Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

Marie-Anne Hervé Du Penhoat,Rodolphe Vuilleumier,Anis Hamila,Marie-Françoise Politis,Kentaro Fujii,Akinari Yokoya,Marie-Pierre Gaigeot

doi:10.3390/qubs3040024

Abstract

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

Highlights

Ionizing radiations, such as hard X-rays, high-energy electrons, or swift ions, are used in cancer therapies to kill malignant cells
In a previous paper [17], we have modeled the dynamics induced by the removal of oxygen K-shell electrons from a deoxyribose molecule embedded in liquid water
Two additional Molecular Dynamics (MD) were performed, in which the core hole was localized on a water molecule donating an hydrogen bond (HB) either to O1 or O4

Summary

Introduction

Ionizing radiations, such as hard X-rays, high-energy electrons, or swift ions, are used in cancer therapies to kill malignant cells. It has been suggested that inner-shell ionization in DNA constituent atoms could be partly responsible for cell death upon irradiation with heavy ions [1] or γ-rays [2]. Core ionization leads to the double ionization of the molecule and to the emission of two few hundred electronvolts electrons. In the sub-keV energy range, electrons have inelastic mean free paths of a few nanometers [3], and may induce clusters of ionizations in the vicinity of the core-ionized molecule. If taking place in DNA, or its hydration layer, inner-shell ionizations are expected to induce complex, irreparable, DNA damage [4]

Methods

Results

Conclusion