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首页> 外文期刊>Quantum Beam Science >Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays
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Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

机译：AB Initio分子动力学模拟以通过同步X射线解释脱氧氧纤维中诱导的分子碎片

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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.
机译：已经提出，DNA原子中的核心电离可以诱导复杂，无法弥补的损伤。 Synchrotron软X射线已被用于探测DNA组分薄膜中这些事件引起的损伤。以互补方法，我们研究了在2-脱氧-D-核糖（DR）中的碳或氧k-壳电离后的碎片动力学，DNA链中的主要组分。还研究了糖水合层的核心电离。为此，我们使用最先进的AB初始密度泛函理论的分子动力学（MD）模拟。核心电离分子的超快解离动力学，先前的螺旋螺旋衰减是约10 fs的建模。我们表明，在螺旋衰减之前，DR或其水合层内的氧原子的核原子的核原子可以诱导质子转移到附近分子。在第二步中，我们模拟了核心孔动力学开始或结束时发生的螺旋钻效果。从最初核离子化氧原子（O *）定位的最深的价分子轨道中除去两种电子，并且该电子状态通过EHERFEST MD繁殖。我们展示了DR2 +分子C-O *键的超快解离，在大多数情况下，这似乎与螺旋衰减发生的时间无关。

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