Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

0475019 - ÚOCHB 2018 RIV US eng J - Journal Article
Kolář, Michal H. - Kubař, T.
Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer.
Journal of Physical Chemistry B. Roč. 121, č. 7 (2017), s. 1520-1532. ISSN 1520-6106. E-ISSN 1520-5207
Institutional support: RVO:61388963
Keywords : excited-state dynamics * excitation energy transfer * solvation dynamics
OECD category: Physical chemistry
Impact factor: 3.146, year: 2017

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
Permanent Link: http://hdl.handle.net/11104/0271902