Effects of single water molecule on proton transfer reaction in uracil dimer cation
Effects of single water molecule on proton transfer reaction in uracil dimer cation
复制标题
DOI：
10.1007/s00214-016-1807-y
复制
发表时间：
2016-02
影响因子：
1.7
通讯作者：
H. Tachikawa
中科院分区：
文献类型：
--
作者：
H. Tachikawa
DNA 的电离辐射有时会引起 DNA 损伤。在本报告中，通过直接从头分子动力学（AIMD）方法研究了尿嘧啶二聚体（U）2及其水复合物（U）2-H2O的电离动力学，以阐明单个水分子对DNA模型碱基对中质子转移（PT）反应速率的影响。 (U)2二聚体被广泛用作 Watson-Crick 碱基对的简化模拟模型。静态从头计算表明，两个构象异构体以(U)2-H2O的中性络合物形式存在。 (U)2–H2O 电离过程的直接 AIMD 计算表明，即使单个水分子也会影响 PT 速率，而它取决于 (U)2 周围 H2O 的位置。水分子与(U)2的相互作用影响PT的势能曲线。特别是，与一个 H2O 分子的相互作用显着改变了沿 PT 坐标的活化势垒。在理论结果的基础上讨论了一个H2O分子对PT过程的影响。
Ionizing radiation to DNA induces sometimes the DNA damage. In this report, the ionization dynamics of uracil dimer (U)2and its water complex (U)2–H2O have been investigated by means of direct ab initio molecular dynamics (AIMD) method in order to elucidate the effects of single water molecule on the reaction rate of proton transfer (PT) in DNA model base pair. The (U)2dimer is widely used as a simplified mimetic model of Watson–Crick base pair. The static ab initio calculation showed that two conformers exist as neutral complex of (U)2–H2O. The direct AIMD calculation of ionization process of (U)2–H2O showed that the rate of PT is affected even by a single water molecule, while it was dependent on the position of H2O around (U)2. The interaction of water molecule with (U)2affected the potential energy curve for PT. Especially, the activation barrier along the PT coordinate was significantly changed by the interaction with one H2O molecule. The effects of one H2O molecule on the PT process were discussed on the basis of theoretical results.