2004 Fiscal Year Final Research Report Summary
Development of many body potential for simulation of mucleic acid base
| Project/Area Number |
14540475
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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 |
Physical chemistry
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| Research Institution | Kinjo Gakuin University |
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Principal Investigator |
NAKAGAWA Setsuko Kinjo Gakuin University, Faculty of Human Life and Environment, Peofessor, 生活環境学部, 教授 (50050711)
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| Project Period (FY) |
2002 – 2004
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| Keywords | nucleic adic base / multicenter polarizability / polarizable potential / quantum chemistry calculation / polarizable one-elctron potential |
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| Research Abstract |
A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculation results. The level of the molecular orbital calculation is MP2/6-31+G^*. The PMP function consists of Coulomb, Lennard-Jones, and polarization terms. The partial point charges of the Coulomb term are determined by using electrostatic potential method. The multicenter polarizabilities of the polarization term are determined by using polarizable one-electronic potential method. Atomic polarizabilities are adopted as the multicenter polarizabilities. The atomic polarization model reproduce well the polarization of the nucleic acid. In the calculations using PMP function, the interaction energies of Watson-Crick type A-T and G-C base pairs were -15.6 and -29.2 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.7 kcal/mol. These results reproduce well the quantum chemistry calculations of MP2/6-311++G(3df,2pd). The stacking energies of A-T and C-G were -9.3 and -10.7 kcal/mol, respectively. These results reproduce well the calculations of MP2/6-311++G (2d,2p). Moreover, the potential energy surfaces of the models in which a sodium ion or a chloride ion is adjacent to the nucleic acid bases are calculated. The reproduction of the energy surfaces was very well. The potential function in which a high-level quantum chemistry calculation results are reproduced well by taking the simple atomic polarizabilities can be made though the nucleic acid base is a molecule with a very large polarization anisotropy.
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