Essentials of Computational Chemistry

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Global minimum, 23, 46, 97, 146, 383 Glucose, 60, 150–151, 193, 235, 240, 385 Gradient, corrected density functionals, (see Generalized gradient approximation) electron density, 263–264 potential energy surface, 43–45, 133, 144, 196–198, 221, 234–235, 238, 243, 260, 291, 319, 401, 472, 477, 497, 505, 522, 532, 573 Green’s function, (see Propagator method) Grid, 62–64, 260, 308, 318, 338, 399–401, 466–467 docking, 62–64 for ESP charge, 318 integration over, 260, 338, 399–400 GROMOS, 54, 60, 99 Ground state, 109, 115, 360, 487–504, 507–508, 511, 513–515 Group theory, (see Point group and Symmetry) GVB, 209 H&H, 266, 296 Half-electron method, (see Hartree-Fock theory) Half-life, 521 Hamiltonian, 72, 106–111, 119–122, 154, 157, 166, 179, 203, 212, 215, 219–220, 223, 249–250, 252–255, 262, 321, 325–327, 387, 396–397, 434, 436, 457, 459, 461, 478, 496, 508, 562, 572–575 determination from electron density, 249–250, 252–254, 475 EVB, 477–482 including radiation field, 508 non-interacting, 122, 219–220, 255–256, 265 QM/MM, 457, 459–462, 467–469 Hardness, 270 Harmonic oscillator, 61, 72–74, 336–342, 356, 364–365, 376, 484, 527, 531, 539 Harris functional, 269 Hartree product, 120–122 Hartree-Fock theory, 126–129 ab initio, 126–129, 165–199, 203–205, 327 and DFT, 258, 267 half-electron, 148 instability, 234 limit, 128–129, 165–166, 173, 176–178, 228, 230 INDEX 587 periodic, 192 predictions from, 192–199, 281, 287–289, 292–294, 322–323, 330–331, 338–340, 346–348 projected, 506, 571–574 QM/MM modifications, 462 restricted, 126–128, 190, 197, 205, 234, 487 restricted open-shell, 188–190, 206, 325, 328–329 semiempirical, 128, 131–147 TS structures, 197–198 unrestricted, 148, 188–190, 234, 244, 272, 324–325, 328, 506, 545, 571–574 Hartree-Fock-Slater method, 252 HCTH, 264, 274, 283, 285, 287, 289, 292, 296 Heat capacity, 366, 445–446 Heat <strong>of</strong> formation, 37, 40–41, 142, 147–148, 155, 192, 240–244, 356, 366–375, 378, 381–383 Heaviside function, 534 Heisenberg spin ladder, 505 Hellmann-Feynman theorem, 264, 326 Hessian, 44–46, 185, 191, 221, 260, 336–338, 365–366 Hexachloroethane, 422–424 HF/3–21G/OPLS, (see QM/MM) Hindered rotor, 376–377 Histogram, 83–86, 439, 541 Hohenberg-Kohn theorems, 252–254, 273, 494 Hole function, 251, 257, 278 Hooke’s law, 18 Hückel theory, 115–119, 269 extended, 134–136, 181 Hund’s rule, 204 Hybrid DFT, (see Adiabatic connection) Hydrazine, 138–139, 151 Hydrogen bonding, 33, 50, 112, 145, 149–151, 156, 158, 193, 195, 198, 279, 293, 309, 386, 407, 433, 449, 460, 463, 513 Hydrogen cyanide, 316, 322, 347, 430–435 Hydrogen electrode, 410, 414, 423 Hydrogen fluoride, 176, 236, 294, 347–349 Hydrogen-atom transfer, 267, 286, 537–538 Hydrophobicity, 152, 388, 407–408, 449, 452 Hydroxylamine, 381–383 8-Hydroxyquinoline, 513–515 Hyperconjugation, 24–25, 313, 578–579 Hyperfine coupling, 10, 189, 305, 327–330, 343–344
588 INDEX Hyperpolarizability, 325–327 Hypervalency, 143, 148, 153–155, 174–175, 197 Hysteresis, 434 Ideal gas assumption, 358–359, 361–362, 379, 527 IGLO, 345 IMOMM, (see QM/MM) Implicit solvation, (see Solvation) Improper torsions, 27 Index <strong>of</strong> refraction, 409, 512, 542 INDO, 139–143, 153, 181 INDO/S, 139–141, 153, 497, 502, 514–515 Infrared spectroscopy, (see Vibrational spectroscopy) Intensity, (see Frequency) Internal coordinates, 6–7, 29, 34, 36, 46–48, 82, 336, 459, 522, 539, 541 Internal energy, 92, 356, 358–366, 376–377, 430–432, 444, 453, 525 Intrinsic reaction coordinate, (see Reaction coordinate) Ion convention, 378 Ionic strength, 394–395 Ionization potential, 116, 135, 137, 194–195, 270, 272, 285, 311, 330–331, 414, 502 predicted values, 141, 143, 149, 194–195, 288–290, 423 valence-shell, 135 IPCM, (see Solvation) IRC, (see Minimum-energy path) Irreversible reaction, 520, 522, 524 ISM, 264, 296 Isodesmic equation, 166, 372–375, 381–382, 413 Isogyric, 373–374 Isotope effect, 357, 528–531 kinetic, 482–484, 528–531, 533, 537–538 Jahn-Teller distortion, 206 Jellium, 250 KCIS, 264, 296 Kinetic-energy density, 264 Kinetic-energy functional, 250, 255–258, 262, 264, 274–275 Kinetic-energy operator, 107, 266, 269, 274, 332, 344 Kinetic isotope effect, (see Isotope effect) Kinetics, 199, 267, 334, 344, 390, 393, 421, 482–483, 519, 523, 537 Kirkwood-Onsager equation, 396–397 KMLYP, 286–288, 296 Kohn-Sham theory, (see also Self-consistent field), 255–257, 274–278, 397, 448, 578 QM/MM modifications, 461–462 Koopmans’ theorem, 149, 194–195, 272, 330–331 Kramers-Grote-Hynes theory, 539 Kronecker δ, 107, 224 Landau-Zener model, 541 Langevin dipole, 466–467 Langevin dynamics, 80, 539 Lap correlation, 264, 297 Laplacian operator, 107, 127, 562 LCAO approach, 111–113 Leapfrog algorithm, 77–78, 101 Lennard-Jones potential, 29–30, 33, 47, 155, 271, 461–463, 478 Lewis structure, 209, 578–579 LG exchange, 263, 297 Line search, 44 Linear response theory, 387 Linear scaling, (see Scaling behavior) Link atom, 473–477 Liquid crystal, 417 Local density approximation, 258–263, 266 Local minimum, 6, 41–46, 61, 69, 183, 185–186, 235, 291, 337–338, 377–378, 419, 522–523 Local spin density approximation, 259–267, 278, 282, 285–286, 288–289, 291–292, 294, 345–348 Locally enhanced sampling, 98 London forces, (see Dispersion) LT2A, 297 LYP correlation, 263, 266, 291, 297 MACROMODEL, 50–51 Magnetic multipole moment, (see Multipole moment, magnetic) Marcus theory, 541–544 Markov chain, 82 Mass-velocity relativistic correction, 223 Mataga-Nishimoto integral, 137
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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 548 and 549: 532 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
Page 582 and 583: SPIN ALGEBRA 569 + = 1 1 ( 2 2 α(
Page 584 and 585: C.3 UHF Wave Functions SPIN ALGEBRA
Page 586 and 587: SPIN ALGEBRA 573 = 〈cs s |H |cs s
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 596 and 597: 584 INDEX Convergence (continued) f
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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