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Title: Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

Abstract

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

Authors:
;  [1];  [2]
  1. Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse (France)
  2. Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay (France)
Publication Date:
OSTI Identifier:
22679020
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 145; Journal Issue: 5; Other Information: (c) 2016 Author(s); Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; CARBON MONOXIDE; COBALT; DEGREES OF FREEDOM; MOLECULAR DYNAMICS METHOD; MOLECULAR STRUCTURE; PROTEINS; RELAXATION; SIMULATION; VIBRATIONAL STATES

Citation Formats

Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr, Meier, Christoph, and Falvo, Cyril. Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein. United States: N. p., 2016. Web. doi:10.1063/1.4959859.
Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr, Meier, Christoph, & Falvo, Cyril. Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein. United States. doi:10.1063/1.4959859.
Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr, Meier, Christoph, and Falvo, Cyril. Sun . "Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein". United States. doi:10.1063/1.4959859.
@article{osti_22679020,
title = {Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein},
author = {Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr and Meier, Christoph and Falvo, Cyril},
abstractNote = {We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.},
doi = {10.1063/1.4959859},
journal = {Journal of Chemical Physics},
number = 5,
volume = 145,
place = {United States},
year = {Sun Aug 07 00:00:00 EDT 2016},
month = {Sun Aug 07 00:00:00 EDT 2016}
}
  • The probability for deactivation of CO(v = 2) and CO/sub 2/(101) on collision with polycrystalline silver surfaces has been measured. The deactivation probability for CO(v = 2) was found to decrease from 0.33 at 300 K to 0.20 at 440 K, while the deactivation probability for CO/sub 2/ (101) was found to decrease from 0.72 at 300 K to 0.37 at 440 K. Since no population was observed in the CO(v = 1) and CO/sub 2/ (001) intermediate levels, it appears that each deactivation proceeds completely to produce the vibrational ground level. The magnitudes for the deactivation probabilities and themore » temperature dependencies indicate that a dominant mechanism for relaxation involves trapping and subsequent deactivation by one or more of several mechanisms, including electron--hole pair formation, vibration-to-rotation energy transfer, or perhaps even transfer of energy to the surface phonons. The experiments were performed in a UHV chamber by using a tunable infrared laser source to excite gas-phase molecules vibrationally before their collision with the surface and by measuring the population of vibrationally excited molecules through their time-resolved infrared fluorescence.« less
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