QM/MM模拟溶液中腺嘌呤-尿嘧啶碱基对的氢键动力学。几何关联与红外光谱
QM/MM Simulation of the Hydrogen Bond Dynamics of an Adenine:Uracil Base Pair in Solution. Geometric Correlations and Infrared Spectrum
摘要：
采用量子力学（QM，DFT）/分子动力学模拟（MM，分子动力学模拟）方法，对9-乙基-8-苯基腺嘌呤和1-环己基尿嘧啶在氘代氯仿溶液中的Watson-Crick碱基对进行了模拟.轨迹进行了分析，特别注意碱基对中的$\NHN$和$\NHO$氢键的几何相关性。此外，根据氢键键长和NH伸缩振动频率之间的经验关系，得到了NH伸缩振动频率沿轨道的涨落。利用与时间相关的频率，红外线的线形确定假设的有效性的二阶累积展开。与实验值相比，计算得到的基本跃迁频率的偏差小于2%。$\NHN$键的光谱宽度与实验结果基本一致，而$\NHO$键的光谱宽度被本模型低估。比较不同的赝势的性能，它被发现，Troullier-Martins赝势与70 Ry截止产生最好的协议。
英文摘要：
Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting special attention to the geometric correlations of the $\NHN$ and $\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuations are obtained along the trajectory. Using the time dependent frequencies the infrared lineshape is determined assuming the validity of a second order cumulant expansion. The deviations for the fundamental transition frequencies are calculated to amount to less than 2% as compared with experiment. The width of the spectrum for the $\NHN$ bond is in reasonable agreement with experiment while that for the $\NHO$ case is underestimated by the present model. Comparing the performance of different pseudopotentials it is found that the Troullier-Martins pseudopotential with a 70 Ry cut-off yields the best agreement.
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