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Abstract
Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals
is of particular importance to reveal the effect of hydroxyl radicals produced by
the secondary effect of radiation. Previous studies address the problem with truncated
DNA bases as ab-initio quantum simulation required to study such electronic spin dependent
processes are computationally expensive. Here, for the first time, we employ a multiscale
and hybrid Quantum-Mechanical-Molecular-Mechanical simulation to study the interaction
of OH radicals with guanine-deoxyribose-phosphate DNA molecular unit in the presence
of water where all the water molecules and the deoxyribose-phosphate fragment are
treated with the simplistic classical Molecular-Mechanical scheme. Our result illustrates
that the presence of water strongly alters the hydrogen-abstraction reaction as the
hydrogen bonding of OH radicals with water restricts the relative orientation of the
OH-radicals with respective to the the DNA base (here guanine). This results in an
angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen
abstraction mechanisms than previously anticipated for identical system in vacuum.
The method can easily be extended to single and double stranded DNA without any appreciable
computational cost as these molecular units can be treated in the classical subsystem
as has been demonstrated here.