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Time resolved analysis of the first order phase transition of nucleotide hydrates

Research Project

Project/Area Number 12440108
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field 物性一般(含基礎論)
Research InstitutionKitasato University

Principal Investigator

SUGAWARA Yoko  Kitasato University, School of Science, Professor, 理学部, 教授 (10167455)

Co-Investigator(Kenkyū-buntansha) URABE Hisako  Tokyo Kasei Gakuin University, Faculty of Home Economics, Associate Professor, 家政学部, 助教授 (00193970)
YAMAMURA Shigefumi  Kitasato University, School of Science, Assistant Professor, 理学部, 助手 (40286373)
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥15,500,000 (Direct Cost: ¥15,500,000)
Fiscal Year 2002: ¥1,500,000 (Direct Cost: ¥1,500,000)
Fiscal Year 2001: ¥1,500,000 (Direct Cost: ¥1,500,000)
Fiscal Year 2000: ¥12,500,000 (Direct Cost: ¥12,500,000)
Keywordsnucleotide / first order phase transition / hydrate / molecular dynamics simulation / neutron diffraction analysis / phonon / 一次相移転 / ヌクレオチドチオ結晶 / 結晶水
Research Abstract

Concerning the dynamics of humidity-induced first order phase transition of nucleotides, following information was obtained.
1. Time dependence of Bragg reflections coincides with the rate of increase or decrease of the number of crystal water molecules monitored by gravimetric measurements. The transition rate becomes infinite at the critical vapor-pressure of water or temperature. The phenomenon would be attributed to energy barrier of the first-order phase transition at the critical point, and is consistent with the observation of hysteresis. In most cases, there exists no intermediate state. However, in the case of Na_2UMP, transient super-structures were found, the cell lengths of which are twice as long as the original one. They are attributed to reorientation of sodium ions and crystal water molecules during the phase transition.
2. Neutron diffraction analysis of Na_2IMP. 7H_2O was carried out to examine the hydrogen positions in the hydrogen-bond networks. There are disordered water molecules, and the nuclear distribution of oxygen and hydrogen atoms was found to reflect three types of librational motions of water molecules with large amplitude.
3. Calculations of molecular dynamics simulation of guanosine dihydrate was carried out to obtain the complemental information to the experimental results. The difference in mobilities of interlayer and intralayer crystal water molecules was revealed, and translocation of water molecules occurred. It would be in close relation to the desorption pass of crystal water molecules. The phonon, whose origin would be common to that of the S-mode observed in Raman spectra of nucleic acid, was assigned to the translational vibration of bases along the stacking direction.

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (14 results)

All Other

All Publications (14 results)

  • [Publications] Y.Sugawara, A.Nakamura, Y.Iimura, K.Kobayashi, H.Urabe: "Crystallographic investigation of humidity-induced phase transition of disodium cytidine 5'-monophoshate and crystal structure of three hydrates"J. Phys. Chem. B. 106. 10363-10368 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Shindo, A.Naito, S.Tuzi, Y.Sugawara, H.Urabe, H.Saito: "Stepwise conformational transition of crystalline disodium adenosine 5'-triphosphate with relative humidity as studied by high resolution solid state ^<13>C and ^<13>P NMR"J. Mol. Struc.. 602-603. 389-397 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara, S.Yamamura, H.Osamura, H.Kimura, Y.Noda: "Neutron diffraction analysis of hydrogen bonding networks of the inosine 5'-monophosphate hydrate in medium humidity range"ISSP Activity Report on Neutron Scattering Research. (in press).

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 菅原洋子: "有機結晶の一次相転移"分子科学研究所平成11年度前期研究会「多体相互作用系へのアプローチ-ブレインストーミング-」報告書. 42-45 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 山村滋典: "回折データのイメージングによる固体中水素の化学結合"KEK Proceedings. 2001-17. 63-67 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] 菅原洋子: "ヌクレオシド、ヌクレオチド水和物結晶にみられる水蒸気圧誘起一次相転移の研究"日本結晶学会誌. 45. 103-109 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara, A.Nakamura, Y.Iimura, K.Kobayashi, and H.Urabe: "Crystallographic investigation of humidity-induced phase transition of disodium cytidine 5'-monophosphate and crystal structure of three hydrates"J.Phys.Chem.B. 106. 10363-10368 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Shindo, A.Naito, S.Tuzi, Y.Sugawara, H.Urabe, and H.Saito: "Stepwise conformational transition of crystalline disodium adenosine 5'-triphosphate with relative humidity as studied by high resolution solid state 13C and 31P NMR"J.Mol.Struc.. 602-603. 389-397 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara, S.Yamamura, H.Osamura, H.Kimura, and Y.Noda: "Neutron diffraction analysis of hydrogen bonding networks of the inosine 5'-monophosphate hydrate stable in medium humidity range"ISSP Activity Report on Neutron Scattering Research. (in press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara: "First order phase transition of organic crystals"Proceedings of IMS Symposium : Approach to multi-interaction system -brainstorming-. (in Japanese). 42-45 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] S.Yamamura: "The nature of hydrogen bonds in solids observed by imaging of reflection data"KEK Proceedings 2001-17. (in Japanese). 63-67 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara: "Investigation of humidity-induced first order phase transition of nucleoside and nucleotide hydrates"J.Crystallogr.Soc.Jpn.. 45, (in Japanese). 103-109 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Sugawara, A.Nakamura, Y.Iimura, K.Kobayashi, H.Urabe: "Crystallographic Investigation of Humidity-Induced Phase Transition of Disodium Cytidine 5'-Monophosphate and Crystal Structure of Three Hydrates"J. Phys. Chem. B. 106(40). 10363-10368 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Y.Shindo, A.Naito, S.Tuzi, Y.Sugawra, H.Urabe, H.Saito: "Stepwise conformational transition of crystalline disodeum adenosine 5'-triphosphatewith relative humidity as studied by high resolution solid state ^<13>C and ^<31>P NMR"J Mci. Struct.. (in press).

    • Related Report
      2001 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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