Variational transition state theory with multidimensional tunneling

Reviews in Computational Chemistry

Volumn 23, Issue , 2007, Pages 125-232

  Fernandez Ramos, Antonio ^a   Ellingson, Benjamin A ^b   Garrett, Bruce C ^c   Truhlar, Donald G ^b  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^b UNIVERSITY OF MINNESOTA   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 67149143279     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: 10.1002/9780470116449.ch3     Document Type: Article

References (198)

1. D. G. Truhlar, A. D. Isaacson, and B. C. Garrett, in Theory of Chemical Reaction Dynamics, Vol. 3, M. Baer, ed., CRC Press, Boca Raton, FL, 1985, pp. 65-137. Generalized Transition State Theory.
2. A. D. Isaacson, D. G. Truhlar, S. N. Rai, R. Steckler, G. C. Hancock, B. C. Garrett, and M. J. Redmon, Comput. Phys. Commun., 47, 91 (1987). POLYRATE: A General Computer Program for Variational Transition State Theory and Semiclassical Tunneling Calculations of Chemical Reaction Rates.
3. D.-h. Lu, T. N. Truong, V. S. Melissas, G. C. Lynch, Y.-P. Liu, B. C. Garrett, R. Steckler, A. D. Isaacson, S.N. Rai, G. C. Hancock, J. G. Lauderdale, T. Joseph, and D. G. Truhlar, Comput. Phys. Commun., 71, 235 (1992). POLYRATE 4: A New Version of a Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics.
4. W.-P. Hu, R. Steckler, G. C. Lynch, Y.-P. Liu, B. C. Garrett, A. D. Isaacson, D.-h. Lu, V. S. Melissas, I. Rossi, J. J. P. Stewart, and D. G. Truhlar, QCPE Bull., 15,32 (1995). POLYRATE -version 6.5 and MORATE -version 6.5/P6.5-M5.05. Two Computer Programs for the Calculation of Chemical Reaction Rates.
5. R. Steckler, W.-P. Hu, Y.-P. Liu, G. C. Lynch, B. C. Garrett, A. D. Isaacson, V. S. Melissas, D.-h. Lu, T. N. Truong, S. N. Rai, G. C. Hancock, J. G. Lauderdale, T. Joseph, and D. G. Truhlar, Comput. Phys. Commun., 88, 341 (1995). POLYRATE 6.5: A New Version of a Computer Program for the Calculation of Reaction Rates for Polyatomics.
6. J. C. Corchado, Y.-Y. Chuang, P. L. Fast, W.-P. Hu, Y.-P. Liu, G. C. Lynch, K. A. Nguyen, C. F. Jackels, A. Fernandez-Ramos, B. A. Ellingson, B. J. Lynch, V. S. Melissas, J. Villà, I. Rossi, E. L. Coitiño, J. Pu, T. V. Albu, R. Steckler, B. C. Garrett, A. D. Isaacson, and D. G. Truhlar, POLYRATE - version 9.4.3. University of Minnesota, Minneapolis, Minnesota, 2006. Available: http://comp.chem.umn.edu/polyrate.
7. S. C. Tucker and D. G. Truhlar, in New Theoretical Concepts for Understanding Organic Reactions, J. Bertrán and I. G. Csizmadia, Eds., Kluwer, Dordrecht, The Netherlands, 1989, pp. 291-346. [NATO ASI Ser. C 267, 291-346 (1989)]. Dynamical Formulation of Transition State Theory: Variational Transition States and Semiclassical Tunneling.
8. H. Eyring, J. Chem. Phys., 3, 107 (1935). The Activated Complex in Chemical Reactions.
9. M. G. Evans and M. Polanyi, Trans. Faraday Soc., 31, 875 (1935). Some Applications of the Transition State Method to the Calculation of Reaction Velocities, Especially in Solution.
10. W. F. K. Wynne-Jones and H. Eyring, J. Chem. Phys., 3, 492 (1935). The Absolute Rate of Reactions in Condensed Phases.
11. R. H. Fowler, Trans. Faraday Soc., 34, 124 (1938). General Discussion.
12. R. K. Boyd, Chem. Rev., 77, 93 (1977). Macroscopic and Microscopic Restrictions on Chemical Kinetics.
13. C. Lim and D. G. Truhlar, J. Phys. Chem., 89, 5 (1985). Internal-State Nonequilibrium Effects for a Fast, Second-Order Reaction.
14. C. Lim and D. G. Truhlar, J. Phys. Chem., 90, 2616 (1986). The Effect of Vibrational- Rotational Disequilibrium on the Rate Constant for an Atom-Transfer Reaction.
15. H. Teitelbaum, J. Phys. Chem., 94, 3328 (1990). Nonequilibrium Kinetics of Bimolecular Exchange Reactions. 3. Application to Some Combustion Reactions.
16. C. Bowes, N. Mina, and H. Teitelbaum, J. Chem. Soc., Faraday Trans., 87, 229 (1991). Non-Equilibrium Kinetics of Bimolecular Exchange Reactions. 2. Improved Formalism and Applications to Hydrogen Atom + Hydrogen Molecule → Hydrogen Molecule + Hydrogen drogen Atom and its Isotopic Variants.
17. H. Teitelbaum, Chem. Phys., 173, 91 (1993). Non-Equlibrium Kinetics of Bimolecular Reactions. IV. Experimental Prediction of the Breakdown of the Kinetic Mass-Action Law.
18. H. Teitelbaum, Chem. Phys. Lett., 202, 242 (1993). Non-Equilibrium Kinetics of Bimolecular Reactions. Effect of Anharmonicity on the Rate Law.
19. P. Pechukas, Annu. Rev. Phys. Chem., 32, 159 (1981). Transition State Theory.
20. B. C. Garrett and D. G. Truhlar, J. Phys. Chem., 83, 1052 (1979); Erratum: 87, 4553 (1983). Generalized Transition State Theory. Classical Mechanical Theory and Applications to Collinear Reactions of Hydrogen Molecules.
21. E. Wigner, J. Chem. Phys., 5, 720 (1937). Calculation of the Rate of Elementary Association Reactions.
22. J. Horiuti, Bull. Chem. Soc. Jpn., 13, 210 (1938). On the Statistical Mechanical Treatment of the Absolute Rates of Chemical Reactions.
23. J. C. Keck, J. Chem. Phys., 32, 1035 (1960). Variational Theory of Chemical Reaction Rates Applied to Three-Body Recombinations.
24. J. C. Keck, Adv. Chem. Phys., 13, 85 (1967). Variational Theory of Reaction Rates.
25. 2 ↔ HF+H.
26. W. H. Miller, J. Chem. Phys., 61, 1823 (1974). Quantum Mechanical Transition State Theory and a New Semiclassical Model for Reaction Rate Constants.
27. B. C. Garrett and D. G. Truhlar, J. Chem. Phys., 70, 1593 (1979). Criterion of Minimum State Density in the Transition State Theory of Bimolecular Reactions.
28. E. B. Wilson, Jr., J. C. Decius, and P. C. Cross, Molecular Vibrations, Dover Publications, Inc., New York, 1955.
29. R. A. Marcus, Discuss. Faraday Soc., 44, 7 (1967). Analytical Mechanics and Almost Vibrationally Adiabatic Chemical Reactions.
30. B. C. Garrett and D. G. Truhlar, J. Phys. Chem., 83, 1079 (1979); Erratum: 87, 4553 (1983). Generalized Transition State Theory. Quantum Effects for Collinear Reactions of Hydrogen Molecules and Isotopically Substituted Hydrogen Molecules.
31. K. Fukui, in The World of Quantum Chemistry, R. Daudel and B. Pullman, Eds., D. Reidel, Dordrecht, The Netherlands, 1974, pp. 113. The Charge and Spin Transfers in Chemical Reaction Paths.
32. G. K. Schenter, B. C. Garrett, and D. G. Truhlar, J. Chem. Phys., 119, 5828 (2003). Generalized Transition State Theory in Terms of the Potential of Mean Force.
33. G. K. Schenter, B. C. Garrett, and D. G. Truhlar, J. Phys. Chem. B, 105, 9672 (2001). The Role of Collective Solvent Coordinates and Nonequilibrium Solvation in Charge-Transfer Reactions.
34. P. L. Fast and D. G. Truhlar, J. Chem. Phys., 109, 3721 (1998). Variational Reaction Path Algorithm.
35. B. C. Garrett and D. G. Truhlar, J. Am. Chem. 50c, 101, 4534 (1979). Generalized Transition State Theory. Bond Energy-Bond Order Method for Canonical Variational Calculations with Application to Hydrogen Atom Transfer Reactions.
36. 2 Systems.
37. J. C. Keck, Adv. Chem. Phys., 13, 85 (1967). Variational Theory of Reaction Rates.
38. E. Wigner, Z. Physik Chem. B, B19, 203 (1932). On the Penetration of Potential Energy Barriers in Chemical Reactions.
39. M. A. Eliason and J. O. Hirschfelder, J. Chem. Phys., 30, 1426 (1956). General Collision Theory Treatment for the Rate of Bimolecular, Gas Phase Reactions.
40. C. Steel and K. J. Laidler, J. Chem. Phys., 34, 1827 (1961). High Frequency Factors in Unimolecular Reactions.
41. B. C. Garrett, D. G. Truhlar, R. S. Grev, and A. W. Magnuson, J. Phys. Chem., 84, 1730 (1980). Improved Treatment of Threshold Contributions in Variational Transition-State Theory.
42. J. O. Hirschfelder and E. Wigner, J. Chem. Phys., 7, 616 (1939). Some Quantum-Mechanical Considerations in the Theory of Reactions Involving an Activation Energy.
43. W. H. Miller, J. Chem. Phys., 65, 2216 (1976). Unified Statistical Model for "Complex" and "Direct" Reaction Mechanisms.
44. B. C. Garrett and D. G. Truhlar, J. Chem. Phys., 76, 1853 (1982). Canonical Unified Statistical Model. Classical Mechanical Theory and Applications to Collinear Reactions.
45. D. G. Truhlar and B. C. Garrett, J. Phys. Chem. A, 107, 4006 (2003). Reduced Mass in the One-Dimensional Treatment of Tunneling.
46. G. Gamow, Z. Phys., 51, 204 (1928). Quantum Theory of the Atomic Nucleus.
47. E. C. Kemble, The Fundamental Principles of Quantum Mechanics With Elementary Applications, Dover Publications, New York, 1937.
48. R. P. Bell, Proc. Royal Soc. A, 139, 466 (1933). The Application of Quantum Mechanics to Chemical Kinetics.
49. R. P. Bell, Trans. Faraday Soc., 55, 1 (1959). The Tunnel Effect Correction for Parabolic Potential Barriers.
50. R. T. Skodje and D. G. Truhlar, J. Phys. Chem., 85, 624 (1981). Parabolic Tunneling Calculations.
51. C. Eckart, Phys. Rev., 35, 1303 (1930). The Penetration of a Potential Barrier by Electrons.
52. R. A. Marcus, J. Chem. Phys., 49, 2617 (1968). Analytical Mechanics of Chemical Reactions. IV. Classical Mechanics of Reactions in Two Dimensions.
53. 3 Potential Surface, Using Transition-State Theory.
54. D. G. Truhlar and A. Kuppermann, J. Am. Chem. Soc., 93, 1840 (1971). Exact Tunneling Calculations.
55. K. Fukui, S. Kato, and H. Fujimoto, J. Am. Chem. Soc., 97, 1 (1975). Constituent Analysis of the Potential Gradient Along a Reaction Coordinate. Method and an Application to Methane + Tritium Reaction.
56. M. C. Flanigan, A. Komornicki, and J. W. McIver, Jr. In Semiempirical Methods of Electronic Structure Calculation, Part B: Applications, G. A. Segal, Ed., Plenum, New York, 1977, pp. 1-47.
57. C. Peng, P. Y. Ayala, H. B. Schlegel, and M. J. Frisch, J. Comput. Chem., 17, 49 (1996). Using Redundant Internal Coordinates to Optimize Equilibrium Geometries and Transition States.
58. P. Y. Ayala and H. B. Schlegel, J. Chem. Phys., 107, 375 (1997). A Combined Method for Determining Reaction Paths, Minima, and Transition State Geometries.
59. V. S. Melissas, D. G. Truhlar, and B. C. Garrett, J. Chem. Phys., 96, 5758 (1992). Optimized Calculations of Reaction Paths and Reaction-Path Functions for Chemical Reactions.
60. M. W. Schmidt, M. S. Gordon, and M. Dupuis, J. Am. Chem. Soc., 107, 2585 (1985). The Intrinsic Reaction Coordinate and the Rotational Barrier in Silaethylene.
61. B. C. Garrett, M. J. Redmon, R. Steckler, D. G. Truhlar, K. K. Baldridge, D. Bartol, M. W. Schmidt, and M. S. Gordon, J. Phys. Chem., 92, 1476 (1988). Algorithms and Accuracy Requirements for Computing Reaction Paths by the Method of Steepest Descent.
62. K. K. Baldridge, M. S. Gordon, R. Steckler, and D. G. Truhlar, J. Phys. Chem., 93, 5107 (1989). Ab Initio Reaction Paths and Direct Dynamics Calculations.
63. M. Page and J. W. McIver, Jr., J. Chem. Phys., 88, 922 (1988). On Evaluating the Reaction Path Hamiltonian.
64. J. Villà and D. G. Truhlar, Theor. Chem. Acc., 97, 317 (1997). Variational Transition State Theory Without the Minimum-Energy Path.
65. W. H. Miller, N. C. Handy, and J. E. Adams, J. Chem. Phys., 72, 99 (1980). Reaction Path Hamiltonian for Polyatomic Molecules.
66. G. A. Natanson, Mol. Phys., 46, 481 (1982). Internal Motion of a Nonrigid Molecule and its Relation to the Reaction Path.
67. G. A. Natanson, B. C. Garrett, T. N. Truong, T. Joseph, and D. G. Truhlar, J. Chem. Phys., 94, 7875 (1991). The Definition of Reaction Coordinates for Reaction-Path Dynamics.
68. C. F. Jackels, Z. Gu, and D. G. Truhlar, J. Chem. Phys., 102, 3188 (1995). Reaction-Path Potential and Vibrational Frequencies in Terms of Curvilinear Internal Coordinates.
69. G. Herzberg, Molecular Spectra and Molecular Structure. II. Infrared and Raman Spectra of Polyatomic Molecules, D. Van Nostrand, Princeton, New Jersey, 1945.
70. 2.
71. P. Pulay and G. Fogarasi, J. Chem. Phys., 96, 2856 (1992). Geometry Optimization in Redundant Internal Coordinates.
72. Y.-Y. Chuang and D. G. Truhlar, J. Phys. Chem. A, 102, 242 (1998). Reaction-Path Dynamics in Redundant Internal Coordinates.
73. D. F. McIntosh and K. H. Michelian, Can. J. Spectrosc., 24, 1 (1979). The Wilson GF Matrix Method of Vibrational Analysis. Part I: General Theory.
74. D. F. McIntosh and K. H. Michelian, Can. J. Spectrosc., 24, 35 (1979). The Wilson GF Matrix Method of Vibrational Analysis. Part II. Theory and Worked Examples of the Construction of the B Matrix.
75. D. F. McIntosh and K. H. Michelian, Can. J. Spectrosc., 24, 65 (1979). The Wilson GF Matrix Method of Vibrational Analysis. Part III: Worked Examples of The Vibrational Analysis of Carbon Dioxide and Water.
76. S. J. Klippenstein, J. Chem. Phys., 94, 6469 (1991). A Bond Length Reaction Coordinate for Unimolecular Reactions. II. Microcanonical and Canonical Implementations with Application to the Dissociation of NCNO.
77. S. J. Klippenstein, J. Chem. Phys., 96, 367 (1992); Erratum: 96, 5558 (1992). Variational Optimizations in the Rice-Ramsperger-Kassel-Marcus Theory Calculations For Unimolecular Dissociations With No Reverse Barrier.
78. 5. Variable Scaling of External Correlation Energy for Association Reactions.
79. J. Villà, J. C. Corchado, A. González-Lafont, J. M. Lluch, and D. G. Truhlar, J. Am. Chem. Soc., 120, 12141 (1998). Explanation of Deuterium and Muonium Kinetic Isotope Effects for Hydrogen Atom Addition to an Olefin.
80. 5.
81. 6 Dissociations.
82. D. M. Wardlaw and R. A. Marcus, Adv. Chem. Phys. 107, 9776 (1988). On the Statistical Theory of Unimolecular Processes.
83. S. J. Klippenstein, J. Phys. Chem. 98, 11459 (1994). An Efficient Procedure for Evaluating the Number of Available States within a Variably Defined Reaction Coordinate Framework.
84. 3 Recombination Reactions.
85. S. C. Smith, J. Chem. Phys., 111, 1830 (1999). Classical Flux Integrals in Transition State Theory: Generalized Reaction Coordinates.
86. S. Robertson, A. F. Wagner, and D. M. Wardlaw, J. Phys. Chem. A, 106, 2598 (2002). Flexible Transition State Theory for a Variable Reaction Coordinate: Analytical Expressions and an Application.
87. 4 Reaction.
88. Y. Georgievskii and S. J. Klippenstein, J. Phys. Chem. A, 107, 9776 (2003). Transition State Theory for Multichannel Addition Reactions: Multifaceted Dividing Surfaces.
89. Y. Georgievskii and S. J. Klippenstein, J. Chem. Phys., 122, 194103 (2005). Long-Range Transition State Theory.
90. Y.-Y. Chuang and D. G. Truhlar, J. Chem. Phys., 112, 1221 (2000); Erratum: 124, 179903 (2006). Statistical Thermodynamics of Bond Torsional Modes.
91. Y.-P. Liu, D.-h. Lu, A. González-Lafont, D. G. Truhlar, and B. C. Garrett, J. Am. Chem. Soc., 115, 7806 (1993). Direct Dynamics Calculation of the Kinetic Isotope Effect for an Organic Hydrogen-Transfer Reaction, Including Corner-Cutting Tunneling in 21 Dimensions.
92. K. S. Pitzer and W. D. Gwinn, J. Chem. Phys., 10, 428 (1942). Energy Levels and Thermodynamic Function for Molecules with Internal Rotation.
93. K. S. Pitzer, J. Chem. Phys., 14, 239 (1946). Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation: II. Unsymmetrical Tops Attached to a Rigid Frame.
94. D. G. Truhlar, J. Comput. Chem., 12, 266 (1991). A Simple Approximation for the Vibrational Partition Function of a Hindered Internal Rotation.
95. B. A. Ellingson, V. A. Lynch, S. L. Mielke, and D. G. Truhlar, J. Chem. Phys., 125, 84305 (2006). Statistical Thermodynamics of Bond Torsional Modes. Tests of Separable, Almost- Separable, and Improved Pitzer-Gwinn Approximations.
96. G. Herzberg, Molecular Spectra and Molecular Structure. I. Spectra of Diatomic Molecules, Van Nostrand Reinhold, Princeton, New Jersey, 1950.
97. A. D. Isaacson and D. G. Truhlar, J. Chem. Phys., 76, 1380 (1982). Polyatomic Canonical Variational Theory for Chemical Reaction Rates. Separable-mode Formalism With Application to Hydroxyl Radical + Diatomic Hydrogen → Water + Atomic Hydrogen.
98. D. G. Truhlar, J. Mol. Spect., 38, 415 (1971). Oscillators with Quartic Anharmonicity: Approximate Energy Levels.
99. B. C. Garrett and D. G. Truhlar, J. Phys. Chem., 83, 1915 (1979). Importance of Quartic Anharmonicity for Bending Partition Functions in Transition-State Theory.
100. K. A. Nguyen, C. F. Jackels, and D. G. Truhlar, J. Chem. Phys., 104, 6491 (1996). Reaction-Path Dynamics in Curvilinear Internal Coordinates Including Torsions.
101. 2.
102. B. C. Garrett and D. G. Truhlar, J. Chem. Phys., 79, 4931 (1983). A Least-Action Variational Method for Calculating Multidimensional Tunneling Probabilities for Chemical Reactions.
103. T. C. Allison and D. G. Truhlar, in Modern Methods for Multidimensional Dynamics Computations in Chemistry, D. L. Thompson, Ed., World Scientific, Singapore, 1998, pp. 618-712. Testing the Accuracy of Practical Semiclassical Methods: Variational Transition State Theory With Optimized Multidimensional Tunneling.
104. Y.-P. Liu, G. C. Lynch, T. N. Truong, D.-h. Lu, D. G. Truhlar, and B. C. Garrett, J. Am. Chem. Soc., 115, 2408 (1993). Molecular Modeling of the Kinetic Isotope Effect for the [1,5]- Sigmatropic Rearrangement of cis-1,3-Pentadiene.
105. D. G. Truhlar and B. C. Garrett, in Annual Review of Physical Chemistry, Vol. 35, B. S. Rabinovitch, J. M. Schurr, and H. L. Strauss, Eds., Annual Reviews, Inc., Palo Alto, California, 1984, pp. 159-189. Variational Transition State Theory.
106. M. M. Kreevoy and D. G. Truhlar, in Investigation of Rates and Mechanisms of Reactions, Fourth edition, Part 1, C. F. Bernasconi, Ed., Wiley, New York, 1986, pp. 13-95. Transition State Theory.
107. D. G. Truhlar and B. C. Garrett, Journal de Chimie Physique, 84, 365 (1987). Dynamical Bottlenecks and Semiclassical Tunneling Paths for Chemical Reactions.
108. B. C. Garrett, T. Joseph, T. N. Truong, and D. G. Truhlar, Chem. Phys., 136, 271 (1989). Application of the Large-Curvature Tunneling Approximation to Polyatomic Molecules: Abstraction of H or D by Methyl Radical.
109. T. N. Truong, D.-h. Lu, G. C. Lynch, Y.-P. Liu, V. S. Melissas, J. J. P. Stewart, R. Steckler, B. C. Garrett, A. D. Isaacson, A. González-Lafont, S. N. Rai, G. C. Hancock, T. Joseph, and D. G. Truhlar, Comput. Phys. Commun., 75, 143 (1993). MORATE: A Program for Direct Dynamics Calculations of Chemical Reaction Rates by Semiempirical Molecular Orbital Theory.
110. A. Fernandez-Ramos and D. G. Truhlar, J. Chem. Phys., 114, 1491 (2001). Improved Algorithm for Corner-Cutting Tunneling Calculations.
111. J. Pu, J. C. Corchado, and D. G. Truhlar, J. Chem. Phys., 115, 6266 (2001). Test of Variational Transition State Theory With Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom System.
112. 3 in an Extended Temperature Interval.
113. R. A. Marcus, J. Chem. Phys., 45, 4493 (1966). On the Analytical Mechanics of Chemical Reactions. Quantum Mechanics of Linear Collisions.
114. A. Kuppermann, J. T. Adams, and D. G. Truhlar, in Abstractions of Papers, VIII ICPEAC, Beograd, 1973, B. C. Cubic and M. V. Kurepa, Eds., Institute of Physics, Belgrade, Serbia. 1973 pp. 149-150.
115. 2+H.
116. R. T. Skodje, D. G. Truhlar, and B. C. Garrett, J. Chem. Phys., 77, 5955 (1982). Vibrationally Adiabatic Models for Reactive Tunneling.
117. M. M. Kreevoy, D. Ostovic, D. G. Truhlar, and B. C. Garrett, J. Phys. Chem., 90, 3766 (1986). Phenomenological Manifestations of Large-Curvature Tunneling in Hydride Transfer Reactions.
118. D. G. Truhlar and M. S. Gordon, Science, 249, 491 (1990). From Force Fields to Dynamics: Classical and Quantal Paths.
119. + Analogues.
120. A. Fernandez-Ramos, D. G. Truhlar, J. C. Corchado, and J. Espinosa-Garcia, J. Phys. Chem. A, 106, 4957 (2002). Interpolated Algorithm for Large-Curvature Tunneling Calculations of Transmission Coefficients for Variational Transition State Theory Calculations of Reaction Rates.
121. A. Fernandez-Ramos and D. G. Truhlar, J. Chem. Theory Comput., 1, 1063 (2005). A New Algorithm for Efficient Direct Dynamics Calculations of Large-Curvature Tunneling and its Application to Radical Reactions with 9-15 Atoms.
122. 3P) with HD.
123. D. C. Chatfield, R. S. Friedman, D. G. Truhlar, and D. W. Schwenke, Faraday Discuss. Chem. Soc., 91, 289 (1991). Quantum-Dynamical Characterization of Reactive Transition States.
124. B. C. Garrett, N. Abusalbi, D. J. Kouri, and D. G. Truhlar, J. Chem. Phys., 83, 2252 (1985). Test of Variational Transition State Theory and the Least-Action Approximation for Multidimensional Tunneling Probabilities Against Accurate Quantal Rate Constants for a Collinear Reaction Involving Tunneling into an Excited State.
125. D. G. Truhlar, J. Chem. Soc. Faraday Trans., 90, 1740 (1994). General Discussion.
126. B. C. Garrett and D. G. Truhlar, J. Phys. Chem., 89, 2204 (1985). Generalized Transition State Theory and Least-Action Tunneling Calculations for the Reaction Rates of Atomic Hydrogen(Deuterium) + Molecular Hydrogen (n = 1)→ Molecular Hydrogen(Hydrogen Deuteride) + Atomic Hydrogen.
127. S. C. Tucker, D. G. Truhlar, B. C. Garrett, and A. D. Isaacson, J. Chem. Phys., 82, 4102 (1985). Variational Transition State Theory With Least-Action Tunneling Calculations for the Kinetic Isotope Effects in the Atomic Chlorine + Molecular Hydrogen Reaction: Tests of Extended-LEPS, Information-Theoretic, and Diatomics-in-Molecules Potential Energy Surfaces.
128. A. Fernandez-Ramos, Z. Smedarchina, M. Zgierski, W. Siebrand, and M. A. Rios, J. Am. Chem. Soc., 121, 6280 (1999). Direct-Dynamics Approaches to Proton Tunneling Rate Constants. A Comparative Test for Molecular Inversions and Application to 7-Azaindole.
129. M. Y. Ovchinnikova, Chem. Phys., 36, 85 (1979). The Tunneling Dynamics of the Low-Temperature Hydrogen Atom Exchange Reactions.
130. V. K. Babamov and R. A. Marcus, J. Chem. Phys., 74, 1790 (1981). Dynamics of Hydrogen Atom and Proton Transfer Reactions. Symmetric Case.
131. D. K. Bondi, J. N. L. Connor, B. C. Garrett, and D. G. Truhlar, J. Chem. Phys., 78, 5981 (1983). Test of Variational Transition State Theory with a Large-Curvature Tunneling Approximation Against Accurate Quantal Reaction Probabilities and Rate Coefficients for Three Collinear Reactions with Large Reaction-Path Curvature: Atomic Chlorine + Hydrogen Chloride, Atomic Chlorine + Deuterium Chloride, and Atomic Chlorine + MuCl.
132. A. González-Lafont, T. N. Truong, and D. G. Truhlar, J. Phys. Chem., 95, 4618 (1991). Direct Dynamics Calculations with NDDO (Neglect of Diatomic Differential Overlap) Molecular Orbital Theory with Specific Reaction Parameters.
133. Y. Kim, J. C. Corchado, J. Villà, J. Xing, and D. G. Truhlar, J. Chem. Phys., 112, 2718 (2000). Multiconfiguration Molecular Mechanics Algorithm for Potential Energy Surfaces of Chemical Reactions.
134. T. V. Albu, J. C. Corchado, and D. G. Truhlar, J. Phys. Chem. A, 105, 8465 (2001). Molecular Mechanics for Chemical Reactions: A Standard Strategy for Using Multiconfiguration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling.
135. H. Lin, J. Pu, T. V. Albu, and D. G. Truhlar, J. Phys. Chem. A, 108, 4112 (2004). Efficient Molecular Mechanics for Chemical Reactions Using Partial Electronic Structure Hessians.
136. Y.-Y. Chuang, P. L. Fast, W.-P. Hu, G. C. Lynch, Y.-P. Liu, and D. G. Truhlar, MORATE- version 8.5. Available: http://comp.chem.umn.edu/morate.
137. J. C. Corchado, Y.-Y. Chuang, E. L. Coitiño, and D. G. Truhlar, GAUSSRATE-version 9.4. Available: http://comp.chem.umn.edu/gaussrate.
138. Y.-Y. Chuang, J. C. Corchado, J. Pu, and D. G. Truhlar, GAMESSPLUSRATE-version 9.3. Available: http://comp.chem.umn.edu/gamessplusrate.
139. J. Pu, J. C. Corchado, B. J. Lynch, P. L. Fast and D. G. Truhlar, MULTILEVELRATE- version 9.3. Available: http://comp.chem.umn.edu/multilevelrate.
140. T. V. Albu, J. C. Corchado, Y. Kim, J. Villà, J. Xing, H. Lin, and D. G. Truhlar, MCTINKERATE- version 9.1. Available: http://comp.chem.umn.edu/mc-tinkerate.
141. M. Garcia-Viloca, C. Alhambra, J. Corchado, M. Luz Sánchez, J. Villà, J. Gao, and D. G. Truhlar, CRATE-version 9.0. Available: http://comp.chem.umn.edu/crate.
142. D. G. Truhlar, in The Reaction Path in Chemistry: Current Approaches and Perspectives, D. Heidrich, Ed., Kluwer, Dordrecht, The Netherlands, 1995, pp. 229-255. Direct Dynamics Method for Calculations of Reaction Rates.
143. 2.
144. I. Rossi and D. G. Truhlar, Chem. Phys. Lett. 223, 231 (1995). Parameterization of NDDO Wavefunctions using Genetic Algorithms: An Evolutionary Approach to Parameterizing Potential Energy Surfaces and Direct Dynamics Calculations for Organic Reactions.
145. J. A. Pople, D. P. Santry, and G. A. Segal, J. Chem. Phys., 43, S129 (1965). Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures.
146. J. A. Pople and D. J. Beveridge, Approximate Molecular Orbital Theory, McGraw-Hill, New York, 1970.
147. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985). Development and Use of Quantum Mechanical Molecular Models. 76. AM1: A New General Purpose Quantum Mechanical Molecular Model.
148. M. J. S. Dewar and E. G. Zoebisch, J. Mol. Struct. (THEOCHEM), 180, 1 (1988). Extension of AM1 to the Halogens.
149. A. Warshel and R. M. Weiss, J. Am. Chem. Soc., 102, 6218 (1980). An Empirical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes.
150. Y. T. Chang and W. H. Miller, J. Phys. Chem., 94, 5884 (1990). An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems.
151. 2 + CO.
152. J. Ischtwan and M. A. Collins, J. Chem. Phys., 100, 8080 (1994). Molecular Potential Energy Surfaces by Interpolation.
153. K. A. Nguyen, I. Rossi, and D. G. Truhlar, J. Chem. Phys., 103, 5222 (1995). A Dual-Level Shepard Interpolation Method for Generating Potential Energy Surfaces for Dynamics Calculations.
154. J. C. Corchado, E. L. Coitiño, Y.-Y. Chuang, P. L. Fast, and D. G. Truhlar, J. Phys. Chem. A, 102, 2424 (1998). Interpolated Variational Transition-State Theory by Mapping.
155. W.-P. Hu, Y.-P. Liu, and D. G. Truhlar, J. Chem. Soc., Faraday Trans., 90, 1715 (1994). Variational Transition-State Theory and Semiclassical Tunneling Calculations With Interpolated Corrections: A New Approach to Interfacing Electronic Structure Theory and Dynamics for Organic Reactions.
156. Y.-Y. Chuang, J. C. Corchado, and D. G. Truhlar, J. Phys. Chem. A, 103, 1140 (1999). Mapped Interpolation Scheme for Single-Point Energy Corrections in Reaction Rate Calculations and a Critical Evaluation of Dual-Level Reaction Path Dynamics Methods.
157. D. G. Truhlar, J. Chem. Educ., 62, 104 (1985). Nearly Encounter-Controlled Reactions: The Equivalence of the Steady-State and Diffusional Viewpoints.
158. K. A. Connors, Chemical Kinetics: The Study of Reaction Rates in Solution; VCH Publishers, New York, 1990, pp. 207-208.
159. Y.-Y. Chuang, C. J. Cramer, and D. G. Truhlar, Int. J. Quantum Chem., 70, 887 (1998). Interface of Electronic Structure and Dynamics for Reactions in Solution.
160. M. J. Pilling and P. W. Seakins, Reaction Kinetics, Oxford University Press, Oxford, United Kingdom, 1995, pp. 155-156.
161. C. J. Cramer and D. G. Truhlar, in Reviews in Computational Chemistry, Vol. 6, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1995, pp. 1-72. Continuum Solvation Models: Classical and Quantum Mechanical Implementations.
162. C. J. Cramer and D. G. Truhlar, in Solvent Effects and Chemical Reactivity, O. Tapia and J. Bertrán, Eds., Kluwer, Dordrecht, The Netherlands, 1996, pp. 1-80. [Understanding Chem. React. 17, 1-80 (1996).] Continuum Solvation Models.
163. D. J. Giesen, C. C. Chambers, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, in Computational Thermochemistry, K. Irikura and D. J. Frurip, Eds., American Chemical Society Symposium Series Volume 677, Washington, D.C., 1998, pp. 285-300. Modeling Free Energies of Solvation and Transfer.
164. G. D. Hawkins, T. Zhu, J. Li, C. C. Chambers, D. J. Giesen, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, in Combined Quantum Mechanical and Molecular Mechanical Methods, J. Gao and M. A. Thompson, Eds., American Chemical Society Symposium Series Volume 712, Washington, D.C., 1998, pp. 201-219. Universal Solvation Models.
165. J. Li, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Chem. Phys. Lett., 288, 293 (1998). Universal Reaction Field Model Based on Ab Initio Hartree-Fock Theory.
166. T. Zhu, J. Li, G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, J. Chem. Phys., 109, 9117 (1998). Density Functional Solvation Model Based on CM2 Atomic Charges.
167. C. J. Cramer and D. G. Truhlar, Chem. Rev., 99, 2161 (1999). Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.
168. J. Li, T. Zhu, G. D. Hawkins, P. Winget, D. A. Liotard, C. J. Cramer, and D. G. Truhlar, Theor. Chem. Acc., 103, 9 (1999). Extension of the Platform of Applicability of the SM5.42R Universal Solvation Model.
169. C. J. Cramer and D. G. Truhlar, in Free Energy Calculations in Rational Drug Design, M. R. Reddy and M. D. Erion, Eds., Kluwer Academic/Plenum, New York, 2001, pp. 63-95. Solvation Thermodynamics and the Treatment of Equilibrium and Nonequilibrium Solvation Effects by Models Based on Collective Solvent Coordinates.
170. J. D. Thompson, C. J. Cramer, and D. G. Truhlar, J. Phys. Chem. A, 108, 6532 (2004). New Universal Solvation Model and Comparison of the Accuracy of Three Continuum Solvation Models, SM5.42R, SM5.43R, and C-PCM, in Aqueous Solution and Organic Solvents and for Vapor Pressures.
171. C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput., 1, 1133 (2005). SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters.
172. D. A. McQuarrie, Statistical Mechanics, Harper & Row, New York, 1976, pp. 266.
173. D. G. Truhlar, Y.-P. Liu, G. K. Schenter, and B. C. Garrett, J. Phys. Chem., 98, 8396 (1994). Tunneling in the Presence of a Bath: A Generalized Transition State Theory Approach.
174. Y.-Y. Chuang, and D. G. Truhlar, J. Am. Chem. Soc., 121, 10157 (1999). Nonequilibrium Solvation Effects for a Polyatomic Reaction in Solution.
175. C. Alhambra, J. Corchado, M. L. Sánchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, J. Phys. Chem. B, 105, 11326 (2001). Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase.
176. D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sánchez, and J. Villà, Acc. Chem. Res., 35, 341 (2002). The Incorporation of Quantum Effects in Enzyme Kinetics Modeling.
177. M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, J. Comput. Chem., 24, 177 (2003). Hydride Transfer Catalyzed by Xylose Isomerase: Mechanism and Quantum Effects.
178. T. D. Poulsen, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, J. Phys. Chem. B,107, 9567 (2003). Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl- CoA Dehydrogenase.
179. D. G. Truhlar, J. Gao, M. Garcia-Viloca, C. Alhambra, J. Corchado, M. L. Sánchez, and T. D. Poulsen, Int. J. Quantum Chem., 100, 1136 (2004). Ensemble-Averaged Variational Transition State Theory with Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions.
180. D. G. Truhlar, in Isotope Effects in Chemistry and Biology, A. Kohen and H.-H. Limbach, Eds., Marcel Dekker, Inc., New York, 2006, pp. 579-620. Variational Transition State Theory and Multidimensional Tunneling for Simple and Complex Reactions in the Gas Phase, Solids, Liquids, and Enzymes.
181. 2 Exchange Reaction.
182. 3 Inversion.
183. D. Heidrich, in The Reaction Path in Chemistry, D. Heidrich, Ed., Kluwer, Dordrecht, The Netherlands, 1995, pp. 1-10. An Introduction to the Nomenclature and Usage of the Reaction Path Concept.
184. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983). CHARMM: A Program for Macromolecular Energy, Minimisation and Dynamics Calculations.
185. G. N. Patey and J. P. Valleau, Chem. Phys. Lett., 21, 297 (1973). The Free Energy of Spheres with Dipoles: Monte Carlo with Multistage Sampling.
186. G. N. Patey and J. P. Valleau, J. Chem. Phys., 63, 2334 (1975). A Monte Carlo Method for Obtaining the Interionic Potential of Mean Force in Ionic Solution.
187. G. M. Torrie and J. P. Valleau, J. Comput. Phys., 23, 187 (1977). Nonphysical Sampling Distributions in Monte Carlo Free Energy Estimation: Umbrella Sampling.
188. M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, J. Chem. Phys., 114, 9953 (2001). Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force.
189. D.C. Chatfield, R.S. Friedman, D.W. Schwenke, and D.G. Truhlar, J. Phys. Chem, 96, 2414 (1992). Control of Chemical Reactivity by Quantized Transition States.
190. N2 Reactions in Polar Solvents.
191. W. P. Kierstad, K. R. Wilson, and J. T. Hynes, J. Chem. Phys., 95, 5256 (1991). Molecular Dynamics of a Model SN1 Reaction in Water.
192. J. T. Hynes, in Solvent Effects and Chemical Reactivity,O. Tapia and J. Bertrán, Eds., Kluwer, Dordrecht, The Netherlands, 1996, pp. 231-258. Crossing the Transition State in Solution.
193. 2.
194. 2 Reaction.
195. 2 Reaction Rate.
196. 2 Reaction. Full Dimensional and Reduced Dimensionality Rate Constants Calculations.
197. C. P. Kelly, J. D. Xidos, J. Li, J. D. Thompson, G. D. Hawkins, P. D. Winget, T. Zhu, D. Rinaldi, D. A. Liotard, C. J. Cramer, D. G. Truhlar, and M. J. Frisch, MN-GSM, version 5.2, Univeristy of Minnesota, Minneapolis, Minnesota, 55455-0431, 2005.
198. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. G. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian 98, Revision A.3, Gaussian, Inc., Pittsburgh, Pennsylvania, 1998.