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Studies of Organic Reactive Intermediates and its Application to the Chemistry of Proteins

Research Project

Project/Area Number 17550032
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Organic chemistry
Research InstitutionThe University of Tokyo

Principal Investigator

TOMODA Shuji  The University of Tokyo, 大学院・総合文化研究科, 教授 (30092282)

Co-Investigator(Kenkyū-buntansha) KANENO Daisuke  東京大学, 大学院・総合文化研究科, 助教 (00361593)
Project Period (FY) 2005 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥4,120,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥420,000)
Fiscal Year 2008: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2007: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2006: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 2005: ¥1,700,000 (Direct Cost: ¥1,700,000)
Keywords量子有機化学 / フロンティア軌道理論 / タンパク質 / 生体分子 / 有機化学 / 化学物理 / 面選択性 / gauche効果 / 分子軌道計算 / 1,2-ジハロエタン / antipeliplanar効果 / ペプチド結合 / hyperconjugation / ab initio / 配座異性 / ジアステレオ面選択性 / 求核付加反応 / シス効果
Research Abstract

エノラート,カルベンなどの有機反応活性種が関与するπ面選択性予測理論の構築をフロンティア軌道理論および溶媒効果理論に基づいて行った. タンパク質データバンクの統計解析によりタンパク質内の微弱相互作用の様式と定量解析およびペプチド結合のシス型の存在様式とその意義について理論研究を行った
申請書に掲載の以下の2つのテーマについて結果をまとめた. 結果をまとめながら, 量子化学の基礎教育に関する教科書を3冊出版した
1. 溶液中における反応化学種の構造解明と面選択性予測理論の構築
α位に電子求引基を有する鎖式ケトンのLiAlH4 還元では従来提唱されていたキレーションモデルが無効なことがわかり, ジメチルエーテル溶媒中での反応遷移状態を求めたところ, 実験の傾向を高精度で再現できた(B3LYP/6-311+G(d, p)). この実験結果はCar-Parinello法による溶媒を含むシミュレーションによって強く支持された. この結果をTetrahedron Lett., 2008, 49, 4223-4226. にまとめた. また, ケトンのNaBH4 還元反応の遷移状態をはじめて求めることが出来た. この場合にもメタノール溶媒が動力学シミュレーションによって関与することが明らかとなり, 溶媒が面選択性に強く関与していることが示された. この結果をJ.Phys.Chem.に投稿してアクセプトされ印刷中の状態になっている. これらの結果はスペインで行われた物理有機国際会議, 春の化学会年会などで口頭発表した
2. タンパク質フォールディング機構の解明を目指したタンパク分子内微弱相互作用の定量評価
タンパク質のシス・トランス異性の問題を追求した. 特に, シス型のペプチド結合がX線データベースで報告されている種々の酵素タンパクの構造や機能を生み出すための役割について, 統計解析を含めた画期的な解析手法を開発しながら研究を進めた. その結果を春の化学会年会で報告し, 現在論文にまとめている最中である. さらにタンパク質のフォールディング機構の解明を目指して, 今年度新しい分子動力学理論を発表した. この新しい手法は従来の3 次元座標を使わず, ポテンシャルを変数にとって解析する全く新しいシミュレーション技術であり記者会見で報告した

Report

(5 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (43 results)

All 2009 2008 2007 2005 Other

All Journal Article (23 results) (of which Peer Reviewed: 19 results) Presentation (15 results) Book (5 results)

  • [Journal Article] The Danishefsky pyranone puzzle : an explanation based on the exterior frontier orbital extension model2009

    • Author(s)
      Kaneno D, Tomoda S.
    • Journal Title

      TETRAHEDRON LETTERS 50

      Pages: 329-332

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Origin of Cis Effect in 1,2-Dihaloethenes : The Quantitative Comparison of Electron Delocalizations and Steric Exchange Repulsions2008

    • Author(s)
      Yamamoto T, Kaneno D, Tomoda S.
    • Journal Title

      BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 81

      Pages: 1415-1422

    • NAID

      10024446409

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Perturbational formulation of principal component analysis in molecular dynamics simulation2008

    • Author(s)
      Koyama YM, Kobayashi TJ, Tomoda S.
    • Journal Title

      PHYSICAL REVIEWE 78

      Pages: 46702-11

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The importance of lone pair delocalizations : Theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes2008

    • Author(s)
      Yamamoto T, Kaneno D, Tomoda S.
    • Journal Title

      JOURNAL OF ORGANIC CHEMISTRY 73

      Pages: 5429-5435

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Direct observation of conformational folding coupled with disulphide rearrangement by using a water-soluble selenoxide Reagent-A case of oxidative regeneration of ribonuclease a under weakly basic conditions2008

    • Author(s)
      Iwaoka M, Kumakura F, Yoneda M, Tomoda S.
    • Journal Title

      JOURNAL OF BIOCHEMISTRY 144

      Pages: 121-130

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Solvent effects on the diastereoselection in LiAlH4 reduction of alpha-substituted ketones2008

    • Author(s)
      Suzuki Y, Kaneno D, Miura M, Tomoda, S.
    • Journal Title

      TETRAHEDRON LETTERS 49

      Pages: 4223-4226

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Danishefsky pyranone puzzle: an explanation based on the exterior fronterorbital extension model2008

    • Author(s)
      Kaneno D, Tomoda S
    • Journal Title

      TETRAHEDRON LETTERS 50(印刷中)

      Pages: 329-331

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Origin of Cis Effect in 1,2-Dihaloethenes: The Quantitative Comparison of Electron Delocalizations and Steric Exchange Repulsions2008

    • Author(s)
      Yamamoto T, Kaneno D, Tomod
    • Journal Title

      BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 81

      Pages: 1415-1422

    • NAID

      10024446409

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Perturbational formulation of principal component analysis in molecular dynamics simulation2008

    • Author(s)
      Koyama YM, Tomoda S
    • Journal Title

      PHYSICAL REVIEW E 78

      Pages: 46702-11

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The importance of lone pair delocalizations: Theoretical investions on the stability of cis and trans isomers in 1,2-halodiazenes2008

    • Author(s)
      Yamamoto T, Kaneno D, Tomod
    • Journal Title

      JOURNAL OF ORGANIC CHEMISTRY 73

      Pages: 5429-5435

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Direct observation of conformational folding coupled with disulphide rearrangement by using a water-soluble selenoxide Reagent - A case of oyidative regeneration of ribonuclease a under weakly hasic conditions2008

    • Author(s)
      Iwaoka M, Kumakura F, Yoneda
    • Journal Title

      JOURNAL OF BIOCHEMISTRY 144

      Pages: 121-130

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Solvent effects on the diastereoselection in LiA1H4 reduction of alpha-substituted ketones2008

    • Author(s)
      Suzuki Y, Kaneno D, Miura M,T
    • Journal Title

      TETRAHEDRON LETTERS 49

      Pages: 4223-4226

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of solvent effect on diastereo selectivity in protonation of methyl 3-fluorobutanoate anion by ethanol : Application of the 3D-RISM theory2007

    • Author(s)
      Ikuta Y, Maruyama Y, Hirata F, Tomoda S.
    • Journal Title

      JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 811

      Pages: 183-190

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Equilibrium and kinetics of the folding and unfolding of canine milk lysozyme2007

    • Author(s)
      Nakatani H, Maki K, Saeki K, Tomoda S.
    • Journal Title

      BIOCHEMISTRY 46

      Pages: 5238-5251

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Studies on the nonbonded interactions of divalent organic selenium2005

    • Author(s)
      Iwaoka M, Tomoda S.
    • Journal Title

      JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN 63

      Pages: 911-920

    • NAID

      130000928549

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] The importance of lone pair electron delocalization in the cis-trans isomers of 1,2-dibromoethenes2005

    • Author(s)
      Yamamoto T, Kaneno D, Tomoda S.
    • Journal Title

      CHEMISTRY LETTERS 34

      Pages: 1190-1191

    • NAID

      10016649667

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Physical- and bio-organic chemstry of nonbonded selenium center dot center dot center dot oxygen interactions.2005

    • Author(s)
      Iwaoka M, Tomoda S
    • Journal Title

      PHOSPHORUS SULFUR AND SILICON AND THE RELATED ELEMENTS. 180

      Pages: 755-766

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Experimental and theoretical studies on the nature of weak nonbonded interactions between divalent selenium and halogen atoms2005

    • Author(s)
      Iwaoka M, Katsuda T, Komatsu H, Tomoda S
    • Journal Title

      JOURNAL OF ORGANIC CHEMISTRY 70

      Pages: 321-327

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Experimental and Theoretical Studies on the Nature of Weak Nonbonded Interactions between Divalent Selenium and Halogen Atoms2005

    • Author(s)
      岩岡道夫
    • Journal Title

      Journal of Organic Chemistry 70・1

      Pages: 321-327

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Physical- and Bio-Organic Chemistry of Nonbonded Selenium ・・・ Oxygen Interactions2005

    • Author(s)
      岩岡道夫
    • Journal Title

      Phosphorus, Sulfur, and Silicon and the Related Elements 180・3-4

      Pages: 755-766

    • Related Report
      2005 Annual Research Report
  • [Journal Article] The Importance of Lone Pair Electron Delocalization in the Cis-Trans Isomers of 1,2-Dibromoethenes2005

    • Author(s)
      山元崇
    • Journal Title

      Chemistry Letters 34・8

      Pages: 1190-1191

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 二価有機セレンの非結合性相互作用に関する研究2005

    • Author(s)
      岩岡道夫
    • Journal Title

      有機合成化学協会誌 63・9

      Pages: 911-920

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Solvent effects on the diastereoselection in LiAlH_4 reduction of α-substituted ketones

    • Author(s)
      鈴木康光、金野大助、友田修司
    • Journal Title

      Tetrahedron Letters 印刷中(掲載確定)

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] グルタチオンペルオキシダーゼの反応機構解明のための理論計算2009

    • Author(s)
      宮沢秀男,金野大助,友田修司
    • Organizer
      日本化学会春季年会
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-30
    • Related Report
      2008 Annual Research Report
  • [Presentation] 酵素タンパクにおけるシス型ペプチド結合の性質と役割の解明2009

    • Author(s)
      平良俊一,金野大助,友田修司
    • Organizer
      日本化学会春季年会
    • Place of Presentation
      日本大学
    • Year and Date
      2009-03-30
    • Related Report
      2008 Annual Research Report
  • [Presentation] Solvent Effects of LiAlH_4 Reduction of a-Substituted Acyclic Ketones2008

    • Author(s)
      Suzuki, Y., Kaneno, D., Tomoda, S
    • Organizer
      IUPAC Physical Organic Chemistry Conference
    • Place of Presentation
      Santiago de Compostela, Spain
    • Year and Date
      2008-07-15
    • Related Report
      2008 Final Research Report
  • [Presentation] Solvent Effects of LiALH4 Reduction of α-Substituted Acyclic Ketones.2008

    • Author(s)
      Suzuki. Y. Kaneno, D, Tomoda, S
    • Organizer
      IUPAC Conference on Physical Organic Chemistry
    • Place of Presentation
      Spain
    • Year and Date
      2008-07-15
    • Related Report
      2008 Annual Research Report
  • [Presentation] NaBH_4還元の遷移状態と溶媒効果2008

    • Author(s)
      鈴木康光, 金野大助, 友田修司
    • Organizer
      日本化学会第89回春季年会
    • Place of Presentation
      千葉, 日本大学
    • Year and Date
      2008-03-30
    • Related Report
      2008 Final Research Report
  • [Presentation] フルタチオンペルオキシダーゼの反応機構解析のための理論計算2008

    • Author(s)
      宮沢秀男, 金野大助, 友田修司
    • Organizer
      日本化学会第89回春季年会
    • Place of Presentation
      千葉, 日本大学
    • Year and Date
      2008-03-30
    • Related Report
      2008 Final Research Report
  • [Presentation] 酵素タンパクにおけるシス型ペプチド結合の性質と役割の解明2008

    • Author(s)
      平良俊一, 金野大助, 友田修司
    • Organizer
      日本化学会第89回春季年会
    • Place of Presentation
      千葉, 日本大学
    • Year and Date
      2008-03-30
    • Related Report
      2008 Final Research Report
  • [Presentation] ペプチド結合におけるトランス形優位性の研究2008

    • Author(s)
      平良俊一、金野大助、友田修司
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-28
    • Related Report
      2007 Annual Research Report
  • [Presentation] 非環状ケトンのLiAlH_4還元におけるジアステレオ面選択性の起源の解明2008

    • Author(s)
      鈴木康光、金野大助、友田修司
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-27
    • Related Report
      2007 Annual Research Report
  • [Presentation] 分子軌道計算法を用いた生体内酵素の過酸化物除去の反応機構解析2008

    • Author(s)
      宮沢秀男、金野大助、友田修司
    • Organizer
      日本化学会第88春季年会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-27
    • Related Report
      2007 Annual Research Report
  • [Presentation] 4-テトラヒドロフラン系のヒドリド還元における面選択性2007

    • Author(s)
      金野大助, 友田修司
    • Organizer
      第57回有機反応化学討論会
    • Place of Presentation
      東広島
    • Year and Date
      2007-09-29
    • Related Report
      2008 Final Research Report
  • [Presentation] 4-テトラヒドロピラノン系のヒドリド還元における面選択性2007

    • Author(s)
      金野大助、友田修司
    • Organizer
      第57回有機反応化学討論会
    • Place of Presentation
      東広島
    • Year and Date
      2007-09-29
    • Related Report
      2007 Annual Research Report
  • [Presentation] 非環状ケトンのLiAlH_4 還元におけるジアステレオ面選択性の起源の解明2007

    • Author(s)
      鈴木康光, 金野大助, 友田修司
    • Organizer
      日本化学会第88回春季年会
    • Place of Presentation
      東京
    • Year and Date
      2007-03-27
    • Related Report
      2008 Final Research Report
  • [Presentation] 分子軌道計算法を用いて生体内酵素の過酸化物除去の反応機構解析2007

    • Author(s)
      宮沢秀男, 金野大助, 友田修司
    • Organizer
      日本化学会第88回春季年会
    • Place of Presentation
      東京
    • Year and Date
      2007-03-27
    • Related Report
      2008 Final Research Report
  • [Presentation] ペプチド結合におけるトランス形優位性の研究2007

    • Author(s)
      平良俊一, 金野大助, 友田修司
    • Organizer
      日本化学会第88回春季年会
    • Place of Presentation
      東京
    • Year and Date
      2007-03-27
    • Related Report
      2008 Final Research Report
  • [Book] はじめての分子軌道法2008

    • Author(s)
      友田修司
    • Total Pages
      230
    • Publisher
      講談社
    • Related Report
      2008 Final Research Report
  • [Book] はじめての分子軌道法-軌道概念によるアプローチ2008

    • Author(s)
      友田修司
    • Total Pages
      230
    • Publisher
      講談社
    • Related Report
      2008 Annual Research Report
  • [Book] 基礎量子化学2007

    • Author(s)
      友田修司
    • Total Pages
      400
    • Publisher
      東大出版会
    • Related Report
      2008 Final Research Report
  • [Book] フロンティア軌道論で化学を考える2007

    • Author(s)
      友田修司
    • Total Pages
      196
    • Publisher
      講談社
    • Related Report
      2008 Final Research Report 2007 Annual Research Report
  • [Book] 基礎量子化学 -軌道概念で化学を考える-2007

    • Author(s)
      友田修司
    • Total Pages
      432
    • Publisher
      東京大学出版会
    • Related Report
      2006 Annual Research Report

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Published: 2005-04-01   Modified: 2016-04-21  

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