 377
Cluster analysis, 457
CN-, 245
CNDO/1, 330, 348
CNDO/2, 331, 333, 348, 429, 435, 436, 438, 463
CNDO/BW, 331
CNDO/S, 329, 332, 333, 356
CO, 180, 181
CO2, 242, 258, 260
CO32-, 243
COBRA, 491, 492
COLUMBUS, 491
Combination rules, 144, 145
Combinatorial explosion, 4, 11, 14
Combinatorial optimization, 28
Commutation relation, 337
Complete neglect of differential overlap (CNDO), 319, 329, 356
Compositional method, 434
Computational biology, 471
Computational chemistry literature, 461
Computational observables, 120, 148, 157
Computer graphics, 19
Computer programs
ALADDIN, 492
Alchemy-II, 486
AMBER, 38, 73, 466, 489
AMPAC, 347, 357, 495
BIOGRAF, 490
BIO-GROMOS, 490
CAChe, 486
CADPAC, 490
CAMSEQ/M, 486
CERIUS, 490
Chem3D Plus, 487
ChemCad+, 487
CHEMLAB-II, 494
CHEM-X, 491
CLOGP, 492
COBRA, 491, 492
COLUMBUS, 491
CONCORD, 486, 492, 496
DAYMENUS, 491
DGEOM, 495
DelPhi, 493
Desktop Molecular Modeller, 487
DGEOM, 495
DISGEO, 495
DMol, 493
ECEPP2, 495
ENZYMIX, 490
GAMESS, 223, 492
GAUSSIAN, 223, 278, 284, 468
GAUSSIAN-86, 224
GAUSSIAN-90, 492
GRADSCF, 151, 492
GRID, 492
GROMOS, 493
HAMOG, 487
Homology, 493
HONDO, 223, 493
IBMOL, 223
INSIGHT/DISCOVER, 493
MacMimic, 487
MacroModel, 494
MAD, 494
MicroChem, 488
MM2, 20, 21, 59, 84, 86-88, 90, 93, 94, 109, 263
MM2/MMP2, 494, 495
MM3, 86-88, 90, 93, 94, 109, 263, 494
MNDO, 285, 315, 338, 343, 344, 348, 355, 356, 429
MNDOC, 338, 495
MOBY, 488
MOLCONN, 413
MOLIDEA, 488
MOPAC, 338, 347, 357, 468, 488, 495
MULTIC, 8, 11, 21
NITRO, 486
NMRGRAF, 490
PCMODEL, 489
PLUTO, 496
POLARIS, 490
POLYATOM, 223
POLYGRAF, 490
Prometheus, 495
Prophet, 495
QPACK, 64, 73
QUANTA/CHARMm, 495
QUEST, 496
SAS, 389
SAVOL2, 492
SYBYL, 486, 496
TOPKAT, 489
TOPMOST, 489, 492
Yeti, 496
ZINDO, 342, 347, 348, 357, 496
Computer-assisted molecular design (CAMD), 469
Computers and Chemistry, 470
CONCORD, 486, 492, 496
Configuration interaction (CI), 172, 175, 177, 223, 225, 256, 313, 335, 348, 353
Configuration space, 129
Conformational analysis, 1, 16-18, 30
Conformational correctness, 67
Conformational diagrams, 15
Conformational energy surface, 2, 25
Conformational entropy, 2
Conformational motifs, 74
Conformational partition function, 3
Conformational sampling, 70
Conformational searching, 2, 3, 21, 58
Conformational space, 1, 10, 11, 15, 16, 20-22, 25-29, 37, 40, 43, 45, 60, 61, 68
Conformational states, 17, 57
Conformational substates, 58, 62
Conformations, 3, 289, 407
Conformers, 2
CONGEN, 9, 10
Conjugate gradients, 33
Connectivity indexes, 390
Connolly surface, 238
Consistent force field (CFF), 73
Constrained molecular mechanics minimization, 45
Contour plots, 231
Core electrons, 330
Core integral, 320
Core-core repulsion term, 339
Core-valence effective potential, 337
Correlation, 185, 189, 191, 205, 328
Correlation coefficient, 296
Correlation effects, 186
Cosine series, 110
COSY, 37
Coulombic interaction, 65, 113, 135, 165, 167, 186
Coulomb's law, 89, 107, 140, 145, 227, 236, 256
Counterpoise correction, 173, 174, 188, 190, 191, 198, 209
Coupled pair functional method (CPF), 172, 198, 206
Coupled-cluster technique, 187, 190, 313
Coupled-electron pair (CEPA), 172
Coupled-perturbed many-electron theory, 313
Coupling force constant, 115
Coupling functions, 114
Covalent radii, 401
Crambin, 73
Cray X-MP, 190
Cross terms, 89, 114, 116, 123
18-Crown-6, 37, 42
Cryptand, 44
Crystal packing forces, 20, 470
Crystallographic databases, 18
Cubane, 302
Cumulative atomic multipole moments (CAMM), 233
Cyanogen, 246
Cycloalkanes, 20
Cyclobutane, 126
Cyclobutanone, 87
Cyclodecane, 88
Cyclododecane, 37
Cycloheptadecane, 20, 21
Cycloheptane, 20
Cyclohexane, 1, 2, 15, 16
Cyclomatic number, 378, 430
Cyclononane, 21
Cyclooctane, 37
Cyclopentane, 91, 126
Cyclopropane, 126, 302
Cyclosporin, 46, 247
Cytochrome c-cytochrome b5 complex, 60
Cytochrome P-450, 388
Cytosine, 275, 276, 279


2D NMR, 37, 45, 47
Daughter (or leaf) nodes, 5
DAYMENUS, 491
Del Re method, 222, 232
DelPhi, 493
Delta chi indexes, 383, 384
Density functional methods, 273, 285, 329
Density matrix, 222, 434-436
Depth-first search, 5
Descriptive centers (DC), 426
Desktop Molecular Modeller, 487
DGEOM, 495
Diagonalization, 317
Dibenzo-p-dioxin, 281, 296
Diborane, 248
Dielectric constant, 70, 114
Difference index, 386, 389
Differential potentials, 132
Diffuse functions, 348
Diffusion equation method, 39
Diffusional relaxation, 62
Dihedral potentials, 110, 129, 132, 133
Diisopropylamine, 92
Dimer-centered basis set (DCBS), 173
Dimethyl ether, 231, 260
Dimethylamine, 231, 245, 260
3,3-Dimethylpentane, 412
Dinitroglycolurile, 291
2,2'-Dinitrophenyl-6,6'-dicarboxylic acid, 87
Dioxins, 281, 283
Diphenylurea, 298
Dipole integrals, 337
Dipole interactions, 88, 89, 170, 177
Dipole length operator, 334, 348
Dipole moments, 89, 149, 152, 219, 221, 224, 225, 243, 346, 356
Dipoles, 27, 258, 286
Discriminant analysis, 368
DISGEO, 495
Dispersion, 112, 168, 170, 171, 175, 184, 186, 187, 189, 209, 220, 393
Dissociation energy, 108
Distance constraints, 60
Distance geometry, 4, 21, 20, 33, 35, 46, 47
Distance space, 39
Distortion energies, 202
Distributed dipole model, 232
Distributed multipole,180, 249
Disulfide bond, 14
DMol, 493
DNA, 13, 14, 38, 275
Double-zeta STOs, 223
Drug-receptor interactions, 280
Drugs, 100
Dynamic correlation, 328
Dynamic programming, 13
DZP, 183, 206


ECEPP, 13, 27, 39, 42, 43, 469
ECEPP2, 495
Edge weights, 370, 375
Edges, 369, 378
Effective core potential, 320
Effective dielectric constant, 63, 89
Electric field, 27, 149
Electric field gradient, 253
Electric potential, 219, 226, 237, 249, 257, 273, 274
Electron affinities, 331
Electron correlation, 167, 168, 170, 172, 184, 194, 209, 220, 223, 284, 285
Electronegativity, 221
Electronic charge, 303
Electronic density, 273, 274, 284, 285, 285, 289
Electronic properties, 432
Electron-topological approach, 423, 431, 437, 456
Electron-topological matrix of congruity (ETMC), 431, 436, 438, 449
Electron-topological submatrix of activity (ETSA), 433, 436, 448, 450, 452
Electrophilic attack, 303
Electrophilic processes, 278
Electropological state index, 415
Electrostatic contribution, 240
Electrostatic energy, 11, 169, 180, 219, 232, 240, 428
Electrostatic interactions, 62, 65, 100, 121, 140, 146, 148, 171, 179, 202
Electrostatic potentials, 148, 273, 282, 284, 429, 430
Electrostatically driven Monte Carlo, 27
Electrostatics, 16, 82, 89, 146, 155.,175, 186, 209, 263
Ellipsoid algorithm, 39, 40
Embedding, 31, 33
Empirical force fields, 99
Empirical pair potentials, 70
Empirical residue contact energies, 69
Energy derivatives, 119
Energy embedding, 37, 38
Energy function, 38, 42, 66
Energy minimization, 5, 21, 39
Energy surface, 84
Energy-biased conformational search, 65
Enkephalin, 28
Entropic effects, 28, 62, 100
Entropy, 2, 60
Enzyme inhibitors, 410
Enzymes, 100
ENZYMIX, 490.
Equilibrium structure, 179
Ergodic assumption, 60
Error function, 33, 72
Essential correlation, 328
Ethane, 2, 110, 124, 126, 129, 132, 134
Ethylene, 153, 154, 231, 240, 259, 260
Ethylphosphine, 91
Eulerian rotation factors, 332
Exchange (EX), 181
Exchange phenomena, 168, 169
Exchange repulsion, 172
(Exponent-6-1) function, 252
Expert systems, 431
Exponents, 330
Extended Hückel theory (EHT), 324, 325, 340, 348, 355, 356, 429, 462, 463
Extended Mulliken schemes, 326


Face-centered cubic lattice, 69
Far-IR, 203
Fenske-Hall scheme, 327
Ferrocene, 321
Filters, 11, 66
Flavodoxin, 64
Flexibility index, 408
Fluorobenzene, 279
Fluorohydrocarbons, 254, 255
Fock equations, 315-318
Fock matrix, 338
Fock-Dirac density matrix, 317
Folded proteins, 65, 66
Folded states, 68
Force constant, 85, 117, 119, 129, 357
Force field, 42, 58, 62, 73, 83, 84, 92, 117, 119, 122, 127, 148
Force parameters, 94, 122
Foreshortened C-H bond length, 241, 252
Formaldehyde, 145, 147, 153, 154, 231, 239, 244, 259-261
Formamide, 104, 105, 120, 145, 153, 154, 231, 239, 247, 259, 260, 284, 286, 288
Formate anion, 111
Formic acid, 231, 244, 260
Four helix bundle motif, 67
Fourier, 23, 87, 135
Fragment, 15, 19, 376, 434
Fragment conformations, 18
Fragment properties, 220
Fragment-based, 17
Fragment-based conformational search, 12
Fragment-joining, 12
Free energy perturbation, 100
Frontier electrons, 462


3-21G, 177, 179, 183, 185, 205, 209, 224
3-21G*, 248
4-21G, 95
4-31G, 205, 209, 224
4-31G*, 198
4-31G**, 248
6-31G, 205, 209, 224, 225, 249
6-31G(d), 183
6-31G(d,p), 183
6-31G*, 95, 124, 126, 183, 185, 198, 205, 284, 286, 288
6-31G**, 145, 151, 175, 198, 200, 225, 228, 234, 238, 239, 243, 244, 255-257
6-31+G(d), 183
6-31+G(d,p), 183
6-31+G**, 193
6-31++G(d), 183
6-311+G(d,p), 183
6-311+G(2df, 2p), 197
6-311++G(2d,2p), 183
6-311++G(3df,3pd), 177, 183
6-311G**, 224
GAMESS, 223, 492
Garlic aroma, 447
Gasteiger charges, 222
GAUSSIAN, 223, 278, 284, 468
GAUSSIAN-86, 224
GAUSSIAN-90, 492
Gaussian basis set, 287
Gaussian-type functions (GTOs), 223
Geometric models, 393
Ghost orbitals, 173, 178
Global energy minimum, 2, 3, 17, 18, 20, 25-29, 42, 58, 73, 200
Global free energy, 28
Globular proteins, 70
Glycine, 10
GRADSCF, 151, 492
Graph edges, 394
Graph theory, 367, 430
Graph vertexes, 394
Graph-based structure analyses, 394
GRID, 492
Grid points, 237, 238
Grid search, 4
GROMOS, 493
Guanine, 10, 279


H2CO, 165, 179, 205, 206, 220
H2NCONH2, 248
H2NCSNH2, 248
H2O, 151, 153, 154, 175, 177-181, 185, 192, 197, 201, 204, 205, 228, 231, 234, 242-244, 254, 259, 260, 289
H2S, 180
H3N, 204
H3P, 204
1-Halonaphthalenes, 282
HAMOG, 487
Hammett constant, 427
Hansch method, 427
Hard-sphere models, 64, 180, 181, 209, 220
Harmonic model, 26, 82, 102, 103, 108, 115, 119, 125, 128, 203
Hartree-Fock, 120, 144, 170, 181, 187, 194, 198, 223, 313, 315
Hartree-Fock limit, 209, 225
Hartree-Fock wavefunctions, 225, 284
HCl, 203, 204, 206, 207, 241
HCN, 167, 181, 206
HCONH2, 246
HCONHMe, 246
HCOOCH3, 242
HCOOH, 248
Heat of atomization, 383
Heats of formation, 91, 93
Heats of sublimination, 89
Heitler-London interaction energy, 169
Helices, 66
Heptane isomers, 414
Hessian, 119, 125, 128, 193, 194, 252, 356
Hexa-aqua Cr(III), 350
Hexafluorobenzene, 254
Hexanes, 379, 395
HF, 153, 154, 178, 179, 181, 182, 192, 196, 203-208, 220, 221
HF dimer, 196
High temperature annealed molecular dynamics, 44
Highest occupied molecular orbital, 427
Hill equation, 88
HIV zinc finger, 38
Hohenberg-Kohn theorem, 285
Homocubane, 302
Homologous proteins, 9, 66
Homology, 493
Homology modeling, 9, 23, 67
HONDO, 223, 493
Hooke's law, 85, 86
Hot spots, 59
Hückel theory, 319
Human carbonic anhydrase, 19
Human growth hormone, 67
Human immuno-deficiency virus (HIV), 67
Human plasminogen, 38
Hybrid force field, 112
Hydration, 24, 100
Hydrazine, 344
Hydrocarbons, 100, 314, 383
Hydrogen bond, 16, 60, 67, 70, 114, 165, 202, 220, 254, 255, 257, 273, 282, 298, 299, 302, 344
Hydrogen fluoride (HF), 231, 234, 241, 259, 260
Hydrogen-suppressed graph, 369, 394
Hydrolysis rates, 392
Hydrophilic residues, 72
Hydrophobic area, 11
Hydrophobic attraction, 72
Hydrophobic core, 63
Hydrophobic residues, 72
Hydrophobicity, 63, 247, 469
Hyperpolarizabilities, 338
Hypervalent compounds, 343
Hypervariable loops, 45, 66


IBMOL, 223
Imidazolidinines, 294
Immediacy index, 471
Immunoglobulins, 66
Impact factor, 471
Improper torsion, 87, 111
INDO, 333, 337, 356
INDO/1, 348, 355
INDO/2, 333, 348
INDO/S, 329, 333, 335, 348, 354-356
Indomethacin, 406
Induced polarization, 62
Inductive effects, 393
Information content, 398
Infrared spectroscopy, 1, 118, 129
INSIGHT/DISCOVER, 493
Interatomic distances, 30
Interleukin-2, 67
Intermediate neglect of differential overlap (INDO), 320, 333
Intermolecular electrostatic energy, 247
Intermolecular interaction, 203, 240
Internal coordinate, 20, 104, 105
Internal coordinate random method, 21
Internal rotation, 110
International Journal of Quantum Chemistry, 470, 474
Inverted lone pair electron sites, 256
Ionization potential, 384
Isodesmic reaction, 303
Isopentane, 376, 377
Iterative extended Hückel theory (IEHT), 341, 348, 356


J-index, 430
Journal of Chemical Information and Computer Sciences, 470
Journal of Chemical Physics, 469, 474
Journal of Chemometrics, 470
Journal of Computational Chemistry, 469-474
Journal of Computer-Aided Molecular Design, 470
Journal of Molecular Graphics, 470
Journal of Molecular Structure, 470, 474
Journal of Physical Chemistry, 469
Journal of the American Chemical Society, 469, 474


Kappa indexes, 367, 368, 396, 399
Knight's move, 69
Knowledge, 16
Knowledge-based modeling, 63, 64, 67
Knowledge-based protein modeling, 58
Koopmans' approximation, 345, 351, 352


Lagrange multiplier, 24
Lanthanide series, 333
Lattice models, 68, 69
Least cost path, 17
Least squares, 235
Lennard-Jones potential, 73, 88, 107, 113, 135, 140, 155
Linear graph, 397
Linear regression statistics, 383
Lipophilicity, 440
Local conformational space, 59
Local conformational subsearches, 63
Local density functions, 180, 284
Local energy minima, 13
Local minima, 2, 39, 275, 446
Logical-structural analysis, 426
London formula, 175
Lone pair sites, 254
Loop conformations, 23, 64, 65
Löwdin-type orbitals, 322
Lower bounds, 41


MacMimic, 487
Macrocyclic structures, 23
MacroModel, 494
MAD, 494
Many-body perturbation approach, 172, 187
Markov process, 26
Markovnikov addition, 277
Matrix of connections of the descriptive centers, 426
Meat odor, 447
Mechanism-free model, 390
Meisenheimer complexes, 289
Met-enkephalin, 13, 26, 29, 42
Methane, 231, 240, 258, 260
Methanol, 231, 240, 244, 260, 261
N-Methyl acetamide, 112, 113
Methyl acetate, 231, 260
Methyl fluoride, 231, 260
Methyl formate, 231, 260
N-Methylacetamide, 231, 247, 260, 261
Methylamine, 231, 245, 260, 261
Methylene chloride, 90
Methylene radical, 223
N-Methylformamide, 231, 247, 260
Metric matrix, 32, 36, 37
Metropolis algorithm, 25-29, 61, 73, 99
Mg-Porphine, 352
MicroChem, 488
Microsomal p-hydroxylation, 388
MINDO, 343-348, 429, 430
MINDO/3, 335, 338, 343, 347
MINI-1, 175, 179, 209
Minimal steric difference (MSD), 393
Minimal topological difference (MTD), 393
Minimization algorithms, 3
Minimization of surface area, 67
Minimum basis set, 329, 345, 285
Minimum energy conformations, 16
Minimum valence basis set, 314
Mixing energy, 170
MM2, 20, 21, 59, 84, 86, 87, 88, 90, 93, 94, 109, 115, 263
MM2/MMP2, 494, 495
MM3, 86-90, 93, 94, 109, 115, 116, 263, 494
MMI, 115
MNDO, 285, 315, 338, 343, 344, 348, 355, 356, 429
MNDOC, 338, 495
MOBY, 488
Model, 313
Model building, 4, 12
Modified neglect of diatomic overlap (MNDO), 338
Molar refraction (MR), 385, 393
Molar volume, 382
MOLCONN, 413
Molecular cavities, 405
Molecular connectivity, 367, 368, 371, 373, 375
Molecular descriptors, 425
Molecular design, 433
Molecular dynamics, 4, 21, 24-26, 38, 42, 47, 48, 59, 73, 99, 254
Molecular electric potential, 146, 152, 219, 235, 259
Molecular flexibility, 406
Molecular graph intersection, 436
Molecular graphics, 12, 430
Molecular graphs, 369, 424
Molecular mechanics, 3, 16, 38, 42, 58, 60, 81, 107, 115, 127, 221, 222, 263, 314, 466, 469
Molecular mechanics energy, 67
Molecular modeling, 12, 481
Molecular moments, 172
Molecular multipoles, 221, 232
Molecular orbital theory, 313
Molecular packing analysis (MPA), 243, 249, 254
Molecular polarity, 232
Molecular shape, 372, 391, 394, 404
Molecular size, 389
Molecular structure, 368
Molecular structure files, 483
MOLIDEA, 488
Møller-Plesset (MP), 172, 177, 181, 184, 186, 190-192, 209, 223, 225, 284
Monomer-centered basis set (MCBS), 173
Monopole, 234, 258, 285
Monte Carlo calculations, 26, 28, 61, 62, 68-70, 73, 99
MOPAC, 338, 347, 357, 468, 488, 495
Morokuma partitioning, 170, 180
Morse potential, 85, 86, 108, 124, 125, 128
Motional behavior, 42
MP2, 177, 183, 184, 186, 190, 194, 198, 200, 206, 288
MP3, 190, 209
MP4, 177, 190, 197, 198, 209
Mulliken approximation, 325
Mulliken electronegativity, 331
Mulliken population analysis, 325, 327, 330, 345, 355
Mulliken valence state electronegativity, 375
MULTIC, 8, 11, 21
Multicenter multipole expansion, 233
Multicenter multipole models, 252, 258
Multiplicity, 316
Multipole expansion, 202, 232, 234, 285
Multipole moments, 100, 175, 187, 189, 219
Musk fragrance, 423, 438, 440, 441


n-31G, 224
n-31G*, 224
n-31G**, 224
NaCl, 101
Naphthalenes, 296
Natural bond length, 85
Natural lengths and angles, 83
NCCN, 245
Negentropy, 398, 400
Neglect of differential diatomic overlap (NDDO), 321, 338,
Net atomic charges, 221, 225
Neural networks, 17
Newton's second law, 42, 59, 148
NH2CH3, 207
NH3, 165, 178, 179, 192, 199-201, 207, 220, 245
NITRO, 486
1-Nitro-2-imidazolidinone, 295
Nitrogen molecule, 323
Nitromusks, 441
NMR, 1, 13, 23, 38, 41, 45, 46, 57, 66, 117, 166
NMRGRAF, 490
NMR NOE, 60
NNDO, 329
NO2, 180
Nobel laureates, 461
Nodes, 5, 17, 70
NOESY, 37
Nonatomic sites, 249
Nonbonded interactions, 11, 112
Nonbonded parameters, 141
Nonbonding pair of electrons, 165
Nonempirical molecular orbital method (NEMO), 340
Normal modes, 26, 62, 72, 107, 120, 122, 124, 128, 202
Nuclear charge, 225
Nucleic acids, 100, 288, 466
Nucleophilic attack, 303
Nucleophilic processes, 289


Object comparisons, 393
Objective function, 41, 42
O(CH3)2, 208
Octupole moments, 221
(OH)3PS, 248
OPLS, 147
Orbital anisotropies, 322
Orbital controlled interaction, 428
Orbital space, 170
Orbital symmetry rules, 462
Oscillator strengths, 334, 348
Othogonalization, 322
Out-of-plane bending, 86, 111
Overlap matrix, 319
Oxyheme, 351


Pairwise potentials, 72
Parabanic acid, 294
Parameterization, 92, 328
Parametric Method 3 (PM3), 339
Pariser-Parr-Pople model (PPP), 319, 332, 348, 463
Partition folding, 28
Path counts, 377, 378, 395, 396
Pattern recognition, 368, 425
Pauli principle, 226
PCMODEL, 489
Pentane, 35, 126
Peptides, 43, 58, 99, 100
Periodic boundary conditions, 62
Perturbation procedure, 168, 181,186, 277, 313, 319
PH3, 248
Pharmocophore, 11, 372, 407
Phase angles, 22
Phase space, 60, 61, 73
Phenanthrene, 282
Phenol toxicity, 387
Phi-psi maps, 10, 17, 27, 62, 73, 99
Pi-electron method, 318
Pitzer acentric factor, 409
Pitzer's steric partition function, 407
Plant growth regulators, 454
PLUTO, 496
PM3, 315, 339, 343-347, 355, 356
Point dipoles, 89, 146
Point multipoles, 179, 209, 146
Poisson's equation, 273, 429
Polar coordinates, 22
POLARIS, 490
Polarizability, 101, 117, 177, 178, 184, 187, 338, 385
Polarization, 171, 181, 224, 257
Polarization energy, 170, 257
Polarization functions, 187, 198, 205, 224, 337
Polyalanines, 29
POLYATOM, 223
POLYGRAF, 490
Poly(L-Ala) peptide, 27
Polymer models, 68
Polypeptide backbone, 65
Polypeptide loop structures, 9
Polypeptides, 3, 13, 17, 19, 26, 27, 226
Population analysis (PA), 225, 234, 249, 345, 461, 463
Population analysis charges, 220
Potential energy, 2, 103
Potential energy function, 2, 58, 82
Potential energy surface, 89, 120, 121, 192, 198, 210
Potential functions, 38
Potential minima, 285
Potential-derived (PD) atomic multipole models, 244, 258
Potential-derived charges, 220, 232, 235
Prediction probability, 446
Projection of differential diatomic overlap (PDDO), 326
Proline, 10
Prometheus, 495
Propane, 126, 136, 137, 139
Prophet, 495
Propyne, 277
Protein conformation, 68
Protein crystal structures, 19
Protein dynamics, 26
Protein engineering, 60
Protein folding, 26, 38, 58, 63, 68
Protein fragments, 13
Protein interaction, 221
Protein loop conformations, 10
Protein simulation, 61
Protein structure, 57
Proteins, 3, 9, 17, 24, 27, 38, 46, 99, 100, 466
Pruning, 5, 11, 16
Pseudo bond, 45
Pseudo-acyclic, 8
Pseudo-energy, 46
Pseudo-exchange repulsion, 179
Pyrazine, 249, 251, 253
Pyridazine, 249, 251
Pyridine, 153, 154, 249, 250, 251, 259, 321, 349, 350
Pyrimidine, 249, 250, 251, 253


QCPE, 484, 488, 495
QCPE Bulletin, 470
QPACK, 64, 73
Quadrupole moments, 180, 221, 243, 244, 254, 256
Quadrupoles, 247, 258, 286
QUANTA/CHARMm, 495
Quantitative structure-activity relationships (QSAR), 367, 371, 380, 393, 423, 424, 469
Quantitative Structure-Activity Relationships, 470
Quantum mechanics, 3
QUEST, 496


Ramachandran plots, 10
Raman NMR, 129
Random correlations, 387
Random distance matrix, 36
Random distortion, 21
Random incremental pulse search (RIPS), 20
Random methods, 4
Random sampling, 17
Random search methods, 20, 23, 24, 46
Random simulations, 25
Random tweak method, 23
Random walk, 21
Randomization, 20
Reaction pathways, 356
Receptor, 11, 427
Rediscovery, 8
Redundancy index, 399
Relational protein database, 19
Relative root-mean-square (rrms), 238, 239, 256
Reliability, 342
Repulsive exchange energy, 220
Residue interaction potentials, 73
Residue solvent accessible surface areas, 64
Residue-based contact interaction potential, 69
Residue-based model, 72
Residues, 17
Resonance integrals, 329
Response surface optimization, 389
Restrained molecular dynamics, 45
Restricted bond dipole, 259, 261
Restricted bond direction, 259
Restricted Hartree-Fock (RHF), 171, 348
Restricted open-shell Hartree-Fock (ROHF), 333, 348
Restricted rotational isomeric model, 65
Retinol-binding protein, 19
Reversed-phase thin-layer chromatographic data, 381
Ring, 377
Ring closure contraints, 8
Ringmaker, 8
rms, 259
rms deviations, 14, 19, 66, 67, 70, 72, 147
rms electric potential, 231, 232
rms error, 205
rms fit, 238, 239, 250
Root node, 5
Rotamer conformations, 19
Rotational energy embedding, 38
Rotational invariance, 319, 321, 329
Rotational isomeric model, 69
Rydberg orbitals, 335
Rydberg states, 348


Saddle point, 193
SAS, 389
SAVOL2, 492
Scaling, 224
SCF, 206
Schrödinger equation, 101, 102, 120, 231, 314, 315
Science Citation Index (SCI) 463
Script, 15
SDTQ-MBPT(4), 190
Search tree, 11, 16
Searching methods, 51
Secondary structure, 17, 57, 66, 68
Self-consistent charge model (SCC-EH), 341
Self-consistent field (SCF), 318
Semiempirical molecular orbital methods, 84, 209, 313, 353
Sequence, 19
Sequence homology, 65
Sequence space, 68
SH2, 248
SHAKE, 43
Shape congruence, 406
Shape identity, 400
Shape index, 396, 397, 398
Shape parameters, 393
Shape similarity, 405
Similarity, 392
Simple delta, 373
Simulated annealing, 61
SINDO1, 320, 336, 346, 347, 355, 356
Site charges, 257
Site multipole series, 234
Skeletal atoms, 378
Slater-Condon factors, 334
Slater-Condon integrals, 321, 333
Slater-type atomic orbital (STO), 223, 330
SN2 reaction, 83
SO2, 179
Software, 481
Solubility, 390
Solvation, 13, 62, 64
Solvatochromic parameters, 298
Solvents, 59, 62, 281, 284, 298
SPC, 151
Spectroscopic force fields, 83, 106, 115, 125
Spectroscopy, 333
SPEEDY, 73
Spin projection operator, 316
Spin-orbit effects, 353
Split-valence gaussian basis sets, 224
Star graph, 397
Statistical Mechanical Algorithm for Predicting Protein Structure (SMAPPS), 27, 28
Statistical weights, 2
Steric accessibility, 440, 441
Steric effects, 392
Steric energies, 83, 92
STO-3G, 174, 175, 179, 183, 185, 205, 224, 240, 245, 276, 285, 296, 347
STO-4G, 224
STO-5G, 279, 283, 285, 291, 292, 296, 298, 299
STO-6G, 224
STO-nG, 174, 209, 223
Stochastic boundary region, 62
Stochastic collisions, 59
Stochastic search, 20
Strained molecules, 16, 92, 278, 280, 301, 303
Structure-activity relationship (SAR), 367, 424
Structure-property modeling, 367, 368
Subgraphs, 376
Substituent constants, 295, 296, 297
Substructural analysis, 426
Substructural fragments, 19
Substructures, 66
Sum index, 389
Supercomputer, 14
Superdelocalizability, 427, 429
Supermolecule approach, 168, 190
Superposition error, 172, 189, 198, 200
Surface area, 393
Surface charge density, 65
Switching functions, 59
SYBYL, 486, 496
Symbolic approaches, 4
Symbolic representations, 12, 15, 16
Symbolic structure, 17
Symmetry, 165, 356
Systematic Conformational Analysis (SCA), 15
Systematic search, 4, 10, 12, 46


Taft Es values, 393
Taft steric parameter, 409, 427
Target function, 34
Target function minimization, 39
Tautomeric transformation, 454
Taylor series, 89, 106, 128
Temperature bath, 59
Template, 9, 16, 65
Template matching, 65
Tertiary structure, 19
Tertiary templates, 19
Tetrahedral lattice, 69
Tetrahedrane, 301, 302
Tetramethylurea, 298
Tetrangle smoothing, 33
Tetranitroglycolurile, 291
THEOCHEM, 469, 470, 474
Theoretica Chimica Acta, 479
Thermal motion, 27
Thermodynamic perturbation, 61
Thrashing, 8
Three-body effect, 135, 137
Three-membered ring compounds, 278
Thymidine phosphorylase, 452
Thymine, 279
Time steps, 59
TiO, 354
Topical indexes, 368, 371, 411
TOPKAT, 489
TOPMOST, 489, 492
Topography, 368
Topological equivalent state, 368, 412, 413
Topological indices, 424, 430
Topology, 368, 394
Torsional angles, 24, 87, 112
Total electric potential, 227
Total energy, 84
Total topological index, 413
Toxicity, 387, 410, 429
Trajectory, 43, 45, 59
Transferability, 103, 114, 119, 125, 135, 137, 144, 146, 258, 261, 263
Transition metal complexes, 348, 355
Transition state, 194, 356
Tree representation, 4
Tree search, 12, 19
Triangle smoothing, 31
s-Triazine, 249, 251, 253
Trifurcated geometry, 198, 199
Trimethylamine, 231, 260, 261
Triple zeta basis set, 95
Tri-tert-butylmethane, 109, 116
Truth maintenance systems, 8
Twist-boat,15
Two-electron integrals, 332
Two-body force field, 20
Two-stage embedding, 38


Uncoupled Hartree-Fock (UCHF), 170
Uniform-usage, 21
United-atom force fields, 112, 117
Units, 94
Unrestricted Hartree-Fock (UHF), 316, 348
Upper bounds, 41
Uracil derivatives, 452
Urea, 248
Ureido, 291
Urey-Bradley, 90, 117


Valence delta value, 373, 412
Valence force field, 100, 115
Valence state ionization potentials (VSIP), 324
Valence structure index, 383
van der Waals, 30, 35
van der Waals atomic radii, 41, 64, 88, 165, 393
van der Waals contact distance, 406
van der Waals envelope, 237, 263
van der Waals interactions, 83, 88, 166
van der Waals overlap, 61
van der Waals parameters, 113
van der Waals volume, 375
Variable retention of diatomic differential overlap (VRDDO), 324
Variational principle, 316
Vector description, 425
Verisimilar reasoning, 426
Vertex degree, 370
Vertex sequence, 412
Vertexes, 369, 426
Vibrational frequencies, 90, 91, 94, 100, 116, 117, 120, 201-203, 206, 210
Vibrational spectroscopy, 166, 171


Water dimer, 156, 166, 167, 169, 171, 182-193, 202, 209, 254, 256, 344
Water structure, 469
Well-tempered basis set, 177, 178
Westheimer method, 83
Wiberg indexes, 438, 453, 454
Wiener index, 380, 430
WIZARD, 16


X-ray conformation, 17, 46
X-ray crystallography, 1, 14, 27, 57, 62, 117, 146, 345, 463


Yeti, 496


Zero differential overlap (ZDO), 318, 355
Zero-order paths, 398
Zero-point vibrational energy, 198
ZINDO, 342, 347, 348, 357, 496

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