REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 5 (1994)

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, 7, 102, 115, 285
AbM
, 418
Accessible surface area, 352
ACES II
, 65, 72, 105, 107, 114, 115, 138, 143, 149, 409
Acetaldehyde, 203
Acetamide, 242
Acetic acid, 237, 242
Acetone, 203, 242
Acridine, 327
Acrolein, 203, 215
Active analog approach (AAA), 361
Active site, 321, 342, 343, 345, 348
Active transport, 278
ADAPT
, 420
Adenine, 242
ADF
, 409
Adiabatic electron affinity, 133, 135
Affinity constant, 359
Aggregation, 286
AGRO-MetabolExpert
, 398
AIMPAC
, 410
Air Force Office of Scientific Research (AFOSR), 34
ALADDIN
, 366, 418
Alchemy
, 400
ALCHEMY II
, 413
Alchemy III
, 385
Alcohols, 203
Aldehydes, 203
Aldrich Catalog
, 391
Alkanes, 190
Alkynes, 190
Allyllithium, 208, 210
Alpha-helix, 245
Alternate hydrocarbons, 11
Alvis
, 420
AM1, 195
AMBER
, 283, 284, 384, 402, 414
American Chemical Society (ACS), 25, 35, 47, 49, 50, 52, 59
Amides, 211
Amorphous Cell
, 405
AMPAC
, 386, 390, 410, 413
Amphipathic molecules, 273
AMSOL
, 413
Analysis
, 405
Analytic first derivatives, 114
Analytic gradient methods, 107
Analytical Chemistry by Open Learning (ACOL)
, 400
Analytical Hessians, 122
Angiotensin II receptor antagonists, 343
Angiotensin-converting enzyme (ACE), 362
Angular correlation, 102
Anharmonic force field, 106
Anharmonicities, 114
ANNEAL-RING
, 402
Antifolates, 365
Antisymmetrized wavefunction, 70
Antiviral agents, 365
Apex-3D
, 405
APSO
, 424
Archie
, 384
Argonne National Laboratory, 50, 51
Argus
, 410
Aromaticity, 221
ARPANet, 48
Array processors, 16
Artificial intelligence, 25, 31
Asp
, 363, 418
ASTERIX
, 410
Atlas of Protein and Genomic Sequences
, 391
ATOM
, 389
Atom-atom potentials, 287, 291
ATOMCI
, 413
Atomic basin, 186
Atomic charges, 216, 221, 231, 235
Atomic Energy Commission (AEC), 35, 37, 47, 50, 51, 53
Atomic natural orbital bases, 103, 144
Atomic overlap matrix, 188
Atomic population, 175, 187
Atomic volume, 184, 220
ATOMPLUS
, 389
ATOMSCF
, 413
Augmented correlation consistent basis sets, 144
AutoDock
, 421
AVS ChemistryViewer
, 421

B2H6, 72
Bacteriorhodopsin, 246
Ball & Stick
, 394
Base stacking, 11
Basis set corrections, 109
Basis set dependence, 195
Basis sets, 101, 104, 177, 216
3-21G, 108, 109, 152, 180, 196, 197, 198, 200
3-21G*, 198
3-21+G, 180, 214
4-31G, 103, 198, 199
6-31G, 103, 144, 152, 200
6-31G*, 102, 108, 136, 144, 152, 172, 187, 195, 196, 197, 198, 200, 203, 203, 207, 211, 212, 215
6-31G**, 102, 198, 199, 210, 212
6-31G+, 144
6-31G+(d,p), 144
6-31+G*, 202, 214
6-31+G**, 210
6-311G, 144
6-311+G*, 198
6-311+G**, 198
DZ, 108, 109, 119, 133
DZP, 82, 88, 94, 102, 103, 108, 111, 116, 118, 119, 121, 123, 132, 133, 136, 144, 147, 149, 152, 158
POL1, 144, 147, 152, 157
PVDZ+, 144
PVQZ+, 144
PVTZ+, 144
STO-3G, 103, 108, 109, 152, 196, 197, 198, 199, 200, 206
TZ+P, 198
TZP, 104, 133, 152
TZ2P, 104, 108, 109, 119, 144, 158
TZ2Pf, 119, 120, 121
BATCHMIN
, 405
Be, 78, 146
Be2, 72, 218
Beilstein database
, 388
BENDER
, 416
Bent bonds, 202, 217
Benzamidine, 358
Benzene, 11, 172, 173, 187, 202, 242
Benzoic acid, 358
Beryllium atom, 145
BESTFIT
, 423
Beta-Lactamase, 349
BH, 83, 88, 94, 96, 161
BH3, 72
Bicyclobutane, 202
Big science, 2, 41, 47, 53, 60
Bigeleisen, J., 52
BIGSTRN3
, 414
Bilayers, 273, 278, 287
Bimolecular rate constants, 251
Binding energies, 242
Binding pockets, 350
Bioavailability, 346
BIOGRAF
, 407
Biomembranes, 269
Biopolymer
, 405
BIOPROP
, 395
BIOSYM, 321, 384
Biradicals, 140
Bisacridine, 323
Bisintercalator, 323
Bitnet, 383
BLDKIT
, 416
BLogP
, 385
BLogW
, 385
BNDPKG2
, 413
Boltzmann distribution, 231
Boltzmann principle, 17
Boltzmann weighting factors, 280
Bond angles, 109, 110, 111
Bond critical points, 184, 186, 189
Bond dissociation energies, 78
Bond lengths, 109, 110, 111
Bond order, 176, 179, 187, 206, 212
Bond path, 186, 202, 217
Bond path network, 189, 218
Bonded interactions, 284
BONDER
, 190
Born-Oppenheimer approximation, 68, 136, 145
BOSS
, 408
Bound water, 288, 293
Boundary lipids, 290
Bounds matrix, 307
Bovine pancreatic trypsin inhibitor (BPTI), 246
Brillouin theorem, 79, 160
Brookhaven Protein Data Bank
, 16, 257, 321, 326, 348
Brooks, H., 47, 50
BROWNIAN
, 413
Brownian dynamics (BD), 229, 249, 255, 283, 291
Browse
, 412
Brueckner orbital, 97
Buffer region, 283, 292
BUILDER
, 357, 419
Bulk lipids, 278, 290
Bulk water, 288
1,3-Butadiene, 200

C2, 218
C2H2, 111, 116, 120, 199, 200
C2H4, 117, 140, 157, 199, 200
C2H6, 199
C3H3-, 180
C3H6, 198
C4, 122, 133, 135
C6H6, 104
CACAO
, 389
CAChe
, 385, 400
CADD software, 367
CADPAC
, 65, 411, 415
Cage critical point, 186
Cambridge Structural Database
, 365, 366
CAMELEON
, 418
CAMEO
, 421
CAMSEQ
, 385
Caprylolactam, 316
Carbonic anhydrase, 253
Carboxylate anions, 214
Carboxylic acids, 211
Cartesian coordinates, 105, 305
CASSCF, 76, 80, 81, 97, 122, 123
CASSCF-CISD, 81, 97, 99
Castor
, 418
Catalyst
, 365, 366, 403
CAVEAT
, 366, 417
CC5SC(TQ), 94
CCD, 91, 92, 94, 96, 107, 126
C(CH3)4, 198
CCP4
, 421
CCSD, 81, 92, 94, 95, 96, 104, 107, 110, 111, 113, 115, 116, 118, 119, 126, 143, 157, 160
CCSD(T), 92, 94, 96, 97, 99, 104, 107, 110, 111, 112, 113, 116, 118, 119, 120, 123, 157
CCSDT, 81, 92, 95, 96, 97, 123
CCSDT-1, 94, 95, 96, 99, 123, 126
CCSDTQ, 94, 95, 96
CDC 7600, 49
C-Design
, 388
Cephalosporins, 13, 343
Cerius
, 407
CH+, 145, 146
CH2Li2, 209
CH2N, 119, 121
CH2O, 111, 112
CH2PH, 131, 132, 133
CH3-, 179
CH3BH2, 197
CH3CH2CH3, 198
CH3CH2(CH3)2, 198
CH3(CH2)2CH3, 198
CH3CH2OH, 214
CH3CH2O-, 214
CH3CH3, 196, 200
CH3F, 196, 197, 198
CH3Li, 199, 200, 209, 210
CH3NH2, 197
CH3OH, 179, 197, 200
(CH3)2SO, 206, 207
(CH3)2SO2, 205, 206, 207
CH3SO2Cl, 206, 207
CH4, 104, 111, 116, 179, 196, 198, 199, 200, 201
CHAIN
, 422
Chain region, 273
Channels, 290
Characterize
, 405
Charge density, 150
CHARMM
, 350, 384, 403, 407
CHELP
, 194, 199, 203
CHELPG
, 195, 212, 411
Chem3D
, 386
Chem3D Plus
, 400
ChemCad+
, 386
ChemCore
, 403, 417
CHEMDBS-1
, 417
ChemDBS-3D
, 367, 417
ChemDIAGRAM
, 395
ChemDraft
, 386
ChemDraw
, 386
ChemEXHIBIT
, 395
ChemFile II
, 398
ChemFinder
, 386
CHEMGRID
, 419
ChemGuide
, 403
Chemical Abstracts Service (CAS), 18, 19, 25, 365
Chemical bonding networks, 218
Chemical Design Ltd., 365
Chemical shifts, 158
CHEMiCALC
, 395, 414
ChemInorganic
, 404
ChemIntosh
, 396
Chemistry Citation Index
, 395
ChemMod II
, 386
ChemModel
, 403
ChemMovie
, 403
ChemOffice
, 386
ChemPolymer
, 404
ChemPrint
, 385
ChemProtect
, 396
ChemProtein
, 404
ChemQM
, 404
ChemQuery
, 391
ChemRXS
, 417
ChemSAVER
, 395
ChemStat
, 404
ChemStock
, 400
ChemVISION
, 395
ChemWhere
, 399
ChemWindow
, 396
ChemWord
, 396
ChemWords
, 396
Chem-X
, 364, 365, 367, 368, 386, 403, 417
Chiral centers, 314
Chiral constraints, 311, 313
Chiral error function, 311
CHIRON
, 396
Cholesky decomposition, 234
Cholesterol, 292
Choline, 273
Chymotrypsin, 321, 323
CI coefficients, 79
CI singles (CIS), 138
CID, 83, 84, 89, 96
CIPSLINE PC
, 391
CISD, 81, 83, 84, 96, 104, 112, 116, 118, 142, 200, 201
CISDT, 83, 84, 90, 96
CISDTQ, 84, 91, 96
Classical mechanics, 7
Clementi, E., 18, 57
CLi4, 199, 209, 210
CLi6, 209, 210
ClO4-, 207
CLOGP
, 408, 418
Closed-shell system, 71
CLUSTER
, 419
Cluster analysis, 317
CMR
, 408, 418
CNDO/2 (Complete Neglect-of-Differential-Overlap), 14
CNDO/S
, 414
CNINDO
, 414
CNINDO/D
, 390
CO, 112, 152, 155, 157, 158, 185, 199, 200, 201, 203
CO2, 111, 117, 120, 152, 153, 157, 158, 201
COBRA
, 365, 417, 418
Cold War era, 38
Collective Index of Chemical Abstracts
, 394
COLUMBUS
, 159, 411
Commission of Crystallographic Computing, 33
Committee on Computers in Chemistry, 42
Committee on Science and Public Policy, 36, 47, 48
Comparative Molecular Field Analysis (CoMFA), 363, 364, 404
COMPARE
, 318
COMPARE-CONFORMER
, 414
Complementary structures, 355
Complete CI, 79
COMPOSER
, 408
Computational biology, 337
Computational chemistry, v, 1, 2, 15, 17, 40, 41, 58, 337, 341, 381
Computational experiment, 22
Computer graphics, 15, 341, 358
Computer simulation, 269
Computer technology, 9
Computer-aided drug design (CADD), 337, 338, 341, 342, 346, 359, 363
Computer-aided molecular design (CAMD), v, 337
Concentration gradient, 278
CONCORD
, 365, 408, 418, 420
CONECT
, 416
Conference on Computational Support for Theoretical Chemistry, 50
Conference on Molecular Quantum Mechanics, 12
Conference on Uses of Computers in Chemistry, 34
Configuration interaction (CI), 67, 78, 81, 83, 115, 138
Conformational analysis, 300, 316, 323
Conformational families, 318
Conformational flexibility, 365, 367
Conformational sampling, 309, 310, 316
Conformational searches, 17, 350
Conformational space, 299, 302, 316, 320, 352
CONGEN
, 350
Congressional Office of Technology Assessment, 340
Conjugate gradient minimization, 233, 303, 315
Connection table, 30, 365
Connolly surface, 194, 351
CONSISTENT
, 405
Constant temperature MD, 282
CONSTRICTOR
, 418
ConSystant
, 399
Continuum electrostatics, 230
Continuum models, 261, 291
Contracted functions, 103
Contracted Gaussian-type orbitals, 74
CONVERT
, 414
Converter
, 405
Core ionization, 127
CORINA
, 396
Correlated analytical Hessians, 115
Correlated methods, 132, 155
Correlation consistent basis sets, 103
Correlation cusp, 78
Correlation, 66, 76, 78, 109, 125, 129
Cosmic force field, 418
Cottage industry, 54
Coulombic interactions, 78, 291
Coulomb's law, 235, 236, 247
Coupled electron-pair approximations (CEPA), 92
Coupled-cluster (CC), 67, 81, 83, 91, 94, 151, 155
Coupled-cluster single, double, and triple excitations (CCSDT), 81
Coupled-perturbed Hartree-Fock, 139, 193
Covalent bond order, 189
Covariance matrix, 306
CPKPDB
, 414
Cray Y-MP, 234
Critical micelle concentration, 273
Critical points, 185, 186, 217
CRSTL
, 405
CRYSTAL
, 414
Crystal Cell
, 405
CRYSTAL VISUALIZER
, 392
Crystal Workbench
, 407
Crystallography, 344
Cubane, 202
Customized Polymer Modeling Program
, 404
Cyclobutane, 202
Cycloheptadecane, 316
Cyclohexanes, 14
Cyclopropane, 189, 202
CYCLOPS
, 401
Cyclosporin, 314
Cytosine, 242

3D structures, 365
DARC Inhouse
, 392
DARC-CHEMLINK
, 392
Database management software, 32
Database searching, 1, 357, 366, 368
Databases, 339, 363, 391, 416
Datalyst II
, 399
Davidson's approximation, 90
Daylight Chemical Information System, 366
DayMenus
, 418
De novo ligands, 353
Dead-end elimination method, 353
Debye, P., 23, 32
Defense Advanced Research Projects Agency (DARPA), 47, 48
Degrees of freedom, 115
DelPhi
, 230, 234, 405
deMon
, 412
DENDRAL
, 26, 27
Dendrogram, 318
Density matrix, 176
Density matrix theory, 11, 107
Department of Defense, 25, 34
Department of Energy, 52
Deprotonation energy, 202
DEREK
, 425
Desk calculators, 8
Desktop Molecular Modeller
, 387
Desolvation, 245, 246
Dewar, M. J. S., 44, 45
DG II
, 316, 405
DGauss
, 415
DGEOM
, 314, 316, 318, 321, 322, 364, 414
DGPLOT
, 416
Diagonal scaling, 234
Diagonalization, 75
DIANA
, 408
DIATOMIC
, 390
Diatomics, 9
Dictionary of Drugs
, 417
Dictionary of Fine Chemicals
, 417
Dictionary of Natural Products
, 391, 417
Dielectric boundary, 232, 247, 248
Dielectric constants, 21, 231, 233, 235, 238, 257
Dielectric inhomogeneities, 248
Diffuse functions, 103, 144, 148
Diffusion, 231, 250, 258, 260, 278
Diffusion constant, 257
Diffusion-controlled rate constant, 250, 255
Diffusion-controlled rate processes, 249
Digital Equipment Corporation (DEC), 15, 30, 54
DIHDRL
, 416
Dihydrofolate reductase, 351, 358
Dihydroxyacetone phosphate, 256
Dilauroylphosphatidylethanolamine (DLPE), 274, 286, 287, 288
Dilithioacetylene, 207
1,2-Dilithioethane, 208
1,2-Dilithioethene, 208, 209
1,3-Dilithiopropane, 208
1,3-Dilithiopropene, 210
Dimethyl ether, 203
Dimyristoylphosphatidylcholine (DMPC), 274, 285
Dipalmitoylphosphatidylcholine (DPPC), 288, 292
Dipole moment derivatives, 157
Dipole moments, 149, 152, 155, 177, 193, 219
Dipole oscillator strengths, 148
Dipole polarizabilities, 157
Dipole potential, 277
Dipole strengths, 146
Directory of Graduate Research
, 400
DISCO
, 408
Disconnected terms, 92
Discover
, 404, 427
Discretization of space, 233
DISGEO
, 414
DISMAN
, 303
DISMAP
, 390
Dispersion forces, 11
Displacement field, 232
Dissociation energy, 76, 99
Distance bounds matrix, 302, 304
Distance constraints, 302, 313, 314, 362
Distance correlation, 309
Distance error function, 311
Distance geometry (DG), 299, 364, 368
Distance map, 361
Distance matrix, 301, 303, 304, 306, 365
Distance selection, 308
Distance space, 303
DISTMAP
, 419
DMol
, 411
DNA, 323, 365
DNA/RNA Builder
, 399
DNMR
, 414
DNMR6
, 414
DOCK
, 351, 356, 357, 418
Docking, 300, 323, 345
Docking ligands, 358
Dopamine, 363, 366
Double harmonic approximation, 114
Double-sided differentiation, 106, 114
DQ-MBPT(4), 95
DRAW
, 390, 414
Drug, 368
Drug Data Report,
391
Drug design, 10, 347, 368
Drug discovery, vi, 337, 339
Drug intervention. 343
DRUGIDEA
, 398, 400
Drugs of the Future
, 391
DSTNCE
, 416
Dynamic correlation, 79, 81, 142
Dynamics, 315

ECEPP
, 14, 387
ECEPP2
, 414
ECEPP/3
, 404
Eckert, J. P., 4
Eckert-Mauchly Computer Corporation, 5
EDD
, 393
EDVAC, 3
Effective cross-sectional areas, 274
Effective density, 108
Effective nuclear charge, 125
Effective potentials, 105
Eigenfunction, 68, 69
Electric field gradients, 150, 153
Electric field strength vector, 154
Electric polarizabilities, 157
Electric quadrupole moment, 152
Electrical fields, 247
Electron affinities, 131, 133, 135
Electron correlation, 78, 82, 108, 138, 155, 193, 199, 203, 216
Electron density, 171, 172, 187, 217
Electron detachment energies, 135
Electron diffraction, 106
Electron photodetachment, 131
Electron repulsion integrals, 12
Electron transfer, 11
Electronic computers, 12
Electronic mail bulletin boards, 384
Electronic mail exploders, 56
Electronic spectra, 136
Electrostatic calculations, 229
Electrostatic double-layer forces, 277
Electrostatic energies, 235
Electrostatic force density, 248
Electrostatic free energy, 232
Electrostatic interactions, 284, 343, 351
Electrostatic potential similarity, 363
Electrostatic potentials, 15, 194, 231, 257, 363
Electrostatic steering, 257
Electrostatic torques, 257
Ellipticity, 190
EluEx
, 398
Embedding, 303, 310
Empirical force field, 346
Empirical scaling factor, 115
EndLink
, 400
EndNote
, 400
EndNotePlus
, 400
Energy Research and Development Administration (ERDA) National Laboratories, 52
ENIAC (Electronic Numerical Integrator and Computer), 3, 4, 9
Ensemble distance geometry method, 320
Entropic forces, 277
Enzyme inhibitors, 338
EnzymeKinetics
, 390
Enzymix
, 407
Equation-of-motion coupled cluster (EOM-CC) method, 131, 135, 143, 149
Equation-of-motion method, 130
EQUIL
, 400
Equilibrium bond lengths, 76, 83
Equilibrium constants, 359
Equilibrium geometries, 99, 106, 114, 145
Equilibrium positions, 113
Equilibrium structure, 105
Ermak-McCammon method, 249
EROS
, 397
Error function, 303, 304, 310
ESCA, 124
ESCALC
, 406
ESP (Experimental Section Processor)
, 390
ESTAR
, 414
Ethane, 201, 202
Ethanol, 214
Ethanolamine, 273
Ethene, 201, 202
Ethylene oxide, 203
Ethyne, 201, 202
Ethynyllithium, 210
EUREKA
, 418
European Center for Atomic and Molecular Calculations (CECAM), 46
Evans & Sutherland Picture System, 15
Ewald sum, 284, 293
Exchange integrals, 12
Excitation energies, 146
Excitations, 86
Excited states, 141, 144
Excluded volume, 362
Experimental chemistry, 46
Explicit solvent, 235, 291
EXPOD
, 422
Exponent-6 potential, 11
Extended Hückel, 385, 390, 414
Extensive property, 160
Extensivity, 81, 89, 91, 92
Extensivity correction, 99
EXTOIN
, 390
EXTREME
, 190, 217
Eyring H., 23

F2, 76, 77, 80, 97, 99, 100, 101, 115
F3D
, 397
F3PO, 207
F3PS, 207
FClO3, 207
FDCALC
, 406
FELIX-Assign,
405
FELIX-MODEL
, 405
Fermions, 69
FH, 83, 88, 94, 96, 161
FIG.P
, 401
File transfer protocol (ftp)
, 383
Finite difference Coulombic potential, 237
Finite difference Poisson-Boltzmann (FDPB), 231, 232, 242, 245
First-order properties, 149, 151
First-order reduced density matrix, 181, 183
FISIPL
, 416
Fixed charge distribution, 231
Flavodoxin, 353
FLEX
, 422
Flexible rings, 300
FlexModel
, 408
3-Fluorotoluene, 106
Fock space multireference coupled-cluster method (FS-MRCC), 131, 135
FOOH, 141
Forbidden reactions, 112
Force constants, 114, 118, 156
Force density, 247
Force field parameters, 300
Force fields, 284, 285
Formaldehyde, 113, 116, 179, 196, 198, 199, 200, 201, 203, 204
Formally balanced basis set, 177
Formamide, 204, 211, 212
Formic acid, 203, 214
Formyl fluoride, 204
FORS (full-optimized reaction space), 81
FORTICON8
, 390, 414
FORTRAN, 15
Four-dimensional refinement, 313, 314
Fourth-dimensional penalty term, 314
Free energies of hydration, 243
Free energy perturbation (FEP), 345, 359
Friction coefficient, 283
FRODO
, 422
Frozen orbital approximation, 139
Full CI (FCI), 79, 81, 82, 88, 90, 96, 97, 107, 133, 145, 161
Funding agencies, 45

GAMESS
, 65, 412
Gas kinetics, 21
Gated rate constant, 260
Gated reactions, 253
Gauge origin problem, 157
Gauge-including atomic orbital (GIAO), 158
GAUSS2
, 389
Gaussian
, 65, 72, 102, 107, 138, 182, 190, 193, 217, 412, 415
Gaussian basis set, 101, 152
Gaussian functions, 190
Gaussian-quadrature integration, 190
Gaussian-type functions, 172
Gauss's law, 232
GCG Package
, 422
GDFB
, 413
GDFMOL/GDFMD
, 413
Gel phase, 274, 286
Gel-to-liquid-crystalline phase transition, 274
GEMINI
, 418
GEMM
, 423
GenBank
, 392
Generalized atomic polar tensor (GAPT) charges, 193, 199, 207
Generalized valence bond (GVB), 73, 74, 76, 77, 80, 81
Generic TOPFRAG
, 392
Geometry optimizations, 107, 109
GEPOL92
, 414
Global minimum, 309, 315
D-Glyceraldehyde-3-phosphate, 256
Goddard Committee, 53, 54
Gopher
, 384, 423
Gordon Research Conference on Computational Chemistry, 59
Government funding, 2, 34, 59
Gradient paths, 186, 189
GRADSCF
, 412
Gramicidin A, 278, 290
GRAMPS
, 421, 423
GRANNY
, 421
Graphical language, 30
Graphics terminals, 15, 16
Green's function, 237
GRID
, 350, 423
GRIN
, 424
GROMOS
, 384, 404
Gross atomic orbital population, 176, 177, 178
Gross atomic population, 176, 183
GROW
, 355, 356
GSTAT
, 420
Guanine, 242
GVB, 81
GVB-CISD, 81, 99

H2, 72, 73, 74, 75, 78, 112, 182
H2ION
, 389
H2NCHO, 200,
H2S, 152, 153, 155, 157, 196
H2SO, 207
H2SO2, 207
H3 radical, 8
H3N, 152, 155
H3PO, 205, 207
H3PS, 207
Hall, K., 33
HAM/3
, 390
Hamiltonian, 67, 78, 85, 107
HAMOG
, 387
Hardwiring, 4
Harmonic force constants, 157
Harmonic force fields, 114
Harmonic frequencies, 114, 116
Harmonic vibrational frequencies, 121
Harris, F., 47
Hartree-Fock approximation, 66, 70, 127, 172
Hartree-Fock instabilities, 140
Hartree-Fock limit, 195
Hartree-Fock-Roothaan procedure, 172
HAZARDEXPERT
, 390
HCl, 196
HCN, 111, 117, 120, 196, 201
HCO2H, 214
Head group, 273, 287, 292
HeH+, 72
HelicalWheel
, 423
Helium atom, 7, 78
Hellmann-Feynman theorem, 151
Helmholz free energy, 359
Heme proteins, 253
Hen egg white lysozyme, 246
Heptadecane, 316
Hessian matrix, 106, 112, 114, 156, 185
Heuristics of organic synthesis, 31
Hexagonal mesophase, 291
Hexagonal tubular phases, 273
Hexalithiomethane, 208
HF, 152, 153, 155, 157, 199, 200, 201
Hierarchical clustering, 318
Highest occupied molecular orbital (HOMO), 125
Hilbert space, 174
HINT
, 424
History, 2
HIV-1 protease, 357, 360
HMO
, 390
HNC, 111
Hole state, 127, 128
Homology
, 405
Homology modeling, 344, 348, 349
HONDO
, 65
HONDO-8
, 413
HPLC-MetabolExpert
, 398
5-HT1a compounds, 362
Hückel molecular orbital, 136
Hückel theory, 13, 137
Human myoglobin, 245
Hund's rule, 137
HYCOIN
, 413
Hydration energies, 239
Hydration force, 276
Hydration pressure, 276
Hydration shells, 288
Hydrides, 9
Hydrocarbons, 201
Hydrodynamic radii, 255, 257
Hydrogen bomb, 5
Hydrogen bonding, 21, 284, 288, 343, 351
Hydrophilic head groups, 273
Hydrophobic effect, 235
Hydrophobic patches, 343
Hydrophobic pocket, 321
Hylleraas wavefunctions, 78
HyperChem
, 384, 387
Hyperfine coupling constants, 150
Hypervalent sulfur, 204, 206

Ibers, J., 49
IBM, 18, 33, 57
IBM 360, 14
IBM 650, 11
IBM 704, 21
IBM 709, 12
IBM 7094, 13
IBM-PC, 56
IBM Stretch computer, 22
IC50, 367
ILIAD database
, 417
Illinois Institute of Technology, 8
Impure spin states, 74
Incompatible distance bounds, 330
Independent particle model, 67, 70, 72, 124, 130, 136
Indiana University, 41
Inextensivity, 90
Infrared intensities, 118
Innovator
, 385
Inorganic Crystal Structure Database
, 392
Insight II
, 404
Insight Xpress
, 405
Insight/Discover
, 321, 349, 365, 368, 404
Institute for Advanced Study, 3, 5
Integrals, 7, 89
Integrated projected populations (IPP), 191, 197, 209
Integrated spatial electron populations (ISEP), 190, 191
Intensities, 114
Interaction energy, 345
Interaction potential, 283
Interaction sites, 358
Interactive computing, 15
Interactive graphics, 323, 328
Interatomic distances, 364
Interchange operator, 69
INTERCHEM
, 414
Intermediate normalization, 85
International Union of Crystallography, 33
Internet, 383
Interphases
, 405
Inverse triangle inequality, 306
Ion channels, 278
Ion-accessible region, 231
Ionic boundary forces, 248
Ionic pressure, 248
Ionizable residues, 244
Ionization equilibrium, 245, 246
Ionization potentials, 72, 124, 125, 126, 132, 133, 134, 141
Ionophores, 278
IRMA
, 405
ISIS
, 419
ISIS-3D
, 367
ISIS/Base
, 419
ISIS/Draw
, 419
Isoelectronic surface, 172
Isopotential contours, 363
IVTANTHERMO database
, 393

Jarvis-Patrick clustering, 318
Journal of Chemical Information and Computer Science
, vi
Journal of Medicinal Chemistry
, vi
Journals in computer-aided chemistry, 55

Kekuké-OCR
, 397
Ketene, 148, 149, 203
Ketones, 203
Keys, 363, 367
KGNGRAF
, 413
KGNMCYL
, 413
KGNMD
, 413
KGNMOL
, 413
KGNNCC
, 413
Kinemage
, 397
Kinetic energy, 68
Koopmans' theorem, 72, 124, 133
Krauss, M., 43

LabADVISOR
, 400
LabSolutions
, 397
LABSWARE
, 398
LabSystant
, 390
LabVantage
, 397
LabVision
, 385, 408
Langevin dynamics, 283
Langridge, R., 24
Laplacian, 185, 189
Lateral diffusion rates, 287
Lateral hopping, 291
Lattice models, 291
Latticepatch
, 424
Lawrence Berkeley Laboratory (LBL), 49, 53
Lead compounds, 357
LEAPFROG
, 408
Leap-frog algorithm, 281
Lennard-Jones potential, 284, 286
Lester, W., Jr., 52
Levinthal, C., 24
LHASA
, 424
Li, 78
Li2, 218
LiBH2, 197
LiCH3, 197
LiCl, 196
LiF, 197, 199, 201
Ligand docking, 321
Ligand families, 357
Ligand volume, 362
Ligands, 345, 368
LIGHT
, 425
LiH, 78, 196, 199
Linear combination of atomic orbitals (LCAO), 171
Linear combination of atomic orbitals--molecular orbital--self-consistent field (LCAO-MO-SCF), 8, 11
Linear structural notation, 27
Linearized embedding, 303
Linearized Poisson-Boltzmann (LPG) equation, 234, 235, 257
Linearized tree structure, 303
LiNH2, 197
Linked-diagram theorem, 90, 91
LiOH, 197
Lipid aggregation, 286
Lipid assemblies, 273
Lipid bilayers, 249, 269
Lipid mobility, 274
Lipid systems, 269
Lipophilicity, 364
Lipscomb, W. N., Jr., 24
Liquid crystalline phase, 274, 276
Local attractors, 186
Local gauge origin, 157
Local maximum, 185
Local minima, 17, 24, 112, 185, 309, 314, 315
Localized orbitals, 92
Logic-centered approach, 29
Long-time dynamics, 291
Long-time-scale motions, 293
Los Alamos National Laboratory, 4, 19, 21, 22
Löwdin, P. O., 11
Löwdin population analysis, 178
Lower bounds, 302, 307, 311, 314
LUDI
, 358, 405
Lykos, P., 8, 47, 54, 56
Lyotropic polymorphism, 274

MACCS
, 419
MACCS-3D
, 367
Machine code, 9
MacImdad
, 397
Mackinac Island meeting, v
MacMimic
, 388
MacroModel
, 16, 17, 405
MADNMR
, 407
MAGE
, 397
MAGIC
, 397
Magnetic susceptibility, 151
Magnetic tape, 6
MANIAC, 5, 20
Man-machine interaction, 23, 25
Many-body perturbation theory (MBPT), 67, 81, 83, 87, 88, 151, 155
Many-body problem, 7
MARDIGRAS+
, 408
Markov chain, 281
MASCA
, 406
Mass spectra, 26
MATCHMOL
, 358
Material Safety Data Sheets (MSDS)
, 391
Mathcad
, 398
Mathlib
, 418
Matrix diagonalization, 12
Matrix equation, 83
Matsen, F. A., 40, 45, 47
Mauchly, J., 4
Maxwell stress tensor, 247
MBPT(2), 87, 96, 104, 107, 110, 111, 112, 113, 115, 116, 118, 119, 120, 123, 151, 157, 158
MBPT(3), 89, 96, 104, 107
MBPT(4), 90, 95, 96, 104, 111, 116, 118, 123, 132
MBPT(5), 91, 96
McLean, D., 8
MD Display
, 414
mdXvu
, 414
MEAD
, 230
Mean square displacements (MSD), 289, 291
Mechanical properties, 7
Medicinal chemistry, 369
MEDIT
, 406
MEDTOOL
, 397
MELD
, 413
Membrane proteins, 269
Membrane transport, 289
METABOLEXPERT
, 398
Methane, 202
Methanol, 242
Methotrexate, 358
Methyl acetate, 242
Methylcyclopropane, 202
Metric matrix method, 303, 304
Metrization, 304, 309
Metropolis method, 20
MgF, 135, 136
Micelles, 273, 286, 291
Michaelis complex, 321
MicroChem
, 388
Microstate, 279
MIDAS parameter set, 248
MidasPlus
, 425
Mie equation, 11
Minicomputers, 15
Minimization, 315, 368
MINP
, 405
MLDC8
, 390, 414
MMI
, 14
MM2
, 14, 21, 56, 385, 386, 388, 390, 414
MM2P, 387
MM3
, 408, 414
MNDO
, 14, 56, 195, 387, 390, 414
MNDOC
, 414
MOBY
, 388
MODEL
, 16, 406
Model-based computational chemistry, 59
Model-based methods, 10
Model-building methods, 299
Modeler
, 398
MoG
, 399
Mohole project, 40
MOIL
, 406
MOLCAD
, 408
MOLCAS-1
, 413
MOLCONN-X
, 399
MOLDEN
, 414
MOLDRAW
, 390
Molecular Animator
, 398
Molecular Design Ltd., 365
Molecular dynamics (MD), 14, 19, 21, 277, 281, 290, 299, 315, 354, 368
Molecular dynamics simulations, 290
Molecular ensemble approach, 364
Molecular field theory, 353
Molecular geometries, 105, 108
Molecular graphics, 337, 368, 394, 420
Molecular Graphics,
398
Molecular mechanics (MM), 10, 14, 247, 300, 323, 350, 354, 359
Molecular modeling, 299, 337, 381, 402
Molecular Motion and Mechanics
, 390
Molecular orbital (MO), 67, 172
Molecular orbital calculations, 354
Molecular orbital theory, 113
Molecular order parameter, 275, 276, 288
Molecular Presentation Graphics (MPG)
, 399
Molecular properties, 149, 186, 341, 368
Molecular replacement, 344
Molecular Silverware
, 408
Molecular similarity, 15, 362
Molecular Spreadsheet
, 408
Molecular structure, 391
Molecular superpositions, 358
Molecular surfaces, 15
Molecular symmetry, 104
Molecular volumes, 360
Molecule building, 368
Molecules
, 399
MOLFIT
, 358, 414
MOLIDEA
, 398
Møller-Plesset (MP) perturbation theory, 81
Møller-Plesset theorem, 151
MOLSCRIPT
, 425
MOLVIB
, 390
MOLVIEW
, 390
MOLY-86
, 414
MOLYROO
, 390
Moments of inertia, 106
Monopole expansion, 194
Monte Carlo importance sampling, 279, 292
Monte Carlo methods, 14, 19, 22
Monte Carlo simulations, 280, 286, 290
MOPAC
, 57, 385, 386, 390, 413
MOPAC Pre-Processor (mpp)
, 399
MOPC
, 390
Morphine, 313, 314, 315
MP2, 200, 201
MP3, 211
MR-CC, 81
MR-CCSD, 149
MR-CI, 97
MR-CISD, 81
MR-MBPT, 81
MS
, 414
MSEED
, 414
MSP
, 425
Mulliken population analysis (MPA), 175, 197, 199
Mulliken, R. S., 7, 34
Multicenter integrals, 8
Multiconfiguration SCF (MCSCF), 80, 81, 107, 115, 142, 151
Multigridding techniques, 234
Multilamellar phases, 273
Multiple minima problem, 353
Multireference (MR) methods, 81, 122, 149
Multireference configuration interaction, 91, 142

N2, 76, 80, 97, 98, 99, 100, 124, 125, 126, 127, 129, 140, 141, 157
N3H3, 118
N5H, 118
NaH, 196
NAMOD
, 390
NanoVision
, 400
Naphthalene, 11
National Academy of Sciences (NAS), 36, 41, 47, 48
National Bureau of Standards (NBS), 5, 6, 8, 43
National Center for Computation in Chemistry (NCCC), 3, 47, 48, 49, 52
National Institutes of Health (NIH), 25, 35
National Register of Scientific and Technical Personnel, 35
National Research Council (NRC), 41, 42, 48, 52
National Resource for Computation in Chemistry (NRCC), 41, 49, 51, 52
National Science Foundation (NSF), 25, 34, 35, 37, 42, 47, 52, 59
Natural atomic orbitals, 181
Natural bond orbitals, 181
Natural minimal basis, 181
Natural orbitals, 142, 181
Natural population analysis (NPA), 180, 197, 203, 207, 217
Natural Rydberg basis, 181
NCSAdisco
, 414
N-DEE
, 406
Neighbor exclusion principle, 328
NEMESIS
, 389
Networks
, 405
NEWHEL92
, 416
Newtonian equations of motion, 22, 281, 354
Newton-Raphson, 106
NEWZMAT
, 412
NH3, 111, 116, 153, 157, 196, 199, 200, 201
Nicotinic agonists, 320
Niemann, C., 36
NIST Crystal Data File
392
NIST Structures and Properties Database
, 393
NITRO
, 408
NM Display
, 414
N-Methyl-D-aspartate (NMDA) receptor, 363
NMR Analysis
, 405
NMR Database
, 405
NMR1
, 408
NMRchitect
, 405
NMRgraf
, 407
NMRZ
, 408
N.N.Charge
, 399
Nobel Prize, 10
NOEL
, 414
NOESY, 326
Nonactin, 278
Nonbonded interactions, 284
Nondynamic correlated methods, 99
Nondynamic correlation, 80
Non-electronic computers, 12
Nonlamellar phases, 291
Nonnuclear attractor, 218
Normal coordinate theory, 113
NorMode
, 390
NSF Chemistry Advisory Committee, 51, 53
NSF Office of Computing Activities, 46
Nuclear magnetic resonance (NMR), 151, 157, 276, 299, 304
Nuclear Overhauser effect (NOE), 302, 314, 323
Nucleic acid, 249
Nucleic Acid Database
, 393
Number crunching, 3, 6, 19
NVE ensemble, 282
NVT ensemble, 282

O
, 425
O2, 73, 74, 131, 134
O2^2-, 141
O3, 81, 122, 123
OCSS
, 30, 31
Ohio Supercomputer Center, 56, 383
Oligopeptides, 353
Omega
, 425
One-electron operator, 68
One-particle density, 108
One-particle operators, 72
OpenMolecules
, 426
OPLS parameter set, 248, 285
Optical rotary dispersion (ORD), 13
ORAC
, 419
Orbital diagram, 73, 127, 135
Orbital energy, 69
Orbital relaxation, 108, 125, 142
Orbital rotations, 128
Orbital symmetry ,13, 112
Orbital-based method, 175, 217
Order parameter profiles, 287, 292
OREX
, 393
Organic chemistry, 347
Organolithium compounds, 207, 209, 210
Organonitrogen compounds, 205
Orientational correlational functions, 289, 291
Origin
, 400
Orthogonalization, 178
OSAC
, 419
Osmotic stress apparatus, 276
Outokumpu HSC Chemistry
, 400
Overlap integrals, 107
Overlap matrix, 175
Overlap population, 175, 179, 183
Overlapping molecules, 15
Overton's rule, 278
Ozone, 109, 140

Packing arrangement, 353
Pair distribution functions, 287, 288
PAP
, 414
Paper tape, 4
Paradox
, 400
Parameterization, 285
Pariser-Pople-Parr (PPP) theory, 12
Partial metrization, 310, 316
Particle-particle ladder (PPL), 89
Partition function, 279
Passive transport, 278
Patentable novelty, 346
Patronage, 32
Pauli exclusion principle, 69, 177
Pauling points, 109, 159
PC-Chemmod
, 386
PCILO/2
, 390
PCILO3,
414
PCMCAD
, 404
PC-Mendeleev
, 390
PCMODEL
, 389, 400, 406
PC-PDF
, 393
PC-PROT+
, 406
PC-TAMMO+
, 406
PDM88
, 414
PDM93
, 414
PDP-1, 30
PeakFit
, 400
PEFF
, 414
Penicillin-recognizing proteins, 348
Pentangle relationship, 308
PepPlot+
, 423
Peptide loop, 258
PEPTIDESTRUCTURE
, 423
Periodic boundary conditions, 280
Permittivity, 231
Permutational symmetry, 69
Perturbation, 85
Perturbed Hamiltonian, 150
PETRA
, 397
pH, 244
PH3, 196, 200, 201, 205
Pharmacophore, 300, 319, 320, 342, 343, 358, 360, 361, 362, 364, 366, 367, 404
Phase Diagram
, 405
Ph.D. degrees, 37
Phenol, 242
Phenylhippurates, 321, 323
Phosphatidylcholine, 271, 277, 293
Phosphatidylethanolamine, 277, 293
Phospholipids, 269, 271
Phosphorus compounds, 205
PHOTO
, 413
Photoelectron spectra, 124
Physically balanced basis set, 177
Pi character, 190
Pi set, 11
Pi-electron theory, 11, 12
PIFF
, 414
PileUp
, 423
Pimms
, 418
Pipeline of discovery, 339
pKa, 245
pKalc
, 398
PLH-91
, 413
PLT2
, 425
PLTCOR
, 400
PLUTO
, 419
PM3, 195
PO4^3-, 207
PO3S^3-, 207
Point charges, 248
Point group symmetry, 105
Poisson equation, 247
Poisson-Boltzmann (PB), 230, 232, 247
Polar region, 273
POLARIS
, 407
Polarizability, 156
Polarization, 102
Polarization functions, 103, 109, 199, 205, 216
Polarization propagator, 149
Polarized basis correlated calculations, 104
Polarized basis sets, 144
POLLY
, 426
POLYATOM
, 390
POLYGRAF
, 407
Polymer modeling, 368
Polymerizer
, 405
Polymorphism, 271
POLYRATE
, 414
Polyview
, 421
POMONA database
, 418
Population analysis, 171, 216
Pores, 278
POSSUM
, 408
Post-Hartree-Fock, 65, 199
Potential energy curve, 68, 72, 73, 74, 77, 97, 98, 100, 101
Potential energy function, 280, 283, 315
Potential of mean force (PMF), 290, 352
Power spectrum, 289
Preconditioner, 234
PREKIN
, 397
Pressure coupling, 282
Primary sequence, 344
Primitive Gaussians, 103
Primitive integrals, 104
Principal component analysis (PCA), 306, 364
Prism
, 405
PROAIM
, 190, 217
Probability density, 69
Probability distribution functions, 291
Probability distribution method, 252
PRODEN
, 414
PRO-EXPLORE
, 406
Professional POLYGRAF,
407
Profiles-3D
, 405
Project MAC, 24
Projected electron density function, 190, 191
ProjectLeader
, 385
PRO-LOGP
, 398
PROLSQ
, 421, 426
Prometheus
, 406
PRONET
, 413
[1.1.1]Propellane, 198
PROPHET
, 407
PRO-QUANTUM
, 406
PRO-SIMULATE
, 406
Prosser, F., 33
PROTEAN II
, 390
PROTECT
, 425
Protein engineering, 354
Protein folding, 10, 353
Protein homology model building, 300, 368
Protein modeling, 352
Protein Predictor
, 399
Protein structure, 300, 304
Protein-protein associations, 351
PROTEINS
, 414
PROTEP
, 408
Proton tunneling, 11
PSDD
, 414
Pseudo potentials, 105
PS-GVB
, 415
PSI77
, 414
PSI88
, 415
PsiBase
, 393
PsiGen
, 393
Punch cards, 15

QCFF/PI
, 414
QCISD, 81, 107, 160
QCISDT, 160
QCISD(T), 107, 123
QCPE (Quantum Chemistry Program Exchange), 33, 43, 44, 48, 55, 56, 364, 382, 390
QMDCP
, 413
QSAR-PC
, 401
QSPR
, 405
QSPR-Polymer
, 407
Quadratic CI (QCISD), 81, 97, 160
Quadratic configuration interaction (QCI), 67, 159, 161, 201
Quadrupole moments, 149
QUANTA
, 407
QUANTA/CHARMm
, 349, 368, 407
Quanta-NMR
, 407
Quantitative Structure-Activity Relationships (QSAR), 13, 321, 342, 368
Quantum chemists, 1, 7, 32, 43
Quantum chemistry, 42, 389
Quantum chemistry calculations, 409
Quantum mechanical observable, 194
Quantum mechanical-molecular mechanics (QM/MM), 346
Quantum mechanics (QM), 11, 171
Quartic force field, 124
QUASAR
, 401
Quasi-restricted Hartree-Fock (QRHF), 122, 128
QUEST
, 419
QUEST3D
, 419

Radial correlation, 101
RAIN
, 401
R & D costs, 340
Random forces, 283
Random phase approximation (RPA), 139
Random sampling, 309
Random search methods, 299, 319
Rank, 185
Ransil, B., 8
RASTER3D
, 426
Rate constant, 250
Rational drug design, 338
2R-CISD, 122
REACCS
, 419
Reaction field energy, 236
Reaction pathway, 112
Reaction potential, 237
Reaction probability, 251, 252
Reaction region, 283, 292
REATOM
, 413
Receptor
, 407, 408
Receptor site, 242, 343, 348, 355, 358, 361, 367
Reduced density function, 180
Reduced temperature, 288
Reference state wavefunction, 79
Refinement, 310
Relative diffusion constant, 255
Relativistic effects, 105
Relaxation techniques, 233
Relaxed density, 108, 118, 155
Remington-Rand, 5
Resonance, 211, 213
Response density, 108
Response vector, 108
Restricted Hartree-Fock (RHF), 71, 76, 99, 107, 115, 140, 199, 201
Restricted open-shell Hartree-Fock (ROHF), 71, 73, 75, 76, 82, 107, 115, 119
Reverse micelles, 273
RHF-CISD, 107
RHF-MBPT, 99
Ribbons
, 426
Rigid template structures, 366
RING
, 390
Ring critical point, 186, 202
RIS
, 405
Rms matrix, 318
Roothaan, C. C. J., 8
Root-mean-square deviation (rmsd), 356
Rotational barrier, 211
Rotational diffusion, 250
Rotational entropies, 14
Rotational spectroscopy, 106
Rotation-translation fitting, 319
RRKM theory, 22
Rydberg states, 144, 147, 148

Sabre
, 386
Saddle points, 112, 114
Sadtler Molecular Structure Search Software
, 393
Sanchez, S., 9
Sanibel Conferences, 11, 41
SAVOL2
, 418
SCARECROW
, 427
SCF approximation, 108
SCF derivatives, 107
SCF equation, 75
SCF frequencies, 115
SCHAKAL
, 401
Scherr, W. C., 8
Schrödinger equation, 7, 10, 18, 68, 85, 92, 130, 138, 143, 150, 156, 171
SciAn
, 427
SciWords
, 400, 401
SDQ-MBPT, 116
SDQ-MBPT(4), 90, 95, 96, 107, 111, 116, 118, 119
SEAC (Standards Eastern Automatic Computer), 3, 6, 8, 32
Search/Compare
, 405
Second derivative, 106
Second-order Møller-Plesset, 193
Second-order properties, 156
Self potential, 236
Self-consistent field (SCF), 66, 76, 77, 110, 111, 112, 113, 115, 116, 118, 119, 123, 152, 157, 158
Semiempirical methods, 14
Semiempirical wavefunctions, 217
Separable wavefunction, 68
Sequence alignment, 348, 352
Serine, 273
Serine proteases, 246
Serratus
, 418
SF4, 200
SF6, 177
SH2, 200
SHAKE algorithm, 259, 282
Shake-up ionization, 129
Shelter Island, 8
Short-range distances, 311
Short-range interactions, 234
Short-time-scale motions, 293
Shull, H., 33, 39, 41, 45, 46, 47, 53
SIBFA
, 414
Sigma set, 11
Signature, 185, 186
SiH4, 196, 201
SIMCA-R
, 427
Similarity matrix, 319
Simulated annealing, 316, 344, 355, 358, 405
SIMVOL/PLTSIM
, 390
Single determinant, 67, 70, 140
Single determinant reference, 68, 71, 78, 91, 97, 112
Single determinant SCF, 81, 122
Singlet instability, 141
SIRIUS
, 353, 413
Sketcher
, 405
Slater determinants, 171, 180
Slater-type functions, 172
SO2, 200
SO2Cl2, 207
SO4^2-, 207
Sodium decanoate-decanol, 287
Sodium octanoate, 291
Softron Substructure Search System
, 394
Software, 381
Solid State suite
, 405
Solids Adjustment
, 405
Solids Builder
, 405
Solids Docking
, 405
Solids Refine
, 405
Solids Simulation
, 405
Solvation effects, 345
Solvation energies, 242, 343
Solvation pressure, 276
Solvation properties, 360
Solvent, 231, 346
Solvent-accessible surface area, 231, 293
Solvent fluctuation, 258
Solvent frictional effects, 249
Solvent reaction field, 247
SOPPA method, 149
Spartan
, 415
SPASMS
, 384, 402
Spatial flexibility, 102
Spatial orbitals, 75
Spatial symmetry, 72
Spatially based population methods, 184
SPCE waters, 287
SpecInfo
, 420
Spectral density function, 289
SPHGEN
, 419
Spin, 119
Spin contamination, 97, 99, 115, 119, 122, 128
Spin density, 154
Spin multiplicity, 77
Spin-orbital effects, 105
Spin orbitals, 69
Spin symmetry, 72, 140
Split-valence basis set, 216
Spreadsheet programs, 364
Standard Drugs File
, 417
Staphylococcal nuclease, 245
State-averaged orbitals, 142
Static correlation, 80
Statistical simulations, 19
STEREO
, 416
STERIMOL
, 390
Steroid, 310
STN EXPRESS
, 394
Stochastic boundary molecular dynamics (SBMD), 283, 292
Stochastic conformational searching, 406
Stochastic dynamics, 249
Stochastic gating, 253
Stored program digital computer, 1, 3
Strain energy, 202
Structural isomorphisms, 26
Structure Image
, 405
Structure Solve
, 405
Structure-based drug design, 337, 338
Substrate binding, 321
Substructure matching, 367
Supercomputers, 16
Superposition algorithms, 358
Superposition errors, 216
SURFACE
, 421
Surface area, 274
Surface force apparatus, 276
Survival probabilities, 252
SYBYL
, 16, 17, 349, 364, 365, 367, 368, 384, 385, 386, 408
SYBYL 3DB/UNITY
, 367, 420
Symmetry breaking, 115
SYNLIB
, 394
Synthesis, 369
Synthia
, 405
Synthetic chemistry, 28
Synthetic feasibility, 359
SynTree
, 390
Systematic search methods, 299

TableCurve
, 400
Tamm-Dancoff approximation, 138, 145
Tanford-Kirkwood model, 246
T(CCSD), 92
TD-CCSD, 82, 149
Teem, J., 51
Template forcing, 328
Tertiary structure, 344, 353
Tetrangle inequality, 308
Tetrangle inequality bound smoothing, 309
Therapeutic ratio, 346
Thermodynamic and Physical Properties database
, 390
Thermodynamic cycle, 359
Thermotropic polymorphism, 274
Thioredoxin, 246
Third-derivative contaminant, 114
Thouless parameterization, 139
Thouless theorem, 128
Three-dimensional database searching 366
Three-dimensional refinement, 314
Thymine, 242
Time scales, 270
Time-dependent Hartree-Fock, 139
Time-sharing, 24
tLEap
, 402
TOPDRAW
, 402
TOPKAT
, 402
TOPMOST
, 402, 418
Topological charge, 203, 207, 209
Topological electron density analysis, 184, 221
Topological populations, 216
Torsional angle driver, 17
Torsional space methods, 303
Toxicity, 346
Trajectory tables, 3
Transition energies, 136
Transition moments, 141
Transition state, 114
Transition state analogs, 338
Transition state structures, 112
Transition temperature, 274
Translational diffusion, 250
Translational steering, 257
TRIAD Base
, 408
TRIAD database
, 417
TRIAD NMR
, 408
Triangle bound smoothing, 302, 304, 306, 330
Triangle inequalities, 306, 309, 330, 364
TRIBL
, 414
Triose phosphate isomerase (TIM), 248, 253, 256, 258
Triple zeta plus polarization (TZP) basis set, 82
Triplet instabilities, 140
Truncated CI, 81, 83, 90
Truncation surface, 250
Trypsin, 358
Tsar
, 418
Turbomole
, 412
Two-determinant reference open-shell singlet (TD-CCSD), 82
Two-particle operator, 78
Two reference CI, 122

UHF-CCSD, 97
Ultraviolet photoelectron spectroscopy (UPS), 124
UniChem
, 415
United atom, 286
United atom models, 312
United atom radii, 351
U. S. Air Force, 6
U. S. Army Ordnance Department, 3, 32
U. S. Atomic Energy Commission, 5
U. S. Navy, 6
Units, 236
UNIVAC (UNIVersal Automatic Computer), 3, 8, 21
UniVersions
, 400
University of Chicago, 8
University of Colorado, 12
University of Houston Brownian Dynamics (UHBD)
, 230, 232, 234, 238, 239, 255
University of Pennsylvania, 4
Unlinked diagrams, 90, 92
Unrelaxed orbital, 129
Unrestricted Hartree-Fock (UHF), 71, 74, 75, 82, 97, 99, 107, 115, 140
Un-Scan-It
, 400
Upper bounds, 302, 307, 311, 314
User-friendly, 24
UV, 124

Vacuum tubes, 4, 5, 6
Valence double zeta, 103
Valence electrons, 13
Valence force fields, 14
Valence topological population, 198
Valinomycin, 278
Van der Waals interactions, 235, 316
Van der Waals radii, 194, 302, 358, 364
Variational collapse, 141
Variational energy, 79
Variational principle, 71, 76, 83
VAX, 56
VAX 11/780, 15, 54
VEGAS
, 397
VEH-91
, 413
Velocity autocorrelation functions, 289
Verlet algorithm, 281
Vertical electron affinity, 133, 135
Vertical electron detachment energy, 133, 135
VESCF (Variable Electronegativity Self-Consistent Field), 12
VIBMOL
, 390
VIBPLT
, 406
VIBRAM
, 390
Vibrational frequencies, 76, 119, 120, 121, 123, 145
Vibrational Schrödinger equation, 68
Vibrational spectra, 113
Vibrationally averaged structures, 106
Vietnam War, 6, 34
Vinyl alcohol, 214
Vinylamine, 215
Vinyllithium, 209
Virial theorem, 186, 217
Virtual orbitals, 75, 78, 112
Viscoelasticity
, 405
Vleduts, G. E., 26
VOID
, 351, 414
Von Neumann, J., 5

Water, 83, 88, 94, 96, 108, 110, 111, 116, 119, 124, 147, 152, 153, 155, 157, 158, 161, 179, 196, 199, 200, 201, 286
Wavefunction, 79, 171, 190
Weiss, A., 8
Westheimer method, 14
Westheimer Report, 36, 38, 40
WHAT IF
, 408
WODCA
, 397
Woodward-Hoffmann rules, 221
Workstations, 270, 341
World War II, 3
Wright Field Air Force Base, 8

xLEap
, 402
XMOL
, 427
Xpdb
, 428
X-PLOR
, 355, 407
XPS, 124
X-ray crystal structure, 300
X-ray structure, 1
Xtalview
, 428

Yak
, 409
Yeti
, 409
Yoshimine, M., 8

Zero-flux surfaces, 184, 186, 190, 217, 220
Zero-point vibrational energy, 127
ZINDO
, 385, 412, 416

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