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Theoretical studies on the electronic states of biological system, applying the effect of protein and solvent molecules.

应用蛋白质和溶剂分子的作用对生物系统的电子态进行理论研究。

基本信息

批准号：
15570134
负责人：
NAKAMURA Haruki
金额：
$ 2.3万
依托单位：
Osaka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2003
资助国家：
日本
起止时间：
2003 至 2004
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15570134/
关键词：
Quantum chemical calculation Molecular dynamics Electron state of protein molecule Simulation calculation Localized molecular orbital Link atom Hybrid-QM MM calculation Algorithm of molecular simulation QM

项目摘要

(1) Development of a new algorithm for the covalent bonds between the quantum and classical regions : In order to overcome the drawback of the Link Atom method, which was often applied at the boundary between the Quantum Mechanical (QM) and the classical Molecular Mechanical (MM) region, we developed a method to introduce a new Pseudu-Quantum Mechanical (PQM) region between the QM and MM regions. The canonical molecular orbitals for the atom groups in the PQM region were replaced by the frozen molecular orbitals, and a new algorithm was established to fuse the QM energy and MM energy in a reasonable manner. This method was applied to small peptide molecules to show its applicability.(2) Inclusion of the long-ranged effect into the QM region by combining the Surface Charges and Dipoles method and the Cell Multipole method : Using the Surface Charges and Dipoles method, where any contributions from outside of any closed surface can be reproduced by the virtual charges and dipoles on the closed surface, the long-ranged interaction between very distant charges and the QM region was able to be calculated with high precision by a newly developed method, combining the cell multipole method. In fact, the contributions from the distant water molecules were correctly calculated for a huge system composed of the fourfold periodic cells, in each of which a benzene and the surrounding 208 water molecules were included. The interaction between the QM regions in the nearest neighbor cells was conventionally calculated by setting the FSP or RESP charges on the atoms in either QM region.

(1)一种新的计算量子区和经典区之间共价键的方法的发展：为了克服链接原子方法在量子力学（QM）区和经典分子力学（MM）区之间的边界处的缺陷，我们发展了一种在QM区和MM区之间引入一个新的伪量子力学（PQM）区的方法。用冻结的分子轨道代替PQM区原子群的正则分子轨道，建立了一种新的算法，将QM能和MM能合理地融合.将该方法应用于小肽分子以显示其适用性。(2)通过结合表面电荷和偶极子方法以及单元多极方法将长程效应纳入QM区域：使用表面电荷和偶极子方法，其中来自任何封闭表面外部的任何贡献可以由封闭表面上的虚电荷和偶极子再现，用一种新发展的方法，结合单元多极方法，能够高精度地计算远距离电荷与QM区之间的长程相互作用。事实上，对于一个由四重周期细胞组成的巨大系统，来自遥远的水分子的贡献被正确地计算出来，每个周期细胞中包括一个苯和周围的208个水分子。在最近邻单元中的QM区域之间的相互作用通常通过在任一QM区域中的原子上设置FSP或RESP电荷来计算。