2004 Fiscal Year Final Research Report Summary
Theoretical studies on the electronic states of biological system, applying the effect of protein and solvent molecules.
| Project/Area Number |
15570134
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Osaka University |
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Principal Investigator |
NAKAMURA Haruki Osaka University, Institute for Protein Research, Professor, 蛋白質研究所, 教授 (80134485)
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| Co-Investigator(Kenkyū-buntansha) |
NAKAJIMA Nobuyuki Kobe University, Clinical Genome Informatics Center, Graduate School of Medicine, Specially Appointed Instructor, 大学院医学系研究科クリニカル・ゲノム・インフォマティクスセンター, 特命講師 (60324852)
YONEZAWA Yasushige Osaka University, Institute for Protein Research, 蛋白質研究所, 産学官連携研究員・客員助教授 (40248753)
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| Project Period (FY) |
2003 – 2004
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| Keywords | 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 |
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| Research Abstract |
(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.
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