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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)
小澤 理樹  豊橋技術科学大学, 大学院・工学研究科, 助手 (30293757)
スラニナ ゼネック  豊橋技術科学大学, 大学院工学研究科, 教授 (10283508)
Project Period (FY) 1998 – 2000
Project Status Completed (Fiscal Year 2001)
Budget Amount *help
¥5,300,000 (Direct Cost: ¥5,300,000)
Fiscal Year 2000: ¥2,700,000 (Direct Cost: ¥2,700,000)
Fiscal Year 1999: ¥2,600,000 (Direct Cost: ¥2,600,000)
Keywordscrystal structure / energy function / inverse probability density / CSD / structural parameters / O-H...O hydrogen bond / Lippincott-Schroder function / fragment structure / 結晶構造からエネルギー関数 / データベース / 分子間相互作用ポテンシャル / 構造パラメーチー確率分布 / O-H…O水素結合 / C-H…パイ相互作用 / C-C結合長平衡値 / ケンブリッジ構造データベース / 水素結合 / 遺伝子アルゴリズム / 分子力学法 / 静電ポテンシャル / Lippincott関数 / 結晶充てん計算 / 結晶力場 / 分子力学計算 / 固体物質予測 / パラメータ最適化
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

Report

(4 results)
  • 2001 Final Research Report Summary
  • 2000 Annual Research Report
  • 1999 Annual Research Report
  • 1998 Annual Research Report
  • Research Products

    (41 results)

All Other

All Publications (41 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
    • Related Report
      2001 Final Research Report Summary
  • [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
    • Related Report
      2001 Final Research Report Summary
  • [Publications] F.Uhlik: "Thermodynamic properties of He@C60"Fullerene Sci. Technol.. 8. 453-460 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] J.Jehlika: "Fullerenes in solid bitumens from pillow lavas of pre-cambrian age (Mitov, Bohemian Massif)"Fullerene Sci. Technol.. 8. 449-452 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] K.H.Lee: "Structures and energetics of regioisomers of C60 dimer and trimers"J.Phys.Chem.. 104. 7038-7042 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Z.Slanina: "Computational modeling of the elemental catalysis in the Stone-Wales Fullerene Rearrangements"J.Organomet.Chem.. 599. 57-61 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] E.Osawa(Ed.): "Perspectives on Fullerene Nanotechnology"Kluwer Academic Publishers. 367 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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
    • Related Report
      2001 Final Research Report Summary
  • [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
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [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
    • Related Report
      2001 Final Research Report Summary
  • [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)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Z.Slanina ほか3名: "Computations of IPR Isomers of C_<88> and C_<90>"nanostruct.mater.. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Z.Slanina ほか4名: "Computations of Metal-covered C_<60> and C_<70>"Comput.mater.Sci.. 18. 308-314 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Z.Slanina ほか3名: "Enthalpy-Entropy Interplay for C_<36> lages : B3LYP/6-3LG^*Calculations"J.Chem.Phys.. 113・12. 4933-4937 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] F.Uhlik ほか2名: "Thermodynamic Properties of He@C_<60>"Fullerene Sci.Technol.. 8・445. 351-367 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Z.Slanina ほか3名: "A Computational Treatment of 35 IPR Isomer of C_<88>"Fullerene Sci.Technol.. 8・445. 433-447 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] K.H.Lee ほか7名: "Structures and Energetics of Regioisomers of C_<60> Dimer and Trimars"J.Phys.Chem.. 104. 7038-7042 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Z.Slanina ほか3名: "Fullerenes-Chemistry,Physics,and Technology"Wiley-Interscience. 283-330 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] 大澤映二: "カーギンナ/チューブーナ/デバイスへの挑戦"化学同人(京都). 47-50 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] E.Osawa: "Natural Fullerenes"Fullerene Sci.Technol.. 7・4. 637-652 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] E.Osawa: "Analysis of the Growth Mechanism of Carbon Nanotubes by C2 Ingestion"Fullerene Sci.Technol.. 7・2. 239-262 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] M.Shibuya: "Detection of Backminsterfullerene in Usual Soot and Commercial Charcoals"Fullerene Sci.Technol.. 7・2. 181-193 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] T.Yu.Ashtakhova: "Numerical Generation of Nanotube Caps"Fullerene Sci.Technol.. 7・2. 223-237 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] M.Ozawa: "Production of Fullerenes by Combustion"Fullerene Sci.Technol.. 7・3. 387-409 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] T.Yu.Ashtakhova: "Numerical Generation of Nanotube Caps II"Fullerene Sci.Technol.. 7・5. 769-779 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Z.Slanina: "Advances in Strained and Interesting Organic Molecules"JAI Press Greenwich. 305 (1998)

    • Related Report
      1999 Annual Research Report
  • [Publications] E.Osawa: "Carbocyclic and Heterocydic Cage Compounds"JAI Press Greenwich. 401 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] E.Osawa ほか: "A Renewed Look at the Stone-Wales Rearrangement" Mol. Mat.10. 1-8 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] E.Osawa ほか: "Combined Topological Energy Analysis of Annealing Process in Fullerene Formation" J.Chem.Soc., Perkin Trans.2. 943-950 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] E.Osawa ほか: "Stone-Wales Rearrangement as the Double Olefin-Carbene 1,2-CC Bond Shift" Fullerene Sci. Technol.6・2. 259-270 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] E.Osawa ほか: "Analysis of the Growth Mechanism of Carbon Nanotubes by CZ Ingestion" Fullerene Sci. Technol.(印刷中). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] M.Ozawa, E.Osawa: "Additives to Improve the Yield of Fullerenes from the Combustion of Benzene" Carbon. (印刷中). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] E.Osawa: "Natural Fullerenes. Will They Offer a Hint to the Selective Synthesis of Fullerenes?" Fullerene Sci. Technol. (印刷中). (1999)

    • Related Report
      1998 Annual Research Report
  • [Publications] E.Osawaほか: "Intermolecular Interactions" Plenum Press, Inc. (New York), 320 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] 大澤映二ほか: "「炭素第三の同素体フラーレンの化学」" 学会出版センター(印刷中), 250 (1999)

    • Related Report
      1998 Annual Research Report

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Published: 1999-04-01   Modified: 2016-04-21  

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