Title: Simulation Methods for Studying Reactions in Proteins

Speaker: Prof. Markus Meuwly, University of Basel, Switzerland

Date/Time: Wednesday, July 28, 2010, 1:30 pm       

Location: CSRI Building/Room 90 (Sandia NM)

Brief Abstract: Chemical reactions involve bond-breaking and bond-forming processes. As such, they are fundamental to chemistry and biology alike. In many cases, mechanistic aspects of the reactions (``which reaction partners interact at which time with each other'') are of interest. However, many details are elusive experimentally, because ``the reaction''itself is a transient process, the transition state is unstable and thus, the most interesting regions along a reaction path can not be investigated experimentally in a direct fashion. To shed light on such questions, theoretical and computational work has become invaluable companions to experimental efforts in understanding particular reaction schemes.
In this seminar I will discuss two recently developed schemes to follow chemical reactions in complex systems. Both approaches have been developed with an emphasis on allowing simulations with "MD speed" - in contrast to ab initio MD simulations. Molecular Mechanics with Proton Transfer (MMPT) is specialized to cases where a proton (PT) or a hydrogen (HT) is transferred between a donor and an acceptor atom. The method builds on a parametrization of accurate ab initio calculations for model PT/HT systems which can be morphed into chemically more representative shapes. Adiabatic reactive MD (ARMD) starts from two separate force fields for the product and educt states and follows the dynamics on the lower of the two. Whenever crossings are energetically possible, the surfaces are mixed and the dynamics is followed through the intersection. Specific applications to ligand transfer in proteins and HT in small molecules are discussed.

CSRI POC: Anatole von Lilienfeld, 505-284-8829