个人简介

lbert Hofmann Centennial Prize - Organic Chemistry Institute, Univeristy of Zurich, 2006 Dirac Medal of the World Association of Theoretically Oriented Chemists, 2000

研究领域

Chemical Biology/Chemical Physics/Chemical Theory & Computation/Organic Chemistry/Energy & Catalysis

We develop computational methods to study systems of biological interest. In each project, we identify a question of biological or chemical significance. Then, we develop the theory and implement it in a computer program to carry out detailed simulations of the system. In particular, we combine quantum mechanics and molecular mechanics (QM/MM) to model large molecular systems, including proteins and nucleic acids. The focus of our group includes (1) development of novel combined QM/MM methods to study chemical and biological reactions, (2) an understanding of the origin of enzyme catalysis, and (3) modeling the diffusion and interactions of macromolecular particles in cellular environment.

近期论文

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Gao, Jiali; Wong, Kin-Yiu; Major, Dan T.; Cembran, Alessandro; Song, Lingchun ; Lin, Yen-lin; Fan, Yao; Ma, Shuhua; "Kinetic Isotope Effects from Hybrid Classical and Quantum Path Integral Computations." In Kinetic Isotoped Effects in Enzyme Catalysis, Eds. R. Alleman and M. Scruton, RSC Biomolecular Sciences, 2009, pp 105-131. Shi, Lei; Cembran, Alessandro; Gao, Jiali; Veglia, Gianluigi; "Tilt and Azymuthal angles of a Transmembrane Peptide: A Comparison of Molecular Dynamics Calculations and Solid-State NMR Data of Sarcolipin in Lipid Membranes." Biophysical Journal, 2009, 96, 3648-3662. Valero, Rosendo; Song, Lingchun; Gao, Jiali; Truhlar, Donald G.; "Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase SN2 Reaction of Acetate Ion with 1,2-Dichloroethane." Journal of Chemical Theory and Computation, 2009, 5, 1-22. Erratum: 5, 2191. Wangshen Xie, Jingzhi Pu and Jiali Gao; "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function." Journal of Physical Chemistry A, 2009, 113, 2109-2116. Lingchun Song, Yirong Mo, and Jiali Gao,; "An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane". Journal of Chemical Theory and Computation, 2009, 5, 174-185. Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G.; Gao, Jiali; "X-Pol Potential: An Electronic Structure Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water." Journal of Chemical Theory and Computation, 2009, 5, 459-467. Lucia Becucci, Alessandro Cembran, Christine B. Karim, David D. Thomas, Rolando Guidelli, Jiali Gao, and Gianluigi Veglia,; "On the Function of Pentameric Phospholamban: Ion Channel or Storage Form?," Biophysical Journal (Letter), 2009, 96, L60-L62. Emilia L. Wu, Kin-Yiu Wong, Xin Zhang, Keli Ha, Jiali Gao,; "Determination of the Structure Form of the Fourth Ligand of Zinc in Acutolysin A using Combined Quantum Mechanical and Molecular Mechanical Simulation," Journal of Physical Chemistry B, 2009, 113, 2477-2485. J. Javier Ruiz-Pernia, Mireia Garcia-Viloca, Sudeep Bhattacharyya, Jiali Gao, Donald G. Truhlar, and Inaki Tunon,; "Critical Role of Substrate Conformational Change in the Proton Transfer Process Catalyzed by 4-Oxalocrotonate Tautomerase," Journal of the American Chemical Society, 2009, 131, 2687-2698. B. B. Brooks, C. L. Brooks III, A. D. MacKerell, Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. D. Wong, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Wang, D. M. York, M. Karplus,; "CHARMM: The Biomolecular Simulation Programm," Journal of Computational Chemistry, 2009, 30, 1545-1614. Kin-Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen-lin Lin, Alessandro Cembran, Jiali Gao,; "Quantum Mechanical Methods for Biomolecular Simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 79-101. DOI 10.1007/078-1-4020-9956-4_4. Tai-Sung Lee, George M. Giambasu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Timothy J. Giese, Jiali Gao and Darrin M. York,; "Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations," in Multi-scale Quantum Models for Biocatalysis, D. M. York and T.-S. Lee eds. 2009, Springer Science+Business Media B. V. pp. 377-408. Lingchun Song, Jaebeom Han, Yen-lin Lin, Jiali Gao,; "Explicit Polarization (X-Pol) Potential Using ab initio Molecular Orbital Theory and Density Functional Theory," Journal of Physical Chemistry A, 2009, 113, 11656-11664. DOI: 10.1021/jp902710a Alessandro Cembran, Lingchun Song, Yirong Mo, and Jiali Gao,; "Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces". Journal of Chemical Theory and Computation, 2009, 5, 2702-2716. DOI: 10.1021/ct9002898 Kin-Yiu Wong, John P. Richard, Jiali Gao,; "Theoretical Analysis of Kinetic Isotope Effects on Proton Transfer Reactions between Substituted _-Methoxystyrenes and Substituted Acetic Acids," Journal of the American Chemical Society, 2009, 131, 13963-13971. Dan T. Major, Annie Heroux, Allen M. Orville, Michael P. Valley, Paul F. Fitzpatrick, Jiali Gao,; "Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction," Proceedings of the National Academy of Sciences, 2009, 106, 20736-20739. Yen-lin Lin, Jiali Gao,; "Protonation State of the External Pyridoxal-5«-phosphate Schiff Base in Dopa Decarboxylase," Biochemistry, 2010, 49, 84-84. Alessandro Cembran, Apirak Payaka, Yen-lin Lin, Wangshen Xie, Yirong Mo, Lingchun Song and Jiali Gao; "A Non-Orthogonal Block-Localized Effective Hamiltonian Approach for Chemical and Enzymatic Reactions," Journal of Chemical Thoery and Computation, 2010, 6, 2242-2251. Jiali Gao, Alessandro Cembran and Yirong Mo;"Generalized X-Pol Theory and Charge Delocalization States." Journal of Chemical Theory and Computation, 2010, 6, 2402-2410. DOI: 10.1021/ct100292g. Alessandro Cembran, Peng Bao, Yingjie Wang, Lingchun Song, Donald G. Truhlar and Jiali Gao"On the Interfragment Exchange in the X-Pol Method." Journal of Chemical Theory and Computation, 2010, 6, 2469-2476. DOI: 10.1021/ct100268p.