Essentials of Computational Chemistry

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REFERENCES 67 Cramer, C. J. 1994. ‘Problems and Questions in the Molecular Modeling of Biomolecules’, Biochem. Ed. 22, 140. Dinur, U. and Hagler, A. T. 1991. ‘New Approaches to Empirical Force Fields’, in Reviews in Computational Chemistry, Vol. 2, Lipkowitz, K. B. and Boyd, D. B., Eds., VCH; New York, 99. Dykstra, C. E. 1993. ‘Electrostatic Interaction Potentials in Molecular Force Fields’, Chem. Rev. 93, 2339. Eksterowicz, J. E. and Houk, K. N. 1993. ‘Transition-state Modeling with Empirical Force Fields’, Chem. Rev. 93, 2439. Jensen, F. 1999. Introduction to Computational Chemistry, Wiley: Chichester. Jensen, F. and Norrby, P.-O. 2003. ‘Transition States from Empirical Force Fields’, Theor. Chem. Acc., 109, 1. Kang, X. S., Shafer, R. H., and Kuntz, I. D. 2004. ‘Calculation of Ligand-nucleic Acid Binding Free Energies with the Generalized-Born Model in DOCK’, Biopolymers, 73, 192. Landis, C. R., Root, D. M., and Cleveland, T. 1995. ‘Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds’ in Reviews in Computational Chemistry, Vol. 6, Lipkowitz, K. B. and Boyd, D. B. Eds., VCH: New York, 73. Lazaridis, T. 2002. ‘Binding Affinity and Specificity from Computational Studies’, Curr. Org. Chem., 6, 1319. Leach, A. R. 2001. Molecular Modelling, 2nd Edn., Prentice Hall: London. Norrby, P.-O. 2001. ‘Recipe for an Organometallic Force Field’, in Computational Organometallic Chemistry, Cundari, T. Ed., Marcel Dekker: New York 7. Pettersson, I. and Liljefors, T. 1996. ‘Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields’, in Reviews in Computational Chemistry, Vol.9, Lipkowitz, K. B. and Boyd, D. B., Eds., VCH: New York, 167. Schlegel, H. B. 2003. ‘Exploring Potential Energy Surfaces for Chemical Reactions: An Overview of Some Practical Methods’, J. Comput. Chem. 124, 1514. References Allinger, N. L., Zhou, X., and Bergsma, J. 1994. J. Mol. Struct. (Theochem.), 312, 69. Barrows, S. E., Storer, J. W., Cramer, C. J., French, A. D., and Truhlar, D. G. 1998. J. Comput. Chem., 19, 1111. Bays, J. P. 1992. J. Chem. Edu., 69, 209. Beachy, M. D., Chasman, D., Murphy, R. B., Halgren, T. A., and Friesner, R. A. 1997. J. Am. Chem. Soc., 119, 5908. Beveridge, D. L. and McConnell, K. J. 2000. Curr. Opin. Struct. Biol., 10, 182. Cohen, N. and Benson, S. W. 1993. Chem. Rev., 93, 2419. Comba, P. and Remenyi, R. 2002. J. Comput. Chem., 23, 697. Dorigo, A. E. and Houk, K. N. 1987. J. Am. Chem. Soc., 109, 3698. Fogarasi, G. and Balázs, A. 1985. J. Mol. Struct. (Thochem), 133, 105. Greengard, L. and Rokhlin, V. 1987. J. Comput. Phys., 73, 325. Gundertofte, K., Liljefors, T., Norrby, P.-O., and Petterson, I. 1996. J. Comput. Chem., 17, 429. Gundertofte, K., Palm, J., Petterson, I., and Stamvick, A. 1991. J. Comput. Chem., 12, 200. Harvey, S. C., Wang, C., Teletchea, S., and Lavery, R. 2003. J. Comput. Chem., 24, 1. Hassinen, T. and Peräkylä, M. 2001. J. Comput. Chem., 22, 1229. Hay, B. P. 1993. Coord. Chem. Rev., 126, 177. Heramingsen, L., Madsen, D. E., Esbensen, S. L., Olsen, L., and Engelsen, S. B. 2004. Carboh. Res., 339, 937. Hill, T. L. 1946. J. Chem. Phys., 14, 465.
68 2 MOLECULAR MECHANICS Jacobson, M. P., Friesner, R. A., Xiang, Z. X., and Honig, B. 2002. J. Mol. Biol., 320, 597. Jalaie, M. and Lipkowitz, K. B. 2000. Rev. Comput. Chem., 14, 441. Jensen, F. 1999. Introduction to Computational Chemistry, Wiley: Chichester, Chapter 14 and references therein. Lazaridis, T. 2002. Curr. Org. Chem., 6, 1319. Leach, A. R. 1991. Rev. Comput. Chem., 2, 1. Li, L., Chen, R., and Weng, Z. P. 2003. Proteins, 53, 693. Meng, E. C., Shoichet, B. K., and Kuntz, I. D. 1992. J. Comput. Chem., 13, 505. Menger, F. 1990. J. Am. Chem. Soc., 112, 8071. Norrby, P.-O. and Brandt, P. 2001. Coord. Chem. Rev., 212, 79. Olsen, P. T. and Jensen, F. 2003. J. Chem. Phys., 118, 3523. Petrella, R. J., Andricioaei, I., Brooks, B., and Karplus, M. 2003. J. Comput. Chem., 24, 222. Price, D. J. and Brooks, C. L. 2002. J. Comput. Chem., 23, 1045. Radom, L., Hehre, W. J., and Pople, J. A. 1971. J. Am. Chem. Soc., 93, 289. Reichardt, C. 1990. Solvents and Solvent Effects in Organic Chemistry, VCH: New York, 12. Salichs, A., López, M., Orozco, M., and Luque, F. J. 2002. J. Comput.-Aid. Mol. Des., 16, 569. Schlick, T. 1992. Rev. Comput. Chem., 3, 1. Shi, S., Yan, L., Yang, Y., Fisher-Shaulsky, J., and Thacher, T. 2003. J. Comput. Chem., 24, 1059. Shoichet, B. K., McGovern, S. L., Wei, B. Q., and Irwin, J. J. 2002. Curr. Opin. Chem. Biol., 6, 439. Skeel, R. D., Tezcan, I., and Hardy, D. J. 2002. J. Comput. Chem., 23, 673. Stahl, M., Schopfer, U., Frenking, G., and Hoffmann, R. W. 1991. J. Am. Chem. Soc., 113, 4792. Westheimer, F. H. and Mayer, J. E. 1946. J. Chem. Phys., 14, 733. Wolfe, S., Rauk, A., Tel, L. M., and Csizmadia, I. G. 1971. J. Chem. Soc. B, 136. Woods, R. J. 1996. Rev. Comput. Chem., 9, 129. York, D. M., Darden, T. A., and Pedersen, L. G. 1993. J. Chem. Phys., 99, 8345. Zou, X. Q., Sun, Y. X., and Kuntz, I. D. 1999. J. Am. Chem. Soc., 121, 8033.
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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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Page 40 and 41: 2.2 POTENTIAL ENERGY FUNCTIONAL FOR
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118 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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