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Dynamical transition in translational and rotational dynamics of water in the grooves of DNA duplex at low temperature

机译:水的平移和旋转动力学的动态转变   在低温下DNa双链的凹槽中

摘要

We have simulated structure and dynamics of water in the grooves of a DNAduplex using moleculear dynamics simulations. We find signatures of a dynamicaltransition in both translational and orientational dynamics of water moleculesin both the major and the minor grooves of a DNA duplex. The transition occursat a slightly higher temperature ($T_{GL} \approx $ 255 K) than the temperature($T_L\approx$ 247 K) where the bulk water is conjectured to undergo a dynamicaltransition. Groove water, however, exhibits markedly different temperaturedependence of its properties from the bulk. Entropy calculations reveal thatthe minor groove water is ordered even at room temperature and the transitionat $T \approx$ 255 K can be characterized as a {\em strong-to-strong} dynamicaltransition. The low temperature water is characterized by pronouncedtetrahedral order, as manifested in the sharp rise near $109^{\circ}$ in theO-O-O angle distribution. We find that Adams-Gibbs relation betweenconfigurational entropy and translational diffusion holds quite well when thetwo quantities are plotted together in a master plot for different region ofaqueous DNA duplex (bulk, major and minor grooves) at different temperatures.The activation energy for the transfer of water molecules between differentregions of DNA is found to be independent of temperature.
机译:我们使用分子动力学模拟对DNAduplex凹槽中水的结构和动力学进行了模拟。我们发现在DNA双链体的主要和次要凹槽中水分子的翻译和定向动力学的动态过渡的签名。过渡发生在温度略高于温度($ T_L \约247 K)的情况下($ T_ {GL} \约$ 255 K),在该温度下,散装水被认为经历了动态过渡。然而,槽水的性质与本体的温度依赖性明显不同。熵计算表明,即使在室温下,次沟水也是有序的,并且在大约255 K时的转变T可以描述为{\ em强到强}动态转变。低温水的特征是明显的四面体有序,表现在O-O-O角分布中的$ 109 ^ {circ} $附近急剧上升。我们发现,当在不同温度下,不同数量的DNA双链体的不同区域(大,小槽和小槽)在主图中将这两个量一起绘制在主图中时,构型熵和平移扩散之间的Adams-Gibbs关系保持得很好。发现DNA不同区域之间的水分子与温度无关。

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