An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting.
An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting.
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DOI：
10.1021/jp107723w
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发表时间：
2011-04-14
影响因子：
3.3
通讯作者：
Singer, Sherwin J.
中科院分区：
文献类型：
--
作者：
Hassanali, Ali A.;Zhong, Dongping;Singer, Sherwin J.
在本文中，我们继续探索环丁烷嘧啶二聚体的修复机制。我们发现，对C5-C5 ‘和C6-C6 ’键分裂的完整描述，除了涉及到内部二聚体坐标的变化外，还需要涉及溶剂坐标的多维处理。非平衡效应可能也很重要，尽管电子正向转移到二聚体后的初始条件，超出了本研究的范围，将最终决定这些效应的重要性。在C5-C5 ‘和C6-C6 ’键分裂的过程中，大量的多余电荷离域到溶剂上。我们已经证实，这不是用于该阴离子系统的电子密度泛函理论（DFT）方法与Schröinger基于方程的量子化学簇计算的产物。电荷离域的量和变异性随反应的进行而变化。C6-C6 ‘键的分裂伴随着C6和C6 ’碳原子上电子密度的增加以及这些原子附近水密度的增加。这些特征在我们的平衡伞采样模拟和非平衡轨迹中都可以观察到。
In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5′ and C6-C6′ bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Non-equilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects. Throughout the splitting of C5-C5′ and C6-C6′ bonds, a significant amount of excess charge is delocalized onto the solvent. We have verified that this is not an artifact of the electronic density functional theory (DFT) method used for this anionic system with Schröinger equation-based quantum chemical cluster calculations. The amount and variability of charge delocalization changes with the course of the reaction. The splitting of the C6-C6′ bond is accompanied by both an increase in electron density on the C6 and C6′ carbon atoms and an increase in the water density near those atoms. These features are observed both in our equilibrium umbrella sampling simulations and non-equilibrium trajectories.
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影响因子：
3.3
作者：
Geissler, PL;Dellago, C;Chandler, D
通讯作者：
Chandler, D
影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
56.9
作者：
Mees, A;Klar, T;Essen, LO
通讯作者：
Essen, LO
影响因子：
--
作者：
REID, PJ;BARBARA, PF
通讯作者：
BARBARA, PF
影响因子：
4.4
作者：
FLYVBJERG, H;PETERSEN, HG
通讯作者：
PETERSEN, HG