Essentials of Computational Chemistry

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ACRONYM GLOSSARY 553 mPW1S mPW1PW91 modified for sugar conformational analysis MRCI Multireference CI MRCISD Multireference CI including single and double excitations MR-MP2 Multireference second-order perturbation theory MST Miertus–Scrocco–Tomasi (polarized continuum) model MST-ST MST model augmented with atomic surface tensions µTST Microcanonical transition state theory µVTST Microcanonical variational transition state theory NAO Natural atomic orbital NBO Natural bond orbital NDDO Neglect of diatomic differential overlap NHE Normal hydrogen electrode NIST National Institute of Standards and Technology (U.S.) NMR Nuclear magnetic resonance nOe Nuclear Overhauser effect NPA Natural population analysis O OPTX exchange functional O3LYP ACM using O exchange and LYP correlation functionals OLYP O exchange and LYP correlation functionals OM1 Orthogonalization method 1 OM2 Orthogonalization method 2 ONIOM Our own n-layered integrated molecular orbital molecular mechanics o.o.p. Out-of-plane OPLS Optimized potentials for liquid simulations ORD Optical rotatory dispersion P Perdew exchange functional P86 Perdew correlation functional PA Proton affinity PB Poisson–Boltzmann PBC Periodic boundary condition PBE Perdew, Burke, and Enzerhof functional PBE1PBE ACM functional derived from PBE PCA Principal components analysis PCM Polarized continuum model pc-n Polarization consistent n-ζ basissetsofJensen PD Pairwise descreening PDDG Pairwise distance directed Gaussian PDFT Projected density functional theory PEG Polyethyleneglycol PEOE Partial equalization of orbital electronegativity PES Potential energy surface PKZB MGGA exchange-correlation functional of Perdew, Kurth, Zupan, and Blaha
554 APPENDIX A PM3 Parameterized (NDDO) model 3 PM3(tm) PM3 with a d orbital extension to transition metals PME Particle-mesh Ewald PMF Potential of mean force PMPn Projected Møller–Plesset theory of order n POS Points on a sphere PP Perfect pairing PPP Pariser–Parr–Pople PUHF Projected UHF PW Perdew–Wang (1991) exchange functional PW91 Perdew–Wang (1991) correlation functional QCISD Quadratic configuration interaction including singles and doubles QCISD(T) QCISD with perturbative estimate for connected triples QEq Charge equilibration QM Quantum mechanics QMHO Quantum mechanical harmonic oscillator QM/MM Quantum mechanics/molecular mechanics hybrid QSPR Quantitative structure–property relationship RAS Restricted active space r.d.f. Radial distribution function RESP Restrained ESP RHF Restricted Hartree–Fock RISM Reference interaction site model RMS Root mean square RMSD Root-mean-square deviation ROHF Restricted open-shell Hartree–Fock ROKS Restricted open-shell Kohn–Sham theory ROSS Restricted open-shell singlet density functional theory RPA Random-phase approximation RRKM Rice–Ramsperger–Kassel–Marcus S Slater exchange functional SAC Scaling all correction SAM1 Semi-ab initio method 1 SAM1D SAM1 with d orbitals SAR Structure–activity relationship SASA Solvent-accessible surface area SCC-DFTB Self-consistent charge density functional tight-binding theory SCF Self-consistent field SCIPCM PCM with a liquid-solution-phase isodensity surface as the cavity surface SCRF Self-consistent reaction field SCS-MP3 Spin-component-scaled MP3 SES Separable equilibrium solvation
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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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Page 536 and 537: 520 15 ADIABATIC REACTION DYNAMICS
Page 564 and 565: Appendix A Acronym Glossary Note: B
Page 566 and 567: ACRONYM GLOSSARY 551 ECP Effective
Page 570 and 571: ACRONYM GLOSSARY 555 SF-CISD Spin-f
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 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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