Femtochemistry of ionized biomolecules immersed in water studied by molecular dynamics and time dependent density functional theory

M. A. HERVÉ DU PENHOAT; M. P. GAIGEOT; R. VUILLEUMIER; C. R. STIA; I. TAVERNELLI; M. F. POLITIS

Urabandai, Fukushima, Japan

Workshop; X International Workshop on Radiation Damage to DNA; 2008

In order to understand, at a molecular level, direct and indirect effects of ionizing radiations in DNA, in the particular case of irradiation by heavy ions, those used in hadron therapy, we are modelling different types of events. We have first modelled the production of HO2 radical in the ion track generated in liquid water irradiated by swift Argon ions with ab initio simulation by a combined Monte Carlo simulation and Car Parrinello Molecular Dynamics [1], and shown a very good agreement with the experimental measurement [2]. In order to complete this study, the early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water is investigated with Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD). Our aim is to verify that the double ionization of one target water molecule immersed in liquid water leads to the formation of an atomic oxygen as a direct consequence of the molecule coulomb explosion. To that end, we used TD-DFT MD in which effective molecular orbitals are propagated in time. We have investigated the double ionization of one target water molecule immersed in bulk water following the removal of two electrons from one of its four molecular orbitals, i.e. 1B1, 3A1, 1B2 and 2A1, in turn. We show that the doubly charged water molecule explodes into its three atomic fragments in less than 4 femtoseconds, leading to the formation of one isolated oxygen atom, while we observe also an ultra fast transfer of electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the most inner shell molecular orbitals. In parallel, we are studying the dissociation of ionized biomolecules in gas phase and in liquid phase. We are, thus, able to simulate the evolution of chemical primary event, in a dozen of femtoseconds, either when the holes are created in water or in the biomolecule. Some examples are shown in the case of the Uracil molecule. 1) M P Gaigeot , et al J. Phys. B: At. Mol. Opt. Phys. 2007 Vol 40 ,12) G. Baldacchino, et al .Nucl. Instrum. Methods. Phys. Res. B., 146:528, 1998.