Essentials of Computational Chemistry

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424 11 IMPLICIT MODELS FOR CONDENSED PHASES Cl Cl Cl Cl Cl Cl Cl Cl + e − Cl Cl Cl 0.0 no barrier Cl Cl Cl Cl + –10.8 Cl Cl Cl or no barrier Cl Cl Cl Cl Cl − Cl – ∆G ‡ = 0.4 Cl + –8.5 Cl Cl Cl Cl + e – Cl Cl Cl Cl Cl Cl Cl Cl Cl Cl + –4.4 Cl Cl HO O Cl − + –3.8 Cl Cl Figure 11.13 Relative aqueous free energies (eV) for various species on different reductive dechlorination paths of hexachloroethane as computed by Patterson and co-workers The relative energies are properly balanced, although for simplicity spectator species are not shown in every case. What is involved in achieving this balance for energy? What about free energy? be kinetically competitive. Such a transfer would generate the acyl chloride equivalent of Cl3CCO2H, which would hydrolyze in short order to the carboxylic acid. This paper provides an example of how accurate continuum models can open the door to the modeling of condensed-phase processes where solvation free energies have a very large influence on reaction energetics. It additionally offers a case study of how to first choose a model on the basis of experimental/theoretical comparisons over a relevant data set, and then apply that model with a greater expectation for its utility. The generality of this approach to other (equilibrium) electrochemical reactions seems promising. Bibliography and Suggested Additional Reading Bashford, D. and Case, D. A. 2000. ‘Generalized Born Models of Macromolecular Solvation Effects’ Annu. Rev. Phys. Chem., 51, 129. Cramer, C. J. and Truhlar, D. G. 1999. ‘Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics’, Chem. Rev., 99, 2160. [O] X Cl Cl −
REFERENCES 425 Cramer, C. J. and Truhlar, D. G., Eds., 1994. Structure and Reactivity in Aqueous Solution, ACS Symposium Series 568, American Chemical Society: Washington, DC. Li, J. Cramer, and Truhlar, D. G. 1999. ‘Application of a Universal Solvation Model to Nucleic Acid Bases. Comparison of Semiempirical Molecular Orbital Theory, Ab Initio, Hartree–Fock Theory, and Density Functional Theory’, Biophys. Chem., 78, 147. Llano, J. and Eriksson, L. A. 2002. ‘First Principles Electrochemistry: Electrons and Protons Reacting as Independent Ions’, J. Chem. Phys., 117, 10193. Orozco, M. and Luque, F. J. 2000. ‘Theoretical Methods for the Description of the Solvent Effect on Biomolecular Systems’, Chem. Rev. 100, 4187. Reichardt, C. 1990. Solvents and Solvent Effects in Organic Chemistry, VCH:NewYork. Roux, B. and Simonson, T., Eds. 1999. Biophys. Chem. 78(1/2), [special issue devoted to implicit solvent models]. Schutz, C. N. and Warshel, A. 2001. ‘What Are the Dielectric “Constants” of Proteins and How to Validate Electrostatic Models?’, Proteins, 44, 400. Tapia, O. and Bertrán, J. 1996. Solvent Effects on Chemical Reactivity, Kluwer: Dordrecht. Winget, P., Cramer, C. J., and Truhlar, D. G. 2004. “Computation of Equilibrium Oxidation and Reduction Potentials for Reversible and Dissociative Electron-Transfer Reactions in Solution”, Theor. Chem. Acc., 112, 217. References Ángyán, J. G. 1992. J. Math. Chem., 10, 93. Baik, M.-H. and Friesner, R. A. 2002. J. Phys. Chem. A, 106, 7407. Banavali, N. K. and Roux, B. 2002. J. Phys. Chem. B, 106, 11026. Banavali, N. K., Im, W., and Roux, B. 2002. J. Chem. Phys., 117, 7381. Barone, V. and Cossi, M. 1998. J. Phys. Chem. A, 102, 1995. Beak, P. 1977. Acc. Chem. Res., 10, 186. Best, S. A., Merz, K. M., and Reynolds, C. H. 1997. J. Phys. Chem. B, 101, 10479. Bordner, A. J., Cavasotto, C. N., and Abagyan, R. A. 2002. J. Phys. Chem. B, 106, 11009. 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. Chandresekhar, J., Smith, S. F., and Jorgensen, W. L. 1985. J. Am. Chem. Soc., 107, 154. Chen, I.-J. and MacKerell, A. D., Jr. 2000. Theor. Chem. Acc., 103, 483. Chen, Y., Noodleman, L., Case, D. A., and Bashford, D. 1994. J. Phys. Chem., 98, 11059. Cheng, A., Best, S. A., Merz, K. M., and Reynolds, C. H. 2000. J. Mol. Graph. Model., 18, 273. Cheng, X. L., Hornak, V., and Simmerling, C. 2004. J. Phys. Chem. B, 108, 426. Chipman, D. M. 2002. Theor. Chem. Acc., 107, 80. Chowdhury, S., Lee, M. C., Xiong, G., Duan, Y. 2003. J. Mol. Biol., 327, 711. Christiansen, O. and Mikkelsen, K. V. 1999. J. Chem. Phys., 110, 1365. Claverie, P. 1978. Perspect. Quantum Chem. Biochem., 2, 69. Colominas, C., Luque, F. J., Teixidó, J., and Orozco, M. 1999. Chem. Phys., 240, 253. Cornell, W., Abseher, R., Nilges, M., and Case, D. A. 2001. J. Mol. Graph. Model., 19, 136. Cossi, M. 2004. Chem. Phys. Lett., 384, 179. Cossi, M. and Barone, V. 2000. J. Phys. Chem. A, 104, 10614. Cossi, M., Barone, V., Cammi, R., and Tomasi, J. 1996. Chem. Phys. Lett., 255, 327. Cossi, M., Scalmani, G., Rega, N., and Barone, V. 2002. J. Chem. Phys., 117, 43. Cullis, P. M.. and Wolfenden, R. 1981. Biochemistry, 20, 3024.
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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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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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