[BANANA] Berkeley Lab - Scientific Computing Seminar, May 11, 2007

[Parry Husbands]

Date: Friday, May 11, 2007
Time: 2:30pm-3:30pm
Location: Building 50F-1647

Seminar Speaker: Edina Rosta
                  Department of Chemistry
                  University of Southern California
                  http://www-rcf.usc.edu/~rosta/

Title: Obtaining Free Energy Profiles of Enzymatic Reactions Using QM/MM
        Simulations: Methods and Applications

Abstract:

Reliable studies of enzymatic reactions by combined quantum mechanical  
/molecular
mechanics (QM/MM) approaches, with an ab initio description of the quantum  
region,
presents a major challenge to computational chemists. The main problem is  
the need
for very large computer time to evaluate the QM energy, which in turn  
makes it
extremely challenging to perform proper configurational sampling. The  
first part
of this talk presents a method for evaluating ab initio QM/MM free energy  
surfaces
and activation free energies of reactions in enzymes and in solutions by  
using the
Empirical Valence Bond (EVB) method as a reference potential and then  
evaluating
the free energies of transfer from the EVB to the QM/MM surfaces. The  
advance
offered by the present approach is particularly significant since it  
evaluates
the free energy associated with both the substrate and the solvent motions.

The second part of this talk is focused on the hydrolysis of phosphate  
ester anions
in solutions and in proteins, which is a problem of a significant current  
interest.
I will discuss an exploration of this problem by systematic calculations  
of the
landscape of the potential surfaces of the reactions of a series of  
phosphate
esters with different leaving groups. These calculations involve ab initio  
studies
with a variety of different implicit solvent models and explicit QM/MM  
simulations.

Sponsor of Seminar: Lin-Wang Wang