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年 報

2010

京都大学
福井謙一記念研究センター

はじめに2010 年度 ( 平成 22 年度 ) の京都大学福井謙一記念研究センターの活動をまとめた
年報をお届けします．当センターは，京都大学本部構内の北，約１キロの高野川沿いの静かな住宅街に独立して位置しております．専任教員は理論研究部門と総合研究部門に准教授各 1 名を持っているに過ぎませんが，センター長のほか，2 名の副セン
ター長と 10 名のスーパーバイザーとして工学研究科，理学研究科，化学研究所所属の教員にご協力頂いており，このメンバーが運営委員会を構成しています．そして優れた博士研究員に研究活動の機会を与える制度を持っており，若手研究者が国際的な雰囲気の中で日夜研究にいそしんでいます．この博士研究員のうち 9 名はセンターの雇用で，福井センターフェローと呼ばれ，自分自身のアイデアで一定期間，自由闊達に研究できる身分を保証しています．また福井謙一記念研究部第一のリサーチリーダ
ーとして世界的な理論化学者の諸熊奎治先生 ( 分子科学研究所名誉教授 ) を米国エモリー大学から招聘し，研究面でのリーダーシップを発揮して頂いております．諸熊先
生は，科学技術振興機構の戦略的創造研究推進事業の予算で 8 名の博士研究員を採用され，全員がセンターで研究に励んでおられます (2011 年 ( 平成 23 年 )11 月現在 )．
さらに 2009 年度 ( 平成 21 年度 ) には福井謙一記念研究部第二も設置し，名古屋大学
名誉教授（前副学長）の大峯巖先生をリサーチリーダーとして招聘し，研究体制を拡大しました．なお，大峯巖先生は 2010 年 ( 平成 22 年 )4 月に分子科学研究所長に転出されました．
私達は，センターが若手研究者の登竜門となることを期待しています．実際に，センターの博士研究員であった方々が京都大学准教授，名古屋大学教授，Tartu 大学 (エストニア共和国 ) 教授，神戸大学准教授，分子科学研究所助教 (3 名 )，Illinois
工科大学客員助教，早稲田大学准教授，九州大学助教，Northwestern 大学研究員等として活躍されております．
当センターの歴史を簡単にご紹介します．ご承知のように故福井謙一京都大学名誉教授はフロンティア軌道理論を提案したご功績により，1981 年 ( 昭和 56 年 ) にわが国で最初のノーベル化学賞を受賞されました．福井先生が京都大学ご退官後に研究を続けられるため，京都市と産業界などのご支援で 1985 年 ( 昭和 60 年 ) に財団法人「基礎化学研究所」が設立されました．専任研究員数名の規模でしたが，研究のレベルは－i－

高く，当時の研究員は現在，東京大学，名古屋大学，分子科学研究所の教授になり，
理論化学分野でトップクラスの研究者として活躍しています．この基礎化学研究所は1998 年（平成 10 年）の福井先生のご逝去の後，2002 年 ( 平成 14 年 ) に本学に寄贈され，福井謙一記念研究センターとなり，現在にいたっています．京都大学の部局となった
後，森島 績，中辻 博，榊 茂好各先生にセンター長としてご指導を頂きました．
当センターは，国際活動も活発で，2005 年 ( 平成 17 年 ) よりチェコおよびスロバ
キアと理論化学・計算化学シンポジウムを定期的に開催しております．日本学術振興会・若手研究者交流支援事業として，タイ，シンガポール，ベトナム ，マレーシア，
フィリピンの東アジア首脳会議参加国からの若手研究者招聘，ベルギーおよびロシアとの 2 国間共同研究も行っております．当センターは，今後も，理論化学・計算化学分野におけるわが国の窓口の役割を果たし，国際協力活動を展開して行きたいと考えております．
例年晩秋に福井センターシンポジウムを開催しており，学外のトップクラスの研究者による特別講演，運営委員の講演，ならびに京都大学内外からのポスター発表を行っております．研究発表のレベルは高く，特別講演に来られた講師からも毎年高い評価を得ております．
当センターは，上述のように規模は大きくありませんが，研究活動は活発です．今後も，京都大学あるいは国内外との共同研究を積極的に進めて行きたいと考えております．とくに実験科学者との共同研究は重要であり，そのような連携研究をさらに活発化したいと考えております．
この年報により，当センターの活動に興味をお持ち頂ければ幸甚です．そして，それが共同研究の契機となり，時間をかけて大きな成果に結実していくことを念願しています．最後になりましたが，当センターの順調な活動も，ひとえに工学研究科，理学研究科，化学研究所のご協力，ご援助の賜物であり，ここに心から御礼申し上げる次第です．

平成 23 年 11 月
京都大学福井謙一記念研究センター長

田中－ ii －

功

目

はじめに

Ⅰ

次

京都大学福井謙一記念研究センター長

田中

功

…………

ⅰ

専任教員・スーパーバイザー
１．教員組織……………………………………………………………………

２．教員プロフィール…………………………………………………………

2………………………………………………………………

2(1) センター長(2) 副センター長……………………………………………………………

(3) スーパーバイザー(4) 専任教員

3………………………………………………………

5…………………………………………………………………

15(5) リサーチリーダー

Ⅱ1………………………………………………………

18(6) 特定助教（白眉）…………………………………………………………

19

博士研究員
１．博士研究員組織……………………………………………………………

２．博士研究員プロフィール

Ⅲ…………………………………………………

20
21

研究広報活動１．福井謙一記念研究センターシンポジウム………………………………

39……………………………………

40……………………………………………………………………

41

２．福井謙一記念研究センターセミナー

Ⅳ

研究業績
１．専任教員

２．リサーチリーダー…………………………………………………………

56

３．特定助教（白眉）……………………………………………………………

60

４．博士研究員

66…………………………………………………………………

－ iii －

資料
１．招へい外国人学者・外国人共同研究者受入れ状況 ……………………
２．海外渡航一覧

143……………………………………………………………… 144

３．福井謙一記念研究センター シンポジウムプログラム ………………… 145
４．福井謙一記念研究センター セミナープログラム・ポスター ………… 154
５．研究業績一覧（2010 年 )…………………………………………………… 155（本冊子は下記アドレス（URL）にて、ウェブ上でも閲覧いただけます。
http://www.fukui.kyoto-u.ac.jp/publication/AnnualReport2010.pdf ）－ iv －

Ⅰ 専任教員 ･ スーパーバイザー (2010)

Ⅰ専任教員 ･ スーパーバイザー
１. 教員組織
平成 22 年度
職

名

氏

センター長

名

備

考

田 中

功 工学研究科材料工学専攻
博

物質－細胞統合システム拠点( 工学研究科分子工学専攻 )総合研究部門副センター長今 堀

理論研究部門副センター長太 田

工学研究科長小 森

理学研究科長吉 川

研 一 理学研究科物理学 ･ 宇宙物理学専攻

化学研究所長時 任

宣 博 化学研究所物質創製化学研究系

協 議 員

総合研究部門スーパーバイザー

理論研究部門スーパーバイザー

総合研究部門隆 夫 理学研究科物理学・宇宙物理学専攻
悟 工学研究科機械理工学専攻

教

授

赤 木

和 夫 工学研究科高分子化学専攻

教

授

田 中

勝 久 工学研究科材料化学専攻

教

授

佐 藤

直 樹 化学研究所複合基盤化学研究系

教

授

北 川

教

授

吉 川

研 一 理学研究科物理学・宇宙物理学専攻

教

授

谷 村

吉 隆 理学研究科化学専攻

教

授

田 中

一 義 工学研究科分子工学専攻

教

授

山 本

量 一 工学研究科化学工学専攻

准 教 授

高 田

彰 二 理学研究科生物科学専攻

准 教 授

林

重 彦 理学研究科化学専攻

准 教 授

石 田

俊 正

准 教 授

佐 藤

徹

専任：平成 16.3.1 － 22.12.31( 工学研究科分子工学専攻協力講座 )

准 教 授

中 尾

嘉 秀

専任：平成 23.1.1 －( 工学研究科分子工学専攻協力講座 )

リサーチ
リーダー

諸 熊

奎 治 研究員（学術研究奨励）

特定助教( 白眉 )

前 田

リサーチ
リーダー

（欠員中）

進

理論研究部門福井謙一記念研究部第一福井謙一記念研究部第二物質－細胞統合システム拠点( 工学研究科合成・生物化学専攻 )専任( 工学研究科合成・生物化学専攻協力講座 )理 次世代研究者育成センター－1－

Ⅰ 専任教員 ･ スーパーバイザー (2010)

２. 教員プロフィール(1) センター長【氏名（ふりがな）】 田中

功 （たなかいさお）【職名】 センター長、教授【所属】 工学研究科

材料工学専攻【研究室】 吉田キャンパス

工学部物理系校舎

量子材料学研究室【直通電話】 075-753-5465【FAX】 075-753-5447【電子メールアドレス】 tanaka@cms.MTL.kyoto-u.ac.jp【ホームページ】 http://cms.mtl.kyoto-u.ac.jp/tanaka.html【研究分野】 材料科学
【現在の研究課題】 セラミックス基礎科学，計算材料科学【研究内容キーワード】 量子材料設計，第一原理計算，電子ｴﾈﾙｷﾞｰ損失分光，Ｘ線吸収分光【最終学歴】 1987年3月【学位】 1987年3月

大阪大学大学院基礎工学研究科物理系専攻博士後期課程修了
大阪大学工学博士【略歴】 1987年4月 日本学術振興会特別研究員(PD)、1987年6月大阪大学産業科学研究所・助手、1993年4月京都大学工学部・助手、1996年5月京都大学大学院エネルギー科学研究科・助教授、2001年7月京都大学大学院工学研究科・助教授、2003年12月京都大学大学院工学研究科・教授【在外研究歴】 1992年4月-1993年3月 ドイツ マックスプランク金属研究所・客員研究員（アレキサンダー・フォン・フンボルト財団奨学研究員）【所属学会】 日本金属学会、日本セラミックス協会、日本鉄鋼協会，応用物理学会、
American Ceramic Society、Materials Research Society【学会活動】 Journal of American Ceramics Society フェロー・編集委員、World Academy of
Ceramics 会員、Journal of Physics : Condensed Matter 編集委員、日本金属学会
評議員【主な著書、学術論文】 1. A. Seko, F. Oba, I. Tanaka,
Classification of spinel structures based on first-principles cluster expansion analysis,（過去5年以内）
Phys. Rev. B 81 (2010) 054114
2. A. Matsumoto, Y. Koyama, I. Tanaka, Structures and energetics of Bi2O3 polymorphs
in a defective fluorite family derived by systematic first-principles lattice dynamics
calculations, Phys. Rev. B 81 (2010) 094117
3. M. Choi, F. Oba, I. Tanaka, Role of Ti Antisitelike Defects in SrTiO3,
Phys. Rev. Lett. 103 (2009) 185502
4. First-principles investigation of atomic structures and stability of proton-exchanged
layered sodium titanate M. Mori, Y. Kumagai, K. Matsunaga, and I. Tanaka,
Phys. Rev. B ,79 (2009) 144117
5. W. Olovsson, I. Tanaka, T. Mizoguchi, P. Puschnig, and C. Ambrosch-Draxl, All-electron Bethe-Salpeter calculations for shallow-core x-ray absorption near-edge structures
Phys. Rev. B 79, (2009) 041102.
6. K. Yuge, A. Seko, Y. Koyama, F. Oba, and I. Tanaka,
First-principles-based phase diagram of the cubic BNC ternary system
Phys. Rev. B 77, (2008) 094121
7. I. Tanaka and F. Oba,First principles calculations for modern ceramic science and engineering
J. Phys: Condens. Matter 20, (2008) 064215
8. A. Seko, A. Togo, F. Oba, and I. Tanaka,
Structure and stability of a homologous series of tin oxides
Phys. Rev. Lett. 100, (2008) 045702【学術関係の受賞】 ドイツ政府 フィリップ･フランツ･フォン･シーボルト賞（2008年）
ルーマニア科学アカデミー ドラゴミール・フルムゼスコ賞（2006年）
米国セラミックス学会 リチャード・フルラース賞（2004年）－2－

Ⅰ 専任教員 ･ スーパーバイザー (2010)(2) 副センター長【氏名（ふりがな）】 今堀

博 （いまほりひろし）【職名】 教授【所属】 物質－細胞統合システム拠点（工学研究科【研究室】 桂キャンパス

A4棟

分子工学専攻）

002号室【直通電話】 075-383-2566【FAX】 075-383-2571【電子メールアドレス】 imahori@scl.kyoto-u.ac.jp【ホームページ】 http://www.moleng.kyoto-u.ac.jp/~moleng_05/【研究分野】 有機化学・光化学【現在の研究課題】 人工光合成・有機太陽電池・ドラッグデリバリー【研究内容キーワード】 ポルフィリン・フラーレン・ナノチューブ・自己組織化・電子移動【最終学歴】 1990年3月【学位】 1990年3月

京都大学大学院理学研究科博士後期課程修了
理学博士（京都大学）【略歴】 1990年4月米国ソーク生物学研究所博士研究員、1992年4月大阪大学産業科学
研究所助手、1999年11月大阪大学大学院工学研究科助教授、2001年12月科学技術振興機構さきがけ研究代表者（兼任）、2002年2月京都大学大学院工学研
究科教授、2002年9月京都大学福井謙一記念研究センタースーパーバイザー（兼任）、2007年10月京都大学物質－細胞統合システム拠点教授【所属学会】 日本化学会、光化学協会、米国化学会、米国電気化学会【主な著書、学術論文】 1. T. Sagawa, S. Yoshikawa, and H. Imahori,“1-D Nanostructured Semiconduct（過去5年以内）
ing Materials for Organic Photovoltaics,”J. Phys. Chem. Lett. (Perspective), 1,
1020-1025 (2010).
2. H. Imahori, T. Umeyama, and S. Ito,“Large π Aromatic Molecules as Potential Sensitizers in Dye-Sensitized Solar Cells,”Acc. Chem. Res. 42, 1809-1818(2009).
3. Y. Matano and H. Imahori,“Phosphole-Containing Calixpyrroles, Calilxphyrins, and Porphyrins: Synthesis and Coordination Chemistry,”Acc. Chem. Res.
42, 1193-1204 (2009).
4. H. Imahori, T. Umeyama,“Donor-Acceptor Nanoarchitecture on Semiconducting Electrodes for Solar Energy Conversion,”J. Phys. Chem. C (Feature
Article), 113, 9029-9039 (2009).
5. A. Kira, T. Umeyama, Y. Matano, K. Yoshida, S. Isoda, J.-K. Park, D. Kim, H.
Imahori,“Supramolecular Donor-Acceptor Heterojunctions by Vectorial Stepwise Assembly of Porphyrins and Coordination-Bonded Fullerene Arrays for
Photocurrent Generation,”J. Am. Chem. Soc., 131, 3198-3200 (2009).
【学術関係の受賞】 1. 2004年光化学協会賞
2. 2006年日本学術振興会賞
3. 2006年日本化学会学術賞
4. 2007年東京テクノ・フォーラム21ゴールド・メダル賞
5. 2007年大阪科学賞
6. 2007年ナイスステップ研究者－3－

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 太田

隆夫 （おおた

たかお）【職名】 教授【所属】 福井謙一記念研究センター【研究室】 理学部5号館

理論研究部門422【直通電話】 075-753-3740【FAX】 075-753--3811【電子メールアドレス】 takao@scphys.kyoto-u.ac.jp【ホームページ】 http://www.ton.scphys.kyoto-u.ac.jp/nonlinear/【研究分野】 相転移理論・非平衡系の統計物理学【現在の研究課題】 非平衡ソフトマター物理学【研究内容キーワード】 高分子共重合体・ミクロ相分離・共連結構造・パターン形成【最終学歴】 1977年1月【学位】 1977年1月

京都大学大学院理学研究科物理学第一専攻博士課程修了
理学博士（京都大学【略歴】 1979年7月九州大学理学部助手、1987年8月お茶の水女子大学理学部助教授、1991年1月お茶の水女子大学理学部教授、1999年4月広島大学大学院理学研究科教授、2004年1月京都大学基礎物理学研究所教授、2006年7月京都大学大学
院理学研究科教授【在外研究歴】 1978年9月-1979年6月
財団研究員）

米国Pittsburgh大学物理（David. Jansnow教授）（Mellon【所属学会】 日本物理学会、中性子科学会、数理生物学会【学会活動】 JPSJ Head Editor【主な著書、学術論文】 1. T. Ohkuma and T. Ohta, Deformable self-propelled particles with a global cou（過去5年以内）
pling, Chaos 20, 023101(1-13) (2010)
2. T. Hiraiwa and T. Ohta, Viscoelasticity of a Single Semiflexible Polymer Chain,
Macromolecules 42, 7553-7562 (2009)
3. T. Ohta, T. Ohkuma and K. Shitara, Deformation of a self-propelled domain in
an excitable reaction-diffusion system, Phys. Rev. E 80, 056203 (2009)
4. T. Sakaue and T. Ohta, Probing Nonequilibrium Fluctuations through Linear
Response, Phys. Rev. E 77, 050102R (2008)
5. Y. Tonosaki, H. Tokuda, V. Zykov and T. Ohta, Phase Dynamics for Nonlinear
Dissipative Waves under Symmetric Feedback, Europhysics Letters 83 50011-16 (2008)
6. R. Tamate, K. Yamada, J. Vinals, and T. Ohta, Structural rheology of microphase separated diblock copolymers, J. Phys. Soc. Jpn.,77 034802 (2008)
7. M. Yanagisawa, M. Imai, T. Masui, S. Komura, Takao Ohta, Growth Dynamics of Domains in Ternary Fluid Vesicles, Biophysical Journal 92, 115-125 (2007)
8. H. Shoji, K. Yamada, D. Ueyama and Takao Ohta, Turing patterns in three dimensions, Phys. Rev. E 75, 046212(13) (2007)【学術関係の受賞】 アレキサンダー・フォン・フンボルト賞（2008年）－4－

Ⅰ 専任教員 ･ スーパーバイザー (2010)(3) スーパーバイザー【氏名（ふりがな）】 赤木

和夫 （あかぎかずお）【職名】 教授【所属】 工学研究科高分子化学専攻【研究室】 赤木研究室【直通電話】 075-383-2595【FAX】 075-383-2760【電子メールアドレス】 akagi@fps.polym.kyoto-u.ac.jp【ホームページ】 http://www.fps.polym.kyoto-u.ac.jp【研究分野】 高分子化学、液晶化学、物質化学【現在の研究課題】 導電性、液晶性、発光性、階層らせん性の共役系高分子の合成と性質【研究内容キーワード】 導電性高分子、液晶性共役高分子、不斉液晶反応場、階層構造制御【最終学歴】 京都大工学研究科博士後期課程【学位】 工学博士【略歴】 福井大工助手、筑波大物質工講師、助教授、教授、同大学院数理物質科学研
究科教授、学際物質科学研究センター長【在外研究歴】 カリフォルニ大学サンタバーバラ校交換研究員、コーネル大学客員研究員【所属学会】 日本化学会、高分子学会、日本液晶学会、アメリカ化学会【学会活動】 文部科学省科研費（特定領域研究、2005-2008）「次世代共役ポリマーの超階層制御と革新機能」領域代表、Chair of 18th Iketani Conference, International
Conference on Control of Super-Hierarchical Structures and Innovative Functionsof Next-Generation Conjugated Polymers (2008)、Chair of International
Conference on Science and Technology of Synthetic Meatals (2010)【主な著書、学術論文】 1. H. Hayasaka, T. Miyashita, K. Tamura, K. Akagi,“Helically π-Stacked Con（過去5年以内）
jugated Polymers Bearing Photoresponsive and Chiral Moieties in Side Chains:
Reversible Photoisomerization-Enforced Switching between Emission andQuenching of Circularly Polarized Fluorescence”, Adv. Func. Mater., 20, 1243
(2010).
2. M. Goh, G. Piao, M. Kyotani, K. Akagi,“Cis-Rich Helical Polyacetylene Synthesized in Low-Temperature Chiral Nematic Liquid Crystal”, Macromolecules,
42, 8590 (2009).
3. K. Akagi,“Helical Polyacetylene - Asymmetric Polymerization in a Chiral Liquid Crystal Field”, Chem. Rev., 109, 5354 (2009).
4. T. Mori, T. Sato, M. Kyotani, K Akagi,“Macroscopically Aligned Helical Conjugated Polymers in Orientation-Controllable Chiral Nematic Liquid Crystal
Field”, Macromolecules, 42, 1817 (2009).
5. M. Kyotani, S. Matsushita, T. Nagai, Y. Matsui, M. Shimomura, A. Kaito. K.
Akagi,“Helical Carbon and Graphitic Films Prepared from Iodine-Doped Helical Polyacetylene Film using Morphology-Retaining Carbonization”, J. Am.
Chem. Soc., 130, 10880 (2008).
6. M. Goh, M. Kyotani, K. Akagi,“Highly Twisted Helical Polyacetylene with
Morphology Free From Bundle of Fibrils Synthesized in Chiral Liquid Crystal
Reaction Field”, J. Am. Chem. Soc., 129, 8519 (2007).
【学術関係の受賞】 日本化学会学術賞（1999年度）、日産科学賞（2000年度）、日本液晶学会賞論文賞（2001年度）、つくば賞（2001年度）、高分子学会賞（2002年度）、文部科学大臣表彰科学技術賞（2005年度）、筑波大学名誉教授称号授与（2009年度）、日本液晶学会賞業績賞（2010年度）－5－

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 田中

勝久（たなかかつひさ）【職名】 教授【所属】 工学研究科 材料化学専攻【研究室】 桂キャンパス

A3クラスター018【直通電話】 075-383-2801【FAX】 075-383-2420【電子メールアドレス】 tanaka@dipole7.kuic.kyoto-u.ac.jp【ホームページ】 http://dipole7.kuic.kyoto-u.ac.jp/【研究分野】 無機固体化学【現在の研究課題】 酸化物薄膜および非晶質酸化物の磁気的性質・表面プラズモンを利用した光機能材料の作製【研究内容キーワード】 酸化物、薄膜、非晶質、表面プラズモン、磁気的性質、光学的性質【最終学歴】 1984年3月
1986年3月

京都大学工学部工業化学科卒業
京都大学大学院工学研究科工業化学専攻修士課程修了【学位】 1991年3月 京都大学工学博士【略歴】 1986年4月 三重大学工学部助手
1989年4月 京都大学工学部助手
1999年7月 京都工芸繊維大学工芸学部助教授
2004年4月 京都大学大学院工学研究科教授
2009年10月 豊橋技術科学大学客員教授【所属学会】 日本セラミックス協会、日本化学会、応用物理学会、日本物理学会、粉体粉末冶金協会、日本材料学会、Materials Research Society、Optical Society ofAmerica【学会活動】 粉体粉末冶金協会 理事、日本材料学会 理事【主な著書、学術論文】 1. Y. Hasegawa, T. Adachi, A. Tanaka, M. Afzaal, P. O’Brien, T. Doi, Y. Hinat（過去5年以内）
su, K. Fujita, K. Tanaka, and T. Kawai,“Remarkable Magneto-Optical Properties of Europium Selenide Nanoparticles with Wide Energy Gaps”, Journal of
the American Chemical Society 130 (2008) 5710-5715.
2. X. Meng, K. Fujita, S. Murai, and K. Tanaka,“Coherent Random Lasers in
Weakly Scattering Polymer Films Containing Silver Nanoparticles”, PhysicalReview A 79 (2009) 053817-1-7.
3. H. Akamatsu, S. Oku, K. Fujita, S. Murai, and K. Tanaka,“Magnetic Properties of Mixed-Valence Iron Phosphate Glasses”, Physical Review B 80 (2009)
134408-1-9.
4. H. Akamatsu, K. Fujita, S. Murai, and K. Tanaka,“Ferromagnetic Eu2＋-Based
Oxide Glasses with Reentrant Spin Glass Behavior”,Physical Review B 81 (2010)
014423-1-9.
5. X. Meng, K. Fujita, S. Murai, T. Matoba, and K. Tanaka,“Plasmonically Controlled Lasing Resonance with Metallic-Dielectric Core-Shell Nanoparticles”,
Nano Letters 11 (2011) 1374-1378.
【学術関係の受賞】 The Australasian Ceramic Society/Ceramic Society of Japan (ACS/CJS) Joint
Ceramic Award (1997年)、日本セラミックス協会学術賞 (2005年)－6－Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 佐藤

直樹 （さとうなおき）【職名】 教授【所属】 化学研究所

複合基盤化学研究系【研究室】 宇治キャンパス化学研究所本館

分子集合解析研究領域
N-324C号室【直通電話】 0774-38-3080【FAX】 0774-38-3084【電子メールアドレス】 naokis@e.kuicr.kyoto-u.ac.jp【ホームページ】 http://www.kuicr.kyoto-u.ac.jp/labos/is2/scope_J.html【研究分野】 有機物性化学【現在の研究課題】 有機結晶・薄膜の構造・電子構造・電子物性の相関研究【研究内容キーワード】 有機半導体・有機薄膜・分子集合体・電子分光・界面物性・分子系構築【最終学歴】 1976年3月【学位】 1983年3月

東京大学大学院理学系研究科化学専門課程修士課程修了
理学博士（東京大学）【略歴】 1976年4月分子科学研究所分子集団研究系技官、1984年4月熊本大学理学部助手、1987年4月東京大学教養学部助教授、1992年5月京都大学化学研究所教授【在外研究歴】 1989年5月-7月 スウェーデンLinköping大学物理学科（William R. Salaneck教授）（Visiting Scholar）【所属学会】 日本化学会、日本物理学会、日本分光学会、分子科学会【学会活動】 日本化学会有機結晶部会長、日本化学会有機結晶ディビジョン主査、分子科学会運営委員
【主な著書、学術論文】 1. H. Yoshida, K. Inaba and N. Sato, X-ray diffraction reciprocal space mapping（過去5年以内）
study of the thin film phase of pentacene, Appl. Phys. Lett. 90 (2007) 181930.
2. H. Yoshida and N. Sato, The crystallographic and electronic structures of threedifferent polymorphs of pentacene, Phys. Rev. B 77 (2008) 235205.
3. R. Murdey, M. Bouvet, M. Sumimoto, S. Sakaki and N. Sato, Direct observation of the energy gap in lutetium bisphthalocyanine thin films, Synth. Met. 159(2009) 1677-1681.
4. T. Hiramatsu, H.Yoshida and N. Sato, Solvent-dependent strutural and electronic behaviors of a push-pull molecule: {4-[4,5-bis(methylsufanyl)-1,3-dithiol2-ylidene] cyclohexa-2, 5-dien-1-ylidene} malononitrile, J. Phys. Chem. A 113(2009) 9174-9179.
5. J. Tsutsumi, H. Yoshida, R. Murdey, S. Kato and N. Sato, An accurate calculation of electronic contribution to static permittivity tensor for organic molecular crystals on the basis of the charge response kernel theory, J. Phys. Chem. A
113 (2009) 9207-9212.
6. J. Tsutsumi, H. Yoshida, R. Murdey and N. Sato, Decay mechanism of spontaneously built-up surface potential in a thin film of a zwitterionic molecule having noncentrosymmetric crystal structure, J. Phys. Chem. C. 115 (2011) 23562359.
7. H. Yoshida and N. Sato, The depth profile of core energy levels: Electronic
structure of buried organic/metal interface examined by X-ray photoemission
and target factor analysis, Chem. Phys. Lett. 511 (2011) 146-150.
【学術関係の受賞】 1985年4月日本化学会（第34回）進歩賞受賞－7－

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 北川

進 （きたがわすすむ）【職名】 副拠点長【所属】 物質－細胞統合システム拠点【研究室】 桂キャンパス

A4棟

319号室

【直通電話】 075-383-2733【FAX】 075-383-2732【電子メールアドレス】 kitagawa@icems.kyoto-u.ac.jp【ホームページ】 http://www.sbchem.kyoto-u.ac.jp/kitagawa-lab/index.html【研究分野】 錯体化学、無機化学【現在の研究課題】 新規多孔性材料の開拓とその応用【研究内容キーワード】 多孔性配位高分子、金属有機構造体、光機能、超分子構造【最終学歴】 1979年3月【学位】 1979年7月

京都大学大学院石油化学専攻博士課程修了
工学博士（京都大学）【略歴】 1979年4月近畿大学理工学部助手、1983年4月近畿大学理工学部講師、1988年4月近畿大学理工学部助教授、1992年4月東京都立大学理学部化学教室無機化学
第一講座教授、1998年6月京都大学大学院工学研究科合成・生物化学専攻教授、2007年10月京都大学物質-細胞統合システム拠点・副拠点長および京都大学大学院工学研究科合成・生物化学専攻（兼任）教授【在外研究歴】 1986年-1987年Texas A&M大学 Cotton研究室博士研究員【所属学会】 日本化学会、錯体化学会、物理学会、高分子学会、米国学会【主な著書、学術論文】 1. One-dimensional imidazole aggregate in aluminum porous coordination poly（過去5年以内）
mers with high proton conductivity”, S. Bureekaew, S. Horike, M. Higuchi, M.
Mizuno, T. Kawamura, D. Tanaka, N. Yanai and S. Kitagawa, Nature Materials, 2009, 8, 831-836.
2.“Selective sorption of oxygen and nitric oxide by an electron-donating flexible
porous coordination polymer”, S. Shimomura, M. Higuchi, R. Matsuda, K.
Yoneda, Y. Hijikata, Y. Kubota, Y. Mita, J. Kim, M. Takata and S. Kitagawa,Nature Chemistry, 2010, 2, 633-637.
3.“Photoactivation of a nanoporous crystal for on-demand guest trapping andconversion”, H. Sato, R. Matsuda, K. Sugimoto, M. Takata and S. Kitagawa,Nature Materials, 2010, 9, 661-666. (Highlighted in News & Views in the same
issue.).
【学術関係の受賞】 1. 2002年第19回日本化学会学術賞
2. 2007 年 Earl L. Muetterties Memorial Lectureship (University of California,
Berkeley)
3. 2007年平成19年度錯体化学会賞
4. 2008年Humboldt Research Award, Germany
5. 2009年第61回日本化学会賞
6. 2010年トムソン・ロイター引用栄誉賞受賞
7. 2011年平成23年度科学技術分野の文部科学大臣表彰研究部門
8. 2011年平成23年度春の紫綬褒章受章－8－Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 吉川

研一 （よしかわけんいち）【職名】 教授【所属】 理学研究科

物理学・宇宙物理学専攻【研究室】 理学研究科

吉川研究室【直通電話】 075-753-3749【FAX】 075-753-3779【電子メールアドレス】 yoshikaw@scphys.kyoto-u.ac.jp【ホームページ】 http://www.chem.scphys.kyoto-u.ac.jp/【研究分野】 非線形科学・生命物理学【現在の研究課題】 1）非平衡開放系での時間的・空間的秩序の自発的生成に関する研究
2）生命現象の物理学【研究内容キーワード】 非平衡開放系・時空間的秩序の自己生成・自己組織化・高分子物理学【最終学歴】 1976年5月【学位】 1976年5月

京都大学大学院工学研究科博士課程修了
工学博士（京都大学）【略歴】 1976年10月徳島大学教養部講師、1979年4月徳島大学教養部助教授、1988 年 4名古屋大学教養部助教授、1990年11月名古屋大学教養部教授、1991年4月名古屋大学大学院人間情報学研究科教授、1998年4月京都大学大学院理学研究科教授、2002年 9月京都大学福井謙一記念研究センター兼任教授（現在に至る）、
1998年10月～ 1999年6月Universite Louis Pasteur 客員教授、2009年2月 ENS,
Paris 客員教授
【在外研究歴】 長期のものはなし【所属学会】 物理学会、日本化学会、生物物理学会など【学会活動】 Vice Chair, Commission C-6, International Union of Pure and Applied Physicsなど【主な著書、学術論文】 1. M.Horning, A.Isomura, K.Agladze, K.Yoshikawa,“Liberation of a pinned（過去5年以内）spiral wave by a single stimulus in excitable media”, Phys. Rev. E, 79,026218(2009).
2. T.Saito, T.Iwaki, K.Yoshikawa,“Small anion with higher valency retards thecompaction of DNA in the presence of multivalent cation”, Biophys. J., 96,1068(2009).
3. A. Estevez, C. Crozatier, A. Diguet, T. Hara, H. Saito, K. Yoshikawa and D.
Baigl,“ Sequence-independent and reversible photocontrol of transcription/
expression systems using a photosensitive nucleic acid binder”, Proc.Natl.Acad.
Sci., 106, 12219(2009).
4. M. Negishi, T. Sakaue and K. Yoshikawa,”Mismatch of bulk viscosity reduces interfacial diffusivity at an aqueous/oil system”, Phys. Rev. E, 81,
020901(2010).
5. M. Takinoue, Y. Atsumi and K. Yoshikawa,“Rotary motion driven by a direct
current electric field”, Appl. Phys. Lett., 96, 104105(2010).
【学術関係の受賞】 日本 IBM 科学賞（1991）－9－

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 Tanimura Yoshitaka （たにむら

よしたか）【職名】 Professor【所属】 Department of Chemistry【研究室】 Faculty of Science, 6th building #256
【直通電話】 075-753-4017【FAX】 075-753-4018【電子メールアドレス】 tanimura@kuchem.kyoto-u.ac.jp【ホームページ】 http://theochem.kuchem.kyoto-u.ac.jp【研究分野】 Chemical Physics【現在の研究課題】 nonlinear optical response【研究内容キーワード】 statistical physics【最終学歴】 Keio University【学位】 Ph. D【所属学会】 Japanese Physical Soc, American Physical Soc, 日本化学会、American Chemical
Soc.
【学会活動】 2002-2004 日本物理学会理事【主な著書、学術論文】 1. A. G. Dijkstra and Y. Tanimura, Correlated fluctuations in the exciton dynamics
and spectroscopy of DNA, New J. of Phys. 12, 055005 (19pages) (2010).
（過去5年以内）
2. M. Tanaka and Y. Tanimura, Multistate Electron Transfer Dynamics in theCondensed Phase: Exact Calculations from the Reduced Hierarchy Equations of
Motion Approach, J. Chem. Phys. 132, 214502 (11pages) (2010)
3. A. G. Dijkstra and Y. Tanimura, Non-Markovian entanglement dynamics in thepresence of system-bath coherence, Phys. Rev. Lett 104, 250401 (4 pages) (2010).
4. A. Sakurai and Y. Tanimura, Does hbar play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations, J.
Phys. Chem. A 115, 4009-4022 (2011)
5. T. Hasegawa and Y. Tanimura, A polarizable water model for intramolecular and intermolecular vibrational spectroscopies, J. Phys. Chem. B 115, 55455553(2011).

【学術関係の受賞】 Morino Foundation
Humboldt Research Award－ 10 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 田中 一義 （たなかかずよし）

【職名】 教授【所属】 工学研究科

分子工学専攻【研究室】 桂キャンパス

A4棟

205

【直通電話】 075-383-2549【FAX】 075-383-2555【電子メールアドレス】 ktanaka@moleng.kyoto-u.ac.jp【ホームページ】 http://www.moleng.kyoto-u.ac.jp/~moleng_03/index_J.html【研究分野】 物理化学・量子化学【現在の研究課題】 分子ナノ工学、量子機能化学【研究内容キーワード】 単一分子スピン、単一分子発光、元素化学の量子論【最終学歴】 1978年3月【学位】 1978年3月

京都大学工学研究科石油化学専攻博士課程修了
工学博士（京都大学）【略歴】 1979年6月米国エナージー・コンバージョン・デバイシズ社リサーチケミスト、
1981年12月京都大学工学部助手、1988年12月 同 助教授、1996年11月京都大学大学院工学研究科教授【所属学会】 日本化学会・日本物理学会・高分子学会【学会活動】 フラーレン・ナノチューブ・グラフェン学会幹事【主な著書、学術論文】 1. 分子エレクトロニクスの基盤技術と将来展望（共監修および共著, シーエム
（過去5年以内）
シー出版, 2009）
2. 物理化学（化学マスター講座）（共著, 丸善, 2010）（以上著書）
1. A. Ito, Y. Nakano, M. Urabe, T. Kato, and K. Tanaka,“Triradical Cation ofp-Phenylenediamine Having Two Nitroxide Radical Groups: Spin Alignment
Mediated by Delocalized Spin”, J. Am. Chem. Soc., 128, 2948-2953 (2006).
2. Y. Hirao, M. Urabe, A. Ito, and K. Tanaka,“Intramolecular Spin Transfer in a
Spiro-Fused Bis(triarylamine)”, Angew. Chem., Int. Ed., 46, 3300-3303 (2007).
3. A. Ito, Y. Yamagishi, K. Fukui, S. Inoue, Y. Hirao, K. Furukawa, T. Kato, andK. Tanaka,“Trimacrocyclic Arylamine and Its Polycationic States”, Chem.
Commun., 2008, Issue 48 (December 28), 6573-6575 (2008).
4. A. Ito, D. Sakamaki, H. Ino, A. Taniguchi, Y. Hirao, K. Tanaka, K. Kanemoto,and T. Kato,“Polycationic States of Oligoanilines Based on Wurster’s Blue”,
Eur. J. Org. Chem., 2009, Issue 26 (September), 4441-4450 (2009).
5. A. Ito, Y. Yokoyama, R. Aihara, K. Fukui, S. Eguchi, K. Shizu, T. Sato, andK. Tanaka,“Preparation and Characterization of N-Anisyl-Substituted Hexaaza[16]paracyclophane”, Angew. Chem. Int. Ed., 49, 8205-8208 (2010).
6. K. Suzuki, T. Matsuo, D. Hashizume, H. Fueno, K. Tanaka, and K. Tamao,“A Planar Rhombic Charge-Separated Tetrasilacyclobutadiene”, Science, 331,
1306-1309 (2011).
（以上学術論文）【学術関係の受賞】 該当なし

－ 11 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 山本

量一 （やまもと

りょういち）【職名】 教授【所属】 工学研究科

化学工学専攻【研究室】 桂キャンパス

A棟

118号室

【直通電話】 075-383-2661【FAX】 075-383-2651【電子メールアドレス】 ryoichi@cheme.kyoto-u.ac.jp【ホームページ】 http://www-tph.cheme.kyoto-u.ac.jp/【研究分野】 ソフトマターの移動現象【現在の研究課題】 コロイド分散系の計算機シミュレーション【研究内容キーワード】 ソフトマター、コロイド、計算機シミュレーション、ガラス転移【最終学歴】 1992年3月【学位】 1996年3月

神戸大学大学院 工学研究科修士課程化学工学専攻修了
博士（工学）京都大学【略歴】 1994年9月 神戸大学大学院自然科学研究科物質科学専攻助手、1996年3月 京都大学大学院理学研究科物理学・宇宙物理学専攻助手、2000年1月 同講師、2004
年10月 京都大学大学院工学研究科化学工学専攻助教授、2007年4月 同准教授、2008年10月 同教授【在外研究歴】 2000年9月-2001年8月 英国ケンブリッジ大学化学教室（J-P. Hansen教授）（文部省在外研究員（若手））【所属学会】 日本物理学会、化学工学会、高分子学会、分子シミュレーション研究会、日本液晶学会、紛体工学会、日本レオロジー学会【主な著書、学術論文】 1. S. Yasuda and R. Yamamoto,“Dynamic rheology of a supercooled polymer（過去5年以内）
melt in nonuniform oscillating flows between rapidly oscillating plates”, Phys.
Rev. E 84, 031501 (2011).
2. H. Mizuno and R. Yamamoto,“Dynamical heterogeneity in a highly supercooled liquid: Consistent calculations of correlation length, intensity, and lifetime”, Phys. Rev. E 84, 011506 (2011).
3. H. Kobayashi and R. Yamamoto,“Implementation of Lees-Edwards periodic
boundary conditions for direct numerical simulations of particle dispersions
under shear flow”, J. Chem. Phys. 134, 064110 (2011).
4. S. Yasuda and R. Yamamoto,“Rheological properties of polymer melt between
rapidly oscillating plates: an application of multiscale modeling”, Europhys.
Lett. 86, 18002 (2009).
5. Y. Nakayama, K. Kim and R. Yamamoto,“Simulating (electro) hydrodynamic
effects in colloidal dispersions: smoothed profile method”, Eur. Phys. J. E 26,
361 (2008).
【学術関係の受賞】 2007年1月 ホソカワ研究奨励賞、2002年12月 分子シミュレーション研究会学術賞－ 12 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 高田

彰二 （たかだ

しょうじ）【職名】 准教授【所属】 理学研究科【研究室】 理学部

生物科学専攻1号館

生物物理学教室

205号室【直通電話】 075-753-4220【FAX】 075-753-4222【電子メールアドレス】 takada@biophys.kyoto-u.ac.jp【ホームページ】 http://theory.biophys.kyoto-u.ac.jp【研究分野】 理論生物物理学【現在の研究課題】 生体分子の構造機能についての理論およびコンピュータシミュレーション研
究【研究内容キーワード】 タンパク質、分子モーター、分子動力学、生体分子モデリング【最終学歴】 1991年9月総合研究大学院大学数物科学研究科機能分子科学専攻博士後期課程
退学【学位】 1994年3月理学博士（総合研究大学院大学）【略歴】 1991年～ 1995年岡崎国立共同研究機構技官（分子科学研究所）、1995年～
1998年日本学術振興会研究員（イリノイ大学化学科）、1998年～ 2001年神戸大学理学部化学科講師、2001年～ 2007年神戸大学理学部化学科助教授、2007年～京都大学理学研究科生物科学専攻生物物理教室准教授。
【在外研究歴】 1995年5月-1998年3月

米国イリノイ大学化学科（日本学術振興会研究員）【所属学会】 日本生物物理学会、日本物理学会【学会活動】 日本生物物理学会運営委員【主な著書、学術論文】 1. Wenfei Li and Shoji Takada, Self-learning multiscale simulation for achieving（過去5年以内）high accuracy and high efficiency simultaneously, Journal of Chemical Physics,
130: 214108(6 pages), 2009
2. Naoto Hori, George Chikenji, R. Stephen Berry, and Shoji Takada, Folding energy landscape and network dynamics of small globular proteins, Proceedings of
the National Academy of Sciences USA, 106: 73-78, 2009
3. Kei-ichi Okazaki, and Shoji Takada, Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus populationshift mechanisms, Proceedings of the National Academy of Sciences USA, 105:
11182-11187, 2008.
4. Kei-ichi Okazaki, Nobuyasu Koga, Shoji Takada, Jose N Onuchic, and Peter G
Wolynes, Multiple-basin energy landscapes for large amplitude conformationalmotions of proteins: Structure-based molecular dynamics simulations, Proceedings of the National Academy of Sciences USA, 103(No.32):11844-11849, 2006.
5. Nobuyasu Koga and Shoji Takada, Folding-based molecular simulations reveal
mechanisms of the rotary motor F1-ATPase, Proceedings of the National Academy of Sciences USA, 103(No.14):5367-5372, 2006.
【学術関係の受賞】－ 13 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 林

重彦 （はやししげひこ）【職名】 准教授【所属】 理学研究科

化学専攻【研究室】 理学研究科

6 号館

154 号室【直通電話】 075-753-4006【FAX】 075-753-4000【電子メールアドレス】 hayashig@kuchem.kyoto-u.ac.jp【ホームページ】 http://kuchem.kyoto-u.ac.jp/riron/hayashig【研究分野】 理論化学・生物物理学【現在の研究課題】 タンパク質分子機能の理論的研究【研究内容キーワード】 タンパク質機能・分子シミュレーション【最終学歴】 1997 年 11 月
【学位】 1997 年 11 月

京都大学大学院理学研究科化学専攻博士課程修了
博士（理学）（京都大学）【略歴】 1998 年 4 月日本学術振興会特別研究員（名古屋大学）、2000 年 4 月米国イリノイ大学ベックマン研究所博士研究員、2003 年 6 月京都大学福井謙一記念研究センター博士研究員、2003 年 10 月科学技術振興機構さきがけ研究員、2005
年 5 月京都大学大学院理学研究科准教授【所属学会】 生物物理学会【主な著書、学術論文】 1. Local entropy difference upon a substrate binding of a psychrophilic α-amy（過去5年以内）
lase and a mesophilic homologue. Takahiro Kosugi and Shigehiko Hayashi,
Chem. Phys. Lett., 501, 517-522 (2011).
2. Protein collective motions coupled to ligand migration in myoglobin. Yasutaka
Nishihara, Shigeki Kato, and Shigehiko Hayashi, Biophys. J., 98, 1649-1657(2010).
3. Electronic coulombic coupling of excitation-energy transfer in xanthorhodopsin. Kazuhiro Fujimoto, and Shigehiko Hayashi, J. Am. Chem. Soc., 131, 1415214153 (2009).
4. Proton transfer reactions in reaction center of photosynthetic bacteria, Rhodobacter sphaeroides. Yu Kaneko, Shigehiko Hayashi, and Iwao Ohmine, J. Phys.
Chem. B, 113, 8993-9003 (2009).
5. Photochemical reaction dynamics of the primary event of vision studied by ahybrid molecular simulation. Shigehiko Hayashi, Emad Tajkhoshid, and Klaus
Schulten, Biophys. J., 96, 403-416 (2009).

－ 14 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)(4) 専任教員【氏名（ふりがな）】 石田

俊正 （いしだとしまさ）【職名】 准教授【所属】 福井謙一記念研究センター【研究室】 福井記念研究センター

総合研究部門205【直通電話】 075-711-7838【FAX】 075-711-7838【電子メールアドレス】 ishida@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~ishida【研究分野】 計算化学・理論化学【現在の研究課題】 光機能分子の反応・ポテンシャル面生成法【研究内容キーワード】 光機能分子・ポテンシャル面・非断熱遷移【最終学歴】 1989年3月【学位】 1989年3月

東京大学理学系大学院相関理化学専攻博士課程修了
理学博士（東京大学）【略歴】 1989年4月 静岡大学教養部助手、1995年4月静岡大学教養部助教授、1995年
10月静岡大学工学部助教授、2002年4月岡崎国立共同研究機構分子科学研究所
助教授（流動部門）、2004年4月静岡大学工学部助教授、2004年10月京都大学
福井謙一記念研究センター助教授、2007年4月同准教授【在外研究歴】 1996年4月-1997年3月 米国Northwestern大学化学（George C. Schatz教授）（文部省在外研究員（若手）【所属学会】 日本化学会、日本分子化学会、日本コンピュータ化学会、American PhysicalSociety【主な著書、学術論文】 1. Hiroshi Kohguchi, Toshinori Suzuki, Shinkoh Nanbu, Toshimasa Ishida,（過去5年以内）
Gennady V. Mil’nikov, Ponmile Oloyede, Hiroki Nakamura,“Collision
Energy Dependence of the O( 1D) + HCl → OH+Cl(2P) Reaction Studied by
Crossed Beam Scattering and Quasiclassical Trajectory Calculations on abinitio Potential Energy Surfaces”, J. Phys. Chem. A 112(5), 818-825 (2008).
2. Toshimasa Ishida, Shinkoh Nanbu, and Hiroki Nakamura, Non-adiabatic ab
initio dynamics of two models of Schiff base retinal, J. Phys. Chem. A, 113(16),4356-4366 (2009).
3. Toshimasa Ishida and Jun-ichi Aihara, Aromaticity of neutral and doubly
charged polyacenes, Phys. Chem. Chem. Phys. 11, 7197 - 7201 (2009).
4. Wilfredo C. Chung, Shinkoh Nanbu, and Toshimasa Ishida,“Nonadiabatic ab
Initio Dynamics of a Model Protonated Schiff Base of 9-cis Retinal”, J. Phys.
Chem. A, 114 (32), 8190-8201 (2010).
5. Shinkoh Nanbu, Toshimasa Ishida and Hiroki Nakamura,“Future Perspectivesof Nonadiabatic Chemical Dynamics”Chemical Science, 1, 663-674 (2010).

－ 15 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 佐藤

徹 （さとうとおる）【職名】 准教授【所属】 京都大学工学研究科分子工学専攻【研究室】 桂キャンパス

A4棟

203号室

【電話】 075-383-2803【FAX】 075-383-2555【電子メールアドレス】 tsato@scl.kyoto-u.ac.jp【ホームページ】【研究分野】 物性理論化学【現在の研究課題】 振電相互作用, 群論の化学への応用【研究内容キーワード】 Jahn-Teller効果, 有機EL, 量子輸送, フラーレン【最終学歴】 平成9年3月 京都大学大学院工学研究科分子工学専攻博士後期課程修了【学位】 平成9年3月 京都大学博士（工学）【略歴】 平成9年4月日本学術振興会特別研究員PD(財団法人基礎化学研究所) (平成9年12月まで)、平成10年1月 京都大学大学院工学研究科分子工学専攻助手 (平成16年2月まで)、平成15年10月 文部科学省在外研究員(若手)(ベルギー王国ルーヴァンカトリック大学,平成16年4月まで)、平成16年3月 京都大学福井謙一記
念研究センター理論研究部門助教授、平成19年4月 京都大学福井謙一記念研究センター理論研究部門准教授(職名変更, 平成22年12月まで)、平成23年1月
京都大学工学研究科分子工学専攻 准教授【所属学会】 日本化学会、日本物理学会、応用物理学会、日本コンピュータ化学会、有機EL討論会、フラーレン・ナノチューブ学会【学会活動】 日本化学会 学会賞等支部推薦委員（平成19年度-20年度）、Jahn-Teller
Steering Committee（2009-）、第21回ヤーン・テラー効果に関する国際会議組
織委員会 副委員長（2010-）【主な著書、学術論文】 1. "Vibronic Coupling in Cyclopentadienyl Radical: A Method for Calculation of Vibronic
Coupling Constant and Vibronic Coupling Density Analysis", Tohru Sato, Ken Tokunaga,（過去5年以内）

and Kazuyoshi Tanaka, J. Chem. Phys. 124, 024314 1-12(2006).
2. "Vibronic coupling in benzene cation and anion:Vibronic coupling and frontier electron
density in Jahn-Teller molecules" Tohru Sato, Ken Tokunaga, and Kazuyoshi Tanaka, J.
Chem. Phys. 124, 154303 1-10(2006).
3. "Vibronic and spin-orbit coupling of a d 9 transition-metal ion encapsulated in an
icosahedral cage: The ( Γ 8+ Γ 9) × (g+2h) Jahn-Teller problem", Tohru Sato and Arnout
Ceulemans, J. Chem. Phys. 126, 184501 1-9(2007) .
4. "Vibronic coupling constant and vibronic coupling density", Tohru Sato, Ken Tokunaga,
Naoya Iwahara, Katsuyuki Shizu, and Kazuyoshi Tanaka,in "The Jahn-Teller Effect:
Fundamentals and Implications for Physics and Chemistry", Springer Series in Chemical
Physics 97, H. Koeppel, H. Barentzen, and D. R. Yarkony (Eds)
5. "Vibronic coupling in naphthalene anion: Vibronic coupling density analysis for totallysymmetric modes", Tohru Sato, Ken Tokunaga, and Kazuyoshi Tanaka, J. Phys. Chem. A
112, 758-767 (2008).
6. "Electron-vibration interactions in carrier transport material: Vibronic coupling density
analysis in TPD", Tohru Sato, Katsuyuki Shizu, Takako Kuga, Kazuyoshi Tanaka,
Hironori Kaji, Chem. Phys. Lett. 458, 152-156 (2008).
7. "A Boron-Containing Molecule as an Efficient Electron-Transporting Material with LowPower Consumption", Katsuyuki Shizu, Tohru Sato, Kazuyoshi Tanaka, and Hironori
Kaji, Appl. Phys. Lett. 97, 142111 1-3(2010).
8. "Vibronic coupling in C 60 - anion revisited: Precise derivations from photoelectron
spectra and DFT calculations", Naoya Iwahara, Tohru Sato, Kazuyoshi Tanaka, Liviu F.
Chibotaru, Phys. Rev. B, 82, 245409 1-10 (2010).

【学術関係の受賞など】 Erasumus Mundus Scholar（欧州連合, 2011）－ 16 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)【氏名（ふりがな）】 中尾

嘉秀（なかおよしひで）【職名】 准教授【所属】 福井謙一記念研究センター【研究室】 京都大学桂A4棟

理論研究部門

024号室【直通電話】 075-383-2546【FAX】 075-383-2799【電子メールアドレス】 nakao@fukui.kyoto-u.ac.jp【ホームページ】 http://www.moleng.kyoto-u.ac.jp/~moleng_10/index_J.html【研究分野】 理論化学・計算化学【現在の研究課題】 物性の理論化学・計算化学【研究内容キーワード】 機能性分子・励起状態・スピン物性【最終学歴】 2003年3月 東京大学大学院工学系研究科応用化学専攻博士課程 修了【学位】 2003年3月 博士(工学) 東京大学
【略歴】 2003年4月 京都大学大学院工学研究科分子工学専攻助手、2007年4月 京都大学
大学院工学研究科分子工学専攻助教、2011年1月 京都大学福井謙一記念研究センター准教授【所属学会】 日本化学会、分子科学会【主な著書、学術論文】 1. H. Ando, Y. Nakao, H. Sato and S. Sakaki, Theoretical Study of Low-Spin,（過去5年以内）
High-Spin, and Intermediate-Spin States of [FeIII(pap)2]+ (pap = N-2-pyridylmethylidene-2-hydroxyphenylaminato). Mechanism of Light-Induced Excited
Spin State Trapping. J. Phys. Chem. A 111, 5515-5522 (2007).
2. K. Umakoshi, T. Kojima, K. Saito, S. Akatsu., M. Onishi, S. Ishizaka, N. Kitamura, Y. Nakao, S. Sakai, Y. Ozawa, Heteropolynuclear Complexes of 3,5-Dimethylpyrazolate [Pt2M4(Me2pz)8] (M = Ag, Cu). Highly Luminescent Character of the Triplet Excited State Based on Mixed-Metal Cores. Inorg. Chem.
47, 5033-5035 (2008).
3. Y. Nakao, K. Saito, S. Sakaki, Theoretical investigation of μ -O-bridged dinuclear Re complexes. Electronic structure, bonding nature, and absorption
spectra, Int. J. Quant. Chem. 109, 2319-2327 (2009).
4. Y. I. Kurokawa, Y. Nakao, S. Sakaki, Bonding nature of open-lantern-type dinuclear Cr(II) complexes. Theoretical study with the MRMP2 method. J. Phys.
Chem. A 113, 3202-3209 (2009).
5. Y. I. Kurokawa, Y. Nakao, S. Sakaki, Inverted Sandwich Type Dinuclear
Chromium(I) Complex and Its Analogues of Scandium(I), Titanium(I),
Vanadium(I), Manganese(I), and Iron(I): Theoretical Study of Electronic
Structure and Bonding Nature, J. Phys. Chem. A, 114, 1191-1199 (2010).

－ 17 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)(5) リサーチリーダー【氏名（ふりがな）】 諸熊

奎治 （もろくまけいじ）【職名】 リサーチリーダー【所属】 福井謙一記念研究センター

福井謙一記念研究部門第一【研究室】 福井謙一記念研究センター 202【直通電話】 075-711-7843【FAX】 075-781-4757【電子メールアドレス】 morokuma@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~morokuma; http://kmweb.fukui.kyoto-u.ac.jp/【研究分野】 理論化学・計算化学【現在の研究課題】 複雑分子系の複合分子理論によるシミュレーション【研究内容キーワード】 複合分子理論、複雑分子系、シミュレーション、ナノ構造、酵素反応【最終学歴】 1962年3月京都大学大学院工学研究科博士課程単位修得退学【学位】 1963年3月工学博士（京都大学）【略歴】 1962年4月京都大学工学部助手、1964年9月Columbia大学客員助教授、1966年9月Harvard大学博士研究員、1967年9月Rochester大学助教授、1971年9月同教授、1976年12月分子科学研究所教授、1993年1月Emory大学William H. Emerson教
授、2006年9月Emory大学名誉教授、2006年9月京都大学福井謙一記念研究センターリサーチリーダー【所属学会】 日本化学会、American Chemical Society、分子科学会【主な著書、学術論文】 過去 5 年間に約 130 報（過去5年以内） 1. S. Sekharan and K. Morokuma, QM/MM Study of the Structure, Energy
Storage and Origin of the Bathochromic Shift in Vertebrate and Invertebrate
Bathorhodopsins. J. Am. Chem. Soc, 133, 4734-4737 (2011).
2. S. Maeda, S. Komagawa, M. Uchiyama, and K. Morokuma. Finding Reaction
Pathways for Multicomponent Reactions: The Passerini Reaction Is a FourComponent Reaction. Angew, Chem. Int. Ed. 50, 644-649. (2011).
3. A. J. Page, K. R. S. Chandrakumar, S. Irle, and K. Morokuma, SWNT Nucleation from Carbon-Coated SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism. J. Am. Chem. Soc. 133, 621-628 (2011).
4. H. Hirao and K. Morokuma, Ferric Superoxide and Ferric Hydroxide Are
Used in the Catalytic Mechanism of Hydroxyethylphosphonate Dioxygenase(HEPD): A Density Functional Theory Investigation, J. Am. Chem. Soc. 132,
17901-17909 (2010).
5. X. Li, L. W. Chung, A. Miyawaki and K. Morokuma, Primary Events of Photodynamics in Reversibly Photoswitching Fluorescent Protein Dronpa, J. Phys.
Chem. Lett. 1, 3328-3333 (2010).
6. K. Nozaki, S. Kusumoto, S. Noda, T. Kochi, L. W. Chung, and K. Morokuma,
Why Did Incorporation of Acrylonitrile to a Linear Polyethylene Become
Possible? Comparison of Phosphine-Sulfonate Ligand with Diphosphine andImine-Phenolate Ligands in the Pd-Catalyzed Ethyelene/Acrylonitrile Copolymerization; J. Am. Chem. Soc. 132, 16030-16042 (2010).
7. A. J. Page, Y. Ohta, S. Irle and K. Morokuma, Mechanisms of Single-Walled
Carbon Nanotube Nucleation, Growth and Healing Determined Using QM/
MD Methods, Acc. Chem. Res. 43. 1375-1385 (2010).
【学術関係の受賞】 Alfred P. Sloan Research Fellowship, 1970-72; International Academy of Quantum Molecular Science (IAQMS); 日本化学会賞, 1992; The Schrödinger Medal,
The World Association of Theoretical Organic Chemists (WATOC), 1993; The
Fukui Medal, Asian Pacific Association of Theoretical & Computational Chemists, 2005;
恩賜賞、日本学士院賞、2008; 瑞宝中綬章、2010－ 18 －

Ⅰ 専任教員 ･ スーパーバイザー (2010)(6) 特定助教（白眉）【氏名（ふりがな）
】 前田

理（まえだ

さとし）

【職名】 特定助教【所属】 京都大学次世代研究者育成センター・京都大学福井謙一記念研究センター【研究室】 福井謙一記念研究センター

208号室【直通電話】 075-711-7894【電子メールアドレス】 075-781-4757【研究分野】 smaeda@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~maeda
https://sites.google.com/site/satoshimaedakyotouniv/【研究分野】 理論化学・計算化学【現在の研究課題】 化学反応経路自動探索法の開発と応用【研究内容キーワード】 ポテンシャルエネルギー曲面・遷移状態・反応経路・非断熱反応経路【学歴】 2004年3月
2007年3月

東北大学大学院理学研究科修士課程 修了
東北大学大学院理学研究科博士課程 修了【学位】 2007年3月

理学博士（東北大学）【略歴】 2004年4月

日本学術振興会特別研究員（DC1）
日本学術振興会特別研究員（PD）
京都大学次世代研究者育成センター（特定助教）

2007年4月
2010年4月【所属学会】 日本化学会・日本物理学会・分子科学会【主な著書、学術論文】 1. Maeda, S.; Ohno, K.; Morokuma, K. Updated Branching Plane for Finding（過去5年以内）】
Conical Intersections without Coupling Derivative Vectors. J. Chem. Theory
Comput. 2010, 6, 1538-1545.
2. Maeda, S.; Ohno, K.; Morokuma, K. A Theoretical Study on the Photodissociation of Acetone: An Insight into the Slow Intersystem Crossing and Explorationof Nonadiabatic Pathways to the Ground State. J. Phys. Chem. Lett. 2010, 1,
1841-1845.
3. Maeda, S.; Morokuma, K. Communications: A Systematic Method for Locating
Transition Structures of A + B → X Type Reactions. J. Chem. Phys. 2010, 132,
241102/1-4.
4. Maeda, S.; Komagawa, S.; Uchiyama, M.; Morokuma, K. Finding Reaction
Pathways for Multicomponent Reactions: The Passerini Reaction Is a FourComponent Reaction. Angew. Chem. Int. Ed. 2011, 50, 644-649.
5. Maeda, S.; Saito, R.; Morokuma, K. Finding Minimum Structures on Seam of
Crossing in Reactions of Type A + B → X: Exploration of Nonadiabatic Ignition Pathways of Unsaturated Hydrocarbons. J. Phys. Chem. Lett. 2011, 2, 852857.
【学術関係の受賞など】 2004年度－2006年度 日本学術振興会特別研究員（DC1）
2007年3月 青葉理学振興会賞
2007年3月 東北大学総長賞
2004年度－2006年度 日本学術振興会特別研究員（PD）
2008年10月 平成20年度分子科学討論会優秀講演賞
2010年度－現在 京都大学白眉研究者－ 19 －

Ⅱ 博士研究員 (2010)

Ⅱ 博士研究員
１. 博士研究員組織

職

名

氏

福井センターフェロー
福井センターフェロー

福井謙一記念研究部第一

名

Biswajit Saha
平尾一

福井センターフェロー

Zhuofeng Ke

福井センターフェロー

Joonghan Kim

福井センターフェロー

Alister Page

（JST）フェロー

Xin Li（JST）フェロー

K.R.S. Chandrakumar（JST）フェロー

Fengyi Liu（JST）フェロー

Parameswaran Pattiyil（JST）フェロー

Hong-Yan Xiao

（JST）フェロー

Lina Ding（JST）フェロー

Haibei Li（JST）フェロー

Lung Wa Chung（JST）フェロー

Galina Petrova

福井センターフェロー

Wilfredo Credo Chung

福井センターフェロー

岩城貴史

福井センターフェロー

池野豪一

福井センターフェロー

義永

那津人

－ 20 －

Ⅱ 博士研究員 (2010)

２. 博士研究員プロフィール【氏名】 Biswajit Saha
【職名】 FIFC Fellow【所属】 Morokuma Group, Fukui Institute for Fundamental Chemistry【研究室】 Room

203

【直通電話】 075-711-7834【FAX】 075-781-4757【電子メールアドレス】 saha@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~saha【研究分野】 Computational Chemistry【現在の研究課題】 Molecular dynamics (MD) simulations and electronic structure calculations of
nano-materials【研究内容キーワード】 Fullerene, nano-tube, metallofullerene, polycyclic aromatic hydrocarbon, DFTB
【学歴】 November 1998, Master of Science (M. Sc.), Calcutta University, India
December 2003, Doctor of Science (Ph. D.), Indian Association for the
Cultivation of Science (IACS), Jadavpur University, India【学位】 Ph. D. (Science)【略歴】 December 2003, Postdoctoral fellow, University of Kassel, Germany
September 2004, JSPS postdoctoral fellow, Kyoto University, Japan
November 2006, Postdoctoral fellow, FIFC, Kyoto University, Japan【所属学会】 Life member, IACS, India
Member, American Chemical Society【主な著書、学術論文】 1. B. Saha, S. Irle, K. Morokuma,“Hot giant fullerenes eject and capture C2 molecules: QM/MD simulations with constant density”, J. Phys. Chem. (Submitted)（過去5年以内）
2. B. Saha, S. Irle, K. Morokuma,“Formation mechanism of polycyclic aromatichydrocarbons (PAHs) in benzene combustion: Quantum chemical molecular
dynamics simulations”, J. Chem. Phys. 132, 224303 (2010)
3. B. Saha, S. Shindo, S. Irle, K. Morokuma,“Quantum chemical molecular dynamics (QM/MD) simulations of fullerene from benzene”, ACS Nano 3, 2241
(2009)
4. B. Saha, M. Ehara, H. Nakatsuji,“Investigation of electronic spectra andExcited-state geometries of poly-para-phenylene vinylene (PPV) and poly-paraphenylene by symmetry adapted configuration-interaction (SAC-CI) method”,
J. Phys. Chem. A 111, 5473, (2007)【学術関係の受賞など】 JSPS postdoctoral fellowship, 2004-2006
Research fellowship, IACS, India, 1999 - 2003
National scholarship, Indian Government, 1990-1995－ 21 －

Ⅱ 博士研究員 (2010)【氏名（ふりがな）】 Hajime Hirao（はじめひらお）【職名】 Assistant Professor【所属】

Division of Chemistry and Biological Chemistry, School of Physical andMathematical Sciences, Nanyang Technological University【研究室】 #04-01【直通電話】 (65) 6592-2644【FAX】 (65) 6791-1961【電子メールアドレス】 hirao@fukui.kyoto-u.ac.jp
Computational bioinorganic chemistry, Metalloenzymes, Transition-metal【研究分野】
catalysts【現在の研究課題】 Computational studies of bioinorganic systems【研究内容キーワード】 metalloenzymes, chemical reactions, electronic excited states, spectroscopy,
ONIOM, QM/MM, medicinal chemistry, molecular interactions【学歴】 Mar. 1998 BSc, Department of Engineering, Kyoto University
Mar. 2000 MSc, Graduate School of Engineering, Kyoto University【学位】 Nov. 2004, PhD, The University of Tokyo【略歴】 Jan. 2002-Dec. 2004 Lab associate at Novartis Pharma K.K.
Jan. 2005-Mar. 2007 Postdoc at The Hebrew University of Jerusalem
Apr. 2007-Mar. 2009 JSPS Postdoctoral Fellow for Research Abroad (Hebrew
University/Emory University)
Apr. 2009-Oct. 2010 FIFC Fellow at Kyoto University
Nov. 2010-Feb. 2011 Associate Professor Extraordinary at Kobe University
Mar. 2011-present Assistant Professor at Nanyang Technological University【所属学会】 American Chemical Society; The Chemical Society of Japan【主な著書、学術論文】 1. H. Hirao, K. Morokuma,“Ferric Superoxide and Ferric Hydroxide Are
Used in the Catalytic Mechanism of Hydroxyethylphosphonate Dioxygenase（過去5年以内）(HEPD): A Density Functional Theory Investigation,”J. Am. Chem. Soc. 2010,
132, 17901-17909
2. H. Hirao, K. Morokuma,“What is the Real Nature of Ferrous Soybean
Lipoxygenase-1? A New Two-Conformation Model Based on Combined
ONIOM(DFT:MM) and Multireference Configuration Interaction Characterization,”J. Phys. Chem. Lett. 2010, 1, 901-906.
3. H. Hirao, K. Morokuma,“Insights into the (Superoxo)Fe(III)Fe(III) Intermediate and Reaction Mechanism of myo-Inositol Oxygenase: DFT and
ONIOM(DFT:MM) Study,”J. Am. Chem. Soc. 2009, 131, 17206-17214.
4. O. Irie, T. Kosaka, T. Ehara, F. Yokokawa, T. Kanazawa, H. Hirao, A. Iwasaki, J. Sakaki, N. Teno, Y. Hitomi, G. Iwasaki, H. Fukaya, K. Nonomura, K.
Tanabe, S. Koizumi, N. Uchiyama, S. J. Bevan, M. Malcangio, C. Gentry, A. J.
Fox, M. Yaqoob, A. J. Culshaw, A. Hallett,“Discovery of Orally Bioavailable
Cathepsin S Inhibitors for the Reversal of Neuropathic Pain,”J. Med. Chem.
2008, 51, 5502-5505.
5. S. Shaik, H. Hirao, D. Kumar,“Reactivity Patterns of High-Valent Iron Oxo
Species in Enzymes and Synthetic Reagents: A Tale of Many States,”Acc.
Chem. Res. 2007, 40, 532-542.
6. H. Hirao, D. Kumar, L. Que, Jr., S. Shaik,“Two-State Reactivity in Alkane
Hydroxylation by Nonheme Iron-Oxo Complexes,”J. Am. Chem. Soc. 2006,
128, 8590-8606.
7. H. Hirao, D. Kumar, W. Thiel, S. Shaik,“Two States and Two More in the
Mechanisms of Hydroxylation and Epoxidation by Cytochrome P450,”J. Am.
Chem. Soc. 2005, 127, 13007-13018.
【学術関係の受賞など】 Oct. 2006-Mar. 2007 Golda Meir Fellowship
Apr. 2007-Mar. 2009 JSPS Postdoctoral Fellowship for Research Abroad
Oct. 2009-Mar. 2011 Kyoto Univ. Startup Grant for Young Researchers
Mar. 2010 Kurata Grant
Jul. 2010 Takeda Science Foundation Grant
2011 Nanyang Assistant Professorship 2010－ 22 －

Ⅱ 博士研究員 (2010)【氏名】 Zhuofeng Ke【職名】 FIFC Fellow【所属】 Morokuma Group, Fukui Institute For Fundamental Chemistry【研究室】 Room 207【直通電話】 075-711-7893【電子メールアドレス】 zhuofeng.ke@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 DNA-based asymmetric catalysis, pMMO enzymatic catalysis.
【研究内容キーワード】 Computational study of catalysis processes in organometallic systems and biosystems【学歴】 2002 B.Sc. in Chemistry, Sun Yat-sen University,
2005 M.Sc. in Polymer Chemistry and Physics, Sun Yat-sen University
2007 Jointly Educating Ph.D. in computational organometallic chemistry,
University of North Texas,
2009 Ph.D. in Physical Chemistry (Theoretical and Computational Chemistry),
Sun Yat-sen University【学位】 Ph.D. in Physical Chemistry (Theoretical and Computational Chemistry), Sun
Yat-sen University【所属学会】 American Chemical Society【学会活動】 241st ACS National Meeting in Anaheim, CA.
【主な著書、学術論文】 1. Ke Zhuofeng, Abe, Satoshi, Ueno, Takafumi, & Morokuma, Keiji, Rh-catalyzed Polymerization of
Phenylacetylene: Theoretical Studies of the Reaction Mechanism, Regioselectivity and Stereoregular（過去5年以内）
ity. J. Am. Chem. Soc., Accepted.
2. Gao, H., Ke, Zhuofeng, DeYonker N. J., Wang J., Xu H., Mao Z.-W., Phillips, D.L., & Zhao C., Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A
Density Functional Theory Study. J. Am. Chem. Soc., 2011, 133 (9), 2904-2915
3. Ke, Zhuofeng & Cundari, T.R., Palladium-Catalyzed C-H Activation/C-N Bond Formation Reactions: DFT Study of Reaction Mechanisms and Reactive Intermediates. Organometallics 29 (4), 821834 (2010). (Top10 Most Accessed Articles of Organometallics in 2010)
4. Guo, Z.; Xue, Jiadan; Ke, Zhuofeng; Phillips, D. L.*; Zhao, C.Y.*“Influence of Water Hydrogen
Bonding on the Reactions of Arylnitrenium Ions With Guanosine: Hydrogen-Bonding Effects Can Favor Reaction at the C8 Site”J. Phys. Chem. B, 2009, 113, 6528-6532.
5. Foley, N. A.; Lee, J. P.; Ke, Zhuofeng; Gunnoe, T. B.*; and Cundari, T. R.*“Ru(II) Catalysts Supported by Hydridotris(pyrazolyl)borate for the Hydroarylation of Olefins: Reaction Scope, Mechanistic Studies, and Guides for the Development of Improved Catalysts”Acc. Chem. Res. 2009, 42, 585-597
6. Lee, J. P.; Ke, Zhuofeng; Ramrez M. A.; Gunnoe, T. B.*; Cundari T. R.*; Boyle, P. D.; Petersen, J. L.
“Six-, Five-, and Four-Coordinate Ruthenium(II) Hydride Complexes Supported by N-Heterocyclic
Carbene Ligands: Synthesis, Characterization, Fundamental Reactivity, and Catalytic Hydrogenationof Olefins, Aldehydes, and Ketones”Organometallics 2009, 28, 1758-1775
7. Liu, Yan; Ke, Zhuofeng; Cui, Jianfang; Chen, Wen-Hua; Ma, Lin; Wang Bo*.“Synthesis, Inhibitory Activities and QSAR Study of Xanthone Derivatives as α-Glucosidase Inhibitors”Bioorg. Med.
Chem. 2008, 16, 7185-7192.
8. Foley, Nicholas A.; Ke, Zhuofeng; Gunnoe, T. Brent*; Cundari, Thomas R.*; and Petersen, Jeffrey
L.“Aromatic C-H Activation and Catalytic Hydrophenylation of Ethylene by TpRu{P(OCH2)3CEt}(NCMe)Ph”Organometallics 2008, 27, 3007-3017.
9. Guo, Zhen; Ke, Zhuofeng; Phillips, David Lee*; Zhao, Cunyuan*.“Intrinsic Reaction Coordinate
Analysis of the Activation of CH4 by Molybdenum atoms: A Density Functional Theory Study of the
Crossing Seams of the Potential Energy Surfaces”Organometallics 2008, 27, 181-188.
10. Gao, Haiyang; Ke, Zhuofeng; Pei, Lixia; Song, Keming; Wu, Qing*.“Drastic ligand electronic effecton anilidoeimino nickel catalysts toward ethylene polymerization”Polymer 2007, 48, 7249-7254.
11.Lin, Xufeng; Zhao, Cunyuan; Che, Chi-Ming*; Ke, Zhuofeng; Phillips, David Lee.“A DFT Study on
the Mechanism of Rh2II,II-Catalyzed Intramolecular Amidation of Carbamates”Chem. Asian J. 2007,
2, 1101-1108
12.Ke, Zhuofeng; Zhou, Yubing; Gao, Hui; Zhao, Cunyuan*, Phillips, David Lee.“On the Mechanismand Stereochemistry of Chiral Lithium Carbenoid Promoted Cyclopropanation Reactions”Chem. Eur.
J. 2007, 13, 6724-6731.
13.Fang, Ran; Ke, Zhuofeng; Shen, Yong; Zhao, Cunyuan*; Phillips, David Lee.“Concurrent Cyclopropanation by Carbenes and Carbanions? A Density Functional Theory Study on the Reaction Pathways”J. Org. Chem. 2007, 72, 5139−5145.
14.Ke, Zhuofeng; Zhao, Cunyuan*; Phillips, David Lee.“Methylene Transfer or Carbometalation? A
Theoretical Study to Determine the Mechanism of Lithium Carbenoid Promoted Cyclopropanation
Reactions in Aggregation and Solvation States.”J. Org. Chem. 2007, 72, 848−860.

【学術関係の受賞など】 Sun Yat-sen University Fellow 2009
State Scholarship Funds, China Scholarship Council (CSC) 2007
－ 23 －

Ⅱ 博士研究員 (2010)【氏名】 Joonghan Kim【職名】 FIFC Fellow【所属】 Fukui Kenichi Memorial Research Group 1, Fukui Institute for Fundamental
Chemistry【研究室】 Room

216

【直通電話】 075-711-7708【FAX】 075-781-4757【電子メールアドレス】 Joonghan@fukui.kyoto-u.ac.jp; quatum99@gmail.com【研究分野】 Computational Chemistry【現在の研究課題】 DFTB-MD simulation of chirality controlled carbon nanotube growth,
determination of local chirality of carbon nanotube【研究内容キーワード】 Carbon nanotube, density-functional tight-binding, chirality【学歴】 2004 B. Sc., Hanyang University, Seoul, Korea
2010 Ph. D., KAIST, Daejeon, Korea【学位】 Doctor of Philosophy, KAIST, Daejeon, Korea【略歴】 2010, Postdoctoral fellow, KAIST, Daejeon, Korea【所属学会】 Korean Chemical Society【主な著書、学術論文】 1. Qingyu Kong, Michael Wulff, Savo Bratos, Rudolphe Vuilleumier, Joonghan（過去5年以内）
Kim and Hyotcherl Ihee,“Structure of the Photodissociation Products of CCl4,
CBr4 and CI4 in Solution Studied by DFT and Ab Initio Calculations”, J. Phys.
Chem. A 110, 11178-11187 (2006).
2. Joonghan Kim, Yoon Sup Lee and Hyotcherl Ihee,“Density Functional and
Ab Initio Studies on Structures and Energies of the Ground State of CrCO”,
Int. J. Quant. Chem. 107, 458 (2007).
3. Joonghan Kim, Tae Kyu Kim, Jangbae Kim, Yoon Sup Lee and Hyotcherl
Ihee,“Density Functional and Ab Initio Study of Cr(CO)n (n = 1−6) Complexes”, J. Phys. Chem. A 111, 4697-4710 (2007).
4. Joonghan Kim, Sunhong Jun, Jeongho Kim and Hyotcherl Ihee,“Density
Functional and Ab Initio Investigation of CF2 ICF2I and CF2 CF2I Radicals in
Gas and Solution Phases”, J. Phys. Chem. A 113, 11059-11066 (2009).
5. Joonghan Kim, Tae Kyu Kim and Hyotcherl Ihee,“Theoretical Study on theReaction of Ti+ with Acetone and the Role of Intersystem Crossing”, J. Phys.
Chem. A 113, 11382-11389 (2009).
6. Jeewon Kang, Joonghan Kim, Hyotcherl Ihee and Yoon Sup Lee,“Molecular
Structures, Energetics and Electronic Properties of Neutral and Charged Hgn
Clusters (n= 2-8)”, J. Phys. Chem. A 114, 5630-5639 (2010).
7. Joonghan Kim, Hyotcherl Ihee and Yoon Sup Lee,“Spin-Orbit Density Functional and Ab Initio Study of HgX n (X=F, Cl, Br, and I; n=1, 2, and 4)”, J.
Chem. Phys. 133, 144309 (2010).
8. Joonghan Kim, Hyotcherl Ihee and Yoon Sup Lee,“Spin-orbit ab initio studyof two low-lying states of chloroiodomethane cation”, Theor. Chem. Acc. 129,343-347 (2011).
9. Joonghan Kim, Tae Kyu Kim and Hyotcherl Ihee,“Density Functional andSpin-Orbit Ab Initio Study of CF3Br: Molecular Properties and Electronic
Curve-Crossing”, J. Phys. Chem. A 115, 1264-1271 (2011).
10.Joonghan Kim and Hyotcherl Ihee,“Theoretical Study on the Reaction of
Butadiynyl Radical (C4H) with Ethylene (C2H4) to Form C6H4 and H”, Int. J.
Quant. Chem. DOI : 10. 1002/qua. 23/47.

－ 24 －

Ⅱ 博士研究員 (2010)【氏名】 Alister Page
【職名】 FIFC Fellow【所属】 Fukui Kenichi Memorial Research Group 1, Fukui Institute for Fundamental
Chemistry【研究室】 Room

03

【直通電話】 075-711-7831【FAX】 095-781-4757【電子メールアドレス】 alisterpage@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Molecular Dynamics simulations and electronic structure calculations of
nanoscale self-assembly processes (in particular, carbon nanotube nucleation andgrowth).
【研究内容キーワード】 Single-walled carbon nanotube, self-assembly, nucleation, growth, healing, (n,m)
chirality, density-functional tight-binding【学歴】 2004, Bachelor of Mathematics (Honours Class I), The University of Newcastle,
Australia
2004, Bachelor of Science (Honours Class I), The University of Newcastle,
Australia
2008, Doctor of Philosophy, The University of Newcastle, Australia【学位】 Doctor of Philosophy, The University of Newcastle, Australia【略歴】 2008, Postdoctoral Research Associate, Priority Research Centre for Energy,
Department of Chemical Engineering, The University of Newcastle,
Australia
2009-2010, CREST Postdoctoral Research Fellow, Fukui Institute for
Fundamental Chemistry, Kyoto University, Japan【所属学会】 American Chemical Society, Royal Australian Chemistry Institute【主な著書、学術論文】 1. A. J. Page, K.R.S. Chandrakumar, S. Irle, K. Morokuma,“SWNT Nucleation（過去5年以内from Carbon-Coated SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism”,
J. Am. Chem. Soc., 132, 15699, (2011)
2. A. J. Page, Y. Ohta, S. Irle, K. Morokuma,“Mechanisms of Single-Walled Carbon Nanotube Nucleation, Growth and Healing Determined using QM/MD
Methods”, Acc. Chem. Res., 43, 1375, (2010)
3. A. J. Page, Y. Ohta, Y. Okamoto, S. Irle, K. Morokuma,“Defect Healing During Single-Walled Carbon Nanotube Growth: A Density-Functional TightBinding Molecular Dynamics Investigation”, J. Phys. Chem. C, 113, 20198,(2009)
4. A. J. Page, B. Moghtaderi,“Molecular Dynamics Simulation of the Low-Temperature Partial Oxidation of CH4”, J. Phys. Chem. A, 20, 1539, (2009)
5. A. J. Page, E. I. von Nagy-Felsobuki,“Rovibrational Spectra of LiH2+, LiHD+, J. Phys. Chem. A, 111,
and LiD2+ Determined using FCI Property Surfaces”
4478, (2007)【学術関係の受賞など】 Australian Post-Graduate Award (2005-2008)
RACI Chemistry Honours Prize (2004)
Deans Medal, Faculty of Science and IT, The University of Newcastle (2004)－ 25 －

Ⅱ 博士研究員 (2010)【氏名】 Xin Li【職名】 JST Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room212

【直通電話】 075-711-7647【電子メールアドレス】 lixin@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 1. Radical Reaction Mechanism in B12-Dependent Methylmalonyl-CoA Mutase
2. Reversibly Photoswitchable Fluorescent Protein: Dronpa
3. Irreversible Photoconversion Fluorescent Protein: Kaede【研究内容キーワード】 Reaction mechanisms of metalloenzymes and photobiology【学歴】 June 2005, Ph. D., College of Chemistry, Liaoning Normal University【学位】 Ph. D. in Physical Chemistry from Liaoning Normal University【略歴】 July 2005-May 2007, Postdoctoral Fellow, Peking University【主な著書、学術論文】 1. Ling Xu, Xin Li, et al.,“Ion-Specific Swelling of Poly (Styrene Sulfonic Acid)（過去5年以内）
Hydrogel”, J. Phys. Chem. B 111(13), 3391-3397 (2007).
2. Fu-Qiang Shi, Xin Li, et al.,“DFT Study of the Mechanisms of In Water
Au(I)-Catalyzed Tandem [3,3]-Rearrangement/Nazarov Reaction/[1,2]-Hydrogen Shift of Enynyl Acetates: A Proton-Transport Catalysis Strategy in the
Water-Catalyzed [1,2]-Hydrogen Shift”, J. Am. Chem. Soc. 129, 15503-15512(2007).
3. Xin Li, Si-Yu Ye, Chuan He, and Zhi-Xiang Yu,“Mechanisms of Brønsted
Acid Catalyzed Additions of Phenols and Protected Amines to Olefins: A DFTStudy”, Eur. J. Org. Chem. 4296-4303 (2008).
4. Lung Wa Chung, Xin Li, Hiroshi Sugimoto, Yoshitsugu Shiro, Keiji. Morokuma,“A DFT Study on a Missing Piece in Understanding of Heme Chemistry:
The Reaction Mechanism for Indoleamine 2,3-Dioxygenase (IDO) and Tryptophan 2,3-Dioxygenase (TDO)”, J. Am. Chem. Soc. 131, 12298 (2008).
5. Xin Li, Lung Wa Chung, Piotr Paneth, and Keiji Morokuma,“DFT and
ONIOM(DFT:MM) Studies on Co-C Bond Cleavage and Hydrogen Transfer
in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism?”, J. Am. Chem. Soc. 131, 5115-5125 (2009).
6. Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma,“A Theoretical Study on the Nature of On- and Off-States of Reversibly
Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation and Raman”, J. Phys. Chem. B 114, 1114-1126 (2010).
7. Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma,“Primary Events of Photodynamics in Reversible Photoswitching Fluorescent Protein Dronpa”, J. Phys. Chem. Lett. 1, 3328-3333 (2010).
8. Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma,“Competitive Mechanistic Pathways for Green-to-Red Photoconversion
in the Fluorescent Protein Kaede: A Computational Study”, J. Phys. Chem. B
114, 16666-16675 (2010).
【学術関係の受賞など】 Postdoctoral Science Fund of China in Peking University, 2006.

－ 26 －

Ⅱ 博士研究員 (2010)【氏名】 K. R. S. Chandrakumar【職名】 JST fellow【所属】

Fukui Kenichi Memorial Research Group 1, Fukui Institute for Fundamental
Chemistry【研究室】 Room

203

【直通電話】 075-711-7834【FAX】 075-781-4757【電子メールアドレス】 krsc@fukui.kyoto-u.ac.jp;
krschandrakumar@gmail.com【研究分野】 Computational Chemistry【現在の研究課題】 DFTB-MD simulation of carbon nanotube growth from the metal decorated
carbon nanocones【研究内容キーワード】 carbon nanotube, nanocones, self-assembly, nanocapsules, density-functionaltight-binding【学歴】 B.Sc., with distinction, Madurai Kamaraj University, (General Chemistry with
Physics and Mathematics as ancillary subjects) 1994
M.Sc., with first class, Madurai Kamaraj University, (specialization in Physical
Chemistry) 1996
Ph.D., Pune University, National Chemical Laboratory, 2003
Thesis Title: Theoretical studies on some aspects of chemical reactivity using
density based descriptors.
【学位】 Doctor of Philosophy, Pune University, National Chemical Laboratory【略歴】 Since 2004, working as a Scientific Officer at Bhabha Atomic Research Centre,India【所属学会】 Chemical Research Society of India.
【主な著書、学術論文】 1. A. J. Page, K. R. S. Chandrakumar, S. Irle, and K. Morokuma,“SWNT Nucle（過去5年以内）
ation from Carbon-Coated SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism”, J. Am. Chem. Soc. 2011, 133, 621-628
2. A. J. Page, K. R. S. Chandrakumar, S. Irle, and K. Morokuma,“Do SiO2 andCarbon-Doped SiO2 Nanoparticles Melt? Insights from QM/MD Simulations
and Ramifications Regarding Carbon Nanotube Growth”, Chem. Phys. Lett.
doi:10.1016/j.cplett.2011.01.075
3. N. K. Jena, K. R. S. Chandrakumar and S. K. Ghosh,“Theoretical Investigation on the Structure and Electronic Properties of Hydrogen- and Alkali-MetalDoped Gold Clusters and Their Interaction with CO: Enhanced Reactivity ofHydrogen-Doped Gold Clusters”, J. Phys. Chem. C, 2009, 113, 17885-17892.
4. K. R. S. Chandrakumar, K. Srinivasu and S. K. Ghosh,“Nanoscale Curvature
Induced Hydrogen Adsorption in Alkali Metal Doped Carbon Nanomaterials”,
J. Phys. Chem. C, 2008, 112, 15670-15679.
5. K. R. S. Chandrakumar and S. K. Ghosh,“Alkali-Metal-Induced Enhancement, Nano Lett. 2008,of Hydrogen Adsorption in C60 Fullerene:An ab initio Study”
8, 13-19.
【学術関係の受賞など】 Indo-European Collaborative Project Grant (FP7); Project Title: Modeling of
Nano-scaled Advanced Materials Intelligently (MONAMI)
Young Scientist Award in 2008 from Department of Atomic Energy (DAE)
Young Scientist Medal Award in 2005 from the Indian National Science Academy(INSA)－ 27 －

Ⅱ 博士研究員 (2010)【氏名】 Fengyi Liu【職名】 JST Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

207

【直通電話】 075-711-7893【電子メールアドレス】 fengyiliu@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Theoretical calculation of molecular motor and switch【研究内容キーワード】 Artificial/biological molecular motor, molecular switch【学歴】 Jun. 1998, B. Sc. in Chemistry, Hebei Normal University, China
Jun. 2001, M. Sc. in Chemistry, Hebei Normal University, China
Dec. 2005, Ph.D. in Chemistry, Beijing University of Chemical Technology,
China【学位】 Ph. D. in Applied Chemistry, Beijing University of Chemical Technology【略歴】 Sep. 2007-Jun. 2009, Postdoctoral researcher, Lund University, Sweden【主な著書、学術論文】 1. Fengyi Liu and Keiji Morokuma, Rationalization of Light-Driven Rotary Mo（過去5年以内）
lecular Motor: An Theoretical Study on the Photoisomerization of an Stiff Stilbene, manuscript in preparation.
2. Fengyi Liu, Yajun liu, Luca De Vico, Roland Lindh, A CASSCF/CASPT2Approach to the Decomposition of Thiazole-Substituted Dioxetanone: Substitution Effects and Charge-Transfer Induced Electron Excitation, Chem. Phys.
Lett. 2009,484,69-75.
3. Fengyi Liu, Yajun Liu, Luca De Vico, Roland Lindh, Theoretical Study of the
Chemiluminescent Decomposition of Dioxetanone, J. Am. Chem. Soc., 2009,
131, 6181-6188.
4. Shu-Feng Chen,Feng-Yi Liu, Ya-Jun Liu, An ab initio investigation of themechanisms of photodissociation in bromobenzene and iodobenzene, J. Chem.
Phys., 2009, 131, 124304.
5. Fengyi Liu, Lingpeng Meng, Shijun Zheng, Small Fullerenes with BN Belts: a
Density Functional Theory Investigation, J. Phys. Chem. B, 2006, 110, 66666672.
6. Fengyi Liu, Lingpeng Meng, Zheng Sun, Shijun Zheng, Insights into the Mechanism of BN Generation via Boron Triazide Precursor: A Theoretical Study, J.
Phys. Chem. A, 2006, 110, 10591-10600.

－ 28 －

Ⅱ 博士研究員 (2010)【氏名】 Parameswaran Pattiyil【職名】 Assistant Professor【所属】 National Institute of Technology【研究室】 Department of Chemistry, NIT Calicut, Kerala, India【直通電話】 0091-9400282159【電子メールアドレス】 param@nitc.ac.in【ホームページ】 http://nitc.ac.in/index.php/?url=users/view/283/15/3【研究分野】 Computational Chemistry【現在の研究課題】 Electronic structure calculations and molecular dynamics simulations ofmolecules, clusters and solids【研究内容キーワード】 Dynamics, DFTB, nanowire, growth, DFT【学歴】 1998, Bachelor of Sci., St. Thomas’College, Thrissur, University of Calicut
2000, Master of Sci., St. Thomas’College, Thrissur, University of Calicut【学位】 Ph. D in Chemistry from University of Hyderabad【略歴】 Mar. 2007 - Oct. 2007 : Research Associate, Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore
Nov. 2007 - Sept. 2009 : Alexander von Humboldt Research Fellow, PhilippsUniversität Marburg, Germany
Oct. 2009 - June 2010 : Postdoctoral Research Fellow, Fukui Institute for Fundamental Chemistry, Kyoto University
July 2010- Till date : Assistant Professor, Department of Chemistry, NIT Calicut【主な著書、学術論文】 1. Melaimi, M.; Parameswaran, P.; Donnadieu, B.; Frenking, G.; Bertrand. G.
（過去5年以内） “Synthesis and Ligand Properties of a Persistent All-Carbon Four-Membered
Ring Allene”, Angew. Chem. Int. Ed. 48, 4792-4795 (2009).
2. P a r a m e s w a r a n , P . ; F r e n k i n g , G . “ T r a n s i t i o n M e t a l C o m p l e x e s[(PMe3)2Cl2M(E)] and [(PMe3)2(CO)2M(E)] with Naked Group 14 Atoms (E= C - Sn) as Ligands; Part 1: Parent Compounds”, Chem. Eur. J. 15, 8807-8816(2009).
3. P a r a m e s w a r a n , P . ; F r e n k i n g , G . “ T r a n s i t i o n M e t a l C o m p l e x e s[(PMe3)2Cl2M(E)] and [(PMe3)2(CO)2M(E)] with Naked Group 14 Atoms (E, Chem. Eur. J. 15,= C - Sn) as Ligands; Part 2: Complexation with W(CO)5”
8817-8824 (2009).
4. Aldeco-Perez, E.; Rosenthal, A.; Donnadieu, B.; Parameswaran, P.; Frenking,G.; Bertrand. G..“Isolation of a C-5-Deprotonated Imidazolium, a Crystalline
Abnormal N-Heterocyclic Carbene”, Science, 326, 556-559 (2009).
5. Back, O.; Donnadieu, B.; Parameswaran, P.; Frenking, G.; Bertrand. G.“Isolation of Crystalline Carbene-Stabilized P2-Radical Cations and P2-Dication”,
Nature Chemistry, 2, 369-373 (2010).
【学術関係の受賞など】 Alexander von Humboldt Research Fellow 2007-2009－ 29 －

Ⅱ 博士研究員 (2010)【氏名】 Hong-Yan Xiao
【職名】 JST Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

208

【直通電話】 075-711-7894【電子メールアドレス】 hyxiao@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Exploring photodissociation mechanism of small molecules by GRRM and AFIR
programs【研究内容キーワード】 Photodissociation, excited state, conical intersection, nonadiabatic transition【学歴】 Jun. 2002, B. Sc. in Chemistry, Liaoning Normal University, China
Jun. 2005, M. Sc. in Physical Chemistry, Liaoning Normal University, China
Jun. 2008, Ph.D. in Physical Chemistry, Beijing Normal University, China【学位】 Ph. D. in Physical Chemistry, Beijing Normal University【略歴】 Since July 2008, working as an assistant researcher at Technical Institute ofPhysics and Chemistry, Chinese Academy of Science【主な著書、学術論文】 1. Hong-Yan Xiao, Jun Cao, Ya-Jun Liu, Wei-Hai Fang, Hiroto Tachikawa,
Masaru Shiotani. Structures and cis-to-trans photoisomerization of hexafluoro（過去5年以内
1,3-butadiene radical cation: electron spin resonance and computational studies.
J. Phys. Chem. A 111, 5192-5200 (2007)
2. Hong-Yan Xiao, Ya-Jun Liu, Wei-Hai Fang. Multireference theoretical investigation on selectivity of the bond fissions in photodissociation of acetyl cyanide.
J. Chem. Phys. 127, 244313-1~244313-7 (2007)
3. Ya-Jun Liu, Hong-Yan Xiao, Meng-Tao Sun, Wei-Hai Fang. Spin-orbit abinitio investigation of the photodissociation of dibromomethane in the gas andsolution phases. J. Comput. Chem. 29, 2513-2519 (2008)
4. Isabelle Navizet, Ya-Jun Liu, Nicolas Ferré, Hong-Yan Xiao, Wei-Hai Fang
and Roland Lindh. Color-tuning mechanism of firefly investigated by multiconfigurational perturbation method. J. Am. Chem. Soc. 132, 706-712 (2010)
5. Hong-Yan Xiao, Zhen Zhen, Huan-Quan Sun, Xu-Long Cao, Zhen-Quan Li,
Xin-Wang Song, Xiao-Hong Cui and Xin-Hou Liu. Molecular dynamics simulation of anionic surfactant at the water/n-alkane interface. Acta Phys. -Chim.
Sin. 26, 422-428 (2010)
6. Hong-Yan Xiao, Satoshi Maeda and Keiji Morokuma. Excited-state roaming
dynamics in photolysis of a nitrate radical. J. Phys. Chem. Lett. 2, 934-938 (2011)【学術関係の受賞など】 Qiu Shi Graduate Student Scholarship in Beijing Normal University (2007)
National Natural Science Foundation of China (2010)－ 30 －

Ⅱ 博士研究員 (2010)【氏名】 Lina Ding
【職名】 JST Fellow【所属】 Fukui Institute For Fundamental Chemistry【研究室】 Room212

【直通電話】 075-711-7631【FAX】 075-781-4757【電子メールアドレス】 ding@fukui.kyoto-u.ac.jp【現在の研究課題】 Photobiology【研究内容キーワード】 Reaction mechanism of photobiology【学歴】 Jun. 2004, B. Sc. in Chemistry, Zhengzhou University, China
Jun. 2007, M. Sc. in Organic Chemistry, Zhengzhou University, China
Jun. 2010, Ph.D. in Physical Chemistry, Beijing Normal University, China【学位】 Ph.D. in Physical Chemistry, Beijing Normal University, China【主な著書、学術論文】 1. Lina Ding, Wei-Hai Fang*, Exploring Light-Induced Decarboxylation Mecha（過去5年以内）
nism of o-Acetylphenyl-Acetic Acid from the Combined CASSCF and DFT
Studies, J. Org. Chem. 2010, 75, 1630-1636.
2. Lina Ding, Lin Shen, Xue-Bo Chen, Wei-Hai Fang*, Solvent Effects on photoreactivity of Valerophenone: A Combined QM and MM Study, J. Org. Chem.
Featured Article 2009, 74, 8956-8962.
3. Lina Ding, Xue-Bo Chen*, Wei-Hai Fang*, Ultrafast Asynchronous Concerted
Excited-State Intramolecular Proton Transfer and Photodecarboxylation of oAcetylphenylacetic Acid Explored by Combined CASPT2 and CASSCF Studies, Org. Lett. 2009, 11(7), 1495-1498.
4. Ganglong Cui, Lina Ding, Feng Feng, Yajun Liu, and Weihai Fang, Insights
into Mechanistic Photochemistry of Urea, J. Chem. Phys. 2010, 132, 194308;【学術関係の受賞など】 Beijing Normal University, Academic Excellence Award, 2009.
Beijing Normal University, Scientific Achievement Award, 2010.

－ 31 －

Ⅱ 博士研究員 (2010)【氏名】 Haibei Li【職名】 JST Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

203

【直通電話】 075-711-7834【電子メールアドレス】 hpli@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 MD simulations of the formation and growth of carbon nanostructures:
fullerenes, and nanotubes【研究内容キーワード】

Fullerene, Hydrocarbon combustions, Self-assembly, Single-walled carbon
nanotube, Chirality, Density-functional tight-bingding【学歴】 2004, Bachelor of Chemistry, Qufu Normal University, China
2007, Master of Chemical Physics, University of Science and Technology ofChina, China
2010, Doctor of Chemical Physics, University of Science and Technology ofChina, China【学位】 Doctor of Chemical Physics, University of Science and Technology of China【主な著書、学術論文】 1. Haibei Li, Shanxi Tian, and Jinlong Yang. Theoretical study of the stepwise（過去5年以内）
protonation of the dioxo Manganese (V) porphyrin, J. Phys. Chem. B, 112,
15807, 2008
2. Haibei Li, Shanxi Tian, and Jinlong Yang. Chemical bonds and electronic
strucures of the methonium cations CH62+ and CH73+, J. Theor. Comp. Chem. 7,
139, 2008
3. Haibei Li, Yubin Bai, Shanxi Tian, and Jinlong Yang. Electron topological andenergetic study of the intermolecular non-hydrogen bonding interactions incomplexes H2O M (M=F2, ClF, and CF4), J. Theor. Comp. Chem. 8, 615, 2009
4. Haibei Li, Shanxi Tian, and Jinlong Yang. Propene oxidation with anionic cluster V4O11 − : selective epoxidation, Chem. Eur. J (communications) 15, 10747,
2009
5. Haibei Li, Shanxi Tian, and Jinlong Yang. Propene oxidation on V4O11− cluster:reaction dynamics to acrolein, J. Phys. Chem. A, 114, 6542, 2010

【学術関係の受賞など】 Qiu Shi Graduate Student Scholarship (2009)
Supported by the Scientific Research Foundation of Graduate School of USTC
(2008)－ 32 －

Ⅱ 博士研究員 (2010)【氏名】 Lung Wa Chung【職名】 FIFC Fellow (till Oct 2011); JST Fellow (Oct 2011-)
Fukui Kennichi Memorial Research Group 1, Fukui Institute For Fundamental【所属】
Chemistry【研究室】 Room 212【直通電話】 075-711-7631【電子メールアドレス】 chung@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry, Biochemistry and Biophysics【現在の研究課題】 Metalloenzymes, photobiology, multi-scale simulations
Reaction mechanism of metalloenzymes, photobiology, bio-inspired systems and【研究内容キーワード】
catalysis; multi-scale simulations development【学歴】 Aug. 2000, B.Sc. in Chemistry (1st Hon.), The Hong Kong University of Science& Technology;
Aug. 2003, M. Phil. in Chemistry, The Hong Kong University of Science &Technology;
Aug. 2006, Ph. D. in Chemistry, The Hong Kong University of Science &Technology【学位】 Ph. D. in chemistry, The Hong Kong University of Science & Technology【主な著書、学術論文】 1. Chung, L. W.; Li, X.; Sugimoto, H.; Shiro, Y.; Morokuma, K.“A DFT Studyon a Missing Piece in Understanding of Heme Chemistry: The Reaction Mecha（過去5年以内）
nism for Indoleamine 2,3-Dioxygenase (IDO) and Tryptophan 2,3-Dioxygenase(TDO)”, J. Am. Chem. Soc. 2008, 130, 12298.
2. Chung, L. W.; Hayashi, S.; Lundberg, M.; Nakatsu, T.; Kato, H.; Morokuma, K.
“Mechanism of Efficient Firefly Bioluminescence via Adiabatic Transition Stateand Seam of Sloped Conical Intersection”, J. Am. Chem. Soc. 2008, 130, 12880.
3. Li.X.; Chung, L. W.; Paneth, P.; Morokuma, K.“DFT and ONIOM(DFT:MM)
Studies on Co-C Bond Cleavage and Hydrogen Transfer in B12-Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism?”, J. Am. Chem. Soc.
2009, 131, 5115.
4. Li. X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K.“A Theoretical
Study on the Natures of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation and Raman”, J. Phys.
Chem. B 2010, 114, 1114
5. Noda, S.; Nakamura, A.; Kochi, T.; Chung, L. W.; Morokuma, K.; Nozaki, K.
“Mechanistic Studies on the Formation of Linear Polyethylene Chain Catalyzed
by Palladium Phosphine-Sulfonate Complexes: Experiment and Theoretical Studies”, J. Am. Chem. Soc. 2009, 131, 14088
6. Chung, L. W.; Li, X.; Sugimoto, H.; Shiro, Y.; Morokuma, K.“ONIOM Study ona Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan
2,3-Dioxygenase with Dual Oxidants”, J. Am. Chem. Soc. 2010, 115, 11993.
7. Nozaki, K.; Kusumoto, S.; Noda, S.; Kochi, T.; Chung, L. W.; Morokuma, K.;“Why Did Incorporation of Acrylonitrile to a Linear Polyethylene Become Possible? Comparison of Phosphine‒Sulfonate Ligand with Diphosphine and Imine‒
Phenolate Ligands in the Pd-Catalyzed Ethyelene/Acrylonitrile Copolymerization”, J. Am. Chem. Soc. 2010, 132, 16030.
8. Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K.“Primary Eventsof Photodynamic in Reversibly Photoswitching Fluorescent Protein Dronpa”, J.
Phys. Chem. Lett. 2010, 1, 3328.
9. Nakamura, A.; Munakata, K.; Ito, S.; Kochi, T.; Chung, L. W.; Morokuma, K.;
Nozaki, K. “Pd-Catalyzed Copolymerization of Methyl Acrylate with Carbon
Monoxide: Structures, Properties and Mechanistic Aspects toward Ligand Design”, J. Am. Chem. Soc. 2011, 133, 6761.
10. Chung, L. W.; Hirao, H.; Li, X.; Morokuma, K.“The ONIOM Method: Its
Foundation and Applications to Metalloenzymes and Photobiology”, WIREs
Comput. Mol. Sci. 2011, doi: 10.1002/wcm. 85－ 33 －

Ⅱ 博士研究員 (2010)【氏名】 Galina Petrova【職名】 JST Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

214

【直通電話】 075-711-7838【電子メールアドレス】 petrova@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Hetero- and homogeneous catalysis【研究内容キーワード】 Metalloenzymes, reaction mechanism, transition metal clusters, zeolites【学歴】 2009, Ph.D. degree in Organic chemistry, University of Sofia, Bulgaria
2003, B.Sc. in Chemistry (Theoretical and physical chemistry), University of
Sofia, Bulgaria【学位】 Ph.D. in Organic chemistry, University of Sofia, Bulgaria【略歴】 02-11/2010, Postdoctoral Scholar at the Faculty of Chemistry, University of Sofia
06/2009-01/2010, Postdoctoral Scholar at the Faculty of Chemistry, University of
Sofia & Excellence Centre for Advanced Materials UNION
7/2008-5/2009, Research chemist at the Faculty of Chemistry, University of Sofia【所属学会】 Bulgarian Catalytic Club, Bulgarian Zeolite Association【主な著書、学術論文】 1. N. Rösch, G. P. Petrova, P. St. Petkov, A. Genest, S. Krüger, H. A. Aleksan（過去5年以内）
drov, G. N. Vayssilov,“Impurity Atoms on Small Transition Metal Clusters.
Insights from Density Functional Model Studies”, Topics in Catalysis, 54, 363377 (2011).
2. M. A. Rangelov, G. P. Petrova, V. M. Yomtova, G. N. Vayssilov,“Catalytic
Role of Vicinal OH in Ester Aminolysis - Proton Shuttle versus HydrogenBonds Stabilization”, J. Org. Chem., 75, 6782-6792 (2010).
3. G. P. Petrova, G. N. Vayssilov, N. Rösch,“Redox behavior of small metalclusters with respect to hydrogen. The effect of the cluster charge from density
functional results”, Phys. Chem. Chem. Phys., 12, 11015-11020 (2010).
4. G. P. Petrova, G. N. Vayssilov, N. Rösch,“Hydrogen Adsorption on ZeoliteSupported Tetrairidium Clusters. Thermodynamic Modeling from Density
Functional Calculations”, J. Phys. Chem. C, 112, 18572-18577 (2008).
5. G. N. Vayssilov, H. A. Aleksandrov, G. P. Petrova, P. St. Petkov,“Computational Modelling of Nanoporous Materials”, Chapter 8 in Ordered Porous
Solids; Valtchev, Mintova, Tsapatsis (Eds.), Elsevier, Amsterdam, pp. 209-236(2008).
6. G. P. Petrova, G. N. Vayssilov, N. Rösch,“Density Functional Modeling of Reverse Hydrogen Spillover on Zeolite-Supported Tetrairidum Clusters”, Chem.
Phys. Lett., 444, 215-219 (2007).
【学術関係の受賞など】 Student award for high academic achievements of the Foundation for support ofthe Bulgarian Higher Education named after Prof. Michael Klett (2003)－ 34 －

Ⅱ 博士研究員 (2010)【氏名】 Wilfredo Credo Chung【職名】 FIFC Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

209

【直通電話】 075 711 7902
【FAX】 075 781 4757
【電子メールアドレス】 wchung@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Theoretical elucidation of reaction mechanisms and dynamics of important
molecules in the electronic ground and excited states【研究内容キーワード】 Ptential energy surface, wave packet dynamics, conical intersection, diabatic
representation, QM/MM【学歴】 March 1991, Bachelor of Science in Chemical Engineering, University of San
Carlos, Cebu City, Philippines
October 1999, Master of Science in Chemistry, Mindanao State University−Iligan
Institute of Technology, Iligan City, Philippines
March 2007, Doctor of Science, Graduate School of Science, Tohoku University【学位】 Doctor of Science, Tohoku University【略歴】 March 1992 − June 1993 Research and Development Chemist, Treasure Island
Industrial Corporation, Cebu City, Philippines
June 1994 − October 1996 Lecturer, Colleges of Arts, Sciences and Engineering,Saint Joseph Institute of Technology, Butuan City, Philippines
November 1996 − March 2003 Lecturer, Department of Chemistry, Northern
Mindanao State Institute of Science and Technology, Butuan City,
Philippines
August 2007 − September 2007 Postdoctoral Fellow, Laboratory of Theoretical
Chemistry, Tohoku University
October 2007 − present Center Fellow, Fukui Institute for Fundamental
Chemistry, Kyoto University【所属学会】 Chemical Society of Japan, Japan Society for Molecular Science, Chemical
Society of the Philipines, Samahang Pisika ng Visayas at Mindanao【主な著書、学術論文】 1. W. C. Chung, Z. Lan, Y. Ohtsuki, N. Shimakura, W. Domcke and Y. Fujimura,
Conical intersections involving the dissociative 1 π σ * state in 9H-adenine:（過去5年以内）a quantum chemical ab initio study, Phys. Chem. Chem. Phys. 9, 2075-2084(2007).
2. M. Yamaki, K. Hoki, T. Teranishi, W. C. Chung, F. Pichierri, H. Kono and Y.
Fujimura, Theoretical design of an aromatic hydrocarbon rotor driven by a circularly polarized electric field, J. Phys. Chem. A, 111, 9374-9378 (2007).
3. W. M. I. Hassan, W. C. Chung, N. Shimakura, S. Koseki, H. Kono and Y. Fujimura Ultrafast radiationless transition pathways through conical intersections
in photo-excited 9H-adenine, Phys. Chem. Chem. Phys., 12, 5317-5328 (2010).
4. W. C. Chung, S. Nanbu and T. Ishida, Nonadiabatic ab initio dynamics of amodel protonated Schiff base of 9-cis retinal, J. Phys. Chem. A 114, 8190-8201(2010).
－ 35 －

Ⅱ 博士研究員 (2010)【氏名（ふりがな）】 Takafumi Iwaki （たかふみいわき）【職名】 FIFC Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room

209

【直通電話】 075-711-7902【電子メールアドレス】 iwaki@fukui.kyoto-u.ac.jp【研究分野】 Soft Matter, Biological Physics【現在の研究課題】 Interfacial Phenomena, Simulation Method【研究内容キーワード】 Polyelectrolyte, DNA folding transition, Thermofluid, Photophoresis【学歴】 March 2001, Master of Sci., Graduate School of Science, Kyoto University
March 2004, Doctor of Sci., Graduate School of Science, Kyoto University【学位】 Doctor of Science from Kyoto University【略歴】 Apr. 2004, Postdoctoral Fellow at The City University of New York, USA
Apr. 2005, Okayama Institute for Quantum Physics【所属学会】 The Physical Society of Japan【主な著書、学術論文】 1. T. Iwaki, N. Makita and K. Yoshikawa,“Folding transition of a single semi（過去5年以内）
flexible polyelectrolyte chain through toroidal bundling of loop structures”,
The Journal of Chemical Physics 129(6), 065103 (13 pages) (2008)
2. T. Saito, T. Iwaki, and K. Yoshikawa,“DNA compaction induced by neutralpolymer is retarded more effectively by divalent anion than monovalent anion”,
Chemical Physics Letters 465(1-3), 40-44(2008)
3. T. Saito, T. Iwaki, and K. Yoshikawa,“Small anion with higher valency retards
the compaction of DNA in the presence of multivalent cation”, BiophysicalJournal 96(3), 1068-1075 (2009)
4. S Araki, K. Hizume, T. Iwaki, Y. Suzuki, K. Takeyasu, and K. Yoshikawa,“Nucleosomal arrays reconstituted from ring and linear DNA”, Chemical
Physics Letters 479, 284-289 (2009)
5. T. Iwaki,“Effect of internal flow on the photophoresis of a micron-sized liquid
droplet”, Physical Review E 81, 066315 (13 pages) (2010)－ 36 －

Ⅱ 博士研究員 (2010)【氏名（ふりがな）】 池野

豪一 （いけのひでかず）【職名】 福井センターフェロー【所属】 福井謙一記念研究センター【研究室】 福井謙一記念研究センター

204【直通電話】 075-711-7863【FAX】 075-781-4757【電子メールアドレス】 ikeno@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~ikeno【研究分野】 計算材料化学・電子分光の理論【現在の研究課題】 電子分光法の理論および第一原理計算による解析【研究内容キーワード】 X線分光・電子線エネルギー損失分光・多重項・強相関【学歴】 京都大学大学院工学研究科材料工学専攻博士後期課程修了【学位】 2007年3月 京都大学 博士（工学）【略歴】 2007年4月 - 2009年3月 京都大学大学院工学研究科 博士研究員
2009年4月 - 2010年3月ユトレヒト大学（オランダ）博士研究員
2010年4月 - 現在 福井謙一記念研究センター フェロー
【所属学会】 日本物理学会，日本金属学会【主な著書、学術論文】 1. Hidekazu Ikeno, Teruyasu Mizoguchi and Isao Tanaka,“Ab initio charge（過去5年以内）transfer multiplet calculations on the L2,3 XANES and ELNES of 3d transition
metal oxides”, Phys. Rev. B 83, 155107 (2011).
2. Teruyasu Mizoguchi, Weine Olovsson, Hidekazu Ikeno and Isao Tanaka,“Theoretical ELNES using one-particle an multi-particle calculations”, Micron 41,
695-709, (2010).
3. Hidekazu Ikeno , Frank M.F. de Groot, Eli Stavitski and Isao Tanaka,“Multiplet calculations of L2,3 x-ray absorption near-edge structures for 3d transitionmetal compounds”, J. Phys.: Condens. Matter 21, 104208 (2009).
4. Hidekazu Ikeno, Teruyasu Mizoguchi, Yukinori Koyama, Yu Kumagai andIsao Tanaka,“First-principles calculations for L2,3 ELNES/XANES of 3d transition metal monooxides, Ultramicroscopy 106, 970-975 (2006).
5. Hidekazu Ikeno, Isao Tanaka, Yukinori Koyama, Teruyasu Mizoguchi andKazuyoshi Ogasawara,“First-principles calculations of Ni L2,3 NEXAFS for
LiNiO2 and related compounds”, Phys. Rev. B 72, 075123 (2005).
【学術関係の受賞など】 日本学術振興会特別研究員(DC2) 2005-2006－ 37 －

Ⅱ 博士研究員 (2010)【氏名（ふりがな）】 義永

那津人 （よしながなつひこ）【職名】 FIFCフェロー【所属】 京都大学

福井謙一記念研究センター【研究室】 204
【直通電話】 075-711-7863【FAX】 075-781-4757【電子メールアドレス】 yoshinaga@fukui.kyoto-u.ac.jp【ホームページ】 http://daisy.phys.s.u-tokyo.ac.jp/yoshinaga/【研究分野】 ソフトマター物理、生物物理【現在の研究課題】 Self-propulsion and deformation of reactive droplet【研究内容キーワード】 Self-propulsion, free boundary problem, hydrodynamics, thermophoresis【学歴】 2007年3月京都大学理学研究科

物理学・宇宙物理学専攻

博士課程修了【学位】 2007年3月理学博士（京都大学）【略歴】 2007年4月東京大学理学系研究科 日本学術振興会特別研究員PD
2010年4月京都大学福井謙一記念研究センター特定研究員【所属学会】 日本物理学会【主な著書、学術論文】 1. Hong-Ren JIANG, Natsuhiko YOSHINAGA, and Masaki SANO,“Active（過去5年以内）
Motion of Janus Particle by Self-thermophoresis in Defocused Laser Beam”,
Physical Review Letters, 105, 268302 (2010)
Editor’s suggestion and Viewpoint in Physics, 3, 108 (2010) Debut of a hot“fantastic voyager”
2. Natsuhiko YOSHINAGA, Jean-Francois JOANNY, Jacques PROST and
Pilippe MARCQ,“Polarity patterns of stress fibers”, Physical Review Letters,
105, 238103 (2010)
3. Takahiro SAKAUE and Natsuhiko YOSHINAGA,“Dynamics of Polymer
Decompression: Expansion, Unfolding and Ejection”, Physical Review Letters,
102, 148302 (2009).
4. Hong-Ren JIANG, Hirofumi WADA, Natsuhiko YOSHINAGA, and Masaki
SANO,“Manipulation of Colloids by Nonequilibrium Depletion Force in Temperature Gradient”, Physical Review Letters, 102, 208301 (2009).
5. Natsuhiko YOSHINAGA, Efim KATS and Avraham HALPERIN,“On the
Adsorption of Two-State Polymers”, Macromolecules, 41, 7744-7751 (2008)
6. Natsuhiko YOSHINAGA,“Folding and unfolding transition in a single semiflexible polymer”, Physical Review E, 77, 061805 (2008)－ 38 －

Ⅲ 研究広報活動 (2009)

Ⅲ 研究広報活動
１. 福井謙一記念研究センターシンポジウム
第 8 回京都大学福井謙一記念研究センターシンポジウム

日時

平成 22(2010) 年 12 月 3 日 ( 金 )10:00 － 19:00

場

所

京都大学福井謙一記念研究センター （３Ｆ大会議室）

開 会 の辞田中功（セン ター長）

10: 00- 1 0 : 0 5

ご 挨 拶

小森

悟 （京大 ・工学研究科長）

9:40- 9 : 5 0

講

演
中村

宏樹 ( 国立交通大 学（台湾）、前分子科学研究所長 ) 10:15-1 1 : 1 5「非断熱化学動力学―分子科学に新次元を」谷村

吉隆 （京大・院理）

11:30-1 2 : 3 0「散逸系の階層型量子運動方程式と多次元分光」
山本

量一 （京大・院工）14:00-1 5 : 0 0「粗視化モデリングのすすめ：分子科学とソフトマター科学の接点 」
ポ ス ターセッション

15:15-1 7 : 1 5

懇 親 会（１Ｆ多目的ルーム ）17:30-1 9 : 0 0－ 39 －

Ⅲ 研究広報活動 (2009)

２. センターセミナー
第８回福井センターセミナー (2010 年６月 21 日 ( 月 )15:00 ～ 15:30

15:00-17:00）

Satoshi Maeda (Hakubi Center, FIFC)"Systematic Exploration of Photochemical Reaction Pathways:
Applications to Ketones and Aldehydes”"
15:30 ～ 16:00

Alister Page (FIFC)“Carbon Nanotube Nucleation on Traditional and Non-Traditional Catalysts:
Insights from QM/MD Simulations”
16:00 ～ 17:00

Alexey Timoshkin (St. Petersburg State University)“From Donor-Acceptor Complexes to Nanorods”－ 40 －

Ⅳ 研究業績 (2010)

Ⅳ

研究業績（2010）

１. 専任教員
総合研究部門
准教授

石田

専任教員

俊正

General Division Fulltime Faculty

Associate Professor Toshimasa Ishida

1. Summary of the research of the year
(1) Theoretical study on reaction of CooA protein with carbon monoxide
Heme-containing gas sensor proteins have a
new function for heme. The heme acts as anactive site for sensing gas molecules such as O2,
CO and NO. CooA is one of the proteins, and isa CO-sensing transcriptional activator found in aphotosynthetic bacterium. The binding of CO tothe heme group stimulates the transcriptional

Figure 1. Ligand exchanges for various
forms of CooA reaction center

activator activity of CooA. CooA has a ferrous form with histidine(His77) and prorine (Pro2 in the other subunit) amino acids as axial
ligands before the protein binds to CO instead of Pro although, inthe rest state, it has a ferric form with Pro2 and Cys75. Figure 1
shows the ligand exchanges for various forms. Here, weinvestigate the reaction during CO-sensing theoretically.
We carried out quantum chemical calculations on a model
system of this reaction. Several models are employed, butessentially includes porphyrin ring, imidazole and pyrrolidine,
where the two latter compounds are models for His and Pro. We
used the Hay-Wadt basis set and effective core potential for ironand the 6-31G(d) basis set at the B3LYP level. We used neutralmodel and anion model where proton is removed from pyrrolidine
in the single as well as triplet states. Figure 2 is the optimized

Figure2.

The

optimized

geometry of the product in theneutral singlet state of themodel compound.

geometry of the product in the neutral singlet state of the model compound.
The distances for Fe-N(Pro) and Fe-N(His) in the optimized geometry are 2.19 and 2.02 Å inthe neutral model and 2.04 and 2.15 Å in the anion model whereas the experimental values fromEXAFS analyses are 2.16 and 2.02 Å. Table 1 shows the distances for singlet and triplet states. The
neutral model is, thus, favorable from this comparison. The products is lower than the reactants inthe neutral and anion models by 4.1 and 28.7 kcal mol-1. CO is attached to Fe with the carbon atomin the products and the Fe-C-O angle is almost 180°, which is in agreement with the previous－ 41 －

Ⅳ 研究業績 (2010)

theoretical

study.

The transition state
is not found so far:the reaction probably
proceeds

withnobarrier on the single
surface.

Table

2Table 1 The distances between Fe-N for Prolin and Histidine ligands andenergy differences for singlets and triplets.

1Neutral
3Neutral
1Deprotonated3Deprotonated
EXAFS

R(Fe-N(Pro))(Å)
2.188
2.493
2.040
1.839
2.16

R(Fe-N(His))(Å) ΔE(kcal/mol)
2.016
0
2.484
7.1
2.152
0
2.124
-2.1
2.02
-

shows the Charges, multiplicities energy differences, bond distances for ferrous and ferriccompounds. For the ferrous form, the His-coordination is more stable than the Cys-coordination,
which is in agreement with experimental observations. For the ferric form, however, the His
coordination is more stable again, which is not consistent with experiments. A QM/MM treatment
would be needed to reproduce the experimental result.
Table 2 Charges, multiplicities energy differences, bond distances for ferrous and ferriccompounds(2) Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal
The dynamics of the photoisomerization of a model protonated Schiff base of 9-cis retinal inisorhodopsin is investigated using nonadiabatic molecular dynamics simulation combined with abinitio quantum chemical calculations on-the-fly. The quantum chemical part is treated at thecomplete-active space self-consistent field level for six electrons in six active π orbitals with the
6-31G basis set (CASSCF(6,6)/6-31G). The probabilities of nonadiabatic transitions between the S1(1ππ*)and S0 states are estimated in light of the Zhu-Nakamura theory. The photoinduced

cis-trans isomerization of 9-cis retinal proceeds slower than that of its 11-cis analogue and at alower quantum yield, confirming experimental observations. An energetic barrier in the excitedstate impedes the elongation and twist of the C9=C10 stretch and torsion coordinates, respectively,
resulting in the trapping of trajectories before transition. Consequently, the isomerization takes
longer time and the transition more often occurs at smaller twist angle of =C8-C9=C10-C11=,
which leads to regeneration of the 9-cis reactant. Thus, neither the smaller twist observed in the－ 42 －

Ⅳ 研究業績 (2010)

x-ray crystal nor the slower movement of nuclei in the transition region would be the main reason
for the longer reaction time and lower yield. A well-known space-saving asynchronous bicycle
pedal or crankshaft photoisomerization mechanism is found to be operational in 9-cis retinal. The
simulation in vacuo suggests that the excited-state barrier and the photoisomerization itself are
intrinsic properties of the visual chromophore and not triggered mainly by the protein environmentthat surrounds the chromophore.
(3) Syntheses,

crystalstructures

and

DFT

calculationsof

2-[4,5-bis(ethylsulfanyl)-1,3-dithiol-2-ylidene]-5- (4,5-diiodo-1,3-dithiol-2ylidene)-1,3-dithiolan-4-thione and -one
Iodine substituted 2,5-di(1,3-dithiol-2-ylidene)-1,3-dithiolan-4-thione and –one derivatives, namely
2-[4,5-bis(ethylsulfanyl)-1,3-dithiole-2-ylidene]-5-(4,5-diiodo-1,3-dithiol-2-ylidene)-1,3-dithiolan-4-thione (1a) and -one (1b), were synthesized.

1a was obtained from the reaction ofbis(tetraethylammonium)bis[2-[4,5-bis(ethylsulfanyl)-1,3- dithiol-2-ylidene]-1,3-dithiole-4,5bis(thiolato)]zinc and 4,5-diiodo-2-methylsulfanyl-1,3- dithiole-2-ylium tetrafluoroborate.

1b wasobtained from the reaction of 1a and mercury(II) acetate. Recrystallization of 1a and 1b fromcarbondisulfide/n-hexane gave single crystals suitable for X-ray structure analysis. In the crystals,
both 1a and 1b were stacked to form one-dimensional columns and the interplanar distances in thecolumns were greater than a π-cloud thickness.

Some effective side-by-side contacts wereobserved between molecules of adjacent columns. The interactions were accomplished throughS…I contacts for 1a, and S…I and O…I contacts for 1b.

The interesting features of thesestructures are the intermolecular C=S…I contacts for 1a and the intermolecular C=O…I contacts
for 1b which are respectively 16% and 17% shorter than the sum of van der Waals radii ofcorresponding atoms.

DFT calculations suggest that the effective geometry of 1a molecules forcharge transfer from the moiety interacting with sulfur to the moiety interacting with iodine plays
an important role for molecular packing through in the crystal system.
(4) Unusually High Aromaticity and Diatropicity of Bond-Alternate BenzeneBenzene
Enormous effort has been devoted to the elucidation of possible effects of bond-length alternationon the benzene π-system. Benzene tends to stay highly aromatic and highly diatropic even if strong
bond-length alternation is introduced artificially into the π-system. Such peculiar aromatic andmagnetic characters of benzene were justified consistently and unambiguously within a single
theoretical framework. From all physically sound points of view, bond-alternate benzene is highly
aromatic with a large aromatic stabilization energy. We confirmed that in the annulene family－ 43 －

Ⅳ 研究業績 (2010)

benzene is least sensitive in aromaticity to bond-length alternation.
2. Original papers(1) Aihara, Jun-ichi; Ishida, Toshimasa,"Unusually High Aromaticity and Diatropicity of Bond-Alternate Benzene"
J. Phys. Chem. A, 114 (2), 1093–1097 (2010).
(2) K. Ueda, K. Suzuki, K. Suzuki, K. Yoza, T. Ishida,“Syntheses, crystal structures and DFT calculations of
2-[4,5-bis(ethylsulfanyl)-1,3-dithiol-2-ylidene]-5-(4,5-diiodo-1,3-dithiol-2-ylidene)1,3-dithiolan-4-thione and –one”
Physica B 405, S69–S74 (2010).
(3) Wilfredo C. Chung, Shinkoh Nanbu, and Toshimasa Ishida,“Nonadiabatic ab Initio Dynamics of a Model Protonated Schiff Base of 9-cis Retinal”,
J. Phys. Chem. A, 114 (32), 8190–8201 (2010).
3. Presentation at academic conferences(1) Wilfredo C. Chung, Shinkoh Nanbu, Toshimasa Ishida
9-cis レチナールの光異性化の理論的研究
第 13 回理論化学討論会 1P03

札幌 2010/5/23(2) Ishida, Toshimasa and Aono, Shigetoshi,“Theoretical study on reaction of CooA protein with carbon monoxide”,
第 26 回化学反応討論会 1P46

東広島 2010/6/2(3) Wilfredo Credo Chung, Shinkoh Nanbu, Toshimasa Ishida,“Nonadiabatic ab initio dynamics of an isorhodopsin model system based on the
Zhu-Nakamura theory”
第 26 回化学反応討論会(4) 石田

俊正、青野

2P45

東広島 2010/6/3

重利「CooA タンパク質の CO との一連の反応に関する理論的研究」
第 4 回分子科学討論会 2010 2P089 豊中 2010/9/15(5) Chung Wilfredo Credo，南部 伸孝，石田 俊正“Hindered cis-trans isomerization in 9-cis retinal: a two-state model dynamics simulation”
第 4 回分子科学討論会 2010 4P092 豊中 2010/9/17(6) Ishida, Toshimasa; Chung, Wilfredo Credo; Nanbu, Shinkoh,“Nonadiabatic ab initio dynamics of 11-cis retinal”－ 44 －

Ⅳ 研究業績 (2010)

The international Chemical Congress of Pacific Basin Societies (Pacifichem2010), Honolulu,
Hawaii, USA. Dec. 17, 2010.
(7) Chung, Wilfredo Credo; Nanbu, Shinkoh, Ishida, Toshimasa"Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal”,
The international Chemical Congress of Pacific Basin Societies (Pacifichem2010), Honolulu,
Hawaii, USA. Dec. 18, 2010.
4. Others(1) 石田俊正「ペニングイオン化の理論的研究」
化学反応のポテンシャル曲面とダイナミックス～加藤重樹先生の足跡をたどって～

京都 2010/6/19(2) Toshimasa Ishida,“Theoretical Study on Photoionization”,
Colloquium on Computational Chemistry, Mindanao State University-Iligan Institute ofTechnology, Iligan, Philippines, Sep. 6, 2010 (Invited)(3) Toshimasa Ishida,“Theoretical Study on Photoionization”,
Mindanao State University of Science and Technology, Cagayan de Oro, Philippines, Sep.
7, 2010 (Invited)(4) 石田 俊正、青野 重利
CooA タンパク質と CO との反応に関する理論的研究
第 8 回 京都大学福井謙一記念研究センターシンポジウム 京都 2010/12/3(5) Wilfredo Credo Chung and Toshimasa Ishida
On the mechanism of the structural decoy action of LMP1 over CD40 in relation to
Epstein-Barr virus infection: an essential dynamics approach
第 8 回 京都大学福井謙一記念研究センターシンポジウム 京都 2010/12/3(6) Wilfredo C. Chung1, Shinkoh Nanbu2, Toshimasa Ishida1
Comparison of the 9-cis retinal photoisomeriation with the 11-cis counterpart
文部科学省「最先端・高性能汎用スーパーコンピュータの開発利用」プロジェクト
次世代ナノ統合シミュレーションソフトウェアの研究開発 第５回 公開シンポ
ジウム P102 2011/2/23

神戸(7) 南部伸孝，石田俊正，徳江郁雄、関谷 博，中園 博
非断熱遷移を利用した分子設計
文部科学省「最先端・高性能汎用スーパーコンピュータの開発利用」プロジェクト
次世代ナノ統合シミュレーションソフトウェアの研究開発 第５回 公開シンポ－ 45 －

Ⅳ 研究業績 (2010)

ジウム P103 2011/2/23

神戸(8) 日本国特許「光学活性分子の絶対配置決定方法、絶対配置決定装置、及びプログラム 」
公開日

2006/10/19

出願人

国立大学法人

発明者

田中康隆・石田俊正

出願番号

特願 2005-105319

出願日

静岡大学

2005/3/31

公開番号

特開 2006-284390

登録番号

特許 4547499

登録日

2010/7/16－ 46 －

Ⅳ 研究業績 (2010)

佐藤理論研究部門徹
准教授

1� 今年度の��の要�
今年度は振電相互作用密度の概念を用いて、新規な電子輸送材料の分子設計を行った。
【����】高効率な有機 EL 素子の開発のために、高い移動度を有するキャリア輸送材料が必要とされている。現在知られている電子輸送材料の移動度は、多くの場合、ホール輸送材料のそれよりも小さく、移動度の違いに起因するキャリアバランスの問題が高効率化の妨げとなっている[1]。
分子レベルで設計可能な因子として、フロンティア軌道準位とともに振電相互作用をあげることができる。振電相互作用が小さいことは、高移動度・低エネルギー散逸の必要条件である。
我々は、最近、振電相互作用密度の概念を提案している[2,3]。振電相互作用密度解析によれば、
振電相互作用を電子構造と振動構造との関係から理解することが可能となり、さらには、振電相互作用を制御することができる。
ここでは、既知である 3TPYMB の振電相互作用密度解析を通じて、キャリア輸送分子の設計指針を示し、設計した新規な電子輸送分子を示す。
【方�】振電相互作用密度 ηα は、イオン化状態と中性状態の間の差電子密度 Δρ とポテンシャル導関
数 υα の積で定義される。
ηα = Δρ × υα(1)

ここで、ポテンシャル導関数は、ひとつの電子に全ての核から作用する核-電子ポテンシャル u の規
準座標 Qα に関する導関数である。
υα =

∂u
∂Qα

(2)

振電相互作用定数 Vα は、振電相互作用密度の積分に等しい。
Vα =∫ ηα (r)d r
3(3)

従って、電子構造から求められる Δρ と振動構造から定まる υα の関係から振電相互作用定数を理解することができる。
振電相互作用密度 ηα は、正負の値を取る。原子核近傍では、υα は対称的に正負の値を持って分布する。したがって、 Δρ が原子上に局在すると ηα は、正負の値に対称的に分布し、相殺がおこる。
このような系では、小さな振電相互作用を与える。
【分子設計指針】図 1 に示す 3TPYMB は、電子輸送材料としてよく知られる Alq3 よりも高い電子移動度を有することが知られている。図 2 と図 3 は、それぞれ Alq3 と 3TPYMB の計算された振電相互作用定数である。3TPYMB の方が小さな振電相互作用を有することがわかる。3TPYMB の差
電子密度を図 2 に示す。差電子密度がホウ素原子上に局在していることがわかる。このため、原子ごとの寄与を表す原子振電相互作用定数はホウ素原子上では、0 となっている。また、3 回対称軸を有するため、選択則により相互作用モードの数も少ない。
従って、以下のような設計指針が得られる[4]。(1)差電子密度が原子上に局在した(2)対称性の高い－ 47 －

Ⅳ 研究業績 (2010)

分子がキャリア輸送分子として望ましい。
このような設計指針に基づき図 5 に示す HBCP を設計した[5]。計算された最適化構造は、6 回対称軸を持ち、差電子密度もホウ素原子上に局在している。
図 6 に計算した振電相互作用定数を示す。3TPYMB よりも小さな振電相互作用を有することが示された。

図 1. 3TPYMB

図 4. 3TPYMB の差電子密度

図 2. Alq3 の振電相互作用定数

図 3. 3TPYMB の振電相互作用定数

図 5.新規に設計した HCBP

図 6. HCBP の振電相互作用定数【���[1] Chopra, N., Lee, J., Zheng, Y., Eom, S.-H., Xue, J., and So, F., “Effect of the charge balanceon high-efficiency blue-phosphorescent organic light-emitting diodes," Appl. Mater. Interfaces 1,1169 (2009).
[2] Sato, T., Tokunaga, K., and Tanaka, K., “Vibronic coupling in naphthalene anion: Vibronic
coupling density analysis for totally symmetric vibrational modes," J. Phys. Chem. A 112,758-767 (2008).
[3] Sato, T., Tokunaga, K., Shizu, K., and Tanaka, K., “Vibronic coupling constant and vibronic
coupling density," in [The Jahn-Teller Effect: Fundamentals and Implications for Physics andChemistry], K oppel, H., Barentzen, H., and Yarkony, D. R., eds., Springer Series in Chemical

Physics 97, 99-129, Springer-Verlag, Heidelberg Berlin (2009).

－ 48 －

Ⅳ 研究業績 (2010)[4] Shizu, K., Sato, T., Ito, A., Kaji, H., and Tanaka, K., “Theoretical design of ahole-transporting molecule: Hexaaza[16]parabiphenylophane," J. Mater. Chem. 21, 6375-6382(2011).
[5] Shizu, K., Sato, T., Tanaka, K., and Kaji, H., “A boron-containing molecule as an efficientelectron-transporting material with low-power consumption," Appl. Phys. Lett. 97, 142111 1-3(2010).

2. ��(1)“Vibronic Coupling Density Analysis of Hole-Transporting Materials:
Electron-Density Difference in DFT and HF Methods”, Katsuyuki Shizu, Tohru Sato,
Kazuyoshi Tanaka, Hironori Kaji, Organic Electronics 11, 1277-1287(2010).

(2)“Inelastic Electron Tunneling Spectra and Vibronic Coupling Density Analysis
of 2,5-Dimercapto-1,3,4-thiadiazole and Tetrathiafulvalene Dithiol”,
Katsuyuki Shizu, Tohru Sato, Kazuyoshi Tanaka, Nanoscale 2, 2186-2194(2010).
“N-Anisyl-Substituted Hexaaza[16]paracyclophane”,A. Ito, Y. Yokoyama, R.
Aihara, K. Fukui, S. Eguchi, K. Shizu, T. Sato, K.Tanaka, Angew. Chem. Int. Ed.
49, 8205-8208(2010).
“Revealing
Bipolar
Charge-Transport
Propertyof
4,4'-N,N'-dicarbazolylbiphenyl (CBP) by Quantum Chemical Calculations”,
Tomonori Yamada, Furitsu Suzuki, Atsushi Goto, Tohru Sato, Kazuyoshi Tanaka,
Hironori Kaji, Organic Electronics 12, 169-178(2010).
“A Boron-Containing Molecule as an Efficient Electron-Transporting Material
with Low-Power Consumption”, Katsuyuki Shizu, Tohru Sato, Kazuyoshi Tanaka,and Hironori Kaji, Appl. Phys. Lett. 97, 142111 1-3(2010).
“Vibronic coupling in C60- anion revisited: Precise derivations fromphotoelectron spectra and DFT calculations”, Naoya Iwahara, Tohru Sato,
Kazuyoshi Tanaka, Liviu F. Chibotaru, Phys. Rev. B 82, 245409 1-10(2010).

(3)

(4)

(5)

(6)

(7)
(8)
(9)

“Molecular design for high-spin molecules in view of vibronic couplings”,
Naoya Iwahara, Tohru Sato, Kazuyoshi Tanaka, Polyhedron 印刷中.
“Vibronic Coupling Density Analysis for Free-Base Porphin Cation”, Katsuyuki
Shizu Tohru Sato, Kazuyoshi Tanaka, Chem. Phys. Lett. 505, 42-46 (2010).
“Theoretical
DesignofaHole-Transporting
Molecule:
Hexaaza[16]parabiphenylophane”, Katsuyuki Shizu Tohru Sato, Akihiro Ito,

Hironori Kaji, Kazuyoshi Tanaka, J. Mater. Chem. 21, 6375-6382(2011).
(10) “Vibronic Interactions in Hole-Transporting Molecules: An Interplay with
Electron-Hole Interactions”, Tohru Sato, Katsuyuki Shizu; Keisuke Uegaito;
Naoya Iwahara; Kazuyoshi Tanaka; Hironori Kaji, Chem. Phys. Lett. 507,
151-156(2011).

－ 49 －

Ⅳ 研究業績 (2010)

3.総�
該当なし
4.��
該当なし
5.学会��
(1) [招待講演] “Vibronic coupling density analysis”,20th International Symposiumon the Jahn-Teller Effect, 2010年8月16日-20日, University of Fribourg Campus
Perolles II, Fribourg, Switzerland(2) Naoya Iwahara, Tohru Sato, Kazuyoshi Tanaka, Liviu F. Chibotaru, “Vibronic
coupling in C60 monoanion”,フラーレンナノチューブ学会 第 39 回フラーレン・ナノチ
ューブ総合シンポジウム, 2010 年 9 月 5 日-7 日, 京都大学百周年記念ホール, 京都市(3) 佐藤徹, Arnout Ceulemans, “Ih 対称における振電相互作用とスピン-軌道相互作用:(Gamma8 + Gamma9) X (g + 2h) Jahn-Teller 問題”, 日本コンピュータ化学会 ２０１０
秋季年会, 2010 年 10 月 22-23 日, 長岡技術科学大学, 新潟県長岡市(4)上島基之, 佐藤徹, 田中一義, “二原子分子における結合次数と振電相互作用密度”,
日本コンピュータ化学会 ２０１０秋季年会, 2010 年 10 月 22-23 日, 長岡技術科学大学,
新潟県長岡市(5)新井友春, 岩原直也, 佐藤徹, 田中一義, 田中庸裕, “アルカリ金属イオン添加バナ
ジウム酸化物における光触媒作用と振電相互作用”,日本コンピュータ化学会 ２０１０
秋季年会, 2010 年 10 月 22-23 日, 長岡技術科学大学, 新潟県長岡市(6)春田直毅, 佐藤徹, 田中一義,“Cyclopentadienyl radical における振電相互作用”,
日本コンピュータ化学会 2010 秋季年会,2010 年 10 月 22-23 日, 長岡技術科学大学, 新潟
県長岡市(7) 岩原直也、佐藤徹、田中一義、Liviu F. Chibotaru, “C60-における光電子スペクトルと振電相互作用”, 京都大学工学研究科 桂インテックセンター高等研究院 第 3 回 融合ナノ基盤工学研空部門 若手研究者交流会 2010 年 7 月 2 日, 京都大学桂キャンパス、－ 50 －

Ⅳ 研究業績 (2010)

京都市(8) Naoya Iwahara, Tohru Sato, Kazuyoshi Tanaka, Liviu F. Chibotaru
Photoelectron spectrum and vibronic couplings in C6020th International Symposium on the Jahn-Teller Effect2010 年 8 月 16 日-20 日
University of Fribourg Campus Perolles II, Fribourg, Switzerland(9) 岩原直也、佐藤徹、田中一義、Liviu F. Chibotaru,“C60-における光電子スペクトルと振電相互作用”, 日本物理学会 2010 年秋季大会, 2010 年 9 月 23 日-26 日, 大阪府立大学中百舌鳥キャンパス、大阪市(10) Naoya Iwahara, Tohru Sato, Kazuyoshi Tanaka, “Vibronic Couplings in High- and
Low-Spin States of Phenylene Diamines”, The 12th International Conference on
Molecule-Based Magnets, 2010 年 10 月 8 日-12 日, Four Points by Sheraton Beijing,
Haidian、北京、中国(11)志津功将、佐藤徹、田中一義、梶弘典, ”電子輸送材料 Alq3 ならびに 3TPYMB における振電相互作用の理論解析”, 有機 EL 討論会第 10 回例会, 2010 年 6 月 17-18 日, 日本科
学未来館、みらい CAN ホール（東京）(12)上島基之，佐藤徹，田中一義,“CO+の基底状態における振電相互作用定数”, 日本コ
ンピュータ化学会 年会：2010 春季年会, 2010 年 5 月 20 日(木)-21 日(金) , 東京工業大学大岡山キャンパス
(13)上島基之, 佐藤徹, 田中一義, 梶弘典, “Alq3 の励起状態における振電相互作用密度解析:構造異性と振電相互作用”, 有機ＥＬ討論会 第 11 回例会, 2010 年 11 月 2 日（火-3 日(水), 名古屋大学 豊田講堂,
6.�の�特許(1) 新規な環状化合物、電子輸送材料および有機エレクトロルミネッセンス素子
出願番号： 特願２０１１−４８７２５
発明者: 佐藤 徹、志津 功将、俣野
権利者: 京都大学、九州大学

善博、田中－ 51 －一義、梶弘典

Ⅳ 研究業績 (2010)

中尾

嘉秀

理論研究部門

准教授

�� 今年度の研究の��
今年度は遷移金属元素を含んだ機能性金属錯体の物性について研究を行った。
䇼ᆎ䉄䈮䇽㩷 遷移金属元素を含んだ金属錯体は様々な配位子との組み合わせで、多様な構造や電子状態をとることができ、様々な機能が発現することがある。発光性錯体は発光素子に、高スピン状態を保つ錯体は記憶素子などに応用できる可能性がある。これらの機能が発現する仕組みを理解する
ことは機能性金属錯体の制御や設計に繋がるため、機能の発現機構の理論的解明が求められている。
今年度はサーモクロミック銅(II)錯体の色変化に対して、量子化学計算と分子動力学法により解明を行った。また、メカノクロミズムを示す金(I)錯体の発光機構について、金-金間相互作用に着目
して発光色の変化を理論的に解明した。
䇼䉰䊷䊝䉪䊨䊚䉾䉪㌃㩿㪠㪠㪀㍲૕䈮㑐䈜䉎⎇ⓥ䇽㩷
温度変化により物質の色が変化する現象はサーモクロミズムと呼ばEt

れ、インキやディスプレイ材料への応用が期待されている。Scheme 1

Etに示した銅(II)錯体 Cu(dieten)2 [dieten = N,N-diethylethylenediamine]の

Cu
N
H2

ClO4 塩は温度を上昇させると、316 K で赤色から青紫色へと可逆的に色が変化することが報告されている[1]。低温相(293 K)、高温相(329 K)の X 線構造解析から、低温相では銅に対して四つの窒素原子が平面四

H2
N

N

N
Et

Et

Scheme 1. Cu(dieten)2 錯体

配位しているのに対して、高温相ではわずかに四面体歪みした配位構造をとることが分かっている[2]。本研究では、量子化学計算により高温相と低温相構造の安定性を評価し、吸収スペクトルの解析を行った。次に、第一原理分子動力学法である Car-Parrinello Molecular Dynamics (CPMD)を用いて温度による構造変化の解析を行って、錯体の色変化と相転移の関係を明らかにした。
構造最適化及びエネルギー評価、振動計算には B3LYP 法を用い、吸収スペクトルの評価には
TD-B3LYP 法を用いた。Cu の内殻電子は Stuttgart-Dresden-Bonn の有効内殻ポテンシャル(ECP)で置
き換え、原子価軌道は triple zeta の基底関数を用いた。N, H, C の基底関数は cc-pVDZ を、O,Cl の基
底関数は aug-cc-pVDZ を用いた。以上の計算には Gaussian 03 を用いた。相転移のダイナミクスを明らかにするために、CPMD 法を用いて 50 K, 150 K, 250 K, 350 K の温度で結晶状態の構造変化の解析を行った。CPMD 計算では、
擬ポテンシャルと平面波(cutoff = 90 Ry.)を基底に、汎関数は BLYP、
時間の刻み幅は 0.1 fs、仮想電子質量を 400 a.u.として、CPMD 3.13 を用いた。
X 線構造解析で得られた構造から Cu(dieten)2 錯体のみを B3LYP 法で構造最適化すると、低温相(L)と高温相構造(H)のそれぞれに 4 通りの安定構造が得られた。各構造の相対安定性と、配位子と金属のなす 2 つの面の角度 d を平面からのずれとして、Table 1 に示した。TD-B3LYP 計算から、平面からのずれが大きい Hc 構造のみが 490 nm 付近に d-d 遷移が存在することが分かった。周期的境界条件を考慮して、これらの結晶状態の構造を最適化すると、低温相構造では La 構造だけが、高温－ 52 －

Ⅳ 研究業績 (2010)相構造では 4 つ全てが安定に存在した。10 ps の CPMD 計算から得られた平面からのずれ d の分布を Figure 1 に示した。50 K では低温相構造は 3.6 度、高温相構造では 13.9 度と平面からのずれは小さいが、350 K では 17.7 度と 24.3 度と大きな値をとる。Cu(dieten)2 錯体は高温では四面体歪が大きくなり、d-d 遷移が許容となり色変化が起こることが明らかになった。Figure 2 に La 構造を初期構造とした 350K での CPMD 計算から得られた二面角 CuNCC と二面角 NCCN と d 値の時間変化を示した。6 ps までは La 構造を保持し、16 ps から Hd 構造へと構造変化が起こった。50K, 150K, 250K では高温構造への変化は見られなかった。

0.12

L
Lb(50K)a (50K)Ha (50K)
Ha(50K)La (350K)
Lb(350K)
Ha (350K)
Ha(350K)

arbitray unit

0.10
0.08
0.06
0.04
0.02
0.00
0.0

10.0

20.0

30.0

40.0

d / degree

Figure 1. 平面からのずれ d の分布

d(NCCN) / degreed(CuNCC) / degree

Table 1. 各構造の相対安定性(kcal mol-1)と平面からのずれ d(括弧内、degree)
B3LYP
BLYP
BLYP+PBC
La 0.00( 0.0) 0.00( 0.0)
0.00( 1.8)－
Lb 2.35( 0.1) 2.14( 0.0)－
Lc 1.15( 5.0) 1.04( 5.6)－
Ld 1.15( 5.0) 1.04( 5.2)
0.04(12.9)
Ha 1.35( 8.5) 1.26( 7.9)
0.05(13.1)
Hb 1.35( 8.5) 1.26( 7.9)
0.21( 8.8)
Hc 2.18(22.3) 2.10(14.7)
0.01(16.7)
Hd 0.40( 3.5) 0.33( 9.2)

La

Hdt / pst / psFigure 2. 350K での二面角 CuNCC と二面角 NCCN と d 値の時間変化

䇼㊄㩿㪠㪀ੑᩭ㍲૕䈍䉋䈶䈠䈱㓸Ⓧ㍲૕䈱ๆ෼䊶⊒శ䉴䊕䉪䊃䊦䈮㑐䈜䉎⎇ⓥ䇽㩷
量子収率が高いリン光性の金属錯体は、変換効率の高い発光素子への応用が期待され、興味が持たれている。中でも一価の金錯体の発光現象に関しては数多くの興味深い報告例が存在する。例えば、三核金属錯体 [M3(R2pz)3] (M = Au; R = CH3, CF3) では金属-金属間の相互作用に由来する温度や溶媒に依存する発光が報告されている[3]。最近、金(I)二核錯体 [(C6F5Au)2(dicb)] (dicb = 1,4-diisocyanobenzene)(Scheme 2) の発光現象に関する興味深い報告がなされた[4]。この分子は結晶および CH2Cl2 溶液中でそれぞれ 415, 418 nm の発光を示し、結晶をスパチュラで擦りつぶすなどの機械的刺激を加えることで、長波長側の 533 nm に発光が変化する非常に珍しいメカノクロミ
ズムを示す。また、類似の単核錯体では短波長側の発光のみ観測
され、類似の三核錯体では長波長側の発光のみ観測される。メカ
ノクロミズムなどの特殊な発光現象に関する理論計算の報告例
は非常に少なく、発光機構の理論的解明は新規錯体の発光を制－ 53 －

Scheme 2. [(C6F5Au)2(dicb)] 錯体

Ⅳ 研究業績 (2010)

御・設計する上でも重要である。
S0 状態及び T1 状態の構造最適化と振動解析は B3LYP 法で、吸収スペクトルの検討は TD-B3LYP 法で行った。Au の内殻電子は Christiansen の有効内殻ポテンシャルで置き換え、価電子には (541/551/211)
基底を用いた。H, C, N, F には Dunning の cc-pVDZ を基底関数として用いた。B3LYP 法では Au-Au 間の分子間力を再現できないため、MP2 法を用いて Au-Au 間距離に対するポテンシャルエネルギー曲線(PEC)の計算を行い、Au-Au 間の相互作用を評価した。溶液中の吸収・発光エネルギーの計算ではPolarizable Continuum Model(PCM)法を用いた。二核錯体の単量体および二量体の発光エネルギー評価には、交換汎関数に長距離補正を取り込んだ LC-BLYP 法も用いた。LC-BLYP 法による計算には GAMESSを用いて、それ以外の計算には Gaussian 03 を用いた。
金二核錯体の単量体の T1 状態では Figure 3 に示したπ, π* 軌道が一電子占有軌道となっており、S0 状
態では上の軌道が LUMO に相当する。リン光は π* → π 遷移に帰属され、リン光エネルギーは B3LYP
法では 2.37 eV と計算され、短波長側の実験値 2.99 eV に比べて小さくなった。B3LYP 法では大きなπ共役系を含む分子の長距離相関をうまく表すことができないため、長距離補正を組み込んだ LC-BLYP 法を用いてTable 2. 二核錯体の単量体および二量体のリン
光エネルギー(eV)

計算を行ったところ、リン光エネルギーは 2.73 eV とな
り、短波長側の実験値とよく一致した(Table 2)。次に、金二核錯体の二量体の構造とリン光エネルギーの検討を行

単量体
二量体

B3LYP

LC-BLYP

Expt

2.37
2.50

2.73
3.18

2.99
2.33

った。S0 状態では Au-Au 間距離が 4.752 Å と離れており Au-Au 間に相互作用は存在しないが、H-F 間距離が 2.307, 2.419 Å と短いので、水素結合のみで二量体が安定化している。一方、T1 状態では Au-Au 間
距離が 2.853 Å、H-F 間距離は S0 状態よりわずかに長く 2.520, 2.918 Å
で、Au-Au 間の金属間結合および水素結合により系が安定化していると考えられる。Figure 4 に金二核錯体の単量体の最低励起三重項状態

Figure 3. 二核錯体の単量体のT1 状態の一電子占有軌道(T1)の一電子占有軌道を示した。T1 状態における一電子占有軌道はAu-Au 間の 5dσ*軌道と中心の-C6H4-NC-Au-のπ* 軌道であり、S0 状態
では上の軌道が LUMO に相当する。リン光は π* → 5dσ* 遷移に帰属され、リン光エネルギーは 2.50 eV となり実験値とよく一致した。つまり、機械的刺激後の長波長側の発光は Au-Au 間の金属間結合に起因することが明らかになった。TD-B3LYP 法で吸収スペクトルを求めると、単量体、二量体ともに 4.0～5.0 eV 付近の吸収は、π(dicb) →**π (dicb), π(C6F5) → (5dπ-π) (-Au-C-N-) 遷移に帰属された。

Figure 4. 二核錯体の二量体のT1 状態の一電子占有軌道

����(1) L. Fabbrizzi, M. Micheloni, and P. Paoletti, Inorg. Chem. 13, 3019-3021 (1974).
(2) P. Naumov, K. Sakurai, T. Asaka, A. A. Belik, S. Adachi, J. Takahashi, and S. Koshihara, P. Naumov,
Inorg. Chem. 45, 5027-5033 (2006).
(3) Omary, M. A.;Rawashdeh-Omary, M. A.; Gonser, M. W. A.; Elbjeirami, O.; Grimes, T.; Cundari, T. R.;
Diyabalanage, H. V. K.; Gamage, C. S. P.; Dias, H. V. R. Inorg. Chem. 44, 8200-8210 (2005).
(4) Ito, H.; Saito, T.; Oshima, N.; Kitamura, N.; Ishizaka, S.; Hinatsu, Y.; Wakeshima, M.; Kato, M.; Tsuge,
K.; Sawamura, M. J. Am. Chem. Soc., 130, 10044-10045 (2008).

－ 54 －

Ⅳ 研究業績 (2010)2� 論文(1) T. Umeyama, N. Tezuka, S. Seki, Y. Matano, M. Nishi, K. Hirao, H. Lehtivuori, N. V.
Tkachenko, H. Lemmetyinen, Y. Nakao, S. Sakaki, H. Imahori,
Selective formation and efficient photocurrent generation of [70] fullerene-single-walledcarbon nanotube composites
Adv. Mater. 22, 1767-1770 (2010).
(2) H. Ando, Y. Nakao, H. Sato, S. Sakaki,Comparison of Electronic Structures and Light-induced Excited Spin State Trapping
between [Fe(2-picolylamine)3]2+ and Its Iron(III) Analogue
Dalton Trans. 39, 3279-3289 (2010).
(3) Y. Nakajima, Y. Nakao, S. Sakaki, Y. Tamada, T. Ono, F. Ozawa,
Electronic structure of four-coordinate iron(I) complexbis(phosphaethenyl)pyridine ligand

supportedbyaJ. Am. Chem. Soc. 132, 9934-9936 (2010).
(4) K. Saito, Y. Nakao, K. Umakoshi, S. Sakaki,
Theoretical study of excited states of pyrazolate- and pyridinethiolate-bridged dinuclear
platinum(II) complexes: relationship between geometries of excited states andphosphorescence spectra.
Inorg. Chem. Soc. 49, 8977-8985 (2010).
3� 学会発�(1) 中尾嘉秀, 山田裕, 榊茂好, 伊藤肇, 澤村正也
「金(I)二核錯体およびその集積錯体の吸収・発光スペクトルに関する理論的研究」
第 60 回錯体化学討論会, 大阪国際交流センター, 2010 年 9 月 27 日～30 日, 2B-07(2) 竹中裕喜雄, 黒川悠索, 中尾嘉秀, 佐藤啓文, 榊茂好「逆サンドイッチ型二核金属錯体に関する理論的研究」
第4回分子科学討論会, 大阪大学豊中キャンパス, 2010年9月14日～17日, 2P108(3) 中尾嘉秀，山田裕, 榊茂好, 伊藤肇, 澤村正也
「金(I)二核錯体およびその集積錯体の吸収・発光スペクトルに関する理論的研究」
第 4 回分子科学討論会, 大阪大学豊中キャンパス, 2010 年 9 月 14 日～17 日, 1P116(4) 吉本亜矢, 石川敦之, 佐藤啓文, 中尾嘉秀
「リンや硫黄を含んだ梯子型π共役化合物の光物性の理論的研究」
日本化学会第91春季年会, 神奈川大学横浜キャンパス, 2011年3月26日～29日,
2PC-167－ 55 －

Ⅳ 研究業績 (2010)

２. リサーチリーダー

Keiji MOROKUMA
Research Leader, Kenichi Fukui Memorial Research Group 1

1. Summary of the research of the year
Multi-level Simulation of Complex Molecular Systems
The goals of the research of this group are 1. to develop further the hybrid theoretical methods (suchas ONIOM) already proposed by us, 2. to demonstrate that such hybrid methods can be used for
simulations of structures, reactions and dynamics and 3. to solve some of the important problems in eachfield. Our research is supported in part by the Institute and in large fraction by a 5-year grant in the areaof High Performance Computing for Multi-Scale and Multi-Physics Phenomena from CREST (Core
Research for Evolutional Science and Technology) program of JST (Japan Science and Technology
Agency) until March 2012. With ten to twelve postdoctoral fellows (both Fukui fellows and JST fellows),
a few visiting graduate students and several research assistants in the group, as well as in collaboration
with my group at Emory University, the group of Prof. Stephan Irle (a CREST collaborator) of Nagoya
University as well as Prof. Satoshi Maeda, Assistant Professor at Hakubi Center, Kyoto University, we
have a strong team of theoretical/computational chemists working together toward a common goal. Since
detailed description on individual projects can be found in the reports of postdoctoral fellows, here theareas of studies and titles of individual projects are summarized.

I. Simulation of Biomolecular Systems

In the area of multi-level simulation of biomolecular systems, in recent years we have studied
structures and reactions of metalloenzyme systems mainly using the active site models in which only theactive site atoms are explicitly included in the QM calculations. In the last few years we have explicitly
included the effects of protein employing the ONIOM QM/MM scheme. We optimized the structures ofintermediates and transition states of enzymatic reactions, and in some cases included the statisticaleffects of protein by QM/MM molecular dynamics, In a few examples we have found that the protein
effects completely changed the mechanism of reaction, compared to the active-site models. We also
perform direct dynamics calculations using QM and QM/MM methods to study the primary events ofphotochemical processes of biomolecular chromophore. We recently expanded our theoretical studies ofcatalytic reactions that take place in the nano cavity created by the protein.
a) Density
Functional
TheoryInvestigationoftheCatalytic
Mechanismof
Hydroxyethylphosphonate Dioxygenase (See research activities of Dr. Hirao)b) Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H2O2 and a Nonheme
Iron(II) Complex: O–O Cleavage Involving Proton-Coupled Electron Transfer (See research
activities of Dr. Hirao)c) Comparative Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in Heme and non-Heme
Complexes (See research activities of Dr. Chung)d) Towards understanding the HppE catalytic mechanism (See research activities of Dr. Petrova)e) Theoretical Studies of the Reaction Mechanism, Regioselectivity and Stereoregularity (Seeresearch activities of Dr. Ke)f) Theoretical Study of Artificial Metalloenzymes (See research activities of Dr. Ke)g) Theoretical Investigation on Light-Driven Molecular Rotary Motors (See research activities of
Dr. Liu)h) Ring-Opening and Ring-Closure Mechanism of Spiropyran-Merocyanine Photochromic
Reaction (See research activities of Dr. Liu)i) Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol
Solution (See research activities of Dr. Xing Li)j) Mechanistic study on photo-induced decarboxylation of the Photoactivable Green Fluorescent－ 56 －

Ⅳ 研究業績 (2010)

Protein: A theoretical ONIOM(QM:MM) calculation (See research activities of Dr. Ding)

II. Simulation of Nanomaterials

In the area of simulation of nanomaterials, we continued our research efforts on quantum chemicalmolecular dynamics (QM/MD) computations of carbon and other nanostructure formation based on
density functional tight binding (DFTB). Single-walled carbon nanotubes (SWNTs) have been one ofrepresentative nanotechnology materials and their various potential applications. Although SWNTs are
known to be efficiently synthesized using metal catalyst, its growth mechanism is still not wellunderstood. In order to understand interplay among feedstock carbon, nanotube, and metal, we have
implemented growth simulations of metal-catalyzed SWNT using DFTB MD simulations. Previously wesucceeded in simulating continued growth SWNT on Fe cluster in our simulation studies. Since then we
have successfully simulated SWNT growth from scratch (without seed SWNT) under a variety ofconditions and our understanding of the growth process has given insight to its mechanism which has notbeen seen previously from either experimental or theoretical studies. We also studied the nucleation of
SWNT cap from Si-bases materials.
a) Annealing of hot giant fullerenes: DFTB MD simulations (See research activities of Dr. Saha)b) Determination of Local Chirality in Irregular Single-Walled Carbon Nanotube Based on
Individual Hexagons (See research activities of Dr. Kim)c) QM/MD Investigation of Single-Walled Carbon Nanotube Nucleation from Si-Based Catalysts:
A Vapor-Solid-Solid Mechanism (See research activities of Dr. Page)d) DFT QM/MD Investigation of the Nucleation of Single-walled Carbon nanotubes on theNonmetallic Silicon Nanoparticles (See research activities of Dr. Chandrakumar)e) Is SWNT Nucleation on Silicon Nanoparticles Preceded by a Carbide Phase or a
Carbon-Coated Surface? (See research activities of Dr. Chandrakumar)f) Melting Behavior of the Pure and carbon-doped Silicon Nanoparticles: Carbon Induced
Liquid-to-Solid Phase Transition in Silicon Nanoparticles (See research activities of Dr.
Chandrakumar)g) Fullerene formation from hydrocarbon combustions: Quantum chemical molecular dynamics
study (See research activities of Dr. Haibei Li)h) Armchair-type SWCNT growth from bottom-up organic synthesis (See research activities of Dr.
Haibei Li)i) QM/MD Investigation of Haeckelite and Graphene Growth on Transition Metal Surfaces
synthesis (See research activities of Dr. Page)

III. Method Developments and Applications

Last year we have extended the Global Reaction Route Mapping (GRRM) method developed
previously by Ohno and Maeda to automatic search of the minimum of seam of crossing (MSX)including the conical intersection. This year we further developed the MSX search method based on the
updating of the branching plane without calculating derivative coupling vector. Further more, this method
was applied to elucidation of the mechanism of photodissociation reactions of acetone and methyl ethyl
ketone.
A new method, artificial force-induced reaction (AFIR) method, suitable to determining the transition
and intermediates of reactions of two or more molecules A + B (+C…) → X, has been developed basedon imposing an artificial attractive force between the reactant molecules. The application of this method
to the Passerini reaction, which has been known in textbooks as an example of three-molecule reaction,
showed that it actually involved four molecules in the reaction. Application to other multicomponent
reactions is in progress.
(Work in collaboration with Prof. Maeda, who is Assistant Professor at Hakubi Center of Kyoto
University and Visiting Assistant Professor at FIFC. See also his Research Activities)a). Theoretical Study of NO3 Photodissociation (See research activities of Dr. Xiao)－ 57 －

Ⅳ 研究業績 (2010)

2. Original papers

1. A. J. Page, K. R. S. Chandrakumar, S. Irle, and K. Morokuma, Do SiO2 and Carbon-Doped SiO2
Nanoparticles Melt? Insights from QM/MD Simulations and Ramifications Regarding Carbon Nanotube
Growth, Chem. Phys. Lett. 508, 235–241 (2011).
2. A. Nakamura, K. Munakata, S. Ito, T. Kochi, L. W. Chung, K. Morokuma and K. Nozaki, Pd-Catalyzed
Copolymerization of Methyl Acrylate with Carbon Monoxide: Structures, Properties and Mechanistic
Aspects toward Ligand Design, J. Am. Chem. Soc. 133, 6761-6779 (2011).
3. H. Xiao, S. Maeda and K. Morokuma, Excited State Roaming Dynamics in Photolysis of Nitrate Radical.
J. Phys. Chem. Lett. 2, 934–938 (2011). DOI: 10.1021/jz2003364; featured in S. North, Natue Chem. 3,
504-504 (2011).
4. S. Maeda, R. Saito, and K. Morokuma, Finding Minimum Structures on Seam of Crossing in Reactions ofType A + B → X: Exploration of Nonadiabatic Ignition Pathways of Unsaturated Hydrocarbons. J. Phys.
Chem. Lett. 2, 852–857 (2011).
5. S. Sekharan and K. Morokuma, QM/MM Study of the Structure, Energy Storage and Origin of the
Bathochromic Shift in Vertebrate and Invertebrate Bathorhodopsins. J. Am. Chem. Soc, 133, 4734-4737(2011).
6. Kawatsu, M. Lundberg and K. Morokuma. Protein Free Energy Corrections in ONIOM QM:MM
Modeling: A Case Study for Isopenicillin N Synthase (IPNS) J. Chem. Theo. Comp. 7, 390-401 (2011).
7. S. Maeda, S. Komagawa, M. Uchiyama, and K. Morokuma. Finding Reaction Pathways forMulticomponent Reactions: The Passerini Reaction Is a Four-Component Reaction. Angew, Chem. Int.
Ed. 50, 644-649. (2011).
8. A. J. Page, K. R. S. Chandrakumar, S. Irle, and K. Morokuma, SWNT Nucleation from Carbon-Coated
SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism. J. Am. Chem. Soc. 133, 621-628 (2011).
9. H. Hirao and K. Morokuma, Ferric Superoxide and Ferric Hydroxide Are Used in the Catalytic
Mechanism of Hydroxyethylphosphonate Dioxygenase (HEPD): A Density Functional Theory
Investigation, J. Am. Chem. Soc. 132, 17901-17909 (2010).
10. N. Bera, S. Maeda, K. Morokuma and A. A. Viggiano, Theoretical study of proton affinity and fluoride
affinity of nerve agent VX. J. Phys. Chem. A 114, 13189-13197 (2010).
11. R. Nádasdi, G. L. Zügner, M. Farkas, S. Dóbé, S. Maeda, and K. Morokuma, Photochemistry of Methyl
Ethyl Ketone: Quantum Yields and S1/S0-Diradical Mechanism of Photodissociation, Phys. Chem. Phys.
11, 3883–3895 (2010).
12. X. Li, L. W. Chung, A. Miyawaki and K. Morokuma, Primary Events of Photodynamics in Reversibly
Photoswitching Fluorescent Protein Dronpa, J. Phys. Chem. Lett. 1, 3328–3333 (2010).
13. X. Li, L.W. Chung, A. Miyawaki, and K. Morokuma, Competitive Mechanistic Pathways for Green-to-Red
Photoconversion in the Fluorescent Protein Kaede: A Computational Study, J. Phys. Chem. B, 114,
16666-16675 (2010).
14. K. Nozaki, S. Kusumoto, S. Noda, T. Kochi, L. W. Chung, and K. Morokuma, Why Did Incorporation of
Acrylonitrile to a Linear Polyethylene Become Possible? Comparison of Phosphine-Sulfonate Ligand with
Diphosphine and Imine-Phenolate Ligands in the Pd-Catalyzed Ethyelene/Acrylonitrile Copolymerization;
J. Am. Chem. Soc. 132, 16030-16042 (2010).
15. S. Sekharan, A. Altun, and K. Morokuma, Retinal QM/MM Study of Dehydro and Dihydro β-Ionone
Retinal Analogues in Squid and Bovine Rhodopsins: Implications for Vision in Salamander Rhodopsin, J.
Am. Chem. Soc. 132, 15856-15859 (2010),
16. A. J. Page, H. Yamane, Y. Ohta, S. Irle, and K. Morokuma, QM/MD Simulation of SWNT Nucleationfrom Transition-Metal Carbide Nanoparticles, J. Am. Chem. Soc. 132, 15699–15707 (2010
17. A. J. Page, Y. Ohta, S. Irle and K. Morokuma, Mechanisms of Single-Walled Carbon Nanotube
Nucleation, Growth and Healing Determined Using QM/MD Methods, Acc. Chem. Res. 43. 1375-1385(2010).
18. J. Jakowski, S. Irle and K. Morokuma, Collision-induced fusion of two C60 fullerenes: quantum chemicalmolecular dynamics simulations, Phys. Rev. B 82, 125443/1-8 (2010).
19. P. V. Avramov, S.Minami, S. Irle, L. A. Chernozatonskii, and K. Morokuma. Atomic Structure andEnergetic Stability of Complex Chiral Silicon Nanowires, J. Phys. Chem. C, 114, 16692-14696 (2010).
20. L. W. Chung, X. Li, H. Sugimoto, Y. Shiro, and K. Morokuma, ONIOM Study on a Missing Piece in Our
Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants. J. Am.
Chem. Soc. 132, 11993-12005 (2010).
21. S. Maeda and K. Morokuma, Communications: A Systematic Method for Locating Transition Structures of
A + B → X Type Reactions, J. Chem. Phys. 24, 241102/1-4 (2010).
22. S. Maeda, K. Ohno, and K. Morokuma, A Theoretical Study on the Photodissociation of Acetone: An
Insight into the Slow Intersystem Crossing and Exploration of Nonadiabatic Pathways to the Ground State,－ 58 －

Ⅳ 研究業績 (2010)

J. Phys. Chem. Lett. 1, 1841-1845 (2010).
23. A. J. Page, S. Minami, Y. Ohta, S. Irle and K. Morokuma, Comparison of Single-Walled Carbon Nanotube
Growth from Fe and Ni Nanoparticles using quantum chemical molecular dynamics methods, Carbon,
48, 3014-3026 (2010).
24. B. Saha, S. Irle and K. Morokuma, Formation mechanism of polycyclic aromatic hydrocarbons (PAH) inthe benzene flame: Density functional tight binding molecular dynamics simulations, J. Chem. Phys. 132,
224303/1-11 (2010)
25. V. P. Ananikov, D. G. Musaev, and K. Morokuma, Real size of ligands, substrates and catalysts: studies ofstructure, reactivity and selectivily by ONIOM and other hybrid computational approaches, J. Mol. Cat. A.
24, 104–119 (2010).
26. S. Maeda, K. Ohno, and K. Morokuma, Updated Branching Plane for Finding Conical Intersections
without Derivative Coupling Vectors. J. Chem. Theo. Comp. 6, 1538–1545 (2010).

3. Review article

J. Jakowski, S. Irle and K. Morokuma, Quantum Chemistry: Propagation of Electronic Structure on aGPU, in “GPU Compute Gems Emerald Edition” ed. W. W. Hwu, Morgan Kaufmann (Elsevier), 59-74(2011).

4. BooksNone

5. Presentation at academic conferences

1. May 10, 2010, Harry King symposium, University of Buffalo, NY, USA, Exciting World of Theoretical
Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures, Catalysts, and Enzymatic
Reactions.
2. May 26, 2010, Molecular Quantum Mechanics conference, Berkeley, CA, USA, ONIOM Studies of
Photochemical Processes and Chemical Reactions of Biomolecular Systems in Protein
3. July 20,2010, Gordon Conf- Atomic and Molecular Interaction, Colby Sawyer college, New London,
USA: Theoretical studies of excited state structure, spectroscopy and dynamics of some gas phase andbiomolecular systems
4. November 29, 2010, invited seminar at Oak Ridge National Laboratory, Oak Ridge, TN USA, Exciting
World of Theoretical Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures,
Catalysts, and Enzymatic Reactions
5. December 1, 2010, invited seminar at University of Tennessee, TN, Nashville, USA, Exciting World of
Theoretical Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures, Catalysts, andEnzymatic Reactions
6. December 17, 2010, Pacifichem 2010, Symposium on Computational Quantum Chemistry: Theory andInteractions with Experiment, Honolulu, HI, USA, History and Overview of Quantum Chemistry in Japan,
on the Occasion of Honoring Profs. Hiroshi Nakatsuji, Kimihiko Hirao, and Shigeru Nagase
7. December 18, 2010, Pacifichem 2010, Symposium on Challenges and Solutions to Accurate Calculations
on Large Molecular Systems and Condensed Phases, Honolulu, HI, USA, ONIOM Studies of
Photochemical Processes and Chemical Reactions of Biomolecular Systems in Protein
8. 2011 年２月７日原子力科学研究所 金曜セミナー、複雑分子系の分子理論によるシミュレーション
9. March 30, 2011, Fatih University, Department of Physics, Istanbul, Turkey, Exciting World of Theoretical
Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures, Catalysts, and Enzymatic
Reaction,－ 59 －

Ⅳ 研究業績 (2010)

３. 特定助教（白眉）Satoshi MAEDA
Visiting Assistant Professor (The Hakubi Center, Kyoto University),
Kenichi Fukui Memorial Research Group 1

1. Summary of the research of the year
1-0. Introduction
The mechanism of chemical reactions can be elucidated by exploring quantum chemical potential
energy surfaces (PESs) for reaction pathways [1,2]. Search for transition state (TS) structures is theprimal task in such studies, since a reaction path can be computed easily by the intrinsic reaction
coordinate (IRC) method [3] once a corresponding TS structure is found. Reaction mechanisms ofnumerous chemical reactions have been elucidated by calculations of TS structures andcorresponding reaction pathways.
One TS structure can be found by a geometry optimization starting from an initial guess
structure. However, an initial guess structure leads only to a TS structure anticipated from it. For
finding unexpected pathways as well as anticipated ones, systematic search is necessary using an
automated reaction path search method.
There had been no general method which can explore chemical reaction pathways automaticallyon quantum mechanical PESs until very recently. Hence, we have developed two such methods: theglobal reaction route mapping (GRRM) method [4-6] and the artificial force induced reaction(AFIR) method [original paper 9]. These two are independent but complementally to each other.
Reaction pathways of type A → X (isomerization) and A → X + Y (dissociation) can be explored by
GRRM, while AFIR can search for A + B → X (+ Y) type synthetic pathways.
We applied these methods to some complex chemical reactions: photolysis of atmosphericmolecules [original papers 1, 7, and 10], combustion reactions of unsaturated hydrocarbons [original
paper 2], an organic multicomponent reaction [original paper 4], a photoionization reaction in ahydrogen-bond cluster [original paper 6], and a surface oxidation reaction [original paper 8].
We also investigated on the infrared spectra of benzene [original paper 3] and ion-molecule
reactions of nerve-agent VX [original paper 5] to make analyses of experimental data.
Works in original papers 4, 5, 6, 7, and 8 were conducted with experimental groups.
[1] Schlegel, H. B. J. Comput. Chem. 2003, 24, 1514.
[2] Jensen, F. Introduction to Computational Chemistry, 2nd edn., Wiley, Chichester, 2007.
[3] Fukui, K. Acc. Chem. Res. 1981, 14, 363.
[4] Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277.
[5] Maeda, S.; Ohno, K. J. Phys. Chem. A 2005, 109, 5742.
[6] Ohno, K.; Maeda, S. J. Phys. Chem. A 2006, 110, 8933.
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Ⅳ 研究業績 (2010)

1-1. Excited-State Roaming Dynamics in Photolysis of a Nitrate Radical (original paper 1)
Roaming dynamics has been recognized as one of the key mechanisms in atmospheric andcombustion processes. In this Letter, we report the first example of roaming dynamics that occurs on
an excited-state potential energy surface. In the photodissociation of a nitrate radical, systematic
CASPT2 reaction path search and DFT dynamics calculations show that the roaming dynamics
occurs on the first excited doublet state (D1). The direct dissociation on D1 gives the minor
vibrationally cold O2, while the indirect dissociation after the nonadiabatic transition to the grounddoublet state (D0) produces the major vibrationally hot O2; this proposal explains the recent
experimental results. (This article was highlighted in News & Views of Nature Chemistry: see, S. W.
North, Roaming in the Dark., Nat. Chem., 2011, 3, 504-505.)
2-2. Finding Minimum Structures on the Seam of Crossing in Reactions of Type A + B → X:
Exploration of Nonadiabatic Ignition Pathways of Unsaturated Hydrocarbons (original paper2)
A new theoretical approach is proposed for finding automatically minimum structures on the seam ofcrossing (MSX) in reactions of type A + B → X, where the artificial-force-induced reaction (AFIR)
method is combined with the seam model function (SMF) approach. Its application to reactions
between triplet dioxygen and unsaturated hydrocarbons provided many MSX structures. In addition
to known ignition pathways, we discovered a pathway through a new type of MSX in the reaction of
dioxygen with aromatic hydrocarbons; for benzene, this new pathway requires a lower energy thanthose of three known ignition pathways and is likely to be the most important. This demonstrates
that the AFIR-SMF approach has the ability to discover unknown/unexpected MSX structures
without prejudice for presumed pathways or mechanisms.
2-3. Ab Initio Anharmonic Calculations of Vibrational Frequencies of Benzene by Means of
Efficient Construction of Potential Energy Functions (original paper 3)
An efficient technique constructing anharmonic potential energy functions was applied to ab initio
vibrational analysis of benzene. Anharmonic potentials including the 6-order terms, much higher
than the full quartic force field, were automatically generated by a second-order algorithm using thescaled hypersphere search method, and vibrational calculations were performed at the level of
VQDPT[1+2]. In comparison with previously reported anharmonic calculations, the present
approach gave an excellent ab initio result for in-plane modes including the b2u so called Kekulé
mode. Characteristic properties of various approaches were discussed in connection with theanharmonic effects and the strong vibronic effects.
2-4. Finding Reaction Pathways for Multicomponent Reactions: The Passerini Reaction Is a
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Ⅳ 研究業績 (2010)

Four-Component Reaction (original paper 4)
The Passerini three-component reaction of a carboxylic acid, an aldehyde (or ketone), and an
isocyanide to give an α-acyloxycarboxamide actually follows a four-component mechanism
involving an additional molecule of carboxylic acid (see scheme). The discovery was made by
applyinganew“reaction

route

explorer”

tothesimplest

Passerini

reaction(HCOOH+HCHO+CH3NC).
2-5. Theoretical Proton Affinity and Fluoride Affinity of Nerve Agent VX (original paper 5)
Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at
the

RI-MP2/cc-pVTZ//B3LYP/6-31G*

andRI-MP2/aug-cc-pVTZ//B3LYP/6-31+G*

levels,+respectively. The protonation leads to various unique structures, with H attached to oxygen,nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of−ΔE ~ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H2, CH4dissociation as well as destruction channels have been found, among which the CH4 +[Et−O−P(═O)(Me)−S−(CH2)2−N+(iPr)═CHMe] product and the destruction product forming
Et−O−P(═O)(Me)−SMe + CH2═N+(iPr)2 are only 9 kcal/mol less stable than the most stable
N-protonated product. For fluoridization, the S−P destruction channel to give Et−O−P(═O)(Me)(F)+ [S−(CH2)2−N−(iPr)2]− is energetically the most favorable, with a fluoride affinity of −ΔE ~ 44 kcal.
Various F− ion−molecule complexes are also found, with the one having F− interacting with twohydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction
product. These results suggest VX behaves quite differently from surrogate systems.
2-6. Long-Range Migration of a Water Molecule To Catalyze a Tautomerization in
Photoionization of the Hydrated Formamide Cluster (original paper 6)
The dynamics on the vacuum-ultraviolet one-photon ionization of a formamide−water cluster isinvestigated by a combination of theoretical reaction-path search and infrared spectroscopic methods.
A keto−enol tautomerization of the formamide moiety occurs after photoionization by a catalytic
action of the water molecule accompanied with its long-distance migration; the water molecule inthe cluster migrates almost one turn around the formamide moiety. During the migration, the watermolecule abstracts the proton of CH in the formamide moiety and carries it to the O atom side in the
carbonyl group through a “catch and release”-type catalytic action.
2-7. Photochemistry of Methyl Ethyl Ketone: Quantum Yields and S1/S0-Diradical Mechanismof Photodissociation (original paper 7)
Pulsed laser photolysis (PLP) at λ = 248 and 308 nm coupled with gas-chromatographic analysis isapplied to determine the photodissociation quantum yield (QY) of methyl ethyl ketone (MEK).
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Ⅳ 研究業績 (2010)

Temperature dependent UV absorption cross-sections [σMEK(λ,T)] are also determined. At 308 nm,
the QY decreases with decreasing temperature (T = 323–233 K) and with increasing pressure (P =67-998 mbar synthetic air). Stern–Volmer (SV) analysis of the T and P dependent QYs provides theexperimental estimate of ES1 = 398 ± 9 kJ mol−1 (= 300 ± 6 nm) for the barrier of the first excited
singlet state (S1). The QY at 248 nm is close to unity and independent of pressure (T = 298 K).
Theoretical reaction pathways are examined systematically on the basis of CASPT2/6-31+G*
calculations. Among three possible pathways, a S1/S0-diradical mechanism, which involves H atomtransfer on the S1 surface, followed by a nonadiabatic transition at a diradical isomer of MEK,
explains the experimental data very well. Therefore, this unusual mechanism, which is not seen inany smaller carbonyl compounds, is proposed as an important pathway for the MEK dissociation.
Our study supports the view that both the absorption cross-sections and the QYs of carbonyls havesignificant temperature dependences that should be taken into account for accurate modeling of
atmospheric chemistry. (This article was featured on the inside cover.)2-8. Theoretical Investigation of the Reaction Pathway of O Atom on Si(001)-(2 × 1) (original
paper 8)Structural, energetic, and mechanistic features of the initial steps of the reaction of an O atom with
Si(001)-(2 × 1) were modeled by the use of a Si9H12 + O system. Transition state structures (TSs)and equilibrium structures (EQs) as well as dissociation channels (DCs) were systematicallysearched using a global reaction route mapping (GRRM) technique on the potential energy surface(PES) based on the scaled hypersphere search (SHS) algorithm. The first six low-energy structures
were consistent with known structure models for oxygen adsorption on the dimer of Si(001)-(2 × 1).
Other structures with higher energies could be well interpreted as intermediates leading toward
reaction paths for migration/dissociation occurring at high temperatures.
2-9. A Systematic Method for Locating Transition Structures of A + B → X Type Reactions(original paper 9)
Search for transition structures (TSs) as first-order saddles is one of the most important tasks intheoretical study of chemical reaction. Although automated search has been established either bystarting from a local minimum (MIN) or by connecting two MINs, there is no systematic method
which can locate TSs of A + B → X (+ Y) type reactions starting from separated reactants. We
propose such an approach for the first time; it was demonstrated to work very well in the SN2,
Diels–Alder, and Wittig reactions.
2-10. A Theoretical Study on the Photodissociation of Acetone: An Insight into the Slow
Intersystem Crossing and Exploration of Nonadiabatic Pathways to the Ground State (original－ 63 －

Ⅳ 研究業績 (2010)

paper 10)Structures of transition states (TSs) and minima on seam of crossing (MSXs) for potential energy
surfaces (PESs) of acetone of the S0, S1, and T1 states were explored. On the basis of the results, we
propose a new mechanism, slow intersystem crossing from S1 to T1 without seam of crossing,followed by CH3 dissociation via a TS on T1; this slow pathway will be overtaken by a more
efficient S1 pathway for higher energy. This is consistent with the observed long lifetime of the S1
species. Moreover, four channels, including three new ones, were found to regenerate the groundstate acetone from the S1 PES, and they all may be involved in the roaming channel that has been
proposed recently as a new route of CO generation in a 230 nm photolysis. There are significant
differences in MSX structures and energies between the present CASPT2 results and previous
CASSCF results.
2. List of original papers(1) H. Xiao, S. Maeda, K. Morokuma, Excited State Roaming Dynamics in Photolysis of Nitrate
Radical., J. Phys. Chem. Lett., 2011, 2, 934-938.
(2) S. Maeda, R. Saito, K. Morokuma, Finding Minimum Structures on the Seam of Crossing in
Reactions of Type A + B → X: Exploration of Nonadiabatic Ignition Pathways of Unsaturated
Hydrocarbons., J. Phys. Chem. Lett., 2011, 2, 852-857.
(3) K. Ohno, S. Maeda, Ab Initio Anharmonic Calculations of Vibrational Frequencies of Benzene
by Means of Efficient Construction of Potential Energy Functions., Chem. Phys. Lett., 2011,
503, 322-326.
(4) S. Maeda, S. Komagawa, M. Uchiyama, K. Morokuma, Finding Reaction Pathways forMulticomponent Reactions: The Passerini Reaction Is a Four-Component Reaction., Angew.
Chem. Int. Ed., 2011, 50, 644-649.
(5) N. C. Bera, S. Maeda, K. Morokuma, A. A. Viggiano, Theoretical Proton Affinity and Fluoride
Affinity of Nerve Agent VX., J. Phys. Chem. A, 2010, 114, 13189-13197.
(6) S. Maeda, Y. Matsuda, S. Mizutani, A. Fujii, K. Ohno, Long-Range Migration of a Water
Molecule To Catalyze a Tautomerization in Photoionization of the Hydrated Formamide
Cluster., J. Phys. Chem. A, 2010, 114, 11896-11899.
(7) R. Nadasdi, G. L. Zugner, M. Farkas, S. Dobe, S. Maeda, K. Morokuma, Photochemistry of
Methyl Ethyl Ketone: Quantum Yields and S1/S0-Diradical Mechanism of Photodissociation.,
ChemPhysChem, 2010, 11, 3883-3895.
(8) S. Ohno, K. Shudo, M. Tanaka, S. Maeda, K. Ohno, Theoretical Investigation of the Reaction
Pathway of O Atom on Si(001)-(2 × 1)., J. Phys. Chem. C, 2010, 114, 15671-15677.
(9) S. Maeda, K. Morokuma, Communication: A Systematic Method for Locating Transition
Structures of A + B → X Type Reactions., J. Chem. Phys., 2010, 132, 241102/1-4.
－ 64 －

Ⅳ 研究業績 (2010)(10) S. Maeda, K. Ohno, K. Morokuma, A Theoretical Study on the Photodissociation of Acetone:
An Insight into the Slow Intersystem Crossing and Exploration of Nonadiabatic Pathways to the
Ground State., J. Phys. Chem. Lett., 2010, 1, 1841-1845.
3. List of review articles(1) 前田理・大野公一・諸熊奎治、「分子の反応経路の自動探索が可能になった」、現代
化学、2011, 478, 32-37.
4. List of books
5. List of presentations at meetings(1) (Oral) S. Maeda, K. Ohno, K. Morokuma, Theoretical Studies on Gas-Phase Photochemical
Reaction Mechanisms of Small Organic Molecules Using the Global Reaction Route Mapping
Method., The 2010 International Chemical Congress of Pacific Basin Societies (Pacifichem),
Honolulu, Hawaii, USA, December 15-20, 2010(2) (Poster) S. Maeda, K. Ohno, K. Morokuma, Efficient Optimizations of Conical Intersection
Geometries Using New Algorithms., The 2010 International Chemical Congress of PacificBasin Societies (Pacifichem), Honolulu, Hawaii, USA, December 15-20, 2010(3) (Invited talk) S. Maeda, Development of Automated Reaction Path Search Methods andApplications to Hydrogen-bonded Clusters., Molecular Photoscience Research Center
International Symposium "New Horizons of Cluster Chemistry", Kobe University, Japan,
October 9-10, 2010(4) (招待講演)「反応経路探索法の新展開」、シンポジウム「化学反応経路探索のニューフ
ロンティア 2010」、京都大学福井謙一記念研究センター、2010 年 9 月 13 日
(5) (口頭発表)前田理・駒川晋輔・内山真伸・諸熊奎治、「多成分反応の遷移構造の自動的な系統探索」、第 4 回分子科学討論会、大阪大学豊中キャンパス、2010 年 9 月 14-17日(6) (Oral) S. Maeda, Systematic Exploration of Photochemical Reaction Pathways: Applications to
Ketones and Aldehydes., The 8th FIFC Seminar, Fukui Institute for Fundamental Chemistry,
Kyoto University, June 21, 2010(7) (Oral) S. Maeda, K. Ohno, K. Morokuma, Photodissociation Mechanisms of Aldehydes and
Ketones., 26th Symposium on Chemical Kinetics and Dynamics, Hiroshima University Satake
Memorial Hall, June 2-4, 2010
6. Others－ 65 －

Ⅳ 研究業績 (2010)

４. 博士研究員

Biswajit SAHAFIFC Fellow, Fukui kenichi Memorial Research Group 1（To 30 Apr. 2010）

1. Summary of the research of the year FY2010(A) Annealing of hot giant fullerenes: DFTB MD simulations

To understand the fullerene formation process, Irle, Morokuma, and coworkers had performed earlier aseries of density-functional tight-binding (DFTB)-based quantum chemical molecular dynamics (QM/MD)
simulations. These extensive nonequilibrium MD studies led to the formulation of the “Shrinking Hot Giant”(SHG) road of fullerene formation, according to which at first giant fullerenes (GFs) Cn with n > 80 self-assemble
through irreversible interactions and autocatalytic reactions of polyyne chains or macrocycles (‘size up’), whichthen shrink in size down to smaller, kinetically more stable fullerenes such as C70 and C60, initially by polyyne“antenna” ‘fall-off’ and later by continued and irreversible C2 evaporation (‘size down’). The latter cage shrinking
process resembles Smalley’s ‘shrink-wrap’ mechanism of laser-induced C2 elimination from C60, and occurs underthe effect of thermal excitation in the case of defect-bearing fullerene cages, even though the shrinking processitself is endothermic.
Although thermal shrinking has been established as a widely accepted mechanism, recent HRTEM
observations of direct fullerene formation from a graphene flake and of catalyst-free fullerene growth inside
nanotubes, as well as the symmetric smooth size distributions of fullerene laser coalescence products around main
BF dimer (C118), trimer (C178), etc. peaks are seemingly at odds with the SHG road. We note however that in thecage growth and coalescence experiments a tightly sealed environment is required, and that C2 can presumably notescape in such an experimental setup. It therefore appears that in addition to C2 evaporation, the reverse process,namely C2 capture, should occur as well, consistent with the principle of microscopic reversibility.
In the present study we therefore revisit the size-down shrinking process of hot GFs as well as the growthmechanism by maintaining constant carbon density in a QM/MD simulation with periodic boundary conditions, tosimulate the effect of an environment where C2 cannot escape. We explicitly include noble gas (Ng) atoms in themodel system to increase the pressure. Interactions with Ng atoms were included using nonbonded molecularmechanics Lennard-Jones potentials, resulting in the use of a mixed QM/MM potential. We describe details of
isokinetic, high-temperature QM/MD trajectories for C2 ejection and capture processes of GFs that wereself-assembled in previous simulations, and focus on the structure and energetics of “antenna fall-off”, “C2 popout” and “C2 incorporation” events under the constant density conditions. Our study is qualitative and not aimed
at quantitatively evaluating shrinking and growth rates and their dependence on fullerene cage isomer, carbon
density, buffer gas pressure, and temperature, as such a study would exceed present computational capabilities.
Molecular dynamics (MD) simulations were performed using the density-functional tight-binding (DFTB)
method within non-charge-consistent (NCC) approximation. The Gamma-point approximation was employed in
the periodic boundary calculations. C-Ng and Ng-Ng interactions were evaluated using Lennard-Jones (LJ) pairpotentials. The C-He, He-He, C-Ar, and Ar-Ar LJ parameters were taken from literature.

－ 66 －

Ⅳ 研究業績 (2010)

Shrinking Mechanism
We describe the shrinking mechanism in the present simulations briefly by giving examples in Figure 1.
At first stage antenna fall-off event occurred very fast where polyyne chains are detached from the cage. The
second stage of the shrinking process is C2 pop-out. Figure 1 shows a sequence of events leading up to C2
elimination from a divalent carbon (in the following named “carbene”) defect. There are four rings participating inthis ejection, marked in blue: a heptagon, two hexagons, and a pentagon. At first, the seven-membered ring
containing the carbene produced a kink at 36.33 ps. The kink site and the four participating rings converted to two
joint 10-membered ring openings, with the carbene defect being converted to a C3 bridge at 36.34 ps. At 36.39
ps these 10-membered rings converted to
two abutting pentagons and two fused
7-membered rings in which the bridge
was shortened to two carbons. Around37.07 ps the bridge broke and a wobblingC2 unit was formed. Much later, ataround 90.19 ps, this wobbling C2 brokeoff, leaving behind a carbene-bearing
octagon joint to the two abutting
pentagons.

Furtherringtransforms

occurred at 108.03 ps when this structuretransformed into a carbene-containing
Figure 1. C2-fragment emission and shrinking mechanism.
7/5/6 structure.

Overall, this process

corresponds to a carbene-containing 7/6/6/5 structure transforming into a carbene-containing 7/5/6 structure where
one C2 unit was ejected. The periodic boundary conditions allow future reactions with the fullerene cage and theejected C2 molecules, resulting in C2 capture as described in the next paragraph.

Growth Mechanism
Cage growth only occurs in trajectories where a sufficient number of carbon fragments were present in
the system, allowing reactions of Cn fragments with the giant fullerene during the simulation time.
Representative snapshots of C2 capture processes are shown in Figure 2. No significant difference is observed insimulations using different thermal control conditions (VS, He or Ar). In this Figure, the newly added C atoms areindicated by red color while the C atoms of the participating ring structures are indicated by blue color. We notethat C2 incorporation can occur either via breaking of the original C2 bond, or the captured C2 molecule becomes
subsequently “swallowed whole”, leaving its original C-C bond intact as shown in Figure 2. It is observed that ingeneral the C2 unit is incorporated via three distinct stages: (i) reaction of C2 with a cage C which is shared byadjacent five-and six-membered rings/five- and seven membered rings/six- and seven-membered rings(chemisorptions), (ii) large ring formation in which C2 is attached to form a bridge, and (iii) C2 is consumed by thecage via ring transformation and thus forming five- and six-membered rings. In some cases the two C’s of the C2
unit are consumed in two steps.

－ 67 －

Ⅳ 研究業績 (2010)

The growth mechanism proceeds in our simulations exclusively by the more probable edge-on attack of
C2 and subsequent cage incorporation. The reorganization of the exothermic reaction energy due to GF-C2 bondformation in the carbon network is crucial toachieve a lifetime long enough to proceed via
the cage ingestion processes described above.
Our simulations show that the cage ingestion
occurs on the order of several tens ofpicoseconds after initial C2 capture.
Constant

temperature/constantdensity direct quantum chemical/molecularmechanics (QM/MM) molecular dynamics(MD)simulationsofdynamically

self-assembled, hot giant fullerenes (GFs)
Figure 2 C2-fragment incorporation events.
with their attached polyyne antennas were
performed on the nanosecond timescale to investigate the C2 ejection and cage incorporation rates associated with
GF cage shrinking and growth. It was found that hot GFs are able to shrink as well as grow during continued hightemperature simulations, on the order of several carbon atoms per nanosecond.
It was observed that larger GFs (>100 cage carbons) have a tendency to shrink whereas smaller GFs (<100cage carbons) tend to grow. However, the C2 ejection and insertion rates depend strongly on the concentration ofavailable carbon outside the cages: A larger number of free carbons increases the growth rate, whereas a smaller
number increases the shrinking rate.

2. Original papers

1.

B. Saha, S. Irle, K. Morokuma, “Formation mechanism of polycyclic aromatic hydrocarbons (PAHs) inbenzene combustion: Quantum chemical molecular dynamics simulations”, J. Chem. Phys. 132, 224303(2010)

3. Presentation at academic conferences

4. Others－ 68 －

Ⅳ 研究業績 (2010)

Hajime HIRAOFIFC Fellow, Fukui Kenichi Memorial Research Group 1（To 31 Oct. 2010）

1. Summary of the research of the year: Computational studies of bioinorganic chemistry
Metalloenzymes are finely tuned catalytic machines that drive energetically unfavorable reactions under mild
conditions, often with surprisingly high selectivity. Detailed understanding of the catalytic functions ofmetalloenzymes is of considerable importance in the sense that it would open up new avenues for practicalapplications such as rational design of potent enzyme inhibitors and development of powerful biomimetic
catalysts. A fundamental prerequisite for that is a full understanding of the enzymatic reaction mechanism,and quantum mechanical (QM) calculations and hybrid QM/MM methods such as ONIOM(QM:MM) haveuseful roles to play in such efforts. Another approach to elucidate the catalytic machineries ofmetalloenzymes should be to investigate mechanisms of simpler synthetic complexes that have someresemblance to metalloenzymes. Studies of biomimetic systems may provide us with clues as to how
enzymes operate in physiological conditions, as well as how enzyme-like competent catalysts could
rationally be designed. This year, the author studied both metalloenzymes and transition-metal complexes
actively.

1-1. Density Functional Theory Investigation
Hydroxyethylphosphonate Dioxygenase

of

the

Catalytic

Mechanismof

Hydroxyethylphosphonate dioxygenase (HEPD) is a mononuclear nonheme iron enzyme that utilizes an O2
molecule to cleave a C−C bond in 2-hydroxyethylphosphonate and produce hydroxymethylphosphonate (HMP)and formic acid. Density functional theory calculations were performed on an enzyme active-site model of HEPD
to understand its catalytic mechanism. The reaction starts with H-abstraction from the C2 position of 2-HEP by aferric superoxide-type (Fe(III)-OO•−) intermediate, in a similar manner to the H-abstraction in the reaction of thedinuclear iron enzyme myo-inositol oxygenase. The resultant Fe(II)-OOH intermediate may follow either ahydroperoxylation or hydroxylation pathway, the former process being energetically more favorable. In thehydroperoxylation pathway, a ferrous-alkylhydroperoxo
intermediate is formed, and then its O − O bond ishomolytically cleaved to yield a complex of ferrichydroxide with a gem-diol radical. Subsequent C−C bondcleavage within the gem-diol leads to formation of an
R-CH2• species and one of the two products (i.e., formicacid). The R-CH2• then intramolecularly forms a C−O
bond with the ferric hydroxide to provide the otherproduct, HMP. The overall reaction pathway does not
require the use of a high-valent ferryl intermediate but
does require ferric superoxide and ferric hydroxideintermediates.

－ 69 －

Figure 1. X-ray crystal structure of HEPD.

Ⅳ 研究業績 (2010)

1-2. Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H2O2 and a
Nonheme Iron(II) Complex: O–O Cleavage Involving Proton-Coupled Electron TransferIt

hasrecently

been

shown

that

the

nonhemeoxoiron(IV)species

supportedbythe

1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane ligand (TMC) can be generated in near-quantitative
yield by reacting [FeII(TMC)(OTf)2] with a stoichiometric amount of H2O2 in CH3CN in the presence of
2,6-lutidine (Li, F.; England, J.; Que, L., Jr. J. Am. Chem. Soc. 2010, 132, 2134−2135). This finding has
major implications for O–O bond cleavage events in both Fenton chemistry and nonheme iron enzymes. To
understand the mechanism of this process, especially the intimate details of the O–O bond cleavage step, aseries of density functional theory (DFT) calculations and analyses have been carried out. Two distinct
reaction paths (A and B) were identified. Path A consists of two principal steps: (1) coordination of H2O2 toFe(II) and (2) a combination of partial homolytic O–O bond cleavage and proton-coupled electron transfer(PCET). The latter combination renders the rate-limiting O–O cleavage effectively a heterolytic process. Path
B proceeds via a simultaneous homolytic O–O bond cleavage of H2O2 and Fe–O bond formation. This isfollowed by H abstraction from the resultant Fe(III)–OH species by an •OH radical. Calculations suggest thatpath B is plausible in the absence of base. However, once 2,6-lutidine is added to the reacting system, thereaction barrier is lowered and more importantly the mechanistic path switches to path A, where 2,6-lutidine
plays an essential role as an acid–base catalyst in a manner similar to how the distal histidine or glutamate
residue assists in compound I formation in heme peroxidases. The reaction was found to proceed
predominantly on the quintet spin state surface, and a transition to the triplet state, the experimentally known
ground state for the TMC-oxoiron(IV) species, occurs in the last stage of the oxoiron(IV) formation process.

Figure 2. Key transitions states for paths A and B.
2. Original papers(1) Hajime Hirao and Keiji Morokuma
Ferric Superoxide and Ferric Hydroxide Are Used in the Catalytic Mechanism ofHydroxyethylphosphonate Dioxygenase (HEPD): A Density Functional Theory
Investigation－ 70 －

Ⅳ 研究業績 (2010)

J. Am. Chem. Soc. 2010, 132, 17901-17909.
(2) Hajime Hirao
Correlation Diagram Approach as a Tool for Understanding Chemistry: An Introductory
Overview
WIREs: Computational Molecular Science, 2011, 1, 337-349.
(3) Lung Wa Chung, Hajime Hirao, Xin Li, and Keiji Morokuma
The ONIOM Method: Its Foundation and Applications to Metalloenzymes andPhotobiology
WIREs: Computational Molecular Science, in press.
(4) Hajime Hirao and Keiji Morokuma
Recent Progress in the Theoretical Studies of Structure, Function, and Reaction of
Biological Molecules
Yakugaku Zasshi-J. Pharm. Soc. Jpn. 2011, 131, 1151-1161.
(5) Hajime Hirao, Feifei Li, Lawrence Que, Jr., and Keiji Morokuma
Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H2O2 and a Nonheme
Iron(II) Complex: O–O Cleavage Involving Proton-Coupled Electron Transfer
Inorg. Chem. 2011, 50, 6637-6648.
(6) Hajime Hirao
Energy Decomposition Analysis of the Protein Environmental Effect: The Case of
Cytochrome P450cam Compound I
Chem. Lett. in press.
(7) Witcha Treesuwan, Hajime Hirao, Supa Hannongbua and Keiji Morokuma
Characteristic Vibration Patterns and Protein Binding of Odor Compounds
from Bread Baking Volatiles: Density Functional and ONIOM Study and Principle
Component Analysis (PCA)
J. Mol. Model. in press.
3. Presentation at academic conferences(1) Hajime Hirao, Lawrence Que, Jr., Keiji Morokuma (Oral: 5T02)
How is Fe(IV)=O Formed from H2O2 and a Nonheme Fe(II) Complex? A Density
Functional Theory StudyICTAC-13: 13th International Conference on Computational Catalysis, Matsushima (Miyagi,
Japan), June 25, 2010.
(2) Hajime Hirao, Keiji Morokuma (Poster: 3P125)
シトクロム P450cam の化学反応における環境効果のエネルギー分割解析
4th Annual Meeting of Japan Society for Molecular Science (2010), Osaka University(Osaka), September 16, 2010.

－ 71 －

Ⅳ 研究業績 (2010)

4. Others
4-1. Other presentations(1) Hajime Hirao (Oral)
計算量子化学による鉄酵素の反応メカニズムの理解
70th Colloquium of Computational Sciences. University of Tsukuba (Tsukuba), April 8,
2010.
(2) Hajime Hirao (Oral)
Biology-Related Activities at the Morokuma Group (Part 1)
JENESYS meeting, Kyoto University (Kyoto), June 17, 2010.
(3) Hajime Hirao (Oral)
Computational Studies of Molecular Interactions and Chemical Reactions: From Simple
Molecules to Complex Systems
An open seminar, Nanyang Technological University (Singapore), July 27, 2010.
(4) Hajime Hirao (Oral)
Valence-shell electron pair repulsion (VSEPR) theory and molecular shape
An open lecture, Nanyang Technological University (Singapore), July 28, 2010.
4-2. Competitive external research grants(1) The Kyoto University Foundation Grant (Travel stipend to attend Pacifichem2010,
Declined because I left Kyoto University)(2) Takeda Science Foundation Grant (Life Science)
4-3. Competitive external computer resources(1) Collaborative Research Program for Young Scientists of ACCMS and IIMC, Kyoto
University.

－ 72 －

Ⅳ 研究業績 (2010)

Zhuofeng KE
FIFC Fellow, Fukui kenichi Memorial Research Group 1

1. Summary of the research of the year (3-5 pages, includes appropriate figures and tables)
I. Theoretical Studies of the Reaction Mechanism, Regioselectivity and Stereoregularity.
Poly(phenylacetylene) (PPA) is aconducting polymer with especiallyintriguing properties. Its stability,
solubility in organic solvents, helicalconformation, and unique magnetic andelectrical properties have prompted
development of PPA-derived materials
for numerous high-tech applications,
including optical polarizing films andasymmetric electrodes. The
properties of PPA depend much
RhI inerstion
on its structure. To tailor the PPA
RhIII insertion
RhC metathesis
structure, it is necessary tounderstand
the
exact
mechanisms
ofthepolymerization
process.
However, it has remained a

Scheme 1. Rh-Catalyzed Polymerization of Phenylacetylene

H pel

ΔH (kcal/mol)

H
H

40
30
20
10
0

RhIII

III-1

L

Rh

pel
pel

RhI

pel
Ph

III-2
Ph

Ph
H

C

RhI

Pel

III-1 (4.2) PA
I-1 (0.0)

RhI

L

H
RhIII

Ph

III-TS1(32.5)
Ph

H

Pel

RhI

C-TS1(16.7)

Ph

C

L

H
Ph
RhIII

RhI

Ph

C
Pel

H

III-3(-1.0)

Ph
RhI

pel

Pel

C-2(8.6)
I-2 (1.9)pel

Ph III-3

I-TS1(14.0)

Ph

-10

pel

Ph

C

III-2 (10.7)
C-1(5.5)

RhIII

pel

III

Ph
RhI

pel

C-TS2(-8.3)

pel

I-3 (-14.9)

Ph

H

RhI

pel

PA

ΔΗ ≠ = 23.7

C
H

C-4(-17.2)

Phchallenge to selectively produce
PPA materials with desiredI-4 (-26.9)-30
C-3(-32.0)
structures, partially due to theI-5 (-56.5)
mechanism is not well known-60
yet. Rh-based catalysts offer
numerous advantages over otherFigure 1. Potential energy surfaces of the RhI/RhIII-insertion, andtransition metal catalysts for themetathesis mechanisms for the Rh-Catalyzed Polymerization ofsynthesisof
PPA-derived
materials. The Rh-catalyzed polymerization is tolerant toward polar functionalized PA derivatives,
can be used to construct screw-sense, helical materials. Herein, we used sophisticatedcomputational methods - density functional theory, ONIOM method, and molecular dynamics - togain insight into the rhodium-catalyzed polymerization process and the factors that control theregiochemistry and stereochemistry of the resulting polymer. The computational findings havepossible applications in the design of catalysts tailored for PPA polymerizations.
-20

pel

pel

I-TS2 (-18.7)

Ph

Rh

Ph

C

III

Rh

Pel

Ph
H

Ph

H

Rh

pel

H

pel

Ph

Ph

Rh

Ph

－ 73 －

Ph

H

H

pel

Ⅳ 研究業績 (2010)

Figure 2. Regioselectivity origin: electronic characteristics of the
conjugative insertion transition state and its molecular orbital diagram.

We found that the
Rh-catalyzed polymerizationof PA proceeds via the RhI
insertionmechanism,
although all the RhI, RhIII,
and Rh-carbene types ofintermediates are calculated
to be thermodynamically andkinetically feasible at room
temperature in solution. The
RhI insertion mechanism iscalculated
to
have
a
propagation
activation
enthalpy of ‫׽‬9 kcal/mol,much lower than those of the

Rh-carbene metathesis mechanism (ΔH≠ ≈ 25 kcal/mol for the rate-determining step) and the RhIII
insertion mechanism (ΔH≠ ≈ 22 kcal/mol).
The RhI insertion mechanism prefers a 2,1-insertion, leading to head-to-tail regioselective PPA.
The preference for 2,1-insertion over 1,2-insertion increases with increasing bulk of the propagatedchain. The 2,1-insertion is favored over 1,2-insertion by up to 7.9 kcal/mol with the ONIOM
models. Our study found a unique π-conjugative characteristic for the insertion transition state, inwhich a conjugative network is formed by the conjugative PA, the Rh dπ orbital, and the π acceptor
nbd ligand, to gain extra
stabilization energy. This
conjugative characteristicof the insertion transition
state always causes steric
repulsion between thephenyl group of PA and thebulky propagation chain,probably
exclusively
preferring the 2,1-insertion.
This provides a newunderstanding for tuning
2,1-/1,2-selectivity during
polymerization of PA.
Figure 3. Stereoregularity origin: Steric repulsion in the transition states leading to
Kinetic factors play adifferent stereoconformers of PPA.
key
role
in
the
stereoconformational selectivity. PA monomer highly prefers to insert into a parent propagation－ 74 －

Ⅳ 研究業績 (2010)

chain in a cis-transoidal conformer rather than a cis-cisoidal conformer (ΔΔH≠ ≥ 4.8 kcal/mol). The
propagation chain can easily adopt a cis-transoidal conformation via single bond rotation before thenext insertion. The kinetic difference mainly originates from steric repulsion caused by the
conformational constraint of the parent propagation chain during insertion. To tailor thestereoregularity of the PPA catalyzed by Rh catalysts, it is important to distinguish kinetic control
from thermodynamic control.
II. Theoretical Study of Artificial Metalloenzymes.
The efficiency and specify of enzymes in nature
inspire scientists to design and construct artificial
enzyme to reproduce their catalytic function or todevelop novel enzyme-like catalysis. One of thepromising strategies is to incorporate a catalytic
metal complex into a host protein to construct an
artificial metalloenzyme with novel catalytic
features in the well-defined “womb” of protein.
Figure 4. Rh-catalyzed Polymerization of
However, the design of new artificial
Phenylacetylene in Nano-Cavity of apo-Ferritin
metalloenzyme is rather challenging. The structuresof metal complexes are much variable and the interaction between metal complex and protein israther tricky leading to complicated binding sites for the catalysis inside artificial metalloenzyme.
Understanding the active site and the catalysis process inside artificial metalloenzyme is extremely
important to advance its rational design and development. However, the characterization of thestructural details of artificial metalloenzyme is very difficult. Even with some structural snapshotsof the catalytic precursor or intermediates, we are still far from understanding the active site and thereaction mechanism inside artificial metalloenzymes. In this study, we demonstrated an example
with QM/MM studies to illustrate the complicated mechanism in artificial metalloenzyme based on
our recently developed artificial metalloenzyme for polymerization.

Figure 5. The solvated apo-Ferritin structures with 24 sub-units, the mono-unit structure with immobilized rhodium
complexes, and the structures for binding site C, D and E on each mono-unite－ 75 －

Ⅳ 研究業績 (2010)

We have evaluated the possible mechanisms for all binding sites suggested by X-ray crystal
structure, i.e. site C, D and E. We
found that site C, D and E themselves
are only precursors, not the true active
site for the polymerization of PA. The
active site should be a RhI-center
located at a hydrophobic pocket nearsite D. The RhI-insertion is the mostplausible polymerization mechanism.
The active site is first generated by theabstraction of rhodium-PA complex
from site D. After the insertion, themetal center doesn’t recombine to
His49 of site D, remaining in the

Figure 6. The plausible active site in hydrophobic pocket near site
D and the 4-fold channel.

Figure 7. The overview mechanism of the polymerization of PA in
the studied artificial metalloenzyme system.

－ 76 －hydrophobic
pocketforthepropagation.
The hydrophobic pocket, which
composed of residues Phe50, Lys143,
and Leu170, plays a key role for thepolymerization behavior in the studied
artificial metalloenzyme. The active
site, the nonpolar 4-fold channel ofFerritin, and other hydrophobic
resides nearby compose a hydrophobic
regionforthetransportation,
coordination and insertion of PA
during the polymerization. Notably,
this hydrophobic pocket can maintainthe stereoselectivity feature of the
Rh-catalyzed polymerization. This
study highlights the importance oftheoretical study in mechanistic
understanding and rational design ofartificial metalloenzyme, and indicatesthat even though with the X-ray
crystal structure in hand, the active
site and the catalytic mechanism arestill far from fully understanding.

Ⅳ 研究業績 (2010)

2. Original papers(1) Ke, Zhuofeng, Abe, S., Ueno, T., & Morokuma, Keiji, Understanding the ComplicatedMechanism in Artificial Metalloenzymes: QM/MM study of catalyzed polymerization by
Rhodium Complex Encapsulated in apo-Ferritin. In preparation.

(2) Ke, Zhuofeng, Abe, S., Ueno, T., & Morokuma, Keiji, Rh-catalyzed Polymerization of
Phenylacetylene: Theoretical Studies of the Reaction Mechanism, Regioselectivity andStereoregularity. J. Am. Chem. Soc. 133 (20), 7926-7941 (2011). (JACS beta Select issue 13:

Current Applications of Computational Chemistry in JACS - Molecules, Mechanisms andMaterials)

3. Presentation at academic conferences(1) Ke, Zhuofeng, Morokuma, K. "Catalyzed polymerization in Bio-Nano Cavity of Protein". The

4th Annual Meeting of Japan Society for Molecular Science, Osaka University, Osaka, Japan.
Sep. 14-17, 2010. (talk)(2) Ke, Zhuofeng, Abe,S., Ueno, T., Morokuma, K., Rh-catalyzed polymerization in bionano
cavity of apo-ferritin. the 241st American Chemical Society National Meeting, Anaheim, CA,
USA. Mar. 27-31,2011. (poster)

4. Others(1) Yan, Y., Ke, Zhuofeng, Liu, Shuwen, Chen, Wen-Hua, Jiang, Shibo; Jiang, Zhi-Hong.
"Betulinic Acid-Polyphenol Conjugates as HIV Inhibitors Targeting gp41". ChemMedChem
6 (9), 1654-1664 (2011)(2) Gao, H., Ke, Zhuofeng, DeYonker N.J., Wang J., Xu H., Mao Z.-W., Phillips, D.L., Zhao C.,
Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted
Mechanism: A Density Functional Theory Study. J. Am. Chem. Soc. 133 (9), 2904–2915(2011).

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Ⅳ 研究業績 (2010)

Joonghan KIM
FIFC Fellow, Fukui kenichi Memorial Research Group 1（From 8 Nov. 2010）

1. Summary of the research of the year
Determination of Local Chirality in Irregular Single-Walled Carbon Nanotube Based on
Individual Hexagons
The chirality of single-walled carbon nanotubes (SWCNTs) has great importance since their physicaland electronic properties strongly depend on it. In this respect the chirality-controlled SWCNT growth is an
essential prerequisite for useful applications in nanotechnology. For the chirality-controlled growth, thepreservation of predefined chirality of initial structures such as cap and seed SWCNTs is essential during the
growth process. However, the chirality of irregular structures of SWCNTs, especially, those formed during
the growth process, was difficult to define in contrast to the definition of the chirality of ideal SWCNTs,
usually done using a graphene sheet with the direction of roll-up vector. For example, as shown in Fig. 1, if
an incoming C2 (magenta in Fig. 1(b)) is attached and a new hexagon is formed on a preexisting armchair(AC)-type SWCNT in Fig. 1(a), the determination of chirality of SWCNT that involves the newly added
hexagon is ambiguous; the black line in Fig. 1(b) indicates that the chirality of SWCNT is still AC-typewhile the red line shows that the chirality is zigzag (ZZ)-type. This means that a new method is urgently
required to define the chirality based noton the whole tube structure but on theindividual hexagons that are formed
during the growth process. Thus, we
propose a robust theoretical method forthe determination of the chirality ofarbitrary SWCNT structures that does notrely on the edge structure. This method
extracts information of the chirality basedon individual hexagons that compose
SWCNT. Thus, the chirality of SWCNT
canbedetermined

by

the

local

information, viz. the local chirality ofFig. 1 (a) Ideal AC(5,5) SWCNT (cyan). (b) Incoming C2(magenta) is attached to SWCNT and one new hexagon forms.
The black and red lines show AC and ZZ edges, respectively.

individual hexagons.
The scheme for the calculation of the local chiral angles is shown in Figs. 2(a)-(e). Firstly, all
Cartesian coordinates of C atoms in SWCNT are extracted and all other atoms (Fe and H atoms in this case)are removed from the original structure. Secondly the principal axes (PAs) X, Y, Z of the whole SWCNT
structure, which we call the global PAs (GPAs) (called GPAX, GPAY, and GPAZ axes in Fig. 2 (b), are－ 78 －

Ⅳ 研究業績 (2010)

calculated, with the standard order of momenta of inertia, I Z ≥ I X , IY . The Cartesian coordinates of all the
carbon atoms are then transformed into this XYZ coordinate system for easy representation in the following
calculations. In particular, the Z axis of GPA (GPAZ) plays a crucial role in the calculations of the chiralangles. In a regular, or almost regular, long SWCNT, GPAZ is (almost) equal to the growth axis of SWCNT.
In the next step, all hexagons with their Cartesian coordinates in the nanostructure are found. The PAs withthe standard order of momenta of inertia, Iz ≥ I x , Iy , of each individual hexagon (for instance the magenta
hexagon in Fig. 2(b)), called the local principal axes (LPAs), are also calculated (see Fig. 2(c)). The
directional cosines of LPAs in the GPA system are LPAx (lx, mx, nx), LPAy (ly, my, ny) and LPAz (lz, mz, nz).
LPAz shown in Fig. 2(c) plays an important role in distinguishing between suitable and ill-suited hexagons
or in determining the suitable and ill-suited hexagon components of a given hexagon, as will be discussed
later. Other PAs of a hexagon, viz. LPAx and LPAy are not used in the analysis because of the degeneracy ofhexagon-like structures: the values of the principal moment of inertia of LPAx and LPAy are almost equal toeach other.
In an ideal SWCNT, theplanes of all the hexagons thatmake up the sidewall are parallelto Z, and the tilt angle φ as
defined between GPAZ and LPAz
(see Fig. 2(c)) is exactly 90° forall hexagons. These hexagons
may be called suitable hexagons.
However, in irregular SWCNTs or
SWCNT fragments such as a cap
structure, the angle φ of a hexagon
can deviate substantially from 90°.
For instance, the angle φ of a Fig. 2 Schematic description for the calculation of the local chiral angle.
hexagons located near the top site (a) An example of an irregular SWCNT (C: cyan, Fe: brown, and H:of the C40 cap is deviated from 90°. white). (b) Irregular SWCNT after removal of other atoms except C

In an extreme case of φ = 0°, atom from the structure in (a) in XYZ coordinate system. (c) One of thenamely when the hexagon plane is individual hexagons from the structure in (b) with LPAz and theperpendicular to GPAZ or the definition of the angle (φ) between GPAZ and LPAz. (d) The plane L
LPAz is parallel to GPAZ (the with its normal unit vector n. (e) The definition of the angle (θ )directional

cosinenz=1),

the between the plane L and GPAZ.
calculation of the chiral angle

1loses its meaning completely, i.e. the distinction between AC and ZZ is totally lost; the hexagon with φ = 0°
may be called an ill-suited hexagon. Between these two extremes, (90°– φ) is an indicator of the suitability ofa hexagon, namely how much the plane of the hexagon is deviated from being parallel to GPAZ. We actually－ 79 －

Ⅳ 研究業績 (2010)use sin2φ and cos2φ (which is equal to (nz)2) as the magnitude of the suitable and ill-suited tilt components,
respectively, of a hexagon. A suitable hexagon (φ = 90°) has 100% of the suitable component and the otherextreme case of the hexagon (φ = 0°) has 100% of the ill-suited component. Between the two extremes, thecomponents change smoothly. In the succeeding calculations of the local chiral angles, we have chosen to
remove any hexagon with the ill-suited component larger than 75 %, in other words, if the suitablecomponent is less than 25 %; the local chirality of this hexagon is considered indefinable.
In the next step, we calculate the local chiral angles only of the hexagons that have more than 25 %of the suitable component. Firstly, the center of mass of a chosen hexagon is moved to the origin of the XYZCartesian coordinate. Next, the coordinates of the hexagon are transformed from the GPA system to the LPA
system. This transformation, represented by the matrix of directional cosines, can be accomplished by the
Euler formula with two consecutive rotations. As shown in Fig. 2(d), next we choose two C atoms in the para
position of the hexagon (for instance, C1 and C4). The plane L is defined to be parallel to LPAz and also to
contain C1 and C4. The angle θ1 in Fig. 2(e) between GPAZ (red arrow) and the plane L is calculated using asimple inner product between GPAZ and the normal unit vector n of plane L. For the same hexagon, twomore angles, θ2 and θ3, are also calculated using the C3-C6 pair and the C2-C5 pair, respectively. The three
angles (θ1, θ2, and θ3) were averaged effectively using Eq. (1).

θ=

θ1 + θ 2 + θ 3
3− 60°.

(1)

The ranges of the three angles are 0° ≤ θ1 ≤ 30°, 60° ≤ θ2 ≤ 90°, and 120° ≤ θ3 ≤ 150°, respectively, and therange of the average angle is 0° ≤ θ ≤ 30°. For a regular hexagon in an ideal SWCNT, θ2 and θ3 are equal toθ1 + 60° and θ1 + 120°, respectively, and thus, the average angle θ should be equal to θ1 using Eq. (1). For
example, the above formula gives θ to be 30° (= (30 + 90 + 150)/3 − 60) and 0° (= (0 + 60 + 120)/3 − 60) asθ for ideal AC and ZZ SWCNT, respectively. They are exactly equivalent to the chiral angle α (with 0° ≤ α ≤30°) of AC (n, m = n) and ZZ (n, m = 0) SWCNT given by Eq. (2).

sin α =

3m
2

2

2 n + m + nm.

(2)This average angle θ can be defined clearly also for irregular hexagons with different bond lengths
and/or different bond angles. Thus, just one angle θ represents the critical information concerning thechirality of a hexagon in SWCNT and will be called the local chiral angle. We named the present method, theanalysis according to the local chiral angle, LOcal Chirality Index (LOCI). The analysis for various examples
including ideal nanotubes as well as irregular SWCNTs is in progress.

2. Original papers(1) Joonghan Kim, Stephan Irle, and Keiji Morokuma,“Determination of Local Chirality in Irregular Single-Walled Carbon Nanotube Based on
Individual Hexagons”, manuscript in preparation.

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Ⅳ 研究業績 (2010)

Alister PAGE
FIFC Fellow, Fukui kenichi Memorial Research Group 1

1.

Summary of the Research of the Year(A) QM/MD Investigation of Single-Walled Carbon Nanotube Nucleationfrom Si-Based Catalysts: A Vapor-Solid-Solid Mechanism
The ability of non-metal catalysts, notably SiO2, to assist the nucleation andgrowth of single-walled carbon nanotubes (SWNTs) via chemical vapour
decomposition (CVD) has been established experimentally within the last decade.
Recent speculation indicated that the traditional vapour-liquid solid mechanism(established for transition-metal catalysts) is possibly responsible for SWCNT
nucleation on silica nanoparticles also. However, the exact mechanism by which thisnew breed of catalysts assists the nucleation and growth of SWNTs remains unknown.
We have addressed this issue by investigating the atomistic mechanism of SWNT
nucleation on SiO2 catalyst nanoparticles, based on QM/MD simulations of CH4 CVD.
In agreement with experiment, we found that CO was produced as the main chemical
product of this CH4 CVD process (Fig. 1). The production of CO in this case, and thenucleation of CNTs in general, necessitate the abstraction of atomic hydrogen fromthe CO carbon. We have therefore observed the mechanism by which this removal
takes place in the case of SiO2 catalysts. The production of CO during CH4 CVD
resulted in the carbothermal reduction of the SiO2 nanoparticle, resulting in a catalyst
nanoparticle consisting of a SiO2 ‘core’ surrounded by an amorphous SiC ‘shell’. The
first stage of the SWNT nucleation process featured the coalescence of carbon atoms
on the SiO2 surface, resulting in the formation of extended polyyne chains. At higher
carbon concentrations, the isomerization of these polyyne chains resulted in theformation of isolated sp2-carbon networks on the SiO2 surface, and ultimately, theformation of a SWNT cap structure (Fig. 2). The surface saturation of the SiO2
nanoparticle was a necessary prerequisite for SWNT nucleation. This is consistent
with the experimental hypothesis of a ‘carbon-coated’ nanoparticle precursor(Homma et al. Nano Res., 2, 793 (2009)). The SiO2/SiC nanoparticle remained in thesolid phase throughout the nucleation process. Moreover, QM/MD thermal annealing
simulations of SiO2 and carbon-doped SiO2 nanoparticles between temperatures of1000 and 3000 K revealed that these nanoparticles did not undergo a solid – liquid
phase transition. Instead, sublimation of the solid phase nanoparticle, yielding SiO andCO vapor was observed. Such phenomena are irreconcilable with those of a VLS-typemechanism. It was thus concluded that SiO2-catalyzed SWNT nucleation proceeds
according to a VSS mechanism, and so is comparable to the growth of a number ofother inorganic nanostructures. Consequently, it is evident that the processes of
SWNT nucleation on SiO2 and ‘traditional’ catalysts (such as Fe and Ni27,28) differ at
the most fundamental level. This VSS proposal has since been corroborated
experimentally (Liu et al., J. Am. Chem. Soc., 133, 197 (2011)).
Following the observation of the surface reduction of SiO2 nanoparticles
discussed above, the role of oxygen on the SWNT nucleation mechanism on SiO2
catalysts was further elucidated. To this end, QM/MD thermal annealing simulationsof SiC nanoparticles were performed between 1200 and 2500 K. SWNT nucleation in－ 81 －

Ⅳ 研究業績 (2010)

Fig. 2. SiO2-catalyzed SWNT nucleation
following CH4 CVD simulation using SCCDFTB/MD. Colour conventions as in Figure 1.

nucleation at temperatures below 2600 K
occurred in the solid, or quasi-solid,
phase. Thus, the traditional vapor-liquidsolid mechanism of SWNT nucleation
once more did not apply in the case of
SiC nanoparticles, with a VSS
mechanism appearing to dictate the
SWNT nucleation process Such a marked
similarity between the atomistic SWNT
nucleation mechanisms on SiC and SiO2
catalysts provided the first evidence of a
Fig. 1. SCC-DFTB/MD simulation of CH4 CVD
on SiO2 nanoparticles (following 35 ps of catalyst-independent SWNT nucleation
simulation). Blue, red, cyan and white spheres mechanism with respect to ‘nonrepresent Si, O, C and H atoms, respectively.
traditional’ SWNT catalyst species.
this case is preceded by a change of the
SiC structure from a crystalline one to
one in which silicon and carbon atoms
became segregated (Fig. 3). This
structural transformation
ultimately
resulted in the formation of extended
polyyne chains on the SiC nanoparticle
surface.
These
polyynechainssubsequently coalesced, forming an
extended sp2-hybridized carbon cap on
the SiC nanoparticle. The kinetics of thisprocess were enhanced significantly athigher temperatures (2500 K), comparedto lower temperatures (1200 K) and sodirectly correlated to the surface
premelting behavior of the nanoparticle
structure. Analysis of the SiC
nanoparticle Lindemann index between
1000 and 3000 K indicated that SWNT

(B)
QM/MD
Investigationof
Haeckelite and Graphene Growth on
Transition Metal Surfaces
Graphene exhibits remarkableelectronic, optical, and mechanicalproperties.
Thisphenomenal
nanomaterial has therefore been ascribeda number of potential applications inelectronic, spintronic, sensor, andmechanical devices. Its electronic
properties depend explicitly on the edge
structure, which provides an additional
control parameter for the purpose ofelectronic or spintronic property tuning.
Haeckelite, on the other hand, is ahypothetical planar carbon compoundthat is intrinsically metallic, irrespectiveof its edge structure. Haeckelite’s－ 82 －

Ⅳ 研究業績 (2010)

Fig. 3. Thermal annealing of SiC nanoparticles
yields SWNT nucleation, as shown by SCCDFTB/MD simulations. Blue and cyan spheres
represent Si and C atoms, respectively.

structure can be formally derived fromgraphene by periodical replacement ofhexagon pairs with pentagon/heptagon
defects. At present, it is only ahypothetical structure, having never been
experimentally
synthesizedandcharacterized. Its formation mechanismis therefore unknown.
To this end, QM/MD simulationsof ensembles of C2 molecules on aNi(111) terrace (Fig. 4) show that, in theabsence of a hexagonal template or stepedge, Haeckelite is preferentiallynucleated over graphene. The nucleation
process is dominated by the swift
transition of long carbon chains towards
a fully connected sp2 carbon network.
Starting from a pentagon as nucleus,
pentagons and heptagons condense
during ring collapse reactions, which
results in zero overall curvature. To thecontrary, in the presence of a coronenelike C24 template, hexagonal ring

Fig. 4. Comparison of Haeckelite and graphene
nucleation on a Ni(111) terrace. In the absence ofa molecular template, Haeckelite forms as astructure rich in pentagon and heptagon defects
from a random ensemble of C2 fragments. Brown
and cyan spheres represent Ni and C atoms,
respectively.

formation is clearly promoted, inagreement with recent suggestions fromexperiments. Neverthless, analysis of thefree energy of Haeckelite and graphenesystems during nucleation shows theformer structure to be ca. 0.1 eV/carbon
atom higher in energy compared to thelatter. This suggests that Haeckelite is ametastable intermediate formed during
graphene nucleation in the absence ofmolecular templates. In such a scenario,
graphene nucleation follows Ostwald’s‘rule of stages’ cascade of metastablestates, from linear carbon chains, via
Haeckelite islands that finally anneal toform the pristine hexagonal carbon latticeof graphene.

－ 83 －

Ⅳ 研究業績 (2010)2.

Original Papers(1) A. J. Page, S. Minami, Y. Ohta, S. Irle and K. Morokuma, “Comparison of SingleWalled Carbon Nanotube Growth from Fe and Ni Nanoparticles using QM/MD
Simulations”, Carbon, 48, 3014 (2010).
(2) A. J. Page, S. Irle, Y. Ohta and K. Morokuma, “Metal-Catalyzed Single-Walled Carbon
Nanotube Nucleation, Growth and Healing Mechansims Determined Using QM/MD
Methods”, Acc. Chem. Res., 43, 1375 (2010).
(3) A. J. Page, D. J. D. Wilson, E. I. von Nagy-Felsobuki, “Trends in MH2n+ Ion-Quadrupole
Complexes (M = Li, Na, K, Be, Mg, Ca; n = 1, 2) using Ab Initio Methods”, Physical
Chemistry Chemical Physics, 12, 13788 (2010).
(4) A. J. Page, H. Yamane, Y. Ohta, S. Irle and K. Morokuma, “QM/MD Simulation of
SWNT Nucleation from Transition-Metal Carbide Nanoparticles”, Journal of theAmerican Chemical Society, 132, 15699 (2010).
(5) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, “SWNT Nucleation from
Carbon-Coated SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism”, Journal of theAmerican Chemical Society, 133, 621 (2011).
(6) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, “Do SiO2 and Carbon-Doped
SiO2 Nanoparticles Melt? Insights From QM/MD Simulations, and Ramifications
Regarding Carbon Nanotube Growth”, Chemical Physics Letters, 508, 235 (2011).
(7) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, “Thermal Annealing of SiC
Nanoparticles Induces SWNT Nucleation: Evidence for a Catalyst-Independent SWNT
Nucleation Mechanism”, Physical Chemistry Chemical Physics, 13, 15673 (2011).
(8) Y. Okamoto, Y. Ohta, A. J. Page, S. Irle, K. Morokuma, “QM/MD Study of Transition
Metal Catalyst Particle Melting and Carbide Formation During SWCNT Nucleation”,
Journal of Theoretical and Computational Nanoscience, 8, 1755, (2011).
(9) Y. Wang, A. J. Page, H.-J Qian, Y. Nishimoto, S. Irle, K. Morokuma, “Template Effectin the Competition Between Haeckelite and Graphene Growth on Ni(111): QuantumChemical Molecular Dynamics Simulations”, Journal of the American Chemical Society,In press.

3.

Presentations at Academic Conferences(1) “Methane CVD on SiO2 Nanoparticles Investigated using QM/MD Methods”. (Poster) A.
J. Page, S. Irle, K. Morokuma, NT2010 - The 11th International Conference on the
Science and Application of Nanotubes, Abstract Page 141, Montreal, Canada (2010).
(2) “QM/MD Simulations of Single-Walled Carbon Nanotube Nucleation on Transition
Metal Catalysts”. (Poster) A. J. Page, H. Yamane, S. Irle, K. Morokuma, NT2010 - The
11th International Conference on the Science and Application of Nanotubes, Abstract
Page 109, Montreal, Canada (2010).
(3) “QM/MD Investigation of SWNT Nucleation on SiO2 via CH4 CVD”. (Oral) A. J. Page,
S. Irle, K. Morokuma, The 39th Fullerenes-Nanotubes General Symposium, Abstract
Page 1-13, Kyoto University, Japan (2010).
(4) “SWNT Nucleation on Si-Based Catalysts via a Vapor-Solid-Solid Mechanism”. (Poster)A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, The Fifth NASA – Air Force
Research Laboratory and Rice University Workshop on Nucleation and Growth
Mechanisms of Single Wall Carbon Nanotubes, Abstract Page 50, San Antonio, Texas,
USA (2011).
(5) “Modelling Carbon Nanotube Growth with Quantum-Mechanical Molecular Dynamics”.
(Poster) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, Theoretical
Modelling of Materials, Abstract Page 67, Barcelona, Spain (2011).
(6) “Understanding Nanoscale Self-Assembly Processes Using QM/MD: Mechanisms ofCarbon Nanotube Nucleation and Growth”. (Talk) A. J. Page, K. R. S. Chandrakumar, S.
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Ⅳ 研究業績 (2010)

Irle, K. Morokuma, 2011 World Congress of WATOC, Abstract Page OC098, Santiago
de Compostela, Spain (2011).
(7) “Mechanisms of Carbon-Based Nanostructure Self-Assembly: Insights from DensityFunctional Tight-Binding Molecular Dynamics”. (Talk) A. J. Page, K. R. S.
Chandrakumar, S. Irle, K. Morokuma, 7th Congress of the International Society for
Theoretical Chemical Physics, Abstract Page 6A2-2C, Tokyo, Japan (2011).

4.

Book Chapters(1) “Mechanisms of Single-Walled Carbon Nanotube Nucleation, Growth and ChiralityControl: Insights from QM/MD Simulations” in Electronic Properties of Carbon
Nanotubes, A. J. Page, Y. Wang, K. R. S. Chandrakumar, S. Irle and K. Morokuma, ed.
Jose Mauricio Marulanda. InTech, Vienna, Austria, p. 521-558. ISBN: 978-953-307499-3.
(2) “Atomistic Mechanism of Carbon Nanostructure Self-Assembly as Predicted by
QM/MD Simulations” in Practical Aspects of Computational Chemistry: An Overview of
the Last Two Decades and Current Trends. S. Irle, A. J. Page, B. Saha, Y. Wang, K. R. S.
Chandrakumar, Y. Nishimoto, H.-J. Qian, K. Morokuma, Springer, New York, USA, In
press. ISBN: 978-94-007-0918-8.

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Ⅳ 研究業績 (2010)

Xin LIJST Fellow, Fukui kenichi Memorial Research Group 1

1. Summary of the research of the year

Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin
and Methanol Solution

Bacteriorhodopsin (bR) is a transmembrane protein in the purple membrane of
Halobacterium salinarium. All-trans retinal protonated Schiff base (RPSB) is
covalently linked to Lys216 of the protein in the light-adapted bR. Absorption of aphoton by RPSB can trigger a photocycle with several photostationary states (seeScheme 1). Photodynamics of light-induced all-trans RPSB is sharply different in bR
and in homogeneous solutions, leading to different photoproducts and excited-state
lifetimes. Primary events of photodynamics of all-trans RPSB in bR and methanol
solution were elucidated by non-adiabatic ONIOM(QM:MM) molecular dynamics
simulations. Our simulations showed that the photoisomerization in bR isbond-specific (leading to the 13-cis form) and unidirectional, as well as thephotoisomerization along the C11=C12 bond is suppressed. Comparatively, thephotoisomerization is not bond-specific and unidirectional in methanol solution, in
which the rotation along the C11=C12 bond is dominant. As shown in Figure 1,
photo-excited RPSB underwent ultrafast radiationless decay (S1S0) exclusively via
a torsional change along φ13 in bR. In methanol, however, the nearly planar RPSB
takes a longer time to decay via one of three torsional changes: φ9, φ11 or φ13.
Therefore, bR catalyzes the photoisomerization to afford the meta-stable 13-cis form,
which should efficiently store energy and thus promote the subsequent proton
pumping and protein conformational change processes. In addition, a bicycle-pedal
like mechanism was found to be the major decay pathway in bR and methanol
solution. The reaction mechanism and environmental effects on the photodynamics
have been extensively investigated.

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Ⅳ 研究業績 (2010)

Scheme 1

Figure 1. Changes of the rotating dihedral in S1 until CS: (a) φ13 in bR and (b) φ11 inmethanol. (c) Excited-state population for photoisomerization in bR and methanol.

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Ⅳ 研究業績 (2010)

2. Original papers(1) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji
Morokuma, “Primary Events of Photodynamics in Reversible Photoswitching
Fluorescent Protein Dronpa”, J. Phys. Chem. Lett. 1, 3328-3333 (2010).
(2) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji
Morokuma, “Competitive Mechanistic Pathways for Green-to-Red Photoconversion
in the Fluorescent Protein Kaede: A Computational Study”, J. Phys. Chem. B 114,
16666-16675 (2010).
(3) Xin Li, Lung Wa Chung, and Keiji Morokuma, “Photodynamics of All-transRetinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution”, J.
Chem. Theory Comp. (letter) 7, 2694-2698 (2011).
3. Presentation at academic conferences(1) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji
Morokuma, “Primary Events of Photodynamics in Reversible Photoswitching
Fluorescent Protein Dronpa”, American Chemical Society 241th National Meeting,Anaheim, California, March 27-31, 2011.
(2) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma,“Primary Events of Photodynamics of GFP Chromophores in Proteins, Solution, andGas-phase”, 9th Triennial Congress of the World Association of Theoretical andComputational Chemists, Santiago de Compostela, Spain, July 17-22, 2011.
(3) Xin Li, Lung Wa Chung, and Keiji Morokuma, “Primary Events of
Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin,
Methanol Solution and Gas Phase”, 5th Asia and Oceania Conference on
Photobiology, Nara, Japan, July 30-August 1, 2011.

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Ⅳ 研究業績 (2010)

K. R. S. CHANDRAKUMAR
JST Fellow, Fukui kenichi Memorial Research Group 1

1.

Summary of the research of the year 2010

DFT QM/MD Investigation of the Nucleation of Single-walled Carbon nanotubes on theNonmetallic Silicon Nanoparticles
Carbon nanotubes (CNTs) and single-walled CNTs (SWNTs) have attracted greatinterest in recent years due to their unique physical and chemical properties, and their rangeof potential applications. Many of these applications require the physical properties of CNTs
(i.e. chirality, diameter and density) to be precisely controlled. In recent years, muchprogress has been made regarding the synthesis via the chemical vapor deposition (CVD)method. Significant progress has also been achieved in obtaining large yields of CNTs by
the optimization of CVD catalysts, substrates, experimental conditions, etc. Despite theseadvances, a method by which a SWNT of a specific chirality, diameter etc. may besynthesized remains elusive to date. This is largely due to the difficulty in observing
nucleation and growth processes in situ. A detailed understanding of the nucleation andgrowth mechanisms on various catalyst particles is therefore crucial. With respect totraditional, transition metal catalysts (such as Fe, Co, Ni etc. and alloys thereof), thevapor-liquid-solid (VLS) mechanism is one such mechanism. Although the nucleation andgrowth processes of single-walled carbon nanotubes have been experimentally andtheoretically studied, the precise atomistic mechanism explaining SWNT growth on
nontraditional catalysts, such as silicon, has not yet been reported. In this work, we will
present a systematic study of the SWNT nucleation mechanism on Si nanoparticles using
quantum mechanical molecular dynamics (QM/MD) simulations. SWNT nucleation here is
induced using a model CVD process, in which gas phase C2 moieties are adsorbed onto amodel Si58 nanoparticle 1250 K. We have considered the nucleation of SWNT induced by
the low and high carbon concentration (Si58C100 and Si58C150). Our results indicate that thecatalyst is stable upon the addition of C2 species and the outer layer of the catalyst surface isdisrupted to a sm:ll extent. Some of the representative figures are shown in figure 1.

Figure 1: Nucleation of SWCNT on silicon nanoparticles－ 89 －

Ⅳ 研究業績 (2010)

Following the adsorption of C2 onto the Si58 nanoparticle surface, the resultant surface
structure resembled an amorphous SiC phase, while the core of the Si nanoparticle remained
pristine. As shown in Figure 1, most of these carbon units are found to be at the siliconsurface and only few carbon atoms are found to penetrate inside the cluster. The incident
carbon species supplied to the silicon catalysts mostly form the linear and short/long polyyne
chains with the number of carbon atoms extending up to ~3-6. Both the ends of the polyyne
chains are connected to the silicon particles and they are found to be very stable for a long
period of time. It is also noted that since the silicon particles act like clamped surface forthe carbon polyyne chains, the flexibility or mobility of these chains are restricted. The
resulting final structures, as shown in Figure 1, are thus typically characterized by theformation of amorphous SiC structure at the surface along with carbon polyyne chains andthe core of the nanoparticle is continued to exist with the Si atoms. These results reveal
certain interesting features, especially on the mechanism of the CNT cap-nucleation, which
are found to be strikingly different from the traditional catalysts. In particular, oursimulation results indicate that the growth of the sp2-carbon network is exclusively dependent
on the dynamics of the vibrational/translational motion of the polyyne chains formed at thecatalyst surface. The process of nucleation stage begins only after the saturation of suchcarbon networks (sufficiently higher carbon based ring networks) at the catalysts surface.
Is SWNT Nucleation on Silicon Nanoparticles Preceded by a Carbide Phase or a
Carbon-Coated Surface?
A detailed understanding of the mechanism of the formation of CNT, especiallythrough the CVD method is very crucial for obtaining precisely controlled the physical andchemical properties of the carbon nanotubes (chirality, density and metallic or nonmetallic
property). In this regard, one pertinent question often asked is on the nature of theintermediate stage for the nucleation of the CNTs. Few experimental and theoretical studies
have been carried out in the past and some of the results are conspicuously different fromeach other. The important intermediate stage for the CNT cap-nucleation with the traditional
catalyst is either the carbide phase and/or the precipitation of carbon at the catalyst surface
through the bulk/surface diffusion of the carbon adatoms to the boundary of thecatalyst. However, for the case of non-traditional catalysts, the detailed mechanism for eachstage of the nucleation/growth mechanism is yet to be established. In particular, we willaddress the question of whether or not a Si-carbide phase precedes the SWNT nucleation
process. To this end, we have monitored the radial distribution of carbon within the Si58
catalyst (with respect to the Si58 center of mass) throughout the thermal annealing period,
averaged over intervals of 20 ps. It is noted here that the radius of the cluster is approximately
4.5 Å. These data are shown in Figure 2a. It is evident that the populations of carbon atoms
at the core and surface of the Si58 nanoparticle are very distinct from each other. For example,
only two carbon atoms are found 4 Å from the Si58 center of mass at 20 ps, a population
which is maintained until 200 ps. At a distance of 4.5 Å from the Si58 center of mass (i.e. the－ 90 －

Ⅳ 研究業績 (2010)

catalyst surface), this population increases to five carbon atoms, whereas a maximum of 14
carbon atoms are observed at 7 Å. At larger distances, the number of carbon atoms decreases.

Figure 2: Solubility of carbon species inside the silicon cluster for (A) low[C] and (B)high[C]. Number of carbon atoms present inside a sphere of radius equivalent to the
distance of each carbon atom from the center-of-mass of the cluster.
A similar pattern is also found for the high [C] case (Figure 2b). For example, atdistances of 4, 4.5 and 7.5 Å from the Si58 center of mass, the populations of carbon atoms is
two, three and 21, respectively, are observed. Interestingly, no significant change in thisgeneral pattern is observed even after a further 200 ps, for both carbon concentrations.
Approximately 97% of all carbon atoms are found to be at the Si nanoparticle surface. The
remaining carbon atoms penetrate the surface and reside in the Si nanoparticle subsurface.
The possibility of the diffusion of carbon within the nanoparticle bulk is therefore very
unlikely, and the catalyst surface is uniformly covered by sp- and sp2-hybridized carbon.
These results demonstrate that the formation of a carbide phase, and the subsequent diffusionof carbon to the catalyst surface, are not necessary conditions for the SWNT nucleation for Si
catalysts. On the other hand, these two stages are generally accepted to precede SWNT
nucleation and growth on transition metal catalysts. Indeed, such diffusion of carbon fromthe catalyst bulk to the catalyst surface is central to the traditional VLS mechanism of SWNT
nucleation and growth. This is consistent with the activation energy for the diffusion ofcarbon in iron (0.75 eV), compared to that of carbon in Si (2.93 eV) in the temperature rangeof 1200-1650 K. From these results, one can unquestionably argue that, contrary toestablished phenomena using transition metal catalysts: (i) carbon atoms neither dissolve nor
diffuse through Si nanoparticles, hence, a Si-carbide phase is not observed; (ii) SWNT
nucleation is driven by the formation of a carbon network through the linear polyyne carbon
chains on the Si nanoparticle surface; and (iii) the polyyne chains are exceptionally stable andtheir constrained rotational/translational motion impedes the formation of sp2-carbon
networks (and thus SWNT nucleation) on the Si surface. An important consequence of thesefacts is that the SWNT yield on Si-catalysts should be much lower than for iron group metal－ 91 －

Ⅳ 研究業績 (2010)

catalysts. These observations also suggest that the VLS type of mechanism may not beapplicable in the case of Si nanoparticles. Two prerequisites for VLS growth of CNTs are thatcarbon is soluble in the catalyst nanoparticles, and that the growth temperature should beabove the eutectic melting point. As shown above, the solubility of carbon inside the Si
catalyst is essentially negligible.
Melting Behavior of the Pure and carbon-doped Silicon Nanoparticles: Carbon Induced
Liquid-to-Solid Phase Transition in Silicon Nanoparticles
Since the phase of the catalyst determines the dynamics and kinetics of CNT
nucleation, herein, our objective is to investigate the nature of the phase of the silicon catalyst
during the nucleation/growth of the CNT. It is well known that the mechanism for the CNT
growth with the transition metal catalyst is shown to be vapor-Liquid-Solid (VLS), i.e. thestate of the catalyst is in the molten state and the carbon species are dissolved from vapor
phase into the molten “liquid-like” catalyst particle and forms the carbide phase. The
carbon super saturation in these metal-carbide precursors subsequently induces precipitationof carbon from the nanoparticle bulk to the surface, at which point the solid phase CNTs
nucleate and grow. Conversely, CNT growth on a diverse range of covalent catalysts (suchas Al2O3, SiC, Si, Ge or SiO2) proposed that during CNT growth the catalyst exists as a solid
nanoparticle. During the chemical vapor decomposition (CVD) process, a high carbon density
builds upon the surface of this nanoparticle resulting in a ‘carbon-coated’ particle. Thisultimately results in the formation of an sp2- hybridized carbon patch (i.e. a ‘grapheneisland’). Continued CNT growth from this solid structure then ensues. Thus, it would beinteresting to verify the experimental hypothesis on the nature of the phase of the siliconcatalyst and the CNT nucleation/growth mechanism .
The melting phenomena of pristine and carbon-doped Si nanoparticles have been
investigated using the Lindemann Index.
2 where N is the number of atoms, rij is therij2 − rij
T instantaneous distance between atoms i and j, and T
1
T
δ=
∑
∑
denotes thermal averaging at temperature T. In thisN ( N − 1)riji≤ N i ≠ j
Twork, all thermal averaging has been performed
using 1 ps periods. The Lindemann criterion, introduced in 1910, measures the atomic
vibrational amplitude in units of the lattice constant of a crystal. If this ratio, which is definedas the disorder parameter reaches a certain value, it is presumed that fluctuations cannot
increase without damaging or destroying the lattice. Experiments and simulations show thatthe critical value of this index for simple solids is in the range of 0.10–0.15. The criticalvalue has been found to be relatively independent of the types of substance, the nature of theinteraction potential, and the crystal structure.
The melting pattern for the Si58 cluster obtained from the DFTB based QM/MD
method is represented in Figure 3a. It is evident from the above figure that the Si58 cluster
starts melting at 900 K and above1600 K it exists as liquid. The experimental melting point－ 92 －

Ⅳ 研究業績 (2010)

for the bulk silicon is 1687 K and for the cluster with different sizes, the calculated melting
point is in the range of 900–1400 K. It may be noted that the CNT growth experiment with
Si nanoparticle was performed at 1250 K and hence, it can be mentioned that the silion
nanocluster is in the liquid state. Does that mean VLS mechanism can explain the growth of
CNT? Although it appears that VLS mechanism can explain the CNT growth, the answer
for this question can be provided if we also analyze the melting pattern for the carbon-doped
silicon nanocluster system. Accordingly, we have systematically considered 3 different
carbon-doped silicon clusters, namely Si58C100 (Low), Si58C150 (Medium), Si58C208 (High) andthe corresponding melting pattern curves are given in Figure 3b, 3c and 3d, respectively.

Figure 3: Melting curve for the silicon and carbon-doped silicon clusters
It is clear from the above figures that addition of carbon into the silicon cluster substantially
increases the melting temperature of the carbon-doped silicon nanoclusters. For instance,
Si58C100 starts melting at 1600 K and above 2600 K, it may exist as liquid and for the case of
Si58C150, the melting temperature is ~1750 K and existence of liquid region is estimated to be
above 3000 K. More interestingly, it appears that the higher level doping of carbon into thesilicon cluster increases their stability and the melting of the cluster starts above 2250 K. It isalso interesting to note that both the medium and high-carbon-doped silicon clusters areobserved to disintegrate into smaller fragments at above 3000 K and hence, it can be－ 93 －

Ⅳ 研究業績 (2010)

mentioned that these clusters sublimes directly without having the liquid phase. Our
simulations show that no liquid phase catalyst carbide precursor can exist during CNT
synthesis on Si nanoparticles, since the experimental/simulation temperature is 1250 K. In
other words, the VLS mechanism can be ruled out for the Si-catalyzed SWNT nucleation andgrowth and our results point to a VSS mechanism. Thus, the mechanisms of SWNT
nucleation and growth on traditional and non-traditional catalysts are therefore offundamentally different natures. Based on the above discussions, we conclude that although
the mechanism at the initial stage appears to be VLS, once the chemical vapor deposition
process begins (as the concentration of carbon increases in silicon nanocluster), themechanism changes from VLS to VSS. These results can have important implications for
the CNT nucleation and growth mechanism with silicon catalyst.
DFTB based QM/MD Investigation on the Formation of Fullerene Molecule fromGraphene Sheet
Although fullerenes have been synthesized by different methods especially from thegraphite based starting materials, the recent experiment has opened up another interestingvenue for generating fullerenes from graphene sheets. The mechanism of fullerene formationfrom graphene sheets has been investigated using the DFTB QM/MD methods with different
graphene models of finite sizes. Our findings reveal that the creation of the defects in themodel graphene sheets is identified as an important step, which facilitates the transformationof sheet into fullerene. At the lower temperature (less than 3000 K), the sheet is found to bestable except at the peripheral regions and leads to the structure with small curvature. The
effect of temperature is observed to be very substantial and the successful transformation
occurs at 3000 K accompanying by the loss of few C2 units from the peripheral regions andthe formation of polyyne chains. In most of the cases, the pentagons are formed either by
the interaction of these polyyne chains or reorganization of the deformed 6m-rings. In
addition, the pentagons are never formed at the center of the sheet and they are rather formedby pushing from outer most layers to penultimate inner layer of the hexagonal sheet. The timescale for this transformation is found to be around 200-400ps depends on the size of the sheets
as well as the temperature.

C84 at 2500 K for 400ps

Figure 4: (a) Snapshots for the formation of fullerene molecule from the C84 graphene sheet
and (b) the polygonal ring formation dynamics－ 94 －

Ⅳ 研究業績 (2010)2.

Original Papers
1. Do SiO2 and carbon-doped SiO2 nanoparticles melt? Insights from QM/MD
simulations and ramifications regarding carbon nanotube growth; Alister J. Page,
K.R.S. Chandrakumar, Stephan Irle and Keiji Morokuma; Chem. Phys. Lett. 508(2011) 235-241.
2. SWNT Nucleation from Carbon-Coated SiO2 Nanoparticles via a Vapor−Solid−Solid
Mechanism Alister J. Page, K. R. S. Chandrakumar, Stephan Irle, and Keiji
Morokuma; J. Am. Chem. Soc., 133 (2011) 621–628.
3. Thermal Annealing of SiC Nanoparticles Induces SWNT Nucleation: Evidence for a
Catalyst-Independent VSS Mechanism; Alister J. Page, K. R. S. Chandrakumar,
Stephan Irle, and Keiji Morokuma; Phys. Chem. Chem. Phys. 13 (2011) 15673-15680

3.

Presentations at Academic Conferences
1. K. R. S. Chandrakumar, S. Irle and K. Morokuma “Carbon Nanotube Growth from
Carbon Nanocones catalyzed by Iron Nanoparticles” (Poster) Presented inInternational Symposium on "Molecular Theory for Real Systems" Kyoto University,
Kyoto, Japan (2010).
2. K. R. S. Chandrakumar, S. Irle and K. Morokuma “DFTB-MD simulation of carbon
nanotube growth from metal decorated carbon nanocones” (Poster) presented in, 50th
Sanibel Symposium, St.Simons Island, Georgia, USA, (2010).
3. K. R. S. Chandrakumar, S. Irle and K. Morokuma "Growth of Nanotubes/
Nanocapsules from Metal Decorated Carbon Nanocone Aggregates: Insights from
DFTB-MD Simulations" (Oral Presentation) Presented in, 39th Fullerenes-Nanotubes
General Symposium, Kyoto University, Kyoto, Japan. Oral Presentation (2010).
4. K. R. S. Chandrakumar, A. J. Page, S. Irle and K. Morokuma”QM/MD Investigationof the Nucleation of Carbon Nanotube on the Nonmetallic Silicon Nanocluster: Is theIntermediate Stage Carbide or Carbon Coated Surface?” (Poster) Presented in 8th
Fukui Institute for Fundamental chemistry Symposium, FIFC, Kyoto University,
Kyoto. (2010).

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Ⅳ 研究業績 (2010)

Fengyi LIU
JST Fellow, Fukui kenichi Memorial Research Group 1

1. Summary of the research of the yeara) Theoretical Investigation on Light-Driven Molecular Rotary Motors
Light-driven molecular rotary motors undergoing repetitive and unidirectional rotation (in similar mannerto that of their biological counterparts, e.g., the bacterial flagella motor and ATPase) have been recently
synthesized and attracted wide interest. The photophysics and photochemistry behind these genius designs
are crucial in fully understanding the working mechanism of the currently synthesized rotary molecularmotors and in designing promising nanoscale molecular devices. However, the necessary information of thephoto-initiated ultrafast processes of the involved molecules, for instance the reaction paths on the groundand excited state potential energy surface (PES),

the nonadiabatic decay governed by the interactions

between the PESs (i.e., conical intersections (CIs) or avoided crossings) , is not sufficient. In order tounderstand their working mechanism, we investigated the light-driven molecular rotary motors by using the
CASPT2//CASSCF methods.
Driving Force—the Engine Powers the Rotation: Driving forces are perquisite for molecular motors. It
stimulates the relative mechanistic movement of one component of the molecule with respect to the other.
According to quantum mechanistic theory, stable molecules are trapped in the well on theirfundamental-state potential energy surface (PESs), with all nuclei in optimal distributions. Upon external
perturbation, the molecule is promoted off the equilibrium state (either geometrically or electronically) toanother high-energy, nonequilibrium state. In order to regain the equilibrium, the molecule adjusts the nuclei
coordinates until it finds the optimal distribution again. In this process, the re-stabilization along with thegeometry relaxation will act as the driving force.
Among the many ways to create such nonequilibrium state, light is an ideal source of energy input. In
light-initiated processes, the nonequilibrium state is electronic excited state (ES), more specifically, the FC
structure on ES PES. It has demonstrated in numerous cases that the landscape of excited-state (ES) PESs
can evidently differ from the ground-state (GS) ones; therefore the ES FC structure (with the same geometry
to the GS minimum) could be highly unstable compared with the actual relaxed ES minimum. Along theadiabatic ES decay path started from the region (to ES intermediate or other crucial region such as conicalintersection (CI), avoided crossing and intersecting seams, etc.), the energy change drives the geometry
relaxation, namely the relative mechanistic movement. This is also valid for the consequent GS decay
process, which is connected with the ES decay by possible ESÆGS nonadiabatic transition, though the
nonadiabatic decay through CI could be more complicated. For instance, excited from either the cis- ortrans-isomer of free-stilbene (FS) which are more or less with planar geometries, the ES FC points aregeometrically far from and energetically less stable than the perpendicular ES intermediate. These
differences generate the bond rotation around the central C-C bond.
Without considering the dynamics of the atoms, the minimal geometry relaxation path corresponds to theminimal reaction path (MEP). Therefore, the sloppiness of the PES along MEP could qualitatively predict the－ 96 －

Ⅳ 研究業績 (2010)

rotary potential of a given molecule. The steeper the slope is, the larger the driving force is and the fasterrelaxation takes place. The shape of the ES PES in the vicinity of the FC region, which generates the initialmomentum of the molecule, is the most important and fundamental one. The sloped PES near FC region
fascinates large initial momentum, while well-shape PES more or less hinders (or at least slows down) the
rotation. The latter case may be overcome by carefully chosen the excitation wavelength (i.e., exciting
molecule to higher electronic state or "hot" vibrational state, etc.), but which is beyond the scope of this
discussion. Another major factor is the overall potential energy change against the whole reaction path,
which reflects the average driving force of the geometry relaxation. In general, large driving force is can beachieved by increase the stability of the final state or decrease the stability of the initial state. In stilbene
motor (SR), the ES FC structures are actually strongly decreased by the methyl-methyl repulsion between thesubstituents in the "fjord" region.

Figure 1. The different shape of PESs in the vicinity of the ES FC region. (FS: free-stilbene; SS: stiff
stilbene; SR: stilbene rotary motor)
Directionality of Rotation: Nondirectional-(Bidirectional-), Directional- and Unidirectional Rotation:
Though bond rotation is an abundant phenomenon in stereochemistry, the direction of bond rotation is
generally ignored in nonchiral chemistry (because the two rotation processes, clockwise- andanticlockwise-rotation and their resulting products are undistinguishable). For instance, the simplest
photo-active C-C bond rotary system is ethylene. From the concept of the molecular rotary motor, the rotor
part (with respect to the stator part) of the molecule can rotate clockwise or anticlockwise towards to the
perp*(-90) and perp*(90) ES intermediate, however, these two perp* structures are stereochemical the same.
The excited FC ethylene is located on the ridge of the two intersected rotation PES, therefore the rotation
opportunities towards the clockwise- and anticlockwise- directions are equal. Such kind of the bond rotationis thus no direction-preferential (nondirectional), or bidirectional. Similar situations are found in thephotoisomerization of trans-FS. Commonly, the nondirectional/bidirectional rotations are governed by thehigh symmetric PES resulted from the high symmetry of the molecule. In order to initiate directional
movement, the symmetry of the molecule (as well as the PES) has to be lowered (or broken) and two paths
have to be distinguishable. This can be achieved by introducing asymmetric substitutions, secondary
structure (helicity), or both.
Strictly speaking, any asymmetric rotary PESs could generate rotation with more or less directionality.
However, only in the case that one direction is evidently more favorable than the other could be regarded as－ 97 －

Ⅳ 研究業績 (2010)

directional rotation. cis-FS will be good example representing a directional rotation on ES PES. The cis-FS
molecule is weakly heical-twisted by the repulsion between the near edges of the two benzene moieties.
Started from one of the two helically chiral enantiomers (for instance, right-hand or P,P'- cis-FS) to
perp*(90) intermediate, the anticlockwise rotation is energetically favorable, while the reversed direction isunfavorable due to the uphill PES caused by the repulsion. Meantime, the M,M'- enantiomer prefers
clockwise rotation to the anticlockwise one. Though for each of them the ES decay follows a directional way,
the overall decay doesn't show directionality due to the barrier between these two enantiomers are rather low
and one could easily isomerization to the other. Only if the helical inversion barrier is high enough to hinder
the thermal isomerization of the P- and M- enantiomers, they could be separated and a light-driven
directional decay is possible. In cis-3, the methyl- substituents on the "fjord" region significantly increase thebarrier height, which makes the separation of the P- and M- conformers possible. Similarly, on trans-SR-3,
the repulsion forces the two benzene moieties twisted along the P- or M- directions (The ideal planar
structure as in free stilbene now actually corresponds to the helical-inversion barrier between P- andM-conformer). The directional rotation started from FC-trans-SR is also expected, though the MEPs are nottotally downhill.
Unidirectionality, which is one of the ultimate goals of artificial molecular rotary motor, can be achievedby the couple of several directional rotations. A series of the directional along the same direction (clockwiseor anticlockwise) compose unidirectional rotation as showed in SR; while two or more directional rotationin reversed direction is possible to be utilized as molecular switch (and similar fancy concepts of functional
molecular devices such as molecular elevator, molecular truck, etc.).
Directional Rotation in Nonadiabatic Decay: The
above discussions of directionality only focus on
adiabatic PES. In fact, the photo-induced process
is more complicated since they involve in the
nonadiabatic transitions. For instance, the decay
through nonadiabatic coupling region strongly
depends on the nature and location of crucial
points (or seam). In stilbene, the ES decay does
not terminated at ES intermediate; instead, themolecule goes further though CIs and relaxes on
GS PES. In SR 3, t wo types of crossings arefound in the rotary process: 1) the 1B/2A seams,
which are located along the 1B-MEP and the slopeof the interesting seam is roughly in parallel with

Figure 2. The 2A/1A nonadiabatic decays (a) U- via
CI2A/1A(85),

(b)U+

via

CI2A/1A(108)incis-SRÆunstable-trans-SR photoisomerization. U- is
the more favorable pathway.

that of the decay path. They are classified as directional nonadiabatic decay. 2) The 2A/1A CIs, which are
off the reaction path along the orthogonal C1/C1′ pyramidalization coordinate and also high in energy,
therefore are classified as poorly directional nonadiabatic decay. In the latter case, the pyramidalizationrather than the primary C-C rotation coordinate controls the 2AÆ1A decay, it could slows down the rotation－ 98 －

Ⅳ 研究業績 (2010)

and eliminates the directionality of rotation. Therefore, the 2A/1A nonadiabatic decay is the key issue in
stilbene rotary motor. In order to design unidirectional rotary motor based on stilbene, the directionality of
the 2A/1A decay has to be improved. Our CASPT2//CASSCF calculations reveal that the 2A/1A CIs in
motor 3 is, though not as comparable with 1B/2A seams, still directional. These are because: 1) The helicaltorsional MEP approaches the 2A/1A CIs along non-perpendicular direction; 2) The repulsions (between thecrowded substituents) push the reaction path close to one of the CIs against the other. These will to largest
extend, maintain the direction of the rotation and the inertial velocity of the molecular.

b) Ring-Opening and Ring-Closure Mechanism of Spiropyran-Merocyanine Photochromic
Reaction
The photochromic reaction of spiropyran (SP)-Merocyanine(MC) photochromic reaction has been widelyused in molecular devices. However, due to the complicity of the potential energy surface of this reaction(conical intersections of the ground- and excited-state potential energy surfaces, excited singlet and triplet
state reactions and unusual intersystem crossing properties of spiropyrans), the details of the reaction havenot been well understood. We carried out CASPT2//CASSCF calculation to explore the ground- andexcited-state PESs of the model molecule (especially the excited-state PES which has been poorly described)
and to uncover the conical intersection based internal conversation processes in this reaction.
H H

H H
UV(365nm)
N

O

H

Vis,D

H

O

N+
H
Merocyanine(MC)Spiropyran(SP)H

Figure 3. SP-MC photochromic reaction (Unsubstituted-SP)
The SP-MC ring-opening reaction takes place in
two steps: 1) Photocleavage of C-O bond. Twoparallel C-O cleavage paths were found on the S1
PES (to S0 C-O cleavage). Starting from theFC(S0-SP), the molecules follow two primary
reaction paths, S1-SPÆ S1-TCC and S1-SPÆS1-CCC,
both are barrierless downhill MEP. Along theS1-MEP, the S0 and S1 curve intersect with each otherand form extensive state-interacting regions (S1-S0
gaps lower than 10 kcal/mol). The torsional modes(especially the N3—C1—C4—C7) corresponding todihedral angle α, β and γ regulate the branching ratio
in the initio step, and are responsible for the strong
state-interacting region along the reaction path. 2)
Isomerization between MC Isomers. In principle,

Figure 2. The variation of dihedral angles α, β and
γ (in degree) along the S1-MEP.

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Ⅳ 研究業績 (2010)

OBF, HT and BP can take place in MC photoisomerization. Considering of their relative long life time(~10ps), low isomerization barriers and flexible reaction paths, all MC conformers can be generated from the
CCC and TCC. Several CIs were located at the CASSCF level and are responsible to produce ground-state
MC isomers, though CASPT2 show large discrepancy with CASSCF results.
The ring-closure mechanism of MC chromic reaction is studied. It is found the bond rotations around β are
crucial for ring-closure, γ less important, and α bond are highly unfeasible. The most efficient reaction pathcorresponds to FC-TTC(S2)Æ CI (S2/S1,β2)Æ TS(β2,S1) Æ TCC(S1) Æ CI2S1/S0ÆSP(S0). These results
agree with the experimental findings.

2. Original papers(1) Fengyi LIU, Keiji MOROKUMA,“A CASSCF/CASPT2 Study on the Working Mechanism of Stilbene Light-Driven
Molecular Rotary Motor: Sloped Minimal Energy Path and Unidirectional Nonadiabatic
Decay”
to be submitted.
(2) Fengyi LIU, Keiji MOROKUMA,"Photochemistry and Photophysics behind Light-Driven Molecular Rotary Motor: What
We Learnt from Stiff Stilbene Rotary Motor”
manuscript in preparation.
(3) Fengyi LIU, Keiji MOROKUMA,"Ring-Opening and Ring-Closure Mechanism of the Spiropyran-Merocyanine
Photochromic Reaction: A CASSCF/CASPT2 Study”
manuscript in preparation.
3. Presentation at academic conferences(1) Fengyi LIU, Keiji MOROKUMA, Poster on:“A Theoretical Study on the Photoisomerization of Stiff Stilbene: A Model of Light-Driven
Rotary Molecular Motor”
Annual Meeting of Japan Society for Molecular Science (2010), Osaka, Sept 14-17, 2010.
(2) Fengyi LIU, Keiji MOROKUMA, Poster on:“Mechanism of Spiropyran-Merocyanine Photochromic Reaction: A CASPT2//CASSCF
Study”
第 8 回 京都大学福井謙一記念研究センターシンポジウム, Kyoto, Dec 3, 2010.

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Ⅳ 研究業績 (2010)

Parameswaran PATTIYIL
JST Fellow, Fukui kenichi Memorial Research Group 1（To 15 Jun. 2010）

1. Summary of the research of the year

Growth Mechanism for Aluminum-Catalyzed Silicon Nanowires : Density Functional Tight
Binding Molecular Dynamics Simulations
Silicon nanowires are identified as one of the important components for future micro electronic
revolution. Several metal-catalyzed silicon nanowires have been reported in the literature. The metal catalyst
is believed to play an essential role in the nucleation and growth of silicon nanowires. The control over thegrowth of nanowires is nevertheless essential for various technological applications. Recent report ofAl-catalyzed Si-nanowire growth demonstrated that the tip is mainly consists of Al atoms whereas nanowire
part is mainly consisting of Si atoms. It is to be noted that these Al-catalyzed Si-nanowires are grown in thelower temperature range of 430°C to 490°C.
It is well known that Si-Si π-bond (≈ 25kcal/mol) is rather weak as compared to C-C π-bond (≈60kcal/mol). This in turn destabilizes planar coordination in silicon and hence planar, tabular and fullerene
type nano scale structures are less stable as compared to carbon. Thus nanoclusters and nanowires are
suitable candidates for nanoscale properties for silicon. In this study, we are investigating the nucleation andgrowth of the silicon nanowire using aluminum catalyst at different temperatures by self-consistent-charge
density functional tight binding molecular dynamics simulations (SCC-DFTB).
Three model systems have been used to understand the mechanism of growth of Si-nanowire (Figure1). Al34 cluster was used as a cap to Si-nanowires. All the dangling valencies of Si atoms are satisfied byhydrogen atoms in model-I (Al34-Si28H33), where as model-II (Al34-Si16) and model-III (Al34-Si42) do not have
any hydrogen atoms. The nuclear temperature of the system was controlled by the Nose Hoover chain
thermostat and electronic temperature is set to 1500K. Periodic boundary conditions were imposed with a
cubic box of side 100Å. The simulation involving model-I was carried out two different temperature 500K
and 750K to study the effect of temperature.

I

II

III

Figure 1: SCC-DFTB optimized geometries of model Al-capped Si-nanowires. Green, pink and blue
spheres represent Al, Si and H-atoms respectively.

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(a)

(b)

(c)

(d)

Figure 2: Snapshots after supplying 50 Si atoms on model-I at temperature (a) 500K and (b)750K and snapshots after supplying 60 Si atoms on (c) model-II and (d) model-III at 500K. Green,pink and blue spheres represent Al, Si and H-atoms respectively and black spheres represent newly added
Si-atoms.
Si atoms were supplied at the interval of 0.5ps at the interface of Al-Si cluster in model-I. Our
simulations at 500K and 750K showed the formation of several 3-7 membered rings which finally leads to
Si-nanoclusters (Figures 2a and 2b). Some of the hydrogen atoms attached to Si-atoms has migrated to
Al-cluster and form Al-H bonds. The number of Si-rings increases with time and the number of six
membered rings is always greater than other rings (Figures 3a and 3b). A few of the added Si-atoms havediffused into Al-cluster. The simulation at two different temperatures shows that mixing between Al and Si asa result of diffusion of added Si-atoms is higher at 750K as compared to 500K. It is to be noted that Si-Si
bond strength is only a little higher than Al-Si bond strength. The Si-Si bond strength in Si2H6 is
96.0kcal/mol while Al-Si bond strength in H3SiAlH2 is 85.6kcal/mol. It can be concluded from thissimulation that lower temperature shows more cluster formation, however even after supplying 50 Si atoms
no significant uni-directional growth has been observed.

On the other hand a Si-nanocluster growth has

been observed (Figure 2a). This might be due to the hydrogen atoms on Si-nanowire which prevent
uni-directional growth. In order to understand this factor we supplied silicon atoms at the centre of mass of
Si-atoms in models-II and III.
Si-rings at 500K,
Average of ten trajectories
for model-I

80

80

(a)
3
4
5
6
7
Total

70

70

3
4
5
6
7
Total

50
40

60

Ring Count

Ring Count60

50Si-rings at 750K,
Average of ten trajectories
for model-I

(b)

40
30

30
20

20
10

10
0

0
0

0

5

10

15

20

5

10

15

20

25

25

ps

ps

Figure 3: The plots of average ring count for ten trajectories versus time in ps at (a) 500K and (b) 750K
for model-I.

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Addition of Si-atoms on model-II and model-III results in mixed Al-Si nanocluster formation withlower part mainly consists of Al-atoms where as upper part is mainly Si-atoms (Figures 2c and 2d). Herealso a few of the added Si-atoms have diffused into Al-cluster. The number of Si-ring increases with time;
however the formations of 3-membered rings are lesser as compared to other rings (Figures 4a and 4b).
The number of ring formation is more for the model-II than the model-III.
A general conclusion observed from these simulations is that a few of the supplied Si-atoms are
diffused into Al-cluster, while other Si-atoms form nanocluster on the surface of Al-cluster.

110

100
90

80

80

3
4
5
6
7
Total

60
50
40

Ring Count

Ring Count

(c)

90

70

Si-rings at 500K,
Average of ten trajectories
for model-III

110

Si-rings at 500K,
Average of ten trajectories
for model-II

100

(b)

3
4
5
6
7
Total

70
60
50
40

30

30

20

20

10

10

0

0

0

5

10

15

20

25

0

ps

5

10

15

20

25

ps

Figure 4: The plots of average ring count for ten trajectories versus time in ps at 500K for (a) model-IIand (b) model-III.

2. Original papers(1) Back, O.; Donnadieu, B.; Parameswaran, P.; Frenking, G.; Bertrand. G. “Isolation of
Crystalline Carbene-Stabilized P2-Radical Cations and P2-Dications”
Nature Chemistry, 2, 369-373 (2010).
(2) Parameswaran P.; Frenking, G.
“Chemical Bonding in Transition Metal Complexes with Beryllium Ligands[(PMe3)2M-BeCl2], [(PMe3)2M-BeClMe] and [(PMe3)2M-BeMe2] (M = Ni, Pd, Pt)”
J. Phys. Chem. A, 114, 8529-8535 (2010).

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Hongyan XIAOJST Fellow, Fukui kenichi Memorial Research Group 1（From 1 Jul. 2010）

1. Summary of the research of the year
I. Theoretical Study of NO3 Photodissociation
The nitrate radical (NO3) is known to play an important role in the atmospheric chemistry, and has been
extensively investigated both experimentally and theoretically. Photodissociation of NO3 has two productchannels in the visible region.
NO3 + hv → NO + O2

(1)

→ NO2 + O

(2)

The thresholds for both channels are very close in energy. In a narrow wavelength range of 585−595 nm
channel (1) occurs, while in the higher energy channel (2) dominates. Recently, the product energy
distribution of channel (1) at 588 nm photolysis was measured by North and coworkers. They showed a clear
evidence of existence of two dissociation pathways: (1A) a path generating vibrationally hot O2 moleculesand (1B) a path giving vibrationally cold O2 molecules. They postulated that the former path involves
dynamics of a roaming oxygen-atom. There is no clear interpretation of the latter path.
Based on PES characterization and ab initio dynamics, we propose that both (1A) and (1B) involve
roaming dynamics of an oxygen atom on the first excited doublet state PES, and that the branching between
the two paths occurs during the roaming dynamics in the partially dissociated (NO2…O) region through a

1.481

conical intersection (CI).

hν

D3/D2

D4/D3

D3
187.9
(192.0)

D2/D1

D2/D1

D0-TS2

200.8

195.4
(185.0)D0-TS1

D1-TS1

166.5(155.1)

171.5

D1-LM1

D0-LM1162.8
162.8 D /D
(153.3) 1 0

160.6(150.9)588 nm ≈ 203.4 kJ/mol
D1-TS2

O+NO2

199.1
(188.8)198.9(186.3)

118.5
D1
86.2
(82.7)

O2+NO
23.00
(7.8)

D0-GM
0.0
(0.0)

Figure 1 The photodissociation processes of NO3 by MS-CAS(11,8)PT2/6-31+G*－ 104 －

Ⅳ 研究業績 (2010)

As shown in Figure 1, upon excitation of NO3 at 588 nm, it reaches D4/D3 crossing point at the Franck
Condon region, then a series of radiationless decay follows D4/D3 → D3 → D3/D2 → D2/D1 → D1, and at
final the roaming pathways of decomposition of NO3 to NO + O2 occur on the D1 and D0 surfaces. Ab initio
classical trajectory calculation further differentiates product O2 vibrational states in the different dissociation
pathways, see Figure 2. The O−O vibration range in the D0 curve is larger than that in the D1 curve. That is
to say, elimination of O2 on the D0 surface gave a vibrationally hot O2 product, while elimination of O2 on theD1 surface gave a cold one.

In conclusion, both of the two O2 elimination
pathways observed in a recent experiment originate
from the excited state roaming dynamics. The
branching into two products occurs during the D1roaming

dynamics

througha

D1/D0

conicalintersection; the indirect dissociation after the
nonadiabatic transition to D0 produces the major
vibrationally hot O2 product, while the direct
dissociation on the D1 PES gives the minor
vibrationally cold O2 product.

Figure 2. The classical trajectory of O2 elimination
at the (TD)UB3LYP/6-31+G* level

II. Theoretical Study of HNO3 Photodissociation
Nitric acid (HNO3) molecule plays an important role in the atmospheric chemistry. Depending on theirradiation wavelength, the photodissociation of HNO3 has rich photochemical decay channels.

HNO 3 + hν → OH( X 2 Π ) + NO 2 ( X 2 A1 ) ΔH 0 = 200 kJ/mol→ OH( X 2 Π ) + NO 2 ( A 2 B 2 )→ O( D) + HONO( X A′)
1

1→ O( P) + HONO(a A′′)
3

3

→ O( P) + HONO( X A′)
3

1

ΔH 0 = 315 kJ/mol

(1)
(2)

0

(3)

0

(4)

0

(5)

ΔH = 490 kJ/mol
ΔH = 550 kJ/mol
ΔH = 300 kJ/mol

Experimental observed results are that pathway (1) is dominant at 308 nm (388.4 kJ/mol),pathway (2) is dominant at 248 nm (482.3 kJ/mol), and pathway (3) is open at 222 nm (538.8 kJ/mol) andis primary at 193 nm (619.8 kJ/mol).

Till now, there is no clear theoretical explanation on HNO3

photodissociation.
Therefore, we undertook a systematic study on the dissociation pathways of HNO3 involving S3, S2, S1and S0 states. Some new structures and pathways were reported and the dissociation thresholds were

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explained.
S3-LM1-TS2
642.2

hν 193 nm=619.8 kJ/molhν 222 nm=538.8 kJ/mol

S3/S2
S2-LM1-TS2b

O(1D)+cis-HONO
509.1

534.3

S2-INT
532.6

S2-LM1-TS2a

S3-LM1

534.6

522.9

S2-GM-TS2b

554.2
S2-GM-TS2a

S2/S1-1

521.2

512.7

S2-TS

S2-LM1-TS1
496.9

501.5

S2-GM-TS2c S2/S1-2
493.9

S2-LM1hν 248 nm=482.3 kJ/mol

481.8

533.5

488.3

S2-GM

O(1D)+trans-HONO
506.2(490)aS2-GM-TS1
481.5

459.0

hν 308 nm=388.4 kJ/mol

S1/S0-1

S1/S0-2
388.8

392.0
S1-TS1
360.2

S1-GM

OH(X)+NO2(A 2B2)

344.1

OH(X)+NO2(A 2B2)328.7(315)a
OH(X)+NO2(X 2A1)

328.7(315)aa : Exp. dissociation energy

S0-GM

219.3
(200)a0.0

Figure 3. The potential energy (kJ/mol) profiles of photodissociation of HNO3 by 3S-CASPT2(12,8)/6-31+G*(except for those involving S3 by 4S-CASPT2(12,8)/6-31+G*)The S0 → S1(nπ*), S0 → S2(nπ*) and S0 → S3(ππ*) translations strongly localized on the NO2 group of
HNO3. As shown in Figure 3, at the short wavelength (193 nm), S3 has a strong absorption (oscillator
strength: 0.193). Pathway (3) is impossible on the S3 state due to a very high barrier. S3 may decay to S2 via
S3/S2 conical intersection, and then pathway (3) occurring on the S2 state becomes the primary pathway withan increase of photon energy. At longer wavelengths, S2 and S1 have weak absorption (oscillator strengths:
1.03 ×10-4and 1.72 ×10-6). Pathway (1) takes place on the S1 state and pathway (2) occurs on the S2 state.

III. Proline-catalyzed Direct Asymmetric Aldol Reactions
Small organic molecules recently emerged as a third class of broadly useful asymmetric catalysts that
direct reactions to yield predominantly one chiral product, complementing enzymes and metal complexes.
The amino acid proline and its derivatives are useful for the catalytic activation of carbonyl compounds andforming carbon-carbon bond in Aldol and Mannich reactions. Scheme 1 shows the generally acceptedmechanism of the proline-catalyzed asymmetric aldol reaction (single proline enamine mechanism). Recently,
some studies reported a new role of the oxazolidinones in the proline-catalyzed asymmetric aldol reaction. In
order to have an insight into the whole processes of the proline-catalyzed asymmetric aldol reaction, first we
used the AFIR method to follow the previously proposed mechanism. Our calculated results indicate that thepreviously proposed mechanism does not explain the experimental results well and has some problems suchthat (i) how to form enamine intermediate from oxazolidinone; (ii) terminate reactions at the intermediatewith lower energy other than the products; (iii) the function (M06) or SCRF model (PCM and CPCM) aresuitable for the aldol reaction or not. From the present results we think that the proline-catalyzed asymmetric
aldol reaction has another new lower energy reaction pathway and we will further explore the reaction－ 106 －

Ⅳ 研究業績 (2010)

mechanism.

2. Original papers(1) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma“Excited-state roaming dynamics in photolysis of a nitrate radical”
J. Phys. Chem. Lett. 2, 934-938 (2011).
3. Presentation at academic conferences
4. Others(1) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma (Poster)“A theoretical study on the photodissociation of NO3”
The 8th FIFC symposium, Kyoto, December 3, 2010.

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Lina DINGJST Fellow, Fukui kenichi Memorial Research Group 1（Form 1 Jul. 2010）

1. Summary of the research of the year
Mechanistic study on photo-induced decarboxylation of the PhotoactivableGreen Fluorescent Protein: A theoretical ONIOM(QM:MM) calculation
The Photo-induced decarboxylation of the green fluorescent protein (GFP) and its variants
have received wide attention since GFP has revolutionized GFP-technology to visualize themolecular events that occur within living cells, which marks the improvement in biologicalimaging and analysis, as recently honored by Nobel Prize in chemistry to three pioneers in thefield. The reported quantum yield 0.03~0.002 for this irreversible photo-decarboxylation ismuch lower than that 0.8 for reversible process in WT-GFP which indicates that both
irreversible and reversible process are involved in GFP photo-transformation with different
kinetics and quantum yields. Recently, X-ray crystal structures of native and photoactivatedstates of PA-GFP were also reported. Rate measurements for photoactivation in WT and
PA-GFP reveal similar kinetics in both proteins.

http://zeiss-campus.magnet.fsu.edu/tutorials/fluorescentproteins/pagfpchroma/index.html

Scheme 1 Proposed Klobe-mechanism
However, the photo-decarboxylation mechanism is still mystery and the detailed study at the－ 108 －

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atomic level remains unresolved up to now despite Kolbe mechanism is well-accepted(Scheme 1).

Fig. 1 Seven active orbitals

Backbone atom position
X-ray (R) & AMBERMin(G)Setup Stru. for Amber-Min
Initial ONIOM Structure
residues:6814; Atoms:23322
residues: 227 Crystal WT:157[ 227,157crystal WT,7Na+];
Atom: 4046; QM: 39
Fig. 2 Structures in MD and ONIOM setup(PDB:3GJ1(1.80 Å))

In this work, we report the first theoretical mechanistic study on the photo-induced
decarboxylation of GFP by using ONIOM(SA6-CASSCF(10e,7o)/6-31G*:Amber)-MEUC
and ONIOM(SS-CASPT2(10e,7o)/6-31G*:Amber)//ONIOM(SA6-CASSCF(10e,7o)/6-31G*:Amber)-MEUC methods. The active space includes two n, one p, π and π* orbitals (8e/5o) of
COO- in Glu219, one pair π and π* orbitals (2e/2o) of chromophore (Fig. 1). All the structures
involved in molecular dynamics and initial ONIOM setup are given in Fig. 2. All calculations
were performed by Molcas74 and Gaussian09. It was found that the decarboxylation process
is initiated on an intra-molecular charge transfer excited state (Intra CT) PES, which thentriggers an ultrafast decarboxylation process via an avoided conical intersection (CI) of an－ 109 －

Ⅳ 研究業績 (2010)

intra-molecular charge transfer excited state (Intra CT) and an inter-molecular charge transfer
excited state(Inter CT). The inter CT excited state plays a key important role in thephoto-induced irreversible process, and finally decays to the ground state via the second
avoided conical intersection (CI) of Inter CT excited state and ground state. The initialprocess on the Intra CT PES is rate-determined step while on the Inter CT PES is ultrafast.

2. Presentation at academic conferences(1) Lina Ding, Lung Wa Chung, Keiji Morokuma“QM/MM study on the Photoinduced decarboxylation mechanism of PhotoactivableGreen Fluorescent Protein”
7th Congress of the International Society for Theoretical Chemical Physics(4PP-62),
Tokyo, Sep. 2-8. 2011

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Hai-Bei LI
JST Fellow, Fukui kenichi Memorial Research Group 1（From 27 Jul. 2010）

1. Summary of the research of the year
(A) Fullerene formation from hydrocarbon combustions: Quantum chemicalmolecular dynamics study
The formation of polycyclic aromatic hydrocarbon (PAH) and fullerenes have been
investigated in great detail. Combustion of hydrocarbon fuels in lean oxygen flame offers
advantages for large-scale fullerene production. Saha et al. performed high temperature
simulations of benzene combustion by gradually reducing hydrogen atoms randomly using
density-functional tight-binding (DFTB)-based quantum chemical molecular dynamics(QM/MD). In this work, we simulate fullerene formation from naphthalene combustion at
1500 K and 2500 K. All QM/MD simulations were performed by employing a Nose Hoover
chain thermostat, and carbon densities of 0.119 and 0.026 g/cm3, respectively. A Monte
Carlo-based hydrogen removal strategy was devised where we calculate the probability factor
for each candidate structure after removing two hydrogen atoms in randomly selected
positions, and select the candidate hydrogen pair randomly under consideration of Boltzmann
weights for the environmental temperature. One hydrogen pair is removed every 0.235 ps and
0.470 ps at 1500 K and 2500 K, respectively, until all hydrogen is removed from the system.
One selected trajectory is shown in the Figure 1. Although the mechanism of fullerene
formation is similar to previous results, in our simulation, lower carbon density and lower
temperature favor the formation of smaller size fullerenes (Figure 2). Our new hydrogen
removal scheme tends to produce more cage structures than the random removal scheme in
Saha’s work.

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4.97ps

8.57ps

10.97ps

15.77ps

20.09ps25.30ps

40.20ps65.04ps

Figure 1. Snapshots from one trajectory showing the key events during the hydrogen removal
and self-assembly processes.

Figure 2. Formation statistics of average rings counting at different temperature as a functionof simulation time. (a) Tn=1500K, (b) Tn=2500K.

(B) AC SWCNT growth from bottom-up organic synthesis
Cycloparaphenylenes(CPPs) as the shortest units of armchair SWCNTs have been usedas the promising precursors to produce the controllable SWCNT in diameter and orientation.
(6,6) SWCNT growth has been modeled using quantum chemical molecular dynamics(QM/MD) in conjunction with feeding of C2H radicals to [6]CPP seed at low temperature
500K. About 7.5-Å-long (6,6) SWCNT with almost 5 belts is produced within 500 ps. The
present QM/MD simulations have shown that C2H radicals can facilitate the H abstraction,
and act as sidewall growth agent, that is, the successful growth of (6,6) SWCNT is proposedby H-abstraction and C2H insertion mechanism, as shown in Figure 3. From our QM/MD－ 112 －

Ⅳ 研究業績 (2010)

simulation, it has been demonstrated that uniform armchair SWCNTs in fixed diameter could
grow in a controlled way by adding C2H radical species. Figure 4 shows the six-memberedring counting statistics as a function of simulation times. In comparison to previously
proposed SWCNT growth mechanisms based on repeated DA cycloadditions, such a radical
addition based mechanism exhibits extremely competitive energetics. The addition of C2H2 tothe growing SWCNT fragment, following hydrogen abstraction by C2H, is also a much moreenergetically favorable process compared to DA cycloaddition. However, in both cases, therate of reaction is determined by the presence of terminating hydrogen atoms at the ‘bay’ areaof the nanotube sidewall.

Figure 3. The snapshots of SCC-DFTB/MD simulations of (6,6)-SWCNT growth.

Figure 4. Six-membered ring counting statistics as a function of simulation times.
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2. Original papers(1) H. B. Li, S. Irle, A. M. Mebel and K. Morokuma, “Fullerene Formation from Hydrocarbon
Combustions: Quantum Chemical Molecular Dynamics Study” Manuscript in preparation.
(2) H. B. Li, A. J. Page, S. Irle and K. Morokuma, “(6,6) SWCNT Growth from a[6]Cycloparaphenylene Seed Molecule: Nonequilibrium Quantum Chemical Molecular
Dynamics Simulations”, Submitted.
(3) H. B. Li, S. Irle and K. Morokuma, “The Roles of Hydrogen in the Fullerene Formation”
Manuscript in preparation.

3. Presentations at Academic Conferences

H. Li, S. Irle and K. Morokuma, “Fullerene Formation from Hydrocarbon Combustions:
Quantum Chemical MD Study”, 7th Congress of the International Society for Theoretical
Chemical Physics, Abstract page 4PP-78, Tokyo, Japan (Septemper 2~8, 2011)－ 114 －

Ⅳ 研究業績 (2010)

Lung Wa CHUNG
JST Fellow, Fukui kenichi Memorial Research Group 1

1. Summary of the research of the year
Comparative Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in Heme and non-Heme
Complexes
Heme- and non-heme-containing oxygenases and oxidases play vital roles in many selective and efficientbiochemical oxidation. Several species including ferryl-oxo, ferric-hydroperoxo and ferric-peroxy were
proposed or found to act as oxidants in these enzymes. In addition to the well-known high-valent ferryl-oxo
species, not-well-characterized lower-valent ferric-superoxo species have recently been suggested orobserved to be an alternative electrophilic oxidant, e.g. in isopenicillin N synthase (IPNS),
hydroxyethylphosphonate dioxygenase (HEPD), and tryptophan 2, 3-dioxygenase (TDO). Furthermore,some recent synthetic ferric-superoxo and other metal superoxo complexes were reported to be capable ofcatalyzing oxidation, including C-H bond activation. Notably, many non-heme enzymes can use
ferric-superoxo species as an oxidant, but only few heme enzymes (TDO, IDO and NOD so far) use
ferric-superoxo species! In this study, we theoretically and systematically compare reactivity of several key
ferric-superoxo and ferryl-oxo model complexes (Scheme 1).
Scheme 1

Our calculations show that different ferric-superoxo species can adopt different O2 coordination and/or
spin state. For instance, ground-state heme ferric-superoxo complexes 11S and 12S favor low-spin and end-on
O2 coordination, whereas ground-state non-heme or synthetic model complexes 73S, 74S, 75S and 78S preferhigh-spin and side-on mode. However, 57S is computed to be similar in energy to less-bulky 5-coordinate
complex 77′S in the gas phase and even 77′S becomes the most stable form in solution (ΔΔE = 3.0 (gas) and-16.5~-18.0 (acetonitrile, ACN) kcal/mol). Driven further by entropy, the 5-coordinate complex 77′S shouldbe the resting state of the recent not-yet-characterized synthetic model, whereas the corresponding ferryl-oxo
complex was observed to be 6-coordinate. The ferric-superoxo can be stabilized by an anti-ferromagnetic
coupling (AFC) between the Fe d electrons and superoxo radical in the singlet heme and quintet non-heme
complexes, or by a ferromagnetic coupling (FC) in the triplet heme and septet non-heme complexes (Scheme2). Electronic structures for most of the end-on ferric-superoxo complexes are schematically illustrated in
Scheme 2. Surprisingly, key electronic structures of complexes 6S-8S are different, in which the out-of-plane
π*(O2) orbital becomes fully occupied and the in-plane π*(O2) orbital is singly occupied. Additionally,－ 115 －

Ⅳ 研究業績 (2010)

compared to the low-spin heme ferric-superoxo complexes, a much smaller coupling was found in a
non-heme end-on ferric-superoxo dioxygenase experimentally (J ~ 6 cm-1) and in our model complexes. In
comparison, geometry and electronic configuration of the ferryl-oxo complexes are much simpler andgenerally favor the triplet state.
Scheme 2.

Scheme 2 conceptually illustrates the oxidative processes of the ferric-superoxo and ferryl-oxo complexes.
For the former ones, one electron is formally transferred from the substrate to the half-filled π*(O2) orbital(reduction of the superoxo), but not to the metal, and thus, the strong π(O2) bond is broken as well as the
Fe-O bond is strengthened. Therefore, the coupling (AFC or FC) between the ferric metal and superoxo parts
is quenched partly in transition states and completely in products. Since the electronic configuration of themetal does not change, the effect of exchange interactions of the metal on the reaction should be small. In
contrast, for the ferryl-oxo oxidants, one electron is formally transferred from the substrate to the ferryl metal(reduction of the metal) to weaken the Fe=O bond via a ferric-oxo transition state. Hence, the reactivity of
the ferryl-oxo complexes can be affected by the spin state to change the exchange interactions.
Our key results for the reactivity of the ferric-superoxo and ferryl-oxo oxidants towards a model substratepropene are summarized as follows. First, the neutral or anionic heme ferric-superoxo and ferryl-oxooxidants (1-2) are usually less reactive than the non-heme oxidants (3-8): the reactivity qualitatively
in-creases with increasing positive charge of the oxidants and stability of the products (i.e. thermodynamic
driving force). Remarkably, a good linear correlation (Figure 1) between the computed barrier and reactionenergy of hydrogen atom transfer (HAT) is found for various ferric-superoxo oxidants with different charges
and spin states. A similar linear correlation is also observed for the ferryl-oxo oxidants. Second, thehigher-valent ferryl-oxo oxidants generally have higher reactivity of HAT and radical addition (RA) than thecorresponding ferric-superoxo oxidants. Third, the reaction barrier for an intramolecular HAT in 77′S is high－ 116 －

Ⅳ 研究業績 (2010)(about 26-30 kcal/mol), and higher than the intermolecular HAT with propene (by 26.0 (gas) and 6.3 (ACN)kcal/mol). Hence, self-decay of 77′S is less feasible, due to larger strain in the transition state.

Figure 1. Correlations between the calculated barrier and reaction energy (relative to the most stable
reactant) for HAT with the ferric-superoxo and ferryl-oxo species.
These oxidation reactions involve an electron transfer from the substrate to the iron oxidants. The more
electrophilic complex with a lower-lying electron-accepting orbital (e.g. the half-filled π*(O2) orbital of
the ferric-superoxo complexes) can enhance both the reactivity and thermodynamic driving force. As
shown in Table 1, the cationic non-heme complexes have higher electron affinity, which can promote thereactivity, especially for the di-cationic complexes 7S, 77′S and 7O. Importantly, even for the neutral
complexes 1S and 3S, the electron-accepting half-filled π*(O2) orbital for the reactions in 1,53S islower-lying than 11S. Therefore, the lower reactivity and driving force of the neutral and anionic heme
ferric-superoxo complexes is partly attributed to their lower electrophilicity. Moreover, as discussed
previously, the more pronounced quenching of anti-ferromagnetic coupling in the low-spin heme
ferric-superoxo complexes than the high-spin non-heme superoxo complexes should further decrease thereactivity and thermodynamic driving force of the heme ferric-superoxo complexes.
Table 1. Calculated adiabatic electron and proton affinity of the key FeIII-O2- and FeIV=O species(kcal/mol, with ZPE) in gas phase and acetonitrile solution and barrier for HAT.

Surprisingly, the lower-valent ferric-superoxo oxidants are calculated to have higher electron affinity than

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the high-valent ferryl-oxo species. However, besides electrophilicity of the oxidants, the high-valent
ferryl-oxo species is found to have higher proton affinity (and basicity), which is another key factor for thehigher reactivity than the ferric-superoxo species. In addition, as found by different groups, the additional
gain of large exchange stabilization for the high-spin non-heme ferryl-oxo species further contributes to thehigher reactivity and driving force (exchange-enhanced reactivity and thermodynamic driving force).
The importance of the driving force on the reactivity makes us further investigate effects of the ligand or
metal on HAT. Bond dissociation energy of the new O-H bond (BDEO-H) can offer “qualitative
understanding” of HAT reactivity. Therefore, BDEO-H of the key ferric-superoxo, ferryl-oxo (including
high-spin ferryl-oxo in TauD and cationic ferryl-oxo in P450) and other common oxidants were evaluatedand compared (Table 2) to understand different mechanistic strategies as well as to help rationally design
reactive heme ferric-superoxo oxidants.
Table 2. Calculated bond dissociation energy (BDEO-H, kcal/mol, with ZPE) of the O-H bond forming.

A trend of the computed BDEO-H is consistent with the above-discussed reactivity and driving force. The
less reactive heme oxidants are endowed with the smaller BDEO-H than the non-heme oxidants (even for
low-spin 13S and 14S). Also, the ferric-superoxo oxidants intrinsically give smaller BDEO-H than theferryl-oxo oxidants, presumably due to the strong π(O2) bond broken and AFC quenching in the former ones
and the exchange stabilization gain for the latter ones. Comparatively, a very reactive cationic low-spin
ferryl-oxo oxidant (Compound I) employed in P450 heme enzymes is driven by the very large BDEO-H (86.8
kcal/mol) so that it can react with inert substrates. On the other hand, the extra exchange stabilization gainedin the high-spin ferryl-oxo oxidants in TauD or synthetic model complexes increases the BDEO-H (81.0-87.8
kcal/mol) and, thus, increases the reactivity. The highest-valent metal-oxo oxidants [MnO4]- and MO4 (M =Ru or Os) give rather small BDEO-H (53.9-70.7 kcal/mol), explaining why stepwise HAT is less favorable
than the concerted [3+2] pathway. As to the heme ferric-superoxo, replacing Fe in 1S by other first-row－ 118 －

Ⅳ 研究業績 (2010)transition metals gives only smaller or similar BDEO-H, while using Ru or Os affords a slightly higher
BDEO-H. Based on these results, we finally used a mono-anionic 21-oxaporphyrin ligand to generate acationic heme-like ferric-superoxo complex 1Soxa. We are pleased to find that 1Soxa gives a lower HAT
barrier with propene (19.3 vs. 24.2 kcal/mol for 1S), as well as higher BDEO-H.
In summary, the reactivity of several key ferric-superoxo and ferryl-oxo model complexes are found tocorrelate well with the driving force and can be enhanced by using more electrophilic complexes. Moreover,the ferryl-oxo complexes with the higher driving force are usually more reactive than the ferric-superoxo
ones. Compared to the non-heme ferric-superoxo oxidants, the lower electrophilicity and more pronounced
quenching of anti-ferromagnetic coupling in the heme ferric-superoxo complexes lower the reactivity. In
addition, the non-heme Fe center is often coordinately-unsaturated and flexible: the substrate can be directly
activated through ligation for intramolecular reactions (and even forms a strong C=S or C=O bond after
HAT). These may be the reasons why nature prefers to use the transient non-heme ferric-superoxo species foroxidation, to a larger extent than the heme superoxo species. The latter may be tailored to function mainly as
oxygen storage or carrier, and be activated by electron and/or proton transfer to generate more powerfuloxidants. Having various oxidants with different reactivity in nature, the milder ferric-superoxo oxidantsshould render the oxidation more selective with the reactive substrates and atomically-economic. The
reactivity and driving force of the ferric-superoxo species could be further enhanced in enzymes by stronger
electrostatic interactions with the reacting (more charged and polar) O-H moieties. Our comparative results
may help design more reactive ferric-superoxo oxidants or artificial heme enzymes.

2. Original papers(1) Chung, L. W.; Li, X.; Sugimoto, H.; Shiro, Y.; Morokuma, K. “ONIOM Study on a Missing Piece
in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2, 3-Dioxygenase with Dual
Oxidants”, J. Am. Chem. Soc. 2010, 115, 11993.
(2) Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. “Primary Events of Photodynamic
in Reversibly Photoswitching Fluorescent Protein Dronpa” J. Phys. Chem. Lett. 2010, 1, 3328.
(3) Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Morokuma, K. “Competitive Mechanistic
Pathways for Green-to-Red Photoconversion in the Fluorescent Protein Kaede: A Computational
Study” J. Phys. Chem. B 2010, 114, 16666.
(4) Chung, L. W.; Hirao, H.; Li, X.; Morokuma, K. “The ONIOM Method: Its Foundation andApplications to Metalloenzymes and Photobiology”, Wiley Interdisciplinary Reviews: Comput. Mol.
Sci. 2011, doi: 10.1002/wcms.85.
(5) Abdel-Azeim, S.; Li, X.; Chung, L. W.; Morokuma, K. “Zinc-Homocysteine Displacement in
Cobalamin-Dependent Methionine Synthase and its Role in Substrate Activation: DFT and ONIOM
Study”, J. Comput. Chem. 2011, 32, 3154.
(6) Li, X.; Chung, L. W.; Morokuma, K. “Primary Events of Photodynamics of All-trans ProtonatedRetinal Schiff Base in Bacteriorhodopsin, Methanol Solution and Gas Phase” J. Chem. Theory－ 119 －

Ⅳ 研究業績 (2010)

Comput. (Lett.) 2011, 7, 2694.
(7) Chung, L. W.; Li, X.; Hirao, H.; Morokuma, K. “Comparative Reactivity of Ferric-Superoxo andFerryl-Oxo Species in Heme and non-Heme Complexes” j. Am. Chem. Soc.(Commun) 2011,(doi:10.1021/ja2084898).

3. Presentation at academic conferences(1) Lung Wa Chung, Xin Li, Hiroshi Sugimoto, Yoshitsugu Shiro, Keiji Morokuma “ONIOM
Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan
2,3-Dioxygenase with Dual Oxidants”, (oral) ACS 240th National Meeting, Boston,
Massachusetts, August 22, 2010.
(2) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, Keiji Morokuma “Reaction
Mechanisms of Novel Fluorescent Proteins”, (oral) the seventh Congress of theInternational Society for Theoretical Chemical Physics, Tokyo, September 4, 2011.
(3) Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, Keiji Morokuma “Reaction
Mechanisms of Photophysics and Photochemistry of New Fluorescent Proteins”, 5th Asiaand Oceania Conference for Photobiology, Nara, July, 31, 2011.

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Galina PETROVAJST Fellow, Fukui kenichi Memorial Research Group 1（From 1 Dec. 2010）

1. Summary of the research of the year

Towards understanding the HppE catalytic mechanism
The hydroxypropylphosphonic acid epoxidase (HppE) is a non-heme redox-active iron containing
enzyme involved into the biosynthesis of (1R,2S)-epoxypropylphosphonic acid also referred to as
fosfomycin – a clinically applied antibiotic inhibiting the first committed step of bacterial cell wallbiosynthesis. By this reason the enzyme has been an object of many experimental studies aiming at
defining its properties and understanding the detailed mechanism of its catalytic action. Thoughmost of the natural epoxides are biosynthesized from alkanes via oxygen insertion by
α-ketoglutarate dependant non-heme monooxygenases or by the heme cytochrome P450 enzymes,
HppE does not require the presence of α-ketoglutarate to function as the substrate itself(2-hydroxypropylphosphonic acid) activates the metal center for O2-binding. On the other hand, theenzyme is not selective with respect to the enantiomeric form of the substrate but does convert
stereospecifically each enantiomer into a specific product; thus, only fosfomycin is obtained from
2S-form of the substrate while the reaction with (R)-2-hydroxypropylphosphomic acid results in
ketone product (Fig. 1a).

Figure 1. (a) Reaction products depending on the enantiomeric form of the substrate. (b) Structureof the active center of HppE as the isolated model includes Glu142, His180 and His138 residues.

The current project is focused on the theoretical modeling of the different reaction mechanisms inorder to understand and explain the catalytic role of HppE in the formation of fosfomycin as well as
the differences observed in the enzyme behavior towards different substrates. The first stage of the－ 121 －

Ⅳ 研究業績 (2010)

study is based on isolated gas-phase model of the active center including the iron ion, the substrate
and the first shell of amino acid residues of the peptide (see Fig. 1b) as two different reactive
species were considered – ferric superoxo, Fe(III)OO•–, and ferryl oxo, Fe(IV)=O. At the next stepof the modeling a QMMM computational scheme will be applied in order to estimate the influenceof the enzyme surrounding.
The formation of fosfomycin from theinitial(S)-2-hydroxypropyl-

phosphomic acid could proceed into
two main steps: (i) H-abstraction fromC1 atom of the substrate, and (ii)further cyclization of the radical
intermediate to epoxide structure. Theenergy profile of the reaction in thecase of ferric superoxo active species
for quintet and septet state of thesystem is presented on Fig. 2a as the
structures

of

the

correspondingtransition states are provided in panelsb and c for the hydrogenated (i.e. thehydroxyl group at C2 is considered
intact) and dehydrogenated substrate,
respectively.
According to the obtained results, theFigure 2. (a) Energy diagram of the reaction in case of(S)-2-hydroxypropylphosphonic acid: blue/red forquintet/septet state, solid/dashed lines for hydrogenated/
dehydrogenated substrate. Examples of structures for tsh
and ts-epox states for hydrogenated (b) anddehydrogenated (c) substrate. Relative energy (ZPE
corrected) is estimated with respect to the most stable
reaction complex.

reactionbarrierforhydrogenabstraction from C1 atom is quite
high, above 25 kcal/mol. Significant
decrease of the energy barrier for H
abstraction by ca. 10 kcal/mol wasobserved in case of ferryl-oxo active
species.
The reaction was modeled also with(R)-2-hydroxypropylphosphomic acidas reactant in which case the hydrogen atom at the C2 atom is also available for abstraction. For
ferric superoxo species the abstraction from C2 is preferred by 5-10 kcal/mol while the energy
barriers for the ferryl oxo structures are very similar for both C1 and C2 abstraction.

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Ⅳ 研究業績 (2010)

Wilfredo Credo CHUNG
FIFC Fellow

1.

Summary of research for the year
A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin: Chemical
Dynamics Reasons Behind Selection of Rhodopsin by Life

Rhodopsin (Rh) has 11-cis retinal as chromophore and is the photosensitive chemical found on
the outer segment of rod-like cells in the retina, the light-sensing structure of the eye.1 Isorhodopsin(isoRh) is an Rh analogue that contains 9-cis retinal embedded in the same opsin environment.2, 3Both are known to yield bathorhodopsin (bathoRh), a photoisomer that contains all-trans retinal, via
cis-trans isomerization of the 11 or 9 position upon absorption of a photon. Despite their similarity,
the photoisomerization period and quantum yield is largely different. Rhodopsin photoisomerization
is experimentally known to be faster (tRh = 200 fs4, 5, tisoRh = 600 fs6) and more efficient (quantum
yield: ΦRh = 0.657, ΦisoRh = 0.228).
We carried out a Quantum Mechanics/Molecular Mechanics (QM/MM) trajectory surface
hopping (TSH) direct dynamics calculations in order to understand the origin of the discrepancy.
Comparison is also made with our previous calculations9, 10 The transition probability is estimatedusing the Zhu-Nakamura (ZN) theory11 of nonadiabatic transitions. We call the present scheme the
ZN-QM/MM-TSH scheme. The QM region is essentially a protonated Schiff base of retinal (seeFigure 1 of reference 9 and Figure 2 of reference 10). The rest of the molecules were treated with
MM using mechanical embedding. The QM treatment was the 6-electron-6-orbital complete active
space self-consistent field (CASSCF) technique12, 13 with the 6-31G basis set14. The MM part was
described by AMBER parameters15 in Gaussian 0316. 162 trajectories were calculated in total forboth Rh and isoRh starting material at 300 K. Geometries of minima in the ground state andminimum energy conical intersections (MECI) are identified to analyze the dynamics results.
We have already shown9, 10 that retinal molecule without opsin leads to rotations of φ11 and φ9
rotates in a direction opposite to each other. Thus, the essential feature of isomerization motion after
photo-excitation is intrinsic in retinal itself.
The experimental photoisomerization period and bathoRh quantum yield are reproduced
reasonably (see Table 1). The slight discrepancy between the simulation and experiments are due tothe failure of the chosen QM/MM treatment to reproduce a barrier8, 17 in the excited state in isoRhreported in experiments. Even a tiny barrier would have slowed down the photoisomerization bytrapping the trajectories in the excited state and yield a quantitatively accurate timescale andquantum yield.
Table 1 also shows thatphotoexcitation of Rh gives
bathoRh (and the reactant)whereas the isoRh excitation
yields a 9,11-dicis analog in
addition to bathoRh (and thereactant).
This
byproduct
formationinisoRhphotoisomerization is anotherreason why life uses Rh rather
than isoRh. Shown in Figure 1
are the plots of the time

Table 1. The ratio of photo products, quantum yield and photoisomerization
period of rhodopsin in comparison with isorhodopsin. The values in square
brackets are taken from the corresponding gas-phase PSB calculationsa.
reactants
Rh(11-cis)
isoRh(9-cis)
photoproducts
bathoRh(all-trans)
52 [27]31 [13]
isoRh(9-cis)
0 [22]
65 [82](%)
Rh(11-cis)
48 [51]0 [5]9,11-dicisRh
0 [0]
4 [0]
quantum yield
calc.
0.52
0.31
expt.
0.657
0.228
photoisomerization
calc.
187[185]344[665]
expt.
2004, 56006
period (fs)aReferences 9 and 10.

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Ⅳ 研究業績 (2010)

evolution of theactivedihedralangles(=C10-C11=C12-C13=
and
or
φ11
=C8-C9=C10-C11=
or φ9, respectively)
for the (a) Rh and
(b)
isoRh
trajectories. Clearly
Figure 1. Time evolution of the dihedral angle of the twisting bond for the (a) Rh and (b)seen in Figure 1a is,
isoRh systems. Blue triangles are transition points from the excited state to the ground state.
for Rh, the lack ofaccessoftrajectories to a clockwise twist in φ11 in addition to rapid change in φ11 to -90°, where an MECI is
located. Figure 1a shows that most of trajectories are in a similar and simultaneous way in the
excited state, consistent with vibrational coherence revealed in an experiment on Rh18 although thepresent treatment of the nuclei is classical except for transitions. In the case of isoRh (Figure 1b), a
few trajectories are initiated by a clockwise twist of φ9 in the excited state although the twist is
unsuccessful and isoRh is regenerated in the ground state (S0). Thus, all bathoRh photoproducts areformed via counterclockwise twist of the active dihedral φ9 or φ11. This obviously hinderedisomerization is due to the constraints offered by the opsin environment especially by amino acidresidues close to the binding pocket. In contrast, in our previous gas-phase PSB simulations, twists
in both directions take place (cf. Figure 6, reference 10). The slower twist in isoRh is in the excitedstate. This is another consequence of the slower isoRh excited-state dynamics.
Figure 2showsthediagram of theactivetwist
angle and thelength of theactive bondforfivetypicaltrajectories
for Rh andisoRh.
Fast
Figure 2. Change in length of the active bond -Cn-Cn+1- against the absolute value of the dihedral
andangle Cn-1-Cn-Cn+1-Cn+2 for typical (a) Rh (n = 11) and (b) isoRh (n = 9) trajectories leading tostraightforwar
the all-trans form. The solid and dashed lines shows that trajectories are in the excited and groundd dynamics instates and the black triangles correspond to transition from the excitated state to the ground state.
Rh is shownin Figure 2a whereas complicated excited-state dynamics is evident in the isoRh case in Figure 2b.
Why is the isoRh photoisomerization more difficult compared to that of Rh? One reason is theatomic displacements required by the chromophore at the excited state potential energy surface toreach the conical intersection region. Shown in Figure 3 is a superimposed image of the S0
optimized geometry and the geometry adapted by the chromophore at the crossing region. The
pocket that contains the retinal chromophore is similar in shape for both the Rh and isoRh case.
Opsin residues Thr118 and Tyr268 create a narrow gap near the -C9=C10-C11= region of the retinal
chain with the two residues coming as close as 7 Å to each other. The isoRh photoisomerization ismore difficult compared to that of Rh because of at least two reasons: (1) the isoRh isomerization
requires more space than that of Rh and (2) the dihedral that needs to be twisted in the isoRh case(-C9=C10-) is situated within the narrow gap between Thr118 and Tyr268.

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Another reason is the initial acceleration ofretinal atoms induced by surrounding residues. The
initial force between two atoms for a few
retinal-opsin atom pairs is listed in Table 2. Cys187,
Thr118 and Tyr268 are close enough to thechromophore to significantly influence theisomerization. For example, for the atomic distance
between the C12 hydrogen in retinal and the oxygen in
Cys187, the projected inter-atomic force for Rh isabout 15 times larger than the counterpart for isoRh.
Also, a five-fold difference is found for the force
between retinal C10 and Tyr268. Such differences
partially explain the discrepancy in the speed andefficiency of the cis-trans isomerization between the
Rh and isoRh chromophores.
Table 2. Initial interatomic forces between most
relevant chromophore-opsin atom pairs
Force (hartree-bohr-1)
Rh

isoRh

Ret C12-H-Cys187 O

2.5 × 10-3

1.7 × 10-4

Ret C10-Tyr268 CE2

2.2 × 10-3

4.5 × 10-4

Ret C11-Thr118 N

1.8 × 10-3

1.6 × 10-3

CE2 = Tyr's second ε-carbon.

Comparison with the previous gas-phasesimulations reveals three other consequences shown
below.

Figure 3. Superimposed structures of the S0
optimized geometry (gray) and geometry at the
MECI (pink) for the (a) Rh and (b) isoRh case.
Also shown is the opsin pocket that contains thechromophore. The pocket surface is the overlappedenvelope of amino residues surrounding the retinal
chromophore, which is generated using the S0
optimized geometry wherein the retinal
chromophore is artificially removed.

The protein causes (almost) one-way twist of the active angle. In Figure 4, the values of theactivedihedralangles φ9 and φ11at the time of
hopping
areplotted (comparewith Figure 11,
reference 9 and
Figure10,reference 10). All
Rh trajectories gothough only one
MECI region withclockwise-twisted
φ9andcounterclockwisetwisted
φ11 Figure 4. Diagram of the twist angles of -C11=C12- (φ11) and -C9=C10- (φ9) at the transition
points. The minima in the ground state (open blue circles) and conical intersections (filled(Figure 4a). This blue circles) obtained in the present calculations are plotted in the diagram. Rh = rhodopsin,
MECI branches isoRh = isorhodopsin, bathoRh = bathorhodopsin, 9,11-dicisRh = 9,11-dicis rhodopsin,
towards
the CI=minimum energy conical intersection.

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Ⅳ 研究業績 (2010)

formation of bathoRh and the regeneration of the reactant. The relaxation of the excited state of
isoRh, on the other hand, goes through two MECI regions. Most of trajectories from isoRh go
through the MECI region with φ9 ~ -90° and clockwise-twisted φ11, which is shown as
CI(isoRh->BathoRh) in Figure 4b. This MECI is responsible for all of bathoRh generation. A few
trajectories go through another MECI region (CI(isoRh->9,11-dicisRh)), which is responsible forthe generation of a photoproduct with 9,11-dicis retinal as chromophore (we call this as9,11-dicisRh hereafter). Thus, photoexcitation of Rh only gives bathoRh as a product whereas isoRhyields 9,11-dicisRh in addition to bathoRh, as shown in Table 1. Note that the reaction speeds
through the two MECI in isoRh are significantly different. The reaction time is longer throughCI(isoRh->BathoRh) (τave=233 fs) than that through CI(isoRh->9,11-dicisRh) (τave=188 fs). The
difference is revealed in the dissimilarity in the twist speed of φ9 in Figure 1(b).
Secondly, the protein environment enhances the production of bathoRh. When the opsin
environment was totally ignored, the calculated bathoRh (all-trans PSB) quantum yield was only
0.27 and 0.13, respectively (in square brackets of Table 1). Explicit consideration of the opsin
residues that envelop the chromophore significantly improves the theoretical quantum yield to 0.51
and 0.31, respectively. This is partly due to the unidirectional rotation in opsin environment.
The third effect of the opsin on the dynamics is to cause transitions to take place near MECIs.
Comparison of transition points in Figure 4 with those in Figure 11 in reference 9 and Figure 10 inreference 10 reveals that the present transition points with the opsin environment are nearer the
MECI points than the points without the opsin. In our previous opsin-free simulations, it wasobserved that inefficient, premature hops (excited-to-ground state hops that occur far from the
MECI region) occur often especially in the isoRh case. The opsin environment enhances the
dynamics by drastically reducing the probability of premature hopping, in particular in the isoRhcase with transitions occurring near the MECI region. The protein may keep large energy gaps
between the excited state and S0 except for the MECI region.
In conclusion, the faster and more efficient photoisomerization of Rh than of isoRh is due to astraightforward and fast excited-state dynamics for Rh in contrast with a complicated dynamics in aback and forth fashion especially in the excited state for isoRh. The dynamics is governed by thedifferences (1) in volume-saving motions of retinal molecules, (2) in space gaps formed bysurrounding residues, and (3) in the initial acceleration by repulsive force from the surrounding
amino residues. The formation of 9,11-dicis Rh byproduct from isoRh photoisomerization isanother reason why organisms adopt rhodopsin rather than isorhodopsin. The other effects of the
opsin environment are (1) to cause the active dihedral angle in retinal to rotate one way, (2) toenhance the bathoRh quantum yield and (3) to cause transitions to take place near the MECIs. The
present ZN-QM/MM-TSH scheme is found to be applicable to photoreactions of biomolecules.
References
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G. Wald, P. K. Brown, R. Hubbard, Proc. Natl. Acad. Sci. U. S. A. 1955, 41, 438.
R. W. Schoenlein, L. A. Peteanu, R. A. Mathies, C. V. Shank, Science 1991, 254, 412.
L. A. Peteanu, R. W. Schoenlein, Q. Wang, R. A. Mathies, C. V. Shank, Proc. Natl. Acad. Sci.
1993, 90, 11762.
6 R. W. Schoenlein, L. A. Peteanu, Q. Wang, R. A. Mathies, C. V. Shank, J. Phys. Chem. 1993,
97, 12087.
7 J. E. Kim, M. J. Tauber, R. A. Mathies, Biochemistry (Mosc). 2001, 40, 13774.
8 J. B. Hurley, T. G. Ebrey, B. Honig, M. Ottolenghi, Nature 1977, 270, 540.
9 T. Ishida, S. Nanbu, H. Nakamura, J. Phys. Chem. A 2009, 113, 4356.
10 W. C. Chung, S. Nanbu, T. Ishida, J. Phys. Chem. A 2010, 114, 8190.
11 H. Nakamura, Nonadiabatic Transition: Concepts, Basic Theories and Applications, World
Scientific Publishing Co. Pte. Ltd., Singapore, 2002, pp. 376.

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H.-J. Werner, P. J. Knowles, J. Chem. Phys. 1985, 82, 5053.
P. J. Knowles, H.-J. Werner, Chem. Phys. Lett. 1985, 115, 259.
W. J. Hehre, R. Ditchfield, J. A. Pople, J. Chem. Phys. 1972, 56, 2257.
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C.
Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179.
16 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J.
B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, C. Gonzalez,
M. Challacombe, P. M. W. Gill, B. G. Johnson, W. C. M. Head-Gordon, E. S. Replogle, J. A.
Pople, Gaussian 03 (Revision D.01), Gaussian, Inc., Pittsburgh, PA, 2003.
17 R. R. Birge, C. M. Einterz, H. M. Knapp, L. P. Murray, Biophys. J. 1988, 53, 367.
18 R. M. Weiss, A. Warshel, J. Am. Chem. Soc. 1979, 101, 6131.

12
13
14
15

2. Original Paper
1. W. C. Chung, S. Nanbu and T. Ishida, Nonadiabatic ab initio dynamics of a model
protonated Schiff base of 9-cis retinal, J. Phys. Chem. A 114, 8190–8201 (2010).
3. Presentation at academic conferences
1. W. C. Chung, S. Nanbu and T. Ishida Nonadiabatic ab initio dynamics of an isorhodopsin
model system based on the Zhu-Nakamura theory 第26回化学反応討論会
平成22(2010)年6月2-4日広島大学東広島キャ ンパス (Poster)
2. W. C. Chung Computational Studies on Some Important Molecules In-House Seminar on
Computational Chemistry, MSU-IIT (Iligan City) and MUST (Cagayan de Oro City)
Philipines, September 7-8, 2010 (Invited Talk)
3. W. C. Chung, S. Nanbu and T. Ishida Hindered cis-trans isomerization in 9-cis retinal: atwo-state model dynamics simulation 第4回分子科学討論会 大阪大学豊中キャ ンパス
2010年9月14日～17日 (Poster)
4. W. C. Chung and T. Ishida On the mechanism of the structural decoy action of LMP1 overCD40 in relation to Epstein-Barr virus infection: an essential dynamics approach
第8回福井謙一記念研究センターシンポジウム 京都大学福井謙一記念研究センター3 December 2010
(Poster)
5. W. C. Chung, S. Nanbu and T. Ishida Nonadiabatic ab initio dynamics of a model
protonated Schiff base of 9-cis retinal The 2010 International Chemical Congress ofPacific Basin Societies (Pacifichem) Honolulu, Hawaii, USA, December 15-20, 2010
(Poster)－ 127 －

Ⅳ 研究業績 (2010)

Takafumi IWAKIFIFC Fellow

1. Summary of the research of the year
Theoretical Study of Nonlinear Photophoretic Motion of a Micro Droplet
When a temperature has a gradient, it sometimes induces a convectional flow, coupledwith a body force such as the gravity. This type of convection is called a natural convection,
which is commonly recognized in our daily life. On the other hand, there are convections ofwhich mechanisms rely on a more delicate effect upon a surface of the object. One example ofthis is the Marangoni convection arising from a gradient in surface energy, and another is theradiometric effect arising from an inelastic reflection of gas molecules at the solid surface with atemperature different from ambient gas (Fig. 1).
So far, the photophoresis caused by the inelastic reflections of gas molecules has beenstudied for a solid colloidal object, and yet there have been not so much consideration on thephotophoresis of the liquid droplet. According to the research in the preceding year, we haveadvanced a theoretical analysis for this case on the basis of the linearized Boltzmann equation
with Maxwell-type kinetic boundary condition, which was summarized as one original paper inthis year.

Figure 1: A schematic representation of the radiometric effect. The Maxwell
temperature of impinging gas particles is different from that of outgoing gas
particles influenced by a surface temperature of an object. On the other hand,the densities of gas particles are same before and after the reflection. This
induces the difference of the pressure according to the temperature difference.
For the case of a slightly rarefied gas, interactions between gas molecules heats－ 128 －

Ⅳ 研究業績 (2010)

the impinging particles, and the temperature difference between impinging andoutgoing particles decreases as compared with the free molecular case. For
comparison, schematic of thermophoresis is also sketched.
The solution for the linearized Boltzmann equation coupled with the Navier-Stokes
equation for a spherical liquid droplet was obtained by a spectral method for the system with anaxial symmetry. It is notable that the photophoretic velocity and the Peclet number are linearly
dependent on the surface temperature gradient, respectively. When light intensity becomeslarger, the system shifts from a temperature diffusion dominant region to a temperatureadvection dominant region. According to this shift, the scaling exponent of the photophoretic
velocity shifts from 1 to about 0.5.
Response functions for P1(cos θ) heat sources monotonically decrease as the Peclet
number increases. On the other hand, response functions for other modes of heat source
functions show a peak at around the Peclet number of 10. For a small Peclet number, an
advection carries energy from other modes. For a large Peclet number, stirring by the advection
becomes too strong and the temperature distribution is equalized in all modes. When internal
flow is slow, a temperature distribution inside the droplet is determined by the diffusion
equation. In this case, the photophoretic velocity linearly scales to the radiation intensity. Only
difference with the case of a solid sphere is its coefficient. When internal flow is fast, thetemperature advection changes the behavior of the system in a qualitative manner. The mostcharacteristic point is the occurrence of an asymmetric flow field induced by a homogeneousmode of the radiation intensity distribution inside the droplet. Figure 2 is a schematic
representation of the mechanism of the occurrence of this flow. When there is a small flow, it
carries heat and makes a surface temperature gradient. The surface temperature gradient resultsin the photophoretic motion of the droplet. The drag force between air and droplet thenstrengthen the internal flow. This positive feed-back process induces the spontaneous breaking
of symmetry.

Figure 2: Positive feed-back process between internal flow and a photophoretic－ 129 －

Ⅳ 研究業績 (2010)

motion for a micron-sized droplet.

Figure 3: The Peclet number at a steady state divided by the size of the droplet
versus the size of the droplet. ξ� and ξ�� are nondimensional coefficients
relating to each flow modes.

is an intensity of an irradiated laser, andindicates a homogeneous mode and the first Legendre mode for the heat source
distribution inside the droplet.
Figure 3 shows the size-dependence of the Peclet number at a steady state divided by theradius of a droplet. In the present analysis, the photophoretic velocity linearly depends on thePeclet number. The figure shows that the direction of a photophoretic motion reverses as thesize of the droplet increases. This reverse of the direction indicates that the dominant effect tothe motion of the whole droplet changes from a radiometric force to the Marangoni convection.
In principle, the Marangoni convection moves a droplet toward the warm side of the droplet justlike a breast stroke. However, when the droplet is very small, this effect is invisible behind theradiometric force. When the size of the droplet increases, the Knudsen number becomes smaller.
The system then gets far from the rarefied gas. The radiometric force vanishes rapidly in thiscontinuous limit of the ambient gas.
In relation to this work, we advance two researches. One is the analysis of the actual
experiment for the photophoretic velocity of the aerosol particles under micro-gravity. In the
beginning, the experiment seemed to show the nonlinear dependence of the photophoretic
velocity on a light intensity. Unfortunately, a detailed analysis showed that this was wrong.

－ 130 －

Ⅳ 研究業績 (2010)

Theoretical analysis based on the Boltzmann equation well explains a linear relation found in
the experiment including its coefficient. From the comparison with the experiment on the
ground, we clarified that the microgravity experiment essentially reduces the “noise” of thenatural convection, which enables to obtain a clear result.
In addition we built CFD software on an irregular lattice as an implicit solver of the finite
volume method to simulate a Marangoni convection of thermo-fluid droplet. For Marangoni
convection, an advection term sometimes plays an essential role. The shape of the droplet is also
important factor. To consider such a problem, computer simulation is very useful. As concerns
this research, an important result was not obtained in this year, and the research is now
continued.

Theoretical Study of a Linear Polymer Morphology Confined in a Sphere
Biopolymers are normally confined in a very tiny space. For example, DNA in vivo isusually confined in a nucleus of which size is extremely smaller than the contour length of DNA.
Readout of gene information is done in such a narrow confinement. However, with a very dense
condition, it is not known how DNA unfolds its expedient part selectively to offer atranscription reaction. Moreover, the structure and the statistical property of a confined linear
polymer have not yet fully understood.

Figure 4: Snapshots of the folding transition of linear polymer chains. (a) A
flexible polymer in a free solution. (b) A confined flexible polymer. (c) A－ 131 －

Ⅳ 研究業績 (2010)semiflexible polymer in a free solution. (d) A confined semiflexible polymer.
We performed a Langevin dynamics simulation of a simplified model polymer confinedin a spherical cavity to get insight into this problem. Figure 4 shows typical snapshots ofpolymeric chain undergoing a folding transition. Folding transition of a flexible polymer is acontinuous transition, and the folded structure is in a liquid-like or amorphous state. On theother hand, a semiflexible polymer undergoes a discontinuous transition, and the folded
structure is in an ordered state. From a sequence of simulations, the confinement was found to
shift transition point of a linear polymer folding in the opposite direction between a flexible
polymer and a semiflexible polymer. We successfully explained this qualitative difference of theconfinement effect by a simple scaling argument. These results are summarized in a paper
coming next year.

2. Original Papers(1) Takafumi Iwaki,“Effect of internal flow on the photophoresis of a micro liquid droplet”,
PRE 81(6),066315-(1-13) (2010)
3. Presentation at academic conferences(1) “液滴の光泳動におけるサイズ依存性” (“Size-dependence of photophoretic velocity of a
micro droplet”), (poster), Takafumi Iwaki, 2010 Autumn meeting of Japan physical society,
Osaka, September 23-26, 2010

(2) “レーザーによる熱流体駆動の数値解析” (“Numerical analysis of thermo-fluid driven
by laser irradiation”), (poster), Takafumi Iwaki, The 20-th workshop of nonlinear reaction
and cooperative phenomena, Kagoshima, January 8-9, 2011(3) “Transportation of a micro droplet by light irradiation: The influence of an advection and
the Marangoni effect.” (invited), T. Iwaki, Optics in the Life Science Congress, Monterey,
USA (April 4-6, 2011)

4. Others(1) ““細胞の自己組織化”に物理の視点から迫る” (“Physical approach toward a“self-organization of a biological cell””), Kenichi Yoshikawa and Takafumi Iwaki, パリティ
(parity), vol. 26, No. 05, pp. 13-21 (issued on Apr. 25, 2011)－ 132 －

Ⅳ 研究業績 (2010)

Hidekazu IKENO
FIFC Fellow

1. Summary of the research of the year

Ab initio multiplet calculation for 3d transition metal L2,3 x-ray absorption and electronenergy loss spectroscopy

Both x-ray absorption near-edge structure (XANES) and electron energy-loss near-edge structure(ELNES) are powerful techniques to observe the electronic structure of selected elements in materials. They
monitor the electronic transition from core states to unoccupied states. Thus, they reflect information about
the oxidation states, spin states, chemical bonding, and atomic coordinates of the element of interest. To
extract such information from experimental spectra, however, a good theoretical tool that has predictive
performance without using adjustable parameters is indispensable.
Density functional calculations using a large periodic supercell with inclusion of a core-hole arewidely used to compute XANES/ELNES theoretically. Most of K XANES/ELNES, which corresponds to theelectronic transition from 1s to unoccupied p orbitals, are reproduced well following the “recipe”[1,2].
However, in the case of 3d transition metal (TM) L2,3 XANES/ELNES, which are dominated by the 2p-3dtransition, the independent particle approximation breaks down. Because of the strong interactions amongcore TM-2p and 3d electrons, the shape of L2,3 XANES/ENLES is strongly modified from the empty 3ddensity of states: this is known as multiplet effects. In order to treat the electronic transition from core levels,
relativistic effects should also be considered. The most prevalent and conventional theoretical approach forthe analysis of TM-L2,3 XANES/ELNES is the semi-empirical charge transfer multiplet method, where
crystal field effects are incorporated into an atomic multiplet calculation using the group theoreticalformalism. In this approach, the ligand field effects are considered using the empirical parameters. Hence it
has little predictive performance of the multiplet structures a priori. An ab initio calculation that takes
multiplet effects into account is therefore strongly desirable.
For this purpose, we have developed an ab initio multiplet method based on the relativistic
configuration interaction (CI) theory. As the first step, the Dirac-Kohn-Sham equation was solved using amodel cluster within the framework of local density approximation (LDA). Then, Slater determinants wereconstructed as the basis of many-electron wavefunctions using four-component molecular spinors. All
possible determinants corresponding to (φ3d)n and (φ2p)5(φ3d)n+1 configurations were considered for rigorously
taking the exchange-correlation interaction among the 2p core-hole and 3d electrons, where φ3d (φ2p) denotes
the molecular spinors mainly composed of 3d (2p) atomic spinors. The many-electron eigenvalues andeigenfunctions for all possible initial and final states were computed by fully diagonalizing the
many-electron Hamiltonian matrix. Then the oscillator strength of the electric dipole transition is evaluatedas－ 133 －

Ⅳ 研究業績 (2010)

where Ψi and Ψf are the many-electron wavefunctions for the initial and final states, while Ei and Ef are theirenergies, respectively. A theoretical spectrum was obtained by convolving the oscillator strength of electric
dipole transition with a Lorentzian function.
Figure 1 shows experimental and theoretical Ni-L2,3 XANES of NiO and Ni-doped ZnO. Excellent
agreement between the experimental and theoretical spectra is found. The differences of the experimental
spectra due to the difference of the coordination number and symmetry around Ni ions, such as the presenceor absence of the splitting at L3 main peaks and difference of L2 line-shapes, are well reproduced. The results
demonstrate that the oxidation states, spin states and local coordination of TM ions in materials can berevealed using theoretical fingerprinting obtained by the ab initio CI method. The present method is also
useful for characterizing TM ions in more complex hosts, such as in interface, surface and amorphous
structures.
NiO

ZnO:Ni

PACS (x10-22 m2/atom)

Intensity(arb. units)

exp.

exp.

L3

L3
L2

L2

0.6
0.5 calc.

calc.

0.4
0.3
0.2
0.1
0
845 850 855 860 865 870 875 880 845 850 855 860 865 870 875 880 885

Energy (eV)Energy (eV)Fig. 1 Theoretical Ni-L2,3 XANES of NiO (Mn2+, CN=6) and Ni dopant in ZnO(Mn2+, CN=4) obtained by the relativistic CI method. Experimental spectra arealso shown for comparison.

In many 3d TM compounds, neighboring ligand atoms contribute to the spectral shapes of L2,3
XANES/ELNES. In the case of 3d TM oxides, The charge transfer (CT) from ligand oxygen ions to the TM
ions plays an important role in the spectral shapes of the TM-L2,3 XANES/ELNES. In the ab initio CI
method described above, part of this charge transfer through the covalent bonding between TM-3d and O-2p
is automatically included by using molecular spinors. The other part of the CT effect can be included byconsidering the additional configurations (Slater determinants) with a hole(s) on the φO-2p levels in the CI. In
order to quantitatively understand the effects of CT on spectra, TM-L2,3 XANES/ELNES for 3d TM oxides－ 134 －

Ⅳ 研究業績 (2010)

with various d-electron numbers and symmetries are systematically calculated using the ab inito CI method.
In these calculations, the additional single electron excitation from φO-2p to φ3d spinors is explicitly includedin the CI. The results are summarized in ref. [4].
First, the influences of the covalency on TM L2,3-edges were discussed. The important consequenceof the covalent bonding between O-2p and TM-3d is the reduction of inter-electron interactions. The
covalent bonding between TM elements and oxygen increased the spatial distribution of TM-3d spinors,
which resulted in the reduction of inter-electron interaction energies among TM-2p and 3d electrons. Hence,
it changed the multiplet structures (eigenvalues and eigenfunctions) and the transition probabilities in the
TM-L2,3 XANES/ELNES. Then, the influences of the from φO-2p to φ3d on TM L2,3-edges have been discussed.
We found that the contribution of φO-2p→φ3d excitation to the initial state eigenfunction increased withincreasing atomic number and valency of TM ions in the oxides. This tendency is similar to that of thecovalent bonding between TM-3d and O-2p spinors. The stronger the covalency, the larger the φO-2p→φ3d
excitation becomes. We also found that the
φO-2p→φ3d

excitation

significantly

modifythespectral features of TM-L2,3 XANES/ELNES forstrongly covalent systems. In the case of Ti-L2,3
XANES/ELNES of SrTiO3, for instance, the Ti-L2
peaks are much broadened by considering φO-2p→φ3d
excitation in the CI as shown in Fig. 2. One can alsofind that the intensity ratio between the two L3 main
peaks is changed. In addition, small satellite peaks
appears around 470-472 eV. It should be noted thatthe extra broadening of the L2 peaks in SrTiO3 hasbeen explained by the shorter lifetime of the corehole in 2p1/2 than in 2p3/2 and by Coster-Kronig
Auger decay. The present result clearly shows that
the CT from the ligand oxygen to the Ti ion also
contributes to the broadening of the L2 peaks in
SrTiO3.
Through this work, the power of the ab initio CI
method to quantitatively reproduce the spectra isFig. 2demonstrated.

compared with the experimental spectrum[6].

References[1] I. Tanaka et al., J. Am. Ceram. Soc.
[2] T. Mizoguchi et al., Micron 41, 695 (2010).
[3] H. Ikeno et al., J. Phys.: Condens. Matter 21, 104208 (2009).
[4] H. Ikeno et al., Phys. Rev. B 83, 155107 (2011).

－ 135 －

Theoretical Ti-L2,3 XANES of SrTiO3

Ⅳ 研究業績 (2010)[5] F.M.F. de Groot et al., Phys. Rev. B 41, 928 (1990).
[6] Y. Uehara et al., Appl. Phys. A 65, 179 (1997).

2. Original papers(1) Mizoguchi Teruyasu, Weine Olovsson, Hidekazu Ikeno and Isao Tanaka“Theoretical ELNES using one-particle, and multi-particle calculations”
Micron 41, 695-709 (2010).
(2) P.S. Miedema, H. Ikeno, and F.M.F. de Groot“First principles multiplet calculations of the calcium L2,3 x-ray absorption spectra of CaO
and CaF2”
J. Phys.: Condens. Matter 23, 144501 (2011).
(3) Hidekazu Ikeno, Teruyasu Mizoguchi and Isao Tanaka“Ab initio charge transfer multiplet calculations on the L2,3 XANES and ELNES of 3dtransition metal oxides”
Phys. Rev. B 83, 155107 (2011).

3. Presentation at academic conferences(1) Hidekazu Ikeno“Relativistic Configuration Interaction Approach to the 3d Transition Metal L2,3 X-ray
Absorption Spectra”
The Electronic Structure of Transition Metal Systems (Oct 21, 2010, Utrecht, theNetherlands)

4. Others(1) 池野豪一「相対論CI法によるX線吸収分光の理論計算」
第8回 福井謙一記念研究センターシンポジウム (2010年12月3日，京都)(2) Hidekazu Ikeno“Introduction of Ab-initio Multiplet Method for X-ray Absorption Spectroscopy”
Institut de minéralogie et de physique des milieux condensés CNRS, Université Pierre etMarie Curie (Feb 11, 2011, Paris)－ 136 －

Ⅳ 研究業績 (2010)

Natsuhiko YOSHINAGAFIFC Fellow

1. Summary of the research of the year (3-5 pages, includes appropriate figures and tables)
Self-propulsion of a drop driven by Marangoni flow
Spontaneous motion or self-propulsion have been attracting attention in last decades for its potential
application to biological problems such as cell motility and wound healing. Recently several modelexperiments showing spontaneous motion

have been proposed. The systems in these works consist of

relatively simple ingredients for instance oil drops in water nevertheless the motion is as if the drops arealive. The key questions are why the particle moves without external force and why it breaks symmetry andchooses one direction.
The first point has been discussed in hydrodynamics of the Marangoni effect in which a liquid droplet
is driven by a gradient of surface tension. The mechanism is that the gradient induces convective flow insideand outside of a drop, which leads to swimming motion of the drop itself. The second point was lessdiscussed, but has been discussed in the field of nonlinear dynamics as drift instability. In fact, the mode
equations of drift instability and deformation have been derived with symmetry consideration and from
specific reaction diffusion equations.
Thus far there are only few attempts to discuss the spontaneous symmetry breaking fromhydrodynamics points of view. In this work, we derive the nonlinear equations exhibiting drift instability.
This is of importance because all the coefficients are determined with physical quantities.

Fig. 1: Schematics of our system. Surfactants dissolve in the outer bulk and are absorbed onto theinterface, resulting in reduction of the surface tension. (A) Isotropic distribution of the surfactants when adrop is stationary. (B) When the distribution breaks symmetry the flow (the red thin arrow) occurs and thedrop starts to move (the black thick arrow).

Polarity patterns of stress fibers
Stress fibers are bundles of actin filaments made contractile by interaction with myosin minifilaments
and elastic by cross-linking with α-actinin and other proteins. They are formed in the cytoskeleton of
nonmuscle animal cells that need either to exert or to resist a mechanical force. Their biological function is－ 137 －

Ⅳ 研究業績 (2010)

exemplified in vivo by myofibroblasts that use the contractility of stress fibers to remodel the extracellularmatrix during wound healing or by vascular endothelial cells in blood vessels that align stress fibers parallelto the direction of flow to resist shear forces. Actin filaments are polar structures, with a plus (or barbed) end
and a minus (or pointed) end. The polarity of actin filaments inside a bundle is determined by decoration ofactin with myosin subfragment-1 and electron microscopy imaging. Noncontractile (or passive) actin bundles
often present uniform polarity, with barbed ends predominantly facing the same direction along the bundle,
as seen in filopodia or in the retraction fibers of postmitotic cells. The polarity profile of stress fibers isalternating, with a majority of barbed ends successively pointing in opposite directions. This periodic
structure, with a wavelength of the order of 1 um, is reminiscent of the sarcomeric organization of muscle
cells. The actomyosin filament bundles of motile fibroblasts, however, exhibit a graded polarity profile: The
proportion of barbed ends in the bundle facing one direction varies gradually and monotonically between 0
and 100% from one end to the other. The direction of the bundle sets the orientation of locomotion: The
formation of graded polarity bundles is an early event in the polarization of fibroblasts prior to migration.
The spatial dependence of polarity in contractile actomyosin bundles contrasts with the uniform polarity
observed in structures such as cilia, filopodia, and retraction fibers, in which motors do not play anorganizing role.
In this work, we aim at identifying the physical mechanisms responsible for the existence of variable
polarity patterns in elastic actin bundles. We show that active contractility, the chemomechanicaltransduction from ATP hydrolysis to motion by myosin motors ‘‘pulling’’ on actin, can generate periodic,
sarcomerelike polarity patterns provided that it exceeds a well-defined threshold. We focus our attention on
ventral stress fibers that span the cell ventral surface and transmit force to the underlying substrate throughend-point focal adhesions. We consider existing actomyosin bundles, with constant total material content,
and ignore the intriguing questions raised by their assembly.

Fig. 2: Schematic representation of an actomyosin bundle with graded (a) and periodic (b) filamentpolarity profile.

Active Motion of a Janus Particle by Self-Thermophoresis
Self-propulsion arouses interest among scientists because of its interesting dynamics, associatedtheoretical challenges to nonequilibrium transport phenomena, and possible applications, including
microswimmers, nanomachines, and drug delivery. Biological self-propelled molecules or biomotors, such as－ 138 －

Ⅳ 研究業績 (2010)

ATPase and myosin, convert chemical energy to mechanical motion through chemomechanical coupling.
Such thermodynamic coupling also causes self-propulsion in physical systems as exemplified by nanorods’
motion in hydrogen peroxide solutions. In contrast to self-propulsion, phoretic motions, such as
electrophoresis, dielectrophoresis, and thermophoresis, generally described by the linear response theory, arethe directional motions of material in given external fields. Making a bridge between a phoresis and aself-phoretic motion would give more insight into the mechanisms for self-propulsion. In this work, we
produced Janus particles (the particle containing two different surfaces on its two sides), by evaporating gold
coat on the hemisphere of silica or polystyrene spheres, and analyzed self-propulsive motion under the laser
irradiation. The Janus particle moves along a local temperature gradient which is generated by absorption oflaser at the metal-coated hemisphere. The local driving gradient and flow near a micro-scale Janus particle
are experimentally observed. To clarify the mechanism, temperature distribution and a thermal slip flow fieldaround a micro-scale Janus particle are measured. With measured temperature drop across the particle, thespeed of self-propulsion is corroborated with the prediction based on accessible parameters.

Fig. 3: Janus particle and its bright field image under microscope. The dark sides of the particles
shown in (b) are the Au coatings (scale bar: 1 μm). The temperature distribution around the particle and thepath of the propelled particle are also shown.

2. Original papers(1) Natsuhiko Yoshinaga, Jean-Francois Joanny, Jacques Prost and Pilippe Marcq,“Polarity patterns of stress fibers”
Phys. Rev. Lett. 105, 238103 (2010).
(2) Hong-Ren Jiang, Natsuhiko Yoshinaga, and Masaki Sano
" Active Motion of Janus Particle by Self-thermophoresis in Defocused Laser Beam"
Phys. Rev. Lett. 105, 268302 (2010).
Editor's suggestion and introduced in Viewpoint in Physics, 3, 108 (2010) Debut of a hot“fantastic voyager”－ 139 －

Ⅳ 研究業績 (2010)

3. Presentation at academic conferences(1) Natsuhiko Yoshinaga, Ken Nagai, and Yutaka Sumino, and Hiroyuki Kitahata
Self-propulsion of a drop driven by Marangoni flow”
Far-from-Equilibrium Dynamics 2011
RIMS Kyoto University, Kyoto, Japan, (4-8 Jan, 2011)(2) Natsuhiko Yoshinaga, Ken Nagai, and Yutaka Sumino, and Hiroyuki Kitahata
Self-propulsion of a drop driven by Marangoni flow”
International Symposium on Non-Equilibrium Soft Matter 2010
Nara, Japan, (17-20 Aug., 2010)(3) Natsuhiko Yoshinaga, Ken Nagai, and Yutaka Sumino, and Hiroyuki Kitahata
Self-propulsion of a drop driven by Marangoni flow”
International Soft Matter Conference 2010
Granada, Spain, (5-8 July, 2010)(4)

Natsuhiko Yoshinaga, Ken Nagai, and Yutaka Sumino, and Hiroyuki Kitahata
Spontaneous deformation of a reactive droplet”
Annual meeting of Japan Physical Society
Osaka, (23-26 September, 2010)(5) Natsuhiko Yoshinaga, Jean-Francois Joanny, Jacques Prost and Pilippe Marcq
Polarity patterns of stress fibers”
Annual meeting of Biophysical Society of Japan
Sendai, (20-22 September, 2010)(6) Natsuhiko Yoshinaga,
Two-state polymers: Folding transition and adsorption”
Memorial Symposium Toyoichi Tanaka
Kyoto, (19-20 November, 2010)

4. Others(1) Natsuhiko Yoshinaga“Drift instability of a drop driven by Marangoni flow”－ 140 －

Ⅳ 研究業績 (2010)

Seminar in Kyoto University, Kyoto, April 16, 2010
(2) Natsuhiko Yoshinaga“Polarity patterns of stress fibers”
Seminar in the University of Tokyo, Tokyo, April 28, 2010

－ 141 －

Ⅳ 研究業績 (2010)－ 142 －

資料 (2010)

招へい外国人学者・外国人共同研究者受入れ状況（平成 22 年度）
氏

名

受入れ身分

受入れ期間

所属機関・職名

受入れ責任者

研 究 内 容Sivakumar
Sekharan

外国人
平成22年4月3日～平 Emory University（アメリカ）
・研究員
共同研究者 成22年4月24日

諸熊 奎治

複雑分子系のシミュレーション

Hasmerya Maarof

招へい
平成22年4月4日～平 Universitiy Teknologiy
Malaysia
外国人学者 成22年7月3日（マレーシア）･講師

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Chulalongkorn
University（タイ）・
研究員

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Chatchawal
Wongchoosuk

外国人
平成22年6月15日～ Mahidol University
共同研究者 平成22年9月13日（タイ）・D2

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Marvin Jose F.
Fernandez

Ateneo de Manila
外国人
平成22年6月3日～平 University（フィリ共同研究者 成22年8月31日
ピン）・大学院生

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Hoa My Nguyen

HaNoi University of
外国人
平成22年6月7日～平 Science（ベトナム）
・共同研究者 成22年9月4日
研究員

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Pham Quoc Buu

HCMCInsititute
外国人
平成22年6月7日～平 for Computational
共同研究者 成22年9月4日
Science & Tech.
（ベトナム）･ 研究員

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Panita Decha

招へい
平成22年6月15日～ Thaksin University
外国人学者 平成22年6月30日（タイ）・講師

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Darinee Sea-tang

招へい
平成22年6月15日～
外国人学者 平成22年6月30日

College of KMITL
Nanotechnology（タイ）・講師

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Thang Ho Viet

外国人
平成22年6月16日～
共同研究者 平成22年6月30日

Danang Universityof Technology,（ベトナム）・講師

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Bokun Cho

外国人
平成22年6月16日～
共同研究者 平成22年6月30日

シンガポール国立大学（シンガポール）
・
大学院生

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Rozana Othman

Universiti Malaya
招へい
平成22年6月16日～ （マレーシア）・
外国人学者 平成22年6月30日
上級講師

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流外国人
平成22年4月16日～
Thanyarat
Udommaneethanakit 共同研究者 平成22年7月15日

外国人
Higinio R. Barros, Jr. 共同研究者 平成22年6月16日～
平成22年6月30日

Ateneo de Manila
University（フィリピン）・大学院生

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Benjoe Rey B.
Visayas外国人
平成22年9月20日～
共同研究者 平成22年12月18日

MSU-Illigan
Institute ofTechnology（フィリ
ピン）
・大学院生

諸熊 奎治

分子理論による複雑分子のシ
ミュレーションに関する共同研
究と研究者交流

Natercia Fernandes
Bras

The University of
外国人
平成22年10月17日～ Porto（ポルトガル）
・
共同研究者 平成22年12月18日
大学院生

諸熊 奎治

複雑分子系のシミュレーション－ 143 －

資料 (2010)

海外渡航一覧（平成 22 年度）
職

名

氏

名

期間（自）

期間（至）

目的地

研究員（学術研究奨励）諸熊奎治

2010/5/4

2010/5/30

アメリカ合衆国研究員（学術研究奨励）

Ke, Zhoufeng

2010/5/8

2010/5/14

中国

特任助教授

Stephan Irle

2010/6/3

2010/6/10

ロシア

特定研究員

KRS Chandrakumar

2010/6/3

2010/6/10

ロシア

特定研究員

義永

那津人

2010/6/16

2010/7/9

フランス、スペイン

特定研究員

Alister Page

2010/6/26

2010/7/7

カナダ

研究員（学術研究奨励）諸熊奎治

2010/7/13

2010/8/17

アメリカ合衆国

特定研究員

平尾

一

2010/7/26

2010/7/29

シンガポール2010/8/20

2010/8/28

アメリカ合衆国

2010/9/5

2010/9/8

フィリピン

Wilfredo C. Chung

2010/9/5

2010/9/8

フィリピン

特定研究員

Alister Page

2010/10/9

2010/10/15

タイ

特任准教授

Stephan Irle

2010/10/8

2010/10/15

タイ

研究員（学術研究奨励）諸熊2010/11/15

2010/12/21

アメリカ合衆国

2010/12/16

2010/12/22

アメリカ合衆国研究員（学術研究奨励）
准教授
研究員（学術研究奨励）

研究員（学術研究奨励）

Lung Wa Chung
石田

俊正

奎治

Wilfredo C. Chung

准教授

石田

俊正

2010/12/16

2010/12/22

アメリカ合衆国

特命准教授

平尾

一

2010/12/19

2010/12/23

ベトナム

特定助教

前田

理

2010/12/16

2010/12/21

アメリカ合衆国

特任准教授

Stephan Irle

2011/3/9

2011/3/18

ロシア

外国人特別研究員

Matt Addicoat

2011/3/9

2011/3/18

ロシア

2011/2/21

2011/3/16

アメリカ合衆国

Li Xin2011/3/26

2011/4/2

アメリカ合衆国

Ke, Zhoufeng

2011/3/26

2011/4/2

アメリカ合衆国研究員（学術研究奨励）
産学官連携研究員
研究員（学術研究奨励）諸熊奎治

－ 144 －

資料 (2010)

第8回
京都大学福井謙一記念研究センター
シンポジウムプ ロ グ ラ ム2010 年 12 月 3 日 (金)10:00-19:00

京都大学福井謙一記念研究センター ３F 大会議室
Fukui Institute for Fundamental Chemistry, Kyoto University
京都市左京区高野西開町３４－４
Tel : 075-711-7708,

Fax : 075-781-4757,

ご関係各位－ 145 －

Web : www.fukui.kyoto-u.ac.jp

資料 (2010)

第8回京都大学福井謙一記念研究センターシンポジウム
プログラム

日時 2010(平成 22)年 12 月 3 日（金）場所 京都大学福井謙一記念研究センター （３Ｆ 大会議室）

・

開会の辞

田中

功

（センター長）10:00-10:05

・

ご挨拶

小森

悟

（京大・工学研究科長）

10:05-10:15

・中村宏樹(国立交通大学（台湾）、前分子科学研究所長)

10:15-11:15「非断熱化学動力学―分子科学に新次元を」
・

谷村

吉隆

（京大・院理）11:30-12:30「散逸系の階層型量子運動方程式と多次元分光」

－昼休み－

・ 山本

量一 （京大・院工）14:00-15:00「粗視化モデリングのすすめ：分子科学とソフトマター科学の接点」

・ ポスターセッション

15:15-17:15

・ 懇親会（１Ｆ多目的ルーム）

17:30-19:00－ 146 －

資料 (2010)

ポスターセッション 15:15-17:15(大会議室)※ 番号が奇数の方は前半(15:15-16:15)に、番号が偶数の方は後半(16:15-17:15)にポスターの場
所にて発表を行ってください。
※ Please present your poster at the first half (15:15-16:15) when your poster number is odd and do itat the second half (16:15-17:15) when the number is even.
1. CooA タンパク質と CO との反応に関する理論的研究（京大福井セ、統合バイオ[2]） ○石田 俊正[1]、青野 重利[2]2. 有機 EL 素子の新規電子輸送材料の分子設計（京大福井セ[1]、京大院工[2]） ◯佐藤 徹[1]、志津功将[2]、田中一義[2]、梶 弘典[2])3. Theoretical analysis of photo-thermal force coupled with internal flow field(FIFC) ○Takafumi Iwaki

4. Vapor-Liquid-Solid versus Vapor-Solid-Solid: How do Single-Walled Carbon Nanotubes
Nucleate on SiO2 Catalysts?
(FIFC, IAR Nagoya Univ.) ○Alister J. Page, K. R. S. Chandrakumar, Stephan Irle, Keiji Morokuma

5. 相対論 CI 法による X 線吸収分光の理論計算(FIFC) ○池野豪一

6. 反応性界面活性剤を用いた液滴の自発的運動（京大福井センター[1]、お茶の水大アカプロ[2]、東大院工[3]、千葉大理[4]、JST[5]）○義永 那津人[1]、永井 健[2]、住野 豊[3]、北畑 裕之[4,5]7. Polymerization in the Bio-Nano Cavity of Apoferritin(FIFC) ○Zhuofeng KE, Keiji MOROKUMA, Takafumi UENO, Satoshi ABE

8. A New Paradigm for Finding Reaction Pathways for Multicomponent Reactions(Hakubi, FIFC, RIKEN, Univ. of Tokyo, Emory Univ.)○Satoshi Maeda, Shinsuke Komagawa, Masanobu Uchiyama, and Keiji Morokuma

9. On the mechanism of the structural decoy action of LMP1 over CD40 in relation to
Epstein-Barr virus infection: an essential dynamics approach（FIFC）○Wilfredo Credo Chung and Toshimasa Ishida－ 147 －

資料 (2010)

10. Computational Studies on Enzymatic Catalytic Mechanisms(FIFC)○Natércia F. Brás, Óscar Chung, Pedro A. Fernandes, Maria J. Ramos and Keiji Morokuma

11. A theoretical study on the photodissociation of NO3.
(FIFC, Hakubi Kyoto Univ.) ○Hongyan Xiao, Satoshi Maeda, Keiji Morokuma

12. ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial
Tryptophan 2,3-Dioxygenase with Dual Oxidants(FIFC & Sping8) ○Lung Wa Chung, Xin Li, Hiroshi Sugimoto, Yoshitsugu Shiro, and Keiji Morokuma

13. QM/MD Investigation of the Nucleation of Carbon Nanotube on the Nonmetallic Silicon
Nanocluster: Is the Intermediate Stage Carbide or Carbon Coated surface?
(FIFC, IAR Nagoya Univ.) ○K. R. S. Chandrakumar, Alister J. Page, Stephan Irle, and Keiji Morokuma

14. Competitive Mechanistic Pathways for Green-to-Red Photoconversion in the FluorescentProtein Kaede: A Computational Study(FIFC) ○Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma

15. Mechanism of the Spiropyran-Merocyanine Photochromic Reacion: A CASSCF/CASPT2
Study(FIFC) ○Fengyi Liu, Keiji Morokuma

16. The fullerene formation mechanism from combustion: quantum chemical MD study(FIFC, IAR Nagoya Univ.) ○Haibei Li, Stephan Irle, Keiji Morokuma

17. 高分子電解質の水中形状解析（東亞合成(株)[1]、名古屋大院工[2]）○飯田優羽[1]、佐々木裕[1]、藤本和士[2]、岡崎進[2]18. 分子動力学シミュレーションによる水蒸気の均一核生成過程の速度論的研究（海洋研究開発機構） ○河野明男 河村洋史 草野完也

19. Ab initio MO 量子マスター方程式法に基づく動的第一超分極率の計算および実空間解析法の開発(阪大院基礎工) ○藤井

宏旭, 岸

亮平,

南

拓也, 重田 育照, 中野

雅由

20. Dicyclopenta-fused acene 系の芳香族性、開殼性に対する分子間相互作用効果と非線形光学特性についての理論的研究(阪大院基礎工) ○元村脩人、 米田京平、福井仁之、重田育照、岸亮平、中野雅由－ 148 －

資料 (2010)

21. フェナレニルユニット連結型一次元グラフェンナノフレークの開殻性と第二超分極率についての理論研究（阪大院基礎工）○米田京平 福井仁之 南拓也 岸亮平 重田育照 中野雅由

22. スピン非制限型 TDDFT 法に基づく量子マスター方程式法による開殻分子系の動的分極率の理論的研究（阪大院基礎工）○岸亮平、南拓也、藤井宏旭、重田育照、中野雅由

23. ペンタセン／C60 ダイマーモデルの励起状態に関する理論的研究（阪大院基礎工[1]、ボルドー大学[2]） ◯南拓也[1]、Frédéric Castet[2]、重田育照[1]、中野雅由[1]24. 半古典ガウス波束伝播法による励起状態動力学―大自由度系への適用（上智大院理工[1]・レブデフ物理研[2]） ○斉田謙一郎[1]、Alexey D. Kondorskiy[2]、南部伸孝[1]25. Kick: Constraining a Stochastic Search Procedure with Molecular Fragments○Matthew A. Addicoat, and Greg F. Metha

26. A Theoretical study of Pt(PR3)2(AlCl3) (R=H, Me, Ph, or Cy); Why does Pt(PR3)2(AlCl3)
take T-shaped structure unlike Y-shaped Pt(PR3)2(C2H4)?
（ICeMS, Kyoto University） ○Shinya Tsukamoto and Shigeyoshi Sakaki

27. Absorption of Gases into Metal Organic Framework: A theoretical Investigation（ICeMS, Kyoto University） ○Milind M.Deshmukh and Shigeyoshi Sakaki

28. Theoretical Study of the Oxoboxyl Complex Formation Reaction and M-BO Bonding
Nature（ICeMS, Kyoto University） ○Guixiang Zeng and Shigeyoshi Sakaki

29. 局在化分子軌道を用いた励起エネルギー移動の研究(京大院工) ○河津 励、長谷川 淳也、松田建児

30. SAC-CI:CIS による脱プロトン化レチナールのオプシンシフトの理論解析（京大院工・京大院理）○長谷川淳也、藤本和宏、浅井康太

31. 鉄触媒クロスカップリング反応における触媒活性種のスピン状態と反応性に関する理論的研究（京大化研元素化学国際研究セ、京大福井セ）○岡田吉弘，畠山琢次，Lung Wa Chung，諸熊奎治，中村正治

32. 14, 15, 16, 17 族高周期ヘテロ元素化合物と炭素ラジカルとの置換反応の理論化学的研究（京大化研、京大福井セ） ○佐伯 昂太郎、茅原 栄一、山子 茂、Lung Wa Oscar、諸熊 奎治－ 149 －

資料 (2010)

33. Folding Pathways of Human Telomeric Type G-quadruplex Structures（京大院理） ○眞下知子、三戸祐太、杉山 弘

34. 脂質マイクロチューブのブラウン運動と形状揺らぎ（京大院理） ○山本暁久、市川正敏

35. 高分子溶液のミクロ相分離パターン：疑似二次元系に対する三次元的効果の検証（京大院理） ○林 仁志、市川正敏

36. テレケリック会合高分子のレオロジーの分子機構（京大院工） ○古賀毅，田中文彦

37. 水/ メタノール混合溶媒中における架橋ポリ N イソプロピルアクリルアミドゲルの再帰的
体積相転移理論（京大院工） ○小島広之・古賀毅・田中文彦

38. すり抜け環モデルを用いた紐状ミセルの分子シミュレーション（京大院工） ○鈴村 圭史・古賀 毅・田中 文彦
39. 水素結合による有機ゲル化剤の超分子構造とダイナミクス（京大院工） ○高橋 孝太郎・古賀 毅・田中 文彦
40. Ir(I)および Ru(II)三員環環状オレフィン錯体と C-C 結合活性化反応の理論的研究（京大院工, 京大 iCeMS） ○谷村雄大 石川敦之 中尾嘉秀 佐藤啓文 榊茂好
41. たんぱく質の水和水、内部水の揺らぎに関する定量的な解析法の開発:
Coil-Ser と Bacteriorhodopsin への応用
（京大院工, 京大 iCeMS） ○平野健司, 横川大輔, 佐藤啓文, 榊茂好
42. 金(I)二核錯体およびその集積錯体の吸収・発光スペクトルに関する理論的研究(京大院工, 京大 iCeMS, 北大院理) ○中尾嘉秀, 山田裕, 榊茂好, 伊藤肇, 澤村正也

43. 逆サンドイッチ型二核金属錯体に関する理論的研究(京大院工, 京大 iCeMS) ○竹中裕喜雄, 黒川悠索, 中尾嘉秀, 佐藤啓文, 榊 茂好

44. 水中におけるフッ化マグネシウム錯体の理論的研究-フッ素配位数、溶媒和エネルギー及び溶媒和構造○（京大院工, 京大 iCeMS）柴田尚人、横川大輔、佐藤啓文、榊茂好－ 150 －

資料 (2010)

45. Symmetric Band Structures and Asymmetric Ultrafast Electron and Hole Relaxations in
Silicon and Germanium Quantum Dots
（京大院理[1]、Univ. of Washington[2]、University of Rochester[3]）○金賢得[1], Angeline B. Madrid[2], Oleg V. Prezhdo[3]46. A stochastic model of neon-liquid surface scattering○Daniel M. Packwood and Leon F. Phillips

47. 複雑な環境における励起子：DNA の不等方緩和（京大院理） ○Arend G. Dijkstra、谷村吉隆

48. フッ化カーボンナノチューブの構造と振動様態の研究：
分子動力学シミュレーションによる赤外応答の解析(京大院理) ○上田哲、谷村吉隆

49. QM/MD 法による分子性液体の IR・RAMAN スペクトルの直接計算（京大院理） ○植野正嗣、谷村吉隆 （神戸大学）天能精一郎

50. 多次元振動分光における散逸と緩和の影響についての理論的研究（京大院理） ○櫻井敦教、谷村吉隆
51. フェノール誘導体の溶液内電子・プロトン移動反応(京大院理) ○稲垣 泰一、山本 武志、加藤 重樹

52. 7-アザインドール２量体の励起状態ダブルプロトン移動反応における反応ダイナミクスの量子動力学法を用いた解析（京大院理) ○安藤耕平、加藤重樹

53. 第一原理計算によるセレンの鎖間相互作用の研究(京大院理) ○松井正冬

54. 溶媒接触表面効果を考慮した pH 一定 MD 法による Melittin の膜挿入過程の研究(京大院理) ○佐井 啓、林 重彦

55. 気相中でのピリジンの超高速緩和過程に関する理論的研究(京大院理[1]、スタンフォード大[2])◯中野勝博[1]、森俊文[2]、加藤重樹[1]56. アルミナテンプレートを用いた有機／無機複合ナノロッドの作製と光電気特性（京大院工） ○北浦真司、張哲、松重和美、梅山有和、俣野善博、今堀博－ 151 －

資料 (2010)

57. Synthesis and Optical Properties of Chemically Converted Graphene Covalently Linked
with Pyrene（京大院工） ◯三原潤也、手塚記庸、梅山有和、俣野善博、今堀博

58. ３次元興奮性反応拡散系における自己推進ドメインの運動（京大院理） ○設楽恭平、平岩徹也、太田隆夫

59. 磁性化合物における構造探索手法の開発(京大院工) ○熊谷悠，(京大 PRU)世古敦人，(京大工)大場史康，田中功

60. ハイブリッド密度汎関数法による Eu2+ぺロブスカイト酸化物の磁性と電子状態(京大院工) ○赤松寛文，熊谷悠，大場史康，藤田晃司，田中勝久，田中功

61. First principles study on Ti antisites and O vacancies in perovskite titanates(Graduate School of Eng., Kyoto Univ.) ○Minseok Choi, Fumiyasu Oba, and Isao Tanaka

62. 水溶液環境下における層状チタン酸化物の構造安定性の第一原理計算（京大院工） ○森 正弘

63. プロトン移動性分子結晶 5-ブロモ-9-ヒドロキシフェナレノンの誘電物性に関する理論的研究（京大院理） ○大滝大樹、安藤耕司－ 152 －

資料 (2010)

第8回福井謙一記念研究センターシンポジウム
2010年（平成22年）12月3日(金)京都大学福井謙一記念研究センター－ 153 －

資料 (2010)

第８回
福井センタ セミナ
福井センターセミナー
The 8th FIFC Seminar
2010年6月21日(月)15:00-17:00

京都大学福井謙一記念研究センター
京都大学福井謙記念研究セ タ
3F 大会議室〒606-8103 京都市左京区高野西開町34-4（℡075-711-7708)

http://www.fukui.kyoto-u.ac.jp/(at FIFC, Kyoto Univ. on June, 21(Mon.), 2010)

15:00～15:30 Satoshi Maeda (Hakubi Center, FIFC)“Systematic
Systematic Exploration of Photochemical Reaction
Pathways: Applications to Ketones and Aldehydes"
15:30～16:00 Alister Page (FIFC)“Carbon Nanotube Nucleation on Traditional and NonTraditional Catalysts: Insights from QM/MD Simulations”
16:00～17:00 Alexey Timoshkin (St. Petersburg State University)“From Donor-Acceptor Complexes to Nanorods”
多数の方のご来場を歓迎いたします
We welcome all of you to join.

－ 154 －

資料 (2010)

研究業績一覧（2010 年度）№

石田Authors

Title

JournalVolume(Number),first page to last
year
page

俊正

Syntheses, crystal structures and DFT
calculations of 2-[4,5-bis (ethylsulfanyl)
K.
Ueda,
K.
Suzuki,
1 K. Suzuki, K. Yoza, T. Ishida -1,3-dithiol-2-ylidene]-5- (4,5-diiodo- Physica B
1,3-dithiol-2-ylidene) -1,3-dithiolan-4thione and -one

405,
S69-S742010

Wilfredo C. Chung,2 Shinkoh Nanbu, andToshimasa Ishida

Nonadiabatic ab Initio Dynamics of a
Model Protonated Schiff Base of 9-cis J. Phys. Chem. A
Retinal114 (32),
8190-8201

2010

Nanbu, Toshimasa
3 Shinkoh
Ishida and Hiroki Nakamura

Future Perspectives of Nonadiabatic Chemical Science 1(6),Chemical Dynamics
663-674

2010

Vibronic Coupling Density Analysis ofHole-Transporting Materials: Electron- Organic
Density Difference in DFT and HF Electronics
Methods

11,1277-1287

2010

Inelastic Electron Tunneling Spectra and
Shizu, Tohru Sato, Vibronic Coupling Density Analysis of Nanoscale
5 Katsuyuki
Kazuyoshi Tanaka
2,5-Dimercapto-1,3,4-thiadiazole andTetrathiafulvalene Dithiol

2,2186-2194

2010

A. Ito, Y. Yokoyama, R.
6 Aihara,K. Fukui, S. Eguchi,
K. Shizu, T. Sato, K.Tanaka

N-Anisyl-Substituted Hexaaza[16] Angew. Chem.
paracyclophaneInt. Ed.

49(44),
8205-8208

2010

Tomonori Yamada, Furitsu
Atsushi Goto,Tohru
7 Suzuki,Sato, Kazuyoshi Tanaka,
Hironori Kaji

Revealing Bipolar Charge-Transport Organic
Property of 4,4'-N, N'-dicarbazolylbiphenyl Electronics(CBP) by Quantum Chemical Calculations

12,
169-178

2010

Katsuyuki Shizu, Tohru
8 Sato, Kazuyoshi Tanaka,andHironori KajiA Boron-Containing Molecule as an
Efficient Electron-Transporting Material Appl. Phys. Lett.
with Low-Power Consumption

97,142111 1-3

2010

Naoya Iwahara, Tohru Sato,
9 Kazuyoshi Tanaka,
Liviu F. Chibotaru

Vibronic coupling in C60 - anion revisited:
Precise derivations from photoelectron Phys. Rev. B
spectra and DFT calculations

82,
245409 1-10

2010

Iwahara, Tohru Sato,
10 NaoyaKazuyoshi Tanaka

Molecular design for high-spin molecules Polyhedronin view of vibronic couplings

In Press

Shizu Tohru Sato,
11 Katsuyuki
Kazuyoshi Tanaka

Vibronic Coupling Density Analysis for Chem. Phys. Lett. 505,
Free-Base Porphin Cation
42-46

Katsuyuki Shizu Tohru Sato,
12 Akihiro Ito, Hironori Kaji,
Kazuyoshi Tanaka

Theoretical Design of a Hole-Transporting J. Mater. Chem.
Molecule:Hexaaza[16]parabiphenylophane

Tohru Sato, Katsuyuki Shizu;
Keisuke Uegaito;
13 Naoya Iwahara;Kazuyoshi Tanaka;
Hironori Kaji

Vibronic Interactions in Hole-Transporting
Molecules: An Interplay with Electron-Hole Chem. Phys. Lett. 507,
151-156
Interactions佐藤徹

Katsuyuki Shizu, Tohru Sato,
4 Kazuyoshi Tanaka,
Hironori Kaji

中尾

21,6375-6382

2011
2011

2011

嘉秀

T. Umeyama, N. Tezuka,
S. Seki, Y. Matano, M. Nishi, S e l e c t i v e f o r m a t i o n a n d e ff i c i e n t
Hirao, H. Lehtivuori,
photocurrent generation of [70] fullerene- Adv. Mater.
14 K.
N. V. Tkachenko,
single-walled carbon nanotube composites
H. Lemmetyinen, Y. Nakao,
S. Sakaki, H. Imahori－ 155 －

22,
1767-1770

2010

資料 (2010)№

Authors

Ando, Y. Nakao, H. Sato,
15 H.
S. Sakaki

Title

JournalComparison of Electronic Structures andLight-induced Excited Spin State Trapping Dalton Trans.
between [Fe(2-picolylamine)3]2+ and Its
Iron(III) Analogue

Volume(Number),first page to last
year
page

39,
3279-3289

2010

Y. Nakajima, Y. Nakao,
Electronic structure of four-coordinate
16 S. Sakaki, Y. Tamada, T. Ono, iron(I) complex supported by a bis J. Am. Chem. Soc. 132,
9934-9936
F. Ozawa(phosphaethenyl) pyridine ligand

2010

Theoretical study of excited states ofpyrazolate- and pyridinethiolate-bridged
dinuclear platinum(II) complexes: Inorg. Chem. Soc. 49,
relationship between geometries of
8977-8985
excited states and phosphorescence
spectra.

2010

QM/MM Study of the Structure,
Energy Storage and Origin of the J. Am. Chem. Soc 133,
B a t h o c h r o m i c S h i f t i n Ve r t e b r a t e
4734-4737
and Invertebrate Bathorhodopsins

2011

Saito, Y. Nakao,
17 K.
K. Umakoshi, S. Sakaki諸熊奎治

18 S. Sekharan and K. orokuma

Free Energy Corrections in
Kawatsu, M. Lundberg and Protein
Chem. Theo.
19 T.
ONIOM QM:MM Modeling: A Case J.Comp.
K. Morokuma
Study for Isopenicillin N Synthase (IPNS)

7,
390-4012011

i n d i n g R e a c t i o n P a t h w a y s f o r Angew, Chem.
Maeda, S. Komagawa, M. F
20 S.
Multicomponent
Reactions: The Passerini Int. Ed.
Uchiyama, and K. Morokuma Reaction Is a Four-Component
Reaction

50,
644-649

2011

A. J. Page, K. R. S.
SWNT Nucleation from Carbon-Coated21 Chandrakumar, S. Irle, and K. SiO2 Nanoparticles via a Vapor-Solid-Solid J. Am. Chem. Soc. 133,
621-628
Morokuma
Mechanism

2010

22 H. Hirao and K. Morokuma

Ferric Superoxide and Ferric Hydroxide
Are Used in the Catalytic Mechanism ofHydroxyethylphosphonate Dioxygenase J. Am. Chem. Soc. 132,
17901-17909(HEPD): A Density Functional Theory
Investigation

2010

N. Bera, S. Maeda, K.
23 Morokuma and A. A.
Viggiano

Theoretical study of proton affinity and J. Phys. Chem. A
fluoride affinity of nerve agent VX

114,
13189-13197

2010

R. Nádasdi, G. L. Zügner, M. Photochemistry of Methyl Ethyl Ketone: Phys. Chem.
24 Farkas, S. Dóbé, S. Maeda,
Quantum Yields and S1/S0-Diradical Phys.
and K. Morokuma
Mechanism of Photodissociation

11,
3883–3895

2010

Primary Events of Photodynamics in J. Phys. Chem.
Li, L. W. Chung, A.
25 X.
Photoswitching Fluorescent Lett.
Miyawaki and K. Morokuma Reversibly
Protein Dronpa

1,3328–3333

2010

Competitive Mechanistic Pathways for
Li, L.W. Chung, A.
Green-to-Red Photoconversion in the
26 X.
Miyawaki, and K. Morokuma Fluorescent Protein Kaede: A Computational J. Phys. Chem. B
Study

114,
16666-16675

2010

Why Did Incorporation of Acrylonitrile toa Linear Polyethylene Become Possible?
Comparison of Phosphine-Sulfonate Ligand J. Am. Chem. Soc 132,
with Diphosphine and Imine-Phenolate
16030-16042
Ligands in the Pd-Catalyzed Ethyelene/
Acrylonitrile Copolymerization

2010

Retinal QM/MM Study of Dehydro andS.
Sekharan,A.
Altun,
andK.
Dihydro β-Ionone Retinal Analogues in J. Am. Chem. Soc 132,
28 Morokuma
Squid and Bovine Rhodopsins: Implications
15856-15859
for Vision in Salamander Rhodopsin

2010

K. Nozaki, S. Kusumoto, S.
27 Noda, T. Kochi, L. W. Chung,and K. Morokuma－ 156 －

資料 (2010)№

Authors

Title

JournalVolume(Number),first page to last
year
page

A. J. Page, H. Yamane,
29 Y. Ohta, S. Irle, and K.
Morokuma

QM/MD Simulation of SWNT Nucleationf r o m T r a n s i t i o n - M e t a l C a r b i d e J. Am. Chem. Soc. 132,
15699–15707
Nanoparticles

2010

J. Page, Y. Ohta, S. Irle
30 A.
and K. Morokuma

Mechanisms of Single-Walled Carbon
Nanotube Nucleation, Growth and Acc. Chem. Res.
Healing Determined Using QM/MD
Methods

43.
1375-1385

2010

Jakowski, S. Irle and K.
31 J.
Morokuma

Collision-induced fusion of two C 60
fullerenes: quantum chemical molecular Phys. Rev. B
dynamics simulations

82,
125443/1-8

2010

P. V. Avramov, S.Minami,
Structure and Energetic Stability J. Phys. Chem. C 114,
32 S. Irle, L. A. Chernozatonskii, AtomicofComplex
Chiral Silicon Nanowires
16692-14696
and K. Morokuma

2010

L. W. Chung, X. Li,
33 H. Sugimoto, Y. Shiro, and
K. Morokuma

ONIOM Study on a Missing Piece in
Our Understanding of Heme Chemistry: J. Am. Chem. Soc. 132,
Bacterial Tryptophan 2,3-Dioxygenase
11993-12005
with Dual Oxidants

2010

34 S. Maeda and K. Morokuma

Communications: A Systematic Methodfor Locating Transition Structures of A + J. Chem. Phys.
B → X Type Reactions

24,241102/1-4

2010

Maeda, K. Ohno, and
35 S.
K. Morokuma

A Theoretical Study on the Photodissociation of Acetone: An Insight into the Slow J. Phys. Chem.
Intersystem Crossing and Exploration of Lett
Nonadiabatic Pathways to the Ground State1,
1841-1845

2010

A. J. Page, S. Minami, Y.
36 Ohta, S. Irle andK. Morokuma

Comparison of Single-Walled Carbon
Nanotube Growth from Fe and Ni Carbon
Nanoparticles using quantum chemicalmolecular dynamics methods

48,
3014-3026

2010

B. Saha, S. Irle and
37 K. Morokuma

Formation mechanism of polycyclicaromatic hydrocarbons (PAH) in thebenzene flame: Density functional tight J. Chem. Phys.
binding molecular dynamics simulations

132,
224303/1-11

2010

P. Ananikov, D. G.
38 V.
Musaev, and K. Morokuma

Real size of ligands, substrates andcatalysts: studies of structure, reactivity J. Mol. Cat. A
and selectivily by ONIOM and otherhybrid computational approaches

24,
104–1192010

Maeda, K. Ohno, and
39 S.
K. Morokuma

Updated Branching Plane for Finding J. Chem. Theo.
Conical Intersections without Derivative Comp.
Coupling Vectors

6, 1538–1545

2010

Maeda, K. Ohno, K.
40 S.
Morokuma

A Theoretical Study on the Photodissociation of Acetone: An Insight into the Slow J. Phys.
Intersystem Crossing and Exploration of Chem. Lett.
Nonadiabatic Pathways to the Ground State1,
1841-18452010

41 S. Maeda, K. Morokuma

Communication: A Systematic Method for
Locating Transition Structures of A + B → J. Chem. Phys.
X Type Reactions

132,
241102/1-4

2010

前田

理

Ohno, K. Shudo,
Theoretical Investigation of the Reaction J. Phys. Chem. C 114,
42 S.
M. Tanaka, S. Maeda, K. Ohno Pathway of O Atom on Si(001)-(2 × 1)
15671-15677

2010

R. Nadasdi, G. L. Zugner,
43 M. Farkas, S. Dobe,
S. Maeda, K. Morokuma

Photochemistry of Methyl Ethyl Ketone:
Quantum Yields and S 1 /S 0 -Diradical ChemPhysChem
Mechanism of Photodissociation

11, 3
883-3895

2010

Maeda, Y. Matsuda,
44 S.
S. Mizutani, A. Fujii, K. Ohno

Long-Range Migration of a Water
Molecule To Catalyze a Tautomerization in J. Phys. Chem. A
Photoionization of the Hydrated Formamide
Cluster

114,
11896-11899

2010－ 157 －

資料 (2010)№

Authors

Title

JournalVolume(Number),first page to last
year
page

C. Bera, S. Maeda,
Theoretical Proton Affinity and Fluoride J. Phys. Chem. A
45 N.
K. Morokuma, A. A. Viggiano Affinity of Nerve Agent VX

114,
13189-13197

2010

F i n d i n g R e a c t i o n P a t h w a y s f o r Angew. Chem.
Maeda, S. Komagawa,
46 S.
Reactions: The Passerini
M. Uchiyama, K. Morokuma Multicomponent
Reaction Is a Four-Component Reaction Int. Ed.

50,
644-6492011

Maeda, R. Saito,
47 S.
K. Morokuma

Finding Minimum Structures on Seam of
Crossing in Reactions of Type A + B → J. Phys. Chem.
X: Exploration of Nonadiabatic Ignition Lett.
Pathways of Unsaturated Hydrocarbons

2, 852-857

2011

Xiao, S. Maeda,
48 H.
K. Morokuma

Excited-State Roaming Dynamics in J. Phys. Chem.
Photolysis of a Nitrate Radical
Lett.

2,
934–9382011

Formation mechanism of polycyclica r o m a t i c h ydrocarbons (PA H s ) in J Chem Phys
benzene combustion: Quantum chemicalmolecular dynamics simulations

132,
224303_1224303_11

2010

Biswajit Saha
Saha, S. Irle,
49 B.
K. Morokuma

平尾一

Hirao and50 Hajime
Keiji Morokuma

Ferric Superoxide and Ferric Hydroxide
Are Used in the Catalytic Mechanism ofHydroxyethylphosphonate Dioxygenase J. Am. Chem. Soc. 132(48),
17901–17909(HEPD): A Density Functional Theory
Investigation

2010

51 Hajime Hirao

Correlation Diagram Approach as a Tool WIREs
Computational
for Interpreting Chemistry: An Introductory Molecular
Overview
Sciences

In Press

2011

Ke Zhuofeng , Abe,52 Satoshi, Ueno, Takafumi, &Morokuma, Keiji

Rh-catalyzed Polymerization of
Phenylacetylene: Theoretical Studies of the J. Am. Chem. Soc. In Press
Reaction Mechanism, Regioselectivity andStereoregularity.

2011

Gao, H., Ke, Zhuofeng,
N. J., Wang J.,
53 DeYonker
Xu H., Mao Z.-W., Phillips,
D.L.,& Zhao C.,

Dinuclear Zn(II) Complex Catalyzed
Phosphodiester Cleavage Proceeds via J. Am. Chem. Soc. 133 (9),a Concerted Mechanism: A Density2904–2915
Functional Theory Study.

2011

Zhuofeng Ke

Joonghan Kim
Jeewon Kang, Joonghan Kim, Molecular Structures, Energetics, and
54 Hyotcherl Ihee, andElectronic Properties of Neutral and J. Phys. Chem. A
Yoon Sup Lee
Charged Hgn clusters (n= 2-8)

114,
5630-5639

2010

Sunhong Jun, Jae Hyuk Lee,
Jeongho Kim, Joonghan Kim,
Kyung Hwan Kim,
55 Qingyu Kong, Tae Kyu Kim,
Manuela Lo Russo,
Michael Wulff, andHyotcherl Ihee

Photochemistry of HgBr 2 in methanolChem.
i n v e s t i g a t e d u s i n g t i m e - r e s o l v e d Phys.
Chem.
Phys.
liquidography

12,11536-11547

2010

Joonghan Kim,
56 Hyotcherl Ihee, andYoon Sup Lee

Spin-orbit density functional and ab initio
study of HgXn (X=F, Cl, Br, and I; n=1, 2, J. Chem. Phys.
and 4)

133,
1443092010

Kim, Tae Kyu Kim,
57 Joonghan
and Hyotcherl Ihee

Density Functional and Spin-Orbit Ab Initio
Study of CF3Br: Molecular Properties and J. Phys. Chem. A
Electronic Curve Crossing

115, 1264-1271

2011－ 158 －

資料 (2010)№

Authors

Title

JournalVolume(Number),first page to last
year
page

Alister Page
J. Page, S. Irle,
58 A.
K. Morokuma

Polyyne Extension and Ring Collapse
Drives Ni-Catalyzed SWNT Growth: A J. Phys. Chem. C 114(18),8206-8211
QM/MD Investigation

2010of Single-Walled Carbon
J. Page, S. Minami, S. Irle, Comparison
59 A.
Nanotube Growth from Fe and Ni Carbon
K. Morokuma
Nanoparticles using QM/MD Simulations

48(11),
3014-3026

2010

Tr e n d s i n M H 2 n + I o n - Q u a d r u p o l e
A.
J.
Page,
D.
J.
D.
Wilson60 and E. I. von Nagy-Felsobuki Complexes (M = Li, Be, Na, Mg, K, Ca; Phys. Chem.
Chem. Phys.
n = 1,2)

12(41),
13788-13797

2010

Metal-Catalyzed Single-Walled Carbon
A.
J.
Page,
S.
Irle,
Y.
Ohta,
K.
Nanotube Nucleation, Growth and Acc. Chem. Res.
61 Morokuma
Healing Mechanisms Determined using
QM/MD Methods

43(10),
1375-1385

2010

J. Page, H. Yamane,
62 A.
S. Irle, K. Morokuma

QM/MD Simulation of SWNT Nuclea15699- 2010tion from Transition-Metal Carbide J. Am. Chem. Soc. 132(44),15707
Nanoparticles

A. J. Page, K. R. S.
63 Chandrakumar, S. Irle, K.
Morokuma

SWNT Nucleation from Carbon-Coated
SiO 2 Nanoparticles via a Vapor-Solid- J. Am. Chem. Soc. 133(3),621-628
Solid Mechanism

A. J. Page,
64 K. R. S. Chandrakumar,
S. Irle, K. Morokuma

Do SiO2 and Carbon-Doped SiO2
Nanoparticles Melt? Insights from QM/ Chem. Phys. Lett. In Press
MD Simulations, and Ramifications
Regarding Carbon Nanotube GrowthY, Okamoto, Y.Ohta,
65 A. J. Page,
S. Irle, K. Morokuma

QM/MD Study of Transition Metal Catalyst J. Comp. Theor.
Particle Melting and Carbide Formation Nanoscience
In Press
During SWCNT Nucleation

2011

Xin LiXin Li, Lung Wa Chung,
Mizuno, Atsushi
66 Hideaki
Miyawaki, and Keiji
Morokuma

A Theoretical Study on the Nature of Onand Off-States of Reversibly Photoswitching J. Phys. Chem. B
Fluorescent Protein Dronpa: Absorption,
Emission, Protonation and Raman

114,
1114-1126

2010

Xin Li, Lung Wa Chung,
Mizuno,67 Hideaki
Atsushi Miyawaki, andKeiji Morokuma

Primary Events of Photodynamics in J. Phys. Chem. 1,
Reversible Photoswitching Fluorescent Lett.
328-3333
Protein Dronpa

2010

Xin Li, Lung Wa Chung,
Mizuno,68 Hideaki
Atsushi Miyawaki, andKeiji Morokuma

Competitive Mechanistic Pathways
for Green-to-Red Photoconversion J. Phys. Chem. B 114,
in the Fluorescent Protein Kaede: A
16666-16675
Computational Study

2010

Alister J. Page, K. R. S.
69 Chandrakumar, Stephan Irle,
and Keiji Morokuma

SWNT Nucleation from Carbon-Coated(3),
SiO2 Nanoparticles via a Vapor-Solid-Solid J. Am. Chem. Soc. 133
621–628
Mechanism

2011

Alister J. Page, K. R. S.
70 Chandrakumar, Stephan Irle,
and Keiji Morokuma

Do SiO2 and Carbon-Doped SiO2
Nanoparticles Melt? Insights from QM/MD Chem. Phys. Lett. In Press
Simulations and Ramifications Regarding
Carbon Nanotube Growth

2011

Isolation of Crystalline Carbene-Stabilized Nature Chemistry 2,
P2-Radical Cations and P2-Dications
369-373

2010

K.R.S. Chandrakumar

Parameswaran Pattiyil
Back, O.; Donnadieu, B.;
71 Parameswaran, P.;
Frenking, G.; Bertrand. G.

－ 159 －

資料 (2010)№

Authors

Title

JournalVolume(Number),first page to last
year
page

Chemical Bonding in Transition Metal
Complexes with Beryllium Ligands J. Phys. Chem. A[(PMe3)2M-BeCl2], [(PMe3)2M-BeClMe]and [(PMe3)2M-BeMe2] (M = Ni, Pd, Pt)

114,
8529-8535

2010

Excited-state roaming dynamics in J. Phys. Chem.
photolysis of a nitrate radical
ett.

2,934-9382011

74 Lina Ding, Wei-Hai Fang*

Exploring Light-Induced Decarboxylation
Mechanism of o-Acetylphenyl-Acetic Acid J. Org. Chem.
from the Combined CASSCF and DFT
Studies75,
1630-1636

2010

Ganglong Cui, Lina Ding,
75 Feng Feng, Yajun Liu, andWeihai Fang

Insights into Mechanistic Photochemistry J. Chem. Phys.
of Urea132,
1943082010

P.;
72 Parameswaran,
Frenking, G.

Hong-yan Xaio
Hongyan Xiao,
73 Atoshi Maeda andKeiji Morokuma

Lina Ding

Lung Wa Chung
Lung Wa Chung, Xin Li,
Sugimoto,
76 Hiroshi
Yoshitsugu Shiro and
Keiji Morokuma

ONIOM Study on a Missing Piece in
Our Understanding of Heme Chemistry: J. Am. Chem. Soc. 132(34),
Bacterial Tryptophan 2,3-Dioxygenase
11993-12005
with Dual Oxidants

2010

Kyoko Nozaki,
Shuhei Kusumoto,77 Shusuke Noda,
Takuya Kochi, Lung Wa
Chung, and Keiji Morokuma

Why Did Incorporation of Acrylonitrile toa Linear Polyethylene Become Possible?
Comparison of Phosphine−Sulfonate Ligand J. Am. Chem. Soc. 132(45),with Diphosphine and Imine−Phenolate
16030-16042
Ligands in the Pd-Catalyzed Ethylene/
Acrylonitrile Copolymerization

2010

Xin Li, Lung Wa Chung,
Mizuno,78 Hideaki
Atsushi Miyawaki, andKeiji Morokuma

Primary Events of Photodynamics in J. Phys. Chem.
Reversible Photoswitching Fluorescent Lett.
Protein Dronpa

1(23),
3328-3333

2010

Xin Li, Lung Wa Chung,
Mizuno,79 Hideaki
Atsushi Miyawaki, andKeiji Morokuma

Competitive Mechanistic Pathways forGreen-to-Red Photoconversion in the J. Phys. Chem. B
Fluorescent Protein Kaede: A ComputationalStudy

114 (49),
16666-16675

2010

Akifumi Nakamura,
Kagehiro Munakata,Ito, Takuya Kochi,
80 Shingo
Lung Wa Chung,
Keiji Morokuma, andKyoko Nozaki

Pd-Catalyzed Copolymerization of
Methyl Acrylate with Carbon Monoxide: J. Am. Chem. Soc. 133 (17),Structures, Properties and Mechanistic
6761-6779
Aspects toward Ligand Design

2011

Galina P. Petrova,
81 Georgi N. Vayssilov,
Notker Rösch

Redox behavior of small metal clusters
with respect to hydrogen. The effect of Phys. Chem.
the cluster charge from density functional Chem. Phys.
results

2010

Petko St. Petkov,
P. Petrova,
82 Galina
Georgi N. Vayssilov,
Notker Rösch

Saturation of Small Supported Metal
Clusters by Adsorbed Hydrogen. A
114,
Computational Study on Tetrahedral J. Phys. Chem. C 8500-8506
Models of Rh4, Ir4, and Pt4

2010

Miroslav A. Rangelov,
P. Petrova,
83 Galina
Vihra M. Yomtova,
Georgi N. Vayssilov

Hierarchical Approach to Conformational Search and Selection of Computa- J. Mol. Graph. 29,
tional Method in Modeling the Mechan- Modelling
246–255
ism of Ester Ammonolysis

2010

Galina Petrova－ 160 －

12,11015-11020

資料 (2010)№

Authors

Title

JournalVolume(Number),first page to last
year
page

Miroslav A. Rangelov,
P. Petrova, V
84 Galina
ihra M. Yomtova,
Georgi N. Vayssilov

Catalytic Role of Vicinal OH in Ester
Aminolysis - Proton Shuttle versus J. Org. Chem.
Hydrogen-Bonds Stabilization

75,
6782-6792

2010

Notker Rösch,Galina P. Petrova,
Petko St. Petkov,
85 Alexander Genest,
Sven Krüger,Hristiyan A. Aleksandrov,
Georgi N. Vayssilov

Impurity Atoms on Small Transition Topics inMetal Clusters. Insights from Density Catalysis
Functional Model Studies

54,363-3772011

Nonadiabatic ab Initio Dynamics of a
Model Protonated Schiff Base of 9-cis J. Phys. Chem. A
Retina114(32),8190-8201

2010

Effect of internal flow on the photophoresis Phys. Rev. E
of a micron-sized liquid droplet

81(6),
066315-(1-13)

2010

Theoretical ELNES using one-particle, Micronand multi-particle calculations

41,695-7092010

principles multiplet calculations of J. Phys.:
S. Miedema, H. Ikeno, and First
89 P.
the
calcium
L2,3 x-ray absorption spectra of Condens. Matter
F. M. F. de Groot
CaO and CaF223,145501

2011

Hidekazu Ikeno,
90 Teruyasu Mizoguchi, andIsao Tanaka

83,
1551072011

Wilfredo Credo Chung
Wilfredo Credo Chung,86 Shinkoh Nanbu, Toshimasa
Ishida岩城貴史

87 Takafumi Iwaki

池野豪一

Mizoguchi Teruyasu,
Olovsson,
88 Weine
Hidekazu Ikeno andIsao Tanaka

義永

Ab initio charge transfer multiplet
calculations on the L 2,3 XANES and Phys. Rev. B
ELNES of 3d transition metal oxides

那津人

Hong-Ren Jiang,
91 Natsuhiko Yoshinaga, andMasaki Sano

Active Motion of Janus Particle by Self- Physical Review 105,
thermophoresis in Defocused Laser Beam Letters
268302(1-4)

2010

Natsuhiko Yoshinaga, Jean92 Francois Joanny,. Jacques
Prost, and Philippe Marcq

Polarity patterns of stress fibers

Physical Review 105,
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2010－ 161 －

京都大学福井謙一記念研究センター

年報

2010

2011 年 12 月 発行
発行人

田中

編

石田俊正

者

功

発行所

京都大学福井謙一記念研究センター（京都市左京区高野西開町 34-4）

印刷所

有限会社 津田印刷（京都市左京区岩倉中大鷲町 14）（無断転載を禁ず）

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