Essentials of Computational Chemistry

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REFERENCES 485 Gao, J., Amara, P., Alhambra, C., and Field, M. J. 1998. ‘A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations’, J. Phys. Chem. A, 102, 4714. Gao, J. and Thompson, M. A., Eds., 1998. Methods and Applications of Hybrid Quantum Mechanical and Molecular Mechanical Methods, ACS Symposium Series, Vol. 712, American Chemical Society: Washington, DC. Orozco, M. and Luque, F. J. 2000. ‘Theoretical Methods for the Description of the Solvent Effect on Biomolecular Systems’, Chem. Rev., 100, 4187. Reuter, N., Dejaegere, A., Maigret, B., and Karplus, M. 2000. ‘Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches’, J. Phys. Chem. A, 104, 1720. Ryde, U. 2003. ‘Combined Quantum and Molecular Mechanics Calculations on Metalloproteins’ Curr. Opin. Chem. Biol., 7, 136. Théry, V., Rinaldi, D., Rivail, J.-L., Maigret, B., and Ferenczy, G. G. 1994. ‘Quantum Mechanical Computations on Very Large Molecular Systems: The Local Self-consistent Field Method’, J. Comput. Chem., 15, 269. Warshel, A. 1991. Computer Modeling of Chemical Reactions in Enzymes and in Solutions, Wiley: New York. Zhang, Y. K., Lee, T. S., and Yang, W. T. 1999. ‘A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods’, J. Chem. Phys., 110, 46. References Abraham, R. J. and Siverns, T. M. 1972. Tetrahedron, 28, 3015. Alhambra, C., Gao, J., Corchado, J. C., Villà, J., and Truhlar, D. G. 1999. J. Am. Chem. Soc., 121, 2253. Alhambra, C., Corchado, J., Sánchez, M. L., Garcia-Viloca, M., Gao, J., and Truhlar, D. G. 2001. J. Am. Chem. Soc., 105, 11326. Amara, P. and Field, M. 2003. Theor. Chem. Acc., 109, 43. Amara, P., Field, M. J., Alhambra, C., and Gao, J. 2000. Theor. Chem. Acc., 104, 336. ˚Aqvist, J. and Warshel, A., 1992. J. Mol. Biol., 224, 7. Bakowies, D. and Thiel, W. 1996. J. Phys. Chem., 100, 10580. Bandyopadhyay, P., Gordon, M. S., Mennucci, B., and Tomasi, J. 2002. J. Chem. Phys., 116, 5023. Banks, J. L., Kaminski, G. A., Zhou, R. H., Mainz, D. T., Berne, B. J., and Friesner, R. A. 1999. J. Chem. Phys., 110, 741. Chambers, C. C., Giesen, D. J., Hawkins, G. D., Vaes, W. H. J., Cramer, C. J., and Truhlar, D. G. 1999. In: Rational Drug Design, Truhlar, D. G., Howe, W. J., Hopfinger, A. J., Blaney, J. M., and Dammkoehler, R. A., Eds., Springer: New York, 51. Chandrasekhar, J., Shariffskul, S., Jorgensen, W. L. 2002. J. Phys. Chem. B, 106, 8078. Chang, Y.-T., Minichino, C., and Miller, W. H. 1992. J. Chem. Phys., 96, 4341. Corchado, J. C. and Truhlar, D. G. 1998. J. Phys. Chem. A, 102, 1895. Cramer, C. J., and Pak, Y. 2001. Theor. Chem. Acc., 105, 477. Cramer, C. J. and Truhlar, D. G. 1992. Chem. Phys. Lett., 198, 74. Cramer, C. J. and Truhlar, D. G. 1993. Chem. Phys. Lett., 202, 567 (erratum). Cui, Q. 2002. J. Chem. Phys., 117, 4720. Deng, L., Woo, T. K., Cavallo, L., Margl, P. M., and Ziegler, T. 1997. J. Am. Chem. Soc., 119, 6177. Depaepe, J.-M. and Ryckaert, J.-P. 1995. Chem. Phys. Lett., 245, 653. Eurenius, K. P., Chatfield, D. C., Brooks, B. R., and Hodoscek, M. 1996. Int. J. Quantum Chem., 60, 1189. Ferenczy, G. G., Rivail, J.-L., Surján,P.R.,andNáray-Szabó, G. 1992. J. Comput. Chem., 13, 830.
486 13 HYBRID QUANTAL/CLASSICAL MODELS Florián, J. and Warshel, A. 1997. J. Phys. Chem. B, 101, 5583. Freedman, H. and Truong, T. N. 2003. Chem. Phys. Lett., 381, 362. Freindorf, M. and Gao, J. 1996. J. Comput. Chem., 17, 386. French, A. D., Kelterer, A.-M., Cramer, C. J., Johnson, G. P., and Dowd, M. K. 2000. Carbohydr. Res., 326, 305. Gao, J. 1994. J. Am. Chem. Soc., 116, 1563. Gao, J. and Xia, X. 1992. Science, 258, 631. Gao, J., Amara, P., Alhambra, C., and Field, M. J. 1998. J. Phys. Chem. A, 102, 4714. Garcia-Viloca, M. and Gao, J. 2004. Theor. Chem. Acc., 111, 280. Humbel, S., Sieber, S., and Morokuma, K. 1996. J. Chem. Phys., 105, 1959. Kaminski, G. and Jorgensen, W. L. 1996. J. Phys. Chem., 100, 18010. Kaminski, G. and Jorgensen, W. L. 1998. J. Phys. Chem. B, 102, 1787. Kerdcharoen, T. and Morokuma, K. 2002. Chem. Phys. Lett., 355, 257. Kim, Y., Corchado, J. C., Villà, J., Xing, J., and Truhlar, D. G. 2000. J. Chem. Phys., 112, 2718. Kongsted, J., Osted, A., Mikkelsen, K. V., Christiansen, O. 2003. J. Phys. Chem. A, 107, 2578. Lee, P. H. and Maggiora, G. M. 1993. J. Phys. Chem., 97, 10175. Loeffler, H. H., Yague, J. I., and Rode, B. M. 2002. J. Phys. Chem. A, 1106, 9529. Luzhkov, V. and Warshel, A. 1992. J. Comput. Chem., 13, 199. Martin, M. E., Aguilar, M. A., Chalmet, S., Ruiz-López, M. F. 2002. Chem. Phys., 284, 607. Maseras, F. and Morokuma, K. 1995. J. Comput. Chem., 16, 1170. Matsubara, T., Maseras, F., Koga, N., and Morokuma, K. 1996. J. Phys. Chem., 100, 2573. Mo, Y. and Gao, J. 2000. J. Phys. Chem. A, 104, 3012. Papazyan, A. and Warshel, A. 1997. J. Phys. Chem. B, 101, 11254. Philipp, D. M. and Friesner, R. A. 1999. J. Comput. Chem., 20, 1468. Pratt, L. R. and Chandler, D. C. 1977. J. Chem. Phys., 67, 3683. Pu, J., Gao, J., and Truhlar, D. G. 2004. J. Phys. Chem. A, 108, 632. Rickard, G. A., Karadakov, P. B., Webb, G. A., and Morokuma, K. 2003. J. Phys. Chem. A, 107, 292. Shao, L., Yu, H. A., and Gao, J. L. 1998. J. Phys. Chem. A, 102, 10366. Sherer, E. C. and Cramer, C. J. 2001. J. Comput. Chem., 22, 1167. Svensson, M., Humbel, S., and Morokuma, K. 1996. J. Chem. Phys., 105, 3654. Svensson, M., Humbel, S., Froese, R. D. J., Matsubara, T., Sieber, S., and Morokuma, K. 1996. J. Phys. Chem., 100, 19357. Swart, M. 2003. Int. J. Quant. Chem., 91, 177. Ten-no, S., Hirata, F., and Kato, S. 1993. Chem. Phys. Lett., 214, 391. Udier-Blagovic, M., Morales de Tirado, P., Pearlman, S. A., and Jorgensen, W. L. 2004. J. Comput. Chem., 25, 1322. Vreven, T., Mennucci, B., da Silva, C. O., Morokuma, K., and Tomasi, J. 2001. J. Chem. Phys., 115, 62. Vreven, T., Morokuma, K., Farkas, Ö., Schlegel, H. B., Frisch, M. J. 2003. J. Comput. Chem., 24, 760. Warshel, A. and Levitt, M. J. 1976. J. Mol. Biol., 103, 227. Warshel, A. and Weiss, R. M. 1980. J. Am. Chem. Soc., 102, 6218. Wiberg, K. B., Keith, T. A., Frisch, M. J., and Murcko, M. 1995. J. Phys. Chem., 99, 9072. Zhang, Y., Lee, T.-S, and Yang, W. 1999. J. Chem. Phys., 110, 46.
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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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12.2 COMPUTING FREE-ENERGY DIFFEREN
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Page 534 and 535: REFERENCES 517 Kim, K., Shavitt, I,
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536 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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