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Research Abstracts Online
January - December 2011

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University of Minnesota Twin Cities
College of Science and Engineering
Department of Chemistry

PI: Jiali Gao, Fellow

Computer Simulation of Chemical and Biochemical Interactions

The Gao group is continuing their investigations in several areas, including: the dynamics and mechanism of enzymatic reactions: the development of a quantal force field, called X-Pol, for biomolecular simulations; the simulation and modeling of macromolecular assembly and diffusion in cells; and solvent effects on chemical reactions and interactions in condensed phases. The researchers’ approach is based on statistical mechanical Monte Carlo and molecular dynamics (MD) simulations, making use of combined quantum mechanical and molecular mechanical (QM/MM) potentials.

The first project area involves MD simulations of enzymatic reactions, including the demethylation reactions catalyzed by a FAD-dependent enzyme and a class of metalloenzymes employing a non-heme high-valent Iron-oxo intermediate, the final step in nucleotide UMP biosynthesis by OMP decarboxylase, and proton-coupled electron transfer processes in ribonucleotide reductase and in photosystem II. These studies will provide a deeper understanding of the reaction mechanism and the origin of catalysis.

The second project aims at the development of the explicit polarization (X-Pol) potential as a next-generation and quantal force field for biomolecular and materials simulations. This work represents a novel approach to describe molecular systems and to determine the potential energy surface. The development of the X-Pol potential is a collaboration with Regents Professor Donald Truhlar (Chemistry).

The third project is aimed at developing a simulation system to understand protein diffusion processes in cellular environment. This is a relatively new project involving methodology and software development.

The final project area focuses on development of novel computational techniques including mixed molecular orbital and valence bond (MOVB) and block-localized density functional theory (BLDFT) and applications to modeling solvent effects on SN2 reactions and the choice of geometrical and energy-gap solvent reaction coordinates in potential of mean force calculations.

Group Members

Peng Bao, Research Associate
Kwok Siang Beh, Undergraduate Student
Alessandro Cembran, Research Associate
Jorge M. Estevez, Graduate Student
Yahid Eyorokon, Collaborator
Jaebeom Han, Graduate Student
Jennifer Hirschi, Research Associate
Miho Isegawa, Research Associate
Pinsker Yen-lin Lin, Graduate Student
Shuhua Ma, Research Associate
Dan T. Major, Research Associate
Michael J. Mazack, Graduate Student
Yirong Mo, Department of Chemistry, Western Michigan University, Kalamazoo, Michigan
Kwangho Nam, Graduate Student
Makenzie Provorse, Graduate Student
Carlos A. Ramirez-Mondragon, Graduate Student
Pavel L. Rehak, Graduate Student
Lingchun Song, Research Associate
Yingjie Wang, Graduate Student
Supachai Wanprakhon, Staff
Kin-Yiu Wong, Graduate Student
Wangshen Xie, Graduate Student
Peng Zhang, Graduate Student
Yong Tiger Zhang, Department of Biochemistry, Albert Einstein College of Medicine, New York, New York
Yan Zhou, Graduate Student