Berkeley Lab Scientific Computing Seminar

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
Scientific Computing

Contact Esmond G. Ng EGNg@lbl.gov