REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 18 (2002)

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 methods, 116, 134, 214, 275
Abraham LSER parameter set, 234
Absorption, 151
Absorption intensity, 193, 195, 200
Absorption transitions, 168, 179
Academic hiring, 301
Accelrys Inc., 35
Acceptance ratios, 99
Acceptor LUMO, 148
ACE (Automatic Computing Engine), 261
Acetylene, 280
Acetonitrile, 201, 205
Acidity, 234, 237, 247
Activation energy, 173
Active site, 73
ADAPT
, 246
Additive models, 51
Adiabatic free energy surfaces, 187
Adiabatic gas-phase basis, 185
Adiabatic polarizable model (APM), 204
Adiabatic states, 149
Adiabatic scalar reaction coordinates, 155
Adiabatic transition dipole moment, 151, 194
Adiabatic wave functions, 154
Adjoined basis sets, 280
Adsorption, distribution, metabolism, and excretion/elimination (ADME), 307, 308
AEG Telefunken, 277
Agglomerative clustering, 4
Agonist-bound state, 67
Ahlrichs, Reinhart, 269, 270
Akademie der Wissenschaften der DDR, 284
ALGOL language, 269
Allen, Leland C., 271
Almost cliques, 22
Alpha-helixes, 125
AM1 (Austin Model 1), 119, 220, 235, 236, 247, 248, 249
AMBER, 50, 51, 63, 65, 72
Ambiguous decision points, 16
American Chemical Society (ACS), 294, 314, 315, 316
AMPAC
, 220, 236, 248
Analog computer, 264
Anisotropic polarizability, 106
Anisotropic potentials, 122
Annihilation operators, 160
Antagonist-bound state, 67
Anthracene, 176
Antibacterial agents, 73
Applequist polarizabilities, 94
Approximate weight of evidence (AWE), 20
Arbeitsgemeinschaft Theoretische Chemie (AGTC), 274, 283
Aromatic rings, 60
Artifacts, 15
Arylesterase, 238
Ascending regression analysis, 231
Atom hardness, 107
Atom-atom charge transfer (AACT), 110
Atom-centered charges, 122
Atomic charges, 219, 221, 246
Atomic group orbitals, 275
Atomic orbitals, 116
Atomic polarizabilities, 94
Atomic solvation parameters, 55
Attractive interactions, 60
Available Chemicals Directory (ACD)
, 31, 72, 74, 86
Average molecular polarizability, 222
Average-link clustering, 8
Avogadro's number, 193
Avoided crossing of states, 280

B2H6, 275
B3P86 functionals, 240
Band gap, 107
Band shape analysis, 180, 191, 206
Barnard Chemical Information Ltd., 22, 34
Barsuhn, Jürgen, 280
Base-pair stacking, 125
BASF, 283
Basicity, 234, 237
Basis set: 3-21G*, 243
Basis set: 6-31+G**, 240
Basis set: adjoined, 280
Basis set: LCGO, 275
Basis set: STO-3G, 119
Basis set: STO-3G*, 240
Basis set: STO-5G*, 240
Batch update classification, 12
Bauer, Friedrich L., 263
Bayer, 283
Bayesian analysis, 1
Bayesian information criteria (BIC), 20
Bazley, N., 274
Benzene, 44, 131, 264
Benzoic acids, 216
Berlin, Free University of, 276
Berthier, Gaston, 270
Bessel function, 201
Beta-sheets, 125
Biermann, Ludwig, 262, 265, 270
Bifurcated hydrogen bonds, 132
Bilinear model, 169
Bilinear solute-solute coupling, 169
Bilinear solute-solvent coupling, 175
Billing, Heinz, 261, 262
Binding affinities, 42, 43, 53, 54
Binding constants, 45, 52
Binding entropy, 54
Bingel, Werner A., 273, 274
Binuclear metal-metal charge transfer complexes, 173
Biological activities, 214, 232
Biological assay, 44
Biological testing, 43
Biotechnology, 312
BIRCH
(Balanced Iterative Reducing and Clustering using Heuristics), 17, 21
Bis(Adamantylidene), 176
Bisecting k-means, 17
Bit strings, 10
BLEEP
, 50
Boiling point, 214, 245, 248
Boltzmann constant, 152
Bond dipole moments, 226
Bond-charge increment (BCI), 110
Bonn, University of, 276, 277
Boolean fingerprints, 15
Born theory of lattice dynamics, 100
Born, Max, viii, 258
Born-Mayer potentials, 103, 127
Born-Oppenheimer (BO) approximation, 104, 155
Botschwina, P., 281
Bottom-up principle, 272, 285
Boundary conditions, 121
Breathing shell, 106
Brickmann, Jürgen, 273
Briegleb, G., 270
BUBBLE
, 17
Buckingham potential, 103, 127
Buenker, Robert J., 281
Bulk metals, 113
Bulk oxides, 113
Bulk properties, 211, 216, 227, 233
Bunsentagung (Physical Chemistry Society), 284
Burden-CAS-University of Texas descriptors (BCUT), 30

c-Means, 19
C2H4, 275
C2H6, 275
C3H6, 275
C6H6, 275
Calorimetry, 45
Canopies, 22
Carbanions, 280
Carbonic anhydrase II (CAII), 72, 73
Carbonic anhydrase inhibitors, 62
Carbonium ions, 280
Cartesian Gaussian functions, 266
Cascaded clustering, 18
Cascaded Jarvis Patrick method, 31
CAST3D
, 31
Categorical data, 20
Cation-[[pi]] interaction, 60
Centroid-based clustering method, 15
Centroids, 19
Cephalosporins, 215
CerBeruS
, 29
CH2, 275
CH4, 275
Chaining, 15, 16, 17
Change, v
Chameleon algorithm, 16
Charge conservation, 110, 120
Charge descriptors, 235
Charge distribution, 133
Charge neutrality constraint, 110
Charge recombination (CR) reorganization energies, 180
Charge separation, 111
Charge separation reactions, 183
Charge separation reorganization energies, 180
Charge transfer (CT), 110, 111, 125, 131, 132, 192
Charge transfer crystals, 173
Charge transfer free energy surfaces, 154, 155, 164, 186
Charge transfer reactions, 147
Charge-assisted hydrogen bonds, 47
Charged partial surface areas (CPSA), 223, 227
CHARMM
, 50
CHARMM force field, 51
Chemical and Engineering News
, 294, 295, 304
Chemical companies, 310
Chemical Computing Group Inc., 34
Chemical data, 16, 23, 25
Chemical databases, 43
Chemical information, v
Chemical potential equalization (CPE), 109, 116, 132
Chemical scoring function, 60
Chemie-Information-Computer (CIC), 283
Cheminformatics, v, 306
Chemistry graduates, 311
ChemScore, 50, 55, 65, 68
Chicago, University of, 265
Chlorine, 108
Chromatographic retention index, 233
Chromophores, 176, 177, 198, 201, 202, 203
Ciba-Geigy, 283
CICLOPS
, 279
City-block distance, 21
Classification of clustering methods, 1, 4
Cliques, 22
Clustan Ltd., 34
Cluster centroid, 6, 10, 13
Cluster density, 15, 20
Cluster features (CF) tree, 17
Cluster identifiers, 12
Cluster medoid, 6
Cluster shape, 15, 20
Cluster size, 15, 20
Cluster-center clustering method, 8
Clustering algorithms, 6
CLustering In QUEst (CLIQUE), 21
Clustering LARge Applications (CLARA), 19
Clustering Large Applications based on RANdomized Search (CLARANS), 20
Clustering methods, 1, 2
Clustering method: Graph-theoretic, 8, 22
Clustering method: Jarvis-Patrick, 10, 18, 22, 23, 31, 32
Clustering method: k-Means, 11, 13, 15, 17, 19, 22, 32
Clustering method: Linkage, 8
Clustering method: Medoid-based, 15
Clustering method: Minimum-diameter, 9, 16, 28
Clustering method: Minimum-variance, 8
Clustering method: Nonhierarchical, 3, 9, 17
Clustering method: Nonparametric, 6
Clustering method: Parametric, 5
Clustering method: Partitioning around medoids (PAM), 19
Clustering method: Reconstructive, 5
Clustering method: Relocation, 5, 11
Clustering method: Single pass, 5, 9
Clustering method: Variable grid, 21
Clustering method: Ward, 8, 15, 22, 23, 25, 28
Clustering tendency, 24
Clustering Using REpresentatives (CURE), 16, 19
Clusters, 115, 122, 282
COBOL language, 269
CODESSA
, 247, 248
Coherence length of a delocalized electron, 111
Collaborations, 306
COLOSSUS, 260
Combinatorial chemistry, vi, 2, 28, 42
Combinatorial classification, 12
Combinatorial libraries, 1, 30, 306
Combinatorial library design, 2
Commonality between nearest neighbors, 5
Communication skills, 306
Complementarity, 45
Complete neglect of differential overlap (CNDO), 279
Complete-link clustering, 7, 14
Compound acquisition, 28
Computational biology, 22, 308
Computational chemistry, v, 1, 276, 293, 306
Computational chemistry in Germany, 257, 276
Computational efficiency, 129
Computer graphics, 41
Computer science, v
Computer simulations, 89
Computer-aided drug design (CADD), 307
Computer-aided ligand design (CALD), 307, 308
Computer-aided synthesis, 278, 283
Computers, 44
Condensed phases, 147, 167, 206
Condensed-phase media, 160
Condensed-phase properties, 128
Configuration interaction (CI), 275
Conformational degrees of freedom, 55
Conformational flexibility, 48
Conjugate gradients, 105
Connectivity index, 249
Consensus scoring, 70
Conserved water molecules, 43, 61, 73
Constitutional descriptors, 219, 248
Contact surface, 55
Continuum solvation models, 51, 52
Contract workers, 314
Contracted Gaussian orbitals, 275
Control Data Corporation (CDC) computers, 276, 277, 278
Convergence limits, 97
Convex computer, 282
Cooperativity effects, 51, 59
Core charges, 100
Corina
, 72
Correlation coefficient, 213, 229, 232
Cost function, 5, 13
Coumarin dye, 203
Counting descriptors, 219, 240, 248
Coupled cluster, 275
Coupled electron pair approach, (CEPA), 275, 279
Covalent H-bond acceptor basicity, 222
Covalent H-bond donor acidity, 222
COX-2 (cyclooxygenase-2), 65, 66, 71
Creation operators, 160
Crisp clustering, 3
Critical point, 124
Cross-validated correlation coefficient, 213, 230, 232
Crossing point, 173
Crystals, 100
Cut-offs, 99
Cyclobutadiene, 275

D-optimal design, 32
D1 Computer, 263
Darmstadt, Technische Hochschule, 261, 263
Data analysis, 1
Data mining, 14
Data reduction, 1
Database creation, 308
Database management, 308
Database mining, 308
Databases, 63, 278, 283
Dataprints, 14, 23
Daylight Chemical Information Systems Inc., 22, 31, 35
De novo design, 42, 57, 73
Decoy solutions, 60
Decoy structures, 58
Deformable shell, 106
Delauney triangulation, 22
Delocalization, 154, 200
Delocalized electrons, 243
Dendrogram, 3
DERA computer, 263
Descending regression analysis, 231
Descriptor reduction, 231
Descriptors, 212, 213, 218, 221
Design of donor-acceptor systems, 184
Density functional theory (DFT), 116, 240
Density of states, 167
Density-based clustering, 5, 13
Density-based spatial clustering of applications with noise (DBSCAN), 21
Descriptor orthogonality, 229
Descriptor space, 5
Descriptors, 2, 9
Desolvation, 46
Deutsche Forschungsgemeinschaft (DFG), 261, 263, 267, 271
Deutsche Rechenzentrum (DRZ), 267, 268
Diabatic basis set, 160, 163, 185
Diabatic electron transfer free energy surfaces, 165
Diabatic solvent reorganization energy, 164
Diabatic states, 149
Diabatic scalar reaction coordinates, 155
Diabatic wave functions, 154
Diatomics, 266, 274
Dielectric constants, 52, 122, 180
Dielectric continuum estimate, 178
Dielectric crystals, 157
Diercksen, Gerd, 270, 273, 274
Diffuse charges, 115
Diffusion constant, 122
Digital computer, 259
Digital Equipment Corporation (DEC) computers, 282
Dimethyl sulfoxide (DMSO), 44
Dipolar hard spheres, 183
Dipole field tensor, 92, 95, 99
Dipole moment calculation, 97
Dipole moments, 89, 91, 101, 111, 121, 205, 219, 222, 225, 226, 236, 249
Dipole operator, 192
Dirac, Paul, 258
Directional interactions, 108
Discrete data, 20
Dispersion molecular surface interaction (MSI), 223
Dissection effect, 17
Distortion, 25
Distribution coefficient, 234
Diversity analysis, 1, 29
Divisive clustering, 4
DNA base pair stacking, 126
DNA gyrase, 73, 74
DOCK
, 50, 52, 55, 60, 62, 70, 72
Docked ligand, 58
Docking, v, 44, 307
Docking programs, 51
Donor HOMO, 148
Donor-acceptor complex, 149, 157, 184
Donor-acceptor overlap, 189
Donor-acceptor pairs, 54, 192
Dresden, 263
Drude model, 176, 177
Drude oscillator model, 100
Drug discovery, 41, 75, 306, 307
Drug-like compounds, 44, 64
Drug-like ligands, 75
DrugScore, 50, 57, 62, 63, 65, 67, 68
Dyes, 200

Effective core potentials, 266
Effective doses, 214
Effective polarizability, 128
Einstein model, 151, 193
Electric field operator, 161
Electric fields, 89, 103, 192
Electrical polarizability, 106
Electron affinity, 107, 225
Electron correlation, 275, 279, 281
Electron delocalization effects, 184
Electron distribution, 219
Electron transfer (ET), 147, 149
Electron transfer free energy surfaces, 150, 155, 182
Electron transfer matrix element, 160, 197
Electronegativity, 107
Electronegativity equalization (EE), 89, 106, 109, 115, 123, 131
Electronic charge distribution, 102, 175
Electronic coupling, 153
Electronic delocalization, 153
Electronic density, 102, 188
Electronic excitation, 193
Electronic polarizability, 159
Electronically delocalized chromophores, 198
Electronically excited states, 279
Electrostatic balance, 241
Electrostatic H-bond acceptor basicity, 222
Electrostatic H-bond donor acidity, 222
Electrostatic induction, 127
Electrostatic interaction, 47
Electrostatic potential (ESP), 90, 132, 226
Electrostatic potential variances, 236
Embedded atom method (EAM) potential, 113
Emission, 151
Emission intensities, 200
Emission rate, 193, 195
Emission transitions, 168, 179
Empirical descriptors, 219, 232
Empirical property, 212
Empirical reactive potentials, 134
Empirical scoring functions, 53, 54, 72
Empirical valence bond (EVP), 119
Employment, 293, 302
Energy descriptors, 235
Energy gap law, 155, 175, 181
Energy gaps, 151, 158, 170, 171, 173, 174, 177, 184, 186, 191, 194, 196
ENIAC, 260, 261
Enrichment factors, 64, 69
Enthalpy-entropy compensation, 46, 56
Entropic effects, 157, 167
Entropy, 55, 59
Entropy penalty, 56
Entropy-driven processes, 48
Enzyme catalysis, 126
Equation of motion (EOM) methods, 280
Equilibrium constant, 216
Erlangen-Nürnberg, University of, 280
EROS
, 279
Estrogen receptor, 65, 68
Euclidean distance, 21
Euclidean metric, 20
European Center for Atomic and Molecular Calculations (CECAM), 276, 278
European Communities Joint Research Center, 32
European Inventory of Existing Chemical Substances (EINECS)
, 32
European Science Foundation, 283
Even-tempered orbital basis, 279
Ewald summation, 99, 130
Exchange correlation, 117
Excited states, 279
Expectation maximization (EM) algorithm, 12, 20, 24
Expert systems, 278
Explicit solvent models, 51, 178
Extended Hückel theory (EHT), 245
Extended Lagrangian method, 98, 113
External electric fields, 125, 175, 225
Extinction coefficient of absorption, 193, 195

F
ratio, 213, 2229, 232
F2O, 275
Factor analysis, 33
False positives, 30, 42, 54, 70, 71
Fano-Anderson model, 165
FAP, 269
Fast multipole methods, 99, 129
Federal agencies, 310
Fermionic annihilation operator, 165
Fermionic creation operator, 165
Fingerprints, 14, 18, 33
First-order predictor algorithm, 97
Fisher index, 232
FK506, 47
FK506-binding protein (FKBP), 47, 70
FKBP inhibitors, 47, 72
Flexible docking, 42, 72
Flexible ligand superposition algorithm, 60
FlexS
, 73
FlexX
, 50, 55, 62, 65, 67, 73
FlexX scoring function, 62, 65
FLOG
, 50, 59, 61, 64
Fluctuating charge method, 110, 123
Fluctuation boundaries, 171, 173
Folding time, 126
Force field-based methods, 51
Force fields, 214
Formate ion, 275
Förster, Th., 270
Fourier integral, 159
Fragment screens, 10
Franck-Condon factor, 156, 157, 162, 195, 198, 201
Franck-Condon optical envelopes, 192
Franck-Condon transfer, 148
Franck-Condon weighted density (FCWD), 149, 153, 194
Frankfort, University of, 270
Free energy, 159, 163, 167, 190, 216, 242
Free energy gap, 150, 184, 185
Free energy of activation, 216
Free energy of binding, 45
Free energy of solvation, 214
Free energy perturbation, 52
Free energy surfaces, 155, 157, 169, 187, 189, 198
Freezing point, 124
Frequency-dependent dielectric constant, 122
Fresno
, 50
Frontier molecular orbital (FMO) theory, 225
Fullerenes, 282
Fuzzy clustering, 3, 5, 18
Fuzzy Jarvis Patrick, 31

Gabriel graph, 22
Gambler
, 65
Gamma function, 166
Gas-liquid chromatography (GLC), 233
Gas-phase dipole moment, 90
Gaussian
, 220, 240, 243
Gaussian solvent model, 161
Gaussian functions, 274, 275
General interaction property function (GIPF), 222, 240
Generalized Born solvation model, 52
Generalized Mulliken-Hush (GMH) basis, 184
Generative clustering methods, 5
Generic drug manufacturers, 303
Genetic algorithm, 218
Geometrical descriptors, 219
German Computing Center (DRZ), 268
German Science Foundation (DFG), 261, 263
Germany, 257
Gesellschaft Deutscher Chemiker (GDCh), 283
Gibbs free energy of activation, 215
Giessen, University of, 261, 270
Glaucoma, 72
GlaxoSmithKline, 28
GOLD
, 54
Golden Rule approximation, 149
Golden Rule perturbation expansion, 165, 197
Google search engine, viii
Gordon Conference on Computational Chemistry, xi
Göttingen computers, 262, 265
Göttingen, University of, 257, 260, 263, 265, 270
Graph-based clustering, 13
Graph-theoretic clustering method, 8, 22
Graph theory, 219
GREEN, 72
Greens function, 281
GRID
, 43, 50, 54

Haas, Arthur, 265
Hahn, Otto, 261
Hamiltonian, 117, 156, 160, 161, 206
Hammerhead
, 50
Hammett-Taft substituent constant, 216, 232
Hamming distance, 21
Hansch QSAR, 243
Hartmann, Hermann, 267, 270, 273, 275
Hartree-Fock model, 243
Health maintenance organizations (HMOs), 298
Heat of formation, 222, 226
Heisenberg, Werner, viii, 261, 262, 265, 270
Heitler, Walter, 257
Heitler-London method, 265
Hellmann, Hans G. A., 258, 265
Heterogeneous discharge, 165
Heterogeneous solvent environments, 134
Hierarchical agglomerative clustering, 6, 22
Hierarchical clustering, 3, 6, 25
Hierarchical divisive clustering, 9
High throughput screening (HTS), 2, 28, 29, 42, 75
Highest occupied molecular orbital (HOMO), 225
HINT
, 50
Hiring trends, 294
History of computational chemistry, 270
Hit rate, 42
HIV protease-inhibitor complexes, 57
Hoechst AG, 283
Hoffmann-LaRoche Ltd., 73, 74, 283
Hohlneicher, Georg, 273
Hollerith machines, 261
Hopping element, 149
Huang-Rhys factor, 195
Hückel, Erich, 258
Hückel calculations, 269
Human immunodeficiency virus (HIV-1) protease, 51, 64, 65
Hund, F., 270
Hybrid model, 202
Hybridization, 126
Hydrogen, 265
Hydrogen bonds, 43, 46, 54, 65, 72, 75, 125, 214, 216, 236, 243, 250
Hydrogen bond acidity, 222, 233
Hydrogen bond basicity, 222, 233
Hydrogen bond acceptor (HBA), 221, 225, 241
Hydrogen bond complementarity, 66
Hydrogen bond donor (HBD), 221, 225, 241
Hydrogen fluoride (HF), 266
Hydrophobic contacts, 56, 72
Hydrophobic environments, 121
Hydrophobic hydration, 125
Hydrophobic interactions, 54, 55, 65, 66
Hyperpolarizability, 130
Hypospherical clusters, 19

IBM computers, 268, 271, 276, 277, 278, 280, 281
Ice, 124
ICM
, 72
Identification of novel leads, 72
IGOR
, 279
Implicit solvation models, 214
Inappropriate assignments, 20
Independent electron pair approach (IEPA), 275
Indiana University, 269
Indiana University-Purdue University Indianapolis, xi
Indicator descriptors, 219
Individual gauge for localized orbitals (IGLO), 282
Induced fit, 42, 64
Induced dipole-induced dipole interaction, 92
Induced dipoles, 92, 102, 225
Inducible dipole moments, 89, 91
Industrial jobs, 300
Industry, 284, 285
Informatics, 306, 308
Information retrieval, 14
Inhibitors, 69
Inhibitory concentrations, 63, 238
Inosine monophosphate dehydrogenase, 65
Instantaneous free energy, 157, 176
Intensity borrowing, 196
Intensity of optical transitions, 150
Interfaces, 121, 122, 125
Intermolecular electron transfer reactions, 184
International Journal of Quantum Chemistry
, 275
Interpersonal skills, 306
Interstellar molecules, 280
Ionic interactions, 54, 55
Ionic materials, 106
Ionic strength, 91
Ionization potential, 107, 225
Isothermal titration calorimetry, 45
Isotropic electrostatic polarizability, 102
Isotropic polarizabilities, 94
Isotropic shell model, 101
Isotropic solute polarizability, 201

Jarvis-Patrick clustering method, 10, 18, 22, 23, 31, 32
JMP
, 231
Job insecurity, 303
Job market, 293
Johnson and Johnson, 29

k-Means clustering method, 11, 13, 15, 17, 19, 22, 32
Karpov Institute, 265
Kekulé, Friedrich August, viii
Kelley plot, 26
Ki values, 62, 63, 73
Kinases, 65, 66
Klessinger, Martin, 269, 270, 273
Knowledge-based scoring functions, 56
Kockel, B., 270
Kohonen maps, 5, 13, 28, 32
Kohonen network, 13
Konig, Edgar, 273
Kuball, Hans Georg, 273
Kuhn, H., 270
Kutzelnigg, Werner, 270, 273, 274

L models, 174, 175
Labhart, H., 273
Lagrangian methods, 103
Lance-Williams matrix-update formula, 7
Lance-Williams recurrence formula, 15
Large chemical data sets, 31
Large systems, 134
Latin language, 275
Leader algorithm, 10, 17, 30
LeadQuest Chemical Compound Libraries
, 72, 87
Lefebre-Brion, Helene, 280
Lehmann, Joachim, 263
Leipzig, University of, 270
Lennard-Jones potentials, 90, 103, 119, 127
Lethal dose (LD50), 218, 232
LHASA
, 278
Library science, v
Liebig, Justus, viii
Ligand binding, 70
Ligand design, 217
Lilly, Eli, and Company, xi, 22, 32
Linear combinations of atomic orbitals (LCAO), 219
Linear free energy relationship methodology, 212
Linear free energy relationships (LFER), 211, 215
Linear response approximation, 153, 162
Linear response theory, 51
Linear solvation energy relationship (LSER), 212
Linkage clustering method, 8
Lipid bilayers, 121
Lipophilic cavities, 65
Lipophilic interactions, 48
Lipophilicity, 44, 232
Liptay, W., 274
LISP, 269
Local dipole moments, 236
Local minima, 19
Local solvent structure, 176
Localized orbitals, 279
Lock-and-key paradigm, 45
Log P, 55, 214, 232, 243, 249
London dispersion energy, 90
London, Fritz, 257
Long-range interactions, 90, 99, 113
Lorquet, Jean-Claude, 280
Löwdin, Per-Olov, 269, 270
Lowest unoccupied molecular orbital (LUMO), 225
LUDI
, 43, 50, 55, 74

MADCAP
, 236
Management, 297, 307
Management of databases, 300
Manhattan distance, 21
Manhattan segmental distance, 21
Many-body interactions, 115
Manz, Jörn, 273, 278, 281
MAP, 269
Mapping, 32
Marburg, University of, 264
Marcus equation, 182
Marcus-Hush (MH) theory, 150, 151, 153, 168, 172, 188, 202
MARK I, 260
Matrix inverson method, 97
Max Planck Institutes, 263, 265, 267, 270, 285
MaxMin, 21, 32
Maybridge library compound databases
, 31, 72
McCoy, Vincent, 280
McGowan volume, 233, 238
MDL Information Systems, Inc., 31, 35
Mechanical polarizability, 106
Mechanical polarization, 127, 128
Mecke, R., 270
Median salaries, 315, 316
Medoid-based clustering method, 15
Medoids, 19
Merck, 64, 283
Merging decisions, 16
Metal surface, 166
Metallo-beta-lactamase, 61
Metals, 167
N
-Methylacetamide (NMA), 125
N
-Methylformamide (NMF), 125
Meyer, W., 281
Minimum-diameter clustering method, 9, 16, 28
Minimum-variance clustering method, 8
Mixing parameters, 188, 199
Mixture model clustering, 5, 12
MM-PBSA method, 63
MM2 force field, 51
Model-based methods, 232
Modified neglect of differential overlap (MNDO), 220, 235, 236
Molar refraction (MR), 233
Molecular descriptors, vii, 213
Molecular design, 306
Molecular Design Ltd. (MDL), 308
Molecular dynamics (MD), 51, 89, 97, 134, 159, 214
Molecular dynamics-based docking algorithm, 62
Molecular electrostatic potential (MEP), 222, 226, 240
Molecular mechanics, 41, 309
Molecular modeling, 300, 306
Molecular orbital (MO) calculations, 220, 269
Molecular polarizabilities, 94
Molecular recognition, 60
Molecular simulations, 308
Molecular size, 59, 225
Molecular surface, 132
Molecular volume, 222
Molecular weight, 214, 219
Møller-Plesset second order (MP2), 275
Molten salts, 106
Monothetic clustering, 5
Monothetic division, 9
Monte Carlo methods, 51, 89, 94, 98, 99, 113, 214
MOPAC
, 215, 220, 236
Moving method, 19
Mulliken electronegativity, 107
Mulliken population analysis, 119, 222, 224
Mulliken, Robert S., 258, 270, 271, 280
Mulliken-Hush, 151, 195, 198
Multiple regression analysis, 54, 212, 213, 217, 227, 231
Multireference configuration interaction (MR-CI), 279
Multireference configuration self-consistent field (MR-SCF) orbitals, 279
München, Technical University of, 263, 276, 278, 280
Murrell mechanism, 196
Mutual neighborhood value (MNV), 18

Nanotubes, 282
Nasal pungency thresholds, 234
National Cancer Institute (NCI), 22, 30
Natural clusters, 24, 33
Natural orbitals, 279
Nearest-neighbor clustering, 10
Nearest-neighbor lists, 10
Nearest-neighbor nonhierarchical clustering, 18
Nearest-neighbor selection, 1, 5
Neglect of diatomic differential overlap (NNDO), 220
Neighborhood conditions, 10
Neighboring clusters, 5
Neural network, 13, 218
Neuraminidase, 62, 65, 66
Newton's equation of motion, 113
Nobel Prize, 258
Noise, 15, 20
Non-Condon effect, 162, 197
Nonadditive effects, 125
Nonadditivity, 89
Nonadiabatic electron transfer rate constant, 149
Noncombinatorial classification, 12
Nonequilibrium process, 157
Nonequilibrium solvent polarization, 191
Nonhierarchical clustering methods, 3, 9, 17
Nonlinear solvation effects, 154, 169, 180, 182, 190
Nonmodel-based methods, 245
Nonorthogonal descriptors, 229
Nonparabolic charge transfer surfaces, 169
Nonparabolic free energy surfaces of electron transfer, 190
Nonparametric clustering methods, 6
Nonpolarizable potential, 90
Nonpolarizable water, 121
Nonspherical charge distributions, 108
Normal coordinates, 152
Northwestern University, 276
Nuclear fluctuations, 161
Nuclear magnetic resonance (NMR), 48
Nuclear magnetic resonance chemical shifts, 282
Nuclear reaction coordinate, 163
Nuclear solvent polarization, 163
Nucleic acid interactions with ions, 126
Nucleic acids, 125

Occupation number, 188
Octanol/water partition coefficients, 55, 214, 232, 243, 249
Off-atom charge sites, 122, 132
One window free energy grid (OWFEG), 52, 63
One-photon transition probability, 193
Online update classification, 12
Oppenheimer, J. Robert, viii
Optical band shape, 191
Optical Franck-Condon factors, 192
OptiSim fast clustering system, 30
Oracle, 308
Orbital energies, 219, 225
Ordering points to identify the clustering structure (OPTICS), 21
Organic donor-acceptor complexes, 173
Organic dyes, 264
Organolithium compounds, 280
Organon, 28
Outliers, 11, 15, 230, 235, 237, 239
Ovality, 223, 249
Overlapping clusters, 3
Oxides, 106
Ozone, 275

p38 MAP kinase, 65, 66
Pair correlation functions, 122
Pair natural orbitals (PNO), 279
Parabola, 168
Parabolic law, 172
Parallel algorithms for hierarchical clustering, 22
Parallel chemistry, 42
Parameterization, 51, 91, 96, 250
Parametric clustering methods, 5
Pariser-Parr-Pople (PPP) MO treatments, 264, 279
Parke, Davis and Company, 29, 32
Partial charge transfer, 111
Partial charges, 108, 118
Partial negative surface area, 227
Partial positive surface area, 227
Particle-mesh methods, 99, 129
Partition coefficients, 55, 214, 232, 243, 249
Partition function, 56
Partitioning Around Medoids clustering method (PAM), 19
Patents, 312, 313
Path integral, 166
Pattern recognition, 283
Pauling, Linus, 258
pC50 values, 238
Penalty functions, 54
Penalty terms, 59
Peptide bond, 119
Peptidic ligands, 75
Periodic boundary conditions, 99
Perkin-Elmer computer, 282
PERM computers, 263, 263
Permanent charges, 92
Peyerimhoff, Sigrid D., 269, 271, 273, 279, 281
Pfizer Central Research, UK, 31
Pfizer Inc., 29
Pharmaceutical companies, 299, 302
Pharmaceutical research, vi
Pharmacophores, 14, 43, 72, 307
Pharmacy benefits management, 298
Phase coexistence properties, 123
Phase diagram, 124
Phonon dispersion curves, 100, 128
Photo-induced charge transfer, 192
Photoelectron spectra (PES), 281
Photoionization cross section, 280
Pi electron distribution, 264
Pi-bond cooperativity, 125
Piecewise linear potential (PLP), 50, 54, 65
Pierson product correlation coefficient, 229
pKa shifts, 61
pKa value, 211
Placement of charge sites, 121
Planck, Max, 258, 261, 297
Planck, Max, Institutes, 263, 265, 267, 270, 285
Platt perimeter model, 279
PM3 (Parametric Model 3), 220, 236, 246
PMF scoring function, 50, 57, 63, 65, 70
Point charges, 115
Point dipoles, 91, 99
Point-polarizable models, 131
Poisson-Boltzmann equation, 52, 63
Polansky, O. E., 273
Polar interactions, 75
Polarity descriptors, 226
Polarity indexes, 226
Polarizability, 89, 129, 133, 176, 178, 219, 225, 234, 238, 240
Polarizability index, 222
Polarizability parameters, 95
Polarizability tensor, 92
Polarizable chromophores, 192, 201
Polarizable donor-acceptor complexes, 175
Polarizable point dipoles (PPD), 91, 97, 103, 107
Polarizable simple point charge (PSPC), 123
Polarizable simulations, 121
Polarizable sites on bonds, 96
Polarizable water models, 134
Polarization, 126, 162
Polarization catastrophe, 94, 103
Polarization energy, 92, 117, 125
Polarization models, 127
Polarons, 157
Polymers, 111
Polythetic clustering, 5
Polythetic division, 9
Postdoctoral positions, 302
Potential energy surface, 219
Potential energy wells, 148
Potential of mean force, 56
PPD models, 132
Predictive ability, 230
Preuss, Heinzwerner, 265, 266, 270, 273, 274
Primitive descriptors, 231
Principal components analysis, 33
Probabilistic clustering, 5
Probability of chance correlation, 213
Probes, 30
Procept, Inc., 31
Proctor and Gamble Company, 29
Profitability, 298
Programmable computer, 262
Programming languages, 306
PROjected CLUSters (PROCLUS), 21
Property filters, 44
Protein binding site, 42
Protein Data Bank (PDB)
, 56, 62
Protein flexibility, 64
Protein folding, 56, 126
Protein structures, 41, 42
Protein-DNA recognition, 60
Protein-ligand complexes, 41, 63
Protein-ligand interactions, 45, 46
Protein-ligand interface, 45
Proteins, 121, 125
Protherics, 55, 68, 86
Protonation state, 61
Proximities, 16
Proximity matrix, 7
Proximity measures, 6
Proximity of clusters, 7
Proximity threshold, 9
Pullman, Bernard, 270

Q model, 170, 171, 172, 174, 175, 182, 183
Q-mode clustering, 33
Quadrupole moment, 121
Quantenchemie, 265
Quantitative structure-activity relationships (QSAR), 28, 32, 212, 232, 250, 284, 306, 308
Quantitative structure-property relationships (QSPR), v, vii, 212, 250
Quantum chemistry, 308
Quantum Chemistry Program Exchange (QCPE), 269
Quantum mechanical descriptors, 211, 219, 235, 248
Quantum mechanical perturbation theory, 193
Quantum mechanical simulations, 134
Quantum mechanics, viii, 211, 257
Quantum polarizable models, 116
Quantum theory, 265

R-mode clustering, 33
Radiative rates, 195, 196
Randic' connectivity index, 249
Random data, 14
Random selection, 20
Rank ordering sets of related ligands, 63
Rapamycin, 47
Rate constants, 149, 214
Reaction coordinate, 155, 186
Reaction activation barrier, 148
Reactive intermediates, 280
Receptor, v
Receptor-ligand binding, 48, 49
Receptor-ligand interface, 55, 60
Reciprocal nearest-neighbor algorithm (RNN), 8, 15, 22
Reclustering, 18
Reconstructive clustering methods, 5
Recursive partitioning, 1, 9, 28
Reduced effective representation (RER), 123
Reducibility property, 8
Refractive index, 193
Regression analysis, 54, 212, 213, 217, 227, 231
Reimers-Watts-Klein (RWK) model, 123
Relative neighborhood graph, 22
Relocation clustering method, 5, 11
Reorganization energy, 150, 152, 178
Research and development (R&D), 298, 299, 310
Resonance Raman spectroscopy, 192
Resonance structures, 119, 125
Reviews in Computational Chemistry
, xi
Reviews in Modern Physics
, 270
Rhone-Poulenc Rorer, 31
RObust Clustering using linKs (ROCK), 15
Roche, 73, 74, 283
Rohm and Haas, 30
Römelt, Joachim, 281
Roothaan, Clemens C. J., 270, 271
Rosmus, P., 281
Rotatable bonds, 48, 55
Ruch, Ernst, 273
Rules of thumb, 98, 213, 228, 229, 230
Rydberg states, 280

Salaries, 314
Salt bridges, 47, 55, 67
SANDOCK
, 72
Sandorfy, Camille, 280
Sandoz AG, 283
SAR-by-NMR technique, 70
SAS Institute Inc., 34
Scaling distance, 95
Schaefer, Henry Fritz, III, 282
Schirmer, J., 281
Schleyer, Paul von Ragué, 280
Schlier, Christoph, 280, 281
Schrödinger equation, 219, 262, 264
Schrödinger, Erwin, viii, 257
Schuster, P., 273
Schwab, Georg Maria, 270
Schwarz, Eugen, 280
Schweig, Armin, 273
Schwerpunktprogramm Theoretische Chemie, 271
Science, v
SCORE, 50
SCORE1, 50, 55, 74
SCORE2, 50
Scoring, 307
Scoring functions, 41, 49
Screening, 96, 133
ScreenScore, 50, 66
Searle, G. D., and Company, 31
Second spectral moments, 152, 174
Second virial coefficient, 122
SECS
, 278
Seeded library, 64
Seeding experiments, 67
Selection, 1
Self-consistent electron pairs (SCEP), 279
Self-diffusion constant, 123
Self-exchange, 189
Self-exchange transitions, 190
Self-organizing map, 13
Semiconductors, 107
Semiempirical Hamiltonians, 220
Semiempirical models, 116, 214
Sequential agglomerative hierarchical nonoverlapping clustering (SAHN), 6, 7
Shell charges, 100
Shell displacement, 104
Shell mass, 105
Shell models, 99, 101, 103, 112, 127, 132
Shielding function, 94
Short-range interactions, 100, 101, 103, 104, 106
SIEMENS AG, 261
Siemens computers, 277
Significance, 228
Similar property principle, 23
Similarity, 1, 2, 16
Simple point charge (SPC), 121
Single pass clustering method, 5, 9
Single-link clustering, 7, 22
Singletons, 4, 11
Size-dependent polarization, 131
Skills in demand, 303
Slater, John, 258
Slater-type functions, 265, 274
SMoG
, 50, 57
Sodium, 108, 265
Sodium chloride, 110, 111
Software, 133, 313
Software companies, 300, 302
Solid-state ionic materials, 99, 106
Solubility, 214, 218
Solute-solute interaction, 161
Solute-solvent interaction, 177, 190, 214, 232
Solvation, 46, 168
Solvation effects, 57, 76
Solvation power, 176
Solvation theories, 182
Solvatochromic parameter set, 233
Solvent, 151, 158, 161, 162, 183, 184, 188
Solvent band shape function, 198
Solvent bath, 225
Solvent-induced line shapes, 202
Solvent-induced Stokes shift, 178
Solvent polarization, 161
Solvent reorganization energy, 179, 191
Sommerfeld, Arnold, 258
Spartan
, 220
Spectral band shape, 151
Spectral moments, 151, 152, 175
Speeding up clustering calculations, 22
SPC/E water model, 124
Spectroscopic observables, 168, 177
Sprik-Klein water model, 112
Square-error, 6
Staemmler, Volker, 270
Standard error of the estimate, 213, 229, 232
Stark spectroscopy, 180
Static dielectric constant, 122, 180
Static field, 93, 99, 102
Steady-state optical band shape, 148
Steepest descent, 104
Stepped hierarchy partition, 27
Stepwise regression, 231
Steric complementarity, 66, 72
Steric effects of a substituent, 232
Steric fit, 45, 60
Stokes shift, 174, 179, 204
Stored-matrix algorithm, 7, 8
Straggly clusters, 15
Strain energy, 53
Streptatividin-biotin, 46
Stromelysin 1, 62
Structural descriptors, 23
Structural fragments, 14
Structure prediction, 61
Structure-activity relationship (SAR), 29
Structure-based ligand design, v, 41, 75, 307
Structure-property relationships, 211
Student's t test, 213, 229, 232, 247
Stuttgart, University of, 276
Supercooled liquid, 124
Supercritical carbon dioxide, 239, 242
Supercritical fluid, 124
Superdelocalizability, 226
Supervised learning, 1, 54
Surface area, 222, 223, 225
Surface properties, 45
Sydney, University of, 262
SYBYL
, 308
SYNCHEM
, 278
SYSTAT
, 231

Tanimoto coefficient, 10, 30
Taylor series expansion, 107, 109, 116
Team environment, 306
Telefunken Rechner (TR) computers, 277
Temperature of maximum density, 124
Test set, 230
Tetraphenylethylene, 176
Theoretica Chimica Acta
, 267, 275, 276
Theoretical chemistry, 267
Theoretical Chemistry Accounts: Theory, Computation, and Modeling
, 276
Theoretical chemistry groups, 269
Theoretical chemistry symposia, 273
Theoretical descriptors, 219, 247
Theoretical Linear Solvation Energy Relationship (TLSER), 235
Thermal bath, 156, 161
Thermolysin, 48
Thymidine kinase, 65
Three-dimensional fingerprints, 24
Three-dimensional QSAR, 217, 308
Thrombin, 65, 69
Thrombin inhibitors, 55
Thrombin-inhibitor complexes, 51
Tied proximities, 16
Time step, 105, 130
Time-dependent external field, 193
TIP4P-FQ model, 114
TIP4P water model, 121, 123, 124
TIP5P water model, 124
TLSER descriptors, 222
Toennies, Peter, 280
Tolerance, 229
Topographic clustering, 5, 13
Topographic electronic index, 226, 248
Topological descriptors, 219, 248
Toxic Substances Control Act (ToSCA) inventory
, 32
Toxicity, 214
Training data, 58
Training sets, 55, 230
Transactivation response element (TAR), 72
Transferability, 121, 123
Transferability of water potentials, 121
Transferable interaction potential, 4 points (TIP4P), 121, 123, 124
Transition dipoles, 175, 186, 193, 194, 195, 196, 197, 200, 205
Transition intensity, 152
Transition moment, 264
Transition probability, 193
Transition state energy, 215
Triethylamine, 216
Tripos Inc., 35, 87
Tunneling, 149
Turing, Alan, 261
Two-dimensional fingerprints, 23, 25
Two-dimensional fragment descriptors, 31
Two-state (TS) model, 160, 169, 196
Two-tailed probability, 228

Ulm, University of, 280
Umbrella sampling, 182
Unconventional interactions, 60
Underbarrier tunneling, 148, 158
Unfavorable interactions, 45, 59
Unfavorable orientation, 59
United States Patent and Trademark Office, 313
UNITY
, 72
UNIVAC, 278
UNIX, 307
Unlikely docking solutions, 75
Unsupervised learning, 1, 13
Urea, viii

VALIDATE, 50, 55
van der Waals interactions, 127, 258
Vancomycin, 48
Vapor pressure, 218, 240, 246
Variable charges, 112
Variable grid clustering method, 21
Variable-length nearest-neighbor lists, 18
Variance, 213
Variance inflation factor (VIF), 213, 229, 232, 239
VAX computer, 282
Veillard, Alain, 280
Vertex Pharmaceuticals, 65, 70
Vibrational excitation, 199
Vibrational reorganization energy, 152, 194
Vibronic band shapes, 173
Vibronic coupling, 281
Vibronic envelope, 194
Virtual libraries, 42, 44
Virtual screening, 43, 52, 62, 72
VisualiSAR
, 29
Volume descriptor, 225
von Laue, Max, 261
von Niessen, W., 281
von Weitzsäcker, Carl Friedrich, 261

Wagniere, G., 273
Walther, Alwin, 261, 268
Ward clustering method, 8, 15, 22, 23, 25, 28
Water, 43, 47, 48, 61, 91, 112, 114, 120, 121, 124, 131
Water dimer, 122
Water structure, 61
Wave function, viii, 117, 170, 186
Weak inhibitors, 69
Weller, A., 274
Werner, H.-J., 281
Willers, Friedrich, 261, 263
Wirtz, K., 265
Within-cluster variance, 6
Wöhler, Friedrich, viii
World Drug Index (WDI)
, 65, 67, 86

X-ray crystallography, 308

Zeil, W., 274
Zeitschrift für Naturforschung
, 266
Zeolites, 106
ZUSE computers, 260, 261, 262, 266, 271
Zwitterionic state, 126

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