Essentials of Computational Chemistry

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REFERENCES 351 The use of computed spectra to bolster structural assignments has seen heavy use in matrix isolation experiments. This is a slightly atypical example, insofar as the species involved actually require some careful attention to non-dynamical correlation, but represents an excellent example of how theory can aid experiment in the identification of short-lived reactive species. Bibliography and Suggested Additional Reading Bachrach, S. 1994. ‘Population Analysis and Electron Densities from Quantum Mechanics’, in Reviews in Computational Chemistry, Vol. 5, Lipkowitz, K. B. and Boyd, D. B. Eds., VCH: New York, 171. Cramer, C. J. 1991. ‘Dependence of Isotropic Hyperfine Coupling in the Fluoromethyl Radical Series on Inversion Angle’ J. Org. Chem., 56, 5229. Hehre, W. J., Radom, L., Schleyer, P. v. R., and Pople, J. A. 1986. Ab Initio Molecular Orbital Theory, Wiley: New York. Helgaker, T., Jaszunski, M., and Ruud, K. 1999. ‘Ab Initio Methods for the Calculation of NMR Shielding and Indirect Spin–spin Coupling Constants’ Chem. Rev., 99, 293. Jensen, F. 1999. Introduction to Computational Chemistry, Wiley: Chichester. Koch, W. and Holthausen, M. C. 2000. A Chemist’s Guide to Density Functional Theory, Wiley-VCH: Weinheim. Kubinyi, H. 2003. ‘Comparative Molecular Field Analysis (CoMFA)’, in Handbook of Chemoinformatics. From Data to Knowledge, Vol. 4, Gasteiger, J., Ed., Wiley-VCH: Weinheim, 1555. Leach, A. R. 2001. Molecular Modelling, 2nd Edn., Prentice Hall: London. Levine, I. N. 1975. Molecular Spectroscopy, Wiley, New York. Malkin, V. G., Malkina, O. L., Eriksson, L. A., and Salahub, D. R. 1995. ‘The Calculation of NMR and ESR Spectroscopy Parameters Using Density Functional Theory’, in Modern Density Functional Theory; A Tool for Chemistry, Politzer, P. and Seminario, J., Eds., Elsevier: Amsterdam, 273. Thompson, J. D., Cramer, C. J., and Truhlar, D. G. 2003. ‘Parameterization of Charge Model 3 for AM1, PM3, BLYP, and B3LYP’, J. Comput. Chem., 24, 1291. Wiberg, K. B. and Rablen, P. R. 1993. ‘Comparison of Atomic Charges Derived via Different Procedures’ J. Comput. Chem., 14, 1504. Wilson, E. B., Jr., Decius, J. C., and Cross, P. C. 1955. Molecular Vibrations, Dover: New York. References Adamo, C. and Barone, V. 1998. J. Chem. Phys., 108, 664. Adamo, C., Cossi, M., and Barone, V. 1999. J. Mol. Struct. (Theochem), 493, 145. Arenas, J. F., Centeno, S. P., Marcos, J. I., Otero, J. C., Soto, J. 2000. J. Chem. Phys., 113, 8472. Bader, R. W. F. 1990. Atoms in Molecules – A Quantum Theory. Oxford University Press: Oxford. Bader, R. W. F. 1991. Chem. Rev., 91, 893. Baker, J., Jarzecki, A. A., and Pulay, P. 1998. J. Phys. Chem. A, 102, 142. Barone, V. 1995. In: Recent Advances in Density Functional Methods, Part 1 , Chong, D. P., Ed., World Scientific: Singapore, 278. Barone, V., Grand, A., Minichino, C., and Subra, R. 1993. J. Chem. Phys., 99, 6787. Barrows, S. E., Cramer, C. J., Truhlar, D. G., Weber, E. J., and Elovitz, M. S. 1996. Environ. Sci. Technol., 30, 3028. Basma, M., Sundara, S., Çalgan, D., Vernali, T., and Woods, R. J. 2001. J. Comput. Chem., 22, 1125. Bauschlicher, C. W. and Partridge, H. 1995. J. Chem. Phys., 103, 1788.
352 9 CHARGE DISTRIBUTION AND SPECTROSCOPIC PROPERTIES Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. 1993. J. Phys. Chem., 97, 10269. Besler, B. H., Merz, K. M., and Kollman, P. A. 1990. J. Comput. Chem., 11, 431. Biegler-Konig, F. and Schonbohm, J. 2002. J. Comput. Chem., 23, 1489. Braden, D. A. and Tyler, D. R. 1998. Organometallics, 17, 4060. Breneman, C. M. and Wiberg, K. B. 1990. J. Comput. Chem., 11, 361. Bytheway, I. and Wong, M. W. 1998. Chem. Phys. Lett., 282, 219. Cheeseman, J. R., Trucks, G. W., Keith, T. A., and Frisch, M. J. 1996. J. Chem. Phys., 104, 5497. Chipman, D. M. 1983. J. Chem. Phys., 78, 3112. Chirlian, L. E. and Francl, M. M. 1987. J. Comput. Chem., 8, 894. Cho, K.-H., Kang, Y. K., No, K. T., and Scheraga, H. A. 2001. J. Phys. Chem. B, 105, 3624. Cioslowski, J. 1989. J. Am. Chem. Soc., 111, 8333. Cornell, W. C., Cieplak, P., Bayly, C. I., and Kollman, P. A. 1993. J. Am. Chem. Soc., 115, 9620. Cramer, C. J. 1991. J. Org. Chem., 56, 5229. Cramer, C. J. and Lim, M. H. 1994. J. Phys. Chem., 98, 5024. Cusachs, L. C. and Politzer, P. 1968. Chem. Phys. Lett., 1, 529. Duffy, E. M. and Jorgensen, W. L. 2000. J. Am. Chem. Soc., 122, 2878. Eriksson, L. A., Malkina, O. L., Malkin, V. G., and Salahub, D. R. 1994. J. Chem. Phys., 100, 5066. Exner, T. E. and Mezey, P. G. 2002. J. Phys. Chem. A, 106, 11791. Francl, M. M. and Chirlian, L. E. 2000. In: Reviews in Computational Chemistry, Vol. 14, Lipkowitz, K. B. and Boyd, D. B., Eds., Wiley: New York, 1. Gasteiger, J. and Marsilli, M. 1980. Tetrahedron, 36, 3219. Giesen, D. J. and Zumbulyadis, N. 2002. Phys. Chem. Chem. Phys., 4, 5498. Gross, K. C., Seybold, P. G., and Hadad, C. M. 2002. Int. J. Quant. Chem., 90, 445. Grunenberg, J. and Herges, R. 1997. J. Comput. Chem., 18, 2050. Guerra, M. 2000. Theor. Chem. Acc., 104, 455. Guerra, C. F., Handegraaf, J. W., Baerends, E. J., and Bickelhaupt, F. M. 2004. J. Comput. Chem., 25, 189. Halls, M. D., Velkovski, J., and Schlegel, H. B. 2001. Theor. Chem. Acc., 105, 413. Jakalian, A., Jack, D. B., and Bayly, C. I. 2002. J. Comput. Chem., 23, 1623. Jaramillo, J. and Scuseria, G. E. 1999. Chem. Phys. Lett., 312, 269. Johnson, B. G., Gill, P. M. W., and Pople, J. A. 1993. J. Chem. Phys., 98, 5612. Kalinowski, J. A., Lesyng, B., Thompson, J. D., Cramer, C. J., and Truhlar, D. G. 2004. J. Phys. Chem. A, 108, 2545. Khandogin, J., Hu, A. G., and York, D. M. 2000. J. Comput. Chem., 21, 1562. Laidig, K. E. 1993. J. Phys. Chem., 97, 12760. Li, J., Xing, J., Cramer, C. J., and Truhlar, D. G. 1999. J. Chem. Phys., 111, 885. Li, J., Zhu, T., Cramer, C. J., and Truhlar, D. G. 1998. J. Phys. Chem. A, 102, 1820. Lim, M. H., Worthington, S. E., Dulles, F. J., and Cramer, C. J. 1996. In: Chemical Applications of Density-functional Theory, ACS Symposium Series, Vol. 629, Laird, B. B., Ross, R. B., and Ziegler, T., Eds., American Chemical Society: Washington, DC, 402. London, F. 1937. J. Phys. Radium, 8, 397. Löwdin, P.-O. 1970. Adv. Quantum Chem., 5, 185. Mayer, I. 1983. Chem. Phys. Lett., 97, 270. Mulliken, R. S. 1955. J. Chem. Phys., 23, 1833, 1841, 2338, 2343. Nguyen, M. T., Creve, S., and Vanquickenborne, L. G. 1997. J. Phys. Chem. A, 101, 3174. No, K. T., Grant, J. A., and Scheraga, H. A. 1990a. J. Phys. Chem., 94, 4732. No, K. T., Grant, J. A., Jhon, M. S., and Scheraga, H. A. 1990b. J. Phys. Chem., 94, 4740. Patchkovskii, S. and Thiel, W. 1999. J. Comput. Chem., 20, 1220. Pople, J. A., Scott, A. P., Wong, M. W., and Radom, L. 1993. Isr. J. Chem., 33, 345.
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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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Page 324 and 325: 9 Charge Distribution and Spectrosc
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402 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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