| Project/Area Number |
16350008
|
|---|
| Research Category |
Grant-in-Aid for Scientific Research (B)
|
| Allocation Type | Single-year Grants |
|---|
| Section | 一般 |
|---|
| Research Field |
Physical chemistry
|
|---|
| Research Institution | Institute for Molecular Science (2005-2006)
Nagoya University (2004) |
|---|
Principal Investigator |
SAITO Shinji Institute for Molecular Science, Department of Theoretical and Computational Molecular Science, Professor, 理論・計算分子科学研究領域, 教授 (70262847)
|
|---|
| Project Period (FY) |
2004 – 2006
|
| Project Status |
Completed (Fiscal Year 2006)
|
| Budget Amount *help |
¥12,100,000 (Direct Cost: ¥12,100,000)
Fiscal Year 2006: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2005: ¥4,000,000 (Direct Cost: ¥4,000,000)
Fiscal Year 2004: ¥4,000,000 (Direct Cost: ¥4,000,000)
|
|---|
| Keywords | water / molecular dynamics simulation / two-dimensional Raman spectroscopy / two-dimensional IR spectroscopy / ion permeation / proton transfer reaction / melting process / 分子動力学シミュレーション / アモルファス氷 / 非平衡分子動力学法 / photoactive yellow protein / 非調和ダイナミクス / 2次元スペクトル / 不均一性 / 多次元振動分光法 / 化学反応 / 相転移ダイナミクス / 非平衡ダイナミクス / 2次元ラマン分法 |
|---|
| Research Abstract |
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 channel
We 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.
|
