Extensive investigation of the ring puckering paths of Glucose using quantum chemical calculation and the molecular design of cellulase

• Project/Area Number: 22500272
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Yokohama National University
• Principal Investigator: UEDA Kazuyoshi 横浜国立大学, 大学院・工学研究院, 教授 (40223458)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: コンピューターシミュレーション / コンピュータシミュレーション / 環変換 / グルコース

Research Abstract

The purpose of this work is to clarify the whole processes of the inter-conversion of the ring conformations of the glucopyranose ring using quantum mechanics calculation. The inter-conversion process can be represented by using Clemer-Pople parameter which is shown by the degrees of the latitude and the longitude on the surface of the globe. The results of this work indicated that there are many pathways which connect north pole 4C1 conformation and south pole 1C4 structure. It also found their transition structures of those paths. This information will help to consider the application of carbohydrate to the industrial use.

Research Products

• [Journal Article] Importance of the CH/? hydrogen bond in the enhancement of CD amplitude of exomethylene steroids (2012)
  • Author(s): Osamu Takahashi, Katsuyoshi Yamasaki, Yuji Kohno, Kazuyoshi Ueda, and Motohiro Nishio
  • Journal Title: RSC Advances Volume: 2 Pages: 10891-10898
  • Peer Reviewed
• [Journal Article] Experimental and theoretical investigation of proton exchange reaction between protic ionic liquid diethylmethylammonium trifluoromethanesulfonate and H2O (2012)
  • Author(s): Kazuki Mori, Takanori Kobayashi, Kazuhisa Sakakibara, and Kazuyoshi Ueda
  • Journal Title: Chemical Physics Letters Volume: 552 Pages: 58-63
  • Peer Reviewed
• [Journal Article] Structure and orientation of bovine lactoferrampin in the bacterial membrane as revealed by Solid-State NMR and molecular dynamics simulation. (2012)
  • Author(s): Atsushi Tsutsumi, Namsrai Javkhlantugs, Atsushi Kira, Masako Umeyama, Izuru Kawamura, Kazuyoshi Ueda and Akira Naito
  • Journal Title: Biophys. J. Volume: 103 Pages: 1735-1743
  • Peer Reviewed
• [Journal Article] Gromacsのための計算支援ソフトGISPの開発 (2012)
  • Author(s): 森一樹、樺島智大、源聡、玉城哲平、上田一義
  • Journal Title: J. Comput. Chem. Soc. Jpn Volume: 11 Pages: 98-103
  • NAID: 130001908172
  • Peer Reviewed
• [Journal Article] Conformational analysis of an extracellular polysaccharide produced by Sphaerotilus natans (2012)
  • Author(s): Keiko Kondo, Minoru Takeda, Masato Katahira, Jun-ichi Koizumi, and Kazuyoshi Ueda
  • Journal Title: Carbohydrate Research Volume: 360 Pages: 102-108
  • Peer Reviewed
• [Journal Article] Ab initio studies of the crystal structure of cellulose triacetate I. (2012)
  • Author(s): Takanori Kobayashi, Daichi Hayakawa, Tegshjargal Khishigjargal and Kazuyoshi Ueda
  • Journal Title: MRS Online Proceedings Library Volume: 1470
  • DOI: 10.1557/opl.2012.1204
  • Peer Reviewed
• [Journal Article] Rare gas bond property ofRg-Be2O2 and Rg-Be2O2-Rg (Rg = He, Ne, Ar, Kr and Xe) as a comparison withRg-BeO (2012)
  • Author(s): Takanori Kobayashi, Yuji Kohno, Toshiyuki Takayanagi, Kanekazu Seki, and Kazuyoshi Ueda
  • Journal Title: Computational and TheoreticalChemistry Volume: 991 Pages: 48-55
  • Peer Reviewed
• [Journal Article] Twisted Coordination Mode of Bis(N-Heterocyclic carbine) Ligands in Octahedral Geometry of Group 6 Transition Metal Complexes : Synthesis, Structure, and Reactivity (2012)
  • Author(s): Kenichi Ogata, Yoshitaka Yamaguchi, Youji Kurihara, Kazuyoshi Ueda, Hirotaka Nagao, Takashi Ito
  • Journal Title: Inorganica Chimica Acta Volume: 390 Pages: 199-209
  • Peer Reviewed
• [Journal Article] Structure and orientation of bovine lactoferrampin in the bacterial membrane as revealed by Solid-State NMR and molecular dynamics simulation. (2012)
  • Author(s): Atsushi Tsutsumi, Namsrai Javkhlantugs, Atsushi Kira, Masako Umeyama, Izuru Kawamura, Kazuyoshi Ueda and Akira Naito
  • Journal Title: Biophycal. Journal Volume: 103 Issue: 8 Pages: 1735-1743
  • DOI: 10.1016/j.bpj.2012.09.010
  • 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] Supermolecular Structure of Cellulose/Amylose Blends Prepared from Aqueous NaOH Solutions and Effects of Amylose on Structural Formation of Cellulose from Its Solution (2011)
  • Author(s): Hitomi Miyamoto, Mariko Ago, Chihiro Yamane, Masaharu Seguchi, Kazuyoshi Ueda, and Kunihiko Okajima
  • Journal Title: Carbohydr. Res. Volume: 346 Pages: 807-814
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Simulation of Bombolitin II in the Dipalmitoylphosphatidylcholine Membrane biyaer (2011)
  • Author(s): Namsrai Javkhlantugs, Akira Naito, Kazuyoshi Ueda
  • Journal Title: Biophys. J. Volume: 101 Issue: 5 Pages: 1212-1220
  • DOI: 10.1016/j.bpj.2011.07.018
  • Peer Reviewed
• [Journal Article] Molecular dynamics simulation of the dissolution process of cellulose triacetate-II nano-size crystal in DMSO (2011)
  • Author(s): Daichi Hayakawa, Kazuyoshi Ueda, Chihiro YAMANE, Hitomi MIYAMOTO and Fumitaka HORII
  • Journal Title: Carbohydr. Res Volume: 346 Issue: 18 Pages: 2940-2947
  • DOI: 10.1016/j.carres.2011.10.019
  • Peer Reviewed
• [Journal Article] Supermolecular Structure of Cellulose/Amylose Blends Prepared from Aqueous NaOH Solutions and Effects of Amylose on Structural Formation of Cellulose from Its Solution (2011)
  • Author(s): Hitomi Miyamoto, Mariko Ago, Chihiro Yamane, Masaharu Seguchi, Kazuyoshi Ueda, Kunihiko Okajima
  • Journal Title: Carbohydrate Research Volume: 346 Pages: 807-814
  • Peer Reviewed
• [Journal Article] Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation (2010)
  • Author(s): Shuichi Toraya, Namsrai Javkhlantugs, Daisuke Mishima, Katsuyuki Nishimura, Kazuyoshi Ueda, Akira Naito
  • Journal Title: Biophys. J. Volume: 99 Pages: 3282-3289
  • Peer Reviewed
• [Journal Article] Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation (2010)
  • Author(s): Shuichi Toraya, Namsrai Javkhlantugs, Daisuke Mishima, Katsuyuki Nishimura, Kazuyoshi Ueda
  • Journal Title: Biophysical Journal Volume: 99 Pages: 3282-3289
  • Peer Reviewed
• [Journal Article] Conformational Study of Ionic Aggregate of Dodecylether Polyethoxylate with Ferric-Thiocyanate Anion through the Intermediary of Potassium Ion (2010)
  • Author(s): Yukio Yokoyama, Hidaka Atsumi, Sayaka Yoshida, Naoyuki Sone, Kazuyoshi Ueda
  • Journal Title: Analytical Science Volume: 26 Pages: 1047-1052
  • Peer Reviewed
• [Presentation] 計算化学によるセルロース系分子の特性と機能解析 (2012)
  • Author(s): 上田一義
  • Organizer: セルロース学会関西支部主催セルロース学会第17回ミクロシンポジウム
  • Place of Presentation: 京都大学化学研究所(招待講演)
  • Year and Date: 2012-01-27
• [Presentation] 平成24年度神奈川県ものづくり技術交 流会予稿集、3PS-11,神奈川県産業技術セ ンター (2012)
  • Author(s): 小林 正人、栗原 庸次、田一義
  • Organizer: 糖α-L-イドピラノースにおける環配座 変換の計算による解析
• [Presentation] Ab initio Studies of the Crystal Structure of Cellulose Triacetate (2012)
  • Author(s): Takanori Kobayashi, Daich Hayakawa, Tegshjargal Khishigjargal, Kazuyoshi Ueda
  • Organizer: 2012 MRS Spring Meeting
  • Place of Presentation: San Francisco, CA, USA
• [Presentation] Computational Study of Optical Properties of Cellulose Triacetate Film (2012)
  • Author(s): Daich Hayakawa, Kazuyoshi UEDA
  • Organizer: 2012 MRS Fall Meeting
  • Place of Presentation: Boston, MA, USA
• [Presentation] 量子化学計算によるグルコース環配座変換経路の検討 (2012)
  • Author(s): 上田一義、栗原庸次、高橋絵理歌
  • Organizer: セルロース学会第１9回年次大会
  • Place of Presentation: 名古屋大学 野依記念学術交流館
• [Presentation] 量子化学計算による1C4グルコース環配座変換経路の探索 (2012)
  • Author(s): 栗原庸次、上田一義、高橋絵理歌
  • Organizer: セルロース学会第１9回年次大会
  • Place of Presentation: 名古屋大学 野依記念学術交流館
• [Presentation] 超臨界状態におけるセルロース I beta結晶クラスターモデルの溶解機構に関する分子動力学シミュレーション (2012)
  • Author(s): 早川大地、上田一義、宮本ひとみ、山根千弘、堀井文敬
  • Organizer: セルロース学会第１9回年次大会
  • Place of Presentation: 名古屋大学 野依記念学術交流館
• [Presentation] セルロース誘導体によるキラル分割機構の自由エネルギー計算による計算化学的考察 (2012)
  • Author(s): 玉城哲平、上田一義、柴田 徹
  • Organizer: セルロース学会第１9回年次大会
  • Place of Presentation: 名古屋大学 野依記念学術交流館
• [Presentation] 分子動力学シミュレーションを用いた水和セルロースの脱水過程 (2012)
  • Author(s): 宮本ひとみ、上田一義、 神戸女子大院家政 山根千弘
  • Organizer: 平成２４年度神奈川県ものづくり技術交流会
  • Place of Presentation: 神奈川県産業技術センター
• [Presentation] 糖α-L-イドピラノースにおける環配座変換の計算による解析 (2012)
  • Author(s): 小林 正人、栗原 庸次、上田 一義
  • Organizer: 平成２４年度神奈川県ものづくり技術交流会
  • Place of Presentation: 神奈川県産業技術センター
• [Presentation] セルローストリアセテートナノサイズ結晶の溶解過程に関する分子動力学シミュレーション (2011)
  • Author(s): 早川大地・上田一義・山根千弘・宮本ひとみ・堀井文敬
  • Organizer: セルロース学会第18回年次大会
  • Place of Presentation: 信州大学工学部
• [Presentation] セルロース誘導体の光学分割機構に対する計算化学的解析 (2011)
  • Author(s): 西村俊秀・上田一義・柴田徹・大西敦・奥山直人
  • Organizer: セルロース学会第18回年次大会
  • Place of Presentation: 信州大学工学部
• [Presentation] Structure and Orientation of Bovine Lactoferrampin in Membranes : Molecular Dynamics Simulation (2011)
  • Author(s): Namsrai JAVKHLANTUGS・内藤晶・上田一義
  • Organizer: 日本化学会第5回関東支部大会
  • Place of Presentation: 東京農工大学小金井キャンパス
• [Presentation] セルローストリアセテートの溶解性向上を目指した計算化学的アプローチ (2011)
  • Author(s): 早川大地・上田一義・山根千弘・宮本ひとみ・堀井文敬
  • Organizer: 平成23年度神奈川県ものづくり技術交流会
  • Place of Presentation: 神奈川県産業技術センター
• [Presentation] セルロース誘導体を用いた光学分割機構の計算化学による解析 (2011)
  • Author(s): 西村俊秀・上田一義・柴田徹・大西敦・奥山直人
  • Organizer: 平成23年度神奈川県ものづくり技術交流会
  • Place of Presentation: 神奈川県産業技術センター
• [Presentation] 無加湿中温形燃料電池用電解質に適したプロトン伝導性イオン液体の分子設計 (2011)
  • Author(s): 森一樹・小林孝徳・上田一義、榊原和久
  • Organizer: 平成23年度神奈川県ものづくり技術交流会
  • Place of Presentation: 神奈川県産業技術センター
• [Presentation] Molecular dynamics simulation of the dissolution process of cellulose triacetate nano-size crystal (2011)
  • Author(s): Daichi HAYAKAWA, Kazuyoshi UEDA, Chihiro YAMANE, Hitomi MIYAMOTO, Fumitaka HORII
  • Organizer: Fall 2011 ACS National Meeting
  • Place of Presentation: Denver, Colorado, USA
• [Presentation] The simulation of FC-domain binding on the polystyrene surface (2011)
  • Author(s): Namsrai JAVKHLANTUGS, Bayarsaikhan Urangoo, Bayar Hexig, Kazuyoshi UEDA
  • Organizer: ISSS-6 International Symposium on Surface Science
  • Place of Presentation: Funabori, Tokyo Japan
• [Presentation] Orientation and interaction of bovine Lactoferrampin in bacterial mimic membrane as performed by molecular dynamics simulation (2010)
  • Author(s): Namsrai Javkhlantugs, AkiraNaito, Kazuyoshi Ueda
  • Organizer: 5^<th> International Peptide Symposium
  • Place of Presentation: Kyoto, Japan
• [Presentation] Structure and orientation of bovine Lactoferrampin in bacterial mimic membrane as investigated by molecular dynamics simulation (2010)
  • Author(s): Namsrai Javkhlantugs, AkiraNaito, Kazuyoshi Ueda
  • Organizer: Mongolian-German Workshop on Advanced Materials
  • Place of Presentation: Ulaanbaatar, Mongol
• [Presentation] Molecular dynamics simulation of Bombolitin II in the DPPC bilayer (2010)
  • Author(s): Namsrai Javkhlantugs, AkiraNaito, Kazuyoshi Ueda
  • Organizer: 2010MRS Spring Meeting
  • Place of Presentation: San Francisco, CA
• [Presentation] Cellulose triacetateII型ナノサイズ結晶の溶解過程に関する分子動力学シミュレーション (2010)
  • Author(s): 早川大地・上田一義、山根千弘・宮本ひとみ 堀井文敬
  • Organizer: セルロース学会第17回年次大会
  • Place of Presentation: 徳島文理大学香川キャンパス
• [Presentation] セルロース誘導体オリゴマーモデルを用いた計算機化学による光学分割機構の解析 (2010)
  • Author(s): 西村俊秀、上田一義、柴田徹、大西敦、奥山直人
  • Organizer: セルロース学会第17回年次大会
  • Place of Presentation: 徳島文理大学香川キャンパス
• [Presentation] セルローストリアセテートーII型ナノサイズ結晶の溶解過程に関する分子動力学シミュレーション (2010)
  • Author(s): 早川大地・上田一義、山根千弘・宮本ひとみ 堀井文敬
  • Organizer: 第59回高分子学会年次大会
  • Place of Presentation: パシフィコ横浜
• [Presentation] セルロース誘導体オリゴマーモデルを用いた計算機化学による光学異性体分離機構の解析 (2010)
  • Author(s): 西村俊秀、上田一義、柴田徹、大西敦、奥山直人
  • Organizer: 第59回高分子学会年次大会
  • Place of Presentation: パシブイコ横浜