Essentials of Computational Chemistry

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Appendix A Acronym Glossary Note: Basis set abbreviations are detailed in Chapter 6 and are, for the most part, not included here. Only the most common combinations of exchange and correlation functionals are included as separate acronyms. Unit abbreviations are not listed. 6-12 The inverse power dependence of Lennard–Jones terms AA All-atom (as opposed to united-atom) ACM Adiabatic connection method ADF Amsterdam density functional code AIM Atoms in molecules AM1 Austin Model 1 AMBER Assisted model building with energy refinement AO Atomic orbital AOC AM1/OPLS/CM1 B Becke (1988) exchange functional B1B95 ACM one-parameter functional B3LYP ACM using B exchange and LYP correlation functionals B3PW91 ACM using B exchange and PW91 correlation functionals B86 Becke (1986) exchange functional B95 Becke correlation functional B97 ACM functional of Becke B97-1 ACM functional of Becke reparameterized by Hamprecht et al. B98 ACM MGGA exchange-correlation functional of Becke BAC Bond-additivity correction BB1K B1B95 optimized for kinetics BD CCD using Brueckner orbitals BH&H Becke half-and-half exchange functional BKO Born–Kirkwood–Onsager BLYP B exchange and LYP correlation functionals Bm Modification of Becke exchange functional for use with τ1 BPW91 B exchange and PW91 correlation functionals Essentials of Computational Chemistry, 2nd Edition Christopher J. Cramer © 2004 John Wiley & Sons, Ltd ISBNs: 0-470-09181-9 (cased); 0-470-09182-7 (pbk)
550 APPENDIX A BR MGGA exchange functional of Becke and Roussel BSSE Basis set superposition error CAM Cambridge GGA exchange functional CAS Complete active space CASPT2 Complete active space second-order perturbation theory CASSCF Complete active space self-consistent field CBS Complete basis set CCD Coupled cluster with double substitution operator CCSD Coupled cluster with single and double substitution operators CCSD(T) CCSD with perturbative estimate for connected triples CCSDT Coupled cluster with single, double, and triple substitution operators CCSDTQ Coupled cluster including single through quadruple excitations CD Circular dichroism CFF Consistent force field CHARMM Chemistry at Harvard molecular mechanics CHELP Charges from electrostatic potentials CI Configuration interaction CID CI including only double electronic excitations CIS CI including only single electronic excitations CISD CI including single and double electronic excitations CIS(D) CIS including a correction for double excitations CISDT CI including single, double, and triple electronic excitations CISDTQ CI including single through quadruple electronic excitations CISD(Q) CISD with Langhoff–Davidson estimate for quadruples CMn Charge model n (where n is a version number) CNDO Complete neglect of differential overlap CoMFA Comparative molecular field analysis COSMIC Computation and structural manipulation in chemistry COSMO Conductor-like screening model CP Counterpoise; Car–Parrinello C-PCM Conductor formulation of PCM CS Correlation functional of Colle and Salvetti CSF Configuration state function CT Charge transfer CVFF Consistent valence force field DFT Density functional theory DFTB Density functional tight-binding theory DFT-SCI Density functional theory singles configuration interaction D-PCM Dielectric formulation of PCM DZ Double zeta (basis set) DZP Double zeta polarized (basis set) EA Electron affinity ECEPP Empirical conformational energy program for peptides
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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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Page 536 and 537: 520 15 ADIABATIC REACTION DYNAMICS
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Page 568 and 569: ACRONYM GLOSSARY 553 mPW1S mPW1PW91
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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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