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

利用多维光谱理论研究化学反应和相变动力学

基本信息

批准号：
16350008
负责人：
SAITO Shinji
金额：
$ 7.74万
依托单位：
Institute for Molecular Science (2005-2006)Nagoya University (2004)
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2004
资助国家：
日本
起止时间：
2004 至 2006
项目状态：
已结题

项目摘要

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.

我们用二维光谱研究了生物体系中的化学反应以及液体和固体水的动力学，分析了离子在模型通道--阴离子掺杂碳纳米管中的渗透机理。用分子动力学(MD)方法分析了其自由能和离子渗透动力学。结果表明，大部分离子被孔道口附近的水分子排斥成块状，只有约10%的离子到达孔道口进入孔道。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)中的质子转移(PT)以及随后的结构变化和氢键重排。这项工作表明了水迁移到生色团区域的重要性，它促进了PT并稳定了PT后的状态。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，由非谐性引起的平移运动对T2&gt；30fs的信号有贡献，而由非线性极化率引起的振转运动对t2&lt；30f的信号有贡献。我们还发现2D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，这项工作表明了多维光谱在相变动力学中的适用性。我们通过分子动力学计算研究了冰的融化过程。五元环和七元环在熔化过程开始时从常规的六元环中产生。随后，三配位水分子的数量在熔融过程中增加。结果表明，当三配位水分子出现时，沿Hb结构重排的势垒降低，聚集的三配位水分子促进了熔化过程。

项目成果

期刊论文数量（25）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A theoretical study on anomalous temperature dependence of pKw of water.

DOI：
10.1063/1.1878712
发表时间：
2005-04
期刊：
The Journal of chemical physics
影响因子：
0
作者：
T. Yagasaki;Kensuke Iwahashi;S. Saito;I. Ohmine
通讯作者：
T. Yagasaki;Kensuke Iwahashi;S. Saito;I. Ohmine

Terahertz Radiation Spectroscopy on Chloroform Confined in Porous Silica Glasses

多孔二氧化硅玻璃中限制的氯仿的太赫兹辐射光谱

DOI：
发表时间：
2004
期刊：
Mat. Res. Soc. Symp. Proc. 790
影响因子：
0
作者：
K.Yamamoto;T.Satoh;H.Okuno;K.Tominaga;S.Saito,.J.Loughnane;A.Scodinu;J.T.Foukas
通讯作者：
J.T.Foukas

実験化学講座 9 物質の構造分光上(5.1 吸収・反射分光概要(理論))

实验化学课程9物质光谱结构1（5.1吸收/反射光谱概述（理论））

DOI：
发表时间：
2006
期刊：
影响因子：
0
作者：
K.Yamamoto;T.Satoh;H.Okuno;K.Tominaga;S.Saito;J.Loughnane A.Scodinu;J.T.Foukas;Y.Ohtsuki;斉藤真司;R.Sahnoun;M.Kanno;斉藤真司
通讯作者：
斉藤真司

Fifth-order two-dimensional Raman spectroscopy of liquid water, crystalline ice Ih and amorphous ices: sensitivity to anharmonic dynamics and local hydrogen bond network structure.