Search

We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1 s pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1 s core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule. [ABSTRACT FROM AUTHOR]

Abstract: Theoretical simulations are particularly well suited to investigate, at a molecular level, direct and indirect effects of ionising radiations in DNA, as in the particular case of irradiation by swift heavy ions such as those used in hadron therapy. In the past recent years, we have developed the modeling at the microscopic level of the early stages of the Coulomb explosion of DNA molecules immersed in liquid water that follows the irradiation by swift heavy ions. To that end, Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD) have been developed where localised Wannier orbitals are propagated. This latter enables to separate molecular orbitals of each water molecule from the molecular orbitals of the biomolecule. Our main objective is to demonstrate that the double ionisation of one molecule of the liquid sample, either one water molecule from the solvent or the biomolecule, may be in some cases responsible for the formation of an atomic oxygen as a direct consequence of the molecule Coulomb explosion. Our hypothesis is that the molecular double ionisation arising from irradiation by swift heavy ions (about 10% of ionisation events by ions whose velocity is about the third of speed of light), as a primary event, though maybe less probable than other events resulting from the electronic cascading (for instance, electronic excitations, electron attachments), may be systematically more damageable (and more lethal), as supported by experiments that have been carried out in our group in the 1990s (in studies of damages created by K holes in DNA). The chemical reactivity of the produced atomic oxygen with other radicals present in the medium will ultimately lead to chemical products that are harmful to DNA. In the present paper, we review our theoretical methodology in an attempt that the community be familiar with our new approach. Results on the production of atomic oxygen as a result of the double ionisation of water or as a result of the double ionisation of the Uracil RNA base will be presented. [Copyright &y& Elsevier]