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1983-1990     1991-1993     1994-1996     1997-1999     2000-2002     2003-2005    2006-2008     2006-present

  1. Garcia-Viloca, M.; Alhambra, C.; Truhlar, D. G.; Gao, J. "Hydride Transfer Catalyzed by Xylose Isomerase: Mechanism and Quantum Effects" Journal of Computational Chemistry, 2003, 24, 177-190.
  2. Devi-Kesavan, L. S.; Gao, J. "Combined QM/MM Study of the Mechanism and Kinetic Isotope Effect of the Nucleophilic Substitution Reaction in Haloalkane Dehalogenase." Journal of the American Chemical Society, 2003, 125, 1532-1540.
  3. Cubero, E.; Luque, F. J.; Orozco, M.; Gao, J. "Perturbation Approach to Combined QM/MM Simulaitons of Solute-Solvent Interactions in Solution" Journal of Physical Chemistry B, 2003, 107, 1464-1471.
  4. Gao, J. "Catalysis Involving Enzyme Conformational Change as Illustrated by Orotidine 5'-Monophosphate Decarboxylase." Current Opinion in Structural Biology, 2003, 13, 184-192.
  5. Devi-Kesavan, L. S.; Gao, J. "Semiempirical QM/MM Potential with Simple Valence Bond (SVB) for Enzyme Reactions. Application to the Nucleophilic Addition Reaction in Haloalkane Dehalogenase." Theoretical Chemistry Accounts, 2003, 109, 133-139.
  6. Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. "Importance of Substrate and Cofactor Polarization in the Active Site of Dihydrofolate Reductase" Journal of Molecular Biology, 2003, 327, 549-560.
  7. Poulsen, T. D.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G."Free Energy Surface, Reaction Path, and Kinetic Isotope Effect of Short-Chain Acyl-CoA Dehydrogenase." Journal of Physical Chemistry B, 2003, 107, 9567-9578.

  8. Rajamani, R.; Naidoo, K. J.; Gao, J. "Implementation of an Adaptive Umbrella Sampling Method for the Calculation of Multidimensional Potential of Mean Force for Chemical Reaction in Solution" Journal of Computational Chemistry, 2003, 24, 1775-1781.

  9. Gao, J.; Garcia-Viloca, M.; Poulsen, T. D.; Mo, Y. "Solvent Effects, Reaction Coordinates, and Reorganization Energies on Nucleophilic Substitution Reactions in Aqueous Solution" Advances in Physical Organic Chemistry, 2003, 38, 161-181.

  10. Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. "Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase" Biochemistry, 2003, 42, 13558-13575.

  11. Wierzchowski, S. J.; Kofke, D. A.; Gao, J. "Hydrogen fluoride phase behavior and molecular structure from a combined QM/MM polarizable potential function" Journal of Chemical Physics, 2003, 119, 7365-7371.

  12. Mo, Y.; Schleyer, P. v. R.; Wu, W.; Lin, M.; Zhang, Q..; Gao, J. "Importance of electronic delocalization on the C-N bond rotation in HCX(NH2) (X = O, NH, CH2, S, and Se)." Journal of Physical Chemistry A, 2003, 107, 10011-10018.

  13. Rajamani, R. ; Gao, J. "Balancing kinetic and thermodynamic control: The mechanism of  carbocation cyclization by squalene cyclase." Journal of the American Chemical Society, 2003, 115, 12768-12781.

  14. Garcia-Viloca, M.; Gao, J.; M. Karplus, Truhlar, D. G. "How enzymes work: Analysis by modern reaction rate theory and computer simulations" Science, 2004, 303, 186-195.

  15. Garcia-Viloca, M.; Gao, J. "Generalized Hybrid Orbital for the Treatment of Boundary Atoms in Combined Quantum Mechanical and Molecular Mechanical Calculations using the Semiempirical Parameterized Model 3 Method." Theoretical Chemistry Accounts, 2004, 111, 280-286.

  16. Pu, J.; Truhlar, D. G.; Gao, J. "The Generalized Hybrid Orbital (GHO) Method for Ab Initio Combined QM/MM Calculations" Journal of Physical Chemistry A, 2004, 108, 632-650.

  17. Gao, J.; Byun, K. L.; Kluger, R. "Catalysis by Protein Conformational Change." Topics in Current Chemistry, 2004, 238, 113-136.

  18. Nam, K.; Prat-Resina, X.; Garcia-Viloca, M.; Devi-Kesavan, L. S.; Gao, J. "Dynamics of an Enzymatic Substitution Reaction in Haloalkane Dehalogenase" Journal of the American Chemical Society, 2004, 126, 1369-1376.

  19. Mo, Y.; Wu, W.; Song, S.; Lin, M.; Zhang, Q.; Gao, J. "The magnitude of hyperconjugation in ethane: A perspective from ab initio valence bond theory" Angewandte Chemie International Edition, 2004, 43, 1986-1990.

  20. Garcia-Viloca, M.; Nam, K.; Alhambra, C.; Gao, J. "Solvent and Protein Effects on the Asymmetric Stretch Frequency of Azide Ligand in the Active Site of Carbonic Anhydrase: a Combined QM/MM  Study" Journal of Physical Chemistry A, 2004, 108, 13501-13512.

  21. Pu, Jingzhi; Gao, Jiali; Truhlar, Donald G. "Combining Self-Consistent-Charge Density-Functional Tight-Binding  (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital  (GHO) Method" Journal of Physical Chemistry A, 2004, 108, 5454-5463.

  22. Xu, Dingguo; Guo, Hua; Gao, Jiali; Cui, Qiang "A QM/MM Study of a Nucleophilic Aromatic Substitution Reaction  Catalyzed by 4-Chlorobenzoyl-CoA Dehalogenase." Chemical Communication, 2004, 892-893.

  23. Garcia-Viloca, Mireia; Poulsen, Tina D.; Truhlar, Donald G.; Gao, Jiali "Sensitivity of Molecular Dynamics Simulations to the Choice of the X-ray Structure Used to Model an Enzymatic Reaction" Protein Science, 2004, 13, 2341-2354.

  24. Hensen, Christian; Hermann, Johannes C.; Nam, K.; Ma, S.; Gao, J.; Höe, Hans-Dieter "A Combined QM/MM Approach to Protein-Ligand Interactions: Polarization Effects of the HIV-1 Protease on Selected High Affinity Inhibitors" Journal of Medicinal Chemistry, 2004, ASAP.

  25. Zhang, Yan; Sham, Yuk Y.; Rajamani, R.; Gao, J.; Portoghese, Philip S. "Mu Opioid Receptor Model in a Membrane-Aqueous System: Homology Modeling and Molecular Dynamic Simulation" ChemBioChem, 2004, in press.

  26. Truhlar, D. G.; Gao, J.; Garcia-Viloca, M.; Alhambra, C.; Corchado, J.; Sanchez, M. L.; Poulsen, T. D. "Ensemble-averaged variational transition state theory with optimized multidimensional tunneling for enzyme kinetics and other condensed-phase reactions" International Journal of Quantum Chemistry, Quantum Chemistry Symposium, 2004, 100, 1136-1152.

  27. Xu, Dingguo; Wei, Yanseng; Wu, Jingbo; Dunaway-Mariano, Debra; Guo, Hua; Cui, Qiang; Gao, Jiali "QM/MM Studies of the Enzyme-Catalyzed De-chlorination of  4-Chlorobenzoyl-CoA Provide Insight into Reaction Energetics." Journal of the American Chemical Society, 2004, 126, 13649-13658.

  28.  Nam, K.; Gao, J.; York, D. M. .An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations.. Journal of Chemical Theory and Computation,  2005, 1, 2-13.

  29. Zhang, Yan; Sham, Yuk Y.; Rajamani, R.; Gao, J.; Portoghese, Philip S. .Mu Opioid Receptor Model in a Membrane-Aqueous System: Homology Modeling and Molecular Dynamic Simulation. ChemBioChem, 2005, 6, 853-859.

  30. Pu, J.; Ma, S.; Gao, J.; Truhlar, D. G. .Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase.. Journal of Physical Chemistry B, 2005, 109, 8551-8556 (communication).

  31. Pu, J.; Gao, J.; Truhlar, D. G. .Generalized Hybrid Orbital Method for Combined Quantum Mechanical and Molecular Mechanical Calculations Based on Density Functional Theory and Hybrid Density Functional Theory.. ChemPhysChem, 2005, 6, 1853-1865.

  32. Major, D. T.; Gao, J. .Implementation of the Bisection Sampling Method in Path Integral Simulations.. Journal of Molecular Graphics and Modeling, 2005, 24, 121-127.

  33. Pu, J.; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. .Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase.. Journal of the American Chemical Society, 2005, 127, 14879-14886.

  34. Major, D. T.; York, D. M.; Gao, J. .Solvent Polarization and Kinetic Isotope Effects in Nitroethane Deprotonation and Implications to the Nitroalkane Oxidase Reaction.. Journal of the American Chemical Society, 2005, 127, 16374-16375.

  35. Bhattacharyya, S.; Ma, S.; Stankovich, M. T.; Truhlar, D. G.; Gao, J. .Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium Chain Acyl-CoA Dehydrogenase: The Effect of Mutaions on Enzyme Catalysis.. Biochemistry, 2005, 44, 16549-16562.


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Revised: November 01, 2006.