2001 Fiscal Year Final Research Report Summary
DERIVATION OF INTERMOLECULAR INTERACTION POTENTIAL FUNCTIONS BASED ON THE CAMBRIDDGE STRUCTURAL DATABASE
| Project/Area Number |
10304052
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| Research Category |
Grant-in-Aid for Scientific Research (A)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Organic chemistry
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| Research Institution | TOYOHASHI UNIVERSITY OF TECHNOLOGY |
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Principal Investigator |
OSAWA Eiji DEPT. KNOWLEDGE-BASED INFORM. ENG., TOYOHASHI UNIVERSITY OF TECHNOLOGY, PROFESSOR, 工学部, 教授 (40001763)
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| Co-Investigator(Kenkyū-buntansha) |
KURITA Noriyuki DEPT. KNOWLEDGE-BASED INFORM. ENG., TOYOHASHI UNIVERSITY OF TECHNOLOGY, ASSISTANT, 工学部, 助手 (40283501)
GOTO Hitoshi DEPT. KNOWLEDGE-BASED INFORM. ENG., TOYOHASHI UNIVERSITY OF TECHNOLOGY, ASSISTANT PROFESSOR, 大学院・工学研究科, 助教授 (60282042)
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| Project Period (FY) |
1998 – 2000
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| Keywords | crystal structure / energy function / inverse probability density / CSD / structural parameters / O-H...O hydrogen bond / Lippincott-Schroder function / fragment structure |
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| Research Abstract |
Derivation of intermolecular potential functions for the atomistic simulation has met difficulties due the lack of appropriate models for intermolecular forces. We propose here an entirely new and non-empirical approach to this problem, which uses Cambridge Structural Database as the source of information on the intermolecular interactions among organic molecules. The method uses inverse probability density distribution of the 3D geometry of pertinent structural fragments to convert structural information into energy functions. We tested the idea by using C=O...H-O ketone/alcohol hydrogen bonding as a test case and modeled its 3D energy surface.
Version 5.16 of CSD was used which contains more than 190,000 crystal structures of organic compounds. Hydrogen bonding structural fragments (631) with high quality were extracted and the distributions of their structural parameters were fit the known potential functions of hydrogen bonding. We found that a combination of modified Lippincott-Sch
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roder potential for bond stretch, single Gaussian for out-of-plane deformation and a linear combination of two Gaussian functions for in-plane deformation fits best.
The first 3D potential function set for the C=O...H-O type hydrogen bond satisfactorily reproduced the well-known 3D energy surface having shallow and double minima along the direction of non-bonded orbitals on a carbonyl group. Extension of this procedure for other types and forms of intermolecular interactions should provide a set of potential functions and a set of appropriate parameters useful for realistic simulations, especially for the dynamic behaviors of bio-molecules including proteins, sugars and DNA. It is well-recognized that by far the most important but the least understood among the steric terms is the intermolecular interactions, but our approach should give a realistic solution to this problem.
One of the ambitious applications of the force field that we will eventually obtain will be a priori determination of crystal structure from chemical formula alone. Less
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Research Products
(17 results)
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[Publications] Shames, A.I. ; Panich, A.M. ; Kempinski, W. ; Alexenskii, A.E. ; Baidakova, M.V. ; Dideikin, A.T. : Osipov, V.Yu. ; Siklitski, V.I. ; Osawa, E. ; Ozawa, M. ; Vul, A.Ya: "Defects and Impurities in Nanodiamonds : EPR, NMR and TEM Study"J. Phys. Chem. Solids. 63. 1993-2001 (2002)
Description
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