Essentials of Computational Chemistry

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584 INDEX Convergence (continued) finite-field calculation, 327 geometry optimization, 40–50, 141, 183, 191 HF SCF, 121, 128–129, 166, 181–182, 207, 262, 491 induced dipole moment, 446 KS SCF, 274, 491, 495 multipole-multipole interactions, 307 quadratic, 181 SCRF, 396–397 simulation, 93–96, 444 solvation free energy, 401 Core electrons, 134, 178–179, 195, 228, 240, 345, 474 Core potential, (see Basis set) Correlation, (see also Electron correlation), 110 Correlation energy density, 259, 263 COSMO, (see Solvation) Coulomb integral, (see Two-electron integral) Coulomb radius, 403–404 Coulomb’s law, 2, 14, 37, 402 Counterpoise correction, 195 Coupled-cluster theory, 224–227, 229–237, 242, 244–246, 336, 401, 465, 574 predictions from, 244–246, 281, 292, 339, 375, 381–382, 422–423, 495, 544–546 scaled, 229–230 spin-flip, 227 Coupling parameter, 265, 433–437, 443–444, 449, 458, 464, 481 Cross terms, 34–36 CS correlation, 296 Curtin-Hammett principle, 300 Cutoff distance, 47, 88–90 CVFF, 53, 60 Cyclobutene, 207–208 d orbitals, 153–155, 167, 285, 291 Darwin relativistic correction, 223–224 Davidson correction, 215 Debye-Hückel parameter, 395, 403 Decay time, 87, 95 Degeneracy, 204–206, 231, 244, 324, 333, 350, 359–364, 498, 563 structural, 364, 563 Degrees of freedom, 6, 20, 34, 42–43, 69, 75, 78–80, 88, 92, 183–186, 338, 342, 394, 429, 442, 523, 525–526, 531–532, 535, 538, 563 Delta SCF, 194–195, 288, 330–331, 494–496, 503 Density functional theory, 249–300, 371 broken symmetry, 275–276, 545 multideterminantal, 276 overdelocalization, 279–280, 294, 330–331 predictions from, (see individual functional names) projected, 494, 506–507 SCI and MRCI, 498, 501 tight-binding, 268–271, 321–322, 404 time-dependent, 497, 501–504, 514–515 Density matrix, 127–128, 181, 188–189, 196, 261–262, 308, 328, 396, 404, 476 spin, 189, 328, 330 spin-difference, 328 Deprotonation, (see Acidity) Diazene, 505–507 1,2-Dichloroethane, 398, 459–460 Didehydrobenzene 1,3-, 197 1,4-, 231–234, 254, 275, 277, 349–350, 374–375 2,5-Didehydropyridinium cation, 231–234, 275 Dielectric constant, 2, 32–33, 98, 101, 394–397, 403, 405, 417, 421, 452, 460, 512, 542 Diels-Alder reaction, 285, 460 Diffusion, 88, 543 Dipole moment, 32–33, 37, 82–84, 143, 152, 198, 294, 306–307, 310, 315, 320–326, 332, 342, 387–388, 397, 411, 445, 463–464 induced, 33, 325, 387–388, 446, 463–464 Dipole-dipole interaction, (see also Electrostatic and Nonbonded interactions), 23–28, 32, 47, 90, 307, 445 Dirac δ, 84–85, 224, 439 Direct dynamics, 532 Direct methods, 13, 191 Dispersion, (see also Nonbonded interaction), 28–29, 149, 155, 192, 195, 198, 271, 293, 371, 388, 406–408, 447, 513 Divide-and-conquer formalism, 274 DNA, (see Nucleic acids) Docking, 62–64, 404, 420, 454 Double-wide sampling, 434 DREIDING, 38, 53 Drug design, 62, 152–153, 309–310 Dry cleaning, 422
Dual topology, 443 Dynamics, molecular, 72–80, 91–96, 273–274, 399, 420–421, 431–434, 438–440, 444, 447–454, 463, 474–477, 482–484, 513, 538 non-adiabatic, 539–544 reaction, 357, 423, 482–484, 519–546 ECEPP, 54 Eckart potential, 536 EDF1, 268, 282, 296 Effective core potential, (see Basis set) Effective fragment potential, 447, 465 Eigenfunction, 106, 111, 120–122, 126, 166, 173, 182, 188, 190, 212, 216–218, 220, 255–256, 324–325, 328, 332, 336, 507–509, 565–570 Eigenvalue, 95, 106–107, 110–111, 121–122, 149, 190, 206, 214, 216, 219–220, 250, 253, 255, 272, 325, 330–333, 335–337, 362, 479, 496, 502, 507, 540, 565–570 Electric multipole moment, (see Multipole moment, electric) Electrochemistry, 410, 413–415, 422–424, 541–544 Electron affinity, 137, 176, 195, 270, 285, 288–290, 311, 330–331, 414, 423 Electron correlation, 111, 128–129, 132–133, 149, 165, 173, 178, 192–195, 203–246, 251, 280, 330, 388, 493, 574 angular, 228 core, 228, 242–243 core-valence, 228, 240–241 dynamical, 203–205, 211, 216, 223, 233, 497, 501 effect on geometries, 197–198, 235 effect on solvation free energy, 401, 406 effect on vibrational intensities, 341 energy, 129, 132–133, 149, 165, 178, 214, 224, 242, 370–372 exchange, 128, 189, 251, 265–267, 274, 278 non-dynamical, 182, 203–205, 209, 212, 216, 223, 246, 275–277, 285, 291, 351, 495, 501 radial, 228 scaled energies, 238–239 Electron density, (see also Density functional theory and Gradient), 61, 112, 249–280, 314–318, 421, 475–476, 577 INDEX 585 Electron spin resonance, 189, 305, 327–330 Electron transfer, 422–424, 541–544 Electronegativity, 23, 31, 152, 171, 270, 307, 310, 313, 318, 474 Electronic energy, 110–111, 121, 148, 154, 203, 206, 220, 238, 332–333, 366, 375, 412, 525 Electronic excited state, 140–141, 176, 186–187, 254, 273, 360–361, 487–513 Electronic g value, 327, 330 Electrostatic interaction, (see also Charge-charge, Dipole-dipole, and Nonbonded interactions), 30–34, 88, 90, 100, 195, 198, 387–388, 393–406, 444, 447, 461–462, 467, 474, 478 Electrostatic potential, (see also Atomic partial charge), 199, 308–309, 318–319, 394–395, 399–400, 405 Electrostriction, 452 Elementary reaction, 519–523, 531 Empirical valence bond, 477–482 Enantiomeric excess, 160 Enediyne, 349–350 Enolase, 482–484 Ensemble, 69, 82, 91–93, 99, 355–366, 432–434, 440, 463 Ensemble average, (see also Expectation value), 70, 83–88, 429, 431–437, 441, 443, 452–454, 463 Enthalpy, (see also Heat of formation), 10, 92, 355–356, 358, 366–378, 381–383, 412, 430, 444, 527–528, 537, 545 Entropy, 355, 358–366, 376–378, 386, 430, 445, 452–453, 527–528, 545 bottleneck, 523, 533 Enzyme-substrate binding, 62–63, 400, 438–439, 442, 452–454, 457–458, 482–484 Equation-of-motion method, (see Propagator method) Equilibration, 92–93, 96, 311 Equilibrium constant, 11, 41, 62, 132, 379–380, 386, 389, 416, 432, 520, 524–525 Equilibrium fraction, 377 Ergodicity, 72, 93, 431 ESFF, 54, 60 Essential dynamics, (see Principal components analysis)
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Essentials of Computational Chemist
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Essentials of Computational Chemist
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For Katherine
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viii CONTENTS 2.5 Menagerie of Mode
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x CONTENTS 7 Including Electron Cor
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xii CONTENTS 11.4 Strengths and Wea
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Preface to the First Edition Comput
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PREFACE TO THE FIRST EDITION xvii d
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xx PREFACE TO THE SECOND EDITION to
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Known Typographical and Other Error
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1 What are Theory, Computation, and
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Activation free energy (kcal mol
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1.3 COMPUTABLE QUANTITIES 5 etc.) f
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a a r 1 1.3 COMPUTABLE QUANTITIES 7
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1.3 COMPUTABLE QUANTITIES 9 path is
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1.4 COST AND EFFICIENCY 11 this is
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1.4 COST AND EFFICIENCY 13 kinds of
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Physical quantity (unit name) BIBLI
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2 Molecular Mechanics 2.1 History a
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2.2 POTENTIAL ENERGY FUNCTIONAL FOR
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2.3 FORCE-FIELD ENERGIES AND THERMO
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Heat of formation A E nb (A) 2.4 GE
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gradient vector, g, which is define
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Eq. (2.38) as 2.4 GEOMETRY OPTIMIZA
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2.4 GEOMETRY OPTIMIZATION 47 that t
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2.4 GEOMETRY OPTIMIZATION 49 is opp
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Table 2.1 Force fields Name (if any
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12 Davies, E. K. and Murrall, N. W.
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5 (MM2(85), MM2(91), Chem-3D) Compr
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2.5 MENAGERIE OF MODERN FORCE FIELD
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2.6 FORCE FIELDS AND DOCKING 63 Fig
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2.7 CASE STUDY: (2R ∗ ,4S ∗ )-1
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REFERENCES 67 Cramer, C. J. 1994.
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3 Simulations of Molecular Ensemble
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3.2 PHASE SPACE AND TRAJECTORIES 71
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m −b r eq −b 3.3 MOLECULAR DYNA
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and 3.3 MOLECULAR DYNAMICS 75 p(t +
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3.3 MOLECULAR DYNAMICS 77 step mean
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3.3 MOLECULAR DYNAMICS 79 of course
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3.4 MONTE CARLO 81 One way to reduc
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3.5 ENSEMBLE AND DYNAMICAL PROPERTY
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3.6 KEY DETAILS IN FORMALISM 89 Fig
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3.6 KEY DETAILS IN FORMALISM 91 alc
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3.6 KEY DETAILS IN FORMALISM 93 mor
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3.6 KEY DETAILS IN FORMALISM 95 der
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3.6 KEY DETAILS IN FORMALISM 97 to
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3.8 CASE STUDY: SILICA SODALITE 99
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BIBLIOGRAPHY AND SUGGESTED ADDITION
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REFERENCES 103 Jaqaman, K. and Orto
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106 4 FOUNDATIONS OF MOLECULAR ORBI
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132 5 SEMIEMPIRICAL IMPLEMENTATIONS
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166 6 AB INITIO HARTREE-FOCK MO THE
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204 7 INCLUDING ELECTRON CORRELATIO
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250 8 DENSITY FUNCTIONAL THEORY num
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252 8 DENSITY FUNCTIONAL THEORY for
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254 8 DENSITY FUNCTIONAL THEORY fun
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256 8 DENSITY FUNCTIONAL THEORY Not
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258 8 DENSITY FUNCTIONAL THEORY emp
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260 8 DENSITY FUNCTIONAL THEORY whe
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264 8 DENSITY FUNCTIONAL THEORY [As
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266 8 DENSITY FUNCTIONAL THEORY som
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268 8 DENSITY FUNCTIONAL THEORY for
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272 8 DENSITY FUNCTIONAL THEORY Ano
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274 8 DENSITY FUNCTIONAL THEORY Eve
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276 8 DENSITY FUNCTIONAL THEORY val
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278 8 DENSITY FUNCTIONAL THEORY acc
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280 8 DENSITY FUNCTIONAL THEORY als
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282 8 DENSITY FUNCTIONAL THEORY Tab
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294 8 DENSITY FUNCTIONAL THEORY con
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300 8 DENSITY FUNCTIONAL THEORY dou
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302 8 DENSITY FUNCTIONAL THEORY Cho
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9 Charge Distribution and Spectrosc
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9.1 PROPERTIES RELATED TO CHARGE DI
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H H P O H H H F Cl Cl P P F H F F P
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9.3 SPECTROSCOPY OF NUCLEAR MOTION
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Energy hn 0→1 9.3 SPECTROSCOPY OF
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9.4 NMR SPECTRAL PROPERTIES 345 The
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9.4 NMR SPECTRAL PROPERTIES 347 Tab
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9.5 CASE STUDY: MATRIX ISOLATION OF
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REFERENCES 351 The use of computed
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REFERENCES 353 Rablen, P. R., Pearl
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356 10 THERMODYNAMIC PROPERTIES of
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358 10 THERMODYNAMIC PROPERTIES whe
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360 10 THERMODYNAMIC PROPERTIES tha
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362 10 THERMODYNAMIC PROPERTIES (Th
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364 10 THERMODYNAMIC PROPERTIES the
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368 10 THERMODYNAMIC PROPERTIES Ene
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372 10 THERMODYNAMIC PROPERTIES 10.
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374 10 THERMODYNAMIC PROPERTIES gen
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382 10 THERMODYNAMIC PROPERTIES Tab
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384 10 THERMODYNAMIC PROPERTIES Clo
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386 11 IMPLICIT MODELS FOR CONDENSE
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12 Explicit Models for Condensed Ph
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12.2 COMPUTING FREE-ENERGY DIFFEREN
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∆G 12.2 COMPUTING FREE-ENERGY DIF
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12.4 SOLVENT MODELS 445 In some cas
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12.4 SOLVENT MODELS 447 increases t
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12.5 RELATIVE MERITS OF EXPLICIT AN
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12.5 RELATIVE MERITS OF EXPLICIT AN
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12.6 CASE STUDY: BINDING OF BIOTIN
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REFERENCES 455 Levy, R. M. and Gall
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13 Hybrid Quantal/Classical Models
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13.2 BOUNDARIES THROUGH SPACE 459 a
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13.2 BOUNDARIES THROUGH SPACE 461 i
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13.2 BOUNDARIES THROUGH SPACE 463 T
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13.2 BOUNDARIES THROUGH SPACE 465 W
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13.3 BOUNDARIES THROUGH BONDS 467 t
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13.3 BOUNDARIES THROUGH BONDS 469 o
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180 180 4 10 15 15 20 150 6 8 150 8
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13.3 BOUNDARIES THROUGH BONDS 473 O
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13.3.3 Frozen Orbitals 13.3 BOUNDAR
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Link atom LSCF GHO 13.4 EMPIRICAL V
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13.4 EMPIRICAL VALENCE BOND METHODS
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13.4 EMPIRICAL VALENCE BOND METHODS
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13.5 CASE STUDY: CATALYTIC MECHANIS
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REFERENCES 485 Gao, J., Amara, P.,
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14 Excited Electronic States 14.1 D
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14.1 DETERMINANTAL/CONFIGURATIONAL
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14.1 DETERMINANTAL/CONFIGURATIONAL
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14.2 SINGLY EXCITED STATES 493 and
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14.2 SINGLY EXCITED STATES 495 Tabl
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14.2 SINGLY EXCITED STATES 497 wher
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14.3 GENERAL EXCITED STATE METHODS
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14.3 GENERAL EXCITED STATE METHODS
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14.4 SUM AND PROJECTION METHODS 503
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14.4 SUM AND PROJECTION METHODS 505
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14.5 TRANSITION PROBABILITIES 507 o
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14.5 TRANSITION PROBABILITIES 509 I
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14.6 SOLVATOCHROMISM 511 overlap) l
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14.7 CASE STUDY: ORGANIC LIGHT EMIT
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BIBLIOGRAPHY AND SUGGESTED ADDITION
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REFERENCES 517 Kim, K., Shavitt, I,
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520 15 ADIABATIC REACTION DYNAMICS
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Page 546 and 547: 530 15 ADIABATIC REACTION DYNAMICS
Page 564 and 565: Appendix A Acronym Glossary Note: B
Page 566 and 567: ACRONYM GLOSSARY 551 ECP Effective
Page 568 and 569: ACRONYM GLOSSARY 553 mPW1S mPW1PW91
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Page 572 and 573: 558 APPENDIX B H 3 C CH 3 H H H a
Page 574 and 575: 560 APPENDIX B Linear molecule? no
Page 576 and 577: 562 APPENDIX B Table B.5 Product ru
Page 578 and 579: Appendix C Spin Algebra C.1 Spin Op
Page 580 and 581: function we have SPIN ALGEBRA 567
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Page 584 and 585: C.3 UHF Wave Functions SPIN ALGEBRA
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Page 588 and 589: Appendix D Orbital Localization D.1
Page 590 and 591: ORBITAL LOCALIZATION 577 〈|H |〉
Page 592 and 593: E rel (kcal mol −1 ) 10 8 6 4 2 0
Page 594 and 595: 582 INDEX B3PW91, 266-267, 284, 288
Page 598 and 599: Global minimum, 23, 46, 97, 146, 38
Page 600 and 601: Matrix diagonalization, (see also S
Page 602 and 603: primitive, 168-173 Slater-type, 134
Page 604 and 605: Reductive dechlorination, 422-424 R
Page 606 and 607: SYBYL, 58 Symmetry, 182-188, 209, 2
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