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

International audienceIt 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

Model potentials in liquid water ionization by fast electron impact

International audienceWe study the ionization of water molecules in liquid phase by fast electron impact. We use our previous first-order model within an independent electron approximation that allows the reduction of the multielectronic problem into a monoelectronic one. The initial molecular states of the liquid water are represented in a realistic way through a Wannier orbital formalism. We complete our previous study by taking into account approximately the influence of the passive electrons of the target by means of different model potentials. We compute multiple differential cross sections for the most external orbital 1B1 and compare them with other results

Double differential cross sections for liquid water ionization by fast electron impact

International audienceIn this work we study theoretically the single ionization of liquid water by impact of energetic electrons. A realistic description of the wavefunction for an isolated water molecule in the liquid phase is made by means of a Wannier orbital formalism. We develop a first order model within the framework of an independent electron approximation in which the relaxation of the target is not taken into account. The double differential cross sections are computed and compared with experimental data and theoretical calculations for gas phase

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

International audienceWe 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

Theoretical study of the ionization of liquid water from its several initial orbitals by fast electron impact

International audienceWe theoretically study the single ionization of liquid water by energetic electrons through one active-electron first-order model. We analyze the angular ejected electron spectra corresponding to the most external orbitals 1B1, 2A1, 1B2 and 1A1 of a single water molecule. We work to create a realistic description of those orbitals corresponding to single molecules in the liquid phase. This goal is achieved by means of a Wannier orbital formalism. Multiple differential cross sections are computed and compared with previous calculations for both liquid and gas phases. In addition, our present results are integrated over all orientations and compared with experimental ones for randomly oriented vapour water molecules, as no experiments currently exist for the liquid phase. Moreover, we estimate the influence of the passive electrons on the reaction by means of a model potential

酸素K殻イオン化によって起こるデオキシリボースの分解過程

本研究では，電離放射線のエネルギー付与直後に起こる初期過程を明らかにすることを目的として，放射光を用いた特定元素のイオン化後のフラグメントイオンの質量分析やX線吸収分光実験を行った．DNA鎖の一部を構成する糖部位（デオキシリボース：dR）の薄膜上に水分子の層を吸着させた試料薄膜に対して酸素K殻イオン化閾値以上のエネルギーを持つ軟X線(560 eV)を照射し，照射中に表面から脱離するイオンの質量分析の結果から分解過程を推察した．その結果イオン化直後の10 fsという早い時間に，dR分子から水和水分子へプロトン移動が起こることによってH3O+が生成することが予想された．さらに，イオン脱離観測前後のX線吸収スペクトルの変化から，乾燥dR薄膜への軟X線照射では，フラノース五員環の分解に由来したC-O結合の切断が観測されたが，水和dR薄膜では，その変化は大幅に抑えられる一方，新たにカルボキシル基の生成に由来したスペクトルの変化が見られた．これらのことから，水和水分子は電離放射線の直接効果によってdR部位が修復困難な構造になることを抑える働きを持つと推察した．第12回分子化学討論会2018福

Soft X-ray Radiation and Monte Carlo Simulations: Good Tools to Describe the Radiation Chemistry of Sub-keV Electrons

International audienceThe description of the biological effects of ionizing radiation requires a good knowledge of the dose deposition processes at both the cellular and molecular scales. However, experimental studies on the energy deposition specificity of sub-keV electrons, produced by most radiations, including high-energy photons and heavy ions, are scarce. Soft X-rays (0.2–2 keV) are here used to probe the physical and physico-chemical events occurring upon exposure of liquid water to sub-keV electrons. Liquid water samples were irradiated with a monochromatic photon beam at the SOLEIL synchrotron. Hydroxyl radical quantification was conducted through HO• scavenging using benzoate to form fluorescent hydroxybenzoate. The yields of HO• radicals exhibit a minimum around 1.5 keV, in good agreement with indirect observation. Moreover, they are relatively independent of the benzoate concentration in the range investigated, which corresponds to scavenging times of 170 ns to 170 ps. These results provide evidence that sub-keV electrons behave as high linear energy transfer particles, since they are able to deposit tens to hundreds of electronvolts in nanometric volumes

Ultrafast nonadiabatic fragmentation dynamics of biomolecules

International audienceFragmentation of doubly charged biomolecules, uracil and amino acids, has been investigated using different ab inito Molecular Dynamics Methods. Time-Dependent Density Functional Theory Molecular Dynamics give a description of the non-adiabatic effects, the charge redistributions that occur in the first few femtoseconds and reveal the importance of the chemical environment. The combination of different techniques allow us to interpret the complex multicoincident spectra obtained experimentally when the molecules collides with ions or are excited with synchrotron radiation