Investigation of the fragmentation of core-ionised deoxyribose: a study as a function of the tautomeric form

Abstract

We have investigated the gas phase fragmentation dynamics following the core ionisation of 2-deoxy-D-ribose (dR), a major component in the DNA chain. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics simulations. The ultrafast dissociation dynamics of the core-ionised biomolecule, prior Auger decay, is first modelled for 10 fs to generate initial configurations (atomic positions and velocities) for the subsequent dynamics of the doubly ionised biomolecule in the ground state. The furanose, linear and pyranose conformations of dR were investigated. We show that fragmentation is relatively independent of the atom struck or of the duration of the core vacancy, but depends rather critically on the molecular orbital removed following Auger decay.

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

“…The elongation of the CO * bonds was always below 0.34 Å at the end of all the 9.7 fs core hole MD. These results are similar to those obtained in the gas phase [20]. Thus, the CO * bonds elongation does not seem to be influenced much by the DR environment.…”

“…Core holes were localized on the different carbon and oxygen atoms of the sugar (direct effect). The results will be compared to simulations of the isolated molecule [20] to infer the role of the environment on the dissociation patterns. Core holes were also localized on the water molecules forming an HB with the sugar (indirect effect).…”

“…On the contrary, although O * H bonds are not much affected by the presence of the K-shell vacancy on O * in the gas phase [20], these bonds may undergo very large elongations in liquid water, as shown in Table 2. In fact, the elongation of the O * H bonds could reach 0.93 Å at the end of the 9.7 fs core hole dynamics.…”

Chemical Understanding of the Limited Site-Specificity in Molecular Inner-Shell Photofragmentation

“…Other works that model x-ray photofragmentation also rely mainly on a statistical model, 21,23,[27][28][29][30] as a theoretical description addressing molecular dissociation after x-ray ionization is challenging. Recently, this statistical model has been challenged by experimental observation that a site-specific fragmentation pattern persists at similar internal energy content 20,24 and that a seemingly minor substitution in a non-ionized site of the molecule can drastically change the fragmentation pattern.…”

“…Our theoretical approach may present a route to efficient modeling of x-ray photofragmentation of molecules, which is complementary to approaches that do not take into account the specificity of the excited electronic states populated after Auger decay. 21,23,[27][28][29][30] Methods…”