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2013 Fiscal Year Final Research Report

Theoretical soft X-ray spectroscopy calculations for biomolecules

Research Project

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Project/Area Number 23540476
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionHiroshima University

Principal Investigator

TAKAHASHI Osamu  広島大学, サステナブル・ディベロップメント実践研究センター, 特任講師 (60253051)

Project Period (FY) 2011 – 2013
Keywords放射線、X線、粒子線 / 生体分子 / 内殻励起 / 化学物理
Research Abstract

In this study, soft X-ray spectroscopy calculations are applied to biomolecular systems. Two computational methods are constructed; one is X-ray natural circular dichroism (XNCD) which is one of specific for biomolecules, the other is double core hole (DCH) spectroscopy which is specially forcus in the use of X-ray free electron laser. For XNCD, a new code has been developed and is applied to several amino acid using cluster models. Our calculations for alanine are consistent with the experiments. For DCH state calculations, we performed calculations for nucleobases, and our calculations can be induced information reflected with chemical environment of molecules.

  • Research Products

    (36 results)

All 2013 2012 2011 Other

All Journal Article (19 results) (of which Peer Reviewed: 19 results) Presentation (16 results) (of which Invited: 1 results) Remarks (1 results)

  • [Journal Article] Site-dependent Si KL_<23>L_<23> resonant Auger electron spectra following inner-shell excitation of Cl_3SiSi(CH_3)_32013

    • Author(s)
      I. H. Suzuki, O. Takahashi (他4名)
    • Journal Title

      J. Chem. Phys

      Volume: 139 Pages: 174314(7)

    • DOI

      10.1063/1.4827860

    • Peer Reviewed
  • [Journal Article] Selective Probing of OH-OD stretch vibrations in liquid water using resonant inelastic soft-X-ray scattering2013

    • Author(s)
      Y. Harada, O. Takahashi (他11名)
    • Journal Title

      Phys. Rev. Lett

      Volume: 111 Pages: 193001

    • DOI

      10.1103/PhysRevLett.111.193001

    • Peer Reviewed
  • [Journal Article] Using covariance mapping to investigate the dynamics of multi-photon ionization processes of Ne atoms exposed to X-FEL pulses2013

    • Author(s)
      V. Zhaunerchyk, O. Takahashi (他32名)
    • Journal Title

      J. Phys. B: At. Mol. Opt. Phys

      Volume: 46 Pages: 164034

    • DOI

      10.1088/0953-4075/46/16/164034

    • Peer Reviewed
  • [Journal Article] Dynamics of hollow atom formation in intense X-ray pulses mapped by partial covariance2013

    • Author(s)
      L. J. Fransinski, O. Takahashi (他31名)
    • Journal Title

      Phys. Rev. Lett

      Volume: 111 Pages: 073002

    • DOI

      10.1103/PhysRevLett.111.073002

    • Peer Reviewed
  • [Journal Article] A variety of characteristic behavior of resonant KL_<23>L_<23> Auger decays following Si K-shell photoexcitation of SiCl_42013

    • Author(s)
      I. H. Suzuki, O. Takahashi (他6名)
    • Journal Title

      J. Phys. B: At. Mol. Opt. Phys

      Volume: 46(7) Pages: 075101(9)

    • DOI

      10.1088/0953-4075/46/7/075101

    • Peer Reviewed
  • [Journal Article] Formation and decay of core-orbital vacancies in the water molecules2013

    • Author(s)
      M. Mucke, O. Takahashi (他5名)
    • Journal Title

      Chem. Phys. Lett

      Volume: 558 Pages: 82-87

    • DOI

      10.1016/j.cplett.2012.11.094

    • Peer Reviewed
  • [Journal Article] Substituent R-effects on the core-electron excitation spectra of hydrogen bonded carboxylic-acid (R-COOH) clusters : Comparison between acetic-acid and formic-acid clusters2013

    • Author(s)
      K. Tabayashi, O. Takahashi (他2名)
    • Journal Title

      Chem. Phys. Lett

      Volume: 557 Pages: 1

    • DOI

      10.1016/j.cplett.2012.10.043

    • Peer Reviewed
  • [Journal Article] Cascade Auger decays following Si KL_<23>L_<23> Auger transitions in SiF_42013

    • Author(s)
      I. H. Suzuki, O. Takahashi (他7名)
    • Journal Title

      J. Chem. Phys

      Volume: 138(2) Pages: 024302(7)

    • DOI

      10.1063/1.4773344

    • Peer Reviewed
  • [Journal Article] Site-specific ion desorption from condensed F_3SiCD_2CH_2Si(CH_3)_3 induced by Si-2p corelevel ionizations studied with photoelectron photoion coincidence (PEPICO) spectroscopy, Auger photoelectron coincidence spectroscopy (APECS) and Auger electron photoion coincidence (AEPICO) spectroscopy2013

    • Author(s)
      K. Mase, O. Takahashi (他7名)
    • Journal Title

      Surf. Sci

      Volume: 607 Pages: 174-180

    • DOI

      10.1016/j.susc.2012.09.003

    • Peer Reviewed
  • [Journal Article] Extracting chemical information of free molecules from K-shell double core-hole spectroscopy2012

    • Author(s)
      K. Ueda and O. Takahashi
    • Journal Title

      J. Elec. Spectrosc. Rel. Phenom

      Volume: 185 Pages: 301-311

    • DOI

      10.1016/j.elspec.2012.04.003

    • Peer Reviewed
  • [Journal Article] Polarization dependent resonant X-ray emission spectroscopy of D_2O and H_2O water : Assignment of the local molecular orbital symmetry2012

    • Author(s)
      T. Tokushima, O. Takahashi (他6名)
    • Journal Title

      J. Chem. Phys

      Volume: 136(4) Pages: 044517-7

    • DOI

      10.1063/1.3678443

    • Peer Reviewed
  • [Journal Article] Core-to-Rydberg band-shift and -broadening of hydrogen bonded ammonia clusters studied with nitrogen K-edge excitation spectroscopy2012

    • Author(s)
      T. Yamanaka, O. Takahashi (他4名)
    • Journal Title

      Chem. Phys

      Volume: 136(1) Pages: 014308-11

    • DOI

      10.1063/1.3673778

    • Peer Reviewed
  • [Journal Article] Molecular double core-hole electron spectroscopy of large molecules for probing molecular size : A series of bridged trihalosilyltrimethylsilyl molecules2011

    • Author(s)
      O. Takahashi (他3名)
    • Journal Title

      Chem. Phys. Lett

      Volume: 518(1-3) Pages: 44-48

    • DOI

      10.1016/j.cplett.2011.11.006

    • Peer Reviewed
  • [Journal Article] Molecular double core hole electron spectroscopy of nucleobases2011

    • Author(s)
      O. Takahashi (他4名)
    • Journal Title

      J. Phys. Chem. A

      Volume: 115(44) Pages: 12070-12082

    • DOI

      10.1021/jp205923m

    • Peer Reviewed
  • [Journal Article] A study to control chemical reactions using Si : 2p core ionization -Site-specific fragmentation-2011

    • Author(s)
      S. Nagaoka, O. Takahashi (他10名)
    • Journal Title

      J. Phys. Chem. A

      Volume: 115(32) Pages: 8822-8831

    • DOI

      10.1021/jp203664r

    • Peer Reviewed
  • [Journal Article] Theoretical spectroscopy on K^<-2>, K^<-1>L^<-1>, and L^<-2> double core hole states of SiX4 (X=H, F, Cl, and CH_3) molecules2011

    • Author(s)
      O. Takahashi (他4名)
    • Journal Title

      Chem. Phys

      Volume: 384 Pages: 28-35

    • DOI

      10.1016/j.chemphys.2011.04.015

    • Peer Reviewed
  • [Journal Article] Site- and geometry-specific CH...O interaction in small acetaldehyde clusters studied with core-electron excitation spectroscopy in the carbon K-edge region2011

    • Author(s)
      K. Tabayashi, O. Takahashi (他8名)
    • Journal Title

      J. Phys. Conf. Ser

      Volume: 288 Pages: 012022-11

    • DOI

      10.1088/1742-6596/288/1/012022

    • Peer Reviewed
  • [Journal Article] Projection of Si 1s photoexcited orbitals into resonant Auger electron spectra in KLL decays of Si(CH_3)_4 and SiF_42011

    • Author(s)
      I. H. Suzuki, O. Takahashi (他7名)
    • Journal Title

      J. Chem. Phys

      Volume: 134 Pages: 084312-7

    • DOI

      10.1063/1.3556942

    • Peer Reviewed
  • [Journal Article] Structure sensitivity of double inner-shell holes in sulfur-containing molecules2011

    • Author(s)
      P. Linusson, O. Takahashi (他3名)
    • Journal Title

      Phys. Rev. A

      Volume: 83 Pages: 022506-4

    • DOI

      10.1103/PhysRevA.83.022506

    • Peer Reviewed
  • [Presentation] Auger decay spectra calculations for some small molecules2013

    • Author(s)
      O. Takahashi, S. Takaki, N. Kunitake, K. Yamasaki
    • Organizer
      5th JCS International Symposium on Theoretical Chemistry
    • Place of Presentation
      Nara, Japan
    • Year and Date
      2013-12-03
    • Invited
  • [Presentation] 軟X線分光に関する理論計算2013

    • Author(s)
      高橋修
    • Organizer
      平成25年度研究集会
    • Place of Presentation
      札幌
    • Year and Date
      2013-11-28
  • [Presentation] 金属原子を含む軟X線吸収分光スペクトルの理論計算2013

    • Author(s)
      高橋修
    • Organizer
      2013年日本化学会中国四国支部大会
    • Place of Presentation
      東広島
    • Year and Date
      2013-11-16
  • [Presentation] 核の運動を含んだオージェ電子分光スペクトルの理論計算2013

    • Author(s)
      高橋修, 高木沙弥, 国武尚登, 山崎勝義
    • Organizer
      日本コンピュータ化学会2013秋季年会
    • Place of Presentation
      福岡
    • Year and Date
      2013-10-18
  • [Presentation] 液体エタノールのX線発光分光に対する理論計算2013

    • Author(s)
      高橋修, Lars Pettersson
    • Organizer
      第7回分子科学討論会
    • Place of Presentation
      京都
    • Year and Date
      2013-09-24
  • [Presentation] Auger decay spectra calculations for some small molecules2013

    • Author(s)
      O. Takahashi, S. Takaki, N. Kunitake, K. Yamasaki
    • Organizer
      XXVIII ICPEAC
    • Place of Presentation
      Lanzhou, China
    • Year and Date
      2013-07-29
  • [Presentation] 液体アルコールのX線発光分光に対する理論計算2013

    • Author(s)
      高橋修, Lars G. M. Pettersson
    • Organizer
      日本コンピュータ化学会2013春季年会
    • Place of Presentation
      東京
    • Year and Date
      2013-05-31
  • [Presentation] 内殻二重正孔状態におけるダイナミクス2013

    • Author(s)
      高橋修, 谷哲龍, 山崎勝義, 上田潔
    • Organizer
      第26回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      名古屋
    • Year and Date
      2013-01-13
  • [Presentation] QCT 法を用いたN_2+O_2 系の振動緩和過程の理論計算2012

    • Author(s)
      大久保康裕, 河野明男, 高橋修, 山崎勝義
    • Organizer
      日本コンピュータ化学会2012秋季年会
    • Place of Presentation
      山形
    • Year and Date
      2012-10-13
  • [Presentation] 分子の二重内殻正孔状態の理論的研究2012

    • Author(s)
      高橋修, 上田潔
    • Organizer
      第35回情報化学討論会
    • Place of Presentation
      東広島
    • Year and Date
      2012-10-05
  • [Presentation] Extracting chemical information of free molecules from K-shell double core-hole spectroscopy2012

    • Author(s)
      O. Takahashi and K. Ueda
    • Organizer
      The 12th international conference on electron spectroscopy and structure (ICESS12)
    • Place of Presentation
      Saint-Malo, France
    • Year and Date
      2012-09-20
  • [Presentation] Theoretical study of photoelectron-Auger electron coincidence spectroscopy of CF_42012

    • Author(s)
      高橋修, T. Arion , U. Hergenhahn
    • Organizer
      第28回化学反応討論会
    • Place of Presentation
      福岡
    • Year and Date
      2012-06-07
  • [Presentation] 軟X線分光法に対する理論計算手法の開発2012

    • Author(s)
      國武尚登, 木元麻衣, 高橋修, 山崎勝義
    • Organizer
      第25回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      鳥栖
    • Year and Date
      2012-01-08
  • [Presentation] アンモニアの光刺激脱離反応に関する理論的研究2012

    • Author(s)
      谷哲龍, 高橋修, 山崎勝義
    • Organizer
      第25回日本放射光学会年会・放射光科学合同シンポジウム
    • Place of Presentation
      鳥栖
    • Year and Date
      2012-01-08
  • [Presentation] 生体分子に対するX 線二重内殻正孔分光理論計算2011

    • Author(s)
      高橋修, 田代基慶, 江原正博, 山崎勝義, 上田 潔
    • Organizer
      第5回分子科学討論会
    • Place of Presentation
      札幌
    • Year and Date
      2011-09-23
  • [Presentation] Theoretical Calculations of Vibrational Relaxation in O_2+N_2 System2011

    • Author(s)
      大久保泰裕, 高橋修, 山崎勝義
    • Organizer
      第27回化学反応討論会
    • Place of Presentation
      東京
    • Year and Date
      2011-06-08
  • [Remarks]

    • URL

      http://home.hiroshima-u.ac.jp/shu/

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Published: 2015-07-16  

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