Theoretical soft X-ray spectroscopy calculations for biomolecules

• Project/Area Number: 23540476
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Biophysics/Chemical physics
• Research Institution: Hiroshima 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
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2011: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• 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

• [Journal Article] Site-dependent Si KL23L23 resonant Auger electron spectra following inner-shell excitation of Cl3SiSi(CH3)3 (2013)
  • Author(s): Isao Suzuki, Hikari Endo, Kanae Nagai, Osamu Takahashi, Yusuke Tamenori, and Shin-ichi Nagaoka
  • Journal Title: J. Chem. Phys. Volume: 139 Issue: 17 Pages: 174314-7
  • DOI: 10.1063/1.4827860
  • Peer Reviewed
• [Journal Article] elective Probing of OH-OD stretch vibrations in liquid water using resonant inelastic soft-X-ray scattering (2013)
  • Author(s): Yoshihisa Harada, Takashi Tokushima, Yuka Horikawa, Osamu Takahashi, Hideharu Niwa, Masaki Kobayashi, Masaharu Oshima, Yasunori Senba, Haruhiko Ohashi, Kjartan Thor Wikfeldt, Anders Nilsson, Lars G. M. Petterson, and Shik Shin
  • Journal Title: Phys. Rev. Lett. Volume: 111 Issue: 19 Pages: 193001-5
  • 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 Pulses (2013)
  • Author(s): V. Zhaunerchyk, L. J. Fransinski, M. Siano, J. H. D. Eland, P. Linusson, R. D. Thomas, M. Larsson, L. Foucar, J. Ullrich, K. Motomura, S. Mondal, K. Ueda, T. Osipiv, L. Fang, B. F. Murphy, N. Berrah, C. Bostedt, J. D. Bozek, S. Schorb, M. Messerschmidt, J. M. Glownia, J. P. Cryan, R. Coffee, O. Takahashi (他10名)
  • Journal Title: J. Phys. B: At. Mol. Opt. Phys. Volume: 46 Issue: 16 Pages: 164034-8
  • DOI: 10.1088/0953-4075/46/16/164034
  • Peer Reviewed
• [Journal Article] Dynamics of hollow atom formation in intense s-ray pulses mapped by partial covariance (2013)
  • Author(s): L. J. Fransinski, P. Linusson, P. v.d. Muelen, P. Salen, R. D. Thomas, M. Larsson, L. Foucar, J. Ullrich, K. Motomura, S. Mondal, K. Ueda, T. Osipiv, L. Fang, B. Murphy, N. Berrah, C. Bostedt, J. D. Bozek, S. Schorb, M. Messerschmidt, J. M. Glownia, J. Cryan, R. Coffee, O. Takahashi, S. Wada (他10名)
  • Journal Title: Phys. Rev. Lett. Volume: 111 Issue: 7 Pages: 73002-5
  • DOI: 10.1103/physrevlett.111.073002
  • Peer Reviewed
• [Journal Article] A vaiety of characteristic behavior of resonant KL23L23 Auger decays following Si K-shell photoexcitation of SiCl4 (2013)
  • Author(s): I. H. Suzuki, Y. Kono, K. Sakai, M. Kimura, K. Ueda, Y. Tamenori, O. Takahashi, and S. Nagaoka
  • Journal Title: J. Phys. B: At. Mol. Opt. Phys. Volume: 46 Issue: 7 Pages: 75101-9
  • DOI: 10.1088/0953-4075/46/7/075101
  • Peer Reviewed
• [Journal Article] Formation and decay of core-orbital vacancies in the water molecules (2013)
  • 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 clusters (2013)
  • Author(s): Tabayashi, K,Takahashi, O,Namatame, H,Taniguchi, M
  • Journal Title: CHEMICAL PHYSICS LETTERS Volume: 557 Pages: 1-9
  • DOI: 10.1016/j.cplett.2012.10.043
  • Peer Reviewed
• [Journal Article] Cascade Auger decays following Si KL23L23 Auger transitions in SiF4 (2013)
  • Author(s): I.H. Suzuki, Y. Kono, A. Ikeda, M. Oi, T. Ouchi, K. Ueda, Y. Tamenori, O. Takahashi and S. Nagaoka
  • Journal Title: J. Chem. Phys. Volume: 138 Issue: 2 Pages: 24302-7
  • DOI: 10.1063/1.4773344
  • Peer Reviewed
• [Journal Article] Site-specific ion desorption from condensed F3SiCD2CH2Si(CH3)3 induced by Si-2p core-level ionizations studied with photoelectron photoion coincidence (PEPICO) spectroscopy, Auger photoelectron coincidence spectroscopy (APECS) and Auger electron photoion coincidence (AEPICO) spectroscopy (2013)
  • Author(s): Kazuhiko Mase, Eiichi Kobayashi, Akira Nambu, Takuhiro Kakiuchi, Osamu Takahashi, Kiyohiko Tabayashi, Joji Ohshita, Shogo Hashimoto, Masatoshi Tanaka, Shin-ichi Nagaoka
  • Journal Title: Surf. Sci. Volume: 607 Pages: 174-180
  • DOI: 10.1016/j.susc.2012.09.003
  • Peer Reviewed
• [Journal Article] Important role of the CH/pi hydrogen bond in the enhancement of CD amplitude of 1,3-diene steroids (2013)
  • Author(s): Osamu Takahashi, Yuji Kohno, Kazuyoshi Ueda, and Motohiro Nishio
  • Journal Title: New J. Chem. Volume: 37 Issue: 3 Pages: 843-849
  • DOI: 10.1039/c2nj40955k
  • Peer Reviewed
• [Journal Article] Influence of the CH/pi hydrogen bond on the enhancement of circular dichroism (CD) amplitude of 5,7-diene steroids: ergosterol, lumisterol, pirocarciferol, isopirocarciferol and structurally related cyclohexadienes (2013)
  • Author(s): Osamu Takahashi, Yuji Kohno and Motohiro Nishio
  • Journal Title: New J. Chem. Volume: 37 Issue: 7 Pages: 2082-2086
  • DOI: 10.1039/c3nj41148f
  • Peer Reviewed
• [Journal Article] Unique Water-Water Coordination Tailored by a Metal Surface (2013)
  • Author(s): T. Schiros, K. Andersson, J. B. MacNaughton, J. Gladh, A. Matsuda, H. Ostrom, O. Takahashi, L.G.M. Pettersson, A. Nilsson, and H. Ogasawara
  • Journal Title: J. Chem. Phys. Volume: 138 Issue: 23 Pages: 234708-7
  • DOI: 10.1063/1.4809680
  • Peer Reviewed
• [Journal Article] Extracting chemical information of free molecules from K-shell double core-hole spectroscopy (2012)
  • Author(s): K. Ueda and O. Takahashi
  • Journal Title: J. Elec. Spectrosc. Rel. Phenom Volume: 185 Issue: 8-9 Pages: 301-311
  • DOI: 10.1016/j.elspec.2012.04.003
  • Peer Reviewed
• [Journal Article] Polarization dependent resonant x-ray emission spectroscopy of D2O and H2O water: Assignment of the local molecular orbital symmetry (2012)
  • Author(s): T. Tokushima, Y. Horikawa, H. Arai, Y. Harada, O. Takahashi, L. G. M. Pettersson, A. Nilsson, S. Shin
  • Journal Title: J. Chem. Phys. Volume: 136 Issue: 4 Pages: 4451707-4451707
  • DOI: 10.1063/1.3678443
  • Peer Reviewed
• [Journal Article] Core-to-Eydberg band-shift and -broadening of hydrogen bonded ammonia clusters studied with nitrogen K-edge excitation spectroscopy (2012)
  • Author(s): 山中武, 田中健一郎, 他4名
  • Journal Title: J.Chem.Phys. Volume: 136(1) Issue: 1 Pages: 1-5
  • DOI: 10.1063/1.3673778
  • Peer Reviewed
• [Journal Article] Influence of the CH/ hydrogen bond on the enhancement of circular dichroism (CD) amplitude of 1,3-cyclohexadiene compounds (2012)
  • Author(s): Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Kazuyoshi Ueda, and Motohiro Nishio
  • Journal Title: RSC Advances Volume: 2 Issue: 29 Pages: 10891-10898
  • DOI: 10.1039/c2ra21446f
  • Peer Reviewed
• [Journal Article] Molecular double core-hole electron spectroscopy of large molecules for probing molecular size : A series of bridged trihalosilyltrimethylsilyl molecules (2011)
  • 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 Nucleobases (2011)
  • Author(s): O. Takahashi, M. Tashiro, M. Ehara, K. Yamasaki, K. Ueda
  • Journal Title: J. Phys. Chem Volume: A115 Issue: 44 Pages: 12070-12082
  • DOI: 10.1021/jp205923m
  • Peer Reviewed
• [Journal Article] A Study to Control Chemical Reactions Using Si:2p Core Ionization : Site-Specifiction (2011)
  • Author(s): S.Nagaoka, H.Fukuzawa, G.Prumper, M.Takemoto, O.Takahashi, K.Yamaguchi, T.Kakiuchi, K.Tabayashi, I.H.Suzuki, J.R.Harries, Y.Tamenori, K.Ueda
  • Journal Title: J.Phys.Chem.A Volume: 115 Issue: 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 SiX_4 (X=H, F, Cl, and CH_3) molecules (2011)
  • Author(s): O.Takahashi, M.Tashiro, M.Ehara, K.Yamasaki, K.Ueda
  • Journal Title: Chem.Phys. Volume: 384 Issue: 1-3 Pages: 28-25
  • 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 region (2011)
  • Author(s): K. Tabayashi, O. Takahashi (他8名)
  • Journal Title: J. Phys. Conf. Ser Volume: 288 Pages: 12022-11
  • 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_4 (2011)
  • Author(s): I. H. Suzuki, O. Takahashi (他7名)
  • Journal Title: J. Chem. Phys Volume: 134 Issue: 8 Pages: 84312-7
  • DOI: 10.1063/1.3556942
  • Peer Reviewed
• [Journal Article] Structure sensitivity of double inner-shell holes in sulfur-containing molecules (2011)
  • Author(s): P. Linusson, O. Takahashi (他3名)
  • Journal Title: Phys. Rev. A Volume: 83 Issue: 2 Pages: 22506-4
  • DOI: 10.1103/physreva.83.022506
  • Peer Reviewed
• [Presentation] Theoretical studies on core-level spectroscopy: Dynamical effects (2014)
  • Author(s): O. Takahashi
  • Organizer: Helmholtz-Zentrum Berlin
  • Place of Presentation: Helmholtz-Zentrum Berlin, Berlin
  • Invited
• [Presentation] Auger decay spectra calculations for some small molecules (2013)
  • 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 molecules (2013)
  • 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] Auger decay spectra calculations for some small molecules (2013)
  • Author(s): Osamu Takahashi, Saya Takaki, Naotake Kunitake, Katsuyoshi Yamasaki
  • Organizer: XXVIII International Conference on Photonic, Electronic and Atomic Collision
  • Place of Presentation: Lanzhou, China
• [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: 東京工業大学大岡山キャンパス
• [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: 九州大学 伊都キャンパス
• [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2013
  • Place of Presentation: 京都 京都テルサ
• [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: 広島大学西条キャンパス
  • Invited
• [Presentation] 軟X線分光に関する理論計算 (2013)
  • Author(s): 高橋 修
  • Organizer: 文部科学省平成25年度科学研究費補助金「新学術領域研究」宇宙における分子進化：星間雲から原子惑星系へ 平成25年度研究集会
  • Place of Presentation: 札幌，低温科学研究所
  • Invited
• [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: 名古屋大学
• [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 spectroscopy (2012)
  • 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_4 (2012)
  • 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] High resolution X-ray emission studies on hydrogen bonded water molecules in liquid and solutions (2012)
  • Author(s): TOKUSHIMA, Takashi; HORIKAWA, Yuka; ARAI, Hidemi; HARADA, Yoshihisa; TAKAHASHI, Osamu; SHIN, Shik
  • Organizer: 化学反応討論会
  • Place of Presentation: 福岡、九州大学筑紫キャンパス
• [Presentation] Theoretical study of photoelectron-Auger electron coincidence spectroscopy of CF4 (2012)
  • Author(s): TAKAHASHI, Osamu; ARION, Tiberiu; HERGENHAHN, Uwe
  • Organizer: 化学反応討論会
  • Place of Presentation: 福岡、九州大学筑紫キャンパス
• [Presentation] Extracting chemical information of free molecules from Kshell (2012)
  • Author(s): O. Takahashi; K. Ueda
  • Organizer: International conference of Electronic spectroscopy and structure
  • Place of Presentation: Palais des Congres &#8211; Saint-Malo, France
• [Presentation] QCT 法を用いたN2＋O2系の振動緩和過程の理論計算 (2012)
  • Author(s): 大久保泰裕、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: 山形大学小白川キャンパス 基盤教育棟2号館
• [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: 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、鳥栖市民文化会館・中央公民館
• [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: 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、鳥栖市民文化会館・中央公民館
• [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 System (2011)
  • 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
• [Presentation] Theoretical Calculations of Vibrational Relaxation in O2+N2 System (2011)
  • Author(s): Okubo,Yasuhiro; Takahashi,Osamu; Yamasaki,Katsuyoshi
  • Organizer: 化学反応討論会
  • Place of Presentation: 東京、東京工業大学(デジタル多目的ホール・コラボレーションルーム)
• [Presentation] Soft X-ray emission spectra of carbonate ions in aqueous solution of alkali carbonates (2011)
  • Author(s): Yoshida,Ayaka; Arai,Hidemi; Horikawa,Yuka; Tokushima,Takashi; Takahashi,Osamu Oura,Masaki; Gejo,Tatsuo; Honma,Kenji; Shin,Siik
  • Organizer: 化学反応討論会
  • Place of Presentation: 東京、東京工業大学(デジタル多目的ホール・コラボレーションルーム)
• [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: 分子科学討論会
  • Place of Presentation: 札幌、札幌コンベンションセンター
• [Remarks]
  • URL: http://home.hiroshima-u.ac.jp/shu/