Theoretical study of chemical reaction and phase transition dynamics by using multi-dimensional spectroscopy

我们利用二维光谱技术研究了生物体系中的化学反应以及液态水和固态水的动力学，并分析了离子在掺杂阴离子的碳纳米管模型通道中的渗透机理。通过分子动力学计算分析了自由能和离子渗透动力学。结果表明，在通道口附近，大部分离子被水分子排斥到通道中，只有约10%的离子到达通道口后能进入通道。我们还用QM/MM方法和分子动力学计算研究了光活性黄蛋白（PYP）的质子转移（PT）过程以及随后的结构变化和氢键重排。这项工作表明，水迁移到发色团区域，这有利于PT和PT后的状态稳定的重要性。我们完成了液体和固体水的二维（2D）拉曼光谱的理论分析。结果表明，当t2> 30 fs时，非谐性引起的平移运动对信号有贡献，而当t2<30 fs时，非线性极化率引起的平移运动对信号有贡献。二维拉曼光谱对局域氢键结构和结构的各向异性非常敏感。因此，这项工作表明多维光谱技术对相变动力学的适用性。我们通过MD计算研究了冰的融化过程。在熔化过程开始时，五元环和七元环从常规的六元环中出现。随后，三配位的水分子的数量沿着熔化过程增加。结果表明，三配位水分子的出现，使HB结构重排的沿着能垒降低，三配位水分子的聚集促进了熔融过程。

We have investigated chemical reactions in biological systems and dynamics of liquid and solid water by using two-dimensional spectroscopies.We analyzed the ion permeation mechanism in a model channel, an anion-doped carbon nanotube. We analyzed the free energy and ion permeation dynamics by using molecular dynamics (MD) calculation. It was found that most of ions are repelled into bulk by the water molecule near the mouth of the channel and that only about 10 % of ions which reach the mouth of the channel can enter the channel. It was revealed that the rate-determining step is the entrance of ion to the channelWe also investigated the proton transfer (PT) and subsequent structural change and hydrogen bond rearrangements in photoactive yellow protein (PYP) by using QM/MM method and MD calculation. This work suggests the importance of water migration into the chromophore region, which facilitates PT and stabilizes the state after PT.We completed the theoretical analysis of two-dimensional (2D) Raman spectroscopy of liquid and solid water. We showed that the translational motion caused by anharmonicity contributes to the signal for t2>30fs, while the librational motion due to nonlinear polarizability does to the signal for t2<30 fs. We also showed that the 2D Raman spectroscopy is very sensitive to the local hydrogen bond structure and anisotropy of structure. Thus, this work suggests the applicability of multidimensional spectroscopy to the phase transition dynamics.We investigated the melting process of ice by using MD calculation. Five-and seven-member rings emerge from the regular six-member rings at the beginning of the melting process. Subsequently, the number of three-coordinated water molecules increases along the melting process. We showed that the energy barrier along HB structural rearrangement becomes low once three-coordinated water molecule appears and the gathering three-coordinated water molecules promotes melting process.