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Research |
| We are applying combined quantum mechanical and molecular mechanical methods both at the semiempirical and ab initio level to enzymatic processes in solution. At present, we focus on three fundamental areas of biological interest: (1) mechanisms of enzymatic reactions including phosphate transfer processes and carbocation cyclizations, (2) electronic and chemical transformations at the electronic excited states, and (3) vibrational energy relaxation and dynamics of substrate-protein interactions in the enzyme active site. |
RNA
| Solvent effects have profound influence on chemical reactions and reactivity. In many cases the direction of a reaction may be altered by changing the solvent. The information gained in computer simulations may be used in rational design of catalytic agents for organic synthesis. Several reactions are currently being investigated, including photoisomerization, pericyclic and nucleophilic addition/substitution reactions. We have recently developed a method, combining features of molecular orbital and modern valence bond theory, to investigate the resonance and stereoelectronic effects in organic molecules. |
| Another exciting area of research is microporous materials and catalysis. In particular, the adsorption, binding and reaction mechanism associated with catalytic processes in zeolites are being studied. Microporous materials such as zeolites are powerful industrial catalysts and have a wide range of applications. Computational methods developed in our laboratory are capable of providing answers at the molecular level to numerous questions of chemical and industrial interest. An understanding of the catalytic mechanism will enable chemists to design and synthesize more powerful catalysts. |
| Undoubtedly, the key factor that determines the success of condensed phase simulations is the availability of accurate intermolecular potential functions. Traditionally, empirical MM potentials are used; however, the form of these functions are not appropriate for describing chemical reactions. The combined QM/MM approach takes advantage of the accuracy and generality of QM calculations but still retains the computational efficiency of the MM force field by treating the solute quantum-mechanically and the surrounding solvent molecules classically. The use of QM methods in statistical mechanical Monte Carlo and molecular dynamics simulations allows us to simulate chemical processes in solution. Current interest includes development of algorithms for even more accurate QM/MM calculations, a mixed molecular orbital-valence bond (MOVB) approach for simulating chemical processes, and molecular orbital-based polarization force fields.. |