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

点击翻译按钮获取中文摘要

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.