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Theoretical Study on Realization of Nonequilibrium Reaction Field Analogs by Unique Aggregated Coordination Space

Research Project

Project/Area Number 16074207
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionNagoya University

Principal Investigator

NAGAOKA Masataka  Nagoya University, Graduate School of Information Sceience, Professor (50201679)

Project Period (FY) 2004 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥11,100,000 (Direct Cost: ¥11,100,000)
Fiscal Year 2007: ¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 2006: ¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 2005: ¥3,100,000 (Direct Cost: ¥3,100,000)
Fiscal Year 2004: ¥2,200,000 (Direct Cost: ¥2,200,000)
KeywordsFree energy gradient method / GCMC method / Molecular mechanics / Ab initio molecular orbital theory / Plane wave based density functional theory / Nanospace chemistry / Microscopic entropy / Structural optimization / スタッガード配座 / QM / MM-MD法 / ミクロエントロピー効果
Research Abstract

In this project, taking microporous coordination polymers as an example, we estimate and clarify the microscopic properties of the pores in materials on the basis of molecular orbital (M0) theory and density functional theory (DFT). Further, through molecular mechanical (MM) and monte carlo (MC) simulation, we will survey the guideline to design the coordination space by investigating the correspondence between the macroscopic and the microscopic ones.
[Results] 1) Microscopic properties of microporous coordination polymer CPL-1 On the basis of Universal Force Field (UFF), we recalibrated the force-field parameters of 02 for the purpose to describe the thermodynamic behaviors satisfactorily, e.g., the ladder structure of 02 dimers in nanochannels in CPL-1. Then, the effective potential of 02-02 interaction was expressed as V02-02, a summation of van der Waals VvdW and quadrupole interaction VEQQ. By fitting V02-02 to the ab initio data, a set of parameters D0-0, Re0-0 and q0 for an oxyg … More en atom of 02 molecule were obtained, i. e., 59.4762 K, 5.9943 a0 and -0.2227 e, respectively.
In addition, q0 could be obtained directly as -0.2518 e at the MP2/6-31G+(d) level of theory by utilizing Gaussian03, so that it could reproduce reasonably the quadrupole moment of 02 and, then, corresponds to the fitting q0 value.
2) Reaction mechanism in specific polymerization in CPL-2 It can be understood that the molecular mechanically optimized structure by using the UFF should also reproduce a specific hydrogen-bonding interaction between an methyl propiolate (MP) monomer and two oxygen atoms in the carboxylate moiety in CPL-2. The -C ≡ CH group of MP is clearly oriented towards the carboxylate oxygen atoms on the pore wall, and the acetylenic hydrogen atom and the oxygen atoms are close enough for an efficient hydrogen bonding (2.8 and 2.9 Å), which is consistent with the experimental results. A schematic illustration is shown in Ref.3 for randomly-aligned MP molecules in the nanochannel in CPL-2, which are found closely-packed in fact for controlling the stereostructure
(the cis and trans chain sequence).
[References]
(l) Y. Ohta, H. Hitomi, M. Nagaoka, R. Matsuda and S. Kitagawa, J. Amer. Chem. Soc. 2007, submitted.
(2) (a) T. Uemura, R. Kitaura, Y. Ohta, M. Nagaoka, S. Kitagawa, Angew. Chem. 2006, 118, 4218; (b) Angew. Chem. Int. Ed. 2006, 45, 4112.
(3) M. Nagaoka, Y. Ohta and H. Hitomi, Coord. Chem. Rev., 2007, 251, 2522. Less

Report

(5 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • Research Products

    (44 results)

All 2008 2007 2006 2005 2004

All Journal Article (18 results) (of which Peer Reviewed: 7 results) Presentation (26 results)

  • [Journal Article] Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace2008

    • Author(s)
      T. Uemura, S. Horike, K. Kitagawa, M. Mizuno, K. Endo, S. Bracco, A. Comotti, P. Sozzani, M. Nagaoka, S. Kitagawa
    • Journal Title

      Journal of the American Chemical Society 130

      Pages: 6781-6788

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Conformation and Molecular Dynamics of Single Polystyrene Chain Confined in Coordination Nanospace2008

    • Author(s)
      T. Uemura, S. Horike, K. Kitagawa, M. Mizuno, K. Endo, S. Bracco, A. Comotti, P. Sozzani, M. Nagaoka, S. Kitagawa.
    • Journal Title

      Journal of the American Chemical Society 130

      Pages: 6781-6788

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Theoretical Characterization of Coordination Space : Adsorption State and Behavior of Small Molecules in Nanochanneled Metal-Organic Frameworks via Electronic State Theory, Molecular Mechanical and Monte Carlo Simulation2007

    • Author(s)
      M. Nagaoka, Y. Ohta, H. Hitomi
    • Journal Title

      Coordination Chemistry Reviews 251

      Pages: 21-24

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Theoretical Characterization of Coordination Space : Adsorption State and Behavior of Small Molecules in Nanochanneled Metal-Organic Frameworks via Electronic State Theory. Molecular Mechanical and Monte Carlo Simulation2007

    • Author(s)
      M. Nagaoka, Y. Ohta, H. Hitomi
    • Journal Title

      Coord. Chem. Rev. 251

      Pages: 2522-2536

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Elongation of Water Residence Time at the Protein Interior in Aqueous Solution with Ectoine2007

    • Author(s)
      I. Yu, M. Nagaoka
    • Journal Title

      Proceedings of International Symposium on Frontiers of Computational Science

      Pages: 269-273

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration2007

    • Author(s)
      I. Yu, Y. Jindo, M. Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 111

      Pages: 10231-10238

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Characterization of Coordination Space: Adsorption State and Behavior of Small Molecules in Nanochanneled Metal-Organic Frameworks via Electronic State Theory, Molecular Mechanical and Monte Carlo Simulation2007

    • Author(s)
      M. Nagaoka, Y. Ohta, H. Hitomi
    • Journal Title

      Coordination Chemistry Reviews 251,21-24

      Pages: 2522-2536

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Body-Centered Cubic Structure of Methyllithium Tetramer Crystal : Staggered Methyl Conformation by Electrostatic Stabilization via Intra-Tetramer Multipolarization2006

    • Author(s)
      Y. Ohta, A. Demura, T. Okamoto, H. Hitomi, M. Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 110, 25

      Pages: 12640-12644

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymer2006

    • Author(s)
      T. Uemura, S. Kitagawa, Y. Ohta, M. Nagaoka
    • Journal Title

      Angewandte Chemie International Edition 45

      Pages: 4218-4222

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] The Body-Centered Cubic Structure of Methyllithium Tetramer Crystal : Staggered Methyl Conformation by Electrostatic Stabilization via Intra-Tetramer Multipolarization2006

    • Author(s)
      Y. Ohta, A Demura, T. Okamoto, H. Hitomi, M. Nagaoka
    • Journal Title

      J. Phys. Chem. A 110

      Pages: 12640-12644

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymers2006

    • Author(s)
      T. Uemura, R. Kitaura, Y. Ohta, M. Nagaoka, S. Kitagawa
    • Journal Title

      Angewandte Chemie International Edition 45

      Pages: 4218-4222

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Anisotropic Structural Relaxation and Its Correlation with the Excess Energy Diffusion in the Incipient Process of Photodissociated MbCO : High-Resolution Analysis via Ensemble Perturbation Method2006

    • Author(s)
      M.Takayanagi, H.Okumura, M.Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 111, 4

      Pages: 864-869

    • Related Report
      2006 Annual Research Report
  • [Journal Article] The Body-Centered Cubic Structure of Methyllithium Tetramer Crystal : Staggered Methyl Conformation by Electrostatic Stabilization via Intra-Tetramer Multipolarization2006

    • Author(s)
      Y.Ohta, A.Demura, T.Okamoto, H.Hitomi, M.Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 110, 25

      Pages: 12640-12644

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Nanochannel-Promoted Polymerization of Substituted Acetylenes in Porous Coordination Polymers2006

    • Author(s)
      T.Uemura, S.Kitagawa, Y.Ohta, M.Nagaoka
    • Journal Title

      Angewandte Chemie International Edition (in press)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Transition-state characterization of ammonia ionization process in aqueous solution via free-energy gradient method2006

    • Author(s)
      Y.Koyano, Y.Oishi, Y.Nagase, M.Nagaoka
    • Journal Title

      The Journal of Physical Chemistry A 110

      Pages: 4555-4563

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Theoretical Study on Stabilities of N-terminal Partial Chains from Apo-Myoglobin2006

    • Author(s)
      M.Takayanagi, I.Yu, M.Nagaoka
    • Journal Title

      Chemical Physics Letters 421

      Pages: 300-304

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Coarse-Grained Approach to Nonequilibrium Molecular Dynamics : Application to Relaxation process of Vibrationally Excited Hydrogen Fluoride in aqueous Solution2005

    • Author(s)
      T.Okamoto, M.Nagaoka
    • Journal Title

      Chemical Physics Letters 407

      Pages: 444-449

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Slowdown of Water Diffusion around Protein in Aqueous Solution with Ectoine2004

    • Author(s)
      I.Yu, M.Nagaoka
    • Journal Title

      Chemical Physics Letters 388

      Pages: 316-321

    • Related Report
      2004 Annual Research Report
  • [Presentation] Toward Understanding Protein Functions: A Computational Chemical Approach2008

    • Author(s)
      M. Nagaoka
    • Organizer
      Joint Symposium of "5th Japan-Chaina Crossover Science Symposium (JCCSS5)
    • Place of Presentation
      Mito
    • Related Report
      2007 Annual Research Report
  • [Presentation] 表面Kirkwood-Buff法による補償溶質エクトイン選択的排除の分子論的理解2008

    • Author(s)
      優 乙石、長岡正隆
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Related Report
      2007 Annual Research Report
  • [Presentation] アンモニア溶解過程の微視的水和機構:溶質QM分極とファンデル・ワールス相互作用のハイブリッド表現の重要性2008

    • Author(s)
      竹中規雄、小谷野哲之、中川幸紀、長岡正隆
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Related Report
      2007 Annual Research Report
  • [Presentation] 自由エネルギー勾配法による水溶液中アンモニアイオン化反応に関する理論的研究2008

    • Author(s)
      中川幸紀, 小谷野哲之, 竹中規夫, 長岡正隆
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Related Report
      2007 Annual Research Report
  • [Presentation] Statistically Studying Condensed-State Chemistry with Molecular Dynamics Simulations2007

    • Author(s)
      M. Nagaoka
    • Organizer
      International Symposium on "Molecular Theory for Real Systems
    • Place of Presentation
      Kyoto
    • Related Report
      2007 Annual Research Report
  • [Presentation] Free Energy Gradient Method: Statistically Studying densed-State Chemistry with Molecular Dynamics Simulations2007

    • Author(s)
      M. Nagaoka
    • Organizer
      The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      Bejing (China)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Anisotropic Structural Expansion of Photodissociated MbCO: Analysis via Ensemble Perturbation Method2007

    • Author(s)
      M. Takayanagi, H. Okumura, M. Nagaoka
    • Organizer
      The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      Bejing (China)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Structural Optimization of Ammonia Ionization Process in Aqueous Solution via Free Energy Gradient Method2007

    • Author(s)
      Y. Koyano, N. Takenaka, Y. Nakagawa, M. Nagaoka
    • Organizer
      The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      Bejing (China)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Surficial Kirkwood-Buff Approach2007

    • Author(s)
      I. Yu, M. Nagaoka
    • Organizer
      The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry
    • Place of Presentation
      Bejing (China)
    • Related Report
      2007 Annual Research Report
  • [Presentation] Anisotropic Structural Expansion of Photodissociated MbCO: Theoretical Analysis via Ensemble Perturbation Method2007

    • Author(s)
      M. Takayanagi, C. Iwahashi, M. Nagaoka
    • Organizer
      The 67th Okazaki Conference Molecular Science and Chemical Biology of Biomolecular Function
    • Place of Presentation
      Okazaki
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular Theoretical Understanding of the Stabilization Effect of Compatible Solute Ectoine on the Structure and Reactivity of Proteins2007

    • Author(s)
      I. Yu, M. Nagaoka
    • Organizer
      The 67th Okazaki Conference Molecular Science and Chemical Biology of Biomolecular Function
    • Place of Presentation
      Okazaki
    • Related Report
      2007 Annual Research Report
  • [Presentation] Theoretical Study on Small Molecules Adsorption in Metal-Organic Frameworks I: An Electronic State Calculation2007

    • Author(s)
      Y. Ohta, H. Hitomi, M. Nagaoka, R. Matsuda, S. Kitagawa
    • Organizer
      Third International Symposium on Chemistry of Coordination Space -ISCCS 2007-
    • Place of Presentation
      Awaji
    • Related Report
      2007 Annual Research Report
  • [Presentation] Theoretical Study on Small Molecules Adsorption in Metal-Organic Frameworks II: A Molecular Mechanical and Monte Carlo Study2007

    • Author(s)
      H. Hitomi, Y. Ohta, M. Nagaoka, R. Matsuda, S. Kitagawa
    • Organizer
      Third International Symposium on Chemistry of Coordination Space -ISCCS 2007-
    • Place of Presentation
      Awaji
    • Related Report
      2007 Annual Research Report
  • [Presentation] エクトイン水溶液中のタンパク質表面における選択的水和発現機構の分子論的考察2007

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Related Report
      2007 Annual Research Report
  • [Presentation] リガンド光解離により生じるMbCO構造変形の理論的解析2007

    • Author(s)
      高柳昌芳、奥村博人、長岡正隆
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Related Report
      2007 Annual Research Report
  • [Presentation] 多孔性配位高分子結晶CPL-1に対する酸素分子吸蔵に関する理論的研究2007

    • Author(s)
      人見晴子、太田雄介, 長岡正隆、松田亮太郎、北川進
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Related Report
      2007 Annual Research Report
  • [Presentation] 凝集反応系における分子熱浴の励起・緩和過程の取り扱い2007

    • Author(s)
      岡本拓也、長岡正隆
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Related Report
      2007 Annual Research Report
  • [Presentation] アンモニアイオン化反応における水和構造変化とエネルギー的安全性の解析2007

    • Author(s)
      小谷野哲之、竹中規雄、中川幸紀、長岡正隆
    • Organizer
      第10回理論化学討論会
    • Place of Presentation
      名古屋
    • Related Report
      2007 Annual Research Report
  • [Presentation] COリガンド光解離により誘起されるヘモグロビンサブユニット構造変形の理論的解析2007

    • Author(s)
      高柳昌芳、岩橋知令、長岡正隆
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] エクトイン水溶液中のタンパク質および小ペプチド表面における選択的水和の微視的描像2007

    • Author(s)
      優乙石、長岡正隆
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 自由エネルギー勾配法による溶質分子の構造最適化:溶媒分子の動的効果2007

    • Author(s)
      小谷野哲之、竹中規雄、中川幸紀、長岡正隆
    • Organizer
      第1回分子科学討論会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 有機溶媒中におけるメチルリチウムの会合状態に関する理論的研究2007

    • Author(s)
      太田雄介、人見晴子、岡本拓也、長岡正隆
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Related Report
      2007 Annual Research Report
  • [Presentation] アンモニアイオン化反応の微視的機構に関する理論的研究2007

    • Author(s)
      中川幸紀, 小谷野哲之, 竹中規夫, 長岡正隆
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Related Report
      2007 Annual Research Report
  • [Presentation] COリガンド光解離により誘起されるヘモグロビンサブユニット構造変形の理論的解析2007

    • Author(s)
      岩橋知令、高柳昌芳、長岡正隆
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Related Report
      2007 Annual Research Report
  • [Presentation] 光解離MbCOにおけるグロビン部内余剰振動エネルギー緩和経路の理論的研究2007

    • Author(s)
      高柳昌芳、岩橋知令、長岡正隆
    • Organizer
      第21回分子シミュレーション討論会
    • Place of Presentation
      金沢
    • Related Report
      2007 Annual Research Report
  • [Presentation] Monte Carlo Simulation on Small Molecules Adsorption in Microporous Coordination Polymers2006

    • Author(s)
      M. Nagaoka
    • Organizer
      XIIth International Congress of Quantum Chemistry Satellite Symposium : Large Molecular Systems
    • Place of Presentation
      Okazaki, Japan
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary

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Published: 2004-04-01   Modified: 2018-03-28  

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