A Abasic Sites, 1902 Ab Initio Methods, 650, 1600 Ab Initio Molecular Dynamics (AIMD), 343–344, 1902, 1923 Simulation, 365–3

Index

A Ag clusters, 1366 Abasic sites, 1902 Agglomerative hierarchical clustering, Ab initio methods, 650, 1600 2102, 2103 Ab initio molecular dynamics (AIMD), Al clusters, 1366 343–344, 1902, 1923 Algebraic approximation, 5 simulation, 365–368 AMBER, 51 Absorption, distribution, metabolism, aminobutyric acid, 2053 excretion (ADME) prediction models, Aminopyrimidine, 1712–1715 2266–2268, 2275 AMOEBA, 45 absoption, 2278–2279 Anaerobic glycolysis, 1559 distribution, 2279–2282 Androgen receptor (AR) antagonists, 2246 excretion, 2287–2288 Angle bending interactions, 361 metabolism, 2282–2287 Anharmonic approximation, 197–198 for oral administration of drugs, 2267 Anionic systems, electronic states of, physicochemical property, 686–689 2268–2274 ANO-RCC, 919 Absorption spectra Anthocyanidins, 2057 coumarin in solution, 1981–1983 Antimicrobial compounds one-photon, 778 benzamides, 2347 two-photon, 778 cinnamic acid, 2347–2348 Acetylcholine, 2053 coumarins, 2346 Acetylcholinesterase, 2053 flavanones, 2348 Active orbitals, 165 furan derivatives, 2349–2350 Additivity, 24 phenolic compounds, 2348–2349 ADFT-GIAO methodology, 820–828 Antisymmetrizer, 111 Adiabatic approximation, 182–188, Apocarotenoid oxygenase (ACO), 1581 202–208 Applicability domain (AD), 2068, 2234 Adiabatic electron affinity (AEA), 688, binary, 2317 1756, 1899 definitions, 2316 Adiabatic local density approximation leverage-based, 2316 (ALDA), 782 Approximation, 22 Adjacency matrix, 2071 Aquatic toxicity, 2329–2330 Adjustable parameter, 25 of personal care products, 2247 Adsorption, hydrogen, 1504 of pharmaceuticals, 2250–2251 Advanced concepts in electronic structure Aquatic toxicity index (ATI), 2249, 2251 (ACES II), 873–874 Armchair graphene ribbon model, 1486 Advanced concepts in electronic structure Artificial light-harvesting systems, 1934–1935 (ACES III), 874 Artificial neural networks (ANNs), 2312

Assumption, 22, 25 Benzamides, 2347 Asymptotic correction, 306 Benzorods, 1481 Atom(s), 78–79 Benzotriazoles, 2238, 2249 Atom-atom approach, 32 Berendsen barostat, 378–379 Atom-atom potential, 26, 32 Berendsen thermostat, 374–375, 413–414 functions, 32 Biasing potential replica exchange MD Atom-atom scheme, 33 (BP-REMD) simulations, 1689 Atom-atom term, 26 Bicycle pedal (BP), 1706 Atomic balance, 891 Bicyclic azoalkane Atomic charge, 26, 2043 ﬂuorescence quenching, 1965–1971 Atomic force microscope (AFM), 1649 photodenitrogenation, 1962–1965 Atomic mean ﬁeld (AMF), 918 Bimolecular systems photoinduced reactions approach, 917 in, 707 molecular dynamics simulations, 339 BiNChE plain enrichment analysis, 2174 Atom-pair (AP) descriptors, 2081, 2307 Biological macromolecules, 2184, 2196 Atoms in molecules (AIM), 783, 2045, Biological system applications, 1930–1935 2056–2057 Biomolecule, 33, 974–976 Atmospheric degradability index, 2240 Bio-ontologies, 2165 Au clusters, 1366, 1385–1391 Biopolymer(s), 30, 399 Aufbau/abbau method, 1366 structure, 22 Auger recombination, 1284–1291 Birefringences, 542–544 Autocorrelation descriptors, 2079–2082 Bismuth vanadate (BiVO4) Auxiliary basis, 307 electronic active centers of, 996–997 Auxiliary density functional theory (ADFT), electronic properties of, 1009–1011 796, 806–808 nanostructures, 1021–1023 Auxiliary density perturbation theory (ADPT), optical behaviour of, 997–998 798, 808–810 structural features of, 1006 Average electrostatic potential, 2056 structural properties of, 994–996 Axial birefringence, 543 Bloch function, 1000, 1427 Axialstrain, 1326 Blood brain barrier (BBB), 2280–2282 B3LYP method, 1778, 1856 Bohr’s formula, 887 B Bond angle bending, 25, 37 Back-donation effect, 1053 Bond critical point, 2057 Band topologies, 944–946 Bonded interactions, 361 Bare cations, 1829–1834 Bond length, 25 Barostats, 378–380 Bond length alteration (BLA), 1704, 1977 Barysz–Sadlej–Snijdars (BSS) approach, 914 Bond-order parameter, 1379 Base pairing, 1808 Bond stretching, 30, 37 Basin hopping algorithm, 1462 Born–Oppenheimer (BO) approximation, 24, Basin hopping method, 1367 134, 188–190, 208–213, 215–216, Basis set cage effects, 687 340–343, 642, 647, 1000, 1362, 1632, Basis Set Superposition Error (BSSE), 1919–1922 302, 315, 608, 709, 718–720, 752, Born–Oppenheimer molecular dynamics 1144, 1811 (BOMD), 343, 380–382, 797 scheme, 1831 Born–Oppenheimer treatment, 289 Basolo–Pearson autocatalytic mechanism, Born–von Kármán (BvK) zone, 1418, 1427 1843 Boron nitride, 1487 B-DNA structure, 1808 Bose–Einstein condensates (BECs), 296 Bead-spring coarse-grained model, 350 Boundary atoms, 349 Beeman’s algorithm, 412–413 Breathing mode relaxation, 1473 Benchmarking studies, 227 Breit operator, 893 Bending, 1326 Breit–Pauli Hamiltonian, 500 “Benign by design” strategy, 2233 Brillouin theorem, 157, 162 Index 2361

Bromofullerenes, 1073 Chemically induced dynamic nuclear 5-Bromouracil (5-BrU), 1784–1785 polarization (CIDNP), 1567 Buckingham potential, 26 Chemical markup language (CML), 2069 Buckminsterfullerene, 1179 Chemical ontology, 2168–2169 Burden matrix, 2075 enrichment analysis, 2172–2173 semantic similarity, 2170–2172 Chemical potential, 2050 C Chemical-probe experiments, 1371 CAM-B3LYP, 789 Chemical reactions, 622 Cambridge Serial Total Energy Package Chemicals of emerging concern (CEC), (CASTEP), 1006 2233 CAMCASP, 327, 783 Chemical space (CS), 2004–2006 Canonical spin orbitals, 654 Chemical text mining, 2170 Carbo index, 2055 Cheminformatics, 2042, 2173–2175 Carbon nanotubes applications, 1240, 1242 Chemistry Development Kit (CDK), 2203 computational approaches, 1202 Chemoinformatics, 2140 discovery, 1195–1200 chemical compound structure, 2007 mechanical properties, 1204 chemical reactions, model structures, 1196 2028 structural forms, 1195 chemical space, 2004–2006 tube diameter and chiral angle, 1197 databases, 2015, 2016 Carbonyl out-of-plane deformation, 1711 deductive learning, 2000 Cardiotonic drugs, 2053 description, 1998 Car–Parrinello MD, 343–344, 382–384, drug design, 2030–2034 1922–1923 Enalos KNIME nodes and Enalos Cloud CASPT2, 1949, 1954 platform, 2205 CASPT2//CASSCF protocol, 1949 fragment-based descriptors, 2028 CASSCF energy profile, 1961 history, 1999–2000 CASSCF level, 1704, 1949, 1960 inductive learning, 2000 CASSCF/AMBER trajectory study, 1985 IUPAC, 2002 Category QSAR, 2314–2315 molecular descriptor, 2021 Cation- interactions, 2046 molecular physicochemical properties, Cauchy moments, 527 2029 Cavitation energy, 762 organic synthesis, 2035 Cavity field factor, 749, 772, 776 physicochemistry-based descriptors, 2028 Cavity size, 762 property prediction, 2018 CCSD. See Coupled-cluster singles-and- software tools for, 2203 doubles (CCSD) structure elucidation, 2034–2035 Cellular uptake prediction, 2211–2214 Chirality molecular topological descriptors Channelrhodopsins (ChRs), 1932–1933 (CMTDs), 2307 Characteristic temperature, 1389 Chromophore, 1881 Charge asymmetry, 213–214 molecular environment, 1971–1974 Charge penetration effect, 762 Cinnamic acid, 2347–2348 Charge transfer, 1965–1971 Circular birefringence, 543 CHARMM, 46 Circular dichroism, 547–550 Chebyshev metric, 2100 Cisplatin, 1860 ChemAxon software, 2306 City block distance, 2100 Chemical entities of biological interest Clamped nuclei approximation, 70 (ChEBI), 2204 Clamped nuclei electronic Hamiltonian ontology, 2168–2170, 2173, 2176, 2177 symmetries, 90–92 Chemical graph, 2008, 2022–2023 Clamped nuclei Hamiltonian, 86–89 Chemical identifier resolver (CIR), 2204 approximate eigenfunctions, 113–119 Chemical information (CHEMINF) ontology, Classical force fields, 355–356 2174, 2175 Classical fullerene, 1185 2362 Index

Classical molecular dynamics (classical MD), Comparative field analysis, 2057 344–347, 1918 Comparative molecular field analysis simulation, 368–370 (CoMFA), 2053 Classical polarizable electrostatical models, descriptors, 2307 359–361 Complete active space (CAS), 1717 Classical valence bond theory, 653 Complete-active-space self-consistent-field Classification and regression tree (CART), (CASSCF) 2238 method, 1949 Classification QSAR model, 2314 approximation, 165 Cleri–Rosato potential, 1365 Complete basis set (CBS) extrapolation Cliffs, 2309 methods, 1811 Cluster geometry, 1340 Complete linkage method, 2102 Cluster growth, 1383 Computational chemistry, 3–17 Cluster (hyper) polarizabilities, 1117 Computational microscope, 1643 Clustering Computational toxicity model, 2325 definition, 2098 Computations hierarchical, 2102–2113 interpretation, 1817–1820 similarity and distance, 2099–2102 level of, 1811–1812 clusters, 1098 quantum chemical techniques, 1806 definition, 1461 Computer-assisted structure elucidation Fe, 1473 (CASE), 2034–2035 germanium, 1468 Computer-assisted synthesis design (CASD), ion mobility, 1466 2035 Ir, 1472 Conductor-like screening model for real mass spectroscopy, 1462 solvents (COSMO-RS), 760, 2270 Mn, 1470 Configuration interaction (CI), 662, 2058 Mo, 1475 Configuration interaction-singles (CIS), 662 Ni, 1475 Configuration-state functions (CSFs), 572 Pb, 1465, 1468 Conformation, 30 Pd, 1473 Confusion Matrix, 2209 potential energy surface, 1461 Conical intersection (CIs), 701–706, 1945 Pt, 1472 charge transfer, 1965–1971 Ta, 1471 photofragmentation, 1962–1965 Cluster property point, 1947 spin configurations, 1348 Conjugate Gradient method, 371–372 fundamental importance, 1340 Connection table (CT), 2011 Landau–Ginsburg–Devonshire theory, 1341 Connectivity matrix, 2075 magnetic features, computation, 1348 Constitutional descriptors, 2070–2071, 2307 magnetic storage devices, 1340 Continuous QSAR, 2313 melting temperatures, 1354 Continuum model, 399–402, 729–732, quantum mechanical procedure, 1349 750, 768 tight-binding molecular dynamics Converse piezoelectric effect, 1450–1454 methodology, 1342 Coproporphyrinogen III oxidase (CPO), CMPSim, 2172 1560 Coarse-grained molecular dynamics, 350–354 Core-excited shape resonances, 1750 simulations, 339, 1478 Core orbitals, 165 Co clusters, 1469 Core/shell particles, 1398 Collaborative drug design (CDD), 2017 Correlation-consistent basis sets, 630–631 Collinear magnetic approximation Correlation time, 1606 atomic MMs directions, 1344 Corrosion inhibitors organic materials as, SO interaction, 1345 2214–2221 TB matrix elements, 1345 Cost-sensitive learning, 2315 ZT-TBMD method, 1347 Cotton–Mouton effect (CME), 551–556 COLUMBUS, 875 Coulomb Hamiltonian, 70 Index 2363

Coumarin(s), 2346 Dendrogram Coumarin in solution, absorption spectra, plot, 2104 1981–1983 types, 2104 Counterpoise correction (CP), 608–609 de novo design, 2223–2225 Coupled cluster (CC), 559 k-means method, 2113 method, 165 medoids, 2116 theory, 1523–1531 modes, 2116 Coupled-cluster singles-and-doubles (CCSD), partitioning algorithm, 2113–2116 626 Density-functional based tight-binding method method, 302, 323, 1812 (DFTB), 1384 model, 2058 Density functional models, 270 Coupled-cluster techniques for computational Density functional theory (DFT), 23, 226, 271, chemistry (CFOUR), 874–875 303, 602, 796, 799, 986, 1001–1005, Coupled Kohn–Sham (CKS), 305, 306 1298, 1922, 1951, 2058 Coupled perturbed Kohn–Sham (CPKS) applicability, 227 methodology, 798 catastrophe, 1455 CPMD program, 1936 complementary, 226 Crossover operation, 1463 computational performance, 241–243 Cross term, 25, 26 development, 227 Cryogenic EPR/ENDOR technique, 1568 orbitals, 258–260 Crystal, 28 electron pairs, 232–235 structure, 32 holes, 232–235 structure prediction, 325–326 methods, 1813, 1905 Cu-Ag clusters, 1377 model proteins molecular mechanics, 1596 Cu clusters, 1366, 1375 performance, 227 Cumulative atomic multipole moments protein interactions ligand binding, 1611 (CAMM), 770 philosophy, 227 Cyclomatic number, 2070 protein hydration, 1609–1610 Cyclopurine lesion, 1908 theoretical chemistry, 228–232 CYP enzymes, 2283 and weight derivatives, 487–491 Cytosine dimer, 707 Density functional zoo, 238 Cytochrome oxidases, 1566–1569 Density matrix, 1423 Cytosine, 1720 Density-ﬁtting (DF), 307 Cytosine-guanine DNA base pair, deactivation Density-functional methods, 1384 mechanism, 1980–1981 Deoxyheme, 1575 2-Deoxyribonolactone, 1909 Deposition, 1381 D Deprotonation, 1710 DALTON, 778 Detour matrix, 2074 Dalton program, 868 DFT-D methods, 23 DALTON 2.0 program, 328 Diagonal Born–Oppenheimer correction, 78 Damped linear response function, 279 Diamagnetic magnetizability operator, 508 Damping functions, 314 Diamagnetic shielding operator, 508 Data sharing, 2017 Diamagnetic spin-orbit operator, 508 DBO, 1966 Diamond, 1176 3db-PSB11, 1959 Diatomic molecules, 189–190 4db-PSB11, 1960, 1962 homonuclear, 190 Deactivation mechanism, cytosine-guanine rotations and vibrations of, 191–196 DNA base pair, 1980–1981 2,3-Diazabicyclo[2.2.1]hept-2-ene (DBH), 555777 Defect, 1482 1962 Defect models, 1503 1,2-Dichloroethane, 471–487 Deformation energy, 297 Dichroism, 542–544 Dehalogenation, 1904 circular, 547–550 deMon program, 797 Dielectric constant, 776, 788 2364 Index

Differential shell approach (DSA), 756, 758 Drug half-life, 2287 5,6-Dihydropyrimidines, 1902 Drug metabolizing enzymes (DMEs), Dioxygen reactions, 1565–1566 2278, 2290 Dipole-dipole interactions, 35 Dyes sensitized solar cells (DSSC), 988 Dipole hyperpolarizability, 523–525 Dipole interaction model, 774 Applequist, 757, 774 E second hyperpolarizabilities, 774 ECEPP. See Empirical conformational energy Dipole moment, 516, 1420–1427, 2043, 2046 program for peptides (ECEPP) Dipole polarizability, 521–523 Ecotoxicity, 2247 Dirac–Coulomb–Breit (DCB) Hamiltonian, Edge adjacency matrix, 2075 893 Effective properties, 750, 762, 767, 771, 777 Dirac electrons, 1492 DRF, 775 Dirac equation, 890, 894 EFISH. See Electric field induced second free-particle Dirac Hamiltonian, 901 harmonic generation (EFISH) free-particle Foldy–Wouthuysen Ehrenfest mean-field dynamics, 1926–1927 transformation, 901 Eigenfunction, 127 Direct piezoelectric effect, 1450 Eigenvalue equation, 127, 133 Directed walks (DWs), 404 Elastic collision, 1748 Disconnected structures, 2088–2089 Elbow method, 2121 Discrete reaction field (DRF), 747, 765, Electric dipole polarizability frequency- 773–777, 782, 786, 789 dependent, 518–521 Disk diffusion studies, 2343 Electric field Dispersion interaction, 28 exciting, 745 Dispersion term, 23 local, 745, 747, 769, 777 Dispersion-corrected atom-centered potential permanent, 747, 772, 783 (DCACP), 605 total, 747 Dissociation, 1399 macroscopic, 744–750, 777 Dissociative electron attachment (DEA), 1748 effective, 775, 777 Distance metrics, 2101 optical, 772 Distributed dispersion coefficients, 320–322 Electric field gradient (EFG), 529–530 Distributed electric properties, 783 Electric-field-gradient-induced birefringence, Distributed hyperpolarizability, 782–783 553–555 Distributed multipole, 316, 782–783 Electric field induced second harmonic Distributed multipole ananlysis (DMA), generation (EFISH), 748, 773, 776, 783–784 787–789 Distributed polarizability, 317, 782 Electric field, Maxwell, 763 Distributing scheme, 751 Electric multipole moment, 515–521, 747 Divisive method, 2103 Electric polarizabilities definitions and theory, DNA, 33, 1804 1114–1128 Docking Electric properties, 515 molecular, 2134, 2147 Electromechanical measurements, 1325 nanostructured materials, 2151 Electron affinity (EA), 1899, 2043 protein-ligand, 2142 Electron delocalization interaction, 29 Double bonds in pentagons (DBIPs), 1068 Electron density difference map (EDDM), Double-strand breaks (DSBs), 1745, 1775, 937 1780, 1901 Electronic structure DFL affinities, 249 Douglas–Kroll–Hess (DKH) method, atomization energies, 250 911–917 energy barriers, 251–253 3D QSAR, 2134 heats formation, 250–251 advantages, 2135 Electron paramagnetic spectroscopy (EPR), developments in, 2141 989, 991, 992, 996 ligand-based, 2135 Electron repulsion integrals, 803 nanostructured materials, 2151–2156 Electron spin, 1561 Index 2365

Electron spin resonance (ESR), 571–581, relative energies, 1061, 1062 1762, 1774, 1784 violation of isolated pentagon rule, effective spin Hamiltonian, 574–576 1065–1066 electronic g-tensor, 576–577 Energy and multiple moments, 514–515 hyperfine coupling tensors, 579–581 Engineered NPs (ENPs), 2212 Electron transmission spectroscopy (ETS), Enthalpy, 2049 1746 Entropy, 1374, 2049 Electron-trap, 1903 Environmental behavior, 2236–2253 Electronegativity, 2052 Environmental effects adding, 679 Electronic circular dichroism (ECD), 547–549 Environmental half-lives, 2243 Electronic couplings computation, 720 Enzyme mechanisms, 1617–1621 Electronic excitations, 641 Equation-of-motion coupled-cluster theory, Electronic ground state, 271 1534–1538 Electronic Hamiltonian, 135, 1632 Estrogen receptor (ER) binders, 2246 Electronic motion, influence of, 200–202 Estrogen-like chemicals, 2245 Electronic Numerical Integrator And Computer Euclidean distance, 2099 (ENIAC), 1630 Exact enumeration technique, 407–408 Electronic stability, 1900 eXact-2-Component (X2C) method, 914–917 Electronic states of anionic systems, 686–689 Excess energy, 1379 Electronic structure calculations, 649 Exchange and correlation energy, 1001 basis sets, 660–661 Exchange correlation energy, 232 excited states, 662–669 Exchange-correlation functional (XCF), general overview, 649–653 931–932 methods, advantages, and drawbacks, Exchange-correlation kernel, 809 653–660 Excitation energy, 530, 677 Electronic structure DFL ionization potentials, Excited state(s) 249 molecular dynamics, 1983–1986 Electronic structure theory, 226 PCM-CC wave functions, 1535–1538 Electronic transitions, 1521 BSSE for, 718–720 Electrophilic superdelocalizability, 2049 properties, 778 Electrostatic effects, 1830 non-adiabatic dynamics, 1716 Electrostatic energy, 311–313 MD, 1919 Electrostatic interactions, 359 Exciton, 1396 Electrostatic potential (ESP) , 2045 in common semiconductor, 1269 fitting, 973 Frenkel, 1271 Electrostatic shielding, 757 nanostructures, 1266–1270 Elimination of small component (ESC), Wannier–Mott, 1272 894, 900 Exciton-polariton, 1260 Embedded atom models (EAM), 1364, 1465 photonic crystals, 1275–1276 Empirical conformational energy program for polarization and optical properties, peptides (ECEPP), 50 1270–1275 Empirical valence bond (EVB) method, Exothermicity, 1230 1974 Experimental descriptors, 2066 Enalos InSilicoNano Cloud platform, Explicit solvent model, 764 2206–2211 Extensive property, 1421 Enalos InSilico platform, 2206–2211, 2213 External forces geometry optimization, Enalos iron oxide platform, 2210 464–465 Enalos KNIME node, 2205 External magnetic field effects (MFE), 1579 Enalos QNAR iron oxide toxicity platform, External validation, 2234, 2318–2319 2211 Endocrine disruptors (EDs), 2245–2247 Endohedral metallofullerenes (EMFs) F metal-cage bonding, 1053 Faraday effect, 550–551 molecular structures, 1062, 1063 Far-bond functions, 309 2366 Index

Fe clusters, 1473 Frontier molecular orbitals, single-walled Fe(II)-Porphyrin-NH3-O2 model, 1572 carbon nanotubes, 1222 Feed-forward back-propagation neural Frontier orbital densities, 2045 networks, 2312 Frozen-density embedding (FDE), 747, 765, Fermi contact (FC) operator, 508 779–782 Feshbach resonances, 1750 Frozen localized orbitals, 349–350 Firefly, 866–867 Fukui functions, 2050 First dipole hyperpolarizability, 523–525 Fullerene(s), 842–847 First-order optical transitions, 1311 applications, 1239 First-order regular approximation canonical spiral, 1036 (FORA), 897 classification, 1185 First-principles plane wave calculations, 1501 13C NMR spectroscopy, 1048, 1184 Fitness parameter, 1463 computational approaches, 1202–1205 Flame Retardants, 2256 computational studies of isomers, Flash vacuum pyrolysis (FVP) technique, 1184 1210–1214 Flavanones, 2348 definition, 1034–1036 Flavin adenine dinucleotide (FAD), DFT calculation, 1043 1559–1561, 1570 discovery, 1180 Fluorescence, 940–942 Euler’s theorem, 1034 Fluorescent proteins (FPs), 1645, 1881–1885 giant, 1214–1215 Fock operator, 150 giant fullerene structures, 1186 Folding table (FT), 1707 hexagonal indices, 1041 Foldy–Wouthuysen transformation, 901, IPR isomers, 1042 902, 913 isolated pentagon rule, 1037, 1191 ForceBalance, 43 molecular structures, 1045 Force fields (FFs), 1363, 1635, 1639–1640 nano-capsules, 1189–1190 Allinger’s, 48–49 natural abundance, 1188–1189 AMBER, 52–55 orbital axis vector analysis, 1039, AMOEBA, 46 1040, 1215 calibration, 2186–2187 POAV pyramidalization angle, 1041, 1042 CHARMM, 56–58 pyramidalization angle, 1215–1218 data, 2059 relative energies, 1038, 1044, 1047 ECEPP-05, 50 Schlegel diagram, 1188, 1189 GROMOS, 56 semiempirical method, 1047 molecular dynamics simulations model, spiral algorithm, 1035 339 steric strain, 1040 MMFF94, 49 Stone–Wales defects, 1193, 1218 OPLS-AA (all atom), 56 structure, 1183 Scheraga’s, 50 synthesis, 1184 Formamide, 1722–1725 thermodynamic stability, 1043 Fragment-based descriptors, 2028 total isomers, 1037 Franck–Condon factors, 645 vacancy defects, 1194, 1219–1221 Franck–Condon point, 1945, 1951 X-ray crystallographic studies, 1050 Franck–Condon principle, 644 Fullerene derivatives Franck–Condon region, 1699 addition patterns, 1069 Freely jointed chain (FJC) model, 399 bond lengths, 1066 Free-particle Dirac Hamiltonian, 901 DFT calculations, 1070 Freeze-and-thaw cycles, 780 energy isomers, 1067 Frenkel exciton, 1271 Full quantum chemical studies, 732–733 Frequency-dependent density susceptibility Fully directed walks (FDWs), 404 (FDDS), 304, 307 Full width at half maximum (FWHM), 995 Frequency-dependent electric dipole Functionalized amino acids (FAAs), 2319 polarizability, 518–521 Funnel, 1946 Frequent subgraph mining approach, 2308 sculpting, 2189–2190 Index 2367

Furan derivatives, 2349–2350 chemisorption energy, 1209 Furocoumarins, 671 computational and experimental studies, Furthest neighbor method, 2102 1180 computational approaches, 1202–1205 defects in, 1180 G description, 1178 Gallium arsenide (GaAs) clusters, 1099, edges chemistry, 1312 1109–1112 hydrogenation, 1209 Gauge, 1419–1420 molecular dynamics simulations, 1208 Gauge invariance, 285–288 Stone–Wales defect, 1205 Gaussian chain model, 399 Graphene nanoribbons (GNRs), 1300, 1303, Gaussian-type functions (GTFs), 660 1311, 1486 GDIIS, 438–439 electronic and mechanical properties, GDMA, 783 1492–1500 Ge clusters, 1399, 1468 electronic properties, 1486 Gene Ontology (GO), 2165 model structure, 1487 General Atomic and Molecular Electronic molecular dynamics computer simulations, Structure System (GAMESS-US), 1487 864–866 structures, 1487 General Atomic and Molecular Electronic Graphene quantum dots, 1503 Structure System (GAMESS-UK), Graph invariants, 2071 867–868 Graphitic systems Generalized gradient approximation (GGA), edge effects, 1318–1323 236, 363, 602, 1298 quantum conﬁnement, 1315 Generalized solvation free energy density Graph-theoretical matrices, 2072 (G-SFED) model, 2271 Green chemistry, 2258 Generalized Tight-Binding Molecular Green ﬂuorescent proteins (GFP), 1601, Dynamics (GTBMD), 1342 1971–1974 Generalized valence bond method in the Green’s function approach, 662 perfect pairing approximation GRIND descriptor, 2308 (GVB-PP), 1717 GRINDOL, 771 Genetic algorithm (GA), 1385, 1463, 2233 GROMACS, 55 Geometrical descriptors, 2082–2085 GROMOS, 55–58 Geometrical distance matrix, 2082 Ground state structures Mn clusters, 1470 Geometries, 1814–1817 Ta clusters, 1471 Geometry optimization and symmetry, Ground-state (GS), 928–929 439–440 structure, 1099–1101 Geranylgeranyltransferase I inhibitors Gupta potential, 1365, 1465 (GGTIs), 2322–2323 Gut physiological model, 2289–2291 GETAWAY descriptors, 2084 Giant fullerenes, 1214–1215 Gibbs free energy, 2049 H Global descriptor, 2008 HAlO, 1391–1396 Global Half Life Index (GHLI), 2241 5-Halouracils, 1905 Global search algorithm(s), 1462 Halonucleobases, 1904 Global search algorithm of minima (GSAM), Hamiltonian 766, 767 matrix, 133 Glucosoxidase model, 1570 scalar potential in, 504–505 Goeppert–Mayer (GM), 1878 vector potential in, 506 Golden cages, 1388 Hamilton operator, 127, 133, 141, 162 Gold standard, 1812 Hard and soft acid-base (HSAB), 2051 Graphene, 1485–1505 Hard sphere, 24, 27 applications, 1238 Harmonic approximation, 194–196, 1373 band gap, 1207 Harmonic potential, 25 2368 Index

Hartree–Fock (HF) Hydrated magnesium cation, 1837 level, 863 Hydrogen adsorption, 1504 mean field approach, 1503 Hydrogen atom transfer, 1907 method, 147–152, 626, 653–660, 1072 Hydrogen bond(ing), 26, 300, 596, potential, 654 1836, 1865 theory, 600–602 acidity, 2052 Hazard of chemical, 2257 basicity, 2052 HD molecule, 213–214 and stacking interactions, nucleic acids, Heat capacity, 1374, 1389 1809–1814 Heat of formation of H2SO2, 634–636 Hydrophobicity, 2049 Hellmann–Feynman theorem, 11 Hyper-functionals, 237 Helmholtz free energy, 972 Hyper-Rayleigh scattering (HRS), 788 Helmholtz free enthalpy, 1374 Hypermagnetizabilities, 551–553 Hermitian operators, 127–129, 132, 159 Hypernetted chain approximation, 966 Hessian matrix and Hessian updates, Hyperpolarizability, 518, 1126–1128, 430–431 1449, 2045 Hexagonal indices, 1040, 1041 distributed, 782–783 Hierarchical cluster analysis (HCA), 2236 effective, 763 Hierarchical clustering DRF effective 789 advantages and disadvantages, 2103 effective, 750 definition, 2102 solute, 748, 750, 763 Hierarchical optimization, 2190–2193 Hypersurface deformation method, 1462 Higher fullerenes Hypothetical perfect computer, 7–10 addition to C70 and, 1078–1082 Hypoxic conditions, 1899 definition, 1032 Hückel’s method, 2057 Higher-order response functions, 281–283 Highest occupied molecular orbital (HOMO), 2045 I High-performance liquid chromatography Impact ionization and Auger recombination, (HPLC), 1780 1284–1291 High throughput screening (HTS), 2344 Implicit solvent model, 759–764, High throughput virtual screening, 2210 1834–1835 Histone deacetylase, 2051 In vitro assays, 2266 Hohenberg–Kohn theorem, 231, 800 In vivo assays, 2266 HOMO-LUMO gaps, 1317 Index of epitaxy, 1382 Homoisoflavanones, 2348 Indigo, 2204 Homology modelling, 1599–1600 Induced dipole moment, 2049 Homonuclear diatomic molecules, 190 Infinite-order two component (IOTC), 913, Homotops, 1376 918, 919 Horseradish peroxidase (HRP), 1566 Infrared (IR), 1444 HSAB principle, 1396 In silico models, 2266, 2267 Hubbard models, 1004 Insubria graph, 2256 Human intestinal absorption (HIA) assay, Integrase inhibitors, 2056 2278, 2279 Intensive property, 1421 Hund’s rule, 1562 Interaction, 26–27 Hybrid quantum mechanics/molecular dispersion, 752, 779 mechanics (QM/MM), 765, electrostatic, 752, 765, 768 1929–1930 energy exchange-dispersion, 752 molecular dynamics, 347–350 exchange, 752 simulations, 340 exchange-induction, 752 Hydrate lattice, 1162, 1167 induced properties, 751–753 Hydrated alkaline earth cations, 1836–1838 induction, 752 Hydrated copper cations, 1838–1840 long-range electrostatic, 766 Hydrated electrons, 1897 polarization, 765 Index 2369

properties distance dependence, 753–754 K many-body effects, 754–756 Kaiser criterion, 2121 short-range, 765 K-Cs clusters, 1366 short-range repulsion, 779 k-nearest neighbor methods, 2312 1-4 Interactions, 27 k-Nearest Neighbors (kNN) technique, Interaction energy, 598–599 2217 charge-transfer, 308–310 k.p method, 1263 components, 301 KcsA channel, 975 definition, 297 Kernel trick, 2311 density-fitting, 307 Kidney physiological model, 2294 DFT, 303 Kinetic stability, 1042 higher-order contributions, 308 Kiteplatin, 1860 many-body contributions, 314–316 Kohn–Sham approximation, 781 multipole expansion, 310–314 Kohn–Sham density functional theory, SAPT(DFT), 303, 304 799–801 two-body interaction energy, 297 Kohn–Sham matrix elements, 816 Interaction-site model, 968 Kohn–Sham variational principle, 2058 Intermediate neglect of differential overlap Konstanz Information Miner (KNIME), 2203 (INDO), 2057 design and prediction, 2221–2225 Intermolecular hydrogen transfer, 1965–1971 Koopman’s theorem, 2050, 2123 Intermolecular interactions, 32 Kovalenko–Hirata closure, 969 BSSE, 1144 Kronecker symbol, 130 classification, 1141 electron correlation, 1143–1144 extrapolation, 1145–1146 L orbital basis set, 1143–1144 Lagrangian dynamics, 1922 Intermolecular proton-transfer reaction, Landau–Zener transition probability, 1701 1849 Langevin dipole model (LD), 735 Internal energy, 1374 Langevin dipoles (QM/LD/MC), 765, 769 Intersystem-crossing (ISC), 642, 1946 Langevin thermostat, 377, 414 Intramolecular interaction, 31 Langevin–Born-type effect, 553 Intrinsic reaction coordinate (IRC), 648 LANL2DZ basis set, 1851 Intrinsically disorder protein (IDP), 1644 Laplacian matrix, 2073 Inverse coordination number, 1471 Lash’s model of CPO oxidation, 1571 Inverse Monte Carlo (IMC) algorithm, 353 Lattice models, 403–404 Inverse Stone–Wales (ISW) defect, 1180 Layered perovskites, 1453 Ion channels, 1647–1648 LCGTO Kohn–Sham method, 801–806 Ionization constant, 2271–2272 LDF approach to exact exchange (LDF-EXX), Ionization potential (IP), 1899, 2043 817 Ir clusters, 1472 Leaching of pesticides, 2236 Iron oxide nanoparticles, 2206 Lead structure, 2030 Isogyric reaction, 625 Leap-frog algorithm, 346, 411 Isolated chromophores, 1956–1971 Lennard–Jones, 26 Isolated pentagon rule (IPR) cluster, 1360 definition, 1037 potential, 779, 1464 endohedral metallofullerenes, 1065–1066 Lhasa Limited nodes, 2204 fullerenes, 1191 Ligand binding, 1610 Iterative Boltzmann inversion (IBI), 352 Ligand field (LF) excitations, 946 Ligand-centered (LC) transitions, 947 Ligand-to-ligand CT (LLCT), 947 J Ligand-to-metal CT (LMCT) excitations, 946 Jablonski diagram, 642, 643 Light-harvesting systems, 1934–1935 Jahn–Teller distortions, 1471 Line notation, 2009, 2010 Jellium model, 1383 Linear birefringence, 542 2370 Index

Linear Combination of Atomic Orbitals mechanism of, 1745–1747 (LCAO) approach, 651 shape resonances of, 1752–1756 Linear combination of Gaussian-type orbitals solvation, effect of, 1760–1766 (LCGTO), 801 5-substituted uracil, 1788–1789 Linear discriminant analysis, 2350 thermodynamic properties and physical Linear free energy relationship (LFER)-based observables, solvated electron, 1763 model, 2269, 2272 TNI formation, 1748 Linear interpolation in internal coordinates Lowest unoccupied molecular orbital (LUMO), (LIIC), 699 1754, 1760, 2045 Linear methods, QSAR, 2311 Lowest-energy isomers, 1469 Linear response function L-shaped GNR models, 1499 anomalous dispersion, 278 conjugation relations, 281 eigenvalue problem solving, 276 M electronic electric dipole, 275 M-DNA crosslink stabilization, 1853 Linkage Machine learning molecular dynamics, definition, 2101 1923–1924 types, 2102 Mackay transition, 1470 Lipinksi rule, 2268 Madin–Darby Canine Kidney (MDCK) cell Lipophilicity (logP), 2273 assay, 2278 Liver physiological model, 2292–2293 Magic number, 1369, 1383, 1462 Liver tissue, 2293 Magic sizes, 1480 Local densities, 235 Magnetic circular dichroism, 555–556 Local density approximation (LDA), 363, 602, Magnetic dipole operator, 507 1002, 1004 Magnetic moments, 1473 Local density-fitting (LDF), 817 Magnetic optical rotatory dispersion Local hardness, 2051 (MORD), 550 Local properties (LoProp), 784–786 Magnetic transition metal clusters, 1349 Local softness, 2050 Magnetic vector potential, 505–506 Local vertex invariants, 2076 Magnetizability, 535–539 Local-field tensor, 749 Magnetization, 1469, 1470 Localized dipole–interaction model (LIM), Manhattan distance, 2100 757 Many-body perturbation theory Long-range correction (LC) scheme, 1003 (MBPT), 659 Long-range dispersion interaction coefficients, MARCH-INSIDE method, 2351 528–529 Marcus and Pekar partitions, 1521 LoProp, 784–786 Markov model, 2351 Lorentz local field model, 773, 777 Martini model, 352 Lorentz-factor tensor, 748, 749, 772 Mass abundance experiment, 1384 Lossless dielectric constant QD dimer systems, Massively Parallel Quantum Chemistry 1282–1283 (MPQC) program, 875 Low-energy electron (LEE)-induced Materials Studio software, 1008 DNA damage Maximum electroshock (MES) test, 2320 basis set, 1760 Maximum likelihood optimization, 5-BrU and radiosensitization activity, 2193–2195 1784–1785 Mean quantization error, 2130 electron-molecule interaction events, Mechanistic model, 23 1747–1748 Metal-cage bonding, endohedral excited states, 1773 metallofullerenes back-donation gas-phase, electron attachment, effect, 1053 1756–1758 electrostatic potential, 1051 hydration of uracil-5-yl radical, formal and actual charge, 1055 1785–1787 ionic model, 1052 ionizing radiation, 1779–1780 kinetic energy density, 1054 Index 2371

Kohn–Sham MO levels, 1052 mapping function, 2345 QTAIM, 1053, 1055 organic synthesis, 2035 Metal coordination selection of, 2344–2345 with base pairs, 1847–1855 structure elucidation, 2034 ions in DNA quadruplexes, 1863–1865 Molecular design, 2030 metal cross-linked DNA structures, Molecular dynamics (MD), 1381, 1629, 2043, 1858–1863 2192, 2195 with platinum complexes, 1856–1858 CHARMM, 1638, 1640 Metal-to-ligand CT (MLCT) excitations, 946 developement of, 1641 Metalation enzymatic activity, mechanism of, exocyclic amino group, 1842 1646–1647 Pt-N7 energies, 1857 force fields, 1635, 1639 preferred sites, 1830 functionally important motions, 1645–1646 Watson–Crick base pairing energy, 1850 GROMACS code, 1639 Metallocarbohedrenes, 1406 history, 1630–1631 Metcars, 1405–1406 IDP, 1644 Micelle-free drugs, 2290 molecular diseases, 1649 Microelectromechanical systems (MEMS), NAMD code, 1639 1323 protein-DNA interactions, 1648–1649 Microsolvation, 766 protein-drug interactions and docking, Mid-bond functions, 309 1644–1645 Minimization, 440–443 protein folding studies, 1643 Minimum cumulative variance criterion, 2121 simulations, 338, 409, 410, 1647, 1918 Minimum energy conical intersections single molecule AFM experiments, 1650 (MECI), 1946 spectroscopy experiments, 1645 Minimum energy path (MEP), 648, 698, 1946, steps in, 1636 1958, 1960 structure optimization/energy Minimum inhibitory concentration (MIC) minimization, 1635 assays, 2343 transport phenomena in proteins, 1647 Mismatched DNA, 1909 Molecular dynamics (MD) simulations, nucleic Mixed quantum-classical approaches, acids, 1676 1700–1702 conformational transitions, 1686 MMFF94, 49 DNA bending, 1683 MM-like terms, 23 induced conformational changes, 1677 Mn clusters, 1470 REMD, 1679 Mo clusters, 1475 replica-exchange and umbrella sampling Model applicability domain, 2256 simulations, 1682 Model proteins RNA, kink-turn motif in, 1685 homology modelling, 1599 molecular dynamics simulation, 27 structure prediction, 1599–1600 Molecular electrostatic potential (MEP), 2043, Modern theory of polarization, 1419, 1433 2053–2056 Modified neglect intermediate neglect of Molecular fingerprints, 2086–2087 differential overlap (MINDO), 2057 Molecular graph, 2010, 2071–2072 Modified Newton–Raphson step, 435–438 Molecular Hamiltonian, 499–510 MOLCAS, 785 Molecular mechanics (MM), 2043, 2059 Molecular Breit–Pauli Hamiltonian, Allinger’s force fields and parameter, 500–504 48–49 Molecular clusters, 463–464 AMBER force fields, 52 Molecular crystal, 30–33 application, 27 Molecular descriptor(s), 2097 CHARMM force field, 56–58 antimicrobial activity, 2345 description, 22 chemical graph, 2008, 2021 formulae and parameters, 41–44 drug design, 2030–2034 intermolecular and non-bonded generation, 2344 interactions, 26 2372 Index

Molecular mechanics (MM) (cont.) Multiconfigurational methods, 651, 679–680 intramolecular contributions, 25–26 Multiconfigurational quantum chemistry, mathematical expressions, 24 1948–1954 MMFF94, 49 Multiconfigurational time-dependent Hartree molecular biology, 33–37 approach (MCTDH), 1715 molecular crystal, 31–33 Multiconfiguration (MC) SCF method, 164 nucleic acid, 37 Multiconfiguration self-consistent field organic molecules, 30 (MCSCF), 1700 Scheraga’s force field, 50 wave function, 651 water molecule, 44 Multidrug Resistance Protein 1 (MDR1), 2286 Molecular operating environment (MOE), Multilayer dielectric continuum model, 757 2306 Multiphoton process, 1283–1284 Molecular orbital configuration of dioxygen, Multiple damage site (MDS), 1743 1564 Multiple moments, energy and, 514–515 Molecular orbitals (MOs), 640 Multiple-carrier processes, 1283–1291 Molecular properties DFL Multiple-spawning, 1947 bond angles, 246–247 Multipolar components, 2046 bond energies, 253 Multipole(s) bond lengths, 244–246 atomic, 774 excited states, 257–258 distributed, 782–783 hydrogen bonding, 253–254 localized, 785 spin states, 256–257 Multipole expansion method (MPE), 760, vibrational frequencies, 247–249 763–764, 786 weak interactions, 254–256 Multipole moments, 778 Molecular Quantum Numbers (MQNs), 2214 Multireference configuration interaction Molecular recognition, 14–16, 34 (MRCI), 662, 1700 Molecular relativistic corrections, 215–217 Multireference coupled-cluster (MRCC) Molecular representation, 2068 methods, 663 Molecular response, 510–514 Multiscale methods, 1478 Molecular structure, 425–426 Multitasking QSAR models (mt-QSAR), curation, 2069–2070 2350–2351 Molecular surface, 13–14 Multivariate explorative methods, 2235–2236 Molecular vibrations, 465–471 Murrell–Mottram potential, 1365 Molecules, 79–86 Møller–Plesset (MP), 273 Møller–Plesset perturbation theory (MPPT), N 152–159, 600–601, 659 Na clusters, 1385 Möller–Plesset second-order perturbation Nanoalloys, 1377 (MP2), 2058 Nanobelts, 1489 MOLPRO 2008, 328 Nano-capsules, 1189–1190 Monomer-centered plus, 310 Nanoclusters, 1098, 2059 Monte Carlo sampling, 27 Nanoelectromechanical (NEMS), 1324 Monte Carlo simulation, 408–409, 2043, 2059 Nanomaterials, 2089, 2151 Motion of nuclei, 178–181 Nanoparticles (NPs), 1461–1464, 2206–2211 MP2 method, 1187 engineered, 2212 Multi criteria decision making (MCDM), 2248 properties, bioactivity and predictions, Multi-configuration self-consistent field 2207 (MCSCF), 863, 2058 via Enalos InSilicoNano platform, Multi-electron molecule, 175–178 2211–2214 Multi photon absorption theory, 1877–1878 Nanoribbons, 1476 Multi-reference model, 2058 electronic properties, 1486 Multi-walled carbon nanotubes graphene, 1476 applications, 1240 Nanoscale, rules of, 16 structure, 1196 Nanoscience, 1098 Index 2373

Nanostrips, 1489 Nonlinear methods, QSAR, 2311 Nanostructure(s), 2151–2156 Nonradiative T-S transitions, 1565 Nanostructure modeling Normalized elimination of small component empirical potential, 1464–1466 (NESC), 898, 914 Lennard–Jones potential, 1465 Normconserving pseudopotentials, 366–367 local optimization, 1466–1475 Nosé–Hoover thermostat, 375–377, one-dimensional, 1475 379–380, 414 zero-dimensional, 1461 np-apomorphine, 2056 Nanotubes, 1476 NP-hard problem, 1360 elastic properties, 1476–1479 Nuclear magnetic resonance (NMR) SiC, 1482 spectroscopy zigzag, 1495 data acquisition, 1593 Nanowires, 1476 effective spin Hamiltonian, 557–559 elastic properties, 1476–1479 indirect spin–spin coupling, 568–571 structural properties, 1479–1481 properties, 778 Natural atomic orbitals, 2045 refinement, 1595 Natural bond orbital, 2045 resonance frequency assignment, 1594 Natural (electronic) circular dichroism, restraint collection, 1594 547–550 sample preparation, 1593 Natural products, 2342 spin-spin coupling constants and Natural selection, 1463 shifts, 1833 Natural transition orbitals (NTO), 934 stability testing, 1593 Negative electron affinities, 690–693 structure calculation, 1595 Neighborhood function, 2126 structure validation, 1595 NEMS applications Nuclear magnetic shielding, 559 carbon nanotubes, 1324–1327 spin-orbit corrections to, 566–567 graphene nanoribbons, 1327–1329 Nuclear motion effects, 288–292 Newton equations, 1630 Nuclear quadrupole coupling constant, Newton–Raphson step, 428–430 529–530 Newton-X program, 1935–1936 Nuclear receptors (NRs), 2286 NH stretching, 1711 NuclearSpin-related properties, 556–571 Ni-Ag clusters, 1377 Nuclear spin-rotation constants (NSRC), Ni clusters, 1366, 1367, 1375, 1475 567–568, 825 Ni-Cu clusters, 1366 Nuclear vibrations NiTiO3 anharmonic approximation, 197–198 electronic properties of, 1012–1013 harmonic approximation, 194–196 nanostructures, 1017–1021 Nuclear wavefunctions, 72 structural features of, 1006 Nucleic acid, 22, 33 Non-adiabatic molecular dynamics, 1924–1930 hydrogen bonding and stacking Non-adiabatic transition probabilities, 1919 interactions, 1809–1814 Non-classical fullerene, 1185 Nucleic acid bases (NABs), 690, 1886–1887 Non-covalent interactions, 595 Nucleobase analogues, 1886 Non-local spin-density approximation (NLSD), Nucleoside analogues 1002 computational investigations of, 1887–1889 Non-relativistic quantum chemistry program NWChem, 870–871 commercial software, 876 free software, 864–876 Non-rigid bicycle pedal (NRBP), 1707 O Non-rigid rotor, 198–200 Octopus program, 1936 Non-symmetric Algebraic Riccati Equation One-bond flip (OBF), 1703, 1704 (nARE), 914, 916 One-dimensional structures, 1475 Nonbonded energy, 24 One-photon absorption (OPA), 530–533, 1876 Nonbonded interaction, 26, 356–361 ONIOM approach, 1203 Noncollinear spin formalism, 1475 ONIOM method, 1855 2374 Index

Online Chemical Modeling Environment p-benzosemiquinone radical anion, 686–689 (OCHEM), 2204 PBT Index, 2255 Onsager local field, 749 PCM cavity field factors, 763 Onsager–Lorentz cavity field factor, 763 PCM-CC equations, 1529–1531 Ontology, 2164–2165 PCM-CCSD analytical gradients, 1531–1534 chemical, 2168–2175 PCM-EOM-CCSD analytical gradients, content and metadata, 2167–2168 1538–1541 languages and logical expressivity, PE-CC2, 778 2165–2167 PE-CCSD, 778, 786 OpenBabel chemoinformatics package, 2204 PE-DFT, 777, 786 Optical absorption coefficient, 1503 PE-HF, 777 Optical rotation, 544 PE-MCSCF, 777 Optimisation algorithms, 370–373 PE-MP2, 777 Optimized Potentials for Liquid Simulations PE-SOPPA, 777 (OPLS), 55–58 Penetration, 311 Orbital model, 12–13 Penrose–Hameroff orchestrated objective ORCA, 871–872 reduction (OOR) model, 1581 Ordinary Least Squares (OLS), 2233 Penta-3,5-dieneiminium cation (PSB3), Organic compounds, 2156 1704–1706 Organic conjugated materials (OCMs), 1933 Pentagonal dodecahedron, 1162 Organic crystals, 324–325 Peptide, 28 Organic materials as corrosion inhibitors, 2214 Perfluoroalkylation of fullerenes, 1075 Organization for Economic Cooperation and PERI-CC2, 778 Development (OECD), 2208 Periodic boundary conditions, 765, 771, ORIENT, 327 1298–1300 Origin invariance, 285–288 Permutational symmetry, 92 Ornstein–Zernike equation, 966 Persistence bioaccumulation toxicity (PBT), Osmium complexes, 1847 2253–2257 Overplotting, 2124 Persistence in environment, 2239–2240 Oversampling, 2315 Persistent organic pollutants (POPs), 2239 Oxaliplatin, 1860 Persistent organic pollutants (POPs) data set 8-Oxoguanine, 1689 k-means method, 2114 Oxyclozanide, 2347 clustering, 2105, 2111 Oxygen revolution, 1559 PCA, 2121 Oxygen-dependent PUVA mechanism, 714 Perutz model, 1562 Oxyheme model, 1572 Pharmacokinetic (PBPK) models, 2288–2295 Phenathrene-based tylophorine derivatives P (PBTs), 2321 P-glycoprotein (P-gP), 2286 Phenolic compounds, 2348–2349 p-Hydroxybenzylideneimidazolinone Phosphorescence, 573–574, 949–951 (HBDI), 1971 Photoactive semiconducting oxides Pair density distribution function, 966 BiVO4, 993–994 Parallel Artificial Membrane Permeability cluster approach, nanocrystals and Assay (PAMPA), 2278 nanostructures, 1005–1006 Paramagnetic spin-orbit operator, 507 computational parameters, 1006–1008 Parameter, 25 crystalline structures, modeling of, Pariser–Parr–Pople (PPP) method, 1753 998–1001 Partially molten clusters, 1354 DFT methodology and functionals, Particle mesh Ewald (PME) methods, 1674 1001–1005 Partition coefficients, 2045 NiTiO3, 1006–1008 Partition function, 1374 TiO2, 987–993 Partitive approach, 2099 Photoactive yellow protein (PYP), 1930–1931 Pauli principle, 91 Photochemical funnel, 1946 Pb clusters, 1468 Photochemical reaction path, 1946 Index 2375

Photodenitrogenation bicyclic azoalkane, Polypeptide, 34 1962–1965 Pople–Nesbet equations, 656 Photodynamic therapy (PDT), 712 Pople-type basis sets, 628–629 Photoelectron spectroscopy (PES), 1187 6-12 Potential, 26 Photoelectronic excitation, 1699 Potential energy, 27, 30 Photoexcitation of proteins, 1721–1722 Potential energy curves (PECs), 708 Photofragmentation Potential energy hypersurfaces (PEHs), conical intersection, 1962–1965 641, 642 DBH, 1964 Potential energy surface (PES), 5, 27, Photoinduced reactions in bimolecular 1631–1633, 1748, 1769, 1921 systems, 707–718 of cluster, 1461 Photoisomerization retinal in different Prehydrated electrons, 1898 environments, 1983–1986 Principal component analysis (PCA), Photonic dispersion QD dimer systems, 1276 2222, 2235 Photophysical and photochemical process, 642 applications, 2118 Photostability, nucleic acid, 1699 correlation-covariance matrix, 2119 Physicochemistry-based descriptors, 2028 covariance, 2119 Physiologically based pharmacokinetic description, 2118 (PBPK) model, 2289 eigenvalues and explained variance, 2121 Piezoelectricity, 1450–1454 POPs, 2121 orbital axis vector (POAV) Prioritisation, 2231–2257 analysis, 1039, 1215–1218 Prolateness parameter, 1467 pyramidalization angle, 1041 Propagator tensor Plane wave basis set, 365–366 dipole-charge, 747 Plane wave-based GGA-DFT method, 1480 dipole-dipole, 747, 748, 772 Plasma protein binding (PPB), 2280 Protein, 22 PM3, 2058 folding, 33, 1643 PM6, 2058 hydration, 1609–1610 Point groups and transformations, 97–111 interactions protein-protein, Polarizability, 1125–1126, 1449 1613–1617 distributed, 774, 782–784 threading, 1600 interaction-induced, 756 Protein crystallography interacting atomic, 774 data collection, 1591 intrinsic, 758 model building, 1592 localized, 778, 785 reﬁnement, 1592 many-body corrected (MBP), 757 sample preparation, 1591 solute intrinsic, 757 structure determination, 1591 net, 757 validation, 1592 transferable atomic, 775 Protein dynamics Polarizability per molecule (PPM), 756 dynamical structures, 1608 Polarizable continuum model (PCM), 679, and molecular dynamics, 1629 760, 761, 786, 932, 1518, 1522–1531, protein-ligand interactions, 1608 1534–1538, 1887, 1905, 1982, 2270 time-scales, 1605 Polarizable embedding (PE), 747, 765, Protein structure(s) 777–779, 786 electrostatics, 1602–1604 Polarization, 29 molecular graphics, 1600–1601 catastrophe, 775 prediction, 2185, 2187–2189 electric, 744, 746, 747 solvent-accessible Surface, 1604–1605 electronic, 770 Proton transfer, 1847 energy, 299 Protonated formamide, 1725 expansion, 298 Protonated Schiff base (PSB) models, orientational, 770 1703 Polyﬂuorinated chemicals (PFCs), 2252 Protonated Schiff base of 11-cis-retinal Polymer and critical phenomena, 404–405 (PSB11), 1947, 1956 2376 Index

Protonation, 1710 Quantitative structure-activity relationship vs. cation coordination, 1830 (QSAR), 2018, 2033, 2042, 2066, energy, 2049 2233–2234, 2267, 2268 Gibbs energy correction, 1855 antimicrobial compounds, 2346–2349 vs. metalation, 1840 description, 2134, 2343 preferred sites, 1830 high throughput screening (HTS), 2344 PSB4 model, 1703, 1705–1708 stages, 2344 Pseudopotentials, 366–368 3D, 2134 PSI3, 872–873 uses, 2134 Psilocybin, 2171 Quantitative structure-activity relationship Psoralen, 671–676 (QSAR) modeling Psoralen CO2, 712–718 anticancer agents, 2321–2322 Pt clusters, 1472 anticonvulsant compunds, 2320 PTDE coupled schemes, 1526–1528 applicability domain, 2315–2317 PTE coupled schemes, 1526–1528 aquatic toxicity, 2329–2330 PTED, 1520 category models, 2314–2315 PUVA mechanism, 714 chemical toxicity and safety, 2323–2324 Pyramidalization angle fullerenes, classiﬁcation, 2314 1215–1218 combinatorial, 2311 single-walled carbon nanotubes, consensus model, 2331 1223 continuous, 2313 Pyrazoline–dichloromethane model data preparation, 2305 pair, 1968 description, 2304 Pyrimidine rings, 1712 external validation, 2318–2319 Pyrrole, 1715–1719 geranylgeranyltransferase I inhibitors, 2322–2323 in vitro and in vivo relationships, Q 2325–2327 QCFF/PI level of theory, 1037, 1038 methods, 2310–2313 QD dimer systems research strategies, 2332–2333 lossless dielectric constant, 1282–1283 steps in, 2305 photonic dispersion, 1276 statistical characteristics, model QM technique performance, 2330 ab initio, 1810 workﬂow, 2310 calculations, 1810 Quantitative structure in vitro-in vivo Quantum mechanical/molecular mechanical relationship (QSIIR) modeling (QM/MM) description, 2327 models, 733–734, 1955 rodent acute toxicity, 2327–2329 method, 973 rodent carcinogenicity, 2327 methodology, 1954–1956 Quantum chemical methods, 1944 technique, 2058 Quantum chemical response theory, 270 QSAR. See Quantitative structure-activity Quantum chemical standard state, 623 relationship (QSAR) Quantum chemistry, 4 QSARINS, 2233 Quantum cluster theory and solvation, QSARINS-Chem, 2243 1518–1552 Quadratic response, 1877, 1879, 1880 Quantum electrodynamics (QED) effects, 211 function, 281–283 Quantum mechanical (QM) approach, 1954 Quadrupolar solvents 1,4-dioxane, 788 Quantum mechanics, 43, 44, 48 Quadrupole moment, 516–518, 2049 Quantum Monte Carlo, 600 Qualitative analysis of adiabatic Quantum theory of atoms in molecules approximations, 184–188 (QTAIM) Quantitative nanostructure-activity atomic charges, 1055 relationships (QNARs), 2206, electron density distribution, 1053 2208, 2211 Quantum topology, 2056 Index 2377

Quartet-doublet (D) transition, 1568 Retinylidene, 1703 Quasi-relativistic-energy-averaged Stuttgart Retinal proteins, spectral tuning, pseudopotentials, 1836 1974–1979 Retinal protonated Schiff base (RPSB), 1702 R Rhodopsin, 1931–1932 Radial breathing mode (RBM), 1199 Rhodopsin chromophore model, Radial distance, 1370, 1381 photoisomerization, 1956–1962 Radiosensitizers, 1896 Rigid body docking, 1611 Radiotherapy, 1896 Rigorous local field method (RLF), 746, 765, Ramachandran map, 27 771, 786, 789 Ramachandran plot, 34 Ring-opening, 1711 Raman, 1444 Ring-puckering, 1711 Raman active modes, 995 Ritz method, 133 Raman spectra, 1854 RNA, 1804 Random forest methods, 2312 Rodent toxicity, 2252 Ranking indexes, 2234–2236 Rotational g Tensor, 539–541 Rational function, 1446 Rule of thumb, 2108 Rb-Cs clusters, 1366 Ruthenium complexes, 1843 RDKit, 2204 Reaction dynamics (RD), 706 Reaction field, 757, 772, 782 S factor, 749 SAPT2008 program, 327 Reaction vectors approach, 2223–2225 Sawtooth-like nanoribbon, 1487 Reciprocal-lattice vectors, 1492 Sawtooth potential, 1418 Reciprocal matrices, 2074 Scalar potential, 1420 Reciprocal space, 1263 in Hamiltonian, 504 Recursive partitioning (RP) methods, 2312 Scaled quantum mechanical force fields, Reference interaction site model (RISM), 478–479 734–735, 969 Schiff base cross-link product, 1909 Refractive index, 776, 788 Schlegel diagram, C70, 1079 Regression analysis, 1073 Schrödinger equation, 127, 134, 142, 643, Rehybridization, 1039 1263, 1631, 1632 Replica-exchange molecular dynamics Screening, 2232 (REMD), 1679 Second dipole hyperpolarizability, 525–527 Repulsive intrinsic stacking energy Second-order induction, 313 terms, 1818 Segmented all-electron relativistically Rescale thermostats, 374 contracted (SARC) Gaussian basis Resonance, 1416 set, 919 RESP. See Restrained electrostatic potential Self-consistent field (SCF), 151, 164 (RESP) Self-consistent reaction field (SCRF), 760, Response functions theory for molecular 2270 solutes, 1541–1550 Self-organizing maps (SOMs) Response theory, 510–515 description, 2124 electric multipole moments, 272 quality assessment, 2129–2130 electronic excited states, 275 structure determination, 2124–2127 magnetic multipole moments, 272 training, 2127–2128 matrix elements, 274 visualization, 2128–2129 software packages, 274 Self-purification of nanomaterials, 1484 standard ground state calculation, 273 Semantic web, 2173–2175 Restrained electrostatic potential (RESP), 51 II-VI Semiconductors, 1396 Restricted open-shell Kohn–Sham (ROKS), III-V Semiconductors, 1396 1923 Semi-empirical PM6-DH2 method, 1860 method, 1703 Semiconducting SWNTs, 1309 2378 Index

Semiconductor clusters Solute properties, 747, 749, 762, 767, 771, (hyper) polarizabilities, 1123–1125 772, 775 III-V and II-VI, 1108–1112 Solute-solvent interactions, 1519 II-VI, 1112–1114 Solvation, 53 structural properties, 1099–1114 effects, 1835 Semiempirical PM3 method, 1833 free energy, 760, 2268 Semiempirical terms, 23 Solvation energy Serial replica exchange molecular dynamics electric properties dispersion term, 762 (SREMD), 1681 electrostatic term, 762 Shape analysis, 1369 Pauli repulsion term, 762 Shape resonances, 1749, 1752 Solvent accessible surface area (SASA), 1605 Si36, 1105–1108 model, 2269 Si6, 1105–1108 Solvent-phase pairing energies, 1860 Si clusters, 1399 Sphere exclusion protocol, 2309 Si-Ge clusters, 1399 Spherical cavity approximation, 750, 764 Si-Ge interface, 1483 Spin and point group symmetry, 111–112 Silhouette index, 2111 Spin-dipole (SD) operator, 509 Silicon clusters, 1103–1108 Spin inversion, 1562 Silver-mediated cytosine, 1853 Spin neuroscience, 1581–1582 Similarity function, 1371, 1403 Spin-orbit coupling (SOC), 929, 1504 Similarity metrics, 2099 constant, 572–573 Simplification, 36 definition, 1564 Simulated annealing method, 1463 in O2 heme interaction, 1574–1578 Single-configuration methods, 650–651 T!S transition, 1571 Single linkage method, 2102 on UV/Vis properties, 948–949 Single-members clusters, 2103 weak, 1565 Single-particle model, 1434 Spin-orbit interaction, 1345 Single point energy calculations, 1834 Spin-polarized DFT method, 1475 Single-strand breaks (SSBs), 1745, 1746, Spin-polarized first-principles, 1500 1767, 1769, 1777, 1901 Spin variables, 125, 126 Single-walled carbon nanotubes, 1300–1302, Spin-valence concept, 1561 1308–1311 Spin-Zeeman operator, 508 armchair, zig-zag and chiral, 1197 Splitting scheme, 751, 756–759 computational studies, 1221–1225 Spurious solutions in anions, 689–690 covalent functionalization, 1225–1231 Stability function, 1368, 1377, 1390 defect formation, 1200 Stabilization energies DFT methods, 1203 adenine and guanine, 1841 electron diffraction, 1199 and binding energies, 1845 heptagon defects, 1200 formula, 1830 hydrogen chemisorption, 1227 vs. Gibb’s free energies, 1839 Raman and electronic spectroscopy, 1199 metal-base complexes, 1831 single-and di-vacancy defects, Pt-cross-linked structures, 1858 1236–1242 Stacking, 596–597 Stone–Wales defects, 1201, 1233 Standardization, 2069, 2098 topological ring defects, 1235–1236 Static response functions, 283–285 Singly occupied molecular orbital (SOMO), Statistical mechanics, 964 1760 Steered molecular dynamics (SMD), 1649 Slater determinants, 112 Steric effects, 2027 Slater rules, 156 Steric strain, 1040, 1041 SMILES, 2069 Stern–Gerlach experiment, 1469 Sodium, 1383 String, 1463 Sodium clusters, 827–832 Structural keys, 2086–2087 Solid-state kp theory, 1261 Structural outliers, 2309 Solubility (logS), 2273–2274 Submolecule approach, 772–773 Index 2379

Substances of very high concern (SVHC), Thomas–Fermi–Dirac (TFD) approach, 2253 2051 Sum-of-molecular fragments, 780 Thomas–Reiche–Kuhn (TRK) sum rule, 532 Sum of squared errors (SSE), 2115 Thymine, 693–698, 1720 Sum-over-states expression (SOS), 1877 Ti clusters, 1366 Superdelocalizability, 2045 Tight-binding Hamiltonian, 1493 Supermolecular approach (SM), 751, 757, 759, Tight-binding molecular dynamics (TBMD), 765, 767, 786 1344 Supermolecular method, 298, 301 Time-dependent density functional theory Supermolecule model, 728 (TD-DFT), 928–957 Superposition approximation, 1376 adequate XCF, 931–932 Supervised machine learning, 2096 approach, 664 Support vector machines (SVMs), 2312 atomic basis set selection, 930–931 Surface(s), 1425 complex environments and biomolecules, Surface hopping, 1927–1929 953–956 Susceptibility, 744–746, 749, 772, 776, electronic transition determination, 783, 786 933–935 cascading, 749 emission and vibronic effects, 939–946 Sutton–Chen potential, 1365 experiments comparison, 935–936 Symmetry-adapted perturbation theory performance, 951–953 (SAPT), 303, 752, 1813 solvent effects, 932–933 Systematic nomenclature scheme, 2009 vertical absorption, 930–939 Time-dependent Hartree–Fock (TDHF) theory, 271, 532 T Time-dependent Schroedinger equation Ta clusters, 1471 (TDSE), 1701 Tamm–Dancoff approach, 663 Tissue distribution Target functions of CYP enzymes, 2283 category QSAR, 2314–2315 of phase II enzymes, 2284 classiﬁcation QSAR model, 2314 Tissue physiological model, 2291 continuous QSAR, 2313–2314 Titanium dioxide (TiO2) Tauc plot, 997 electronic and optical features of, 988 Tautomeric equilibrium, platinum complexex, mesoporous TiO2, synthesis of, 1841–1843 989–993 TDDFT, 1952, 1954 morphology and structural organization, TDDFT/FDE, 782 987 Temporary negative ion (TNI), 686 nanostructures, 1015–1021 Tetrakaidecahedron (T-Cage), 1165–1166 photoactivity of, 987–988 Theoretical descriptors, 2066 structural features of, 1006–1008 Thermochemical calculations, 623–626 Topochemical indices, 2076 accuracy, 624–626 Topographic error, 2130 case study, 626 Topological distance matrix, 2072 chemical reactions, 623 Topological indices (TIs), 2071–2082, 2345 Thermochemistry of species with F–O bonds, Topological representation, 2068 632–634 Topological ring defects, 1235–1236 Thermodynamic Topostructural indices, 2076 cycle, 2272 Torsion, 1326 limit, 1421 Torsional interactions, 361–362 properties, 1373–1376 Torsion energy, 25 stability, 1042, 1900 Total energy, 28 Thermostats, 373–377 Total interaction energy, 300 THG, 776 Toxicity, 2245–2247 Thioguanine base, 1837 Traditional MD, 1918 Thole damping, 774 Transferability, 25 2380 Index

Transient negative ion (TNI) formation van der Waals, 26, 2055 molecular orbital approach, 1748 atom radii, 34 Transition dipole moment (TDM), 644, 645 bonding, 300–301 Transition metal (TM), 1348 interaction, 26, 356–359, 598 complexes photophysics of, 946–953 radii, 27 Transition moment, 530 van der Waals density functional (vdW-DF), Transition state searches, 432–433, 451–458 605 potential scans in, 458–460 Variational principle, 136 Transition temperature, 1376 Variational–perturbational scheme, 752 Translationally invariant Hamiltonian, 76 VB theory, 653 Translational motion separation of, 74 Vector potential, 1420, 1444 Transporter, 2285, 2286 in Hamiltonian, 506–510 Transposition, 93 approach, 1419, 1443–1444 Transthyterin (TTR), 1649 Velocity Verlet algorithm, 346–347, 411–412 Tropospheric oxidants, 2240 Verlet algorithm, 345, 411 Turbomole, 778 Vernalis Research, 2204 Two-dimensional graphene sheet, 1303 Vertical detachment energy (VDE), 1752, Two-level model, 1878–1879 1754, 1756, 1762, 1764, 1899 Two photon absorption (TPA), 533–535, Vertical ionization potential, 2123 1876–1889 Vibrational circular dichroism (VCD) spectra, applications, 1881–1889 1863 computational implementation of, Vibrational feshbach resonances (VFRs), 1750 1879–1880 Vibrational heat capacity, 1389 theory, 1877–1880 Vienna ab initio simulation package (VASP), two-level model, 1878–1879 1204 Two-photon circular dichroism, 549–550 Virtual orbital energies (VOEs), 1754 Two-photon transition matrix, 1877 Virtual orbitals, 165 Visual molecular dynamics (VMD), 1640 Volatile organic compounds (VOCs), U 2240–2241 Ultrafast photodeactivation mechanism, 1981 VolSurf descriptor, 2308 U-matrix, 2128 Volume of distribution (VD), 2280–2281 Umbrella integration (UI) method, 1862 Undersampling, 2315 Uniﬁed distance matrix, 2128 W United atom, 36 Wannier functions, 1435 Unnormalized elimination of the small Wannier–Mott exciton, 1272 component (UESC), 897–898 Ward’s method, 2107 Unoccupied molecular orbital (UMO), 1749, Water clusters 1754 “all-surface” to “internally solvated”, UNRES, 51 1155–1157 Unsupervised machine learning clustering, electronic structure calculations, 2099 1156–1157 data preparation, 2097–2098 intermolecular interactions, 1141–1146 PCA, 2096 2–10 molecules, 1146–1152 self-organizing maps, 2124 pentagonal dodecahedron, 1162–1165 uses, 2096 11ÄnÄ 16 range, 1152–1156 UV-Filters, 2249 spectroscopic signature, 1157 structure, 1157 tetrakaidecahedron (T-Cage), 1165–1166 V vibrational spectra, 1160 Vacancy defects, 1194 Water liquid Valence–Rydberg mixing, 684–685 dc-Pockels effect, 786 Vanderbilt ultrasoft pseudopotentials, 367–368 electric properties, 786 Index 2381

Water model, 43 Wide angle X-ray scattering (WAXS), 989 Water molecule, 43 Wigner–Witmer rules, 678 Water radiolysis, 1897 Williams–Stone–Misquitta (WSM) Wave function distribution, 318–319 coupled cluster approximation, 165–170 Worm like chain (WLC) model, 399 Hartree–Fock method, 147–152, 159 Møller–Plesset perturbation theory, 152–159 X one-electron approximation, 142–147 X-ray crystallographic studies, 1050 perturbation calculus, 137–147 X-ray diffraction, 989 quantum mechanics, 125–133 X ray-like, 1605 variational principle, 136–137 Wave function theory (WFT), 226 Weak intermolecular interactions Y aromatic stacking, 596–597 Y randomization test, 2317 basis sets, 607–608 Yellow fever (YF) inhibitor, 2221–2223 benchmark set, 609–610 Yellow fever ﬂavivirus (YFV), 2221 counterpoise correction, 608–609 Young’s modulus, 1476 coupled cluster, 599–600 density functional theory, 602–603 deoxyribonucleic acid, 595 Z empirical performance considerations, Z-cutoff value, 2317 610–613 Zener tunneling, 1417 Hartree–Fock (HF) theory, 602 Zeolites structure, 833–842 hydrogen-bond, 596 Zero temperature (ZT), 1344 interaction, 596, 597 Zero-dimensional nanomateials, 1461 interaction energy, 598 Zero-ﬁeld splitting (ZFS), 577 molecular mechanics, 606 Zero-point vibrational energy (ZVE), 644 Møller–Plesset perturbation theory, Zeroth-order regular approximation (ZORA), 600–601 917 quantum Monte Carlo, 600 Zigzag graphene ribbon model, 1486 semiempirical methods, 605–606 ZINC database, 2016 Web Ontology Language (OWL), 2165–2167, Zinc-group metal cations, 1836–1838 2175 Zincblende, 1262 Weighted histogram analysis (WHAM) ZnO nanobelts, 1497 method, 1862 Z-transformation, 2098 WHIM descriptors, 2084 ZT-TBMD method, 1347