Abstract
We simulated the interactions of molecules in the compounds in microcosm and used parallel computing to reduce the calculating time by a software of Quantum Physics and Quantum Chemistry in the servers of National Center for High-Performance Computing. The software, Gaussian 98, can simulate the mechanism of cell wall biosynthesis in bacteria. The major component in bacterial cell wall is peptidoglycan which is composed with a group of sugars, N-acetylglucosamine, and N-acetylmuramic acid and different kinds of amino acids. The bacterial enzyme, MurA (UDP-N-acetylglucosamine enolpyruyl transferase), catalyzes the synthesis of peptidoglycan. By transfering enolpyruvate from phosphoenolpyruvate to UDP-N-acetylglucosamine and released an inorganic phosphate .We attempted to identify the transition state and intermediate state of the reaction. To make the simulation more similar to the real environment, the effect of molecules and the solvent in the reaction and the participation of the enzyme were considered. In the calculation, we obtained three kinds of pathway in Transition state search, that would facilitate our understanding on how the enzyme affects the reaction. We anticipate that this research can help other scientists more to understand the mechanism in the future.