尿嘧啶氢键的QM/MM线型模拟CDCl $_3$中腺嘌呤-尿嘧啶碱基对的NH伸缩振动
QM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl$_3$
摘要：
采用Car-Parrinello QM/MM混合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.重点分析了N-H $...$ N氢键的几何构型。利用$\NN$距离和NH伸缩基频之间的经验相关性，得到了该能隙沿轨道的时间依赖性。从间隙-关联函数，我们确定的红外吸收光谱，结合多模振荡器模型的线形理论。得到的平均跃迁频率和谱宽与最近的实验数据是合理的协议。
英文摘要：
A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H$...$N Hydrogen bond geometry. Using an empirical correlation between the $\NN$-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum is in reasonable agreement with recent experimental data.
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