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Yirong Mo, Ph.D.

 

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Research Interests

The research in our groups centers on the development and applications of novel theoretical methods to chemical and biological processes. Our current focuses are:

Inter- and Intra-Molecular Electron Transfer

Over the recent several years, we have been developeing a novel approach called block-localized wavefunction (BLW) method. This method successfully incorporates the characters of both valence bond (VB) and molecular orbital (MO) theories, e.g., the physical intuition of the VB theory and the computational efficiency of the MO theory. In this method, the electrons and primitive orbitals are partitioned into several subgroups and each block molecular orbital is expanded in only one subspace. While block localized molecular orbitals in the same subspace are constrained to be orthogonal, orbitals between different subspaces are free to overlap. In fact, a BLW corresponds to a resonance structure (or diabatic state). Based on the BLW, an energy decomposition scheme (BLW-ED) has been proposed to probe the nature of intermolecular interactions. In addition, we have developed a MOVB method which has been incorporated with quantum mechanical and molecular mechanical Monte Carlo simulation codes. As a consequence, reactions in solution, which is described with a set of resonance structures, can be studied in a QM/MM way.

Currently we are extending the BLW method to the study of electron transfer effect in electron donor-bridge-electron acceptor (DBA) complexes and nonlinear optical (NLO) organic molecules, probe the resonance effect in various conjugated systems, the analysis of inter- and intra-molecular interactions, charge transfer stability across the protein/solvent interface, electronic polarization of the main chain carbonyl groups in proteins and the frequency shifts of hydrogen bonds. In particular, we intend to establish the correlation of the electron transfer efficiency with the donor/acceptor and bridge groups and the media effect for DBA complexes, and explore the structure-property relationships in NLO materials.

Modeling and Engineering of Enzymes

Enzymes are able to catalyze biochemical reactions that could not readily occur without them under mild conditions. Understanding how enzymes work is one of central goals in biochemistry. Computationally, molecular dynamics simulations with combined QM/MM methods have been developed and applied to elucidate the enzymatic reactivity fruitfully. Our interests in this arena are the development of novel approaches to model and engineer pesticide-degrading enzymes with higher activity and diversity.

It has been found that phosphotriesterase (PTE), isolated from wild-type, soil-dwelling bacteria Pseudomonas diminuta, can catalyze the hydrolysis of a few organophosphates, which have been widely used as pesticides and nerve chemical agents. Our research is aimed toward elucidating the catalytic mechanism of bacterial PTE on organophosphates and engineering this enzyme for increased catalytic efficiency and diversity. The fact that PTE is specific only to a few target organophosphate molecules and that PTE exhibits varied activities underscores the necessity and importance of improving our understanding of this enzyme and its mechanism of action. Better understanding will enable the design of novel PTEs having enhanced activity and applicability toward the broad array of organophosphates currently used as pesticides and chemical nerve agents. We hypothesize that a theoretical description of the structure and dynamics of PTE would elucidate the substrate-ligand interactions and the reaction mechanism, and a subsequent computational protein design would lead to novel PTE mutants with high efficiency in catalyzing the hydrolysis of a broad range of organophosphates from the nature and battlefield.

Funding Agencies

 

National Science Foundation (NSF)

National Institute of Health (NIH)

Keck Foundation