**************** The 2nd., Lab Seminar ****************************

Date: Thu, May 21, 2009  PM 2:30-

Place: No.616 Seminar room
　　　　　　 Graduate School of Information Science

Speaker: Yoshiyuki Koyano

Title: Fragment Molecular orbital Method-Based Molecular Dynamics (FMO-MD)
as a Simulator for Chemical Reactions in Explicit Solvation
Y. Komeiji et al., J Comput. Chem., 30, 40 (2009).

Abstract:
 Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., 
Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large 
molecular systems. Here, FMO-MD was implemented to conduct full quantum 
simulations of chemical reactions in explicit solvation. Several FMO-MD 
simulations were performed for a sphere of water to find a suitable simulation 
protocol. It was found that annealing of the initial configuration by a 
classical MD brought the subsequent FMO-MD trajectory to faster stabilization, 
and also that use of bond constraint in the FMO-MD heating stage effectively 
reduced the computation time. Then, the blue moon ensemble method (Sprik 
and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested 
by calculating free energy profiles of the Menschutkin reaction (H3N + CH3Cl 
--> +H3NCH3 + Cl-) in the presence and absence of the solvent water via 
FMO-MD. The obtained free energy profiles were consistent with the Hammond 
postulate in that stabilization of the product by the solvent, namely hydration 
of Cl-, shifted the transition state to the reactant-side. Based on these 
FMO-MD results, plans for further improvement of the method are discussed.

*******************************************************************