Essentials of Computational Chemistry

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5 (MM2(85), MM2(91), Chem-3D) Comprehensive: Burkert, U. and Allinger, N. L. 1982. Molecular Mechanics, ACS Monograph 177, American Chemical MM2 Organics Superseded by MM3 but still widely available in many modified Society: Washington, DC. forms. 2.5 MENAGERIE OF MODERN FORCE FIELDS 55 5 (MM3(92)) Original: Allinger, N. L., Yuh, Y. H., and Lii, J.-H. 1989. J. Am. Chem. Soc., 111, 8551. MM3(94): Allinger, N. L., Zhou, X., and Bergsma, J. 1994. J. Mol. Struct. (Theochem), 312, 69. Recent extension: Stewart, E. L., Nevins, N., Allinger, N. L., and Bowen, J. P. 1999. J. Widely available in many modified forms. MM3 Organics and biomolecules Org. Chem. 64, 5350. Allinger, N. L., Chen, K. S., and Lii, J. H. 1996. J. Comput. Chem., 17, 642; Nevins, N., Chen, K. S., and Allinger, N. L. 1996. J. Comput. Chem., 17, 669; Nevins, N., Lii, J. H., and Allinger, N. L. 1996. J. Comput. Chem., 17, 695; Nevins, N. and Allinger, N. L. 1996. J. Comput. Chem., 17, 730. Recent extension: Lii, J. H., Chen, K. H., and Allinger, N. L. 2004. J. Phys. Chem A, 108, 3006. MM4 Hydrocarbons, alcohols, ethers, and carbohydrates (continued overleaf )
56 2 MOLECULAR MECHANICS Table 2.1 (continued) Name (if any) Range Comments Refs (error) a 4 (MMFF93) Halgren, T. A. 1996. J. Comput. Chem., 17, 490, 520, 553, 616; Halgren, T. A., and Nachbar, R. B. 1996. J. Comput. Chem., 17, 587. Widely available in relatively stable form. MMFF Organics and biomolecules See also www.schrodinger.com BasedonMM2. Seewww.serenas<strong>of</strong>t.com 5 MMX Organics, biomolecules, and inorganics Original: Bernhardt, P. V. and Comba, P. 1992. Inorg. Chem., 31, 2638. Latest generation: Comba, P. and Gyr, T. 1999. Eur. J. Inorg. Chem., 1787 See also MOMEC Transition metal compounds www.uni-heidelberg.de/institute/fak12/AC/ comba/molmod−momec.html Proteins: Jorgensen, W. L., and Tirado-Rives, J. 1988. J. Am. Chem. Soc., 110, 1657; Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., and Jorgensen, W. L. 2001. J. Phys. Chem. B, 105, 6474. Organic parameters are primarily for solvents. All-atom and united-atom versions exist. OPLS Biomolecules, some organics
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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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Page 40 and 41: 2.2 POTENTIAL ENERGY FUNCTIONAL FOR
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Page 88 and 89: REFERENCES 67 Cramer, C. J. 1994.
Page 90 and 91: 3 Simulations of Molecular Ensemble
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Page 122 and 123: BIBLIOGRAPHY AND SUGGESTED ADDITION
Page 124 and 125: 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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Appendix A Acronym Glossary Note: B
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ACRONYM GLOSSARY 551 ECP Effective
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ACRONYM GLOSSARY 553 mPW1S mPW1PW91
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ACRONYM GLOSSARY 555 SF-CISD Spin-f
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558 APPENDIX B H 3 C CH 3 H H H a
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560 APPENDIX B Linear molecule? no
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562 APPENDIX B Table B.5 Product ru
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Appendix C Spin Algebra C.1 Spin Op
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function we have SPIN ALGEBRA 567
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SPIN ALGEBRA 569 + = 1 1 ( 2 2 α(
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C.3 UHF Wave Functions SPIN ALGEBRA
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SPIN ALGEBRA 573 = 〈cs s |H |cs s
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Appendix D Orbital Localization D.1
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ORBITAL LOCALIZATION 577 〈|H |〉
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E rel (kcal mol −1 ) 10 8 6 4 2 0
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582 INDEX B3PW91, 266-267, 284, 288
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584 INDEX Convergence (continued) f
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Global minimum, 23, 46, 97, 146, 38
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Matrix diagonalization, (see also S
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primitive, 168-173 Slater-type, 134
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Reductive dechlorination, 422-424 R
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SYBYL, 58 Symmetry, 182-188, 209, 2
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