Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments
Punwong, Chutintorn
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https://hdl.handle.net/2142/72400
Description
Title
Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments
Author(s)
Punwong, Chutintorn
Issue Date
2009
Doctoral Committee Chair(s)
Martinez, Todd J.
Department of Study
Center for Biophysics and Computational Biology
Discipline
Biophysics and Computational Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Chemistry, Physical
Biophysics, General
Abstract
Retinal Protonated Schiff Base (RPSB) is the chromophore employed by the rhodopsin family of proteins, which includes rhodopsin (Rh), bacteriorhodopsin (bR) and halorhodopsin (hR). Photoisomerization of RPSB from the all-trans to 13-cis conformation triggers ion transport across the cell membrane in hR and bR. Visual perception in the eye is initiated by RPSB isomerization from 11-cis to all-trans conformation in Rh. An important unresolved question is the role of the protein environment in altering the photochemical mechanism. We have investigated the detailed photochemical mechanism in RPSB using the full multiple spawning method to describe quantum mechanical effects of the nuclear degrees of freedom. Simulations are carried out in isolation as well as a solvated (methanol) and protein environments. A reparameterized multireference semiempirical method is used to describe the ground and excited electronic states of the chromophore and the environment is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find good agreement. The results from these simulations provide a much more complete picture of the role of complex environments in influencing photochemical mechanism and achieving bond selectivity in isomerization.
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