REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 13 (1999)

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, 2, 70, 185
Accuracy improvement, 43
ACES II
, 35, 77
Acetylcholinesterase, 268, 293
Acetylene dimer, 44, 45
Acid-base catalysis, 249
Activation energies, 74
Activation entropies, 74
Active electrons, 21
Active site, 250
Active space orbitals, 21, 26, 62, 66, 77, 83
Adiabatic connection models, 42
Adjustable atom, 322
Adjustable bond, 322
ADS
, 315
Aesthetic function of a structure diagram, 386
Affinity of inhibitors, 285
Allene, 172
Allinger, N. L., v
Allyl radical, 11, 12, 17, 20, 23, 25, 33, 43, 48, 58
AM1, xiii, 43, 79
AMBER
, xii
American Chemical Society, v, xiv
Amide hydrogen exchange, 289, 291, 301
AMPAC
, xiii
Analysis of chains, 342
Analytical construction methods, 330
Analytical derivatives, 20, 22, 80
Analytical functions, 204
Analytical gradients, 36, 77
Angle spacing of a structure diagram, 341, 393
Angular demand (AD), 315, 317, 318, 346, 392
Angular momentum, 10
Angular projection operators, 165
Anisotropic polarizability, 233
Anisotropic potential functions, 207
Antisymmetric wavefunctions, 4, 20, 99, 148, 201
Aqueous systems, 183, 250, 257
Arcs in a structure diagram, 363
Argon clusters, 170
ARGOS
, 385
Artifactual symmetry breaking, 21
ASD
(Algorithmic Structure Display), 372, 379, 381
Assembly of a structure diagram, 344, 392
Assignment engine, 333
Atom and bond overlap in a structure diagram, 318
Atom label expansion, 313, 322
Atom prioritization, 328, 382
Atomic orbitals (AOs), 4, 26, 85
Atomic radii, 274
Atomization energies, 72
Attaching a bridged ring, 337
Attaching a fused ring, 337
Automated structure elucidation, 375
Automorphism in a structure diagram, 369
Avoidance heuristics, 393

B3LYP density functionals, 17, 42, 64, 71, 72, 73, 74, 75, 80, 82
Backtracking in a structure diagram, 356, 377, 382
Bacteriorhodopsin, 272
Barium, 167
Barnase stability, 298, 300
Base-catalyzed hydrogen exchange rates, 301
Basis functions, 2, 4, 110
Basis set effects, 105
Basis set extension (BSE), 100
Basis set size, 79
Basis set superposition errors (BSSE), 99, 100, 104, 113, 122
Basis sets, 29, 79, 100, 104, 108, 113, 114, 115, 194
Becke exchange functionals, 42
Benchmark calculations, 166
Benchmarks, 29, 64, 68, 74
Bending in a structure diagram, 358
Ben-Naim--Stillinger (BNS) potential, 221, 222
Benzoquinone radical anion, 79
Benzyl radical, 16, 17, 25, 33, 34, 43
Beryllium, 149, 155
Bessel function, 147
Bijl function, 153
Bimolecular reaction, 175
Binding energy, 103, 168, 173
Binding of inhibitors, 285
Biomacromolecular assemblies, 295
Biomolecular simulations, 228
Biopolymers, 292, 380, 389
Bitmask, 320
Bitstring, 365
Bjerrum potential, 221
BLYP density functionals, 17, 42, 73, 75, 117, 118, 119, 121, 122, 176
Boltzmann distribution, 139, 250, 254, 257, 264
Bond angle, 189, 190
Bond breaking, 5
Bond directions in a structure diagram, 329
Bond dissociation energies, 71, 72
Bond energies, 169
Bond functions, 113
Bond length, 189, 190, 396
Bond orbitals, 104
Bond stretching, 217
Bonding to pi bonds, 362
Born--Oppenheimer approximation, 196
Bosons, 148
BOSS
, xii
Bound water molecules, 273
Boundary conditions, 188
Bovine pancreatic trypsin inhibitor (BPTI), 272, 295, 296, 298, 299
BPW91, 176
Bra-ket notation, 4
Bridged rings in a structure diagram, 318, 330, 374, 376
Bridgehead atoms, 337, 376, 382
Brillouin's theorem, 23, 24, 27
Brownian dynamics simulations, 304
Bulk liquid water, 213
Bulk properties, 187
Buried hydrogens, 289
Buried residues, 271
Butadiene, 43
Butadiene radical cation, 51, 52, 69

C4H4 radical cations, 72
CADPAC
, 35
CambridgeSoft, 392
CAMEO
, 320, 357, 361, 364, 368, 373, 385, 388
Canonical ring description, 367
Canonical structure diagram, 397
Capping group in a structure diagram, 340, 342, 344
Carbenes, 72, 73, 77
Carbohydrates, 361, 389
Carbon clusters, 71, 135, 167
Carbonyl ylide radical cation, 50
Carhart's diagram layout algorithm, 378
CAS-CISD method, 17, 30, 36, 62, 81, 85
CAS-CISD+Q method, 17, 62, 63, 65
CAS-MP2, 36
CASPT2 method, 17, 36, 37, 62, 65, 73, 76, 81, 85
CASREACT
, 379
CAS Registry File, 379
CASSCF (complete active space SCF) calculations, 13, 17, 21, 22, 25, 26, 30, 36, 48, 55, 62, 65, 76, 80, 81, 85
Catalytic residues, 249
Cavity charge, 256
CBS-type calculations, 42, 82, 85
CCSD, 37, 38, 80, 85
CCSDT, 37, 38
CCSD(T), 38, 42, 72, 80, 85, 135
Central force (CF) potentials, 222
Central potentials, 222
Central rings in a structure diagram, 334
Centralized computing facilities, 1
Chain angle, 342
Chain perception, 342
Chain zigzags, 329
Chains, 340
Charge densities, 231
Charge distribution, 204, 216, 250, 262
Charge equilibrium techniques, 213
Charge sites, 208
Charge transfer (CT), 109, 218
Charges, 273, 274, 363
CHARMM
, xii, 259
CHARMM22 parameter set, 260, 262
ChemDraw
, xvi, 314, 321, 327, 340, 361, 371, 373, 388
Chemical Abstracts Service (CAS), 315, 331, 356, 361, 364, 371, 379, 381, 391
Chemical accuracy, 39, 80
Chemical Hamiltonian approach (CHA), 106
Chemical potential, 213
Chemical shift, 191, 278
ChemIntosh/ChemWindow
, 314
Chemsketch
, 314, 364, 371, 392
ChemWindow
, xvi, 371, 373, 392
Chlorine, 166, 167
Chlorobutanone, 344
alpha-Chymotrypsin, 249, 293, 296, 302, 303
Circular dichroism, 286
Circular free sweep (CFS), 323, 339, 393
Circular order of substituents (COS), 321, 329, 393
CISD, 29, 30, 86
Cis/trans bond configuration, 337
Citation analysis, vi
Classical induction energy, 211
Classical mechanics, 185
CLEAN
, 380
Closed-shell molecules, 2, 3, 4
Close-lying electronic states, 20, 44
Clusters, 187, 191, 204, 266
CN radical, 82
CNDO/S method, 76
Coherent scattering lengths, 192
Combating overlap in a structure diagram, 354
Compact Gaussians, 79
Competitive inhibition, 284
Complete basis set (CBS), 42, 82, 85
Complicated ring systems, 371
Compressibility, 225
Computational chemistry, vii, 1
Computer era models, 220
Computer simulations, 183
Computer phobia, xvi
Computers in Chemistry Division of the American Chemical Society (COMP), xiv
Condensed media, 203, 204
Condensed ring systems, 371, 389, 389
Condensed text style, 393
Condensed water, 220
Configuration interaction (CI), 26, 76, 86, 104, 105, 135
Configuration interaction (CI) wavefunction, 5, 22, 28
Conformational flexibility, 259, 270, 271
Conformational stability, 287
Congestion function, 330, 355, 363, 384, 387
Congestion potential, 359
Conical intersection (singularities), 20
Connection table, 313, 316, 325, 367, 393
Construction phase for structure diagrams, 334
Continuous dielectric media, 250
Continuum model, 234, 252, 274
Control flags for structure diagrams, 320, 321, 393
Conventional layouts of a structure diagram, 319
Coordinate systems, 325
Copper hydride, 167, 169
Core chain atoms, 340, 342, 349
Core electrons, 165, 168
Correlation coefficient, ix
Correlation energy, 5, 22, 77, 81, 104, 149, 172
Correlation functional, 41
Correlation-consistent functions, 116
Coulomb energy, 83, 211
Coulomb repulsion, 12, 27, 59
Coulombic interaction, 109, 195, 197, 256
Counterpoise corrections, 106, 107, 112, 120, 123, 125
Counterpoise method, 104, 107
Coupled-cluster (CC) methods, 30, 37, 63, 66, 85, 105, 135
Coupling parameter, 197
Cubane, 330, 384, 389
Cusps, 79
CVFF parameter set, 262, 302
Cyclobutadiene (CB), 56, 61, 62
Cyclobutane radical cation, 51
Cyclobutene, 22, 52
Cycloheptatrienylidene, 67, 68, 72, 73
Cyclooctatetraene (C8H8), 175
Cytochrome, 272

Database search, 374
Davidson correction, 17, 31, 37, 38
Daylight Chemical Information Systems, 382
Daylight Toolkit
, 382
De novo structure diagram generation, 313, 393
Debye--Hückel parameter, 257
Degenerate MOs, 47
Dehydrobenzene singlet diradicals, 82
Delocalized rings, 363
DelPhi
, 256
Denaturation curves, 286
Denaturation free energy, 287
Density, 190
Density functional approximations, 171
Density Functional Theory (DFT), 2, 10, 27, 39, 40, 69, 71, 72, 79, 82, 86, 105, 115, 122, 133, 171, 172, 185, 213
Density of water, 189
Density-pressure relations, 186
DEPICT
, 361, 364, 373, 382, 383
Deputy atoms, 361
Deputy bonds, 362
Design modes for structure diagrams, 320, 393
Desmol
, 373, 386
Deuterated water (D2O), 218, 289
Deviations from harmonicity, 75
Dewar benzene radical cation, 39
Dewar, M. J. S., xii, xiv
DGEOM
, xii
Diamond, 167, 172
Dielectric boundary, 261, 274
Dielectric cavity, 256
Dielectric constant, 188, 190, 225, 229, 230, 250, 258, 275
Dielectric properties, 186, 190
Dielectric saturation effects, 270
Difference schemes, 161
Differential equations, 142
Diffuse functions, 105
Diffuse polarization functions, 108, 110
Diffusion coefficient, 143, 187, 190, 294
Diffusion equation, 138
Diffusion quantum Monte Carlo (DQMC), 137, 141
Diffusion with drift, 140, 152, 162
Diffusional encounter complex, 291
Dimers, 187
Dipole moment, 10, 113, 117, 119, 175, 184, 188, 189, 191, 204, 207, 216, 219, 220, 229, 250, 294
Dipole moment derivatives, 75
Dipole moments of proteins, 267, 276, 292, 302, 303
Dipole polarizability tensor, 200, 233
Dipole polarization, 206
Diradicals, 3, 20, 22, 44, 52, 53, 61, 66, 72, 78, 82, 83
Direct CI methods, 32
Disconnected structures of a structure diagram, 384
Discretized continuum (DC) models, 274
Disjoint diradicals, 66
Disjoint orbitals, 56, 65
Dispersion energy, 109
Dispersion interactions, 115, 199, 201
Dissociation energies, 71, 114, 120
Distortion in a structure diagram, 360
Distortion coordinate, 52
Disulfide bonds, 298
DNA complexes, 295
DOCK
, xii
DOPS
(Distribution of Protonation States), 267
Double excitations, 27, 76
Double-reciprocal plot, 280
Doublet, 11
Doubly excited configuration, 13, 76
Dummy atom, 362
Dynamic electron correlation, 26, 29, 36, 66, 76, 79
Dynamic fitting methods for structure diagrams, 330
Dynamic grid, 364
Dynamic polarizability, 83
Dynamic spin polarization, 58

ECEPP
, xii
Effective charge model, 207
Effective core potentials (ECP), 165
Effective dipole moment, 209
Effective nuclear charge, 165
Effective water potential, 184, 213, 220
Eigenfunction, 87
Eigenvalues, 11, 75
Einstein equation, 143
Einstein relation, 187
Electric field, 199, 211
Electric field pulses, 292, 303
Electrochemical potential, 213
Electrocyclic ring opening, 51
Electrolyte, 250
Electron affinities (EAs), 72, 82
Electron configuration, 5
Electron correlation, 19, 26, 27, 72, 105, 154, 201
Electron density, 40, 113, 171
Electron gas, 135, 171
Electron paramagnetic resonance (EPR), 86
Electron repulsion operator, 28, 31
Electron spin, 10, 87
Electron spin density, 78
Electron spin resonance (ESR), 8, 17, 18, 86
Electron spin resonance spectra, 48, 77, 78, 80
Electronegativity equalization, 232
Electronic spectra, 7
Electrooptical investigations, 292, 304
Electrostatic effects, 274, 291
Electrostatic energy, 109, 208, 209
Electrostatic field, 249, 256
Electrostatic interactions, 184, 198, 205, 207, 210, 250, 255
Electrostatic potential, 255, 256, 258
Empirical water potentials, 184
Enediynes, 82
Energies of atomization, 169
Energy minimization, 259
Ensemble average, 187
Enthalpy, 191, 209
Entropy, 191
Enzymatic reaction mechanism, 281, 285
Enzyme kinetics, 279
Enzyme-product complex, 279
Enzymes, 249
Enzyme-substrate complex, 279
EOM-CCSD method, 77
EPEN empirical potential, 205, 222
EPEN/2 model, 223
Equal angle spacing, 342
Equation-of-motion coupled-cluster method (EOM-CC), 77
Equations of motion, 232
Equilibrium geometries, 14, 69, 73
Ethanol, 69
Ethyl radical, 74
Ethylene, 34, 54
Ethylene oxide radical cation, 48
Ethylene additions, 74
Ewald summation, 210, 225
Exact cancellation methods, 155, 159
Exact solutions, 159
Exchange energy, 41, 58, 109
Exchange functional, 41, 70
Exchange holes, 42
Exchange operator, 99
Exchange rates, 291
Exchange repulsion, 201, 202
Excited states, 22, 32, 36, 75, 83, 88, 164
Expanded text style, 393
Expectation value, 11, 134, 137, 140, 202
Expectation values of spin, 87
Experimental accuracy, 2
Experimental determination of pKas, 277
Experimental properties of water, 234
Explicit solvent, 272
Explicit waters, 275
Explicitly correlated Gaussian functions, 154
Extended single-excitation CI (XCIS) method, 76
External fields, 213
Extinction anisotropy measurements, 293
Extinction coefficient, 294
Extra diffuse functions, 110

F2, 103
Family tree of quantum chemistry, 134
Fermi contact term, 78
Fermi hole, 7
Fermions, 148
Feynman--Hibbs effective potential, 218
Fick's second law of diffusion, 141
Field-induced alignment, 292
Finite basis set, 29
Finite difference Poisson--Boltzmann (FDPB) methods, 251, 256, 257, 258, 274, 287, 304
Fixed angle spacing, 342
First-order energy correction, 197
First-order perturbation energy, 199
Fischer projections, 361
Fixed-charge four-site model, 234
Fixed-charge models, 220, 224, 229
Fixed-node calculations, 155
Fixed-node DQMC, 169, 172
Fixed-node methods, 155, 164
Fixed-node structure, 149
Fleeing heuristic, 355, 382
Flexibility, 224, 226, 231, 271
Flexible 3-center (F3C) potential, 226, 228
Flexible charge model, 216
Flexible nodes, 157
Flexible water models, 227
Fluctuating charge models, 185, 232
Fluorescence spectroscopy, 286
Fluorine, 103
Fokker--Planck equation, 140
Force constant, 20, 75
Force field parameters, 273
Force fields, 185, 234, 250
Form factors, 192
Formaldehyde, 165, 172, 174
Four-site charge model, 208, 234
Fragment for structure diagrams, 395
Fragment interpositioning, 363, 371
Franck--Condon factors, 61
Free circular angle, 317
Free energy, 189, 252, 265
Free energy differences, 253
Free energy interaction matrix, 255
Frozen atom of a structure diagram, 322, 393
Frozen bond, 322, 324, 393
Frozen-core basis sets, 165
Full CI, 6, 10, 21, 28, 38, 135, 166
Full counterpoise procedure (FCP), 107, 112, 120
Full group titration model, 260
Functional space, 110
Functionals, 40
Fused ring systems, 318, 337
Fusion atoms, 337
Fuzzy symmetry algorithm, 389, 390

G1 method, xiv
G2 procedures, 42, 70, 71, 82
GAMESS
, 116, 122, 123, 125
Gas phase ion chemistry, 3
Gauss' theorem, 257
Gaussian
, xii, 17, 29, 33, 36, 71, 78, 84, 116, 122, 125
Gaussian distribution, 144, 212
Gaussian functions, 103
Gaussian ("G") schemes, xiv, 42, 70, 71, 82
Generalized valence bond (GVB), 55, 86, 176
Genetic algorithm (GA), 330
Geometrically distinct topological automorphisms (GDTA), 368, 393
Geometries, 67
Geometry attributes table (GAT), 367, 393
Geometry optimization, 7, 14, 22, 26, 34, 37, 42, 70, 82, 116
Ghost atoms, 123
Ghost orbitals, 107, 111, 113, 118, 119
Gibbs free energy, 267
Globular proteins, 272, 296
Gordon Conference on Computational Chemistry, xiv
Gradient-corrected functionals, 41
Graphite, 172
Green's function quantum Monte Carlo method (GFQMC), 137, 146, 160
Green's function sampling, 157
Green's functions, 160
GROMOS
, xii
Ground state wavefunction, 6, 142
Guided random walk, 140
GVB NBMOs, 59

H2, 102, 103
Hamiltonian, 11, 165, 183, 186, 195, 202
Harmonic approximation, 75
Harmonic oscillator, 143, 144, 159
Hartree product of orbitals, 201
Hartree--Fock calculations, 6, 40, 194
Hartree--Fock exchange, 70, 83
Hartree--Fock limit, 139
Hartree--Fock (HF) theory, 2, 117, 118, 119, 121, 122, 135, 172
Hashing, 365
Haworth drawings, 361
Head atom for structure diagrams, 345, 346, 393
Heat capacities, 63, 65, 189, 190
Heats of formation, 71, 82
HeH, 135, 137, 155, 159
Heisenberg uncertainty principle, 11
Heitler--London energy, 109
Helium, 137, 148, 149, 164
Helium dimer, 100, 106, 112, 135, 154, 155, 159
Helium trimer, 123, 135, 159
Helium tetramer, 161
Hemoglobins, 293
Hen egg white lysozyme (HEWL), 272, 295, 296
Henderson--Hasselbalch equation, 264, 278
Hermitian properties of wavefunctions, 151
Higher order BSSE effects, 113
Highly condensed ring systems, 390
HIV protease, 300
HIV-1 zinc finger peptide, 275, 300
Hohenberg--Kohn (HK) theorem, 40, 135
HOMO energy, 84, 86
Homology modeling, 259
HONDO
, 36
Hückel NBMOs, 59
Hückel theory, 50
Hund's rule, 58
Hybrid approaches, 264, 268
Hybrid functionals, 82
Hybrid HF/DFT methods, 42
Hydrated electrons, 218
Hydrocarbons, 172
Hydrogen, 137, 144, 145, 149, 153, 154, 155, 156
Hydrogen abstraction reactions, 74
Hydrogen bond network, 191, 194, 224, 225, 228, 229, 231
Hydrogen bonds, 101, 107, 184, 188, 192, 201, 203, 210, 217, 229
Hydrogen chloride (HCl), 74, 170
Hydrogen dimer, 135, 137, 149, 155
Hydrogen exchange, 289, 290
Hydrogen fluoride, 149, 170
Hydrogen fluoride clusters, 123, 170
Hydrogen fluoride dimer, 106, 115, 116, 117, 118, 119, 121, 122, 175
Hydrogen ion, 135, 137
Hydrogen trimer, 135, 152, 154, 159, 164, 167
Hylleraas function, 154
Hyperfine coupling (hfc), 8, 14, 78, 86
Hyperpolarizability, 199

Ice, 174, 184, 189, 219, 220, 234
IGOR
, 385
Imaginary frequency, 63
Imaginary time, 142, 144, 164
Importance sampling, 140, 150, 158, 163, 168
Incoming coordinate space for structure diagrams, 325
Incoming orientation, 329
Individual bond alignment, 353
INDO method, 17, 79, 86
INDO/S-CI method, 17, 76
Induced dipole moments, 212
Induced moments, 187, 200, 210, 212, 228, 233
Induced polarization, 191, 223, 225
Induction energy, 109, 113, 114, 211
Inductive effects, 302
Infinite-order perturbation method, 37
Infrared (IR) intensities, 36, 75, 217
Inhibitors, 284, 300
Initial velocity, 280
Inorganic complexes, 389
InsightII
, 259
Institute of Scientific Information, vi
Integral equation methods, 222, 252
Interaction correlation energy, 114
Interaction energy, 109, 113, 119, 120, 121
Interaction free energy matrix, 253, 254, 263
Interaction potential, 217
Interaction sites, 206
Interelectron distances, 139, 153
Inter-fragment positioning, 363, 380
Intermolecular interaction energy, 99, 195, 231
Internal energy, 187
International Association for the Properties of Water and Steam, 189
Intramolecular motion of water, 216
Intrinsic pKa values, 251, 255, 264
Intrinsic reaction coordinate (IRC), 52
Intruder states, 37, 77
Ion polarization, 292
Ionic strength, 250
Ionizable groups, 274, 278, 287
Ionizable residues, 249
Ionization constants, 250, 290
Ionization of acids, 260, 283
Ionization potentials, 72, 82
Ionization states, 249
Ion-molecule interactions, 113
Iron, 166
Irregular rings, 318, 364, 382, 384, 393
ISIS/Draw
, xvi, 314, 330, 371, 381
Isodesmic reactions, 5, 27
Isoionic point, 289, 303
Isotope effects, 73, 75
Isotropic interaction sites, 206
Iterative vertex partitioning, 328
Iterative/predictive methods, 212

Jahn--Teller cusp, 164
Jahn--Teller effect, 47, 61
Jahn--Teller (JT) theorem, 20, 47
Jastrow function, 153, 154, 168

Kinetic mechanism, 280
Kinetics, 73
Kirkwood correlation sphere, 270
Kohn--Sham density functional theory, 40, 135
Kohn--Sham orbitals, 41, 77
Koopmans' theorem, 72
Kozack--Jordan model, 228, 230

Label expansion in a structure diagram, 361
Lac repressors, 293
Lagrangian formulation, 232
Large basis sets, 79
Latent heat of vaporization, 190
Lattice constant, 171
LAYOUT
, 364, 372, 380
LCAO-MO approximation, 4, 86
Lee--Yang--Parr (LYP) correlation functional, 42
Lennard-Jones parameters, 214
Lennard-Jones (LJ) potential, 184, 221, 228, 229
Level-shift techniques, 77
LHASA
, 385
Ligand binding, 250, 289
Linear dichroism, 292, 293
Linear response theory, 209
Linearized Poisson--Boltzmann equation, 255, 257
Linearly polarized light, 292
Lineweaver--Burk plot, 280
Linked diagram theorem, 32
Liquid state models, 224
Liquid water, 173, 192, 205, 206, 214, 220, 223, 228, 232, 234
Lithium, 135, 137, 166, 167, 171
Lithium hydroxide, 157, 161, 164
Lithium hydroxide dimer, 106
Local basis, 112
Local circular free sweep, 393
Local coordinates, 324, 325, 335, 394
Local correlation method, 111
Local density approximation (LDA), 41, 75, 135, 176
Local dielectric constant model, 271, 273
Local electric field, 232
Local energy, 139, 151, 154, 165
Local mode potential, 226
Local order, 194
Local potentials, 165
Localized orbitals, 104, 105, 110
Localized pair correlation, 111
Logical connector, 356
Lone pair sites, 221
Lowest unoccupied molecular orbital (LUMO), 86
Lysozyme, 251, 259, 271, 273, 295, 296

M site of water, 221
MACCS
, 330, 381
Macrocycles, 384, 389
Macroorientation, 351
Macroscopic properties, 231
Magnesium, 167
Magnetic field, 10
Many-body counterpoise correction, 123
Many-body interactions, 195, 204, 223, 224
Many-body perturbation theory (MBPT), 6, 7, 22, 31, 80, 86, 112
Many-body polarization, 206
Many-electron wavefunction, 4
Markush structures, 314
Massively parallel computers, 168
Master substituent sequencing, 346
Matrix inversion techniques, 212
Matrix isolation techniques, 3, 75
Matsuoka--Clementi--Yoshimine (MCY) potential, 222, 223, 231
Maximal velocity, 279
MDL Information Systems, 371, 380
MDRAW
, 373, 385
MEAD
, 256
Mean field approximation, 205, 225, 264, 266
Mean-square displacement, 187
MELD
, 36
Melting, 219
Mesoscopic models, 249, 274
Metal-insulator transition, 171
Metallic lithium, 135, 171
Metastable structure, 72
Methane, 154, 172
Methyl radical, 8, 9
Methylene, 20, 172
Metropolis algorithm, 137
Metropolis sampling, 139, 140
Michaelis constant, 279
Michaelis--Menten relation, 279
MINDO/3, xiii, 43
Minimal basis sets, 28
Minimization, 28
MM2/MM3
, xii
MNDO, xiii
Mobile charges, 250, 257
Mobile electrolyte, 256
Model chemistry, 25
Model of choice, 234
Models, 259
MOLCAS
, 29, 30, 36
MOLCOORD
, 385
Molecular distortion, 20
Molecular dynamics, 183, 185, 221, 222, 271
Molecular dynamics trajectories, 272, 298
Molecular geometry, 20, 206
Molecular ionization constants, 283
Molecular mechanics (MM), 2, 390
Molecular modeling, xvi
Molecular orbitals (MO), 86
Molecular properties, 115
Molecular surface, 250
Molecule in structure diagrams, 395
Molecule flipping, 351
Molfile, 394
Møller--Plesset (MP) perturbation theory, 6, 33, 36, 66, 104
MOLPRO
, 17, 29, 30, 36
Monocyclic rings, 368
Monoradical, 54
Monosaccharides, 389
Monte Carlo (MC) method, 183, 185, 205, 220, 222, 251, 267, 268, 330
MOPAC
, viii, xii
MOPLOT
, 44
Morse potential, 184, 216
Morse quadratic-quartic (MQQ) procedure, 175
Most cited authors, viii, x, xiii
MP2, 33, 35, 38, 42, 86, 110, 112, 117, 118, 119, 121, 122, 135
MP4, 38, 86, 110, 135
MST-FP potential, 231, 234
Mu-bonding in structure diagrams, 362
Mulliken electronegativity, 213
Mulliken spin densities, 9
Multiattached atom labels (MAALs), 361, 394
Multibridged ring system, 390
Multiconfigurational wavefunctions, 21, 26, 36
Multiple ionization equilibria, 263, 266
Multipole expansion, 210
Multipole moment, 113, 184
Multireference CI, 30, 86, 135
Multireference second-order perturbation theory, 66
Myoglobin, 269, 271, 273, 276

N2, 107
Nanomaterials, 2
Naphthalene, 369
Natural orbitals, 56, 176
Neat water, 186
Negative cooperativity, 279
Neon dimer, 110
Neutron diffraction, 188, 192
Nickel oxide, 167
Niesar--Corongiu--Clementi (NCC) potentials, 230, 231
Nobel laureates, viii, ix
Nodal properties, 7, 11, 146, 151
Node structure, 147, 149, 155
Nodeless ground state wavefunctions, 148
NMR chemical shift values, 278
NMR-determined structures, 272
Nonbonding MOs (NBMOs), 56, 59, 87
Nondisjoint orbitals, 59, 66
Nondynamic correlation, 38
Nonempirical molecular orbital (NEMO), 214, 230, 231
Nonempirical potential, 204
Nonhybrid gradient corrected functionals, 75
Noninteracting electrons, 40
Nonlocal effective potentials, 166
Nonlocal operator, 99
Normal mode analysis, 75, 217
Nuclear cusp, 79
Nuclear magnetic resonance (NMR) spectroscopy, 190, 259, 272, 278, 286, 289
Nuclear polarization effect, 206
Nucleic acids, 389

O3, 82
Odd-alternant hydrocarbon radicals, 11, 14
Off-atom sites, 207
Olefins, 74
Oligopeptides, 289
One-electron wavefunctions, 5
Open polygon in a structure diagram, 335, 337
Open-shell CISD calculations, 29
Open-shell molecules, 1, 2, 6, 67, 72, 75
Operators, 10
OPLS parameter set, 262, 273, 302
Optical rotation, 286
Optimizing geometries, 81, 82
Orbital overlap, 201
Orbits, 369
Ordered water molecules, 259
Organic radicals, 8, 7
Organic structures, 388
Organometallics, 388
Orientational decay times, 189
Output coordinate space for a structure diagram, 325
Overlap integral, 202
Overlap rectification, 356
Overlapping atoms, 380
Ovomucid, 272, 295, 296
Oxymyoglobin, 302, 303

Pair correlation functions, 192, 193
Pair distribution functions, 171, 188, 220
Pairwise additive potentials, 214, 230
Pairwise additivity, 210
Pairwise effective potential, 205
Pairwise interactions, 184, 204
Parabolic potential curves, 75
Parameter fitting, 204
Parameters, 262
PARSE parameter set, 262, 274
Partial atomic charges, 213
Partially selected atom, 322, 394
Path integral quantum Monte Carlo method (PIQMC), 137, 138
Path integral statistical mechanics, 218
Pauli exclusion principle, 4, 7, 41, 54, 59, 108, 135, 201
Peeled rings, 365
Peptides, 301
Periodic boundary conditions, 210
Perturbation theory, 32, 65, 99, 105, 106, 172
pH, 249, 279
pH-dependent inhibitor binding, 284
pH-dependent properties of proteins, 249, 284
Phenoxyl radical, 69
Phenylalanine, 259
Phenylcarbene, 67
Photodetachment, 175
Photoelectron spectroscopy (PES), 61, 65
Photosynthetic reaction center, 251
Pi bond in a structure diagram, 362
Pivot atom, 358
pKa algorithm, 268
pKa values, 297
Placing an atom, 350
Placing neighbors, 346
Planar [[pi]] systems, 8, 76, 78
Planar radicals, 16
Plastoquinone, 79
Poisson--Boltzmann (PB) method, 256, 257
Poisson's equation, 257
Polar hydrogens, 259, 271
Polarizability, 113, 210, 211, 229, 231, 250, 259, 273, 294
Polarizability tensor, 233
Polarizable electropole (PE) model, 184, 222
Polarizable point charge (PPC), 230, 232
Polarizable water potentials, 228, 230
Polarization, 109, 184, 185, 187, 199, 200, 213, 223
Polarization catastrophe, 212
Polarization charges, 256
Polarization energy, 203, 224
Polarization function, 19, 28, 82, 110, 114, 118
Polarization of protons, 292
Polarized basis set, 38
Polarized light, 292
Polyacetylene, 14
Polyenes, 14, 15
Polyenyl radicals, 14, 16, 43
Polygons, 319, 335, 377, 383
Polymers, 389
Polypeptides, 289
Polysaccharides, 389
Pople, J. A., ix, xiv
Porphine, 77
Postassembly of a structure diagram, 351
Post-facto reorganization, 356
Post-Hartree--Fock, 106, 115
Post-SCF methods, 6, 27
Potassium, 167
Potential energy curves, 49, 214
Potential energy functions, 184, 185
Potential energy surface (PES), 20, 26, 33, 35, 52, 56, 61, 83, 120, 135, 164, 166, 213, 223
Power series expansion, 37
PPP-CI method, 76
Preassembly analysis, 328
Pre-computer era, 219
Prefabricated unit (PFU), 324, 394
Prefabricated unit deposition, 351
Preservation of molecular macroorientation (PMM), 351, 394
Preservation of style in a structure diagram, 320, 322
Pressure, 187, 225
Principle of minimal tampering, 394
Probability density (PD), 1
Probability density functions, 140
Probability of birth, 145
Program flow for structure diagram generation, 326, 327
Projected UHF (PUHF) wavefunctions, 16, 17, 35, 62, 87
Projected UMP2 (PUMP2) method, 17, 35, 62, 73, 87
Projection operators, 35
Properties, 186
Propyne, 172
Protein conformations, 298
Protein Data Bank (PDB), 259
Protein dipole-Langevin dipole (PDLD) method, 251
Protein folding, 286, 289, 290, 298
Protein interior, 276
Protein stability, 250, 286
Protein-solvent system, 250
Proteins, 2, 249, 251, 274, 289, 389
Proteolytic reactions, 280
Proton transfer, 249
Protonation equilibria, 251
Pseudopotentials, 165, 168, 172
Psips, 144
Pure density functionals, 82
Pure spin states, 8, 9, 17, 21
Pure water, 186, 191, 218

QCISD(T) method, 30, 38, 72, 73, 80, 82, 87
QMagiC
, 135
Quadratic CISD(QCISD), 30, 37, 73, 80, 87
Quadrupole moments, 189, 194, 206, 210
Quantum chemical software, 1
Quantum chemistry, 194
Quantum Monte Carlo (QMC), 133
Quantum simulations, 216
Quantum statistical mechanics, 218
Quartet contaminant, 24

R groups, 356
Radial distribution function, 224, 228
Radical anion, 61, 77
Radical cations, 77
Radical ions, 20, 44, 69, 83
Radicals, 3, 11, 44, 69, 76, 78, 82
Radii of atoms, 273
RAIN
, 385
Random walk, 138, 141
Rate constants, 176, 291
Rate equation, 281
Rayleigh--Ritz variational theory (RRV), 133, 134
RCCSD, 87
RCCSD(T) method, 38, 87
RCISD method, 17, 38, 87
RCISD+Q method, 17
Reaction field, 210, 252, 255, 256
Reaction layout, 391
Reaction path, 175, 250
Reaction path zero-point energy, 175
Redesign for structure diagrams, 394
Redraw of a structure diagram, 394
Redraw queue, 325
Reduced effective representation (RER) potentials, 225, 226, 230
Reduced-site approximation, 251, 264, 288
Reference wavefunctions, 29, 32
Reflection in a structure diagram, 357
Registry File
, 391
Regular polygon, 335, 377, 383
Regular ring, 394
Reimers-Watts-Klein (RWK) potential, 222, 229, 231
Relative energies, 81
Relativistic effects, 172
Relaxation amplitudes, 294
Relaxation electrooptical methods, 292
Relaxation times, 294
Released-node method, 157
Relic databases, 314
Removing atom overlap, 351
Repositioning in a structure diagram, 394
Residues, 249
Resonance stabilization, 71
Restricted open-shell Hartree-Fock (ROHF), 6, 7, 12, 15, 16, 17, 19, 58, 68, 87
Ribonuclease, 298
Ribonuclease A, 272, 295, 296
Ribonuclease T, 296
Rigid, fixed-charge models of water, 226
Rigid models, 206
Ring analysis in a structure diagram, 333, 394
Ring angular demand, 317
Ring construction flowchart, 335, 394
Ring directions, 330
Ring drawing unit (RDU), 331, 394
Ring fusion, 331
Ring Index
, 364, 375
Ring opening reaction, 51
Ring peeling, 331, 332, 382
Ring systems (RS), 330, 394
Ring template database (RTD), 331, 364, 365, 394
Ring templates, 371, 384
Ring topology, 370
Rings, 319, 329
RJOIN
, 380
RMP2 method, 17, 35, 38, 82, 87
RNA, 304
Robust solvent models of water, 224
Rotate--bend--stretch (RBS) heuristic, 356, 357, 382, 394
Rotation to maximum bond alignment (RMBA), 352, 353
Rotational barrier, 16, 17, 18, 33, 43
Rotational velocity, 303
Rowlinson potential, 221
RSCD
, 365
RWK models, 222
RWK2 model, 222, 229, 231
RWK2-M, 222
Rydberg states, 77

Saddle point, 166
Sadtler database
, 392
Salt bridge, 273
Salt effects, 302
SAM1, xiii
Sampling error, 145
Sampling sequence, 157
Scaling, 39, 75
Scaling requirements, 136
Scattering calculations, 168
Schrödinger equation, 133, 136, 138, 141, 144, 146, 147, 148, 151, 159, 195, 197
SDG programs, 372, 374
Second virial coefficient, 219, 223
Secondary basis set superposition error, 113
Second-order Jahn--Teller (SOJT) effect, 47, 48, 49, 87
Second-order saddle point, 51
SECS
, 372, 385
Seed atom, 315, 346, 349, 350, 387, 394
Selecting a bridge for peeling, 334
Selecting a fused ring for peeling, 334
Selective redesign, 322, 388, 394
Self-consistent field (SCF), 5, 87, 135, 154
Self-consistent partial charges, 264
Self-diffusion coefficient, 225
Self-energy, 209, 211
Semiempirical methods, 76
Sensitivity analysis, 234
Sensitivity coefficients, 233
Sequencing a ring, 339
Silicon, 167
Silicon hydrides, 168, 169
Simple point charge (SPC) model, 224, 225, 229
Simulated annealing, 272, 330
Singer polymals, 154
Single excitations, 27
Single reference configuration, 30, 36
Single-determinant wavefunction, 63, 149
Single-electron transfer, 3
Single-site algorithm, 262
Single-site titration model, 260
Singlet carbenes, 73
Singlet diradicals, 66, 82
Singlet--triplet gaps, 39, 61, 66, 72, 73, 83
Singly occupied molecular orbitals (SOMOs), 6, 7, 8, 11, 44, 69, 76, 87
Size consistency, 29
Slater determinant, 4, 5, 12, 43, 86, 154
Slater-type orbital, 103
Smeared charges, 231
SMILES, 313, 322, 382, 384, 388
SMOG
, 373
Sodium, 167
Soft sticky dipole (SSD) potential, 226, 228
Soliton, 14, 18
Solvation, 217, 234
Solvation shell, 234
Solvent-accessible surfaces, 270, 273, 274
Solvent-exposed residues, 271
Source term in QMC, 162
Spanning tree, 384
SPC water model, 214, 216, 226, 227, 234
SPC/E water model, 225, 226, 232, 234
SPC-FP water model, 231
Special functions theory, 102
Spektren
, 372, 380
Spin angular momentum, 10
Spin contamination, 8, 10, 11, 13, 16, 33, 43, 58, 63, 67, 68, 80
Spin density, 8, 9, 18, 78
Spin echo measurement, 8
Spin operator, 11
Spin polarization, 8, 11, 13, 18, 25, 43, 78, 79
Spin projection, 16, 63, 73
Spin states, 10, 11
Spin-coordinate space, 150
Spin-polarized electron gas, 172
Spin-polarized wavefunction, 58
Spiro dilemma in a structure diagram, 395
Spiro junction, 331
Spiro rings, 339
Split-valence plus polarization (SVP), 88
Spurious symmetry breaking, 20
ST2 potential, 221, 224, 231
ST4 potential, 225
Staphylococcal nuclease, 296
State crossings, 20
Static dielectric constant, 276
Statistical mechanical models of water, 219
Steady state kinetics, 279
Steam Tables
, 189
Step-by-step buildup, 3
Stereocenters, 361
Stereochemistry, 360, 371, 374, 380
Steric effects, 302
Steroids, 352, 364, 369
Stillinger (ST2) potential, 222
STN International, 379
Stockmayer potential, 219
STR3
, 372, 375, 377, 380
Stretch frequency, 189, 190, 195
Stretching in a structure diagram, 358
Strontium, 167
Structure cleanup, 314, 320
Structure diagram generation (SDG), xvi, 313, 372, 374, 375, 395
Structure factors, 192
Structure, 395
Strychnine, 332
Stylistic choices in a structure diagram, 322
Styrene, 43
Subjacent MOs, 11, 78
Substituent angular spacing, 347
Substituent placement, 348, 349, 350
Substituent sequencing, 348
Substrate concentration, 280
Supermolecular approach, 100, 102, 196
Surface residues, 276
Surface tension, 186, 189, 190
Symmetric wavefunctions, 148
Symmetrical radical ions, 83
Symmetry, 47, 51, 60
Symmetry breaking, 7, 17, 18, 20, 22, 35, 50, 51
Symmetry perception, 391
Symmetry-adapted perturbation theory (SAPT), 112
Symmetry-constrained MOs, 18
Synthesis planning programs, 314, 385
Systematic error, 157, 159, 166

Tanford--Roxby approximation, 251, 264, 267
Tautomeric equilibria, 275
Tautomeric forms of residues, 269
Taylor series, 198, 201, 233
Template matching algorithm, 370
Templates for structure diagrams, 367
Tet repressors, 293
Thermal corrections, 74
Thermodynamic cycles, 251
Thermodynamic properties, 189, 231
Thermodynamics, 70, 251
Thermostat, 232
Three-dimensional to two-dimensional conversion, 314
Three-electron two-center bonds, 83
Three-site charge model, 208
Tidy function in a structure diagram, 320
Tight polarization functions, 110
Time-dependent density functional response theory (TD-DFRT), 84
TIP3P model, 224, 226, 234
TIP4P model, 214, 224, 226, 229, 232, 234
TIPS2 model, 224
Toluene radical, 45, 46, 71
Topological automorphisms, 368
Transferable intermolecular potential (TIP), 224, 226, 229, 232, 234
Transition metal complexes, 2
Transition state theory, 175
Transition states, 22, 26, 33, 35, 37, 39, 42, 56, 69, 70, 73, 175, 176, 250
Trial wavefunctions, 153
Trimethylenemethane, 52, 58, 61, 64
Triple excitations, 27, 38
Triplet, 11
Triplet diradical, 54, 69
Truncated CI methods, 29, 32
Tryptophan, 259
Tunneling, 218
Turkey ovomucid third domain, 272, 295, 296
Twisted allyl radical, 16
Twisted ethylene, 52, 54
Two configuration SCF (TCSCF), 87
Two-dimensional box, 156
Tyrosine, 259

UB3LYP, 43, 62, 64, 68, 81
UBLYP, 68
UCCSD method, 62, 88
UCCSD(T) method, 17, 62, 73, 88
UCISD method, 17, 62, 88
UDFT, 43
UHBD
, xii
Ultraviolet difference spectroscopy, 286
UMP2 method, 8, 17, 33, 34, 62, 68, 73, 82, 88
UMP3 method, 62
UMP4(SDQ), 62
Units, 151
University of Houston Brownian Dynamics (UHBD), xii, 256, 261, 262
Unrestricted Hartree--Fock (UHF), 7, 8, 10, 12, 15, 16, 17, 34, 43, 45, 62, 68, 88
Upper bound, 134
UQCISD method, 17, 30, 62, 68
UQCISD(T) method, 17, 30, 62, 88

Valence bond description, 60
Valence correlation energy, 166
Valence electrons, 26, 165
van der Waals complexes, 107, 109, 114, 120
van der Waals radii, 273
Variable attachment points, 362
Variational methods, 28, 134
Variational principle, 21, 102
Variational quantum Monte Carlo method (VQMC), 137, 139
Variational transitional state theory, 175
Velocity autocorrelation function, 188
Vibrational analyses, 22
Vibrational corrections, 70
Vibrational density of states, 189
Vibrational frequencies, 170, 174
Vibrational spectra, 75, 75
Vibration-rotation tunneling spectroscopy, 174
Vibronic interaction, 44, 47
Vinyl radical, 20
Virial coefficient, 220
Virial formulation, 187
Virtual counterpoise procedure (VCP), 107
Virtual orbitals, 5, 22, 27, 76, 104, 105, 111
Viscosity, 189

Walkers, 144, 145, 152, 158, 159, 160, 161, 163
Watanabe--Klein (WK) potential, 225, 226
Water (H2O), 119, 149, 157, 174, 183, 186, 206, 209, 217, 218, 219, 220, 234, 251, 259
Water clusters, 174, 175, 194, 213, 228
Water dimer, 106, 111, 115, 116, 117, 118, 119, 121, 122, 191, 192, 194, 201, 202, 203, 207, 208, 214, 215, 223
Water hexamer, 174
Water models, 203, 215, 221, 234
Water potentials, 184, 219
Water properties, 189, 190, 227
Wavefunction, 197
Weakly bound states, 105
Wedge/hash bonds, 321
Weighting factor, 137
Weights, 160
Well-tempered basis sets, 113
Wigner--Kirkwood expansion, 217
Wilson GF matrix method, 75
Wiswesser line notation (WLN), 374, 395
World Wide Web, vii, xvi, 396, 398

X-alpha method, 41, 135
X-ray diffraction, 188, 192, 219
X-ray structures, 274

Zero-order approximation, 32
Zero-order reference wavefunction, 31
Zero-point energy (ZPE), 17, 63, 74, 82, 169, 174, 175
Zigzag preservation, 343

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