POLYRATE BIBLIOGRAPHY

POLYRATE BIBLIOGRAPHY:


Publications from the University of Minnesota based in whole or in part on POLYRATE:

"The Incorporation of Quantum Effects in Generalized Transition State Theory," D. G. Truhlar, A. D. Isaacson, R. T. Skodje, and B. C. Garrett, Journal of Physical Chemistry 86, 2252-2261 (1982).  Erratum:  87, 4554 (1983). 

"Polyatomic Canonical Variational Theory for Chemical Reaction Rates. Separable-Mode Formalism with Application to OH + H2 -> H2O + H," A. D. Isaacson and D. G. Truhlar, Journal of Chemical Physics 76, 1380-1391 (1982).

"Statistical-Diabatic Model for State-Selected Reaction Rates. Theory and Application of Vibrational-Mode Correlation Analysis to OH(nOH) + H2(nHH) ->  H2O + H," D. G. Truhlar and A. D. Isaacson, Journal of Chemical Physics 77, 3516-3522 (1982).

"Recent Progress in Atomic and Molecular Collisions and the Interface with Electronic Structure Theory," D. G. Truhlar, International Journal of Quantum Chemistry, Symposium 17, 77-87 (1983).

"The Current Status of Transition State Theory," D. G. Truhlar, W. L. Hase, and J. T. Hynes, Journal of Physical Chemistry 87, 2664-2682 (1983).  Erratum:  87, 5523 (1983).

"Small-Curvature Adiabatic Approximation for Reaction-Path Reduced-Dimensionality Effective Hamiltonian," R. T. Skodje and D. G. Truhlar, Journal of Chemical Physics 79, 4882-4888 (1983).

"Variational Transition State Theory Calculations for an Atom-Radical Reaction with No Saddle Point: O + OH," S. N. Rai and D. G. Truhlar, Journal of Chemical Physics 79, 6046-6059 (1983).

"Variational Transition State Theory," D. G. Truhlar and B. C. Garrett, in Annual Review of Physical Chemistry, Vol. 35, edited by B. S. Rabinovitch, J. M. Schurr, and H. L. Strauss (Annual Reviews, Inc., Palo Alto, California, 1984), pp. 159–189.

"Generalized Transition State Theory," D. G. Truhlar, A. D. Isaacson, and B. C. Garrett, in Theory of Chemical Reaction Dynamics, edited by M. Baer (CRC Press, Boca Raton, FL, 1985), Vol. 4, pp. 65–137.

"Improved Canonical and Microcanonical Variational Transition State Theory Calculations for a Polyatomic System: OH + H2 -> H2O + H," A. D. Isaacson, M. T. Sund, S. N. Rai, and D. G. Truhlar, Journal of Chemical Physics 82, 1338-1340 (1985).

"Large Tunneling Effects in the Migration of Chemisorbed Hydrogen on a Metal," J. G. Lauderdale and D. G. Truhlar, Journal of the American Chemical Society 107, 4590-4591 (1985).

"Semiclassical Reaction-Path Methods Applied to Calculate the Tunneling Splitting in NH3," F. B. Brown, S. C. Tucker, and D. G. Truhlar, Journal of Chemical Physics 83, 4451-4455 (1985).

"Diffusion of Hydrogen, Deuterium, and Tritium on the (100) Plane of Copper: Reaction-Path Formulation, Variational Transition State Theory, and Tunneling Calculations," J. G. Lauderdale and D. G. Truhlar, Surface Science 164, 558-588 (1985).

"Embedded-Cluster Model for the Effect of Phonons on Hydrogen Surface Diffusion on Copper," J. G. Lauderdale and D. G. Truhlar, Journal of Chemical Physics 84, 1843-1849 (1986).

"Phenomenological Manifestations of Large-Curvature Tunneling in Hydride Transfer Reactions," M. M. Kreevoy, D. Ostovic´   , D. G. Truhlar, and B. C. Garrett, Journal of Physical Chemistry 90, 3766-3774 (1986).

"Reaction-Path Analysis of the Tunneling Splitting in Fluxional Molecules: Application to the Degenerate Rearrangement of Hydrogen Fluoride Dimer," G. C. Hancock, P. Rejto, R. Steckler, F. B. Brown, D. W. Schwenke, and D. G. Truhlar, Journal of Chemical Physics 85, 4997-5003 (1986).

"Transition State Theory," M. M. Kreevoy and D. G. Truhlar, in Investigation of Rates and Mechanisms of Reactions, 4th edition, edited by C. F. Bernasconi (John Wiley and Sons, New York, 1986), Part 1, pp. 13–95.  [Tech. Chem. (N.Y.), 4th ed., 6/Pt. 1, 13-95 (1986)]

"The Representation and Use of Potential Energy Surfaces in the Wide Vicinity of a Reaction Path for Dynamics Calculations on Polyatomic Reactions," D. G. Truhlar, F. B. Brown, R. Steckler, and A. D. Isaacson, in The Theory of Chemical Reaction Dynamics, edited by D. C. Clary (D. Reidel, Dordrecht, Holland, 1986), pp. 285–329.  [NATO ASI Ser. C 170, 285–329 (1986)]

"Dynamical Bottlenecks and Semiclassical Tunneling Paths for Chemical Reactions," D. G. Truhlar and B. C. Garrett, Journal de Chimie Physique 84, 365-369 (1987).

"POLYRATE: A General Computer Program for Variational Transition State Theory and Semiclassical Tunneling Calculations of Chemical Reaction Rates," A. D. Isaacson, D. G. Truhlar, S. N. Rai, R. Steckler, G. C. Hancock, B. C. Garrett, and M. J. Redmon, Computer Physics Communications 47, 91-102 (1987).

"Surface Diffusion of H on Copper: The Effect of Phonon-Adsorbate Coupling on the Diffusion Rate," T. N. Truong and D. G. Truhlar, Journal of Physical Chemistry 91, 6229-6237 (1987).

"A Comparative Study of Potential Energy Surfaces for CH3 + H2 -> CH4 + H," R. Steckler, K. J. Dykema, F. B. Brown, G. C. Hancock, D. G. Truhlar, and T. Valencich, Journal of Chemical Physics 87, 7024-7035 (1987).

"A New Potential Energy Surface for the CH3 + H2 -> CH4 + H Reaction: Calibration, Rate Constants, and Kinetic Isotope Effects by Variational Transition State Theory and Semiclassical Tunneling Calculations," T. Joseph, R. Steckler, and D. G. Truhlar, Journal of Chemical Physics 87, 7036-7049 (1987).

"Algorithms and Accuracy Requirements for Computing Reaction Paths by the Method of Steepest Descent," B. C. Garrett, M. J. Redmon, R. Steckler, D. G. Truhlar, K. K. Baldridge, D. Bartol, M. W. Schmidt, and M. S. Gordon, Journal of Physical Chemistry 92, 1476-1488 (1988).

"An Analytic Representation of the Six-Dimensional Potential Energy Surface of Hydrogen Fluoride Dimer," G. C. Hancock, D. G. Truhlar, and C. E. Dykstra, Journal of Chemical Physics 88, 1786-1796 (1988).

"Surface Diffusion of H, D, and T on a Metal Surface: The Role of Metal Motions in the Kinetic Isotope Effects,"  T. N. Truong and D. G. Truhlar, Journal of Chemical Physics 88, 6611-6619 (1988).

"Calculation of Reaction Rates and Kinetic Isotope Effects for Dissociative Chemisorption of H2 and D2 on Ni(100), Ni(110), and Ni(111) Surfaces," T. N. Truong, G. Hancock, and D. G. Truhlar, Surface Science 214, 523-559 (1989).

"Ab Initio Reaction Paths and Direct Dynamics Calculations," K. K. Baldridge, M. S. Gordon, R. Steckler, and D. G. Truhlar, Journal of Physical Chemistry 93, 5107-5119 (1989).

"Dynamical Formulation of Transition State Theory: Variational Transition States and Semiclassical Tunneling," S. C. Tucker and D. G. Truhlar, in New Theoretical Concepts for Understanding Organic Reactions, edited by J. Bertrán and I. G. Csizmadia (Kluwer, Dordrecht, The Netherlands, 1989), pp. 291–346.  [NATO ASI Ser. C 267, 291–346 (1989)]

"Application of the Large-Curvature Tunneling Approximation to Polyatomic Molecules: Abstraction of H or D by Methyl Radical," B. C. Garrett, T. Joseph, T. N. Truong, and D. G. Truhlar, Chemical Physics 136, 271-284 (1989).  (Special Issue: Spectroscopy and Dynamics of Elementary Proton Transfer in Polyatomic Systems)  Errata:  140, 207 (1990).

"Embedded Diatomics-in-Molecules (EDIM): A Method to Include Delocalized Electronic Interactions in the Treatment of Covalent Chemical Reactions at Metal Surfaces," T. N. Truong, D. G. Truhlar, and B. C. Garrett, Journal of Physical Chemistry 93, 8227-8239 (1989).

"A New Ab Initio Potential Energy Surface for H on Ru(0001) and Its Use for Variational Transition State Theory and Semiclassical Tunneling Calculations of the Surface Diffusion of H and D," T. N. Truong, D. G. Truhlar, J. R. Chelikowsky, and M. Y. Chou, Journal of Physical Chemistry 94, 1973-1981 (1990).

"A Six-Body Potential Energy Surface for the SN2 Reaction Cl-(g) + CH3Cl(g) and a Variational Transition State Theory Calculation of the Rate Constant," S. C. Tucker and D. G. Truhlar, Journal of the American Chemical Society 112, 3338-3347 (1990).

"The Effect of Nonequilibrium Solvation on Chemical Reaction Rates.  Variational Transition State Theory Studies of the Microsolvated Reaction Cl-(H2O)n + CH3Cl," S. C. Tucker and D. G. Truhlar, Journal of the American Chemical Society 112, 3347-3361 (1990).

"The Effects of Steps, Coupling to Substrate Vibrations, and Surface Coverage on Surface Diffusion Rates and Kinetic Isotope Effects: Hydrogen Diffusion on Ni," T. N. Truong and D. G. Truhlar, Journal of Chemical Physics 93, 2125-2138 (1990).

"Effect of Steps and Surface Coverage on Rates and Kinetic Isotope Effects for Reactions Catalyzed by Metallic Surfaces: Chemisorption of Hydrogen on Ni," T. N. Truong and D. G. Truhlar, Journal of Physical Chemistry 94, 8262-8279 (1990).

"Ab Initio Transition State Theory Calculations of the Reaction Rate for OH + CH4 ->  H2O + CH3," T. N. Truong and D. G. Truhlar, Journal of Chemical Physics 93, 1761-1769 (1990).  Erratum:  97, 8820 (1992).

"What is the Effect of Variational Optimization of the Transition State on a-Deuterium Secondary Kinetic Isotope Effects? A Prototype: CD3H + H -> CD3 + H2," D.-h. Lu, D. Maurice, and D. G. Truhlar, Journal of the American Chemical Society 112, 6206-6214 (1990).

"From Force Fields to Dynamics: Classical and Quantal Paths," D. G. Truhlar and M. S. Gordon, Science 249, 491-498 (1990).

"Reaction Path Power Series Analysis of NH3 Inversion," R. Steckler and D. G. Truhlar, Journal of Chemical Physics 93, 6570-6577 (1990).

"Projection Operator Method for Geometry Optimization with Constraints," D.-h. Lu, M. Zhao, and D. G. Truhlar, Journal of Computational Chemistry 12, 376-384 (1991).

"Solvent and Secondary Kinetic Isotope Effects for the Microhydrated SN2 Reaction of Cl-(H2O)n with CH3Cl," X. G. Zhao, S. C. Tucker, and D. G. Truhlar, Journal of the American Chemical Society 113, 826-832 (1991).

"Direct Dynamics Calculations with Neglect of Diatomic Differential Overlap Molecular Orbital Theory with Specific Reaction Parameters," A. Gonzàlez-Lafont, T. N. Truong, and D. G. Truhlar, Journal of Physical Chemistry 95, 4618-4627 (1991).

"The Definition of Reaction Coordinates for Reaction-Path Dynamics," G. A. Natanson, B. C. Garrett, T. N. Truong, T. Joseph, and D. G. Truhlar, Journal of Chemical Physics 94, 7875-7892 (1991).

"An Experimentally Based Family of Potential Surfaces for Hydride Transfer Between NAD+ Analogues," Y. Kim, D. G. Truhlar, and M. M. Kreevoy, Journal of the American Chemical Society 113, 7837-7847 (1991).

"Interpolated Variational Transition State Theory: Practical Methods for Estimating Variational Transition State Properties and Tunneling Contributions to Chemical Reaction Rates from Electronic Structure Calculations," A. Gonzàlez-Lafont, T. N. Truong, and D. G. Truhlar, Journal of Chemical Physics 95, 8875-8894 (1991).

"Temperature Dependence of the Kinetic Isotope Effect for a Gas-Phase SN2 Reaction: Cl- + CH3Br," A. A. Viggiano, J. Paschkewitz, R. A. Morris, J. F. Paulson, A. Gonzàlez-Lafont, and D. G. Truhlar, Journal of the American Chemical Society 113, 9404-9405 (1991).

"Optimized Calculations of Reaction Paths and Reaction-Path Functions for Chemical Reactions," V. S. Melissas, D. G. Truhlar, and B. C. Garrett, Journal of Chemical Physics 96, 5758-5772 (1992).

"POLYRATE 4: A New Version of a Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics," 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, Computer Physics Communications 71, 235-262 (1992).

"Variational Transition State Theory with Multidimensional Semiclassical Ground-State Transmission Coefficients: Applications to Secondary Deuterium Kinetic Isotope Effects in Reactions Involving Methane and Chloromethane," D. G. Truhlar, D.-h. Lu, S. C. Tucker, X. G. Zhao, A. Gonzàlez-Lafont, T. N. Truong, D. Maurice, Y-.P. Liu, and G. C. Lynch, in Isotope Effects in Chemical Reactions and Photodissociation Processes, by J. A. Kaye (American Chemical Society Symposium Series 502, Washington, DC, 1992), pp. 16-36.

"MORATE: A Program for Direct Dynamics Calculations of Chemical Reaction Rates by Semiempirical Molecular Orbital Theory," 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. Gonzàlez-Lafont, S. N. Rai, G. C. Hancock, T. Joseph, and D. G. Truhlar, Computer Physics Communications 75, 143-159 (1993).

"Use of an Improved Ion-Solvent Potential Energy Function to Calculate the Reaction Rate and a-Deuterium and Microsolvation Kinetic Isotope Effects for the Gas-Phase SN2 Reaction of Cl-(H2O) with CH3Cl," X. G. Zhao, D.-h. Lu, Y.-P. Liu, G. C. Lynch, and D. G. Truhlar, Journal of Chemical Physics 97, 6369-6383 (1992).

"Molecular Modeling of the Kinetic Isotope Effect for the [1,5]-Sigmatropic Rearrangement of cis-1,3-Pentadiene," Y.-P. Liu, G. C. Lynch, T. N. Truong, D.-h. Lu, D. G. Truhlar, and B. C. Garrett, Journal of the American Chemical Society 115, 2408-2415 (1993).

"Interpolated Variational Transition State Theory and Tunneling Calculations of the Rate Constant of the Reaction OH + CH4 at 223-2400 K," V. S. Melissas and D. G. Truhlar, Journal of Chemical Physics 99, 1013-1027 (1993).

"Bond-Distance and Bond-Angle Constraints in Reaction-Path Dynamics Calculations," D.-h. Lu and D. G. Truhlar, Journal of Chemical Physics 99, 2723-2738 (1993).

"Direct Dynamics Calculation of the Kinetic Isotope Effect for an Organic Hydrogen-Transfer Reaction, Including Corner-Cutting Tunneling in 21 Dimensions," Y.-P. Liu, D.-h. Lu, A. Gonzàlez-Lafont, D. G. Truhlar, and B. C. Garrett, Journal of the American Chemical Society 115, 7806-7817 (1993).

"Deuterium and Carbon-13 Kinetic Isotope Effects for the Reaction of OH with CH4," V. S. Melissas and D. G. Truhlar, Journal of Chemical Physics 99, 3542-3552 (1993).
"Effect of Phonon Coupling on Hydrogen Tunneling Rates at Gas-Surface Interfaces," S. E. Wonchoba and D. G. Truhlar, Journal of Chemical Physics 99 9637-9651 (1993).

"Variational Transition State Theory and Semiclassical Tunneling Calculations with Interpolated Corrections: A New Approach to Interfacing Electronic Structure Theory and Dynamics for Organic Reactions," W.-P. Hu, Y.-P. Liu, and D. G. Truhlar, Journal of the Chemical Society Faraday Transactions 90, 1715-1725 (1994).

"Tunneling Effects in Hydride Transfer Reactions," Y.-P. Liu and D. G. Truhlar, J. Chem. Soc. Faraday Trans. 90, 1735-1737 (1994).

"Interpolated Variational Transition State Theory and Semiclassical Tunneling Calculations of the Rate Constant of the Reaction OH + C2H6 at 200-3000 K," V. S. Melissas and D. G. Truhlar, Journal of Physical Chemistry 98, 875-886 (1994).

"Reaction Path Approach to Dynamics at a Gas-Solid Interface: Quantum Tunneling Effects for an Adatom on a Non-Rigid Metallic Surface," S. E. Wonchoba, W.-P. Hu, and D. G. Truhlar, in Theoretical and Computational Approaches to Interface Phenomena, edited by H. L. Sellers and J. T. Golab (Plenum, New York, 1994), pp. 1–33.

"Dual-Level Reaction-Path Dynamics (The /// Approach to VTST with Semiclassical Tunneling).  Application to OH + NH3 -> H2O + NH2" J. C. Corchado, J. Espinosa-Garcia, W.-P. Hu, I. Rossi, and D. G. Truhlar, Journal of Physical Chemistry 99, 687-694 (1995).

"Reaction-Path Potential and Vibrational Frequencies in Terms of Curvilinear Internal Coordinates," C. F. Jackels, Z. Gu, and D. G. Truhlar, Journal of Chemical Physics 102, 3188-3201 (1995).

"Surface Diffusion of H on Ni(100). Interpretation of the Transition Temperature," S. E. Wonchoba, W.-P. Hu, and D. G. Truhlar, Physical Review B 51, 9985-10002 (1995).

"Deuterium Kinetic Isotope Effects and their Temperature Dependence in the Gas-Phase SN2 Reactions X- + CH3Y -> CH3X + Y- (X, Y = Cl, Br, I)," W.-P. Hu and D. G. Truhlar, Journal of the American Chemical Society 117, 10726-10734 (1995).

"Direct Dynamics Method for the Calculation of Reaction Rates," D. G. Truhlar, in The Reaction Path in Chemistry: Current Approaches and Perspectives, edited by D. Heidrich (Kluwer, Dordrecht, 1995), pp. 229–255.  [Understanding Chem. React. 16, 229-255 (1995).]

"POLYRATE–version 6.5 and MORATE–version 6.5/P6.5-M5.05.  Two Computer Programs for the Calculation of Chemical Reaction Rates," W.-P. Hu, R. Steckler, G. C. Lynch, Y.-P. Liu, B. C. Garrett, A. D. Isaacson, D.-h. Lu, V. Melissas, I. Rossi, J. J. P. Stewart, and D. G. Truhlar, QCPE Bulletin 15, 32–36 (1995). [brief communication]

"POLYRATE 6.5:  A New Version of Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics," 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, Computer Physics Communications 88, 341-343 (1995). [new version announcement]

"MORATE 6.5:  A New Version of Computer Program for Direct Dynamics Calculations of Chemical Reaction Rate Constants," W.-P. Hu, G. C. Lynch, Y.-P. Liu, I. Rossi, J. J. P. Stewart, R. Steckler, B. C. Garrett, A. D. Isaacson, D.-h. Lu, V. S. Melissas, and D. G. Truhlar, Computer Physics Communications 88, 344-346 (1995). [new version announcement]

"Factors Affecting Competitive Ion-Molecule Reactions:  ClO- + C2H5Cl and C2D5Cl via E2 and SN2 Channels," W.-P. Hu and D. G. Truhlar, Journal of the American Chemical Society 118, 860-869 (1996).

"Current Status of Transition State Theory," D. G. Truhlar, B. C. Garrett, and S. J. Klippenstein, Journal of Physical Chemistry 100, 12771-12800 (1996).

"Reaction-Path Dynamics in Curvilinear Internal Coordinates Including Torsions,"  K. A. Nguyen, C. F. Jackels, and D. G. Truhlar, Journal of Chemical Physics 104, 6491-6496 (1996).

"General Potential-Energy Function for H/Ni and Dynamics Calculations of Surface Diffusion, Bulk Diffusion, Subsurface-to-Surface Transport, and Absorption," S. E. Wonchoba and D. G. Truhlar, Physical Review B 53, 11222–11241 (1996).

"Theoretical Approaches to the Reaction Dynamics of Clusters," A. Gonzàlez-Lafont and D. G. Truhlar, in Chemical Reactions in Clusters, edited by E. R. Bernstein (Oxford University Press, New York, 1996), pp. 1-39.

"Improved Dual-Level Direct Dynamics Method for Reaction Rate Calculations with Inclusion of Multidimensional Tunneling Effects and Validation for the Reaction of H with trans-N2H2," Y.-Y. Chuang and D. G. Truhlar, Journal of Physical Chemistry A 101, 6911-6921 (1997).

"Molecular Modeling of Combustion Kinetics. The Abstraction of Primary and Secondary Hydrogens by Hydroxyl Radical," W.-P. Hu, I. Rossi, J. C. Corchado, and D. G. Truhlar, Journal of Physical Chemistry, in press.

"Reaction-Path Dynamics with Harmonic Vibration Frequencies in Curvilinear Internal Coordinates: H + trans-N2H2 -> NH2 + H2," Y.-Y. Chuang and D. G. Truhlar, Journal of Chemical Physics 107, 83-89 (1997).

"Variational Transition State Theory Without the Minimum Energy Path," J. Villa and D. G. Truhlar, Theoretical Chemistry Accounts 97, 317-323 (1997). (Almlof Memorial Issue)

"The Importance of Quantum Effects for C-H Bond Activation Reactions," J. Espinosa-Garcia, J. C. Corchado, and D. G. Truhlar, Journal of the American Chemical Society 119, 9891-9896 (1997).

"Transition State Theory," B. C. Garrett and D. G. Truhlar, in Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, and H. F. Schaefer III (John Wiley & Sons, Chichester, UK, 1998), Volume 5, pp. 3094-3104.

"Dual-Level Methods for Electronic Structure Calculations of Potential Energy Functions that Use Quantum Mechanics as the Lower Level," J. C. Corchado and D. G. Truhlar, in Combined Quantum Mechanical and Molecular Mechanical Methods, edited by J. Gao and M. A. Thompson (American Chemical Society Symposium Series volume 712, Washington, DC, 1998), pp. 106-127.

"Reaction-Path Dynamics in Redundant Internal Coordinates," Y.-Y. Chuang and D. G. Truhlar, Journal of Physical Chemistry A 102, 242-247 (1998).

"Interpolated Variational Transition State Theory by Mapping," J. C. Corchado, E. L. Coitino, Y.-Y. Chuang, P. L. Fast, and D. G. Truhlar, Journal of Physical Chemistry A 102, 2424-2438 (1998).

"Entropic Effects on the Dynamical Bottleneck Location and Tunneling Contributions for C2H4 + H -> C2H5. Variable Scaling of External Correlation Energy for Association Reactions," J. Villa, A. Gonzalez-Lafont, J. M. Lluch, and D. G. Truhlar, Journal of the American Chemical Society 120, 5559-5567 (1998).

"Variational Transition State Theory and Tunneling Calculations with Reorientation of the Generalized Transition States for Methyl Cation Transfer," A. Gonzalez-Lafont, J. Villa, J. M. Lluch, J. Bertran, R. Steckler, and D. G. Truhlar, Journal of Physical Chemistry A 102, 3420-3428 (1998).

"Dual-Level Direct Dynamics Calculations of Deuterium and Carbon-13 Kinetic Isotope Effects for the Reaction Cl + CH4," by O. Roberto-Neto, E. L. Coitino, and D. G. Truhlar, Journal of Physical Chemistry A 102, 4568-4578 (1998).

"Dual-Level Direct Dynamics Calculations of the Reaction Rates for a Jahn-Teller Reaction: Hydrogen Abstraction from CH4 or CD4 by O(3P)," by J. C. Corchado, J. Espinosa-Garcia, O. Roberto-Neto, Y.-Y. Chuang, and D. G. Truhlar, Journal of Physical Chemistry A 102, 4899-4910 (1998).

"Interface of Electronic Structure and Dynamics for Reactions in Solution," Y.-Y. Chuang, C. J. Cramer, and D. G. Truhlar, International Journal of Quantum Chemistry 70, 887-896 (1998). (Sanibel issue)

"Variational Reaction Path Algorithm," P. L. Fast and D. G. Truhlar, Journal of Chemical Physics 109, 3721-3729 (1998).

"The Calculation of Kinetic Isotope Effects Based on a Single Reaction Path," P. L. Fast, J. C. Corchado, and D. G. Truhlar, Journal of Chemical Physics 109, 6237-6245 (1998).

"Explanation of Deuterium and Muonium Kinetic Isotope Effects for Hydrogen Atom Addition to an Olefin," J. Villa, J. C. Corchado, A. Gonzalez-Lafont, J. M. Lluch, and D. G. Truhlar, Journal of the American Chemical Society 120, 12141-12142 (1998).

"Ethylene Polymerization by Zirconocene Catalysis," P. K. Das, D. W. Dockter, D. R. Fahey, D. E. Lauffer, G. D. Hawkins, J. Li, T. Zhu, C. J. Cramer, D. G. Truhlar, S. Dapprich, R. D. J. Froese, M. C. Holthausen, Z. Liu, K. Mogi, S. Vyboishchikov, D. G. Musaev, and K. Morokuma, in Transition State Modeling for Catalysis, edited by D. G. Truhlar and K. Morokuma (American Chemical Society Symposium Series Volume 721, Washington, DC, 1999), pp. 208-224.

"Thermochemistry, Solvation, and Dynamics," D. G. Truhlar, Y.-Y. Chuang, E. L. Coitino, J. C. Corchado, C. J. Cramer, D. Dolney, J. Espinosa-Garcia, P. L. Fast, G. D. Hawkins, Y. Kim, J. Li, B. Lynch, M. L. Radhakrishnan, O. Roberto-Neto, J. M. Rodgers, M. L. Sánchez, J. Villa, P. Winget, and T. Zhu, in American Chemical Society Division of Fuel Chemistry Preprints of Symposia, Vol. 44 (American Chemical Society, Washington, 1999), pp. 452-458. [long abstract: Prepr. Symp. - Am. Chem. Soc., Div. Fuel Chem. 44(3), 452-458 (1999).]

"Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton-Transfer Reaction," C. Alhambra, J. Gao, J. C. Corchado, J. VillĂ , and D. G. Truhlar, Journal of the American Chemical Society 121, 2253-2258 (1999).

"Mapped Interpolation Scheme for Single-Point Energy Corrections in Reaction Rate Calculations and a Critical Evaluation of Dual-Level Reaction-Path Dynamics Methods," Y.-Y. Chuang, J. C. Corchado, and D. G. Truhlar, Journal of Physical Chemistry A 103, 1140-1149 (1999).

"Variational Transition State Theory with Optimized Orientation of the Dividing Surface and Semiclassical Tunneling Calculations for Deuterium and Muonium Kinetic Isotope Effects in the Free Radical Association Reaction H + C2H4 -> C2H5," J. Villà, J. C. Corchado, A. González-Lafont, J. M. Lluch, and D. G. Truhlar, Journal of Physical Chemistry A 103, 5061-5074 (1999).

"Direct Dynamics for Free Radical Kinetics in Solution: Solvent Effect on the Rate Constant for the Reaction of Methanol with Atomic Hydrogen," Y.-Y. Chuang, M. L. Radhakrishnan, P. L. Fast, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A 103, 4893-4909 (1999).

"Energetic and Structural Features of the CH4 + O(3P) -> CH3 + OH Abstraction Reaction: Does Perturbation Theory from a Multiconfiguration Reference State (Finally) Provide a Balanced Treatment of Transition States?", O. Roberto-Neto, F. B. C. Machado, and D. G. Truhlar, Journal of Chemical Physics 111, 10046-10052 (1999); erratum: 113, 3929 (2000).

"Nonequilibrium Solvation Effects for a Polyatomic Reaction in Solution," Y.-Y. Chuang and D. G. Truhlar, Journal of the American Chemical Society 121, 10157-10167 (1999)

"Vignette: Present-Day View of Transition State Theory," in Physical Chemistry, 2nd ed., edited by R. S. Berry, S. A. Rice, and J. Ross (Oxford University Press, New York, 2000), Section 30.6.

"Statistical Thermodynamics of Bond Torsion Modes," Y.-Y. Chuang and D. G. Truhlar, Journal of Chemical Physics 112, 1221-1228 (2000).

"Potential Energy Surface, Thermal and State-Selected Rate Constants and Kinetic Isotope Effects for Cl + CH4 -> HCl + CH3" J. C. Corchado, D. G. Truhlar, and J. Espinosa-Garcia, Journal of Chemical Physics 112, 9375-9389 (2000).

"Multiconfiguration Molecular Mechanics Algorithm for Potential Energy Surfaces of Chemical Reactions," Y. Kim, J. C. Corchado, J. VillĂ , J. Xing, and D. G. Truhlar, Journal of Chemical Physics 112, 2718-2735 (2000).

"Quantum Dynamics of Hydride Transfer in Enzyme Catalysis," C. Alhambra, J. C. Corchado, M. L. Sanchez, J. Gao, and D. G. Truhlar, Journal of the American Chemical Society 122, 8197-8203 (2000).

"Molecular-Scale Modeling of Reactions and Solvation," D. G. Truhlar, in First International conference on Foundations of Molecular Modeling and Simulation; edited by P. T. Cummings. P. R. Westmoreland, and B. Carnahan (American Institute of Chemical Engineers Symposium Series Vol. 97, New York, 2001), pp. 71-83.

"Improved Algorithm for Corner Cutting Calculations," A. Fernandez-Ramos and D. G. Truhlar, Journal of Chemical Physics 114, 1491-1496 (2001).

"Quantum Mechanical Dynamics of Hydride Transfer in Polycyclic Hydoxy Ketones in the Condensed Phase," R. M. Nicoll, I. H. Hillier, and D. G. Truhlar, Journal of the American Chemical Society 123, 1459-1463 (2001).

"Inclusion of Quantum Mechanical Vibrational Energy in Reactive Potentials of Mean Force," M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, Journal of Chemical Physics 114, 9953-9958 (2001).

"Variational Transition State Theory Evaluation of the Rate Constant for Proton Transfer in a Polar Solvent," R. P. McRae, G. K. Schenter, B. C. Garrett, Z. Svetlicic, and D. G. Truhlar, Journal of Chemical Physics 115, 8460-8480 (2001).

"Molecular Mechanics for Chemical Reactions. A Standard Strategy for Using Multi-Configuration Molecular Mechanics for Variational Transition State Theory with Optimized Multidimensional Tunneling," T. Albu, J. C. Corchado, and D. G. Truhlar, Journal of Physical Chemistry A 105, 8465-8487 (2001).

"Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-dimensional Rate Constant Calculation for a Six-Atom system," J. Pu, J. C. Corchado, and D. G. Truhlar, Journal of Chemical Physics 115, 6266-6267 (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," C. Alhambra, J. Corchado, M. L. Sánchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B 105, 11326-11340 (2001).

"Quantum Mechanical Methods for Enzyme Kinetics ," J. Gao and D. G. Truhlar, in Annual Review of Physical Chemistry, Vol. 53 (Annual Reviews, Inc., Palo Alto, CA, 2002), pp. 467-505.

"Quantum Mechanical Tunneling in Methylamine Dehydrogenase," C. Alhambra, M. L. Sánchez, J. C. Corchado, J. Gao, and D. G. Truhlar, Chemical Physics Letters 347, 512-518 (2001); reprinted correctly: 355, 388-394 (2002).

"The Incorporation of Quantum Effects in Enzyme Kinetics Modeling," D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sánchez, and J. Villà, Accounts of Chemical Research 35, 341-349 (2002). (special issue on Molecular Dynamics Simulations of Biomolecules)

"Parameterized Direct Dynamics Study of Rate Constants of H with CH4 from 250 to 2400 K," J. Pu and D. G. Truhlar, Journal of Chemical Physics 116, 1468-1478 (2002).

"Interpolated Algorithms for Large-Curvature Tunneling Calculations," A. Fernandez-Ramos, D. G. Truhlar, J. C. Corchado, and J. Espinosa-Garcia, Journal of Physical Chemistry A 106, 4957-4960 (2002).

"Tests of Potential Energy Surfaces for H + CH4 <-> CH3 + H2: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," J. Pu and D. G. Truhlar, Journal of Chemical Physics 117, 10675-10687 (2002).

"Dynamics of 1,2-Hydrogen Migration in Carbenes and Ring Expansion in Cyclopropylcarbenes," T. V. Albu, B. J. Lynch, D. G. Truhlar, A. C. Goren, D. A. Hrovat, W. T. Borden, and R. A. Moss, Journal of Physical Chemistry A 106, 5323-5338 (2002).

"Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions Against Accurate Quantum Mechanical Dynamics for H + CH4 -> H2+ CH3 in an Extended Temperature Interval," J. Pu and D. G. Truhlar, Journal of Chemical Physics 117, 1479-1481 (2002).

<"Quantum Dynamics of Hydride Transfer Catalyzed by Bimetallic Electrophilic Catalysis: Synchronous Motion of Mg2+ and H- in Xylose Isomerase," M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, Journal of the American Chemical Society 124, 7268-7269 (2002). (communication)

"Hydride Transfer Catalyzed by Xylose Isomerase: Mechanism and Quantum Effects," M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, Journal of Computational Chemistry 24, 177-190 (2003). (Peter Kollman Memorial Issue)

"Reduced Mass in the One-Dimensional Treatment of Tunneling," D. G. Truhlar and B. C. Garrett, Journal of Physical Chemistry A 107, 4006-4007 (2003).

"Force Field Variations along the Torsional Coordinates of CH3OH and CH3CHO," T. V. Albu and D. G. Truhlar, Journal of Molecular Spectroscopy 219, 129-131 (2003).

"Carbon Tunneling from a Single Quantum State," P. S. Zuev, R. S. Sheridan, T. V. Albu, D. G. Truhlar, D. A. Hrovat, and W. T. Borden, Science 299, 867-870 (2003).

"Free Energy Surface, Reaction Paths, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase, " T. D. Poulsen, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B 107, 9567-9578 (2003).

"Reaction-Path Energetics and Kinetics of the Hydride Transfer Reaction Catalyzed by Dihydrofolate Reductase," M. Garcia-Viloca, D. G. Truhlar, and J. Gao, Biochemistry 42, 13558-13575 (2003).

"Ensemble-Averaged Variational Transition State Theory with Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions," D. G. Truhlar, J. Gao, M. Garcia-Viloca, C. Alhambra, J. Corchado, M. L. Sanchez, and T. D. Poulsen, International Journal of Quantum Chemistry 100, 1136-1152 (2004). (Proceedings of the 2004 Sanibel Symposium).

"Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," H. Lin, Y. Zhao, B. A. Ellingson, J. Pu, and D. G. Truhlar, Journal of the American Chemical Society 127, 2830-2831 (2005).

"Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect is Different for Physiological and Slow Substrate of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures," D. Sicinska, D. G. Truhlar, and P. Paneth, Journal of the American Chemical Society 127, 5414-5422 (2005).

"A New Algorithm for Efficient Direct Dynamics Calculations of Large- Curvature Tunneling and Its Application to Radical Reactions with 9-15 Atoms," A. Fern?ndez-Ramos and D. G. Truhlar, Journal of Chemical Theory and Computation 1, 1063-1078 (2005).

"Combined Valence Bond-Molecular Mechanics Potential Energy Surface and Direct Dynamics Study of Rate constants and Kinetic Isotope Effects for the H + C2H6 Reaction," A. Chakraborty, Y. Zhao, H. Lin, and D. G. Truhlar, Journal of Chemical Physics 124, 044315/1-044315/14 (2006).

"Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and Intramolecular Correlated Motions," J. Pang, J. Pu, J. Gao, D. G. Truhlar, and R. Allemann, Journal of the American Chemical Society 128, 8015-8023 (2006).

"Coupling of Hydrogenic Tunneling to Active-Site Motion in the Hydrogen Radical Transfer Catalyzed by a Coenzyme B12-Dependent Mutase ," A. Dybala-Defratyka, P. Paneth, R. Banerjee and D. G. Truhlar, Proceedings of the National Academy of Sciences of the U.S.A. 104, 10774-10779 (2007).

"Multi-Coefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4 Reaction and its 12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," B. A. Ellingson, J. Pu, H. Lin, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A 111, 11706-11717 (2007).

"Explanation of the Unusual Temperature Dependence of the Atmospherically Important OH + H2S -> H2O + SH Reaction and Prediction of the Rate Constant at Combustion Temperatures," B. A. Ellingson, and D. G. Truhlar, Journal of the American Chemical Society 129, 12765-12771 (2007).

"Reactions of Hydrogen Atom with Hydrogen Peroxide," B. A. Ellingson, D. P. Theis, O. Tishchenko, J. Zheng, and D. G. Truhlar, J. Phys. Chem. A 111, 13554-13566 (2007).

"Density Functional Study of Methyl Radical Association Reaction Kinetics," J. Zheng, S. Zhang, and D. G. Truhlar, Journal of Physical Chemistry A 112, 11509-11513 (2008).

"Mechanistic Analysis of the Base-Catalyzed HF Elimination from 4-Fluoro-4-(4'-nitrophenyl)butane-2-one Based on Liquid-Phase Kinetic Isotope Effects Calculated by Dynamics Modeling with Multidimensional Tunneling," Y. Kim, A. V. Marenich, J. Zheng, K. H. Kim, M. Kołodziejska-Huben, M. Rostkowski, P. Paneth, and D. G. Truhlar, Journal of Chemical Theory and Computation 5, 59-67 (2009).

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