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2001 Fiscal Year Final Research Report Summary

DERIVATION OF INTERMOLECULAR INTERACTION POTENTIAL FUNCTIONS BASED ON THE CAMBRIDDGE STRUCTURAL DATABASE

Research Project

Project/Area Number 10304052
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Organic chemistry
Research InstitutionTOYOHASHI UNIVERSITY OF TECHNOLOGY

Principal Investigator

OSAWA Eiji  DEPT. KNOWLEDGE-BASED INFORM. ENG., TOYOHASHI UNIVERSITY OF TECHNOLOGY, PROFESSOR, 工学部, 教授 (40001763)

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)
Project Period (FY) 1998 – 2000
Keywordscrystal structure / energy function / inverse probability density / CSD / structural parameters / O-H...O hydrogen bond / Lippincott-Schroder function / fragment structure
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 … More 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

  • Research Products

    (17 results)

All Other

All Publications (17 results)

  • [Publications] Z.Slanina: "Relative stabilities of the C92 IPR isomers"J. Mol. Model.. 6. 312-317 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] V.Y.Davidov: "Storage of hydrogen in chemisorbed state in aromatic compounds and fullerene C60 complexes with platinum"Int. Sci. J. Alt. Ener. Ecol.. 1. 182-183 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] F.Uhlik: "Thermodynamic properties of He@C60"Fullerene Sci. Technol.. 8. 453-460 (2000)

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      「研究成果報告書概要(和文)」より
  • [Publications] J.Jehlika: "Fullerenes in solid bitumens from pillow lavas of pre-cambrian age (Mitov, Bohemian Massif)"Fullerene Sci. Technol.. 8. 449-452 (2000)

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      「研究成果報告書概要(和文)」より
  • [Publications] K.H.Lee: "Structures and energetics of regioisomers of C60 dimer and trimers"J.Phys.Chem.. 104. 7038-7042 (2000)

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      「研究成果報告書概要(和文)」より
  • [Publications] Z.Slanina: "Computational modeling of the elemental catalysis in the Stone-Wales Fullerene Rearrangements"J.Organomet.Chem.. 599. 57-61 (2000)

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      「研究成果報告書概要(和文)」より
  • [Publications] E.Osawa(Ed.): "Perspectives on Fullerene Nanotechnology"Kluwer Academic Publishers. 367 (2002)

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      「研究成果報告書概要(和文)」より
  • [Publications] Davydov, V. Ya. ; Sheppard, N. ; Osawa, E.: "An Infrared Spectroscopic Study of the Hydrogenation and Dehydrogenation of the Complexes of Aromatic Compounds and of Fullerene C_<60> with Silica-Supported Platinum"J. Catalysis. 211. 42-52 (2002)

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      「研究成果報告書概要(欧文)」より
  • [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)

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      「研究成果報告書概要(欧文)」より
  • [Publications] Ozawa, M. ; Goto, H. ; Kusunoki, M. ; Osawa, E.: "Continuously Growing Spiral Carbon Nanoparticles as the Intermediates in the Formation of Fullerenes and Nano-onions"J. Phys. Chem. B. 106[29]. 7135-7138 (2002)

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      「研究成果報告書概要(欧文)」より
  • [Publications] Slanina, Z. ; Iida, S. ; Zhao, X. ; Chiang, L.Y. ; Adamowicz, L. ; Osawa, E.: "Computations of Hexa-nitrated and Hexa-anilinated Fullerenes"Synth. Metals. 121. 1101-1102 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Uhlik, F. ; Slanina, Z. ; Osawa, E.: "C78 IPR Fullerenes : Computed B3LYP/6-31G^*//HF/3-21G Temperature-dependent Relative Concentrations"Eur. Phys. J.D.. 16. 349-352 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Slanina, Z. ; Uhlik, F. ; Lee, S.-L. ; Osawa, E.: "Geometrical and Thermodynamic Approaches to the Relative Stabilities of Fullerene Isomers"MATCH. 44. 335-348 (2001)

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      「研究成果報告書概要(欧文)」より
  • [Publications] Braun T. ; Osawa, E. ; Detre, C. ; Toth, I.: "On some analytical aspects of the determination of fullerenes in samples from the permian/triassic boundary layers"Chem. Phys. Lett.. 348. 361-362 (2001)

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  • [Publications] Lee, K.H. ; Park., S.S. ; Suh, Y.S. ; Yamabe, T. ; Osawa, E. ; Luethi, H.P. ; Gutta, P. ; Lee, C.: "Similarity and Difference of (C_<60>)_2^<2-> of (C_<59>N)_2 Conformers"J. Am. Chem. Soc.. 123. 11085-11086 (2001)

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      「研究成果報告書概要(欧文)」より
  • [Publications] Slanina, Z. ; Zhao, X. ; Deota, P. ; Osawa, E.: "Relative Stabilities of the C_<92> IPR Isomers"J. Mol. Model.. 6. 312-317 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Zhao, X. ; Slanina, Z. ; Ozawa, M. ; Osawa, E. ; Deota, P. ; Tanabe, K.: "C_<32> : Computations of the Low-Energy Cages with Four-Membered Rings"Fullerene Sci. Technol.. 8[6]. 595-613 (2000)

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Published: 2003-09-17  

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