年
報
年 報

2010
2011

京都大学
福井謙一記念研究センター

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はじめに2011 年度(平成 23 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。本センターは、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。そして世界中から集めた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。この福井センターフェローと呼ばれる博士研究員は、センター雇用であることによって自分自身のアイディアで一定期間、自由闊達に研究できる身分を保証されています。
2006 年(平成 18 年)9 月に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。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。その後任として、2011 年(平成 23 年)4 月に京都大学物
質―細胞統合システム拠点(iCeMS)特任教授の榊茂好先生を研究部第二のリサーチリーダーとして招聘しました。榊先生は、遷移金属化合物や類縁化合物に関する研究で顕著な業績を挙げておられ、現在は科学研究費補助金「d-電子複合系の理論化学：
新しい高精度大規模計算法による微視的理解と予測」を推進しておられます。榊先生
は、この予算で博士研究員を採用され、そのメンバーもセンターで研究に励んでいます。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多くの方々が、現在、国内外の大学、研究機関で活躍しておられます。
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ように、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)に本学に寄贈されて福井－i－fukui2011_01.indb 3

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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、田中 功の各先生にセンター長としてご指導を頂きました。
本センターは、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。2011 年(平成 23 年)には国内外(主にドイツ、東欧、中国、韓国)から第一線の研究者を招き、第 1 回福井センター理論化学・計算化学国際シンポジウムを開催しました。こうした国際連携活動
をさらに活性化するという観点から、2011 年(平成 23 年)10 月に国際連携研究室を設置し、その運営上必要となるコーディネーター役として、特定准教授及び特定助教各1 名を配置しました。本センターは、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、国際連携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、並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。
さらに社会貢献活動の一環として、2011 年(平成 23 年)が福井先生のノーベル化学賞受賞 30 周年にあたるため、これを節目として本センター玄関ロビーに先生ゆかりの文物の展示コーナーを設置しました。コーナーでは先生が使用された机、椅子、ノーベ
ル賞メダル・賞状(複製)、研究ノート・メモ、写真などを展示し、常設展示として一般に公開しています。
本センターは、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、本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、本センターの順調な活動は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 24 年 11 月
京都大学福井謙一記念研究センター長

田中一義－ ii －

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目
はじめに

Ⅰ

Ⅱ

Ⅲ

次

京都大学福井謙一記念研究センター長

田中一義�������

i

１．教員組織 ����������������������������

1

２．教員プロフィール ������������������������

2(1) センター長 �������������������������

2(2) 副センター長 ������������������������

3(3) スーパーバイザー ����������������������

5(4) 専任教員 ��������������������������

15(5) リサーチリーダー ����������������������

19(6) 特定助教（白眉）������������������������

21

専任教員・スーパーバイザー

博士研究員
１．博士研究員組織 �������������������������

22

２．博士研究員プロフィール ���������������������

23

研究広報活動
１．若い人に贈る福井謙一先生ノーベル化学賞受賞 30 周年記念公開講座― 最近の基礎化学の進展 ― �������������������
２．京都大学ジュニアキャンパス 201153

中学生向けゼミ「化学―フロンティア軌道理論と電子計算機で化学が分かる？」 ����

53

３．Fukui International Symposium for Theoretical Chemistry (FISTC)��

54

４．福井謙一記念研究センターシンポジウム― 福井謙一博士ノーベル賞受賞 30 周年記念 ―Ⅳ�����������

54

５．福井謙一記念研究センターセミナー ����������������

55

６．社会へのアウトリーチ活動 ��������������������

55

７．福井謙一博士記念展示コーナー ������������������

55

研究業績
１．専任教員 ����������������������������

57

２．リサーチリーダー ������������������������

79

３．特定助教（白眉） �������������������������

90

４．博士研究員 ���������������������������

96－ iii －

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資料
１．外国人共同研究者受入れ状況 ………………………………………………… 231
２．海外渡航一覧 …………………………………………………………………… 232
３．研究業績一覧 …………………………………………………………………… 233
４．若い人に贈る福井謙一先生ノーベル化学賞受賞30周年記念公開講座
ポスター・プログラム ………………………………………………………… 245
５．Fukui International Symposium for Theoretical Chemistry (FISTC)
プログラム ……………………………………………………………………… 246
６．京都大学ジュニアキャンパス2011 パンフレット……………………………… 249
７．福井謙一記念研究センター シンポジウム― 福井謙一博士ノーベル賞受賞30周年記念 ― ポスター・プログラム…… 252
８．福井謙一記念研究センターセミナー ポスター・プログラム………………… 261
９．社会へのアウトリーチ活動紹介記事 ………………………………………… 262
１０．福井謙一博士記念展示コーナーパンフレット・
展示コーナー除幕式新聞記事等 ……………………………………………… 263（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/AnnualReport2011.pdf）－ iv －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)Ⅰ

専任教員・スーパーバイザー

１．教員組織平成２３年度
職

名

氏

名

備

考

センター長

田 中

功

工学研究科材料工学専攻

総合研究部門副センター長田 中

一 義

工学研究科分子工学専攻

理論研究部門副センター長太 田隆 夫

理学研究科物理学・宇宙物理学専攻

工学研究科長小 森

悟

理学研究科長山 極

壽 一

理学研究科生物科学専攻

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

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

進

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

今 堀

博

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

総合研究部門准 教 授

長谷川 淳 也

理論研究部門

准 教 授

中 尾

嘉 秀

国際連携研究室

特定准教授

石 田

俊 正

専任

国際連携研究室

特定助教

池 野

豪 一

専任

福井謙一
記念研究部第一

リサーチ
リーダー

諸 熊

奎 治

研究員（学術研究奨励）

福井謙一
記念研究部第二

リサーチ
リーダー

榊

茂 好

研究員（学術研究奨励）

福井謙一
記念研究部第一

特定助教

前 田

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理

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)

物質－細胞統合システム拠点(工学研究科分子工学専攻)

専任(工学研究科合成・生物化学専攻協力講座)

専任(工学研究科分子工学専攻協力講座)

次世代研究者育成センター
特定助教（白眉）－1－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)

２. 教員プロフィール
⑴

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，電子エネルギー損失分光，Ｘ線吸収分光【最終学歴】 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【学位】 1987 年 3 月大阪大学工学博士【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（過去 5 年以内）
principles cluster expansion analysis, Phys. Rev. B 81 (2010) 054114
2. A. Matsumoto, Y. Koyama, I. Tanaka, Structures and energetics of Bi 2 O 3polymorphs 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, Allelectron 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 andengineering, 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 ﾌｨﾘｯﾌﾟ ･ ﾌﾗﾝﾂ ･ ﾌｫﾝ ･ ｼｰﾎﾞﾙﾄ賞 (2008 年）
ﾙｰﾏﾆｱ科学ｱｶﾃﾞﾐｰ ﾄﾞﾗｺﾞﾐｰﾙ・ﾌﾙﾑｾﾞｽｺ賞 (2006 年 )米国ｾﾗﾐｯｸｽ学会 ﾘﾁｬｰﾄﾞ・ﾌﾙﾗｰｽ賞 (2004 年 )－2－fukui2011_01.indb 2

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Ⅰ 専任教員 ･ スーパーバイザー (2011)⑵

副センター長【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 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【学歴】 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【学位】 1978 年 3 月

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（過去 5 年以内）
ムシー出版 , 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, and K.
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, and K.
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, 13061309 (2011).
（以上学術論文）－3－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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

理論研究部門【研究室】 理学部５号館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【学位】 1977 年 1 月理学博士（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 coupling,
Chaos 20, 023101(1-13) (2010)（過去 5 年以内）
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 50011-1-6(2008)
6. R. Tamate, K. Yamada, J. Vinals, and T. Ohta, Structural rheology of microphaseseparated diblock copolymers, J. Phys. Soc. Jpn.,77 034802 (2008)
7. M. Yanagisawa, M. Imai, T. Masui, S. Komura, Takao Ohta, Growth Dynamics ofDomains 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－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)⑶

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】 カリフォルニア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 Functions of
Next-Generation Conjugated Polymers (2008)、Chair of International Conference on
Science and Technolgy of Synthetic Metals (2010).
【主な著書、学術論文】 1. H. Hayasaka, T. Miyashita, K. Tamura, K. Akagi, “Helically π-Stacked Conjugated
Polymers Bearing Photoresponsive and Chiral Moieties in Side Chains: Reversible（過去 5 年以内）
Photoisomerization-Enforced Switching between Emission and Quenching 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 HelicalConjugated 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－fukui2011_01.indb 5

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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【学歴】 1984 年 3 月 京都大学工学部工業化学科卒業
1986 年 3 月 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】 1986 年 3 月 京都大学大学院工学研究科工業化学専攻修士課程修了【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. Hinatsu,（過去 5 年以内）
K. Fujita, K. Tanaka, and T. Kawai, “Remarkable Magneto-Optical Properties
of Europium Selenide Nanoparticles with Wide Energy Gaps”, Journal of theAmerican 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”, Physical Review 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 CeramicAward (1997 年 )、日本セラミックス協会学術賞 (2005 年 )－6－fukui2011_01.indb 6

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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

分子集合解析研究領域【研究室】 宇治キャンパス化学研究所本館 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【学位】 1983 年 3 月理学博士（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. R. Murdey, N. Sato and M. Bouvet, Frontier electronic structures in fluorinated（過去 5 年以内）
copper phthalocyanine thin films studied using ultraviolet and inverse
photoemission spectroscopies, Mol. Cryst. Liq. Cryst. 455 (2006) 211-218.
2. H. Yoshida, K. Inaba and N. Sato, X-ray diffraction reciprocal space mapping studyof the thin ﬁlm phase of pentacene, Appl. Phys. Lett. 90 (2007) 181930.
3. H. Yoshida and N. Sato, The crystallographic and electronic structures of threedifferent polymorphs of pentacene, Phys. Rev. B 77 (2008) 235205.
4. T. Hiramatsu, T. Sasamori, H. Yoshida, N. Tokitoh and N. Sato, Reversible
polymorphic crystalline transition of a push–pull-type molecule:{4-[4,5-bis(methylsulfanyl)-1,3-dithiol-2-ylidene]cyclohexa-2,5-dien-1-ylidene}malononitrile (BMDCM), J. Mol. Struct. 922 (2009) 30-34.
5. R. Murdey, M. Bouvet, M. Sumimoto, S. Sakaki and N. Sato, Direct observationof the energy gap in lutetium bisphthalocyanine thin ﬁlms, Synth. Met. 159 (2009)1677-1681.
6. J. Tsutsumi, H. Yoshida, R. Murdey, S. Kato and N. Sato, An accurate calculation ofelectronic contribution to static permittivity tensor for organic molecular crystals on
the basis of the charge response kernel theory, J. Phys. Chem. A 113 (2009) 92079212.
7. J. Tsutsumi, H. Yoshida, R. Murdey and N. Sato, Spontaneous buildup of surface
potential with a thin ﬁlm of a zwitterionic molecule giving non-centrosymmetriccrystal structure, Appl. Phys. Lett. 95 (2009) 182901.
【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－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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 月京都大学大学院石油化学専攻博士課程修了【学位】 1979 年 7 月工学博士（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 polymers（過去 5 年以内）
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, 831836.
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－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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【研究室】 理学研究科

物理学・宇宙物理学専攻
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.yklab.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―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 月京都大学大学院工学研究科博士課程修了【学位】 1976 年 5 月工学博士（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 月 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】 Vise Chair, Commission C-6, International Union of Pure and Applied Physics、など【主な著書、学術論文】 1. “Large-scale vortex lattice emerging from collectively moving microtubules”,
Yutaka Sumino, Ken H. Nagai, Yuji Shitaka, Dan Tanaka, Kenichi Yoshikawa,（過去 5 年以内）
Hugues Chaté and Kazuhiro Oiwa, Nature, 483(7390), 448–452 (2012)
2. “In Vitro Murine Leukemia Retroviral Integration and Structure Fluctuation of
Target DNA”, Tatsuaki Tsuruyama, Weizhi Liu and Kenichi Yoshikawa, PLoS
ONE, 7(2), e31533/1–8 (2012)

3. “Rigidity Matching between Cells and the Extracellular Matrix Leads to the
Stabilization of Cardiac Conduction”, Marcel Hörning, Satoru Kidoaki, Takahito
Kawano and Kenichi Yoshikawa, Biophysical Journal, 102(3), 379–387 (2012)
4. “Enhancement of DNA compaction by negatively charged nanoparticles: Effect ofnanoparticle size and surfactant chain length”, Sergii Rudiuk, Kenichi Yoshikawa
and Damien Baigl, Journal of Colloid and Interface Science, 368(1), 372–377(2012)

5. “Cell-Sized confinement in microspheres accelerates the reaction of gene
expression”, Ayako Kato, Miho Yanagisawa, Yuko Sato, Kei Fujiwara and Kenichi
Yoshikawa, Scientific Reports (Nature Publishing Group), 2, 283/1–5 (2012)【学術関係の受賞】 日本 IBM 科学賞 (1991)－9－

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【氏名】 Tanimura Yoshitaka【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【学歴】 Keio University【学位】 Ph. D【所属学会】 Japanese Physical Soc【主な著書、学術論文】 1. A. G. Dijkstra and Y. Tanimura, Correlated ﬂuctuations in the exciton dynamics andspectroscopy 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 molecularvibrations, J. Phys. Chem. A 115, 4009-4022 (2011)
5. T. Hasegawa and Y. Tanimura, A polarizable water model for intramolecular andintermolecular vibrational spectroscopies, J. Phys. Chem. B 115, 5545-5553(2011).
【学術関係の受賞】 Morino Foundation－ 10 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【氏名（ふりがな）】 今堀

博 （いまほりひろし）【職名】 教授【所属】 物質－細胞総合システム拠点（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 月京都大学大学院理学研究科博士後期課程修了【学位】 1990 年 3 月理学博士（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 Semiconducting（過去 5 年以内）
Materials for Organic Photovoltaics,” J. Phys. Chem. Lett. (Perspective), 1, 10201025 (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, 11931204 (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－ 11 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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【研究室】 桂キャンパス

化学工学専攻A4 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】 ソフトマターの計算化学【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 月神戸大学大学院 工学研究科修士課程化学工学専攻修了【学位】 1996 年 3 月博士（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、分子シミュレーション研究会【主な著書、学術論文】 1. R. Tatsumi and R. Yamamoto, Direct numerical simulation of dispersed particles in（過去 5 年以内）
a compressible ﬂuid, Phys. Rev. E 85, 066704 (2012).
2. H. Mizuno and R. Yamamoto, Mechanical responses and stress fluctuations of astrongly sheared supercooled liquid, Eur. Phys. J. E, 35, 29 (2012).
3. H. Kobayashi and R. Yamamoto, Implementation of Lees-Edwards periodic
boundary conditions for direct numerical simulations of particle dispersions undershear 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, EPL, 86, 18002(2009).
5. T. Iwashita and R. Yamamoto, Short-time motion of Brownian particles in a shear
ﬂow, Phys. Rev. E, 79, 031401 (2009).
6. Y. Nakayama, K. Kim and R. Yamamoto, Simulating (electro) hydrodynamic
effects in colloidal dispersions: smoothed proﬁle method, Eur. Phys. J. E, 26, 361368 (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 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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

生物科学専攻生物物理学教室【研究室】 理学部 1 号館 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 high
（過去 5 年以内）
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 coupledbinding and protein conformational change: Induced-fit versus population-shiftmechanisms, Proceedings of the National Academy of Sciences USA, 105: 1118211187, 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, Proceedingsof 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 Academyof Sciences USA, 103(No.14):5367-5372, 2006.
－ 13 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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【学歴】 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【学位】 1997 年 11 月

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-amylase and（過去 5 年以内）
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, 14152-14153(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 a hybrid
molecular simulation. Shigehiko Hayashi, Emad Tajkhoshid, and Klaus Schulten,
Biophys. J., 96, 403-416 (2009).

－ 14 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)

⑷

専任教員

【氏名（ふりがな）】 長谷川

淳也 （はせがわ

じゅんや）【職名】 准教授【所属】 福井謙一記念研究センター

総合研究部門【研究室】 福井記念研究センター 206【直通電話】 075-711-7867【FAX】 075-781-4757【電子メールアドレス】 hasegawa@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/~hasegawa【研究分野】 理論化学・量子化学【現在の研究課題】 光機能性蛋白質の発現メカニズムの解明、励起状態理論の開発【研究内容キーワード】 光機能性蛋白質、励起状態理論、電子相関理論【最終学歴】 1998 年 3 月京都大学工学研究科合成・生物化学専攻博士後期課程修了【学位】 1998 年 3 月博士（工学）、京都大学【略歴】 1999 年 11 月京都大学工学研究科合成・生物化学専攻助手、2007 年 4 月京都
大学工学研究科合成・生物化学専攻助教、2008 年 12 月京都大学工学研究科
合成・生物化学専攻講師、2011 年 10 月京都大学福井謙一記念研究センター准教授、2012 年 4 月分子科学研究所客員准教授【在外研究歴】 1998 年 4 月 -1999 年 10 月
デン）

Lund 大学理論化学科（B. O. Roos 教授、スウェー【所属学会】 日本化学会、分子科学会、理論化学研究会、米国化学会、生物物理学会【学会活動】 量子化学研究協会

理事【主な著書、学術論文】 1. T. Kawatsu, K. Matsuda, and J. Hasegawa, “Bridge-Mediated Excitation Energy（過去 5 年以内）
Transfer Pathways through Protein Media: a Slater Determinant-Based Electronic
Coupling Calculation Combined with Localized Molecular Orbitals”, J. Phys.
Chem. A 115(39), 10814-10822 (2011).
2. K. Fujimoto, K. Asai, and J. Hasegawa, “Theoretical Study of the Opsin Shiftof Deprotonated Retinal Schiff Base in the M state of Bacteriorhodopsin”, Phys.
Chem. Chem. Phys. 12(40), 13107-13116 (2010).
3. J. Hasegawa, T. Ise, K. Fujimoto, A. Kikuchi, E. Fukumura, A. Miyawaki, and Y.
Shiro, “Excited States of Fluorescent Proteins, mKO and DsRed: Chromophoreprotein Electrostatic Interaction Behind the Color Variations”, J. Phys. Chem. B,
114(8), 2971-2979 (2010).
4. K. Fujimoto, J. Hasegawa, and H. Nakatsuji, “Color tuning mechanism in humanred, green, and blue cone visual pigments: SAC-CI theoretical study”, Bull. Chem.
Soc. Jpn. 82(9), 1140-1148 (2009).
5. N. Nakatani, J. Hasegawa, and H. Nakatsuji, “Red Light in Chemiluminescenceand Yellow-green Light in Bioluminescence: Color-tuning Mechanism of Fireﬂy,
Photinus pyralis, studied by the SAC-CI method”, J. Am. Chem. Soc. 129, 87568765 (2007).
【学術関係の受賞】 平成 9-11 年 日本学術振興会特別研究員、平成 21 年 9 月 分子科学会奨励賞、
平成 23 年 9 月 QSCP Promising Scientist Prize of CMOA
－ 15 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【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

理論研究部門【研究室】 京都大学桂キャンパス A4-024【直通電話】 075-383-2546【FAX】 075-383-2799【電子メールアドレス】 nakao.yoshihide.5a@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】 計算化学・理論化学【現在の研究課題】 機能性分子の物性の理論的解明【研究内容キーワード】 機能性金属錯体、スピン、発光【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助手、2007 年 4 月 京都大学大学院工学研究科助教、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. Y. Nakao, K. Saito, S. Sakaki, “Theoretical investigation of μ-O-bridged dinuclear（過去 5 年以内）
Re complexes. Electronic structure, bonding nature, and absorption spectra”, Int. J.
Quant. Chem. 109, 2319-2327 (2009).
2. K. Umakoshi, K. Saito, Y. Arikawa, M. Onishi, S. Ishizaka, N. Kitamura, Y. Nakao,
S. Sakaki, “Luminescent Heteropolynuclear Complexes of 3,5-Dimethylpyrazolate[Pt 2Au 2M 2(Me 2pz) 8] (M=Ag, Cu) Showing the Synergistic Effect of Three
Transition Elements in the Excited State”, Chem. Eur. J. 15, 4238-4242 (2009).
3. 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).
4. H. Ando, Y. Nakao, H. Sato, S. Sakaki, “Comparison of Electronic Structures andLight-induced Excited Spin State Trapping between [Fe(2-picolylamine)3]2+ and Its
Iron(III) Analogue”, Dalton Trans. 39, 1836-1845 (2010).
5. Y. Nakajima, Y. Nakao, S. Sakaki, Y. Tamada, T. Ono, F. Ozawa, “Electronic
structure of four-coordinate iron(I) complex supported by a bis(phosphaethenyl)
pyridine ligand”, J. Am. Chem. Soc. 132, 9934-9936 (2010).

－ 16 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【氏名（ふりがな）】 石田

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

国際連携研究室【研究室】 福井記念研究センター 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・生体分子の反応・ポテンシャル面生成法【研究内容キーワード】 光機能分子・生体分子・ポテンシャル面・非断熱遷移【最終学歴】 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【学位】 1989 年 3 月理学博士（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、2011 年 10月同特定准教授【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. Toshimasa Ishida, Shinkoh Nanbu, and Hiroki Nakamura, Non-adiabatic ab initio（過去 5 年以内）
dynamics of two models of Schiff base retinal, J. Phys. Chem. A, 113(16), 4356–
4366 (2009).
2. Toshimasa Ishida and Jun-ichi Aihara, Aromaticity of neutral and doubly charged
polyacenes, Phys. Chem. Chem. Phys. 11, 7197 - 7201 (2009)
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).
4. Shinkoh Nanbu, Toshimasa Ishida and Hiroki Nakamura, “Future Perspectives ofNonadiabatic Chemical Dynamics”, Chemical Science, 1, 663-674 (2010)
5. Wilfredo Credo Chung,* Shinkoh Nanbu, and Toshimasa Ishida, “A Nonadiabatic
Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin: Chemical
Dynamics Reasons Behind Selection of Rhodopsin by Life”, Chem. Lett. 40, 13951397(2011).
－ 17 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【氏名（ふりがな）】 池野

豪一 （いけのひでかず）【職名】 特定助教【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/users/ikeno/index_ja.html【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 – 2011 年 10 月 福井謙一記念研究センター フェロー2011 年 11 月 – 現在 福井謙一記念研究センター 特定助教
【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, Yukinori Koyama, Zenpachi Ogumi,（過去 5 年以内）
YasuharuUchimoto, and Isao Tanaka, “Theoretical Fingerprints of Transition Metal
L2,3 XANES/ELNES for Lithium Transition Metal Oxides by ab initio Multiplet
Calculations”, J. Phys. Chem. C 115, 11871 (2011).
2. Hidekazu Ikeno, Teruyasu Mizoguchi and Isao Tanaka, “Ab initio charge transfer
multiplet calculations on the L 2,3 XANES and ELNES of 3d transition metaloxides”, Phys. Rev. B 83, 155107 (2011).
3. Teruyasu Mizoguchi, Weine Olovsson, Hidekazu Ikeno and Isao Tanaka,“Theoretical ELNES using one-particle an multi-particle calculations”, Micron 41,
695-709, (2010).
4. 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 transition-metalcompounds”, J. Phys.: Condens. Matter 21, 104208 (2009).
5. Hidekazu Ikeno, Teruyasu Mizoguchi, Yukinori Koyama, Yu Kumagai and Isao
Tanaka, “First-principles calculations for L2,3 ELNES/XANES of 3d transition
metal monooxides”, Ultramicroscopy 106, 970-975 (2006).
【学術関係の受賞など】 日本学術振興会特別研究員 (DC2) 2005-2006－ 18 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)⑸

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. H.-B. Li, A. J. Page, S. Irle, and K. Morokuma, Theoretical Insights into ChiralityControlled SWCNT Growth from a Cycloparaphenylene Template. ChemPhysChem
13, 1479-1485 (2012).
2. F. Liu, and K. Morokuma, A Computational Study on the Working Mechanism of
Stilbene Light-Driven Molecular Rotary Motor: Sloped Minimal Energy Path andUnidirectional Nonadiabatic Isomerization. J. Am. Chem. Soc. 134, 4864-4876(2012).
3. M. P. Grubb, M. L. Warter, H.-Y. Xiao, S. Maeda, K. Morokuma, S. W. North,
No Straight Path: Multistate Roaming as the Only Route for the NO3 → NO + O2
Reaction, Science, 335, 1075-1078 (2012).
4. S. Maeda and K. Morokuma, Toward Predicting Full Catalytic Cycles Using
Automatic Reaction Path Search Method: A Case Study on HCo(CO)3-Catalyzed
Hydroformylation, J. Chem. Theo. Comp. 8, 380-385 (2012).
5. J. Pang, X. Li, K. Morokuma, N. S. Scrutton, and M. J. Sutcliffe, Large-scale
Domain Conformational Change Is Coupled to the Activation of the Co-C bond in
the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A Computational Study. J.
Am. Chem. Soc. 134, 2367-2377 (2012).
6. Y. Nishimoto, Z. Wang, K. Morokuma, and S. Irle, Molecular and electronic
structures of endohedral fullerenes, Sc2C2@C3v-C82 and Sc2@C3v-C82:
Benchmark for SCC-DFTB and proposal of new inner cluster structures, Phys.
Status Solidi B, 249, 324-334 (2012).
7. Y. Matsuda, K. Hoki, S. Maeda, K. Hanaue, K. Ohta, K. Morokuma, N. Mikami,
and A. Fujii, Experimental and theoretical investigations of isomerization reactionsof ionized acetone and its dimer. Phys. Chem. Chem. Phys. 14, 712-719 (2012).
【学術関係の受賞】 International Academy of Quantum Molecular Science (IAQMS) Medal, 1978; 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 ofTheoretical & Computational Chemists, 2005; 恩賜賞、日本学士院賞、2008; 瑞宝
中綬章、2010－ 19 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)【氏名（ふりがな）】 榊

茂好 （さかきしげよし）【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第２【研究室】 303
【直通電話】 075-711-7907【FAX】 075-711-4757【電子メールアドレス】 Sakaki.shigeyoshi.47e@st.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/【研究分野】 理論化学・計算化学【現在の研究課題】 遷移金属元素を含む複合電子系の構造、電子状態、反応過程の理論化学【研究内容キーワード】 電子状態理論・遷移金属錯体・反応解析・触媒作用・励起状態【学歴】 1974 年 3 月

京都大学工学研究科燃料化学専攻博士課程単位取得退学【学位】 1974 年 11 月

工学博士（京都大学）【略歴】 1975 年 4 月 熊本大学工学部助手、1982 年 1 月 同助教授、1990 年 4 月 同教授を経て、2002 年 4 月より京都大学工学研究科教授、2010 年 3 月定年、現在に至る。
【所属学会】 日本化学会、触媒学会、近畿化学協会、ケイ素化学協会、American Chemical
Society【主な著書、学術論文】 1. Pd(II)-Promoted Direct Cross-Coupling Reaction of Arenes via Highly Regioselective Aromatic
C-H Activation: A Theoretical Study, A. Ishikawa, Y. Nakao, H. Sato, S. Sakaki, Dalton Trans.,（過去 5 年以内）

39, 3279-3289 (2010).
2. Comparison of Electronic Structures and Light-induced Excited Spin State Trapping between[Fe(2-picolylamine)3]2+ and Its Iron(III) Analogue, H. Ando, Y. Nakao, H. Sato, S. Sakaki,
Dalton Trans., 39, 1836-1845 (2010).
3. Spin-orbit coupling in a model Hamiltonian for d-d excited states of Ni2+ ion aqueous solution, S.
Iuchi, S. Sakaki, Chem. Phys. Lett., 485, 114-118 (2010).
4. 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, Y.-I. Kurokawa, Y. Nakao, S. Sakaki, J. Phys. Chem. A, 114, 1191–1199(2010).
5. Theoretical Study of Excited States of Pyrazolate- and Pyridinethiolate- Bridged Dinuclear
Platinum(II) Complexes: Relationship between Geometries of Excited States andPhosphorescence Spectra, K. Saito, Y. Nakao, K. Umakoshi, S.Sakaki, Inorg. Chem., 49, 8977–
8985 (2010).
6. Multi-State CASPT2 Study of Native Iron(III)-dependent Catechol Dioxygenase and Its
Functional Models: Electronic Structure and Ligand-to-Metal Charge- Transfer Excitation, N.
Nakatani, Y. Hitomi, S. Sakaki, J. Phys. Chem. B, 115, 4781–4789 (2011).
7. Theoretical Study of Photoinduced Epoxidation of Oleﬁns Catalyzed by Ruthenium Porphyrin,
A. Ishikawa, S. Sakaki, J. Phys. Chem. A, 115, 4774–4785 (2011).
8. Noble Reaction Features of Bromoborane in Oxidative Addition of B − Br σ − Bond toM(PMe3)2 (M= Pt or Pd): Theoretical Study, G. Zeng, S. Sakaki, Inorg. Chem., 50, 5290-5297(2011).
9. Theoretical Study of Pt(PR3)2(AlCl3) (R=H, Me, Ph, or Cy) Including an Unsupported Bondbetween Transition Metal and Non-Transition Metal Elements; Geometry, Bond Strength, andPrediction, S. Tsukamoto, S. Sakaki, J. Phys. Chem. A, 115, 8520-8527 (2011).
10.Theoretical study on aquation reaction of cis-platin complex: RISM-SCF-SEDD, a hybrid
aproach of accurate quantum chemical method and statistical mechanics, D. Yokogawa, K. Ono,
H. Sato, S. Sakaki, Dalton Trans, 40 (42), 11125-11130 (2011).
11. Theoretical Study on High-Spin to Low-Spin Transition of Fe(pyrazine) [Pt(CN) 4]}: GuestInduced Entropy Decrease, A. Hideo, Y. Nakao, H. Sato, M. Ohba, S.Kitagawa, S. Sakaki,
Chem. Phys. Lett. 511(4-6), 399-404 (2011).

【学術関係の受賞など】 第１回分子科学会賞 (2009 年 9 月 )－ 20 －

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Ⅰ 専任教員 ･ スーパーバイザー (2011)⑹

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【FAX】 075-781-4757【電子メールアドレス】 smaeda@fukui.kyoto-u.ac.jp【ホームページ】 https://sites.google.com/site/satoshimaedahokkaidouniv/【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
東北大学大学院理学研究科博士課程【学位】 2007 年 3 月

理学博士（東北大学）

修了
修了【略歴】 2004 年 4 月 日本学術振興会特別研究員（DC1）2007 年 4 月 日本学術振興会特別研究員（PD）
2010 年 4 月 京都大学次世代研究者育成センター（特定助教）
2012 年 2 月 北海道大学大学院理学研究院化学部門物理化学分野（助教）【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.; Morokuma, K. A Systematic Method for Locating Transition Structures（過去 5 年以内）
of A + B → X Type Reactions. J. Chem. Phys. 2010, 132, 241102/1-4.
2. 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.
3. 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, 852-857.
4. Maeda, S.; Morokuma, K. Finding Reaction Pathways of Type A + B → X: Toward
Systematic Prediction of Reaction Mechanisms. J. Chem. Theory Comput. 2011, 7,2335-2345.
5. Maeda, S.; Morokuma, K. Toward Predicting Full Catalytic Cycle Using
Automatic Reaction Path Search Method: A Case Study on HCo(CO)3-Catalyzed
Hydroformylation. J. Chem. Theory Comput. 2012, 8, 380-385.
【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 4 月 京都大学白眉研究者
2012 年 3 月 The PCCP Prize for Outstanding Achievement of Young Scientists inPhysical Chemistry and Chemical Physics－ 21 －

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Ⅱ 博士研究員 (2011)

Ⅱ

博士研究員

１．博士研究員組織
平成２３年度職

名

氏

名

Zhuofeng Ke
福井センターフェロー

Joonghan Kim
Alister Page
畑中

美穂

Xin Li
K.R.S. Chandrakumar
Fengyi Liu

福井謙一記念研究部第一Hong-yan Xiao
（JST）フェロー

Lina Ding
Haibei Li
Lung Wa Chung
Galina Petrova
Raman Kumar SinghJSPS 外国人特別研究員

Travis Harris

福井センターフェロー

土方

優

青野

信治

塚本

晋也

Milind Deshmukh
福井謙一記念研究部第二特推研究フェロー

JSPS 特別研究員

會

桂香

髙木

望

中垣

雅之

吉澤

輝高

中谷

直樹

松井

亨

Wilfredo Credo Chung
福井センターフェロー

岩城

貴史

義永

那津人

嶺澤

範行

Kunkun Guo（受入れ研究者）
分子科学研究所 専門研究職員

河津励－ 22 －

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Ⅱ 博士研究員 (2011)

２. 博士研究員プロフィール【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 bio-systems【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, Universityof 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, S., Ueno, T., & Morokuma, Keiji,J. Am. Chem. Soc. 133(20), 7926-7941 (2011) (JACS beta Select issue 13: Current Applications of（過去 5 年以内）
Computational Chemistry in JACS - Molecules, Mechanisms and Materials)
2. Liu, Y., Ke, Zhuofeng, Liu, Shuwen, Chen, Wen-Hua, Jiang, Shibo; Jiang, ZhiHong. ChemMedChem 6 (9), 1654- 1664 (2011)..
3. Gao, H., Ke, Zhuofeng, DeYonker N. J., Wang J., Xu H., Mao Z.-W., Phillips, D.L.,& Zhao C. J. Am. Chem. Soc., 2011, 133 (9), 2904–2915
4. Ke, Zhuofeng & Cundari, T.R. Organometallics 29 (4), 821-834 (2010). (Top10
Most Accessed Articles of Organometallics in 2010)

5. Guo, Z.; Xue, Jiadan; Ke, Zhuofeng; Phillips, D. L.*; Zhao, C.Y. J. Phys. Chem. B,
2009, 113, 6528–6532.
6. Foley, N. A.; Lee, J. P.; Ke, Zhuofeng; Gunnoe, T. B.*; and Cundari, T. R. Acc.
Chem. Res. 2009, 42, 585–597
7. Lee, J. P.; Ke, Zhuofeng; Ramrez M. A.; Gunnoe, T. B.*; Cundari T. R.*; Boyle, P.
D.; Petersen, J. L. Organometallics 2009, 28, 175 8–1775
8. Liu, Yan; Ke, Zhuofeng; Cui, Jianfang; Chen, Wen-Hua; Ma, Lin; Wang Bo*.
Bioorg. Med. Chem. 2008, 16, 7185–7192.
9. Foley, Nicholas A.; Ke, Zhuofeng; Gunnoe, T. Brent*; Cundari, Thomas R.*; andPetersen, Jeffrey L. Organometallics 2008, 27, 3007–3017.
10. Guo, Zhen; Ke, Zhuofeng; Phillips, David Lee*; Zhao, Cunyuan*.
Organometallics 2008, 27, 181–188.
【学術関係の受賞など】 Sun Yat-sen University Fellow 2009
State Scholarship Funds, China Scholarship Council (CSC) 2007
－ 23 －

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Ⅱ 博士研究員 (2011)【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 203【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 anddetermination 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. Joonghan Kim, Yoon Sup Lee, and Hyotcherl Ihee, “Density Functional and Ab（過去 5 年以内）
Initio Studies on Structures and Energies of the Ground State of CrCO”, Int. J.
Quantum Chem. 107, 458 (2007).
2. 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).
3. Joonghan Kim, Sunhong Jun, Jeongho Kim, and Hyotcherl Ihee, “Density
Functional and Ab Initio Investigation of CF2ICF2I and CF2CF2I Radicals in Gas
and Solution Phases”, J. Phys. Chem. A 113, 11059-11066 (2009).
4. 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).
5. Jeewon Kang, Joonghan Kim, Hyotcherl Ihee, and Yoon Sup Lee, “Molecular
Structures, Energetics and Electronic Properties of Neutral and Charged Hg n
Clusters (n= 2–8)”, J. Phys. Chem. A 114, 5630-5639 (2010).
6. Joonghan Kim, Hyotcherl Ihee, and Yoon Sup Lee, “Spin-Orbit Density
Functional and Ab Initio Study of HgXn (X=F, Cl, Br, and I; n=1, 2, and 4)”, J.
Chem. Phys. 133, 144309 (2010).
7. Joonghan Kim, Tae Kyu Kim, and Hyotcherl Ihee, “Density Functional and SpinOrbit Ab Initio Study of CF3Br: Molecular Properties and Electronic CurveCrossing”, J. Phys. Chem. A 115, 1264-1271 (2011).
8. Joonghan Kim, Hyotcherl Ihee, and Yoon Sup Lee, “Spin-orbit ab initio study of
two low-lying states of chloroiodomethane cation”, Theor. Chem. Acc. 129, 343347 (2011).
9. Joonghan Kim, Stephan Irle, and Keiji Morokuma, “Determination of Local
Chirality in Irregular Single-Walled Carbon Nanotubes Based on Individual
Hexagons”, Phys. Rev. Lett. 107, 175505 (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.
Quantum Chem. 112, 1913-1925 (2012).
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Ⅱ 博士研究員 (2011)【氏名】 Alister Page
【職名】 Fukui Fellow【所属】 Fukui Kenichi Memorial Research Group 1, Fukui Institute for Fundamental
Chemistry【研究室】 Room 203【直通電話】 075-711-7831【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 & graphene nucleation andgrowth).
【研究内容キーワード】 Single-walled carbon nanotube, garphene self-assembly, nucleation, growth, healing,(n,m)chirality, functionalization 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
2010-2012, Fukui 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. Y. Wang, A. J. Page, H.-J. Qian, Y. Nishomoto, S. Irle, K. Morokuma, “Template
Effect in the Competition Between Haeckelite and Graphene Growth on Ni(111):（過去 5 年以内）
Quantum Chemical Molecular Dynamics Simulations.”, J. Am. Chem. Soc., 133,
18837, (2011)
2. A. J. Page, K.R.S. Chandrakumar, S. Irle, K. Morokuma, “SWNT Nucleation from
Carbon-Coated SiO2 Nanoparticles via a Vapor-Solid-Solid Mechanism”. J. Am.
Chem. Soc., 132, 15699, (2011)
3. 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)
4. A. J. Page, Y. Ohta, Y. Okamoto, S. Irle, K. Morokuma, “Defect Healing During
Single-Walled Carbon Nanotube Growth: A Density-Functional Tight-Binding
Molecular Dynamics Investigation”, J. Phys. Chem. C, 113, 20198, (2009)
5. A. J. Page, E. I. von Nagy-Felsobuki, “Rovibrational Spectra of LiH 2+, LiHD+
and LiD2+ Determined using FCI Property Surfaces”, J. Phys. Chem. A, 111, 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 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 畑中

美穂 （はたなかみほ）【職名】 福井謙一記念研究センターフェロー【所属】 福井記念研究センター

諸熊グループ【研究室】 福井記念研究センター 212【直通電話】 075-711-7647【電子メールアドレス】 miho@fukui.kyoto-u.ac.jp【研究分野】 計算化学・理論化学【現在の研究課題】 一酸化窒素還元酵素の反応機構に関する理論的研究【研究内容キーワード】 酵素反応・ONIOM 法【学歴】 2011 年 3 月 慶應義塾大学大学院 理工学研究科 基礎理工学専攻 博士課程修了【学位】 2011 年 3 月 博士（理学）（慶應義塾大学）【略歴】 2009 年 4 月－ 2010 年 3 月 慶應義塾大学大学院理工学研究科助教（有期・研究助成）2011 年 4 月 京都大学福井謙一記念研究センターフェロー【所属学会】 日本化学会・分子科学会【主な著書、学術論文】 1. M. Hatanaka, S. Yabushita, “An ab initio study on the f-f hypersensitive transition
intensities of lanthanide tribromide molecules”, Chem. Phys. Lett. 504, pp 193-198（過去 5 年以内）
(2011).
2. M. Hatanaka, S. Yabushita, “Theoretical Study on the f−f Transition Intensities ofLanthanide Trihalide Systems”, J. Phys. Chem. A 113, pp 12615-12625 (2009).
3. T. Ikeno, I. Iwakura, A. Shibahara, M. Hatanaka, A. Kokura, S. Tanaka, T. Nagata,
T. Yamada, “Newly Designed Catalysts for the Enantioselective Borohydride
Reduction: Prediction from the Theoretical Analysis”, Chem. Lett. 36, pp 738-739(2007).
4. I. Iwakura, M. Hatanaka, A. Kokura, H. Teraoka, T. Ikeno, T. Nagata, T. Yamada,“The Reactive Intermediate of Catalytic Borohydride Reduction by Schiff BaseCobalt Complexes”, Chem. Asian J. 1, pp 656-663 (2006).
【学術関係の受賞など】 2011 年 4 月 福井謙一記念研究センターフェロー
2010 年 4 月 公益信託 林女性自然科学者研究助成基金
2009 年 3 月 日本化学会第 89 春季年会 学生講演賞

林フェロー－ 26 －

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Ⅱ 博士研究員 (2011)【氏名】 Xin Li【職名】 Associate professor【所属】 Dalian Institute of Chemical Physics, Chinese Academy of Sciences【研究室】 Room 104【直通電話】 +86-411-84379376【電子メールアドレス】 lixinbj@gmail.com【研究分野】 Computational Biochemistry【現在の研究課題】 Studies of biological systems【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
July 2007-December 2011, Postdoctoral Fellow, Fukui Institute for Fundamental
Chemistry【主な著書、学術論文】 1. Xin Li, Lung Wa Chung, Piotr Paneth, and Keiji Morokuma, “DFT and（過去 5 年以内）
ONIOM(DFT:MM) Studies on Co-C Bond Cleavage and Hydrogen Transfer in B12Dependent Methylmalonyl-CoA Mutase. Stepwise or Concerted Mechanism?” J.
Am. Chem. Soc. 131, 5115-5125 (2009).
2. 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).
3. Xin Li, Lung Wa Chung, Hideaki Mizuno, Atsushi Miyawaki, and Keiji Morokuma,“Primary Events of Photodynamics in Reversible Photoswitching FluorescentProtein Dronpa”, J. Phys. Chem. Lett. 1, 3328-3333 (2010).
4. 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, 1666616675 (2010).
5. Xin Li, Lung Wa Chung, and Keiji Morokuma, “Modeling Photobiology Using
Quantum Mechanics (QM) and Quantum Mechanics/Molecular Mechanics (QM/
MM) Calculations,” In “Computational Methods for Large systems: Electronic
Structure Approaches for Biotechnology and Nanotechnology” Reimers, J. R. Eds.
John Wiley & Sons, Inc., Hoboken, 2011, pp 397-433.
6. Xin Li, Lung Wa Chung, and Keiji Morokuma,“Photodynamics of All-trans Retinal
Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution”, J. Chem.
Theory Comput. (Lett.) 7, 2694–2698 (2011).
7. Lung Wa Chung, Xin Li, Hajime Hirao, and Keiji Morokuma, “Comparative
Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in Heme and Non-Heme
Complexes”, J. Am. Chem. Soc. (Commun.) 133, 20076-20079 (2011).
8. Jiayun Pang, Xin Li, Keiji Morokuma, Nigel S. Scrutton, and Michael J. Sutcliffe,“Large-Scale Domain Conformational Change Is Coupled to the Activation of
the Co−C Bond in the B 12-Dependent Enzyme Ornithine 4,5-Aminomutase: A
Computational Study” J. Am. Chem. Soc. 134, 2367-2377 (2012).
9. Chung, L. W.; Hirao, H.; Li, X.; Morokuma, K. “The ONIOM Method: Its
Foundation and Applications to Metalloenzymes and Photobiology”, WIREs
Comput. Mol. Sci. 2, 327-350 (2012).
【学術関係の受賞など】 Postdoctoral Science Fund of China in Peking University, 2006; WATOC2011 Poster
Prize－ 27 －

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Ⅱ 博士研究員 (2011)【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-functional tightbinding【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. Jena, N. K. Tripathy, M. K., Samanta, A. K., Chandrakumar, K. R. S. and Ghosh,（過去 5 年以内）
S. K. “Water molecule encapsulated in carbon nanotube model systems: effect of
conﬁnement and curvature” Theo. Chem. Acc. 2012, 131, 1-12.
2. Jena, N.K., Chandrakumar, K.R.S; Ghosh, S.K. Beyond the gold-hydrogen analogy:
Doping gold cluster with H-atom-O2 activation and reduction of the reaction barrier
for CO oxidation Journal of Physical Chemistry Letters 2011 2 1476-1480.
3. Page, A.J., Chandrakumar, K.R.S., Irle, S., Morokuma, K. SWNT nucleation fromcarbon-coated SiO 2 nanoparticles via a vapor-solid-solid mechanism J. Am.
Chem. Soc. 2011, 133, 621-628.
4. Page, A.J., Chandrakumar, K.R.S., Irle, S., Morokuma, K. “Thermal annealing of
SiC nanoparticles induces SWNT nucleation: Evidence for a catalyst-independent
VSS mechanism” Physical Chemistry Chemical Physics 2011, 13, 15673-15680
5. Jena, N.K., Chandrakumar, K.R.S. Ghosh, S.K. DNA Base-Gold Nano Cluster
Complex as a Potential Catalyzing Agent: An Attractive Route for CO Oxidation
Process. J. Phys. Chem. C 2012, (In Press).
【学術関係の受賞など】 Indo-European Collaborative Project Grant (FP7); Project Title: Modeling of Nanoscaled 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)－ 28 －

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Ⅱ 博士研究員 (2011)【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, Computational Study on the Working Mechanism（過去 5 年以内）
of a Stilbene Light-Driven Molecular Rotary Motor: Sloped Minimal Energy Pathand Unidirectional Nonadiabatic Photoisomerization, J. Am. Chem. Soc., 2012, 134,
4864–4876.
2. Shu-Feng Chen, Ya-Jun. Liu, Fengyi Liu, Luca De Vico, Roland Lindh,Multireference calculations on the chemical origin and mechanism of fireflybioluminescence, Luminescence, 2010, 25, 89-90.
3. Fengyi Liu, Yajun liu, Luca De Vico, Roland Lindh, A CASSCF/CASPT2 Approachto the Decomposition of Thiazole-Substituted Dioxetanone: Substitution Effects
and Charge-Transfer Induced Electron Excitation, Chem. Phys. Lett. 2009,484,6975.
4. 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.
5. 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.
6. Jie Ren, Fengyi Liu, Yatong Zhang, David Wei Zhang, Initial reaction of HfO2
atomic layer deposition on silicon surfaces with different oxygen levels: A density
functional theory study, Thin Solid Film, 2007, 515, 4702-4708.
【学術関係の受賞など】 Poster Prize on 7th Congress of the International Society for Theoretical Chemical
Physics, 2011, Tokyo, Japan.
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Ⅱ 博士研究員 (2011)【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 of Physics
and Chemistry, Chinese Academy of Science【主な著書、学術論文】 1. Ya-Jun Liu, Hong-Yan Xiao, Meng-Tao Sun, Wei-Hai Fang. Spin-orbit ab initio
investigation of the photodissociation of dibromomethane in the gas and solution（過去 5 年以内）
phases. J. Comput. Chem. 29, 2513-2519 (2008)
2. 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)
3. Hong-Yan Xiao, Zhen Zhen, Huan-Quan Sun, Xu-Long Cao, Zhen-Quan Li, XinWang Song, Xiao-Hong Cui and Xin-Hou Liu. Molecular dynamics simulation ofanionic surfactant at the water/n-alkane interface. Acta Phys. -Chim. Sin. 26, 422428 (2010)
4. Huan-Quan Sun, Hong-Yan Xiao, and Xin-Hou Liu. Structural properties ofhydroxyl-substituted alkyl benzenesulfonates at the water/vapor and water/decaneinterfaces. Sci. China Chem. 54, 1078-1085 (2011)
5. 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)
6. Michael P. Grubb, Michelle L. Warter, Hong-Yan Xiao, Satoshi Maeda, Keiji
Morokuma and Simon W. North. No straight path: roaming in both ground- andexcited-state photolytic channels of NO3 → NO +O2. Science 335, 1075-1078(2012)【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 －

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Ⅱ 博士研究員 (2011)【氏名】 Lina Ding （丁麗娜）【職名】 JST Fellow【所属】 Fukui Institute For Fundamental Chemistry【研究室】 Room 212【直通電話】 075-711-7631【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】 Photo reaction mechanism of biochemical and metal-complexes systems【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, Lung Wa Chung, Keiji Morokuma “Reaction Mechanism of Photo（過去 5 年以内）
induced Decarboxylation of the Photoactivatable Green Fluorescent Protein:An
ONIOM(QM:MM) Study”, To be submitted.
2. Lina Ding, Keiji Morokuma, “Mechanisic study on the Photoisomerization in
Polypyridyl mononuclear ruthenium(II) aquo (PMRA) complexe”, In preparation.
3. Lina Ding, Wei-Hai Fang, “Exploring Light-Induced Decarboxylation Mechanismof o-Acetylphenyl-Acetic Acid from the Combined CASSCF and DFT Studies”, J.
Org. Chem. 2010, 75, 1630-1636.
4. 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.
5. Lina Ding, Xue-Bo Chen, Wei-Hai Fang, “Ultrafast Asynchronous Concerted
Excited-State Intramolecular Proton Transfer and Photodecarboxylation ofo-Acetylphenylacetic Acid Explored by Combined CASPT2 and CASSCF Studies”,
Org. Lett. 2009, 11(7), 1495-1498.
6. 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 －

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Ⅱ 博士研究員 (2011)【氏名】 Hai-Bei 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, andnanotubes【研究内容キーワード】 Fullerene, Hydrocarbon combustions, Self-assembly, Single-walled carbon nanotube,
Chirality, Graphene growth, Density-functional tight-bingding【学歴】 2004, Bachelor of Chemistry, Qufu Normal University, China
2007, Master of Chemical Physics, University of Science and Technology of China,
China
2010, Doctor of Chemical Physics, University of Science and Technology of China,
China【学位】 Doctor of Philosophy, University of Science and Technology of China【主な著書、学術論文】 1. Hai-Bei Li, Aister. J. Page, Sthephan. Irle and K. Morokuma, “Theoretical Insights（過去 5 年以内）
for Chirality-Controlled SWCNT Growth from a Cycloparaphenylene Template”,
ChemPhysChem, 13, 1479, 2012.
2. Hai-Bei Li, Aister. J. Page, Ying Wang, Sthephan. Irle and K. Morokuma,“Sub-Surface Nucleation of Graphene Precursors near a Ni(111) Step- Edge”,
ChemComm, Accepted. DOI:10.1039/c2cc32995f.
3. Hai-Bei Li, Shanxi Tian, and Jinlong Yang. Propene oxidation on V4O11− cluster:reaction dynamics to acrolein, J. Phys. Chem. A, 114, 6542, 2010
4. Hai-Bei Li, Shanxi Tian, and Jinlong Yang. Propene oxidation with anionic cluster
V4O11−: selective epoxidation, Chem. Eur. J (communications) 15, 10747, 2009

5. Hai-Bei Li, Shanxi Tian, and Jinlong Yang. Theoretical study of the stepwise
protonation of the dioxo Manganese (V) porphyrin, J. Phys. Chem. B, 112, 15807,
2008【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 －

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Ⅱ 博士研究員 (2011)【氏名】 Lung Wa Chung【職名】 JST Fellow【所属】 Fukui Kennichi Memorial Research Group 1, Fukui Institute For Fundamental
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【ホームページ】 https://sites.google.com/site/oscarlwchung/home【研究分野】 Computational Chemistry, Biochemistry and Biophysics【現在の研究課題】 Metalloenzymes, photobiology, multi-scale simulations【研究内容キーワード】 Reaction mechanism of metalloenzymes, photobiology, bio-inspired systems andcatalysis; 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 Study ona Missing Piece in Understanding of Heme Chemistry: The Reaction Mechanism（過去 5 年以内）
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. 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.
6. 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.
7. 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.
8. Li, X.; Chung, L. W.; Morokuma, K. “Primary Events of Photodynamics of Alltrans Protonated Retinal Schiff Base in Bacteriorhodopsin, Methanol Solution and
Gas Phase” J. Chem. Theory Comput. (Lett.) 2011, 7, 2694.
9. Chung, L. W.; Hirao, H.; Li, X.; Morokuma, K. “The ONIOM Method: Its
Foundation and Applications to Metalloenzymes and Photobiology”, WIREs
Comput. Mol. Sci. 2012, 2, 327.
10. Chung, L. W.; Li, X.; Hirao, H.; Morokuma, K. “Comparative Reactivity of
Ferric-Superoxo and Ferryl-Oxo Species in Heme and non-Heme Complexes” J.
Am. Chem. Soc. (Commun.) 2011, 133, 20076.
11. Tanaka, R.; Yamashita, M.; Chung, L. W.; Morokuma, K.; Nozaki, K.
“Hydrogenation of Carbon Dioxide Catalyzed by Ir-PNP Complex: Reversibility
and Reaction Mechanism” Organometallics 2011, 30, 6742.
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Ⅱ 博士研究員 (2011)【氏名】 Galina Petrova【職名】 JST fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 208【直通電話】 075-711-7894【FAX】 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, DNA based asymmetric catalysis, reaction mechanisms【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】 12/2010-04/2012, Postdoctoral Scholar at FIFC, Kyoto University, Kyoto, Japan
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 ofSoﬁa & 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. G. N. Vayssilov, G. P. Petrova, E. A. I. Shor, V. A. Nasluzov, A. M. Shor, P. S.
（過去 5 年以内）
Petkov, N. Rösch, “Reverse hydrogen spillover on and hydrogenation of supported
metal clusters: Insights from computational model studies” Phys. Chem. Chem.
Phys. 14, 5879-5890 (2012).
2. G. N. Vayssilov, Y. Lykhach, A. Migani, T. Staudt, G. P. Petrova, N. Tsud, Tomáš
Skála, A. Bruix, F. Illas, K. C. Prince, V. Matolín, K. M. Neyman, J. Libuda,“Support nanostructure boosts oxygen transfer to catalytically active platinum
nanoparticles”, Nature Materials, 10, 310–315 (2011).
3. G. P. Petrova, G. N. Vayssilov, N. Rösch, “Interaction of ethene and ethyne withbare and hydrogenated Ir4 clusters. A density functional study”, Catalysis Science &Technology, 1, 958-970 (2011).
4. N. Rösch, G. P. Petrova, P. St. Petkov, A. Genest, S. Krüger, H. A. Aleksandrov, G.
N. Vayssilov, “Impurity Atoms on Small Transition Metal Clusters. Insights from
Density Functional Model Studies”, Topics in Catalysis, 54, 363-377 (2011).
5. M. A. Rangelov, G. P. Petrova, V. M. Yomtova, G. N. Vayssilov, “Catalytic Roleof Vicinal OH in Ester Aminolysis - Proton Shuttle versus Hydrogen-Bonds
Stabilization”, J. Org. Chem., 75, 6782–6792 (2010).
【学術関係の受賞など】 Student award for high academic achievements of the Foundation for support of the
Bulgarian Higher Education named after Prof. Michael Klett (2003)－ 34 －

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Ⅱ 博士研究員 (2011)【氏名】 Raman Kumar Singh【職名】 Post doctoral Researcher【所属】 Fuel Cell Nanomaterials Centre, University of Yamanashi, Japan【研究室】 6-43 Miyamae-cho, Kofu 400-0021【直通電話】 055-254-7161【FAX】 055-254-7161【電子メールアドレス】 singh@yamanashi.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Electronic structure calculation, electron-molecule resonance, proton conductivity offuel cell membranes, nonlinear optical properties of materials, polyyne nano-fusion
reactions【研究内容キーワード】 Dyson orbital, vibrational excitation cross-sections, Nafion, polyyne, single-wallcarbon nano tube
【学歴】 Dec 2004, Master of Technology, Birla Institute of Technology Mesra, India
Jan 2010, Ph.D. in Chemistry, Indian Institute of Technology Bombay, India【学位】 Ph.D. in Chemistry, Indian Institute of Technology Bombay, India【略歴】 Feb 2010, Postdoctoral Researcher, RIKEN Advanced Science Institute, Japan
April 2011,Postdoctoral Fellow, FIFC, Kyoto University, Japan
Sept 2011, Postdoctoral Researcher, Fuel Cell Nanomaterials Centre, University of
Yamanashi, Japan【主な著書、学術論文】 1. Raman K. Singh, Takao Tsuneda, Kenji Miyatake and Masahiro Watanabe,“Theoretical Investigation of Proton Conductivity in Proton Exchange Membranes（過去 5 年以内）
for Fuel cells”, J. Phys. Chem. B, submitted (2012).
2. Raman K. Singh and Takao Tsuneda, “Reaction Energetics on Long-range
Corrected Density Functional Theory: Diels-Alder Reactions”, J. Comput. Chem.,
revised submitted (2012).
3. Raman K. Singh and M. K. Mishra, “Investigation of Ethynylpyridines using theElectron Propagator Theory”, Int. J. Quant. Chem. 112(2), 426-439 (2012).
4. Raman K. Singh, Takao Tsuneda and Kimihiko Hirao, “An Examination of
Density Functionals on Aldol, Mannich and α-Aminoxylation Reactions Enthalpy
Calculations”, Theor. Chem. Acc. 130 (2-3), 153-160 (2011).
5. Raman K. Singh, J. V. Ortiz and M. K. Mishra, “Tautomeric Forms of Adenine:
Vertical Ionization Energies and Dyson Orbital”, Int. J. Quant. Chem. 110(10),1901-1915 (2010).
6. Raman K. Singh and M. K. Mishra, Investigation of Ethynylfurans using theElectron Propagator Theory, J. Phys. Chem. A, 113(51), 14150-14155 (2009).
7. Raman K. Singh and M. K. Mishra, “Electronic Structure Analysis and Vertical
Ionization Energies of Thiophene and Ethynylthiophenes”, J. Chem. Sci., 121(5),867-872 (2009).
8. J. Melin, Raman K. Singh, M. K. Mishra and J. V. Ortiz, Tautomeric Forms of
Azolide Anions: Vertical Electron Detachment Energies and Dyson Orbitals, J.
Phys. Chem. A, 111(50), 13069-13074 (2007).
9. Raman K. Singh, M Sarma, A Jain, S Adhikari and M K Mishra, “Calculation ofVibrational Excitation Cross-Sections in resonant e-molecule scattering using thetime dependent wave packet(TDWP) approach with application to the 2Π COshape resonance”, J. Chem. Sci., 119(5), 385-389 (2007).
10. Raman K. Singh, M. Sarma and M. K. Mishra, “Approximate construction of
local complex potentials for a time dependent wave packet based treatment ofvibrational excitation cross-sections in resonant e-N2, e-CO and e-H2 scattering”,
Indian J. Phys., 81(10), 983-1002 (2007).
11. M. Sarma, Raman K. Singh and M. K. Mishra, “Local complex potential based
time dependent wave packet approach to calculation of vibrational excitation
cross-sections in e-N2, e-H2 and e-CO scattering,” Computation in Modern
Science and Engineering, Volume 2, Part A (American Institute of Physics),
963,227-230 (2007).
【学術関係の受賞など】 Fellowship for SAARC / IAESTE- Japan Academic Internship Programme 2008
－ 35 －

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Ⅱ 博士研究員 (2011)【氏名】 Travis Harris【職名】 JSPS Foreign Researcher【所属】 Fukui Kenichi Memorial Research Group 1, Fukui Institute for Fundamental
Chemistry【研究室】 212
【直通電話】 075-711-7631【FAX】 075-781-4757【電子メールアドレス】 tvharris@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Computational studies of metalloenzymatic reactions【研究内容キーワード】 Ferritin, ferroxidase, di-iron, non-heme【学歴】 2006, B.A. (summa cum laude), Willamette University, Salem, OR, USA
2011, Ph.D., Montana State University, Bozeman, MT, USA【学位】 Doctor of Philosophy, Montana State University, Bozeman, MT, USA【略歴】 2011, General Chemistry Lab TA, Montana State University
2007, Research Assistant, Montana State University
2006, Biochemistry Lab TA, Willamette University【主な著書、学術論文】 1. Harris, T. V.; Szilagyi, R. K. Comparative Assessment of the Composition and（過去 5 年以内）
Charge State of Nitrogenase FeMo-Cofactor. Inorg. Chem., 2011, 50 (11), 4811.
2. Harris, T. V.; Szilagyi, R. K. Nitrogenase Structure and Function Relationships by
Density Functional Theory. In Nitrogen Fixation: Methods and Protocols; Ribbe, M.
W. Ed.; Humana Press: New York, 2011; pp 267-292.
3. Harris, T. V.; Szilagyi, R. K.; McFarlane Holman, K. L. Electronic Structural
Investigations of Ruthenium Compounds and Anticancer Prodrugs. J. Biol. Inorg.
Chem. 2009, 14 (6), 891.
4. Pool, V. L.; Klem, M. T.; Holroyd, J.; Harris, T.; Arenholz, E.; Young, M.; Douglas,T.; Idzerda, Y. U. Site Determination of Zn Doping in Protein Encapsulated ZnxFe3xO4 Nanoparticles. J. Appl. Phys. 2009, 105 (7), 07B515.
5. Pandey, A. S.; Harris, T. V.; Giles, L. J.; Peters, J. W.; Szilagyi, R. K.
Dithiomethylether as a Ligand in the Hydrogenase H-Cluster. J. Am. Chem. Soc.
2008, 130 (13), 4533.

【学術関係の受賞など】 NSF Materials Computation Center Travel Grant, 2011
Kopriva Graduate Student Fellowship, 2009
Molecular Biosciences Fellowship, 2007–2011
Mildred Livingston Grant, 2007–2008
ACS Montana Travel Grant, 2007
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Ⅱ 博士研究員 (2011)【氏名】 Yuh Hijikata【職名】 FIFC Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 303【直通電話】 075-711-7907【電子メールアドレス】 hijikata@fukui.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/member_e/hijikata.html【研究分野】 Quantum Chemistry, Coordination Chemistry【現在の研究課題】 Gas Adsorption【研究内容キーワード】 Porous Coordination Polymers【学歴】 Mar 2008, Master of Eng., Graduate School of Engineering, Kyoto University
May 2011, Ph.D. of Eng., Graduate School of Engineering, Kyoto University【学位】 Ph.D. of Eng. from Kyoto University【略歴】 Oct. 2011FIFC Fellow (Kyoto University)
Apr. 2011-Sep. 2011 Specially Promoted Research Fellow (Kyoto University)
Apr. 2008-Mar. 2011 JSPS Research Fellow (DC1) (Kyoto University)【所属学会】 Chemical Society of Japan, Japan Society of Coordination Chemistry,
Japan Society for Molecular Science【主な著書、学術論文】 1. Nobuhiro YANAI, Koji KITAYAMA, Yuh HIJIKATA, Hiroshi SATO, Ryotaro（過去 5 年以内）
MATSUDA, Yoshiki KUBOTA, Masaki TAKATA, Motohiro MIZUNO, Takashi
UEMURA, and Susumu KITAGAWA, “Reporting structural transformation of soft
porous crystals for detection of CO2”, Nat. Mater., 10, 787-793 (2011)
2. Yuh HIJIKATA, Satoshi HORIKE, Daisuke TANAKA, Juergen GROLL, Motohiro
MIZUNO, Jungeun KIM, Masaki TAKATA, and Susumu KITAGAWA, Differencesof crystal structure and dynamics between soft porous nanocrystal and bulk
crystal”, Chem. Commun., 47, 7632-7634 (2011)

3. Yuh HIJIKATA, Satoshi HORIKE, Masayuki SUGIMOTO, Hiroshi SATO,
Ryotaro MATSUDA, and Susumu KITAGAWA, “Relationship between Channel
and Sorption Properties in Coordination Polymers with Interdigitated Structures”,
Chem. Eur. J., 17, 5138-5144 (2011)
4. Satoru SHIMOMURA, Masakazu HIGUCHI, Ryotaro MATSUDA, Ko YONEDA,
Yuh HIJIKATA, Yoshiki KUBOTA, Yoshimi MITA, Jugeun KIM, Masaki
TAKATA, and Susumu KITAGAWA, “Selective Sorption of oxygen and nitricoxide by an electron-donating ﬂexible porous coordination polymer”, Nat. Chem., 2,633-637 (2010)
5. Yuh HIJIKATA, Hiroyuki NAKASHIMA, and Hiroshi NAKATSUJI, “Solving
non-Born-Oppenheimer Schrödinger equation for hydrogen molecular ion and its
isotopomers using the free complement method”, J. Chem. Phys., 130, 024102-1-11(2009)【学術関係の受賞など】 JSPS Research Fellowships for Young Scientists (DC1) 2008-2011－ 37 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 青野

信治 （あおのしんじ）【職名】 特推研究フェロー【所属】 京都大学 福井謙一記念研究センター【研究室】 福井記念研究センター 303 号室【直通電話】 075-711-7907【電子メールアドレス】 saono@fukui.kyoto-u.ac.jp【研究分野】 溶液化学・計算化学・理論化学【現在の研究課題】 溶液中の遷移金属錯体の化学反応の理論的解析【研究内容キーワード】 3D-RISM-SCF 法、平均場 QM/MM 法、自由エネルギー解析、溶媒和構造解析、
周期的結晶解析【学歴】 2010 年 3 月 京都大学大学院理学研究科化学専攻博士後期課程研究指導認定退学【学位】 2010 年 9 月 理学博士（京都大学）【略歴】 2010 年 4 月 京都大学大学院理学研究科化学専攻 研修員
2010 年 5 月 京都大学 物質 - 細胞統合システム拠点 教務補佐員
2010 年 10 月 京都大学 物質 - 細胞統合システム拠点 特定研究員
2011 年 4 月 京都大学 福井謙一記念研究センター 特定研究員【主な著書、学術論文】 1. Aono S., Sakaki S., “Proposal of new QM/MM approach for geometry optimization（過去 5 年以内）
of periodic molecular crystal: Self-consistent point charge representation for
crystalline effect on target QM molecule” Chem. Phys. Lett. (accepted 2012).
2. Aono S., Yamamoto T. and Kato S. “Solution reaction space Hamiltonian based onan electrostatic potential representation of solvent dynamics” J. Chem. Phys. 134
144108 (2011).
3. Aono S., Kato S. “Proton Transfer in Phenol-Amine Complexes: Phenol Electronic
Effect on Free Energy Proﬁle in Solution” J. Comput. Chem. 31 2924-2931 (2010).
4. Aono S., Minezawa N. and Kato S. “Electronic spectra of coumarin-151 in polar
solvents: Linear response free energy approach” Chem. Phys. Lett. 492 193-197(2010).

－ 38 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 塚本

晋也 （つかもと

しんや）【職名】 特推研究フェロー【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

福井謙一研究部第二

榊グループ

301

【直通電話】 075-711-7907【FAX】 075-711-4757【電子メールアドレス】 stsukamoto@fukui.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/【研究分野】 計算化学・理論化学【現在の研究課題】 遷移金属錯体の理論研究【研究内容キーワード】 遷移金属
【学歴】 2010 年九州大学大学院総合理工学府量子プロセス理工学専攻博士後期課程修了【学位】 2010 年 3 月博士（理学）（九州大学）【所属学会】 分子科学会、American Chemical Society【主な著書、学術論文】 1. “Experimental and Theoretical Approaches Toward Anion-responsive TripodeLanthanide Complexes: Mixed Donor Ligand Effects on Highly Coordinated（過去 5 年以内）
Complexation and Luminescence Sensing Profiles” Y. Kataoka, D. Paul, H.
Miyoka, T. Yaita, E. Miyoshi, H. Mori, S. Tsukamoto, H. Tatewaki, S. Shinoda, and
H. Tsukube, Chem. A Eur. J. 2008, 14, 5258
2. “CASSCF and CASPT2 calculations for lanthanide trihalides LnX3 using model
core potentials” S. Tsukamoto, H. Mori, H. Tatewaki, and E. Miyoshi, Chem. Phys.
Lett. 2009, 474, 28
3. “Theoretical Study of Pt(PR3)2(AlCl3)(R-H, Me, Ph, or Cy) Including an
Unsupported Bond between Transition Metal and Non-Transition Metal Elements;
Geometry, Bond Strength, and Prediction” S. Tsukamoto and S. Sakaki, J. Phys.
Chem. A, 2011, 115, 8520
4. “Theoretical Study of Metallasilatranes; Bonding Nature and Prediction of New
Metallasilatrane” S. Sakaki, D. Kawai, and S. Tsukamoto, Collect. Czech. Chem.
Comm, 2011, 76, 619－ 39 －

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Ⅱ 博士研究員 (2011)【氏名】 Milind Madhusudan Deshmukh【職名】 SPR Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 304【直通電話】 075-711-7907【電子メールアドレス】 milind@fukui.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/member_j/milind.html【研究分野】 Theoretical and Computational Chemistry【現在の研究課題】 Trapping gas molecules in Metal Organic Framework, Non covalent Interactions【研究内容キーワード】 Metal-Organic Framework, Binding Energy, Potential Energy Surface【学歴】 March 2001, Master of Sci., University of Pune, India
October 2008, Doctor of Philosophy, Department of Chemistry, University of Pune,
India【学位】 Doctor of Philosophy from Department of Chemistry, University of Pune, India【略歴】 August 2008 to April 2010: Postdoctoral Research Fellow, Tata Institute ofFundamental Research, Mumbai, India
June 2010 to present: Postdoctoral Research Fellow, Kyoto University, Japan【主な著書、学術論文】 1. Milind M. Deshmukh, and Shigeyoshi Sakaki, “Two-step Evaluation of Potential（過去 5 年以内）
Energy Surface and Binding Energy of van der Waals Complexes” J. Comput.
Chem. 33 617 (2012).
2. Jayasree K. Kedkar, Milind M. Deshmukh, Shridhar R. Gadre. Shridhar P. Gejji,“Intramolecular Hydrogen Bonding and cooperative interactions in Calix[n]arenes(n = 4, 5)” J. Phys. Chem. A. 116, 3739 (2012).
3. Milind M. Deshmukh and Shigeyoshi Sakaki, “Binding Energy of Gas Moleculewith Two Pyrazine Molecules as Organic Linker in Metal-Organic Framework: Its
Theoretical Evaluation and Understanding of Determining Factors” Theo. Chem.
Acc. 130, 475 (2011).
4. Milind M. Deshmukh, Bartolotti Libero Jr., and Shridhar R. Gadre, “Intramolecular
Hydrogen Bond Energy and Cooperative Interactions in α-, β-, and γ-Cyclodextrin
Conformers”, J. Comput. Chem. 32, 2996 (2011).
5. Milind M. Deshmukh and Shridhar R. Gadre, “Estimation of N-H···O=C
Intramolecular Hydrogen Bond Energy in Polypeptides”, J. Phys. Chem. A. 113,
7927 (2009).
【学術関係の受賞など】 Senior Research Fellowship of Council of Scientiﬁc and Industrial Research (CSIR)
2005-2008. Senior Research Fellowship of Centre for Developing Advanced
Computing (CDAC), Pune, 2004-2005.
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Ⅱ 博士研究員 (2011)【氏名】 Guixiang Zeng
【職名】 SPR Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 303【直通電話】 075-711-7907【電子メールアドレス】 guixang.zeng@fukui.kyoto-u.ac.jp【研究分野】 Computational Chemistry【現在の研究課題】 Unusual Electronic Process of the H − H bond activation across a Ni − B unit
【研究内容キーワード】 H − H bond activation, metal-ligand cooperation mode, ﬁrst-row transition metals【学歴】 June 2010, Ph. D., School of Chemistry & Chemical Engineering, Nanjing University【学位】 Ph. D. in Physical Chemistry from Nanjing University【略歴】 Sep. 2010~, Postdoctoral Fellow, Kyoto University【主な著書、学術論文】 1. Guixiang Zeng, Yong Guo, Shuhua Li, “H2 activation by a (PNP)Ir(C6H5)complex（過去 5 年以内）
via the dearomatization/aromatization process of the PNP ligand: A computational
study” Inorg. Chem. 48, 10257 (2009).
2. Guixiang Zeng, Shuhua Li, “Mechanistic insight on the hydrogenation of
conjugated alkenes with H2 catalyzed by early main-group metal catalysts” Inorg.
Chem. 49, 3361 (2010).
3. Guixiang Zeng, Shuhua Li, “Insights on Dehydrogenative Coupling of Alcohols
and Amines catalyzed by a (PNN)−Ru(II) Hydride Complex: Unusual Metal−
Ligand Cooperation” Inorg. Chem. 50, 10572 (2011).
4. Guixiang Zeng, Shigeyoshi Sakaki, “Noble Reaction Features of Bromoboranein Oxidative Addition of B−Br σ−Bond to [M(PMe3)2] (M= Pt or Pd): Theoretical
Study” Inorg. Chem. 50, 5290 (2011).
5. Guixiang Zeng, Shigeyoshi Sakaki, “Theoretical Study on the Transition-Metal
Oxoboryl Complex: M−BO Bonding Nature, Mechanism of the Formation
Reaction, and Prediction of a New Oxoboryl Complex” Inorg. Chem. 51, 4597
(2012)－ 41 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）
】 高木

望（たかぎ

のぞみ）

【職名】 特推研究フェロー【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

榊研究室【直通電話】 075-711-7907【電子メールアドレス】 takagi@fukui.kyoto-u.ac.jp【研究分野】 計算化学・理論化学【現在の研究課題】 d- 電子複合系の理論化学、新規な化学結合を有する分子の設計と結合解析【研究内容キーワード】 遷移金属元素、高周期典型元素、分子軌道計算【学歴】 1997 年 3 月
1999 年 3 月
2002 年 3 月

立教大学理学部化学科 卒業
東京都立大学大学院理学研究科化学専攻修士士課程 修了
東京都立大学大学院理学研究科化学専攻博士課程 修了【学位】 2002 年 3 月

理学博士（東京都立大学）【略歴】 2002 年 4 月
2005 年 4 月
2007 年 5 月
2011 年 1 月
2011 年 4 月

日本学術振興会 特別研究員 (PD)
自然科学研究機構・分子科学研究所 専門研究職員
ドイツ・フィリップス = マールブルク大学 博士研究員
自然科学研究機構・分子科学研究所 専門研究職員
京都大学・福井謙一記念研究センター 特定研究員【在外研究歴】 2007 年 5 月 -2010 年 12 月 ドイツ・フィリップス = マールブルク大学研究員（Gernot Frenking 教授）

博士【所属学会】 日本化学会【主な著書、学術論文】 1. “A Theoretical Study of Unusual Y-Shaped Three-coordinate Pt Complex: Pt(0) σ-Disilane
Complex or Pt(II) Disilyl Complex?” N. Takagi, S. Sakaki, J. Am. Chem. Soc., in press.
（過去 5 年以内）
2. “Carbodiphosphorane-Analogues E(PPh 3) 2 with E = C - Pb. A Theoretical Study with
implications for ligand design” N. Takagi, R. Tonner, G. Frenking, Chem. Eur. J., 18, 17721780 (2012).

3. “Bonding Situation in “Early-Late” Transition Metal Complexes Cl3M-M’(PCl3)4 (M = Ti, Zr,
Hf; M’= Co, Rh, Ir) - Theoretical Study for a Ligand Fine Tuning of M-M’ Bonds -” N. Takagi,
A. Krapp, G. Frenking, Z. Anorg. Alleg. Chem. 637, 1728-1735 (2011).

4. “Divalent Pb(0) Compounds” N. Takagi, G. Frenking, Theor. Chem. Acc., 129, 615-623 (2011).

5. “Bonding Analysis for Metal-Metal Multiple bonds in R3M-M’R3 (M, M’ = Cr, Mo, W; R = Cl,
NMe2)” N. Takagi, A. Krapp, G. Frenking, Inorg. Chem., 50, 819-826 (2010).

6. “On the nature of homo- and heterodinuclear metal-metal quadruple bonds – Analysis of thebonding situation and benchmarking DFT against wavefunction methods” N. Takagi, A. Krapp,
G. Frenking, Can. J. Chem., 88, 1079-1093 (2010).
7. “Divalent E(0) Compounds (E = Si - Sn)” N Takagi, T. Shimizu, G. Frenking, Chem. Eur. J.,
15, 8593-8604 (2009).

8. “Divalent Si(0) Compounds” N Takagi, T. Shimizu, G. Frenking, Chem. Eur. J., 15, 3448-3456(2009).

9. “Do Lead Analogues of Alkynes Take a Multiply Bonded Structure?” N. Takagi, S. Nagase,
Organometallics, 26, 3627-3629 (2007).
10.“Tin Analogues of Alkynes. Multiply Bonded Structures vs Singly Bonded Structures” N.
Takagi, S. Nagase, Organometallics, 26, 469-471 (2007).

11. “Effects of Bulky Substituent Groups on the Si-Si Triple Bonding in RSi≡SiR and the
Short Ga-Ga Distance in Na2[RGaGaR]. A Theoretical Study” N. Takagi, and S. Nagase, J.
Organomet. Chem. 692, 217-224 (2007).

【学術関係の受賞など】 2002 年 -2005 年

日本学術振興会

特別研究員 (PD)－ 42 －

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Ⅱ 博士研究員 (2011)【氏名】 Masayuki Nakagaki【職名】 SPR Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 303【直通電話】 075-711-7907【電子メールアドレス】 nakagaki@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/【研究分野】 Computational Chemistry【現在の研究課題】 Electronic Structure of Inverted Sandwich Type Complexes【研究内容キーワード】 Electronic Structure of Metal Complex, Multireference Theory【学歴】 March 2005, Master of Sci., Graduate School of Science, Kyushu University
March 2009, Doctor of Sci., Graduate School of Science, Kyushu University【学位】 Doctor of Science from Kyushu University【略歴】 Apr. 2009, Postdoctoral Fellow, Kyushu University【所属学会】 Japan Society for Molecular Science【主な著書、学術論文】 1. M. Nakagaki, E. Nishi, K. Sakota, H. Nakano, H. Sekiya, “A model two（過去 5 年以内）
dimensional potential for internal rotation of 9-methylanthracene studied byelectronic spectroscopy and DFT calculations” Chem. Phys. 328, 190-196 (2006)
2. K. Sakota, Y. Komoto, M. Nakagaki, W. Ishikawa, H. Sekiya “Observ- ation of acatalytic proton/hydrogen atom relay in microsolvated 7-azaindole-methanol cluster
enhanced by a cooperative motion of the hydrogen-bonded network” Chem. Phys.
Lett. 435, 1-4 (2007)
3. X. Zhang, Y. Komoto, K. Sakota, M. Nakagaki, H. Nakano, T. Shinmyozu, H.
Sekiya “Heavy mass effect on excited-state double-proton transfer in 7-azaindole
dimer by Cl substitution” Chem. Phys. Lett. 441, 176-180 (2007)
4. X. Zhang, Y. Komoto, K. Sakota, N. Masayuki, T. Shinmyozu, S. Nanbu, H.
Nakano, H. Sekiya “Remarkable suppression of the excited-state double-protontransfer in the 7-azaindole dimer due to substitution of the dimethylamino groupstudied by electronic spectroscopy in the gas phase” Chem. Phys. Lett. 443, 194198 (2007)－ 43 －

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Ⅱ 博士研究員 (2011)【氏名】 Terutaka Yoshizawa【職名】 SPR Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 303【直通電話】 075-711-7907【FAX】 075-711-4757【電子メールアドレス】 yoshizawa@fukui.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/【研究分野】 Theoretical chemistry【現在の研究課題】 Relativistic quantum chemical calculations of NMR shielding constants【研究内容キーワード】 NMR, DFT, Douglas–Kroll–Hess method, Transition metal complexes【学歴】 March 2006, Master of Sci., Graduate School of Science, Tokyo Metropolitan
University
March 2009, Doctor of Sci., Graduate School of Science and Engineering, Tokyo
Metropolitan University【学位】 Doctor of Science from Tokyo Metropolitan University【略歴】 Apr. 2009, Postdoctoral Fellow, Kyushu University
Jan. 2010, Postdoctoral Fellow, RIKEN
Apr. 2011, (SPR) Fellow, Kyoto University【主な著書、学術論文】 1. T. Yoshizawa and M. Hada, “Calculations of Frequency-Dependent Molecular（過去 5 年以内）
Magnetizabilities with Quasi-Relativistic Time-Dependent Generalized Unrestricted
Hartree-Fock Method”, J. Comput. Chem. 28, 740−747, (2007)
2. T. Yoshizawa and M. Hada, “Relativistic quantum-chemical calculations ofmagnetizabilities of noble gas atoms using the Douglas–Kroll–Hess method”,
Chem. Phys. Lett. 458, 223−226, (2008)
3. T. Yoshizawa and M. Hada, “Relativistic and Electron–Correlation Effects on
Magnetizabilities Investigated by the Douglas–Kroll–Hess Method and the SecondOrder Møller–Plesset Perturbation Theory”, J. Comput. Chem. 30, 2550−2566,(2009)
4. T. Yoshizawa and T. Nakajima, “Second-order generalized unrestricted Moller–
Plesset perturbation theory for the spin–orbit part of zero-ﬁeld splitting tensors”,
Chem. Phys. Lett. 515, 296−301, (2011)【学術関係の受賞など】 JSPS Research Fellowships for Young Scientists(DC) 2007-2009－ 44 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 中谷

直輝 （なかたに

なおき）【職名】 Postdoctral Associate【所属】 Department of Chemistry, Princeton University【研究室】 Frick Chemistry Laboratory, #355
【直通電話】 +1-609-258-9369【電子メールアドレス】 naokin@princeton.edu【研究分野】 理論・計算化学【現在の研究課題】 テンソルネットワークアルゴリズムによる DMRG の多次元化【研究内容キーワード】 DMRG, テンソルネットワーク、デンドリマー、遷移金属錯体【学歴】 2010 年 3 月

京都大学大学院工学研究科分子工学専攻博士課程修了【学位】 2010 年 3 月

工学博士（京都大学）【略歴】 2009 年 4 月 学術振興会特別研究員（DC2）2011 年 4 月 福井謙一記念研究センター研究フェロー【主な著書、学術論文】 1. Naoki Nakatani, Jun-ya Hasegawa, and Hiroshi Nakatsuji, “Red Light in
Chemiluminescence and Yellow-Green Light in Bioluminescence: Color-Tuning（過去 5 年以内）
Mechanism of Fireﬂy, Photinus Pyralis, Studied by the Symmetry-Adapted ClusterConﬁguration Interaction Method” J. Am. Chem. Soc. 129(28), 8756-8765 (2007)
2. Naoki Nakatani, Jun-ya Hasegawa, and Hiroshi Nakatsuji, “Artiﬁcial color tuningof firefly luminescence: Theoretical mutation by tuning electronic interactions
between protein and luciferin” Chem. Phys. Lett. 469, 191-194 (2009)
3. Naoki Nakatani, Yoshihide Nakao, Hirofumi Sato, and Shigeyoshi Sakaki,“Theoretical Study of the Iron Sulfur Cluster-free Hydrogenase (Hmd): What is theActive Center of Hmd?” Chem. Lett. 38(10), 958-959 (2009)
4. Naoki Nakatani, Yoshihide Nakao, Hirofumi Sato, and Shigeyoshi Sakaki,“Theoretical Study of Dioxygen Binding Process in Iron(III) Catechol Dioxygenase:“Oxygen Activation” vs. “Substrate Activation”” J. Phys. Chem. B 113, 48264836 (2009)
5. Naoki Nakatani, Yutaka Hitomi, and Shigeyoshi Sakaki, “Multistate CASPT2 Studyof Native Iron(III)-Dependent Catechol Dioxygenase and Its Functional Models:Electronic Structure and Ligand-to-Metal Charge-Transfer Excitation” J. Phys.
Chem. B 115, 4781-4789 (2011)【学術関係の受賞など】 Poster Award on the 48th Sanibel Symposium (2008)－ 45 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 松井

亨 （まついとおる）【職名】 日本学術振興会 特別研究員 (PD)【所属】 大阪大学大学院 理学研究科 化学専攻
【研究室】 奥村研究室【直通電話】 06-6850-5405【FAX】 06-6850-5550【電子メールアドレス】 tmatsui@fukui.kyoto-u.ac.jp【ホームページ】 http://www.users.iimc.kyoto-u.ac.jp/~z59354/member_j/matsui.html【研究分野】 生物無機化学 , 生物物理化学【現在の研究課題】 酸化還元電位の算出法【研究内容キーワード】 酸化還元電位 , 酸解離定数 , pKa【学歴】 2009 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】 2009 年 3 月 工学博士 ( 東京大学 )【略歴】 2008 年 4 月 日本学術振興会特別研究員 (DC2, 東京大学 ), 2009 年 4 月 日本学術振興会特別研究員 (DC2, 大阪大学 ), 2010 年 4 月 兵庫県立大学大学院生命理学研究科 特任助教 , 2011 年 4 月 日本学術振興会特別研究員 (PD), 福井謙一記
念研究センター 客員研究員【所属学会】 日本化学会 , 日本分子科学会【主な著書、学術論文】 1. T. Matsui, T. Sato and Y. Shigeta, “Sequence dependent proton-transfer reaction instacked GC pair II: The origin of stabilities of proton-transfer products”, Chemical（過去 5 年以内）
Physics Letters, 478, pp.238-242 (2009).
2. T. Matsui, H. Miyachi, Y. Nakanishi, Y. Shigeta, T. Sato, Y. Kitagawa, M. Okumura
and K. Hirao, “Theoretical Studies on Sulfur and Metal Cation (Cu(II), Ni(II),
Pd(II), and Pt(II))-Containing Artiﬁcial DNA”, Journal of Physical Chemistry B,
113, pp.12790-12795 (2008).
3. H. Miyachi, T. Matsui, Y. Shigeta and K. Hirao, “Effects of mercury(II) on
structural properties, electronic structure and UV absorption spectra of a duplex
containing thymine-mercury(II)-thymine nucleobase pairs”, Physical Chemistry
Chemical Physics, pp. 909-917 (2010).
4. T. Matsui, A. Oshiyama and Y. Shigeta, “A Simple Scheme for pKa of 5-substituted
Uracils” Chemical Physics Letters, 502, pp.238-242 (2011).
5. Y. Nakanishi, T. Matsui, Y. Kitagawa, Y. Shigeta, T. Saito, Y. Kataoka, T.
Kawakami, M. Okumura and K. Yamaguchi, “Electron Conductivity in Modiﬁed
Models of Artiﬁcial Metal-DNA Using Green's Function-Based Scattering Theory”,
Bulletin of Chemical Society of Japan, 84, pp.366-375 (2011).
6. T. Matsui, H. Miyachi, T. Baba and Y. Shigeta, “A Theoretical Study on Reaction
Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation”, theJournal of Physical Chemistry A,.115, pp.8524-8531 (2011).
7. K. Kamiya, T. Matsui, T. Sugimura and Y. Shigeta, “Theoretical Insight into
Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin[2+2] Cycloaddition”, The Journal of Physical Chemistry A,116, pp. 1168-1175(2012).
8. T. Matsui, T. Baba, K. Kamiya and Y. Shigeta, “'An accurate density functional
theory based estimation of pKa value of polar residues combined with experimental
data: from amino acids to minimal proteins”, Physical Chemistry Chemical
Physics,14, pp. 4181-4187 (2012).
9. T. Matsui, H. Miyachi, Y. Shigeta and K. Hirao (2012) “Metal-Assisted Proton
Transfer in Guanine-Cytosine Pair: An Approach from Quantum Chemistry”, inSome Applications of Quantum Mechanics, ISBN 978-953-51-0059-1, edited byMohammad Reza Pahlavani , InTech, pp. 167-188.
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Ⅱ 博士研究員 (2011)【氏名】 Wilfredo Credo Chung【職名】 Associate Professor 5【所属】 Department of Chemistry, De La Salle University – Manila, Philippines【研究室】 Room 312, St. Joseph Hall
【直通電話】 +63 2 536 0230
【FAX】 +63 2 524 0451
【電子メールアドレス】 wilfredo.chung@dlsu.edu.ph【研究分野】 Computational Chemistry【現在の研究課題】 Theoretical elucidation of reaction mechanisms and dynamics of important moleculesin the electronic ground and excited states【研究内容キーワード】 potential 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 – September 2011 Center Fellow, Fukui Institute for Fundamental
Chemistry, Kyoto University
May 2012 – present Associate Professor 5, Department of Chemistry, De La Salle
University – Manila, Philippines【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, S. Nanbu and T. Ishida, QM/MM Trajectory Surface Hopping（過去 5 年以内）
Approach to Photoisomerization of Rhodopsin and Isorhodopsin: The Origin of
Faster and More Efﬁcient Isomerization for Rhodopsin, J. Phys. Chem. B, 116 (28),8009–8023 (2012).
2. W. C. Chung, S. Nanbu and T. Ishida, A Nonadiabatic Ab Initio Dynamics Studyon Rhodopsin and Its Analog Isorhodopsin: Chemical Dynamics Reasons behind
Selection of Rhodopsin by Life, Chemistry Letters 40, 1395-1397 (2011).
3. W. C. Chung and T. Ishida, An MD simulation of the decoy action of Epstein–Barrvirus LMP1 protein mimicking the CD40 interaction with TRAF3, Theoretical
Chemistry Accounts 130, 401-410 (2011).
4. 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).
5. W. M. I. Hassan, W. C. Chung, N. Shimakura, S. Koseki, H. Kono and Y. Fujimura
Ultrafast radiationless transition pathways through conical intersections in photoexcited 9H-adenine, Phys. Chem. Chem. Phys., 12, 5317–5328 (2010).
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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 岩城

貴史 （いわきたかふみ）【職名】 FIFC Fellow【所属】 京都大学福井謙一記念研究センター【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【ホームページ】 http://www.fukui.kyoto-u.ac.jp/users/iwaki/topj.htm【研究分野】 Soft Matter, Biological Physics【現在の研究課題】 Interfacial Phenomena, PEMS of coarse-grained model polymer folding【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 semiﬂexible
polyelectrolyte chain through toroidal bundling of loop structures”, The Journal of（過去 5 年以内）
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. Iwaki, “Effect of internal flow on the photophoresis of a micron-sized liquid
droplet”, Physical Review E 81, 066315 (13 pages) (2010)
4. 吉川研一、岩城貴史、“細胞の自己組織化”に物理の視点から迫る”, パリ
ティ 2011年5月号 pp. 13-21
5. Y. Higuchi, K. Yoshikawa, T. Iwaki, “Stiffness causes opposite trend on the folding
transition of a single polymer chain in a conﬁned space”, Physical Review E 84,
021924 (5 pages)－ 48 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 義永

那津人 （よしながなつひこ）【職名】 助教【所属】 東北大学

原子分子材料科学高等研究機構【直通電話】 022-217-6333【FAX】 022-217-6335【電子メールアドレス】 yoshinaga@wpi-aimr.tohoku.ac.jp【ホームページ】 http://www.wpi-aimr.tohoku.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, Contraction of active gels
【学歴】 2007 年 3 月

京都大学理学研究科【学位】 2007 年 3 月

理学博士（京都大学）【略歴】 2007 年 4 月
2010 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、
京都大学福井謙一記念研究センター特定研究員

物理学・宇宙物理学専攻

博士課程修了【所属学会】 日本物理学会【主な著書、学術論文】 1. Hiroyuki Kitahata, Natsuhiko Yoshinaga, Ken H. Nagai, and Yutaka Sumino,“Spontaneous motion of a droplet coupled with a chemical wave” Phys. Rev. E.
（過去 5 年以内）
Rapid Communications 84, 015101 (2011).
2. Philippe Marcq, Natsuhiko Yoshinaga, and Jacques Prost, “Rigidity sensing
explained by active matter theory” Biophys. J. 101, L33-L35 (2011).
3. Hong-Ren JIANG, Natsuhiko YOSHINAGA, and Masaki SANO, “Active Motionof Janus Particle by Self-thermophoresis in Defocused Laser Beam”, PhysicalReview Letters, 105, 268302 (2010)
Editor's suggestion and Viewpoint in Physics, 3, 108 (2010) Debut of a hot “fantastic
voyager”
4. Natsuhiko YOSHINAGA, Jean-Francois JOANNY, Jacques PROST and Pilippe
MARCQ, “Polarity patterns of stress ﬁbers”, Physical Review Letters, 105, 238103(2010)
5. Takahiro SAKAUE and Natsuhiko YOSHINAGA, “Dynamics of Polymer
Decompression: Expansion, Unfolding and Ejection”, Physical Review Letters, 102,148302 (2009).
6. 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).

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 嶺澤

範行（みねざわのりゆき）【職名】 福井センターフェロー【所属】 京都大学福井謙一記念研究センター【研究室】 京都大学福井謙一記念研究センター 209 号室【直通電話】 075-711-7902【FAX】 075-781-4757【電子メールアドレス】 minezawa@fukui.kyoto-u.ac.jp【研究分野】 理論化学・計算化学【現在の研究課題】 時間依存密度汎関数法による非断熱遷移の解析【研究内容キーワード】 時間依存密度汎関数法・円錐交差・非断熱分子動力学【学歴】 2008 年 3 月京都大学大学院理学研究科化学専攻博士課程修了【学位】 2008 年 3 月京都大学理学博士【略歴】 2008 年 5 月米国アイオワ州立大学 (Mark S. Gordon 教授 )2011 年 10 月京都大学福井謙一記念研究センター・センターフェロー【所属学会】 アメリカ化学会【主な著書、学術論文】 1. A. Defusco, N. Minezawa, L. V. Slipchenko, F. Zahariev, and M. S. Gordon,“Modeling solvent effects on electronic excited states”, J. Phys. Chem. Lett. 2,（過去 5 年以内）
2184-2192 (2011).
2. N. Minezawa and M. S. Gordon, “Photoisomerization of stilbene: A spin-flip
density functional theory approach”, J. Phys. Chem. A 115, 7901-7911 (2011).
3. N. Minezawa, N. De Silva, F. Zahariev, and M. S. Gordon, “Implementation of
the analytic energy gradient for the combined time-dependent density functional
theory/effective fragment potential method: Application to excited-state molecular
dynamics simulations”, J. Chem. Phys. 134, article No. 054111 [12 pages] (2011).
4. S. Aono, N. Minezawa, and S. Kato, “Electronic spectra of coumarin-151 in polar
solvents: Linear response free energy approach”, Chem. Phys. Lett. 492, 193-197(2010).
5. N. Minezawa and M. S. Gordon, “Optimizing conical intersections by spin-flip
density functional theory: Application to ethylene”, J. Phys. Chem. A 113, 1274912753 (2009).

－ 50 －

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Ⅱ 博士研究員 (2011)【氏名】 Kunkun Guo【職名】 FIFC Fellow【所属】 Fukui Institute for Fundamental Chemistry【研究室】 Room 204【直通電話】 075-711-7838【FAX】 075-711-7838【電子メールアドレス】 guo@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/【研究分野】 Soft matter physics【現在の研究課題】 Phase separation of aqeuos two polymer system encapsulated by vesicle【研究内容キーワード】 Photo-functional molecules, Potential surfaces, non-adiatbatic transition【学歴】 June 2002, Master of Sci., ICCAS, China
June 2005, Doctor of Sci., Fudan University, China【学位】 Doctor of Science from Fudan University, China【略歴】 August. 2005, Postdoctoral Fellow, Max-Planck Institute for Colloid and Interface,
Germany【所属学会】 Chemical Society of China, American Physics Society【主な著書、学術論文】 1. Kunkun Guo, Wenjia Xiao, Dong Qiu, “Polymerization of actin ﬁlaments coupled（過去 5 年以内）
with adenosine triphosphate hydrolysis: Brownian dynamics and theoreticalanalysis”, J. Chem. Phys. 135(10):105101 (2011).
2. Kunkun Guo, Jianfeng Li, “Exploration of the Shapes of double-walled vesicles
with a conﬁned inner membrane” J. Phys.: Condens. Matter. 23:285103 (2011).
3. Kunkun Guo, Wenchi Han, “Growth of Dynamic Actin Filament via Brownian
Dynamics Simulations,” Acta Chimica Sinica, V69(02):145-152 (2011).
4. Kunkun Guo, JC Shillcock, R Lipowsky, “Treadmilling of Actin Filaments via
Brownian Dynamics Simulations”, J. Chem. Phys. 133(15)155105(20100
5. Jiafang Wang, Kunkun Guo, Lijia An, M. Mueller, ZG Wang, “Micelles of CoilComb Block Copolymers in Selective Solvents: Competition of Length Scales,”Macromolecules, 43, 2037(2010)
6. Kunkun Guo, Jiafang Wang, Feng Qiu, Hongdong Zhang, Yuliang Yang, “Shapes of
ﬂuid vesicles anchored by polymer chains”, Soft matter, 5:1646(2009).

－ 51 －

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Ⅱ 博士研究員 (2011)【氏名（ふりがな）】 河津

励 （かわつつとむ）【職名】 分子科学研究所 専門研究職員【所属】 総合研究部門【研究室】 福井謙一記念研究センター 206【直通電話】 075-711-7867【FAX】 075-781-4757【電子メールアドレス】 kawatsu@fukui.kyoto-u.ac.jp【ホームページ】 http://www.fukui.kyoto-u.ac.jp/ users/kawatsu/index.html【研究分野】 生物物理化学【現在の研究課題】 革命的ハイパフォーマンス・コンピューティング・インフラ (HPCI) の構築【研究内容キーワード】 電子移動、励起エネルギー移動、蛋白質科学、自由エネルギー計算【学歴】 1999 年 3 月
2002 年 2 月

名古屋大学理学研究科物質理学専攻博士前期課程修了
名古屋大学理学研究科物質理学専攻博士後期課程修了【学位】 2002 年 2 月

理学博士（名古屋大学）【略歴】 2002 年 3 月 デューク大学化学科 ポスドク
2005 年 9 月 ジョージア工科大学化学生化学科 ポスドク
2006 年 11 月 京都大学福井謙一記念研究センター JST フェロー2010 年 4 月京都大学工学研究科合成・生物専攻 特定研究員
2011 年 10 月自然科学研究機構分子科学研究所 専門研究職員【所属学会】 American Physical Society、日本生物物理学会【主な著書、学術論文】 1. T. Kawatsu, J. Hasegawa, “Excitation energy transfer in GFP-X-CFP model（過去 5 年以内）
peptides (X = amino acids): Direct Versus through-bridge energy transfers,” Int. J.
Quantum Chem. published online: 23 FEB 2012.
2. T. Kawatsu, J. Hasegawa, K. Matsuda, “Bridge-mediated excitation energy transfer
pathways through protein media: a Slater determinant-based electronic coupling
calculation combined with localized molecular orbitals,” J. Phys. Chem. A 2011,
115, 10814-10822.
3. J. Hasegawa, T. Kawatsu, K. Toyota, K. Matsuda, “Chemical-intuition based LMO
transformation simplifies excited-state wave functions of peptides,” Chem. Phys.
Lett. 2011, 508, 171-176.
4. T. Kawatsu, M. Lundberg, K. Morokuma, “Protein free energy corrections in
ONIOM QM:MM modeling: A case study for isopenicillin N synthesis (IPNS),” J.
Chem. Theory Comput. 2011, 7, 390-401.
5. M. Lundberg, T. Kawatsu, T. Vreven, M. J. Frisch and K. Morokuma, “Transition
states in the protein environment – ONIOM QM:MM modeling of isopenicillin N
synthesis,” J. Chem. Theory Comput. 2009, 5, 222-234.
－ 52 －

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Ⅲ 研究広報活動 (2011)

Ⅲ

研究広報活動Ϫ ◊✲ᗈሗάື
㸯㸬ⱝ࠸ே࡟㉗ࡿ⚟஭ㅬ୍ඛ⏕ࣀ࣮࣋ࣝ໬Ꮫ㈹ཷ㈹  ࿘ᖺグᛕබ㛤ㅮᗙ  ̿᭱㏆ࡢᇶ♏໬Ꮫࡢ㐍ᒎ̿
日時：平成２３年７月３０日（土）13:00-16:00

場所：京都大学福井謙一記念研究センター

３Ｆ大会議室プログラム
13:00-13:10

開会の挨拶

センター長 田中
13:10-13:55

福井謙一博士の生い立ちとノーベル化学賞までの軌跡：

副センター長14:10-14:55

功（京都大学工学研究科教授）

田中一義（京都大学工学研究科教授）

コンピュータで化学反応の世界を探るセンター リサーチリーダー
15:10-15:55

諸熊奎治

基礎化学から応用への展開

センター運営委員

今堀博（京都大学工学研究科教授）

・休憩時間や講座終了後に，福井先生記念の展示物を見学。

（この公開講座は、京都大学ジュニアキャンパス 2011の特別協賛ゼミとしても提供した）㸰㸬ி㒔኱Ꮫࢪࣗࢽ࢔࢟ࣕࣥࣃࢫ  ୰Ꮫ⏕ྥࡅࢮ࣑  ࠕ໬Ꮫ̿ࣇࣟࣥࢸ࢕࢔㌶㐨⌮ㄽ࡜㟁Ꮚィ⟬ᶵ࡛໬Ꮫࡀศ࠿ࡿ㸽ࠖ
日時：平成２３年９月１７日（土）14 時 30 分

榊

14:30-16:00

茂好（福井謙一記念研究センター リサーチリーダー）「原子、分子、電子の軌道、フロンテイア軌道理論」
14 時 55 分

長岡正隆（名古屋大学情報科学研究科教授）「福井謙一先生の思い出」

15 時 25 分

諸熊奎治（福井謙一記念研究センター リサーチリーダー）「コンピュータで化学反応の世界を探る」

15 時 40 分

センター内見学－ 53 －

fukui2011_01.indb 53

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Ⅲ 研究広報活動 (2011)

International
InternationalSymposium
Symposium
Symposium
for
for
for
International
Theoretical
Theoretical
TheoreticalChemistry
Chemistry
Symposium
Chemistry(FISTC)(FISTC)(FISTC)for Theoretical Chemistry (FISTC
㸱㸬Fukui
㸱㸬Fukui
㸱㸬FukuiInternational
㸱㸬Fukui
Place:
Place:
Place:Fukui
Fukui
FukuiInstitute
Institute
Instituteforfor
forPlace:
Fundamental
Fundamental
Fundamental
Fukui
Chemistry,
Chemistry,
Chemistry,
Institute
Kyoto
Kyoto
Kyoto
for University
Fundamental
University
University Chemistry, Kyoto Univers

Schedule:
Schedule:
Schedule:

Wednesday,
Wednesday,
Wednesday,AugustAugustAugustSchedule:31,
31,
31,1300:opening,
1300:opening,
1300:opening,
Wednesday,
lectureslectureslectures
Augustandandandbanquet
banquetbanquet31, 1300:opening, lectures and banquet
Thursday,Thursday,Thursday,September,
September,
September,1,1,
1,2011,
2011,
2011,9:00:
9:00:
9:00:
Thursday,lectures;lectures;lectures;
September,
1700:
1700:
1700:closing
closing
closing
1, 2011, 9:00: lectures; 1700: closing
banquet:banquet:banquet:Aug.
Aug.
Aug.31
31
31PM
PM
PM7:00-9:00
7:00-9:00
7:00-9:00 banquet: Aug. 31 PM 7:00-9:00

Organizers:
Organizers:
Organizers: Keiji
Keiji
KeijiMorokuma,
Morokuma,Morokuma,Shigeyoshi
Shigeyoshi
Shigeyoshi
Organizers:
Sakaki
Sakaki
Sakaki
Keiji Morokuma, Shigeyoshi Sakaki(詳細は資料編(詳細は資料編(詳細は資料編 3.
3.
3. Fukui(詳細は資料編
3. Fukui
Fukui
Fukui International
International
International
Symposium
Symposium
Symposiumforfor
for Theoretical
Theoretical
Theoretical
International
Chemistry
Chemistry
Chemistry
Symposium for Theoretical Chem
(FISTC)参照)(FISTC)参照)(FISTC)参照)(FISTC)参照)㸲㸬⚟஭ㅬ୍グᛕ◊✲ࢭࣥࢱ࣮ࢩ࣏ࣥࢪ࣒࢘
㸲㸬⚟஭ㅬ୍グᛕ◊✲ࢭࣥࢱ࣮ࢩ࣏ࣥࢪ࣒࢘
㸲㸬⚟஭ㅬ୍グᛕ◊✲ࢭࣥࢱ࣮ࢩ࣏ࣥࢪ࣒࢘
㸲㸬⚟஭ㅬ୍グᛕ◊✲ࢭࣥࢱ࣮ࢩ࣏ࣥࢪ࣒࢘
�京都大学福井謙一記念研究センターシンポ��ム�京都大学福井謙一記念研究センターシンポ��ム
第第第999�京都大学福井謙一記念研究センターシンポ��ム
第 9 �京都大学福井謙一記念研究センターシンポ��ム
日
日
日

時
時
時 2012
2012
2012年(平成年(平成年(平成2424
24年)
年)年) 111日
月
月
月666日
日
日
時

2012 年(平成 24 年) 1 月 6 日

場
場
場

所
所
所 京都大学福井謙一記念研究センター（3F
京都大学福井謙一記念研究センター（3F
京都大学福井謙一記念研究センター（3F場
所 京都大学福井謙一記念研究センター（3F
大会議室）
大会議室）
大会議室）
大会議室）

講
講
講

演
演
演 玉尾
玉尾
玉尾 皓平(理化学研究所
皓平(理化学研究所
皓平(理化学研究所
講 基幹研究所
基幹研究所
基幹研究所
演 玉尾 所長)
所長)
所長)
皓平(理化学研究所 基幹研究所 所長)

「深化
「深化
「深化
・
・
・
拡大を続ける有機元素化学
拡大を続ける有機元素化学
拡大を続ける有機元素化学
「深化
：
：
：
実験と理論の連携の舞台」
実験と理論の連携の舞台」
実験と理論の連携の舞台」
・拡大を続ける有機元素化学
11:00―12:00
11:00―12:00
11:00―12:00：実験と理論の連携の舞台」 11:00―
諸熊
諸熊
諸熊 奎治（福井謙一記念研究センター
奎治（福井謙一記念研究センター
奎治（福井謙一記念研究センター
諸熊 奎治（福井謙一記念研究センター
リサーチリーダー）
リサーチリーダー）
リサーチリーダー）
リサーチリーダー）「化学反応の理論研究：フロンティア理論から現在、未来へ」「化学反応の理論研究：フロンティア理論から現在、未来へ」「化学反応の理論研究：フロンティア理論から現在、未来へ」「化学反応の理論研究：フロンティア理論から現在、未来へ」
13:30―14:15
13:30―14:15
13:30―14:15
13:30―
平尾平尾
平尾 公彦（理化学研究所
公彦（理化学研究所
公彦（理化学研究所 計算科学研究機構
計算科学研究機構
計算科学研究機構
平尾 公彦（理化学研究所
機構長）
機構長）
機構長）
計算科学研究機構 機構長）
「コンピュータと福井先生」「コンピュータと福井先生」「コンピュータと福井先生」
ポスターセッション
ポスターセッション
ポスターセッション

懇親会（１F懇親会（１F懇親会（１F多目的ルーム）
多目的ルーム）
多目的ルーム）「コンピュータと福井先生」 14:15―15:00
14:15―15:00
14:15―15:00

ポスターセッション
15:30―17:20
15:30―17:20
15:30―17:20

15:30―17:20――― コーヒーブレイク
コーヒーブレイク
コーヒーブレイク ―――― コーヒーブレイク ―懇親会（１F 多目的ルーム）

14:15―

17:30―19:00
17:30―19:00
17:30―19:00

17:30―－ 54 －

fukui2011_01.indb 54

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Ⅲ 研究広報活動 (2011)����������
第 9 �福井センターセミナー
日時2012 年(平成 24 年) 3 月１6 日

場

所

京都大学福井謙一記念研究センター（3F 大会議室）

14:00－17:00

14：00－15：00 Shinkoh Nanbu (Sophia Univ., Tokyo)“Nonadiabatic dynamics in photochemical processes”
15：00－15：30

Yoshihide Nakao (FIFC)“Theoretical Study of Physical Properties in First-Row
Transition Metal Complexes”

16：00－17：00

Shoji Takada (kyoto Univ.)“Coarse-grained molecular simulasions of Large biomolecules :From theory to applications”

����������
(1) 科学技術フェスタ in Kyoto 2011
榊2011 年(平成 23 年) 12 月１7�1� 日

茂好リサーチリーダが国立京都国際会館にて開催された「科学技術フェスタ in

Kyoto 2011」に出展した。コンピュータを使う化学の研究について、特に、金属などに現れる d 電子、d 軌道の面白さを伝えた。
(2) ウォークイン

サイエンス

2012 年(平成 24 年) 2 月 2��27 日

研究部第一のオフィスアシスタントの三木さん、堀さん、延山さんが理学研究科・
社会交流室が主催する「ウォークイン

サイエンス」に出展し、Zest 御池河原町広場にて理論化学のデモンストレーションを行った。
(3) 京都大学アカデミックデイ
諸熊2012 年(平成 24 年) 3 月 10 日

奎治リサーチリーダーが「京都大学アカデミックデイ」に出展し、理論化学の面白さを伝えた。

����������������
2011 年(平成 23 年)が福井謙一博士のノーベル化学賞受賞 30 周年にあたるため、これを節目として本センター玄関ロビーに博士ゆかりの文物の展示コーナーを設置した。コーナーでは先生が使用された机、椅子、ノーベル賞メダル・賞状(複製)、研究ノート・－ 55 －

fukui2011_01.indb 55

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Ⅲ 研究広報活動 (2011)

メモ、写真などを展示し、常設展示として一般に公開している。
2012 年(平成 24 年) 1 月 6 日に同コーナーの序幕式を行った。
福井謙一��記念展示コーナー�幕式
日時

2012 年(平成 24 年) 1 月 6 日（10:00－10:45）

場

所

京都大学福井謙一記念研究センター（1F 展示コーナー）

・開会の辞

田中

功（福井謙一記念研究センター長）

・挨

拶

江﨑

信芳（京都大学理事・副学長）

・挨

拶

小森

悟（京都大学 工学研究科長）

・テープカット・ご見学－ 56 －

fukui2011_01.indb 56

12.12.12 0:51:54 PM

Ⅳ 研究業績 (2011)

Ⅳ

研究業績

���

１．専任教員

��

�合研究部� ���（平成 23 年 10 月 1 日から）1� 今年度の研究の要�
生体関連分子の励起状態と機能に関する理論的研究【���】� これまで、周辺の分子環境に応じて光吸収・発光エネルギーを大きく変化させる光機能性蛋白質について、理論化学計算によりメカニズムを解析してきた。その結果、色素の電子励起に伴う電荷分布の変化と、蛋白質の偏った静電ポテンシャル分布の協同効果により励起エネルギー準位が変化することを明らかにした。他方で、いくつかのレチナール蛋白質では、周辺アミノ酸の電子状態が励起エネルギーに寄与することを見出している。周辺環境との協同効果による化学現象の制御は、化学における重要なテーマであり、これを記述する理論化学を発展させる必要がある。今
年度は、蛋白質の電子的効果を解析するために、新たに分子軌道の局在化法を開発した。これにより、意図した形状や領域に局在化した分子軌道を得ることが可能になった。今後、色素の励起に対して、蛋白質や溶液における分子環境がどのように応答するかを局在化軌道を用いて解析を進める予定である。また、この方法を応用し、励起エネルギー移動における super-exchange 機構について移動経路の解析を行なった。
ポルフィリン化合物の励起状態に関しても研究を継続的に進めている。今年度は、光化学系Ⅱの光合成反応中心に存在するクロロフィル集合体が示す特異的な光吸収特性に関して、大規模な励起状態計算に基づき解析を行ない、光合成細菌との比較を行なった。また、ポルフィリンの異性体であるポルフィセン化合物について、置換基の導入による光吸収エネルギーと酸化・還元ポテンシャ
ルの特異的変化の起源について解析を行なった。
【ཧ↷㌶㐨ࢆ⏝࠸ࡿᒁᅾ໬ἲࡢ㛤Ⓨ㸸ບ㉳≧ែ࡬ࡢᛂ⏝】これまで局在化分子軌道（LMO）の開発やその応用研究が多く報告されているが、意図した領域に意図した形状の LMOを与える方法はあまり知られていない。本研究では、
minimum orbital deformation (MOD)法と Pipek-Mezey(PM)
法を組み合わせた分子軌道の局在化法を提案し、ペプチド分子の LMO を求め、励起状態の計算に応用した。
図１a のように領域を分割し、フラグメント 1-3 については参照軌道を使用して MOD 法により、その他の部分は PM 法
により局在化した。図１cd に示すように、四角枠内に示した参照軌道によく一致した局在化軌道が得られた。また、
PM 法を用いて局在化した部分についても、ペプチド結合に局在した非共有電子対やπ軌道が得られた(図 1be)。

Fig. 1(a) モ デ ル ペ プ チ ド の 構 造 とfragment への分割。(b-e)本方法による
局在化軌道。四角枠内は各 fragment において用いられた参照軌道。

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Ⅳ 研究業績 (2011)

次に、この局在化軌道を用いて、励起状態の計算を行(a)CMO を用いた場合った。計算には CIS 法を用いた。図 2a には、非局在化した CMO を用いて得られた励起状態の波動関数について示す。局所励起や電荷分離状態などの励起配置が混合し、複雑な電子構造が得られる。図 2b には、本方法の局在化(b)LMO を用いた場合

軌道を用いて得られた波動関数を示す。その結果、同状態が一つのアミノ酸残基の局所励起であることが明らかになる。非局在化した CMO を用いると、局所励起を記述するための軌道回転に相当する電子励起が混合し、波動関数を複雑化する原因になることがわかる。

Fig. 2 モデルペプチドの第一励起状態に お け る CIS 波 動 関 数 の 主 配 置 。
(a)CMO と(b)LMO を用いた場合。

�局在化軌道を用いた励起エネルギー移動経路の解析�
励起エネルギー移動(EET)速度定数は、ドナーとアクセプターの励起状態間の electronic
coupling, TIF の大きさの自乗に比例する。従って、TIF を計算・解析 することで EET のメカニズムを理解できる。本研究では、局在化した分子軌道を用いて、TIF を計算する手法を開発した。また、
EET 経路を解析するための tunneling configuration flux に基づく手法を開発した。これにより、
励起エネルギーの伝播経路に関する詳細な解析が可能となり、励起移動に用いられる軌道ペアの実
空間的、エネルギー空間的な分布を理解することが可能である。
方法論の確認のために行った計算では、図 3 に示したペプチド化合物を用いた。Fragment 1-4
から二つを選択し、ドナー・アクセプター対として TIF を計算した。今回のモデルペプチド分子では、計算された TIF におけるブリッジを介する間接項の寄与は、ドナー―アクセプター間の直接項と比べて小さかった。直接項の値は、クーロン相互作用の多極子展開における最低次でよく近似でき、双極子―双極子相互作用に駆動される Forster 機構によることが分かった。他方でドナーとア
クセプターの配向によっては間接項が支配的になる場合も確認できた。また、間接項において EET
経路を解析したところ、ブリッジのエキシトン状態を介した経路が主要であった。具体的には、図4 に示したように、ペプチド結合部の π-π*遷移などの寄与が明らかになった。今回開発した局在化
法では、参照軌道によく一致するように軌道を変換するので、対象となる系の軌道を化学的直観によく合致するものに変換でき、EET 経路を直観的に理解することが可能となった。

Fig. 3 モデルペプチド化合物の構造と領域分割のために設定した境界。

Fig. 4 局在化分子軌道を用いて計算した、ペプチド結合を介在した励起移動経路。数値は全体の流束に対する比率。

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�PSII 反応中心の励起スペクトルと分子間相互作用の変化の起源に関する��的研究�
光合成色素蛋白質複合体である PSII の反応中心(RC, 図 5 赤線)と紅色細菌反応中心(bRC, 図 5青線)は、進化的に同一の起源を持ち、構造が類似するにもかかわらず、光吸収スペクトルの形状や励起電子移動メカニズムが大きく異なる(図 6ab)。本研究ではシアノバクテリア T. elongatusの RC におけるクロロフィル六量体（図 5）に関する量子化学計算を行い、励起状態の電子構造を解析し、観測される光吸収スペクトルを帰属した。
図 6 に示したように、PSII RC と bRC の計算スペクトルは、実験的に観測される光吸収スペクト
ルを定性的に再現できている。PSII の励起スペクトルにおいて最も振動子強度が大きい励起状態は、
ChlD1 と PD2 の第一励起状態のエキシトンカップリングによるものであり、ChlD1, PD2 の遷移双極子モーメントが互いに強め合うような相互作用がみられた。従来からスペシャルペアと呼ばれる PD1, PD2からなる二量体は、bRC のような強い相互作用は無く、この点において植物と細菌の反応中心の電子構造の違いが明らかになった。また、強い二量体形成が失われたことにより、PSII では P のイオ
ン化ポテンシャルが増加した。これにより、水を酸化するためのエネルギーを獲得できたと考えられる。即ち、PSII における特異的な光吸収スペクトルの変化は、イオン化ポテンシャルの増大と同じ起源を持つことが分かった。
さらに、詳細な解析を行なった結果、PSII RC と bRC との差異の起源は、色素の空間配置と蛋白質の構造に起源を見出した。更に、分子軌道とそのエネルギー準位を比較した。PSII では P が非対称に配向するため(図 5 青)、分子間の結合性と反結合性の軌道間相互作用が互いに打ち消し合い、二量化の効果が小さくなることが分かった。他方で、対称的な紅色細菌型配向(図 5 赤)では PD1 とPD2 の HOMO どうし、LUMO どうしが相互作用しやすいので、HOMO-LUMO ギャップが著しく低下することが分かった。
また、PSII bRC と bRC で PD2 周辺の蛋白質の構造を比較し、PD2 の配向の起源を検討した。その結果、PSII における PD2 の色素配向の変化は D2 subunit の CD helix の変化とよく相関があることが分った。従って、この変化に対応するアミノ酸配列の自然変異が、励起状態の電子構造に影響を及ぼし、結果として水を参加する能力を獲得したと考えられる。

Fig. 5

PSII(緑)と紅色細菌(赤)の色素六量体．

Fig. 6 (a)PSII RC (b)bRC の光吸収スペクトルについて、実験結果と計算結果。励起状態間の分子間相互作用を考慮するため、クロロフィル六量体を超分子として計算し、蛋白質は静電ポテンシャルとして考慮した。計算は CIS/6-31G*レベル。

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Ⅳ 研究業績 (2011)

�トリフルオロメチルポルフィセン化合物における特�的スペクトルシフトの解析�
近年合成された CF3 基置換ポルフィセン化合物は、無置換ポルフィセン化合物と比較して、第一励起状態のエネルギー準位が約 0.25 eV もの赤方シフトを示すことが知られている。高波
長側にシフトしたポルフィリン化合物は光力学
療法への応用が期待されているため、励起エネ
ルギーを制御する手法として CF3 置換効果の解明が必要とされた。
このシフトの原因として、CF3 基による電子的効果と構造歪み効果が考えられた。SAC-CI 計算を行いった結果、0.30 eV の赤方シフトが得られ、定量的に実験結果を再現できた。次に、この結果を解析するため、テトラフルオロポルフィセ
ンにおける構造歪みを無置換ポルフィセンに導入したところ、0.23 eV の赤方シフトが得られた。
従って、全シフトにおいて、構造歪みが 0.23 eV、
電子的効果が 0.07 eV の寄与があることが明らかになった。このような構造歪みの導入がポルフィセン化合物の光吸収スペクトルのみでなく、 Fig. 7 励起に関与する軌道エネルギ―の構造依存
参加還元特性にも変化が現れることが理解できた。

性。ポルフィセン(H2Pc), テトラメチルポルフィセン (H2PcCH3), テ ト ラ フ ル オ ロ ポ ル フ ィ セ ン(H2PcCF3), H2PcCF3 の構造歪を導入した H2Pc.。

2. ��(1) J. Hasegawa, T. Kawatsu, K. Toyoya, and K. Matsuda“Chemical-intuition based LMO transformation simplifies excited-state wave
functions of peptides”
Chem. Phys. Letters, 508(1-3), 171-176 (2011).
(2) Y. Kitagawa, K. Matsuda, and J. Hasegawa“Theoretical Study of the Excited States of the Photosynthetic Reaction
Center in Photosystem II: Electronic Structure, Interactions, and Their
Origin”
Biophys. Chem. 159(2-3), 227-236 (2011).
(3) T. Kawatsu, K. Matsuda, and J. Hasegawa“Bridge-Mediated Excitation Energy Transfer Pathways through Protein Media:
a Slater Determinant-Based Electronic Coupling Calculation Combined with
Localized Molecular Orbitals”－ 60 －

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Ⅳ 研究業績 (2011)

J. Phys. Chem. A 115(39), 10814-10822. (2011).
(4) J. Hasegawa and K. Matsuda“Theoretical study of the excited states and the redox potentials of
unusually distorted β-trifluoromethylporphycene”
Theoret. Chem. Acc. 130(2-3), 175-185 (2011).
(5) Y. Yamamoto, J. Hasegawa, and Y. Ito“Kinetic investigation on carbamate formation from the reaction of carbon
dioxide with amino acids in homogeneous aqueous solution”
J. Phys. Org. Chem., 25(3), 239-247 (2012).
(6) T. Sakano, J. Hasegawa, K. Higashiguchi, and K. Matsuda“Chronological Change from Face-On to Edge-On Ordering of Zinc
Tetraphenylporphyrin at Phenyloctane-HOPG Interface”
Chem. Asian J. 7(2), 394-399 (2012).
(7) T. Kawatsu and J. Hasegawa“Excitation Energy Transfer in GFP-X-CFP Model Peptides (X=amino acids):
direct vs. through-bridge energy transfers”
Int. J. Quantum Chem. (2012) In press.
(8) J. Hasegawa, K. Fujimoto, and H. Nakatsuji“Color tuning in human cone visual pigments: the role of the protein
environment”
Progress in Theoretical Physics and Chemistry (2012) In press.
3. ��(1)Jun-ya HASEGAWA, Kazuhiro FUJIMOTO, and Hiroshi NAKATSUJI,“Color tuning in photo-functional proteins”
ChemPhysChem 12(17), 3106-3115 (2011).
4. ����
(1) J. Hasegawa“Excited states of photo-functional proteins: SAC-CI study”(Invited talk)The 4-th Japan-Czech-Slovakia Symposium on Theoretical Chemistry, Prague,
Czech, 2011.5.18-20.
(2) J. Hasegawa“Laser control of reactions of photo-switching molecules”(Invited talk)
BioInformatics in Torun - BIT11, N. Copernicus University, Torun, Poland,
2011.6.2-4.
(3) J. Hasegawa－ 61 －

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Ⅳ 研究業績 (2011)“Excited states of photo-functional proteins”(Invited talk)
Fukui International Symposium for Theoretical Chemistry, Kyoto, 2011.8.1-9.1.
(4) J. Hasegawa“Theoretical study on the excited states and molecular interactions ofphoto-functional proteins”(Invited talk)The 14-th Asian Chemical Congress, Bangkok, Thailand, 2011.9.2-4.
(5) J. Hasegawa“Excited states of photo-functional proteins: SAC-CI study”(Invited talk)The 16-th Quantum Systems in Chemistry and Physics, Kanazawa, 2011.9.12-17.
(6) 長谷川淳也「光生物学システムの励起状態と機能への理論的アプローチ」（依頼講演）
日本化学会第92春季年会（第２次先端ウオッチング）、慶應義塾大学、平成24年3月25-28日．
(7) 長谷川淳也「光機能性蛋白質における励起状態と分子間相互作用」(招待講演)
計算科学研究センター・ワークショップ「バイオサイエンスに対する計算分子科学
からのアプローチ」、分子科学研究所、平成24年1月24, 25日.
(8) 長谷川 淳也「光機能性蛋白質のカラーチューニング」（依頼講演）
大阪大学蛋白質研究所セミナー“タンパク質科学の未来を語る ―実験・理論研究
者の対話－”，大阪大学，2011年11月21,22日．
(9) 長谷川 淳也、河津 励、松田 建児
参照軌道を用いた分子軌道の局在化法：励起状態への応用(口頭発表)
第5回分子科学討論会、札幌、9月20-23日, 2011.
(10) 長谷川 淳也、河津 励、松田 建児
参照軌道を用いる局在化法：励起状態への応用(Poster)
第14回理論化学討論会、岡山大学、5月12-14日，2011．

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Ⅳ 研究業績 (2011)

中� ��
���
�� 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と梯子型π共役分子の固体中の光物性について研究を行った。
䛆ጞ䜑䛻䛇㻌 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。
今年度はオキサラト架橋した多核金属錯体の磁気異方性とピラゾラト架橋した多核金属錯体の固体中の発光を量子化学計算により明らかにした。また、梯子型π共役化合物の固体中の発光について、周期的境界条件を用いた量子化学計算により明らかにした。
䛆䜸䜻䝃䝷䝖ᯫᶫከ᰾㔠ᒓ㘒య䛾☢Ẽ␗᪉ᛶ䛻㛵䛩䜛◊✲䛇㻌 金属間に強磁性相互作用を持つ多核金属
錯体は、高密度磁気記憶媒体として応用が期待されている。Scheme 1 に示したオキサラト架橋したCr(III)-Co(II)二核錯体(1)と Cr(III)-Co(II)-Cr(III)三核錯体(2)はそれぞれの金属中心に S = 3/2 のスピンが立ち、各金属中心の局所スピン間にも相互作用がある。また、2は低温で大きな磁気異方性が存在することが分かっている[1]。本研究では、金属間のスピン相互作用を理論計算により解明して、
1

磁気異方性の本質を明らかにした。
B3LYP 法で高スピン状態の構造最適化を行い、高スピン状態と低スピン状態の相対エネルギーを Broken Symmetry(BS)法で計算した。局所スピンの組み合わせから考えられる全てのスピン多重度の 1 点計算に State-averaged CASSCF 法と MCQDPT 法を用いた。
基底関数は Cr, Co に Stuttgart-Dresden の ECP と基底関数を、その

N

N
O
O

O

O
O

O

Cr
N

O
N

Co
O

O
O

O
O

Cr
N

2

O

O
O

O

N

Scheme 1. オキサラト架橋多核金属錯体

他の原子に cc-pVDZ を使用した。磁気異方性を明らかにするために、Spin-Orbit Coupling(SOC)ハミ
ルトニアンに外部磁場によって誘起される項を加えて各状態の計算を行い、誘起磁場の大きさを評価した。B3LYP 計算では Gaussian 09 を、その他の計算では GAMESS を用いた。
計算により得られた J 値を Table 1 に示した。1 と 2 は共に高ス
ピン状態が最も安定で、金属間の局在スピンには非常に弱い強磁性相互作用が存在する。B3LYP 計算の結果から山口らの方法[2]でJ 値を評価すると、1 では 2.18 cm-1 となり、実験値の 2.16 cm-1 と良く一致した。CASSCF 計算を用いて計算した結果は 0.25 cm-1 と実験値や B3LYP 法と比べて非常に小さい値となった。次に、低温

Table 1. J value (cm-1)
Method

1

2

B3LYP

2.18

2.56

CASSCF

0.25

0.23

MCQDPT

0.74

Expt.[1]

2.16

1.81

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Ⅳ 研究業績 (2011)

部の磁気異方性を解明するために、外部磁場による項を加えた SOC 計算を行い、ボルツマン分布を用いて温度と磁化率(M)を調べた。温度磁化率曲線は CASSCF 計算で得られ た J 値で は 実 験 を再 現 せ ず、Figure 1 に示したように B3LYP 計算で得られた J 値の場合によく再現した。Figure 2 に 2 に対して x, y, z 軸

Figure 1. 温度-磁化率曲線

Figure 2. 2 の磁気異方性

方向から外部磁場をかけた場合の温度-磁化率曲線を示した。10 K 以下の低温では金属間で強磁性相互作用したスピンが x 軸方向に向いていることが明らかとなった。
䛆䝢䝷䝌䝷䝖ᯫᶫከ᰾㔠ᒓ㘒య䛾ᅛయ୰䛾Ⓨග䛻㛵䛩䜛◊✲䛇 リン光性の錯体は量子収率が高いことが知られており、発光デバイスへの応用が期待されている。[Pt2M2(Bpym)2(Bupz)4](PF6)2 (M = Au(3),Ag(4)) (Bpym = 2,2'-Bipyrimidine, Bupz = 3-tert- butylpyrazole)は特徴的なリン光を示す[3]。3 のリン光
スペクトルは π 共役系の振動準位に由来する微細構造を持ち、4 のスペクトルも 150 K 以下で同様の微細構造を持つ。本研究では隣接するカウンターイオンと錯体の影響を考慮した量子化学計算を行い、固体中で発光する機構を理論的に解明した。
Pt, Au, Ag には Christiansen の有効内殼ポテンシャルと基底関数を、配位子には cc-pVDZ を用いた。構造最適化とエネルギーの評価には B3LYP 法を用いた。固体中の環境を再現するように隣接イオンや錯体の影響を点電荷で表現したモデル(固体モデル)を用いて構造最適化を行い、固体中の発光スペクトルを評価した。点電荷は NAO(Natural Atomic Orbital)法で決定し、

M
Pt

Pt

M

固体モデルでの構造最適化では Buckingham Potential を用いた。全ての計算
は Gaussian 09 で行った。
カウンターイオン無しで錯体のみの理論計算から、3 と 4 の発光は LLCT

Figure 1. 固体モデル(π*(Bpym) → π(Bupz))であり、発光エネルギーはそれぞれ 2.33 eV, 2.23 eV となった。しかし、LLCT
では振動準位に由来する微細構造が見られることは考えられず、実験の発光スペクトルと矛盾する。
3 と 4 の基底状態の最適化構造での M-M 間距離は、X 線構造のものと比べそれぞれ 0.39 Å, 0. 30 Å
長くなり、Bupz の向きは最適化構造と X 線構造とでは異なっていた。従って、固体中での錯体の電子状態を評価するには、隣接するカウンターイオン PF6- や錯体の効果を考慮した固体モデルで電子状態を考える必要がある。始めに、錯体に隣接する 12 個の PF6- の P 中心のみ点電荷を置いたモデル(Figure 1)で、点電荷を 0 から-1 まで変化させた計算を行った。点電荷を強くするに従い、1
重項と 3 重項の全エネルギーは共に上昇し、3 と 4 の 2 状態間のエネルギー差も 0.07 eV, 0.10 eV とそれぞれ上昇した。3 と 4 の T1 状態では LLCT と MLCT の励起状態をとり、カウンターイオンに近い Bpym(π*)に電荷が移動するため、電荷移動型の励起状態は不安定になる。また、錯体の NAO
電荷は点電荷の変化に伴い大きく変化したので、更に外側の錯体の電荷を考慮したモデルを考えた。
錯体に隣接する PF6- を NAO 電荷で表現し、点電荷を隣接する錯体の中心に置いたモデルで、点電－ 64 －

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Ⅳ 研究業績 (2011)

Table 2. Emission Energies (eV)
錯体のみ
固体モデル
計算を行ったところ、錯体の
MLCT LLCT π-π*
MLCT LLCTNAO 電荷の変化は小さかった。
1
2.44 2.33 2.37
2.44―
この電荷を隣接する錯体の電2― 2.23 2.20―
2.62
荷として用いて、固体モデル
荷を 0 から 2 まで変化させた

Exp.[3]
2.52
2.40

π-π*
2.32
2.29

中で S0, T1 状態の構造最適化を行って、発光エネルギーを評価した。Table 2 に示したように、固体
中では 3 と 4 は LLCT や MLCT よりも π-π*遷移の励起状態がエネルギー的に安定となった。固体モデルを導入することで、3 と 4 のリン光は π*-π 遷移由来の発光であることが明らかになった。
䛆ᲓᏊᆺ䃟ඹᙺ໬ྜ≀䛾ᅛయ୰䛾Ⓨග䛻㛵䛩䜛◊✲䛇㻌 多環式骨格を含む Scheme 2 に示すような梯子型 π 共役系分子は平坦で硬い分子構造を持ち、非常に安定で秩序だった結晶構造をとることが知られている[4]。また、π 共役系にヘテロ元素を導入して電子状態を制御できるため、新しい有機エレクトロニクス材料として非常に注目されている。しかしながら、固体中の π 共役化合物の発光に関して理論計算はほとんど行われておらず、設計の面からも電子状態の解明が求められている。本研究では梯子型 π 共
役分子について、ヘテロ元素の寄与を明らかにし、気相中と固体中の安Scheme 2定構造を求めることで、吸収・発光エネルギーを明らかにした。

気相中の計算では cc-pVDZ を基底関数として用いた。B3LYP 法及び TD-B3LYP 法で構造最適化を行い、励起エネルギーは TD-BLYP 法と TD-B3LYP 法、GMCPT 法で求めた。計算パッケージとして GMCPT 法のみ GAMESS を用い、他は全て Gaussian 09 で行った。固体中の構造最適化は CPMD
パッケージで平面波基底、擬ポテンシャル及び周期的境界条件を用いて行った。ただし、固体中の励起エネルギーは気相中と同様に Gaussian 09 によって TD-B3LYP 法で評価した。
気相中における吸収・発光エネルギーについて TD-BLYP 法、TD-B3LYP 法、GMCPT 法で求めた結果を Table 3 に示した。この吸収・発光には HOMO-LUMO 間の遷移が大きく寄与しているため、S1 状態の最適化構造はキノイド型となり、発光エネルギーは約 0.4 eV と大きくストークスシフト
する。THF 中の吸収エネルギーの実験値は 2.94 eV であるが、TD-BLYP 法は吸収エネルギーを小さく見積もり、GMCPT 法は計算コストを抑えるため励起配置の制限を課したので吸収エネルギーを大きく見積もった。従って、吸収・発光エネルギーの評価には THF 中の実験値と比較的よく一致した TD-B3LYP 法を用いることにした。
ケイ素原子が π 共役系に与える影響を調べたところ、LUMO で σ*(Si-H)の反結合性相互作用が π共役系に寄与するため、吸収・発光エネルギーを約
0.2 eV 低下させることが示された。また、ケイ素同士の位置が近い方が吸収・発光エネルギー共に小さくな

Table 3. 気相中の吸収・発光エネルギー(eV)
TD
TD
Exp.
GMCPT
-BLYP -B3LYP
in THFることが明らかになった。固体中における S0 状態のAbsorption

2.60

2.96

3.40

2.94

構造は気相中とほぼ同じであり、吸収エネルギーもほEmission

2.26

2.53

2.96

2.81

とんど変わらなかった。結晶構造が三斜晶をとるため、CPMD パ
ッケージでは S1 状態の構造最適化が不可能であり、振動子強度が得られない。側鎖を水素に置換した分子について、T1 状態の最適化構造がそれぞれ Gaussian 09 と CPMD パッケージでほぼ同

Table 4 吸収・発光エネルギー(eV)in solid

Exp. in solid

Absorption

2.90

―

Emission

2.41

2.61

－ 65 －

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Ⅳ 研究業績 (2011)

じであること、気相中の S1 状態及び T1 状態の構造が大きく変わらず、吸収・発光エネルギーも近い値をとることを確認した。よって、固体中の S1 状態の構造は T1 状態の構造を代用することにして、固体中の吸収・発光エネルギーを Table 4 にまとめた。固体中の励起状態の構造は気相中と同様にキノイド型をとり、固体中の発光エネルギーは約 0.5 eV と大きくストークスシフトすることが明らかになった。今後、励起状態の構造緩和を明らかにするために、CPMD 法により解析する予
定である。
䛆ᩥ⊩䛇
[1] J. Vallejo, I. Castro, J. Ferrando-Soria, M. del Pino Dénis-Hernandez, C. Ruiz-Pérez, F. Lloret, M. Julve, R.
Ruiz-García, J. Cano, Inorg. Chem., 50, 2073 (2011).
[2] K. Yamaguchi, T. Tsunekawa, Y. Toyoda, T. Fueno, Chem. Phys. Lett., 143, 371-376 (1988).
[3] K. Umakoshi (private communication).
[4] H. Yamada, C. Xu, A. Wakamiya, S. Yamaguchi, Macromol Chem. Phys. 210, 904-916 (2009).

�� �文(1) Hideo Ando, Yoshihide Nakao, Hirofumi Sato, Masaaki Ohba, Susumu Kitagawa, Shigeyoshi
Sakaki,"Theoretical study on high-spin to low-spin transition of {Fe(pyrazine)[Pt(CN)4]}: Guest-induced
entropy decrease”
Chem. Phys. Lett. 511, 399-404 (2011).
(2) Yusaku I. Kurokawa, Yoshihide Nakao, Shigeyoshi Sakaki,“Theoretical Study of Inverted Sandwich Type Complexes of 4d Transition Metal Elements:
Interesting Similarities to and Differences from 3d Transition Metal Complexes”
J. Phys. Chem. A 116, 2292–2299 (2012).
(3) Yoshihiro Matano, Kazuaki Matsumoto, Hironobu Hayashi, Yoshihide Nakao, Tatu Kumpulainen,
Vladimir Chukharev, Nikolai V. Tkachenko, Helge Lemmetyinen, Soji Shimizu, Nagao Kobayashi,
Daisuke Sakamaki, Akihiro Ito, Kazuyoshi Tanaka, and Hiroshi Imahori,“Effects of Carbon–Metal–Carbon Linkages on the Optical, Photophysical, and Electrochemical
Properties of Phosphametallacycle-Linked Coplanar Porphyrin Dimers”
J. Am. Chem. Soc. 134, 1825–1839 (2012).
(4) Ken Saito, Yoshinori Eishiro, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki,“Oscillator strength of symmetry-forbidden d-d absorption of octahedral transition metal complex:
theoretical evaluation.”
Inorg. Chem. 51, 2785-2792 (2012).

�� ��発�(1) 中尾嘉秀、竹中裕喜雄、佐藤啓文－ 66 －

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Ⅳ 研究業績 (2011)「第一原理分子動力学法によるサーモクロミック銅(II)錯体に関する理論的研究」
第14回理論化学討論会, 岡山, 2011/5/14, 3E5b(2) Yoshihide Nakao“Theoretical Study of Structures and Absorption Spectra of Thermochromic

Copper(II) Complex”

Fukui International Symposium for Theoretical Chemistry (FISTC), Kyoto, 2011/8/31(3) 中尾嘉秀「貨幣金属を含んだ多核金属錯体の発光現象に関する理論研究」
第61回錯体化学討論会, 岡山, 2011/9/18, S2-6
(4) 成田真弘、佐藤啓文、中尾嘉秀「梯子型π共役化合物の固体中の発光に関する理論研究」
日本化学会第92春季年会, 2012/3/25, 1A4-10(5) 野口純樹、佐藤啓文、中尾嘉秀「オキサラト架橋した多核金属錯体の磁性に関する理論的研究」
日本化学会第92春季年会, 2012/3/25, 1A4-32

�� �の�
(1) 中尾 嘉秀「CPMD法による金属錯体のダイナミクス」
化学反応経路探索シンポジウム, 北海道, 2011/9/24(2) 中尾嘉秀、竹中裕喜雄、佐藤啓文「第一原理分子動力学法によるサーモクロミック銅(II)錯体に関する理論的研究」
第9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, 2012/1/6, 41(3) Yoshihide Nakao“Theoretical Study of Physical Properties in First-Row Transition Metal Complexes”
第9回福井センターセミナー, 京都, 2012/3/16－ 67 －

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Ⅳ 研究業績 (2011)�������
�����

��

��

International Relationship Office

Program-specific Associate Professor Toshimasa ISHIDA

1. Summary of the research of the year
(1) A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin
Rhodopsin (Rh) has 11-cis retinal as chromophore and is the photosensitive chemical found on theoutersegment of rod-like cells in the retina, the light-sensing structure of the eye. Isorhodopsin(isoRh) is an Rh analogue that contains 9-cis retinal embedded in the same opsin environment. Bothare 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 fs, tisoRh = 600 fs) and more efficient (quantum yield:
ΦRh = 0.65, ΦisoRh = 0.22). We carried out non-adiabatic ab initio dynamics calculations on the twomolecules.
The

experimental

photoisomerization

period and bathoRh quantum yield werereproduced

reasonably.

Onedifferences

betweensimulation

the

of

slightandexperiments are due to the failure of thechosen QM/MM treatment to reproduce a ~0.2
kcal mol-1 barrier at the isoRh excited state
reported in experiments. In our previous
calculation, we found a 10 kcal mol-1 barrier atthe excited-state potential energy surface of an
isoRh model system that caused trapping oftrajectories. Even a tiny barrier in the present

Figure 1. Change in length of the active bond -Cn-Cn+1against the absolute value of the dihedral angle
Cn-1-Cn-Cn+1-Cn+2 for typical (a) Rh (n = 11) and (b)isoRh (n = 9) trajectories leading to the all-trans form.
The solid and dashed lines show that trajectories are in
the excited and ground states and the black triangles
correspond to transition from the excitated state to theground state.

case would have slowed down the photoisomerization by trapping the trajectories in the excitedstate and yield a quantitatively accurate timescale and quantum yield. Figure 1 shows the diagramof the active twist angle and the length of the active bond for five typical trajectories for Rh andisoRh. Fast and straightforward dynamics in Rh is shown in Figure 1a whereas complicatedexcited-state dynamics is evident in the isoRh case in Figure 1b. Why is the isoRhphotoisomerization more difficult compared to that of Rh? One reason is the atomic displacements
required by the chromophore at the excited state potential energy surface to reach the conical－ 68 －

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Ⅳ 研究業績 (2011)

intersection region. Shown in Figure 2 is a superimposed image of the S0 optimized geometry andthe geometry adapted by the chromophore at the crossing region. The pocket that contains theretinal chromophore is similar in shape for both the Rh and isoRh case. Opsin residues Thr118 andTyr268 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 is more difficult compared tothat of Rh because of at least two reasons: (1) the isoRh isomerization requires more space than thatof 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.
Another
acceleration

reasonof

would

retinal

be

atoms

the

initialinducedbysurrounding residues. The initial force between
two atoms for a few retinal-opsin atom pairs islisted in Table 2. Cys187 and Tyr268 are closeenough to the chromophore to significantly
influence the isomerization. For example, for theatomic distance between the C12 hydrogen in
retinal and the oxygen in Cys187, the projectedinter-atomic force for Rh is about 15 times larger
than the counterpart for isoRh. Also, a five-folddifference is found for the force between retinal
C10 and Tyr268. Such differences partially explain
the discrepancy in the rate and efficiency of thecis-trans isomerization between the Rh and isoRhchromophores.
Comparison with the previous gas-phasesimulations reveals three other consequences
shown below.
The protein causes (almost) one-way
twist of the active angle. As shown in Figure3(a), all of the Rh trajectories go through only
one MECI region with clockwise-twisted 9 andcounterclockwise-twisted

11.

This

MECI

branches towards the formation of bathoRh (andthe regeneration of the reactant). The relaxationof the excited state of isoRh, on the other hand,

Figure 2. 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 pocketthat contains the chromophore. The pocket surface is theoverlapped envelope of amino residues surrounding theretinal chromophore, which is generated using the S0
optimized geometry wherein the retinal chromophore is
artificially removed.

goes through two MECI regions, shown in Figure 3(b). Most of trajectories from isoRh go through－ 69 －

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Ⅳ 研究業績 (2011)

the MECI region with 9 ~ -90° andclockwise-twisted 11, which is
shown

as

CI(isoRh->BathoRh).

This MECI is responsible for all ofbathoRh

generation.

trajectories

goA

throughfew
another

MECI

region(CI(isoRh->9,11-dicisRh)),which

is responsible for 9,11-dicisRh. Thus,

Figure 3. Diagram of the twist angles of -C11=C12- (11) andphotoexcitation of Rh only gives-C9=C10- (9) at the transition points. The minima in the groundbathoRh as a product whereas isoRhstate (open blue circles) and conical intersections (filled blue

yields 9,11-dicisRh in addition tocircles) obtained in the present calculations are plotted in thebathoRh. Note that the reaction time

diagram. Rh = rhodopsin, isoRh = isorhodopsin, bathoRh =isbathorhodopsin,longerCI(isoRh->BathoRh)
than

that

through(ave=233

fs)

9,11-dicisRh=

9,11-dicis

rhodopsin,

CI=minimum energy conical intersection.

through

CI(isoRh->9,11-dicisRh) (ave=188 fs). Secondly, the protein environment enhances the productionof bathoRh. When the opsin environment was totally ignored, the calculated bathoRh (all-trans
PSB) quantum yield was only 0.27 and 0.13, respectively. Explicit consideration of the opsin
residues significantly improves the theoretical quantum yield to 0.51 and 0.31, respectively. This
would be mainly 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 3 with those in the calculations in vacuo reveals that the present transition points
with the opsin environment are nearer the MECI points than the points without the opsin. The opsin
would prevent inefficient, premature hops especially in the isoRh case.
(2) Changes in the Electronic Structures of a Single Sheet of Sashlike Polydiacetylene Atomic
Sash upon Structural Transformations
Atomic sash (AS) is a single sheet of a sashlike macromolecule comprising a column of alkyl
chains bridged by a polydiacetylene (PD) chain. The AS is produced by the intramonolayer
polymerization of 17,19-hexatriacontadiyne molecules laid flat on a graphite (0001) surface underultrahigh vacuum. In an AS conformer initially formed at low temperature (AS-I), the PD chain andthe R carbon atoms of the alkyl chains are raised higher than other carbons of methylenes in contact
with the substrate; with rising temperature, the AS-I is transformed to another conformer AS-II, in
which all the carbon atoms are placed in a common plane. A simplified model is constructed in this－ 70 －

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Ⅳ 研究業績 (2011)

study to obtain an optimized geometric structure of the AS-I, and its electronic structures arecompared with those of the AS-II. The first-principles calculations for the model under periodic
boundary conditions reveal that their energies are almost the same. The optimization also tells us
the existence of the third stable conformer AS-III that has been suggested on the basis of STM
images. In addition, it is found that the HOMO-LUMO energy gap of the AS-I is larger than that of
the AS-II, and the orbital shapes dependent on the conformation successfully explain the result.
This means that the AS-I → AS-II transformation of the ideal infinite polymer is not related to thechromatic transition of bulk PDs(3) An MD simulation of the decoy action of Epstein–Barr virus LMP1 protein mimicking theCD40 interaction with TRAF3
The Epstein–Barr virus (EBV) is associated with a variety of malignancies and chronic active
EBV infection is a severe systemic disease associated with high rates of mortality and morbidity. In
this paper, the dynamics of the interaction of EBV-expressed latent membrane protein 1 (LMP1)
with cellular signaling intermediate tumor necrosis factor receptor (TNFR)-associated factor 3(TRAF3) is simulated using standard classical molecular dynamics (MD) protocols. For comparison,
the dynamics of the interaction of TRAF3 with CD40, a TNFR mimicked by LMP1 to effect EBV
infection is also calculated under similar conditions. Essential dynamics (ED) analysis is carried out
to identify important degrees of vibrational freedom that relate to protein function and virus
infection. Both the MD simulation and ED analysis reveal novel interactions that help explain the
structural decoy action of LMP1 over CD40. These interactions involve the consensus sequence
PXQXTXX shared by CD40 and LMP1. In LMP1, we have found novel interaction of Asp 209
with TRAF3 and the interaction is crucial although the adjacent Asp 210 was suggested to be
essential by the X-ray analysis. In CD40, it is found that the hairpin formation is not indispensablefor the interaction with TRAF3.
(4) Electronic and Magnetic Characteristics of Polycyclic Aromatic Hydrocarbons with
Factorizable Kekul_e Structure Counts
The Kekulé structure count (K) for some types of polycyclic aromatic hydrocarbons (PAHs),
such as fluoranthene and perylene, can be factorized into the product of those for two or morearomatic subunits. The ring-current map for these PAHs placed in a perpendicular magnetic field
exhibits a substantial localization on aromatic subunits. We found that such localization of π
circulation is a characteristic of fairly small K-factorizable species in the neutral electronic state.
Even in such a case, no single π molecular orbital (πMO) is associated with localized π circulation.

－ 71 －

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Ⅳ 研究業績 (2011)

Apparent localization of π circulation is caused by the superposition of currents induced by all
occupied πMOs. π circulation is less localized in larger K-factorizable species.
2. Original papers(1) Suhara, Masanori; Ozaki, Hiroyuki; Endo, Osamu; Ishida, Toshimasa; Katagiri, Hideki;
Egawa, Toru; Katouda, Michio"Changes in the Electronic Structures of a Single Sheet of Sashlike

Polydiacetylene Atomic

Sash upon Structural Transformations"J. Phys. Chem. C, 115(19)，9518-9525(2011)(2) Wilfredo Credo Chung and Toshimasa Ishida*,
An MD simulation of the decoy action of Epstein-Barr virus LMP1 protein mimicking theCD40 interaction with TRAF3
Theo. Chem. Acc. 130(2), 401-410 (2011).
(3) Jun-ichi Aihara*, Rika Sekine and Toshimasa Ishida
Electronic and Magnetic Characteristics of Polycyclic Aromatic Hydrocarbons with
Factorizable Kekule Structure Count
J. Phys. Chem. A. 115(33), 9314-9321 (2011)(4) Wilfredo Credo Chung,* Shinkoh Nanbu, and Toshimasa Ishida“A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin:
Chemical Dynamics Reasons Behind Selection of Rhodopsin by Life”,
Chem. Lett. 40(12), 1395-1397(2011).
3. Presentation at academic conferences(1)

Wilfredo C. Chung, Shinkoh Nanbu, Toshimasa IshidaComparison 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
P102 2011/2/23

(2)

第５回

公開シンポジウム神戸

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
P103 2011/2/23

(3)

第５回

公開シンポジウム

神戸

Ishida, Toshimasa; Aono, Shigetoshi“A QM/MM study on reactions of the axial ligand exchange in CooA protein”－ 72 －

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Ⅳ 研究業績 (2011)

第 27 回化学反応討論会 1P20 2011/6/8 東京工業大学（東京）(4) Chung, Wilfredo Credo; Nanbu, Shinkoh; Ishida, Toshimasa“Nonadiabatic ab initio dynamics of rhodopsin and isorhodopsin: a QM/MM trajectory surface
hopping (TSH) approach based on the Zhu-Nakamura theory”
第 27 回化学反応討論会 1P23 2011/6/8 東京工業大学（東京）(5)Toshimasa Ishida, Wilfredo Credo Chung; Shinkoh Nanbu, and Hiroki Nakamura“Non-adiabatic ab initio dynamics of 11-cis retinal photoisomerization
Ninth Triennial Congress of the WORLD ASSOCIATION OF THEORETICAL AND
COMPUTATIONAL CHEMISTS(WATOC 2011)”, July 17, 2011, Santiago de Compostela,
Spain

(6)

S. Nanbu , T. Ishida, and A. D. Kondorskiy“Non-adiabatic dynamics with semiclassical trajectories: applications to photo-isomerization”
Ninth Triennial Congress of the WORLD ASSOCIATION OF THEORETICAL AND
COMPUTATIONAL CHEMISTS WATOC (WATOC 2011), July 19, 2011 Santiago deCompostela, Spain(7) T. Murakami, K. Saita, W. C. Chung, T. Ishida and S Nanbu“Theoretical study of photo-physical properties of indolylmaleimides
Ninth Triennial Congress of the WORLD ASSOCIATION OF THEORETICAL AND
COMPUTATIONAL CHEMISTS WATOC (WATOC 2011)”, July 21, 2011 Santiago deCompostela, Spain(8) Toshimasa Ishida, Wilfredo Credo Chung; Shinkoh Nanbu, and Hiroki Nakamura
Non-adiabatic ab initio dynamics of 11- and 9-cis retinal photoisomerizationNon-adiabatic ab
initio dynamics of 11-cis retinal photoisomerization
Excitedstatesandnon-adiabatic

processes

incomplexsystems.

Theoretical

approaches(WATOC2011 Satellite Meeting), July 25, 2011 Sant Feliu de Guíxols, Spain(9) Toshimasa Ishida,
Photoisomerization dynamics of 11-cis and 9-cis retinal.

An origin of difference between

rhodopsin and its analog
Fukui International Symposium for Theoretical Chemistry, Aug. 31, 2011, Kyoto, Japan(10) Wilfredo C. Chung、南部 伸孝、石田 俊正
A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin
第 9 回福井謙一記念研究センターシンポジウム(P42)2012 年 1 月 6 日

京都(11) 村上龍大、石田俊正、南部伸孝、「インドリルマレイミドの光物理家庭の非断熱力学」
日本化学会第 92 春季年会

(4A4-01)2012 年 3 月 28 日

日吉

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Ⅳ 研究業績 (2011)

4. Others(1) 石田俊正「レチナール光異性化反応のシミュレーション」
静岡大学理学部化学科講演会

2011/6/3 静岡(2) 石田俊正「ロドプシンとイソロドプシンの動力学の理論的研究 － なぜ生物はロドプシンを選んだか」2011 年度 上智大学理工学部物質生命理工学科コロキウム

2011 年 10 月 24 日

上智大学（東京）－ 74 －

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Ⅳ 研究業績 (2011)

Hidekazu IKENO
Assistant Professor
1. Summary of the research of the year
Theoretical Fingerprints of Transition Metal L2,3 XANES/ELNES for Lithium Transition
Metal Oxides
Transition metal oxide crystals with topotactic and reversible lithium insertion/extraction capability,
such as LiCoO2, LiNiO2, LiMn2O4, and their alloys, have been used as cathodes of a lithium ion battery.
Although they have already been used commercially, many studies for improving their electrochemical
performance, such as lifetime and rate capability, are still ongoing. Characterization of the transition metal
ions in the cathodes during the charge/discharge cycles is one of the essential points for such studies. Amongthe many techniques, spectroscopic methods to measure X-ray absorption near-edge structures (XANES) andelectron energy loss near-edge structures (ELNES) at transition metal L2,3-edges (M L2,3-edges) are very
powerful to selectively observe the electronic states and local environment of transition metal ions.
It is known that M-L2,3 XANES/ELNES show widely spread multiplet structure because of the strong
electronic correlation among 2p core-hole and 3d electrons. For simulating these spectra, the present authors
have developed an ab initio multiplet method based on the relativistic configuration interaction theory.
Experimental M-L2,3 XANES/ELNES with different d-electron numbers, coordination numbers, andsymmetries have been successfully reproduced without any adjustable parameters[1,2].
In this work, we aim at providing theoretical fingerprints of M-L2,3 XANES/ELNES for for LiMO2 (M= Mn, Fe, Co, Ni) and Li-extracted MO2 that should be useful for the analysis of experimental spectra.
Theoretical spectra obtained by the ab initio multiplet method are given for six set of oxides with several
different crystal structures. The effects of oxidation states, spin states, and crystal structures including that of
the Jahn-Teller (JT) distortion on the M-L2,3 XANES/ELNES are discussed[3].
First, the variations of M-L2,3 spectra with M in the layered structures were studied. The results are
summarized in Fig. 1. It is clearly seen that the spin state and oxidation state can be unambiguously
determined using these theoretical fingerprints.
The variations of M-L2,3 spectra of LiMO2 and Li-extracted MO2 with the crystal structures were
examined for M = Mn and Fe. The dependence of spectral shapes on crystal structure was very small in thecase of LiMO2. The spectral difference became larger in the case of Li-extracted MO2, which originated fromthe stronger covalent bonding between M-3d and O-2p orbitals in MO2 than in LiMO2.
The L3/(L3+L2) branching ratio was also calculated. The branching ratio changes with the atomic
number, oxidation state, and spin state. The results imply that the branching ratio can be used to identify theoxidation and spin states, except for the case of Fe4+. However, the branching ratio was insensitive to the
crystalline structure.

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The effects of the JT distortion on M-L2,3 spectra for two compounds with d4 high-spin state, namely,
LiMnO2 and FeO2 with layered structures, were examined. The presence and orientation of the distortion canbe easily and clearly detected by measuring the orientation dependence of the spectra, although theorientationally averaged spectra do not change so much with the JT distortion.
The ab initio multiplet calculations can well reproduce experimental spectra. It therefore has thepredictive performance of theoretical fingerprints of M-L2,3 XANES/ELNES for transition metal compoundswith arbitrary atomic arrangement and symmetry. High-quality XANES/ELNES measurements and reliable
theoretical fingerprint calculations should be a powerful and unique combination for the characterization of
M ions during the charge/discharge cycles in the cathodes of lithium ion batteries.
Mn

0.5

PACS (10-22 m2/atom)

BR*
0.4 0.67
0.62
0.3

HS (t2g)3(eg)1
LS (t2g)4

0.2

0.1
0

HS (t2g)3(eg)2LS (t2g)5

0.4

BR
0.61

0

m-MnO20.3

HS/LS (t2g)3

0.3

BR
0.66
0.66

m-FeO2HS (t2g) (eg)LS (t2g)43

1

0630 635 640 645 650 655 660 665

Energy (eV)HS (t2g)4(eg)2LS (t2g)6

0.4

r-CoO2

0.2

0

0.4

HS (t2g)3(eg)2LS (t2g)5

0.76
0.5
0.70
0.3

r-LiNiO2
HS (t2g)5(eg)2LS (t2g)6(eg)1

BR

r-NiO20.70

HS (t2g)4(eg)2LS (t2g)6

0.8 0.74
0.6
0.4
0.2

0.1
0
770 775 780 785 790 795 800 805 810

Energy (eV)BR
0.3 0.83
0.69

0.1

0
0.6 BR0700 705 710 715 720 725 730 735

Ni

0.4

r-LiCoO2

0.2

0.1

0.1

BR
0.6 0.77
0.65

0.2

0.2

0.2

Co

0.8

r-LiFeO2BR
0.6 0.75
0.69

0.2

0.4

Fe

0.8

m-LiMnO2

Energy (eV)0845 850 855 860 865 870 875 880 885

Energy (eV)Fig. 1 Theoretical M-L2,3 XANES/ELNES of LiMO2 and Li-extracted MO2 (M=Co, Ni) with layered
structures. Theoretical spectra from the high-spin (HS) and low-spin (LS) states are drawn in the black andred lines, respectively, for each compound.
without JT distortion

0.5 r-LiMnO2

E // c

PACS (10-22 m2/atom)

0.4

E

0.3

c

0.2
0.1
0

0.5 m-LiMnO2
0.4
0.3

with JT distortion†c c

E // aE // b
E // c†

b

a

0.2
0.1
0

630 635 640 645 650 655 660 665

Energy (eV)Fig. 2 Jahn-Teller effect on the theoretical Mn-L2,3 XANES/ELNES of LiMnO2 with layered structures.
Theoretical spectra are averaged over all directions.

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Relativistic Configuration Interaction Calculations of X-ray Magnetic Circular Dichroism(XMCD)
Soft x-ray absorption spectroscopy (XAS) and its magnetic circular dichroism (XMCD) are widelyused to investigate the electronic and magnetic structures of the selected element in materials. The XMCD isa difference of two XAS spectra taken in the magnetic field: the one is taken with left circularly polarized(LCP) light, and the other is taken with right circularly polarized (RCP) light. By using circularly polarized
light, we can utilize not only the selection rule for angular momentu (L = ±1), but also that for magnetic
momentum number: when LCP (RCP) light is irradiated, only electric dipole transitions with M = +1 (M= -1) are allowed. XMCD is usually interpreted using the sum-rules introduced by Thole and Carra[4,5]which enable us to determine the expectation values of orbital moment <Lz> and spin moment <Sz> at the
ground state by just integrating observed spectra. However, it is known that the effective moment obtainedby these sum-rules have large errors up to 30% in the real systems. The detailed analysis of XMCD by the
first principle calculations is thus strongly desired.
In this study, we have extended the relativistic configuration interaction (CI) method to compute theelectronic structure under the external magnetic field, and applied to the calculation of transition metal L2,3
XMCD spectra. In order to include the effect of external magnetic field in the CI, the Zeeman term,

H Zeeman    B (l k  2sk ) B ,k

1.4

the external magnetic field, and B is the Bohr

1.2

magneton. After digonalizing the Hamiltonian matrix,

1.0

the oscillator strengths of electric dipole transition are

0.8

calculated for left and right-circularly polarized light,
respectively, to obtain the XMCD spectra.
Fig. 3 shows L2,3 XAS and XMCD of isolated
Fe3+ ion (d5, 6S5/2 ground state) with various magnetic
field. As the magnetic field stronger, the absolute
amplitude of XMCD signal becomes larger because
the Zeeman splitting at the initial state is larger. Inside
the magnetic compounds, the exchange interaction
among transition metals further split the multiplet
levels. This effect can be mimicked by add themolecular field, Bm, into B. The spin and orbital
contribution to the magnetic moment can also be
obtained numerically from the eigenfunctions.

PACS (x10-22 m-2/atom)

is added to the many-electron Hamiltonian. Here B is

XAS

0.6
0.4
0.2
0
0.1

XMCD

0
-0.1

0T
5T
10T
20T
30T
40T
50T

-0.2
-0.3
-0.4
-0.5
700

705

710

715

720

725

Energy (eV)

730

735

740

Fig 3. Theoretical L2,3 XAS and XMCD spectra of
the isolated Fe3+ ion with various magnetic field.

References[1] H. Ikeno et al., Phys. Rev. B 83, 155107 (2011).

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Ⅳ 研究業績 (2011)[2] H. Ikeno et al., J. Phys.: Condens. Matter 21, 104208 (2009).
[3] H. Ikeno et al., J. Phys. Chem. C 115, 11871 (2011).
[4] B. T. Thole et al., Phys. Rev. Lett. 68, 1943 (1992).
[5] P. Carra et al., Phys. Rev. Lett. 70, 694 (1993).

Original papers(1) Hidekazu Ikeno, Teruyasu Mizoguchi, Yukinori Koyama, Zenpachi Ogumi, YasuharuUchimoto,and Isao Tanaka,“Theoretical Fingerprints of Transition Metal L2,3 XANES/ELNES for Lithium Transition Metal
Oxides by ab Initio Multiplet Calculations”
J. Phys. Chem. C 115, 11871-11879 (2011)(2) S. Ootsuki, H. Ikeno, Y. Umeda, H. Moriwake, A. Kuwabara, O. Kido, S. Ueda, I. Tanaka, Y.
Fujikawa, and T. Mizoguch“Ab-initio multiplet calculation of oxygen vacancy effect on Ti-L2,3 electron energy loss near edge
structures of BaTiO3”
J. Phys.: Condens. Matter 23, 144501 (2011).

2. Presentation at academic conferences(1) H. Ikeno, F. Oba and I. Tanaka“Ab Initio Multiplet Method for L2,3 XANES and ELNES of 3d Transition Metal Compounds”
The 15th International Conference on Thin Films (ICTF-15), (Nov. 8-11, 2011, Kyoto, Japan)(2) Piter S. Miedema, Hidekazu Ikeno, Frank M.F. de Groot“First principles multiplet calculations of the calcium 2p XAS spectra of CaO and CaF2”
X-ray Spectroscopy: Recent Advances in Modeling and New Challenges, (Jul. 13-15, 2011, Zurich,
Switzerland)

3. Others(1) 池野豪一「遷移金属酸化物におけるX線磁気円二色性の第一原理計算」
第9回 福井謙一記念研究センターシンポジウム (2012年1月6日，京都)(2) 池野豪一「強相関計におけるXASおよびXMCDの第一原理計算」
強磁場X線・中性子線実験の発展 (2012年3月23日，神戸)－ 78 －

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Ⅳ 研究業績 (2011)

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 (such as
ONIOM) already proposed by us, 2. to demonstrate that such hybrid methods can be used for simulations ofstructures, reactions and dynamics and 3. to solve some of the important problems in each field. Our research is
supported in part by the Institute and in large fraction by a 5-year grant in the area of High Performance
Computing for Multi-Scale and Multi-Physics Phenomena from CREST (Core Research for Evolutional Scienceand 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 and from November 2011 at Hokkaido University, we have a strong team oftheoretical/computational chemists working together toward a common goal. Since detailed description on
individual projects can be found in the reports of postdoctoral fellows, here the areas of studies and titles ofindividual projects are summarized.

I. Simulation of Reactions and Dynamics of Complex and Biomolecular Systems

In the area of multi-level simulation of complex and biomolecular systems, in recent years we have studied
structures and reactions of metalloenzyme systems mainly using the active site models in which only the active
site atoms are explicitly included in the QM calculations. In the last few years we have explicitly included theeffects of protein employing the ONIOM QM/MM scheme. We optimized the structures of intermediates andtransition states of enzymatic reactions, and in some cases included the statistical effects of protein by QM/MM
molecular dynamics. In a few examples we have found that the protein effects completely changed themechanism 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 of photochemical processes of organic and biomolecularchromophores. We recently expanded our theoretical studies of catalytic reactions that take place in the nanocavity created by the protein and nucleic acids.
a) Reaction Mechanism of Biosynthesis of Antibiotic Fosfomycin in HppE (See research activities of Dr.
Chung and Dr. Petrova)b) DFT study of the mechanism of NO reduction in bacterial nitric oxide reductase (See research activities
of Dr. Hatanaka)c) Effect of protein environment on the NO reduction: An ONIOM study reductase (See research activities
of Dr. Hatanaka)d) Comparative Reactivity of Hydrogen Atom Transfer (HAT) with Important Metal-Oxo andFerric-Superoxo Species (See research activities of Dr. Chung)e) Theoretical modeling of stereochemistry control of copper catalysts based on the chirality of DNA (Seeresearch activities of Dr. Ptrova)f) Theoretical Study of Asymmetric Hydration Catalyzed by DNA-based Artificial Enzyme
Metalloenzymes (See research activities of Dr. Ke)g) Theoretical Study of Polymerization Catalyzed by Artificial Metalloenzymes (See research activities ofDr. Ke)h) ONIOM Investigation of Iron Uptake by Ferritin (See research activities of Dr. Harris)i) Ring-Opening and Ring-Closure Mechanism of Spiropyran-Merocyanine Photochromic Reaction (Seeresearch activities of Dr. Liu)
1
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Ⅳ 研究業績 (2011)j) Photodynamics and Isomerization Mechanisms of All-trans and 13-cis, 15-syn Retinal Protonated
Schiff Base in the light-adapted and dark-adapted Bacteriorhodopsin (See research activities of Dr. Xin
Li)k) Reaction Mechanism of Photo-induced Decarboxylation of the Photoactivatable Green FluorescentProtein:An ONIOM(QM:MM) Study (See research activities of Dr. Ding)l) Mechanistic study on the Photoisomerization in Polypyridyl mononuclear ruthenium(II) aquo (PMRA)
complex (See research activities of Dr. Ding)m) Reaction Mechanism of Hydrogenation of Carbon Dioxide Catalyzed by Ir-PNP Complex (See research
activities of Dr. Chung)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 of representative
nanotechnology materials and their various potential applications. Although SWNTs are known to be efficiently
synthesized using metal catalyst, its growth mechanism is still not well understood. In order to understandinterplay among feedstock carbon, nanotube, and metal, we have implemented growth simulations ofmetal-catalyzed SWNT using DFTB MD simulations. This year we invented a theoretical method to define thelocal chirality of irregular carbon nanotubes and used this definition to analyze mechanism of retention and lossof chirality during the growth of carbon nanotubes.
a) Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Non-Equilibrium (Seeresearch activities of Dr. Page)b) Functionalization of Fullerenes Using a Genetic Algorithm (See research activities of Dr. Page)c) The Reaction Pathway for C4H2 Polyyne Fusion Reactions: A Theoretical Investigation (See research
activities of Dr. Signh)d) Determination of Local Chirality in Irregular Single-Walled Carbon Nanotube Based on Individual
Hexagons (See research activities of Dr. Kim)e) Chirality-Controlled Carbon Nanotube Growth from Organic Templates (See research activities of Dr.
Page)f) SWCNT Growth from Chiral Carbon Nanorings: Prediction of Chirality and Diameter Influence on
Growth Rates (See research activities of Dr. Haibei Li)g) Sub-Surface Nucleation of Graphene Precursors near a Ni(111) Step-Edge (See research activities of Dr.
Haibei Li)

III. Method Developments and Applications

Previously 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 conicalintersection. This year we applied this method for elucidation of the mechanism of photodissociation reactions. In
photodissociation of NO3, we found a totally new kind of reaction mechanism, in which the molecule in an
excited state roam around a roaming transition state and branches into the direct excited state dissociation and theground state dissociation after nonadiabatic transition to the ground state. This mechanism since has beenunequivocally proved by an experimental study.
A new method, artificial force-induced reaction (AFIR) method, suitable to determining the transition andintermediates of reactions of two or more molecules A + B (+C…)  X, has been developed based on imposing
an artificial attractive force between the reactant molecules. The application of this method to the Passerini andother multicomponent organic reactions has shown that textbook mechanisms of some of the multicomponent
reactions are wrong, and actually additional molecules are involved as a catalyst. The method has also been used
to determine the best reaction pathway for the full catalytic cycle for the reaction of C2H4 + CO + H2 catalyzed by
HCo(CO)3.
(Work in collaboration with Prof. Maeda, who was Assistant Professor at Hakubi Center of Kyoto University
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Ⅳ 研究業績 (2011)

and Visiting Assistant Professor at FIFC. See also his Research Activities)a) Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction
Mechanismsb) No Straight Path: Roaming in Both Ground- and Excited-State Photolytic Channels of NO3 → NO +O2c) Fitting Global Ab Initio Potential Energy Surfaces for Low-lying Doublet States of NO3 (See research
activities of Dr. Xiao)d) Exploring Multiple Potential Energy Surfaces: Photochemistry of Small Carbonyl Compounds
Experimental and Theoretical Investigations of Isomerization Reactions of Ionized Acetone and Its
Dimere) Theoretical Study of the Photodissociation Dynamic of Ketenef) Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A Case Studyon HCo(CO)3-Catalyzed Hydroformylation
2. Original papers
1. H.-B. Li, A. J. Page, S. Irle, and K. Morokuma, Theoretical Insights into Chirality-Controlled SWCNT Growth from a
Cycloparaphenylene Template. ChemPhysChem 13, 1479-1485 (2012).
2. F. Liu, and K. Morokuma, A Computational Study on the Working Mechanism of Stilbene Light-Driven Molecular
Rotary Motor: Sloped Minimal Energy Path and Unidirectional Nonadiabatic Isomerization. J. Am. Chem. Soc. 134,4864-4876 (2012).
3. M. P. Grubb, M. L. Warter, H.-Y. Xiao, S. Maeda, K. Morokuma, S. W. North, No Straight Path: Multistate Roamingas the Only Route for the NO3 � NO + O2 Reaction, Science, 335, 1075-1078 (2012).
4. S. Maeda and K. Morokuma, Toward Predicting Full Catalytic Cycles Using Automatic Reaction Path Search Method: A
Case Study on HCo(CO)3-Catalyzed Hydroformylation, J. Chem. Theo. Comp. 8, 380-385 (2012).
5. J. Pang, X. Li, K. Morokuma, N. S. Scrutton, and M. J. Sutcliffe, Large-scale Domain Conformational Change Is
Coupled to the Activation of the Co-C bond in the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A
Computational Study. J. Am. Chem. Soc. 134, 2367-2377 (2012).
6. Y. Nishimoto, Z. Wang, K. Morokuma, and S. Irle, Molecular and electronic structures of endohedral fullerenes,
Sc2C2@C3v-C82 and Sc2@C3v-C82: Benchmark for SCC-DFTB and proposal of new inner cluster structures, Phys.
Status Solidi B, 249, 324-334 (2012).
7. Y. Matsuda, K. Hoki, S. Maeda, K. Hanaue, K. Ohta, K. Morokuma, N. Mikami, and A. Fujii, Experimental andtheoretical investigations of isomerization reactions of ionized acetone and its dimer. Phys. Chem. Chem. Phys. 14,
712-719 (2012).
8. S. Sekharan, S. Yokoyama,. K. Morokuma. Quantum Mechanical/Molecular Mechanical Structure, Enantioselectivity
and Spectroscopy of Hydroxyretinals and Insights into the Evolution of Color Vision in Small White Butterflies, J. Phys.
Chem. B. 115, 15380-15388 (2011).
9. J. M. Knaup. K. Morokuma and S. Irle, A simulation of possible carbon nanotubes slitting in a CMOS compatible way,
Mater. Express, 1, 343–349 (2011).
10. H. M. Nguyen, H. Hirao, U. V. Dang, K. Morokuma, Computational Studies of Bacterial Resistance to b-Lactam
Antibiotics: Mechanism of Covalent Inhibition of the Penicillin-Binding Protein 2a (PBP2a), J. Chem. Inf. Model. 51,
3226-3234 (2011).
11. R. Tanaka, M. Yamashita, L. W. Chung, K. Morokuma, and K. Nozaki, Mechanistic Studies on the Reversible
Hydrogenation of Carbon Dioxide Catalyzed by an Ir-PNP complex, Organometallics, 30, 6742–6750 (2011).
12. L. W. Chung, X. Li, H. Hirao and K. Morokuma,, Comparative Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in
Heme and non-Heme Complexes. J. Am. Chem. Soc 133, 20076–20079 (2011).
13. K. Ando and K. Morokuma, DFT and ONIOM Study on the Alkylation of the Lithium Enolate in Solution:
Microsolvation Cluster Models for CH2=CHOLi + CH3Cl + (THF)0-6, Theo. Chem. Acct. 130, 323-331 (2011).
14. Y. Okamoto, F. Kawamura,.Y. Ohta, A. J. Page, S. Irle and K. Morokuma, SCC- DFTB/MD Simulation of Transition
Metal Catalyst Particle Melting and Carbide Formation, J. Comp. Theo. Nanosci. 8, 1755-1763 (2011).
15. B. Saha, S. Irle, and K. Morokuma, Hot giant fullerenes eject capture C2 molecules. QM/MD simulations with constant3－ 81 －

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density. J. Phys. Chem. C, 115, 22707-22716 (2011).
16. S. Sekharan and K. Morokuma, Why 11-Retinal? Why Not 7-, 9- or 13-in the Eye? J. Am. Chem. Soc. 133,
19052-19055 (2011).
17. Y. Wang, A. J. Page, Y. Nishimoto, H.-J. Qian, K. Morokuma and S. Irle, Template Effect in the Competition Between
Haeckelite and Graphene Growth on Ni(111): Quantum Chemical Molecular Dynamics Simulations, J. Am. Chem. Soc.
133, 18837–18842 (2011).
18. J. Kim, S. Irle and K. Morokuma, Determination of Local Chirality of Irregular Single-Walled Carbon Nanotube Basedon Individual Hexagons. Phys. Rev. Lett. 107, 175505/1-5 (2011).
19. W. Zhang, Y. Tang, M. Lei, K. Morokuma, and D. G. Musaev, Ditantalum dinitrogen complex: Reaction of H2
molecule with “end-on-bridged” [TaIV]2(μ-η1:η1-N2) and bis(μ-nitrido) [TaIV]2(μ-N)2 complexes. Inorg. Chem. 50,
9881-9490 (2011).
20. S. Abdel-Azeim, X. Li, L. W. Chung and K. Morokuma,, Zinc–Homocysteine Displacement in Cobalamin-Dependent
Methionine Synthase and its Role in the Substrate Activation: DFT, ONIOM, and QM/MM Molecular Dynamics Studies.
J. Comp. Chem. 32, 3154-3167 (2011).
21. H. Hirao and K. Morokuma, ONIOM(DFT:MM) Study of 2-Hydroxyethylphosphonate Dioxygenase: What Determines
the Destinies of Different Substrates? J. Am. Chem. Soc. 133, 14550-14553 (2011).
22. A. J. Page, K. R. S. Chandrakumar, S. Irle and K. Morokuma, Thermal Annealing of SiC Nanoparticles Induces
SWNT Nucleation: Evidence for a Catalyst-Independent VSS Mechanism. PhysChemChemPhys, 13, 15673-15680(2011).
23. X. Li, L. W. Chung, and K. Morokuma, Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin
and Methanol Solution, J. Chem. Theo. Comp. 7, 2694-2698 (2011).
24. S. Maeda and K. Morokuma, Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of
Reaction Mechanisms, J. Chem. Theo. Comp. 7, 2335-2345 (2011).
25. A. Altun, K. Morokuma and S. Yokoyama, H-bond network around retinal regulates the evolution of ultraviolet andviolet vision, ACS Chem. Bio. 6, 775-780 (2011). DOI: 10.1021/cb200100f
26. H.-J. Qian, A. van Duin, K. Morokuma and S. Irle. Reactive Molecular Dynamics Simulation of Fullerene Combustion
Synthesis: ReaxFF vs DFTB Potentials. J. Chem. Theo. Comp. 7, 2040-2048 (2011). DOI: 10.1021/ct200197v
27. H. Hirao, F. Li, L. Que, Jr., and K. 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. 50,
6637-6648 (2011).DOI: 10.1021/ic200522r
28. Z. Ke, S. Abe, T. Ueno and K. Morokuma, Rh-catalyzed Polymerization of Phenylacetylene: Theoretical Study of theReaction Mechanism, Regioselectivity and Stereoregularity, J. Am. Chem. Soc. 133, 7926–7941 (2011).

3. Review article

1.

2.

3.

4.
5.

S. Sekharan, A. Altun and K. Morokuma, Computational Chemistry of Vision in Vertebrates and Invertebrates, in“Annual Reports in Computational Chemistry”, Vol. 7, ed. R. A Wheeler, Elsevier. 215-233 (2011).
S. Maeda, K. Ohno and K. Morokuma, Exploring Multiple Potential Energy Surfaces: Photochemistry of Small CarbonylCompounds, in Advances in Physical Chemistry "Accurate potential energy surfaces and beyond: chemical reactivity,
binding, long-range interactions and spectroscopy", eds. L. Bytautas, J. Bowman, X. Huang and A. Varandas,
268124/1-1313 (2011).
X. Li, L. W. Chung, and K. Morokuma, Modeling Photobiology Using Quantum Mechanics (QM) and Quantum
Mechanics/Molecular Mechanics (QM/MM) Calculations, in “Computational Methods for Large Systems: Electronic
Structure Approaches for Biotechnology and Nanotechnology”, ed. J. R. Reimers, John Wiley, Hoboken, NJ, pp. 397-434(2011). ISBN: 978-0-470-48788-4.
L.W. Chung, H. Hirao, X. Li and K. Morokuma, The ONIOM Method: Its Foundation and Applications to
Metalloenzymes and Photobiology, WIREs Comput. Mol Sci 2, 327–350 (2012). doi: 10.1002/wcms.85
S. Irle, G. Zheng, Z. Wang and K. Morokuma, Dynamics Simulations of Fullerene and SWCNT Formation, in
Spectroscopy, Dynamics, Moelcular Theory of carbon Plasmas and Vapors, Eds. L. Nemes and S. Irle, World Scientific,
375-416 (2012).

4. Presentation at academic conferences and universities

1. Exciting World of Theoretical Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures,
Catalysts, and Enzymatic Reactions Division of Chemistry and Biological Chemistry. Nanyang Technological
University. March 26, 20124
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2. How much can complex chemical reactions be understood by the use of theoretical and computational chemistry?
Hiratsuka Symposium at Kanagawa University, March 9, 2012
3. Theoretical Studies of Chemical Reactions and Dynamics -- Mainly ONIOM Applications, The workshop“Introduction to Gaussian: Theory and Practice” February 23, 2012. Global Scientific Information and Computing
Center (GSIC) ＆Computational Chemistry Collegium, Tokyo Institute of Technology (TITECH)
4. Two Stories of Chemical Reactions. 1. Exploring Reaction Pathways Using Automated Reaction Route Finders. 2.
Nucleation, Growth and Healing Processes of Single-Walled Carbon Nanotubes. Quantum Molecular Dynamics: A
Conference in Honor of William H. Miller, University of California, January 9-12, 2012
5. Application of molecular simulations to bionaoscience, Supercomputing Workshop, Institute for Molecular Science,
Okazaki, Japan, January 24-25, 2012
6. Theoretical studies of chemical reactions. From the frontier theory to present and future. Fukui Center Symposium,
January 6, 2012
7. Theoretical Studies of Chemical Reactions – From Simple Molecules to Complex Systems. Molecular Science
Symposium, Sapporo, Japan, September 21, 2011.
8. Nucleation, Growth and Healing Processes of Single-Walled Carbon Nanotubes from Metal Clusters and SiO2 and
SiC Surfaces: Density Functional Tight-Binding Molecular Dynamics Simulation, Sixteenth International
Workshop on Quantum Systems in Chemistry and Physics, Kanazawa, Japan, September 11, 2011
9. Theoretical Studies of Chemical Reactions and Dynamics of Biomolecular Systems in Protein, 14th Asian
Chemical Congress (14ACC), Bangkok, Thailand, September 8, 2011
10. Theoretical Studies of Chemical Reactions – Gas Phase Reactions to Nano Structures, Catalyses, and Enzymatic
Reactions in Ground and Excited Electronic States, 7th Congress of the International Society for Theoretical
Chemical Physics, Waseda University, Tokyo, Japan, September 2, 2011
11. Exciting World of Theoretical Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures,
Catalysts, and Enzymatic Reactions, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China,
12. Exploring Reaction Pathways Using Automated Reaction Route Finders. International Conference on Theoretical andHigh Performance Computational Chemistry, Xi'an, China, August 11-14, 2011
13. Computational Studies of Chemical Reactions of Molecular Systems: Overview of Our Recent Activities. 2011 Congressof World Association of Theoretical and Computational Chemistry (WATOC), Santiago de Compostela, Spain, July
16-22, 2011
14. ONIOM QM/MM studies of reactions of transition metal complexes in biological and biomimetic environment. 3rd
Quantum Bioinorganic Chemistry Conference, Český Krumlov, Czech Republic; June 25-28, 2011
15. Exciting World of Theoretical Studies of Chemical Reactions – From Gas Phase Reactions to Nano Structures,
Catalysts, and Enzymatic Reactions. Heyrowsky Institute, Czech Academy of Science, Prague, Czech Republic, June 24,
2011

5. Public talks

1. Let’s Explore the World of Chemical Reactions Using Computer (in Japanese), Open Lectures for High SchoolStudents, in Commemoration of the 30th Anniversary of Prof. Fukui’s Nobel Prize, Fukui Institute for Fundamental
Chemistry, Kyoto University, July 30, 2011.
2. Let’s Explore the World of Chemical Reactions Using Computer (in Japanese), Kyoto University Junior Campus
2011, Fukui Institute for Fundamental Chemistry, Kyoto University, September 19, 2011.
3. Let’s Explore the World of Chemical Reactions Using Computer (in Japanese), Academic Day, Kyoto University,
March 10, 2012.
3. Let’s Explore the World of Chemical Reactions Using Computer (in Japanese), Moriyama High School, Shiga
Prefecture, March 19, 2012.
4. Let’s Explore the World of Chemical Reactions Using Computer, Nanyang Technical University, Singapore, March
26, 2012.

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Shigeyoshi SAKAKI
Research Leader, Kenichi Fukui Memorial Research Groups II
1. Summary of the research of 2011
Molecules and molecular systems which consist of transition metal element, organic moiety,non-transition metal element, and hypervalent element are attractive research targets in wide areas ofchemistry. Actually, those molecules and complexes play important roles as metal enzymes, molecularcatalysts, and molecular devices such as photosensitizer, molecular switch, luminescence material etc.
Their functions deeply relate to their those electronic structures. In this regard, it is worthy elucidating theelectronic structure of the complex system including transition metal element. Moreover, their electronic
structures are interesting from the point of view of theoretical/computational chemistry, because theirelectronic structures are not simple but complicated in many cases. In particular, transition metgal
complexes bearing large correlation effects are challenging research target even nowadays.
This year, we theoretically investigated (i) Noble Reaction Features in Oxidative Addition of
B−Br σ−Bond of Bromoborane to M(PMe3)2 (M= Pt or Pd), (ii) Reaction Mechanism andReaction Features of Epoxidation of alkenes by Ru-porphyrin (iii) MS-CASPT2 study of iron(III)complexes of catechol dioxygenase, (iv) HSLS Transition of the Hoffmann type MOF,
{FeII(pz)[PtII(CN)4]}, by CS2 absorption. We wish to report summary of them.
(i) Noble Reaction Features in Oxidative Addition of B−Br σ−Bond of Bromoborane to M(PMe3)2 (M=Pt or Pd)
Formation processes of cis−boryl complexes via oxidative additions of B−H, B−B, and B−E (E═Si,
Ge, or Sn) bonds to low−valent transition−metal complexes have been clarified theoretically.1 However, themechanism for trans-boryl complex produced by the oxidative addition of B−X (X═Cl, Br, or I) bond toPd(0) and Pt(0) complexes remains unclear yet, in which the cis−trans isomerization is proposed to be
involved. However, the cis-trans isomerization occurs via spin conversion process in general, 2 but thecis-trans isomerization taking place on single potential surface has not been investigated well. Here, wetheoretically investigated the oxidative addition of the B−Br bond of bromoborane Br2B(OSiMe3) toM(PMe3)2 (M ═ Pt or Pd) to explore possible reaction pathways and to clarify the process of the thermal
cis−trans isomerization in this reaction.
The first step is the coordination of Br2B(OSiMe3) with M(PMe3)2 (M ═ Pt or Pd) to form aprecursor complex. The next is the
B−Br bond cleavage. In the Pt
system, two reaction courses are
possible (Scheme 1); one is thenucleophilic attack pathway which
directly affords the trans-product.
The other one is the stepwise
reaction pathway which includes thecis−oxidative addition followed by
the cis−trans isomerization. The
Fig. 1 Schematical geometry changes and energy
former reaction course is more changes in B-Br s-bond activation by Pt(0)favorable. In the Pd system, only theEa (kcal/mol) is Gibbs energy barrier in solvent(toluene),
stepwise pathway was found.

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Interestingly, the thermal cis−trans isomerization was found to occur on the singlet potential
energy surface due to the strong donation ability of the boryl group. The reason is interpreted
in terms of the very strongly donating boryl ligand, as follows: Because the boryl ligand isvery strongly donating, it destabilizes one d orbital, the other four d orbitals become doubly
occupied and hence the closed-shell singlet is the ground state.
(ii) Reaction Mechanism and Reaction Features of Epoxidation of alkenes by Ru-porphyrin
Epoxidation of olefine by [Ru(TMP)(CO)(O)] �(TMP = tetramesitylporphine), which is a key step of
the photocatalyzed epoxidation of olefin by [Ru(TMP)(CO)], is studied mainly with the density functional
theory (DFT) method, where [Ru(Por)(CO)] is employed as a model complex (Por = unsubstituted
porphyrin). This reaction is of considerable interest because dioxygen molecule is not the oxygen source
but water is the oxygen source; in other words, the water is employed as reactant. The CASSCF method was
also
used
to
investigate
theelectronic structureof important species
in the catalytic cycle.
In all of theruthenium porphyrin
species involved in
the catalytic cycle,
the weight of themain configurationof the CASSCF Fig.2 Geometry changes of ethylene epoxidation by Ru-porphyrinwave function islarger than 85%, suggesting that the static
correlation
is
not
very
large.
Also,
unrestricted-DFT-calculated natural orbitals are
essentially the same as CASSCF-calculated ones,
here. On the basis of these results, we employed
the DFT method in this work. Present
computational results show characteristic featuresof this reaction, as follows: (I) The epoxidation
reaction occurs via carboradical-type transition Fig. 3 Energy changes by epoxidation of threestate. Neither carbocation-type nor concerted olefins by Ru-porphyrin
oxene-insertion-type character is observed in thetransition state. (ii) Electron and spin populations transfer from the olefine moiety to the porphyrin ring inthe step of the C_Obond formation. (iii) Electron and spin populations of the olefin and porphyrin moieties
considerably change around the transition state. (iv) The atomic and spin populations of Ru change little in
the reaction, indicating that the Ru center keeps the +II oxidation state in the whole catalytic cycle. (v) The
stability of the olefiene adduct [Ru(Por)(CO)(O)(olefiene) considerably depends on the kind of olefin, suchas ethylene, n-hexene, and styrene. In particular, styrene forms a stable olefin adduct. And, (vi) interestingly,
the difference in the activation barrier among these olefin is small in the quantitative level (within 5kcal/mol), indicating that this catalyst can be applied to various substrates. This is because the stabilities and－ 85 －

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electronic structures of both the olefin adduct and the transition state are similarly influenced by thesubstituent of olefin.
(iii) MS-CASPT2 study of iron(III) complexes of catechol dioxygenase
In bioinorganic chemistry, non-hem ironcomplexes attract a lot of interest, because of theirinteresting catalytic reactions such as oxygenation ofaromatic compounds.
In such non-hem iron(III)catechole dioxygenase, the relation between activity andligand-tometal charge-transfer (LMCT) transitionenergy was pointed out experimentally.
We
theoretically investigated the LMCT excitation of thenative iron(III)-dependent catechol dioxygenase and its
functionalmodel complexes with multistate complete
active space second-order perturbation theory(MS-CASPT2). The ground state calculated by the
MS-CASPT2 method mainly consists of the iron(III)catecholate electron configuration and moderately of the Fig.4 Model Fe(III) complexes examinediron(II) semiquinonate electron configuration for both of here
the enzyme active centers and the Table 1. MS-CASPT2- and CAS-PT2-calculated LMCT
model complexes when the active transition energy of model complounds (in eV)
center exists in the protein environment
Compound
MS-CASPT2 CASPT2 TD-DFT Expt.
and the model complexes exist in thesolution. However, the ground-state PCD-PCA
1.57
0.74
0.81
1.75
+
[Fe(TPA)(CAT)]
1.45
0.46
1.41
1.53
wave function mainly consists of the
+
1.25
0.23
1.45
1.39
iron(II)semiquinonate
electron [Fe(TPA)(DMC)]+
1.54
0.62
1.36
1.58
[Fe(TPA)(3CC)]
configuration for both the enzyme
activesite
without a
proteinenvironment and themodel complexes in vacuo. These results clearly show that the protein environment andsolvent play important roles to determine the electronic structure of the catecholatoiron(III) complex. The
LMCT excitation energy clearly relates to the weight of the iron(III)-catecholate configuration in the groundstate. The reactivity and the LMCT excitation energy directly relate to the ionization potential of thecatecholate (IPCAT) in the model complex. This is because the charge transfer fromthe catecholatemoiety to
the dioxygen molecule plays a key role to activate the dioxygen molecule. However, the reactivity of thenative catechol dioxygenase ismuch larger than those of the model complexes, despite the similar IPCAT
values, suggesting that other factors such as the coordinatively unsaturated iron(III) center of the native
enzyme play a crucial role in the reactivity.
(iv) HSLS Transition of the Hoffmann type MOF, {FeII(pz)[PtII(CN)4]}, by CS2 absorption
It is recently reported that a porous coordination polymer (PCP), {FeII(pz)[PtII(CN)4]} (pz = pyrazine,
Figure 4), adsorbs various guest molecules to induce spin transition between the LS and the HS states atroom temperature. For instance, LS→HS transition is induced by adsorption of guest species whose size or
occupation number per pore is large in many cases. This transition is understood by steric repulsion between
bulky guests and the PCP framework, as follows. The steric repulsion is smaller in the HS framework than in－ 86 －

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the LS one because the HS framework is larger than the LS one. Hence, the HS framework is favorable foradsorption of bulky guests. This is the reason why the LS→HS transition is induced by bulky guests. In thecase of adsorption of CS2, on the other hand, reverse HS→LS transition is unexpectedly induced. The reasonof this reverse transition is not clear at all.
We investigated themechanism
of
the
HS→LS
CS2-induced
transitionofII
II{Fe (pz)[Pt (CN)4]},
consideringhinderedrotational entropy of the pz
ligands. In the guest-free PCP,pz ligands rotate much easier Fig. 4 Hoffmann-type
MOF
in the HS framework than in
Fig. 5 Pyrazyne rotation around Fe-Fe
the LS one, as shown in Fig. 4. This is because the steric axis
repulsion in the HS framework is weaker than in the LS one. Thus, the entropy difference (ΔSrot) between the
LS and the HS states is positive. In CS2 clathrate, however, CS2 molecules are strongly adsorbed between pz
ligands to suppress the pz rotation and to decrease ΔSrot. We evaluated the ΔSrot value and estimated how
much T1/2 shifts through the CS2 adsorption. The results indicate that the decrease in ΔSrot induces the
HS→LS transition. All computational results and discussion are consistent with the experimental ones. Thisis the first clear understanding of the T1/2 shift based on the entropy difference between the LS and the HS
states.
2. Original papers(1) Hirofumi Sato,Chisa Kikumori, Shigeyoshi Sakaki“Solvation structure of coronene-transition metal complex: a RISM-SCF study”
Phys. Chem. Phys. 13,309-313 (2011).
(2) Naoki Nakatani, Yutaka Hitomi, and Shigeyoshi Sakaki"Multi-State CASPT2 Study of Native Iron(III)-dependent Catechol Dioxygenase and Its
Functional Models: Electronic Structure and Ligand-to-Metal Charge-Transfer Excitation”
J. Phys. Chem. B. 115, 4781–4789 (2011).
(3) Atsushi Ishikawa and Shigeyoshi Sakaki,,
Theoretical Study of Photoinduced Epoxidation of Olefins Catalyzed by Ruthenium Porphyrin
J. Phys. Chem. A, 115, 4774–4785 (2011).
(4) Shigeyoshi Sakaki, Daisuke Kawai, and Shinya Tsukamoto
Theoretical Study of Metallasilatranes; Bonding Nature and Prediction of New Metallasilatrane
Collect. Czech. Chem. Commun. 76, 619–629 (2011).
(5) Atsuhi Ikeda, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki,
A resonance theory consistent with Mulliken-population concept
Chem. Phys. Lett., 505, 4-6 (2011).
(6) Guixiang Zeng and Shigeyoshi Sakaki
Noble Reaction Features of Bromoborane in Oxidative Addition of B−Br σ−Bondto M(PMe3)2 (M= Pt or Pd): Theoretical Study
Inorg. Chem., 50, 5290-5297 (2011).
(7) Shinya Tsukamoto and Shigeyoshi Sakaki
Theoretical Study of Pt(PR3)2(AlCl3) (R=H, Me, Ph, or Cy) Including an Unsupported Bondbetween Transition Metal and Non-Transition Metal Elements; Geometry, Bond Strength,
and Prediction
J. Phys. Chem. A, 115, 8520-8527 (2011).

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Ⅳ 研究業績 (2011)(8) Daisuke Yokogawa, Kohei Ono, Hirofumi Sato, Shigeyoshi Sakaki
Theoretical study on aquation reaction of cis-platin complex: RISM-SCF-SEDD, a hybrid aproachof accurate quantum chemical method and statistical mechanics
Dalton Trans., 40, 11125-11130 (2011).
(8) Hideo Ando, Yoshihide Nakao, Hirofumi Sato, Masaaki Ohba, Susumu Kitagawa, Shigeyoshi
Sakaki
Theoretical Study on High-Spin to Low-Spin Transition of {Fe(pyrazine)[Pt(CN)4]}:
Guest-Induced Entropy Decrease
Chem. Phys. Lett., 511, 399-404 (2011).
(9) Shibata, Naoto, Hirofumi Sato, Shigeyoshi Sakaki, Yuji Sugita
Theoretical Study of Magnesium Fluoride in Aqueous Solution
J. Phys. Chem., B, 115, 10553-10559 (2011).
(10) Hiroyuki Sakaba, Hiroyuki Oike, Masaaki Kawai, Masato , Takami, Chizuko Kabuto, Mausumi
Ray, Yoshihide Nakao, Hirofumi Sato, and Shigeyoshi Sakaki
Synthesis, Structure, and Bonding Nature of Ethynediyl-Bridged Bis(silylene)
Dinuclear Complexes of Tungsten and Molybdenum
Organometallics, 30,4515-4531 (2011).
(11) Kazuhide Ichikawa, Ayumu Wagatsuma, Yusaku I. Kurokawa, Shigeyoshi Sakaki, Akitomo
TachibanaInverted-sandwich-type and open-lantern-type dinuclear transition metal complexes: theoretical
study of chemical bonds by electronic stress tensor
Theor. Chem. Acc., 130, 237-250 (2011).
(12) Milind Deshmukh, Shigeyoshi Sakaki
Binding energy of gas molecule with two pyrazine molecules as organic linker inmeal-organic framework: its theoretical evaluation and understanding of determining
factors
Theor. Chem. Acc., 130, 475-482 (2011).
3. Presentation at academic conferences(1) Shigeyoshi Sakaki“Theoretical Study of Dinuclear Transition Metal Complexes: Interesting Electronic Structures andMolecular Properties, 4th Japan-Czech-Slovakia Joint Symposium for Theoretical andComputational Chemistry, Prague, 2011/5/18-20. (Invited Talk)(2) Shigeyoshi Sakaki“Heterolytic C-H -Bond Activation Reaction; Driving Force, Regioselectivity, Orbital Mixing,
and Its Application to Pd-Catalyzed Direct Cross-Coupling Reaction”, 9th World Association ofTheoretical and Computational Chemists (WATOC2011), Sanchiago de Compostella, Spain,
2011/7/17-22. (Invited Talk)(3) Shigeyoshi Sakaki, Milind Deshmukh, Hideo Ando, Yoshihide Nakao, Hirofumi Sato
“Theoretical Study of Gas-Adsorption to Metal-Organic-Framework (MOF)”
7th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII) at Waseda
University, Tokyo, Japan on September 2-8, 2011. (Invited Talk)(4) Shigeyoshi Sakaki“Theoretical Study of -Bond Activation Reaction by Transition Metal Complex and Catalytic
Reaction Including It”, The 14th Asian Chemical Congress 2011 (14 ACC) Sept. 5-8, 2011 in
Bangkok, Thailand. (Invited Talk)(5) Shigeyoshi Sakaki“C-H -Bond Activation Reaction and Catalytic Reactions by Transition Metal Complexes:
Theoretical Study”, The 9th International Conference on Computational Methods for Science andTechnology (ICCMSE), Oct., 2 to 7, Halkidiki, Greece (Invited Talk)
4. Others
(1) 榊

茂好

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Ⅳ 研究業績 (2011)“理論・計算化学の現在の成果と近未来：触媒反応、分子物性へのアプローチを例として”
計算分子科学拠点第１回 産学連携シンポジウム、野村コンファレンスプラザ日本橋、東京、2011年11月24日(2) 榊 茂好 Hiroyuki Tamura, Shinkoh Nanbu, Toshimasa Ishida, and Hiroki Nakamura“理論化学・計算化学と実験化学のインタープレイ：元素戦略への貢献を期待して“、CREST「元素戦略を基軸とする物質・材料の革新的機能の創出」理論と実験の連携強化を目指したシンポジウム（基調講演） 平成24年1月24日 東京（富士ソフトアキバプラザ）(3) 榊 茂好“遷移金属化学種の分子物性と反応過程：電子状態からの微視的理解と予測”、第２２回神奈川大学平塚シンポジウム 平成２４年３月９日 平塚(神奈川大学湘南ひらつかキャンパス)－ 89 －

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３．特定助教（白眉）Satoshi MAEDA
Visiting Assistant Professor (The Hakubi Center, Kyoto University),
Kenichi Fukui Memorial Research Group 1(To 31 Jan. 2012)
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) and finding reaction pathways [1,2]. Search for transition state (TS)structures is the primal 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 of numerous chemical reactions have been elucidated by calculations of TS structuresand corresponding reaction pathways.
One TS structure can be found by a geometry optimization starting from an initial guess
structure [4]. 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:
global reaction route mapping (GRRM) method [5-7] and artificial force induced reaction (AFIR)
method [8, original paper 7]. 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 and 5], an organometallic catalysis [original paper 3], and aphotoionization induced dynamics in a hydrogen-bond cluster [original paper 4].
We developed a set of Li-H-C-O DFTB parameters and it was employed in a simulation study
on sputtering and reflection dynamics of lithiated carbon material bombarded by slow hydrogenatoms [original paper 2]. A very accurate calculation of the energetics of POCl + e− → PO + Cl−
reaction was also performed to analyze experimental data concerned with electron catalyzed mutual
neutralization reactions of POCl3− and POCl2− each with Ar+ and Kr+ [original paper 6].
Works in original papers 1, 2, 4, and 6 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] Schlegel, H. B. WIREs Comput. Mol. Sci. 2011, 1, 790.

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Ⅳ 研究業績 (2011)[5] Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277.
[6] Maeda, S.; Ohno, K. J. Phys. Chem. A 2005, 109, 5742.
[7] Ohno, K.; Maeda, S. J. Phys. Chem. A 2006, 110, 8933.
[8] Maeda, S.; Morokuma, K. J. Chem. Phys. 2010, 132, 241102.
1-1. No Straight Path: Roaming in Both Ground- and Excited-State Photolytic Channels of
NO3 → NO + O2 (original paper 1)
Roaming mechanisms have recently been observed in several chemical reactions alongside
trajectories that pass through a traditional transition state. Here, we demonstrate that the visible
light–induced reaction NO3 → NO + O2 proceeds exclusively by roaming. High-level ab initio
calculations predict specific NO Λ doublet propensities (orientations of the unpaired electron withrespect to the molecular rotation plane) for this mechanism, which we discern experimentally by ion
imaging. The data provide direct evidence for roaming pathways in two different electronic states,
corresponding to both previously documented photolysis channels that produce NO + O2. More
broadly, the results raise intriguing questions about the overall prevalence of this unusual reaction
mechanism.
1-2. Dynamics of Deuterium Retention and Sputtering of Li–C–O Surfaces (original paper 2)
Chemistry as well as sputtering and reflection dynamics of lithiated carbon material, bombarded byslow hydrogen atoms are studied. We present a realistic method for computational simulation of the
dynamics of the polar Li–C–O–H material dynamics. It is based on an approximate, semi-empiricalquantum mechanics of electrons and classical mechanics of nuclei. Results are validated
qualitatively by comparison with experiments and with a first principle DFT computations. In
particular, we explain observed details of the hydrogen bonding chemistry in lithiated carbon,
showing that incoming hydrogen interacts preferably with Li-C rather than C structures.
1-3. Toward Predicting Full Catalytic Cycle Using Automatic Reaction Path Search Method: A
Case Study on HCo(CO)3-Catalyzed Hydroformylation (original paper 3)
Toward systematic prediction of reaction pathways in complex chemical reaction systems byquantum chemical calculations, a new automatic reaction path search approach has been proposed on
the basis of the artificial force induced reaction (AFIR) method [J. Chem. Theory Comput. 2011, 7,2335-2345.]. We demonstrate in this Letter that this approach enabled semi-automatic determinationof the full catalytic cycle of the HCo(CO)3-catalyzed hydroformylation. The search was fullysystematic; no initial guess was required concerning the entire reaction mechanism as well as eachtransition state structure. This approach opens the door to non-empirical prediction of complex
reaction mechanisms involving multiple steps in multiple pathways, such as full cycles of catalytic－ 91 －

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Ⅳ 研究業績 (2011)

reactions.
1-4. Experimental and Theoretical Investigations of Isomerization Reactions of Ionized
Acetone and Its Dimer (original paper 4)
Ionization dynamics of acetone and its dimer in supersonic jets is investigated by a combination ofexperimental and theoretical techniques, both of which have recently been developed. In
experiments, the neutral and the cationic structures are explored by infrared predissociation
spectroscopy with the vacuum-ultraviolet photoionization detection schemes. Reaction paths
following the one-photon ionization of the acetone monomer and its dimer have been studied by thejoint use of several theoretical methods including the ab initio molecular dynamics, the global
reaction route mapping, the intrinsic reaction coordinate, and the artificial force induced reaction
calculations. Upon one-photon ionization, the dimer isomerizes to the H-bonded form, in which theenol cation of acetone is bound to the neutral molecule, while this enolization is energeticallyforbidden in the acetone monomer. The enolization of the dimer cation occurs through a two-step
proton-transfer from the methyl group of the ionized moiety, and is catalyzed by the neutral moiety
within the dimer cation.
1-5. Exploring Multiple Potential Energy Surfaces: Photochemistry of Small CarbonylCompounds (original paper 5)
In theoretical studies of chemical reactions involving multiple potential energy surfaces (PESs) suchas photochemical reactions, seams of intersection among the PESs often complicate the analysis. In
this paper, we review our recipe for exploring multiple PESs by using an automated reaction pathsearch method which has previously been applied to single PESs. Although any such methods for
single PESs can be employed in the recipe, the global reaction route mapping (GRRM) method was
employed in this study. By combining GRRM with the proposed recipe, all critical regions, that is,transition states, conical intersections, intersection seams, and local minima, associated with multiple
PESs, can be explored automatically. As illustrative examples, applications to photochemistry offormaldehyde and acetone are described. In these examples as well as in recent applications to othersystems, the present approach led to discovery of many unexpected nonadiabatic pathways, bywhich some complicated experimental data have been explained very clearly.
1-6. Temperature Dependences of Rate Coefficients for Electron Catalyzed Mutual
Neutralization (original paper 6)
The flowing afterglow technique of variable electron and neutral density attachment mass
spectrometry (VENDAMS) has recently yielded evidence for a novel plasma charge loss process,electron catalyzed mutual neutralization (ECMN), i.e., A+ + B− + e− → A + B + e−. Here, rate

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Ⅳ 研究業績 (2011)

constants for ECMN of two polyatomic species (POCl3− and POCl2−) and one diatomic species(Br2−) each with two monatomic cations (Ar+ and Kr+) are measured using VENDAMS over thetemperature range 300 K-500 K. All rate constants show a steep negative temperature dependence,
consistent with that expected for a three body process involving two ions and an electron. No
variation in rate constants as a function of the cation type is observed outside of uncertainty;
however, rate constants of the polyatomic anions (~1 × 10-18 cm6 s-1 at 300 K) are measurably higher
than that for Br2− [(5.5 ± 2) × 10-19 cm6 s-1 at 300 K].
1-7. Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of
Reaction Mechanisms (original paper 7)
In these five decades, many useful tools have been developed for exploring quantum chemical
potential energy surfaces. The success in theoretical studies of chemical reaction mechanisms has
been greatly supported by these tools. However, systematic prediction of reaction mechanisms
starting only from given reactants and catalysts is still very difficult. Toward this goal, we describe
the artificial force induced reaction (AFIR) method for automatically finding reaction paths of type
A + B → X (+ Y). By imposing an artificial force to given reactants and catalysts, the method canfind their reactive sites very efficiently. Further pressing by the artificial force provides approximatetransition state and product structures, which can be easily reoptimized to the corresponding true
ones. This procedure can be executed very efficiently just by minimizing a single function called the
AFIR function. All important reaction paths can be found by repeating this cycle starting from many
initial orientations. We also discuss perspectives of automated reaction path search methods toward
the above goal.
2. List of original papers(1) M. P. Grubb, M. L. Warter, H. Xiao, S. Maeda, K. Morokuma, S. W. North, No Straight Path:
Roaming in Both Ground- and Excited-State Photolytic Channels of NO3 → NO + O2, Science,
2012, 335, 1075-1078.
(2) P. S. Krstic, J. P. Allain, A. Allouche, J. Jakowski, J. Dadras, C. N. Taylor, Z. Yang, K.
Morokuma, S. Maeda, Dynamics of Deuterium Retention and Sputtering of Li–C–O Surfaces.,
Fusion Eng. Des., [doi:10.1016/j.fusengdes.2011.07.009].
(3) S. Maeda, K. Morokuma, Toward Predicting Full Catalytic Cycle Using Automatic Reaction
Path Search Method: A Case Study on HCo(CO)3-Catalyzed Hydroformylation., J. Chem.
Theory Comput., 2012, 8, 380-385.
(4) Y. Matsuda, K. Hoki, S. Maeda, K.-i. Hanaue, K. Ohta, K. Morokuma, N. Mikami, A. Fujii,
Experimental and Theoretical Investigations of Isomerization Reactions of Ionized Acetone andIts Dimer., Phys. Chem. Chem. Phys., 2012, 14, 712-719.

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Ⅳ 研究業績 (2011)(5) S. Maeda, K. Ohno, K. Morokuma, Exploring Multiple Potential Energy Surfaces:
Photochemistry of Small Carbonyl Compounds., Adv. Phys. Chem., 2012, 2012, 268124 (13pages).
(6) N. S. Shuman, T. M. Miller, J. F. Friedman, A. A. Viggiano, S. Maeda, K. Morokuma,
Temperature Dependences of Rate Coefficients for Electron Catalyzed Mutual Neutralization.,
J. Chem. Phys., 2011, 135, 024204 (8 pages).
(7) S. Maeda, K. Morokuma, Finding Reaction Pathways of Type A + B → X: Toward Systematic
Prediction of Reaction Mechanisms., J. Chem. Theory Comput., 2011, 7, 2335-2345.
3. List of review articles(1) 大野公一・前田理「化学反応経路の自動探索」、Mol. Sci., 2011, 5, A0042 (16 pages).
4. List of books
5. List of presentations at meetings(1) (口頭発表)前田理・諸熊奎治、「反応経路自動探索法による触媒サイクルと選択性の量
子化学的予測」、日本化学会第 92 春季年会(2012)、慶應義塾大学日吉キャンパス・矢
上キャンパス、2012 年 3 月 25-28 日(2) (招待講演) 前田理「人工力誘起反応法（AFIR）による化学反応経路探索」、シンポジ
ウム「化学反応経路探索のニューフロンティア 2011」、北海道大学、2011 年 9 月 23-24
日(3) (口頭発表)前田理・阿部恵里花・諸熊奎治、「反応経路自動探索法の有機金属触媒サイ
クルへの応用」、第 5 回分子科学討論会、札幌コンベンションセンター、2011 年 9 月
20-23 日(4) (Oral) S. Maeda, K. Ohno, K. Morokuma, 16th International Workshop on Quantum Systems in
Chemistry and Physics (QSCP- XVI), Kanazawa, Japan, September 11-17, 2011(5) (Oral) S. Maeda, H. Xiao, R. Saito, K. Morokuma, Nonadiabatic Reactions Studied by
Automated Reaction Path Search Methods., 7th Congress of the International Society for
Theoretical Chemical Physics (ISTCP-VII), Waseda University, Tokyo, Japan, September 2-8,
2011(6) (Invited talk) S. Maeda, Finding Chemical Reaction Pathways: Toward Systematic Predictionof Reaction Mechanisms., FISTC: Fukui International Symposium for Theoretical andComputational Chemistry, Kyoto, Japan, August 31 and September 1, 2011(7) (ポスター発表)前田理・大野公一・諸熊奎治、「化学反応予測に向けた反応経路自動探索法の開発とその超並列化」、計算分子科学研究拠点（ＴＣＣＩ）第２回研究会、理化学研究所計算科学研究機構(AICS)、2011 年 8 月 11-12 日－ 94 －

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Ⅳ 研究業績 (2011)(8) (Invited talk) S. Maeda, Finding Unexpected Reaction Pathways using Automated Reaction
Route Finders., The World Association of Theoretical and Computational Chemists (WATOC)
2011, the Auditorio de Galicia and the Faculty of Medicine of the University of Santiago in
Santiago de Compostela, Spain, July 17-22, 2011(9) (口頭発表)前田理・諸熊奎治、「人工力誘起反応法による A + B → X 型反応経路の自動探索」、第 14 回理論化学討論会、岡山大学創立五十周年記念館、2011 年 5 月 12-14日(10) (Invited talk) S. Maeda, A New Paradigm for Finding Reaction Pathways for Organic
Multicomponent Reactions., The First International Symposium on Computational Sciences(ISCS2011), Shanghai, China, April 18-21, 2011
6. Others－ 95 －

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Ⅳ 研究業績 (2011)

Zhuofeng KE

４．博士研究員

FIFC Fellow, Fukui Kenchi Memorial Research Group 1
1. Summary of the research of the year
I. Theoretical Study of Polymerization Catalyzed by Artificial Metalloenzymes.

Figure 1. Plausible active sites A, B and C inside Rh(nbd)•apo-Fr for the Rh-diene catalyzed polymerization of PA: theRhI-insertion, RhI-metathesis or RhIII-insertion.

Artificial metalloenzyme is a promising strategy to mimic enzyme catalytic functions or todevelop novel enzyme-like catalysis, via combination of metal complex(es) into a host protein,.
This strategy exhibits the advantages of metal complex in easy accessibility, broad substrate scope,and versatile reaction transformation, and the merits of enzyme in high efficiency, specificselectivity, and green chemistry. Therefore, it has intriguing potentials in the application anddevelopment of catalysis, through chemical evolution of metal complexes component and genetic
evolution of the protein component. However, the design of new artificial metalloenzymes is rather
challenging due to the complicated interactions between metal complex and protein, especiallywhen the metal complexes have variable geometries in binding sites. To advance development ofartificial metalloenzymes, it is important to detailedly understand the active site and the exact
reaction mechanism inside host protein. Unfortunately, it is difficult to characterize the active
species for the catalysis inside artificial metalloenzymes. Sometimes, only with some X-ray crystal
structures of catalytic precursors or intermediates, the catalysis process inside artificial
metalloenzyme is still less known. This study will clarify, with QM/MM studies, the complicatedreaction polymerization mechanism for a recently developed artificial metalloenzyme system(Rh(nbd)·apo-Fr), with the X-ray proposed A, B, and C types of binding sites (Figure 1).
We have previously studied computationally the detailed mechanism of polymerization of PA
catalyzed by the homogenous catalyst [Rh(nbd)Cl]2 without protein environment. (J. Am. Chem.
Soc. 2011, 133, 7926-7941). The equilibriums of the reaction intermediates in the solution are more
complicated than generally assumption. The RhI, RhIII, and Rh-carbene types of intermediates are－ 96 －

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Ⅳ 研究業績 (2011)

all thermodynamically and kineticallyfeasible. Among them, the RhI insertion
mechanism is most preferred for thepolymerization. In contrast, the RhIII
insertion and the Rh-carbene metathesis
mechanisms need to overcome higher
reaction barriers. RhI insertion shows
perfectly regio- and stereoselectivity, i.e.
the 2,1-inserion of PA leading to thehead-to-tail cistransoidal PPA. To
elucidatehowdifferentisthepolymerization mechanism inside artificial
metalloenzyme from that in homogeneous
solution, with the influence of the protein
environment, we carried out a QM/MM
study on the complicated polymerization
mechanism for the (Rh(nbd)·apo-Fr)
system, (nbd = norbornene) which iscomposed of a rhodium complex[Rh(nbd)Cl]2 and the recombinant horse
L-chain apo-Ferritin. We found that thebinding sites A, B and C, from X-ray
crystalstructure,are
only
precursors/intermediates, not true active
sites
for
the
polymerizationofphenylacetylene (PA). A new hydrophobic
site D is suggested to be the most plausible
active site for the polymerization. After thecoordination of first monomer PA, theRhI(PA) complex is extruded from site B tothe hydrophobic site D nearby. Then thepolymerization occurs in site D via
RhI-insertion mechanism. Importantly, a
specific “hydrophobic region” composedby the hydrophobic active site D, thenonpolar 4-fold channel and otherhydrophobic resides nearby is found to
facilitate the accumulation, coordinationand insertion of PA for the polymerization.

H

H

Ph

H

Ph

RhI
His
Ferritin

RhI

H-transfer

H

His
Ferritin

DI-3

His
DI-TSHoxidative addition
H

H

H

Ph
I

Rh

Ph

H

RhIII

H
H

Ferritin

Ferritin

DI-TSO

DI-4

reductive elimination
H
H
Ph

H
RhIII
His

His

His
Ferritin

H
H
Ph
H
RhI

H

Ferritin

DI-5

DI-TSE

BI-TSA
34.2
DI-TSH
20.8

E

BI-1

DI-TSO
12.9

BI-2
5.8

0.0

DI-TSD
8.3

DI-TSE
13.5
DI-5
5.5

DI-3
-6.1
BI-PCA-23.9
no re-combination

DI-4
-15.9

DI-PCD-25.8

Figure 2. The plausible active site in hydrophobic pocket near site
D and the 4-fold channel.
Scheme 1. The overview mechanism of the polymerization of
PA in the studied artificial metalloenzyme system.

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Ⅳ 研究業績 (2011)

Our results also demonstrate that the hydrophobic active site D can retain the native regio andstereoselectivity of the Rh-catalyzed polymerization of PA without protein. The preferred potential
energy surfaces, as well as reaction scheme, are shown in Figure 2. The overall reaction mechanism
is shown in Scheme 1. This study highlights the importance of theoretical study in mechanistic
understanding and rational design of artificial metalloenzymes, indicating that even with X-ray
crystal structures at hand we may still be far from fully understanding the active site and thecatalytic mechanism of artificial metalloenzymes.
II. Theoretical Study of Asymmetric Hydration Catalyzed by DNA-based Artificial Enzyme.

Figure 3. The d orbital splitting in the ligand fields oftetrahedral, square planar, square pyramidal and octahedraltransition metal complexes.

Biomacromolecule, like DNA, based
catalysts recently emerges as an attractive
strategytothesynthesisofenantiomericallypurecompounds.
Through recombination of DNA andmetal complexes with a specific ligand,highstereoselectivity
andrate
enhancement had been achieved inseveral important applications, such as
Diels–Alder,Michaeladdition,Friedel–Crafts reactions and hydration
reactions. A novel non-enzymatic
catalytic enantioselective hydration ofenones was recently published by Ben L.
Feringa, Gerard Roelfes and co-workers.
The chiral b-hydroxy ketone product was
obtained in up to 82% enantiomeric
excess. Importantly, this diastereospecificand enantioselective reaction had noequivalent in conventional homogeneous
catalysis. Herein, our theoretical study
aims to understand the mechanism andthe factors that controlling theenantioselectivity,
which
is
of
fundamental
importanttotheFigure 4. The thermodynamic stabilities of the studied CuIIdevelopment of these types hybrid
complexes in aqueous.
catalysis with DNA
First, we studied the geometries and the thermodynamic stabilities of the studied CuII

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Ⅳ 研究業績 (2011)

complexes in aqueous. Copper plays important roles in metal-catalyzed and enzymatic processes.
Natural copper compounds usually exist as CuI and CuII states. CuII with an open-shell d9 electronic
configuration is harder than CuI and softer than CuIII, thus have complicated coordination situation,
especially due to its Jahn-Teller effect(Figure 3). We performed DFT calculations for four, five andsix-coordinated CuII complexes with model systems (L1-Cu-R’) and real systems (L1-Cu-R)(Figure 4). The results for both model and real systems consist well with each other and suggest that
the CuII complexes prefer five and six-coordinated structures with additional axial solvent ligands,
rather than a four-coordinated square planar structure.
Table 1. Binding Energy from Docking Simulation.
Binding Energy

DNA1N(3.75)

DNA2N(3.75)

DNA1L(6.5)

DNA2L(6.5)(kcal/mol)

minor groove

minor groove

into layer

into layer

L1-Cu4-R’

-5.42

-4.58

-5.58

-5.42

L1-Cu5-R’

-6.29

-5.23

-5.95

-5.69

L1-Cu6-R’

-6.16

-5.69

-6.71

-6.50

L2-Cu-R

-8.89

-7.10

-9.25

-8.79

DNA1/2N is oligonucleotides with normal structures whose base-pair distance is 3.75 Å; DNA1/2L is oligonucleotides
with artificial structures whose base-pair distance is elongated to 6.5 Å to estimate the capability of complex to insert
into the DNA base-pair.

Secondly, we used combined docking and MD simulation to evaluate the binding modes andbinding energies of CuII complexes to DNA molecules. The binding manners and binding freeenergies (BE) obtained by docking simulation are summarized in Table 1. We systematicallycompared the docking behaviors for the four-coordinated L1-Cu4-R’, the five-coordinated
L1-Cu5-R’, and the six-coordinated L1-Cu6-R’. It is found that L1-Cu6-R’ and L1-Cu5-R’ havestronger binding affinities to both DNA1 and DNA2 than L1-Cu4-R’ does. Compared with thebinding manner in the minor groove (DNA1/2N, BE = -6.16/-5.69 kcal/mol), the L1-Cu6-R’
prefers to insert into the base-pair of DNA (DNA1/2L, BE = -6.71/-6.50 kcal/mol). As for the
L2-Cu-R complex (model for hydration reaction),
we also found that it prefers a binding manner of
insertion rather docking in the minor groove. The
binding affinity of L2-Cu-R to the minor grooveof DNA1/2N is calculated to be -8.89/-7.10
kcal/mol. A stronger binding free energy(-9.25/-8.79 kcal/mol) is obtained for L2-Cu-R
for its insertion into the layer of DNA1/2L. MD
simulation starting with the obtained docking Figure 5. The plausible stereoselective controllingbinding modes as initial structural also found that factors for the asymmetric catalysis by DNA-based
the intercalations insertion should be more artificial enzyme.
favorable than the minor groove aggregations,and the intercalations prefer specific layer of the base pairs.

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Ⅳ 研究業績 (2011)

Thirdly, to reveal the plausible stereoselective controlling factors (Figure 5) that playing a rolein the asymmetric hydration, we studied the Cu-catalyzed hydration reaction in the aqueous solution.
Our calculation suggested that the general proposed hydration reaction assisted by coordinatedwater molecules is less feasible. Both the 1,4-addition and the 1,2-addition reaction mechanisms
require to overcome reaction barriers of about 30 kcal/mol. However, with a deprotonated aqueous
CuII complexes model, the hydration reaction barrier is only about 16 kcal/mol. Our results indicatethat the acidity/basicity of the coordinated ligand or the base-pair/phosphodiester linkage may play
an important role in the stereoselectivity.
Scheme 2. Generally proposed Cu-catalyzed hydration reaction mechanism.

2. Original papers(1) Ke, Zhuofeng, Abe, S., Ueno, T., & Morokuma, Keiji, Catalytic Mechanism in Artificial
Metalloenzyme: QM/MM Study of Phenylacetylene Polymerization by Rhodium Complex
Encapsulated in apo-Ferritin. J. Am. Chem. Soc. Submitted.

(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, Abe,S., Ueno, T., Morokuma, K., Catalytic Mechanism in Artificial
Metalloenzyme: QM/MM Study of Phenylacetylene Polymerization by Rhodium Complex
Encapsulated in apo-Ferritin. The 7th Symposium of Fukui Institute for Fundamental

Chemistry, FIFC, Kyoto University, Kyoto, Japan. Jan. 6th. 2012. (poster)
4. Others－ 100 －

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Ⅳ 研究業績 (2011)

Joonghan KIM
FIFC Fellow, Fukui Kenichi Memorial Research Group 1
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. This means that a new method isurgently required to define the chirality based not on the whole tube structure but on the individual hexagons
that are formed during the growth process. Thus, we have recently developed the local chirality index(LOCI) method to determine the local chirality of arbitrary SWCNTs. For a growing, straight SWCNT
structure, the principal axes (PAs), denoted as the global PAs (GPAs) may be calculated trivially. The
z-component of the GPAs (GPAZ) is then assumed to be parallel to the growth axis of the SWCNT itself. We
note here that if this assumption does not hold (i.e. if GPAZ and the growth axis are not approximately
parallel) then the straightforward applicability of the LOCI method is limited, and a more involved
methodology is required to determine GPAZ. Each constituent hexagon in the SWCNT structure is thenidentified, and its individual PAs, denoted as the local PAs (LPAs), are calculated. The angle (ϕ) between
GPAZ and the z-axis of each hexagon’s LPAs (LPAz) can then be used to determine the efficacy of the LOCI
method for each hexagon. Hexagons with ϕ = 90º (i.e. the plane of the hexagon is parallel to the growth axisof the SWCNT) are ideally suited to the LOCI method, whereas ϕ = 0º (i.e. the plane of the hexagon isperpendicular to the growth axis of the SWCNT, such as in a cap) are not. All hexagons in the sidewall of an
ideal SWCNT are categorized as the former. Intermediate cases (hexagons with  between 0 and 90º) may betransformed to the suitable hexagon via two consecutive Euler rotations. Having done so, three angles (1, 2,and 3) formed between the planes defined by GPAZ and three pairs of para carbon atoms in the hexagon arecalculated. The effective average, ( = [1 + 2 + 3]/3 – 60), of 1, 2, and 3 is denoted as the local

chiral angle. By definition, 0°    30°, and the overall chirality of a SWCNT can be described using a
distribution of all constituent local chiral angles.
The present method has been applied to various SWCNT-like irregular structures as well as ideal
SWCNTs, and the results of distributions of local chiral angles are shown in Figs. 1(a)-(h). The histograms
were used for the representation of distributions of the local chiral angles  for all hexagons, color-coded
both in the structure and distribution, from red for zigzag (ZZ, =0°) through yellow to green for armchair－ 101 －

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Ⅳ 研究業績 (2011)(AC, =30°) (see inset in Fig.
1(a)).

The

width

of

each

histogram bin is 0.5°. Firstly,
we have calculated the local
chiral angles of ideal seed
SWCNTs of ZZ(10,0) with alength of 11 Å (total 40
hexagons),

AC(5,5)withalength of 10 Å (total 35
hexagons), and chiral(5,3) witha length of 12 Å (total 32
hexagons).

The

results

areshown in Figs. 1(a), (b), and (c),respectively. The histograms inthese figures show only one
peak each as we expected. The
values of the local chiral anglesof

ZZ(10,0),AC(5,5),andchiral(5,3) SWCNT are exactly
equal to the chiral angle, 0°,30°, and 21.8°, respectively.
Moreover, we calculated the
local chiral angles for distorted
Fig. 1. Histograms of the local chiral angles of various ideal and irregular SWCNT-like structures.

C40

Color codes used are illustrated in (a) as a triangle, from red for 0 to green for 30°. (a) Ideal ZZ(10,0)

structures were optimized using

SWCNT with a length of 11 Å. (b) Ideal AC(5,5) SWCNT with a length of 10 Å. (c) Ideal chiral(5,3)

DFTB method in the presence

SWCNT with a length of 12 Å. (d) AC-type distorted C40 cap. (e) ZZ-type distorted C40 cap. (f)of a Fe38 cluster supporting the

Irregular SWCNT obtained from DFTB/MD simulations in the trajectory A (T= 1000 K; at 45 ps ofcap and are distorted from thesimulation). The magenta wire frames show new added C atoms during DFTB/MD simulations. The

ideal C5v structures; they havebars with black borderline indicate new added hexagons during DFTB/MD simulations. (g) Irregularbeen used as an initial structure

SWCNT obtained from DFTB/MD simulations in the trajectory E (T= 1000 K; at 45 ps of simulation).

in DFTB/MD simulations. The(h) Irregular SWCNT obtained by DFTB/MD simulations in the trajectory G (T= 1000 K; at 45 ps ofAC-type

C40

cap

has

ten

simulation).

AC-typeofhexagonsandcap

structures.

These

ZZ-type C40 cap has five AC
and five ZZ-types of hexagons, which can be distinguished visually. Both AC-type and ZZ-type C40 caps
have five ill-suited hexagons near top site of the cap. For the regular C5v-symmetric caps, we should haveobtained two sharp peaks near  = 30° for AC-type and two peaks near  = 30° and 0° for ZZ-type. The
results of these distorted AC- and ZZ-type caps are shown in Figs. 1(d) and 1(e), respectively. The
distributions are not sharply peaked and indicate that the present method can detect subtle changes in the－ 102 －

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chiral angle by distortion of the structure. Thus the present method provides a new accurate tool for detectionof changes of local chiral environment during the dynamics of formation and annealing of SWCNT. The
distributions of local chiral angles of three typical irregular SWCNTs obtained in DFTB/MD simulations ofcontinued growth of a prepared AC hexagons during the growth simulation in Figs. 1(f)-(g). For example, inFig. 1(f) a total of eight new hexagons were added, as shown in the black borderline in the histogram; thelocal chiral angles of preexisting and new added hexagons are found distributed near 30.0°. This result
indicates that the local chirality of SWCNT shown in Fig. 1(f) is essentially retained. However, it does notmean a success of the chirality-controlled SWCNT growth since the one new added hexagon located on theunderneath of SWCNT in Fig. 1(f) fortunately possesses AC chirality despite of the existence of defects(pentagon and heptagon) near the hexagon. This example in Fig. 1(f) shows very good growth of SWCNT
except defects because of many newly added hexagons and the preservation of the original chirality. An
example in Fig. 1(g) shows that all local chiral angles are distributed near 30.0°, except one whose local
chiral angle is 2.9° (red colored hexagon). The value of 2.9° local chiral angle indicates that this hexagon isof ZZ-type. The formation of the ZZ-type hexagon was attributed to the existence of defect (pentagon in thiscase). Therefore, if any defect occurs and a new hexagon is added without healing process, the new added
hexagon cannot maintain the chirality of the existing tube. The initial structure before MD simulation had
twenty hexagons, and the present structure after MD growth process has also twenty hexagons. This
indicates that some preexisting hexagons were broken by incoming feedstock (C atoms in this case) anddefects are formed, which results in the failure of the chirality-controlled growth. Thus, the preservation of
the preexisting hexagons seems to be crucial for the chirality-controlled SWCNT growth. In the example ofFig. 1(h), the distribution of the local chiral angles is very broad; containing hexagons with all kinds of local
chiral angles. In particular, the local chiral angles for some newly added hexagons (with black borderline in
the histogram) are different from those of the preexisting hexagons. As can be seen in these results, the LOCI
method can monitor the state of the growth process and how the chirality is destroyed or maintained during
the growth process.

Dynamics of Local Chirality during SWCNT Growth: Armchair versus Zigzag Nanotubes
We examine the time-evolution of SWCNT chirality and local chiral angles during SWCNT growth(TE-LOCI). This is achieved via monitoring the average local chiral angle or LOCI of all hexagons, and its
standard deviation (σ), as a function of time. Despite of its simplicity, this analysis provides detailed
understanding of the growth process and the dynamics of SWCNT chirality itself. We have applied
TE-LOCI to AC(5,5) and ZZ(8,0) SWCNTs during their growth process. TE-LOCI analysis of trajectory(5,5)slow-B (Fig. 2(a)) shows no dramatic change in the average θ and corresponding σ, from the originalchirality of the SWCNT ((5,5) in this case) for the first 300 ps of growth. However, this does not indicate thesuccess of chirality-controlled SWCNT growth, since SWCNT growth in this trajectory exhibited heptagon
and pentagon defects (Fig. 2(b)). In particular, incoming carbon atoms readily initiated hexagon  heptagontransformation. This fact is reflected in the LOCI analysis; the total number of hexagons in the SWCNT at
300 ps (19 hexagons) was decreased compared to that in the initial SWCNT (20 hexagons). Alternatively,－ 103 －

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the local chirality can change during
the growth process, a phenomenon
typically indicated by a sudden change
in either/both θ and/or σ (for example,
such as that observed at 220 ps intrajectory (5,5)slow-F, Fig. 2(c)). In thiscase, this sudden change was caused by
the formation of a single hexagon witha significantly different local chiralangle; this hexagon was the result of anFig. 2. TE-LOCI analysis of slow (5,5) SWCNT growth, demonstrating (a),(b)incoming carbon atom attacking achirality-controlled (5,5) SWCNT growth observed in trajectory (5,5)slow-B, and (c),(d) apentagonloss of (5,5) SWCNT chirality during growth observed in trajectory (5,5)slow-F.

defect-healing

Data

at

210.28ps

process,(i.e.

asomewhatshown in (a),(b) are average θ values, error bars denote σ deviation. (c) Local chiralironically). Nevertheless, this hexagon

angles of all hexagons in trajectory (5,5)slow-B at 300 ps. (d) Local chiral angles of all

ultimately possessed a local chiral angle

hexagons in trajectory (5,5)slow-F at 220 ps. Red and blue bars denote original and addedthat is more typical of a zigzag SWCNT

hexagons, respectively. Black, white, and brown spheres denote carbon, hydrogen, and(θ=9.7º), since the adjacent heptagon

iron, respectively. Cyan spheres denote carbon atoms discussed in the text.

defectwasnotremoved.

Another

instance of ‘defective’ hexagon formation was observed in this trajectory at 211.36 ps, in this case θ=14.6º.
Both hexagons here remained in the SWCNT structure for the remainder of the simulation. From theseobservations it is concluded that in order to accomplish chirality-controlled SWCNT growth, the preventionof defect formation is a key factor. Thus, chirality-controlled growth is not determined solely by thedefect-healing process (such as in trajectory (5,5)slow-F, Fig. 2(d)), but additionally by the ability to impede
defect formation in the first place.
As can be seen in Fig. 3(a), local
chiralityispreserved

intrajectory(8,0)slow-A during growth. That is, nofluctuation in θ was observed. In addition,
new hexagons exhibiting the ‘original’chirality of the SWCNT were added
during growth. Although this trajectoryshows chirality-controlled growth, at leastin the context of TE-LOCI analysis, it also
exhibited a defect that resulted from theFig. 3. TE-LOCI analysis of slow (8,0) SWCNT growth, demonstrating (a),(b)destruction of preexisting hexagons, aschirality-controlled (8,0) SWCNT growth observed in trajectory (8,0)slow-A, and (c),(d)observed also in the case of (5,5) SWCNT

a loss of (8,0) SWCNT chirality during growth observed in trajectory (8,0)slow-D. Data

growth. Abrupt changes in the local

shown are average θ values, error bars denote σ deviation. (c) Local chiral angles of all

chirality were also observed during (8,0)

hexagons in trajectory (8,0)slow-A at 300 ps. (d) Local chiral angles of all hexagons in

SWCNT growth, as in the case of (5,5)

trajectory (8,0)slow-D at 220 ps. Color schemes as in Fig. 2.

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SWCNT growth. This is illustrated in Fig 3(c), which depicts the TE-LOCI of trajectory (8,0)slow-D. Up until
250 ps, local chirality was conserved during growth at a value essentially equivalent to that of a pristine
zigzag SWCNT. However, as shown in Fig. 3(d), an incoming carbon atom inserted directly into an existing
pentagon defect at 260 ps, thereby creating a hexagon possessing near-armchair chirality (θ=29.2º). This
structure was subsequently maintained for the remainder of the simulation. It is noted that the formation ofthis hexagon takes place via a route commonly associated with defect formation, viz. carbon atom insertion
into an existing C–C bond. Following this result, we conclude that the preservation of local chirality during
growth cannot be achieved in the absence of healing processes that remove defect structures located near the
SWCNT-catalyst interface. That is, healing during SWCNT growth is necessary for the conservation of local
chirality.

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”, Phys. Rev. Lett. 107, 175505 (2011)(2) Joonghan Kim, Alister J. Page, Stephan Irle, and Keiji Morokuma,“Dynamics of Local Chirality during SWCNT Growth: Armchair versus Zigzag
Nanotubes”, submitted
3. Presentation at academic conferences(1) Joonghan Kim and Keiji Morokuma“Determination of Local Chirality of Irregular Single-Walled Carbon Nanotube Based on
Individual Hexagons”
7th Congress of the International Society for Theoretical Chemical Physics, Tokyo, Sep. 4,2011
4. Others(1) Joonghan Kim, Alister J. Page, Stephan Irle, and Keiji Morokuma“The dynamics of Local Chirality during SWCNT Growth: A QM/MD Investigation”
The 9th Symposium of Fukui Institute for Fundamental Chemistry, Kyoto, Jan. 6, 2012

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Alister PAGE
Fukui Fellow, Fukui Kenichi Memorial Research Group 1
1.

Summary of the Research of the Year(A)

Chirality-Controlled Carbon Nanotube Growth from Organic Templates

The electronic properties of single-walledcarbon nanotubes (SWCNTs) are solely
determined by their atomic structure, which is
specified by a pair of chiral indices (n,m). Precise
chirality control during SWCNT synthesis has
become the ‘holy grail’ of nanotube research since
it became clear that conventional high-temperaturesynthetic methods are incapable of achieving suchcontrol. Recent success in the synthesis of[n]cycloparaphenylenes ([n]CPPs) has fueled
speculations on their use as organic templates inthe ‘bottom-up’ synthesis of (n,n) SWCNTs andgeneral carbon nanostructures. We have proposeda mechanism of SWCNT growth from [n]CPPs
based upon the ethynyl (C2H) radical. The
formation of this radical from acetylene (C2H2) is
known experimentally to take place attemperatures as low as 100 K on a variety ofsurfaces, including Fe, alumina and silica. The
benefits of this radical-based mechanism over‘traditional’, Diels-Alder cycloaddition-based
approaches are numerous. Firstly, a decrease in theactivation energy of approximately one order ofmagnitude is obtained using C2H instead of C2H2.
In addition, hydrogen abstraction from the growing
SWCNT edge by C2H (which we show to takeplace ca. 40 % of the time) produces radical
centers on the growing SWCNT, which in turnfacilitate much more labile SWCNT growth via
C2H2 addition, see Fig. 1. For further details of our
QM/MD simulations of SWCNT growth via C2H
addition to [n]CPPs, see the report of Dr Hai-Bei
Li.
We have further demonstrated catalyst-free,chirality-controlled growth of chiral and zigzag
SWCNTs from organic precursors using quantum
chemical simulations. Comparison of C2H- andC2H2-based growth mechanisms highlights the roleof the C2H radical in the growth of chiral andzigzag SWCNTs, as well as the growth of armchair
SWCNTs. In agreement with current experimental
and theoretical data concerning transition-metal
catalyzed SWCNT growth, we have shown herethat the SWCNT growth rate under significantly
different (i.e. low temperature, catalyst-free)conditions correlates directly with the chiral angle
 of the SWCNT fragment. This relationship is

(a)

(b)

Fig. 1 (a) Reactive PES of C2H andbiphenyl/phenanthrene interaction, resulting inhexagon formation. In all cases, prior C2H addition isa barrierless process. (b) Reactive PES of C2H2 andbiphenyl/phenanthrene radical interaction, resulting inhexagon formation. Three possibilities, in which
neither H2/ H2′ have been abstracted (i.e. DA
cylcoaddition, IV), H has been abstracted (V) and both
H2/ H2′ have been abstracted (VI) are shown. All data
computed using B3LYP/6-31G(d); Gibbs freeenergies calculated at 500 K.

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Fig. 2. (a) Reaction mechanism for hexagon addition to [n]CPP precursors (II-R) and H2 renormalization via DA
cycloaddition. (b) G‡(II-TS1), (c) G(II-INT) (d) G‡(II-TS2) and (e) G(II-P), relative to II-R, for [n]CPP
precursors. All data computed using B3LYP/6-31G(d); Gibbs free energies calculated at 500 K.

therefore an intrinsic property of the SWCNT edge structure itself; the trend may presumably only beenhanced or minimized, but hardly reversed, by altering the conditions of growth. On the other hand, resultspresented here suggest that the relationship between the SWCNT’s diameter and its rate of growth depends
explicitly on the growth conditions. Contemporary theories of SWCNT growth rates, which are shown to be
in good agreement with experimental data, are implicitly diameter-independent. Our simulations of C2Hbased SWCNT growth also show diameter-independent SWCNT growth rates. Conversely, the energetics of
SWCNT growth via DA-based cycloaddition of C2H2 is influenced strongly by the SWCNT diameter, withthe growth rate being proportional to the SWCNT diameter, see Fig. 2. Under such conditions, SWCNT
diameter must therefore be taken into account if the mechanism and kinetics of SWCNT growth are to beunderstood. Most notably, our theoretical investigation points to the possibility that, for a given C2H/C2H2
feedstock ratio, a SWCNT diameter/chirality combination that yields a maximum growth rate exists.

(B)

Functionalization of Fullerenes Using a Genetic Algorithm

Functional carbon nanomaterials, such as graphene oxide, are being heralded as a cornerstone of the next
generation of nano- and micro-scale devices. However, our understanding of the factors underpinning thefunctionalization of graphene, SWCNTs and fullerenes is relatively limited at this time. One of the
mitigating factors in this respect is the combinatorial size of the problem; for example, to determine thethermodynamically most favorable hydroxylated adduct of C60 for M OH groups one must consider
M!/[60!(M-60)!] structures (and more generally M!/[n!(M-n)!] for a structure with n possiblefunctionalization sites). Clearly this cannot be achieved using QM methods, even for relatively modest cases.
In the case of C60H5, the number of symmetrically distinct isomers is 45,010 (from a total of 5,461,512
structures in total). One possible alternative is to consider the use of -Hückel theory as an approximation toa full QM description of functionalization, since the disruption to the -conjugation of the carbon
nanostructure presumably accounts for the majority of the energy associated with functionalization. In some－ 107 －

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cases this is certainly true; however, in others -Hückel theory, and other topological approaches (such as the
Zhang-Zhang polynomial approach) fail to describe functionalization completely. We have shown that thisshortcoming of these simplified approximations coincides with those cases in which a large geometricaldeformation of the functionalized structure takes place, see Figs 3 and 4. By definition, these simplified
approaches cannot describe such geometrical considerations, and so in general one must employ moresophisticated methods to describe carbon nanostructure functionalization.
To this end, we have optimized a genetic algorithm (GA) that is designed to predict the most stablestructural isomers of hydrogenated and hydroxylated carbon nanostructures. While this GA wasparameterized using hydrogenated and hydroxylated C20 fullerenes, anticipate that it will applicable to thefunctionalization of any nanostructure, since it only considers energy of a given structure (which it is trying
to minimize). Density functional theory (DFT) and density functional tight binding (DFTB) methods areboth employed to compute isomer energies in the parameterization of the GA. We have shown that DFTB
and DFT levels of theory are in good agreement with each other and that therefore both sets of optimized GA
parameters are very similar. An energy decomposition analysis (EDA) for both C20Hn and C20(OH)n systems
reveals that, for only few functional groups, the relative stabilities of different structure isomers may berationalized simply with recourse to -Hückel theory. However, upon a greater degree of functionalization,
-electronic effects alone are incapable to describe the interaction between the functional groups and the
distorted cage, and both - and -electronic structure must be taken into account in order to understand therelative isomer stabilities.

Fig. 3. (a) EDA of C20H4 functionalization. DFT
Edef(C20) and Eint for 57 distinct isomers shows that theisomers with the most favorable E are those with thelargest Eint. (b), (c) Structural deformation of the (b)most and (c) least stable C20H4 isomers according to
Hückel (left) and DFT/DFTB (right). Structures
shown are DFT-optimized. Functionalized structures
are given in red and the pristine C20 cage is given in
blue.

Fig. 4. (a) EDA of C20(OH)4 functionalization.
DFT Edef(C20) and Eint for 57 distinct isomers
shows that the isomers with the most favorable
E are those with the largest Eint. However,hydrogen bonding between adjacent OH groups isseen to increase Eint substantially as shown in (b).
Conversely, in the absence of these stabilizinghydrogen bonds, Eint is seen to decrease, as shownin (c).

(C)
Effects of Molecular Dynamics Thermostats on Descriptions of Chemical NonEquilibrium－ 108 －

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The performance of popular molecular dynamics (MD) thermostat algorithms in constant temperature
simulations of equilibrium systems is well known. This is not the case, however, in the context of nonequilibrium chemical systems, such as chemical reactions or nanoscale self-assembly processes. We haveinvestigated the effect of popular thermostat algorithms on the natural dynamics of a non-equilibrium,chemically reacting system. By comparing constant-temperature quantum mechanical MD (QM/MD)
simulations of carbon vapor condensation using velocity scaling, Berendsen, Andersen, Langevin and NoséHoover Chain thermostat algorithms with ‘natural’ NVE simulations, we have shown that efficienttemperature control and reliable reaction dynamics are mutually exclusive under conditions of chemical nonequilibrium, see Fig. 5. This problem may be circumvented, however, by placing the reactive system in an
inert He atmosphere which is itself described using NVT MD, see Fig. 6. We have demonstrated that both
realistic temperature control and dynamics consistent with natural NVE dynamics can then be obtained
simultaneously. In essence, the thermal energy created by the natural dynamics of the NVE subsystem isdrained by the thermostat acting on the NVT atmosphere, without adversely affecting the dynamics of thereactive system itself.

Fig 5. Comparison of time-dependent velocity
distributions of a reactive C2 system using (a) NVE
C2 and a Nosé-Hoover Chain thermostat coupled (b)strongly ( = 188.37 ps-1) and (c) weakly ( = 0.19
ps-1) to the degrees of freedom of the system. For
reference, time-dependent Maxwell-Boltzmann
velocity distributions at the corresponding NVE
MDsimulation temperatures are included in (a)(grey lines). Temperature control comes at the costof sacrificing a reliable description of the ‘natural’reaction dynamics.

Fig 6. Comparison of time-dependent velocity
distributions of a reactive C2 system using (a) NVE
C2, (b) NVE C2+He, and (c) NVE(C)-NVT(He)ensembles. For reference, time-dependent MaxwellBoltzmann velocity distributions at the corresponding
NVE MD simulation temperatures are included in (a)(grey lines). NVE/NVE(C)-NVT(He) simulations use
C:He=1:1. P(v) shown only take into account carbon
atom velocities.

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Ⅳ 研究業績 (2011)2.

Original Papers(1) 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 andComputational Nanoscience, 8, 1755 (2011).
(2) Y. Wang, A. J. Page, H.-J Qian, Y. Nishimoto, S. Irle, K. Morokuma, “Template Effect in theCompetition Between Haeckelite and Graphene Growth on Ni(111): Quantum-Chemical Molecular
Dynamics Simulations”, Journal of the American Chemical Society, 133, 18837 (2011).
(3) H.-B. Li, A. J. Page, S. Irle, K. Morokuma, “Theoretical Insights into Chirality-Controlled SWCNT
Growth from a Cycloparaphenylene Template”, ChemPhysChem, 13, 1479 (2012).
(4) M. A. Addicoat, A. J. Page, Z. Brain, L. Flack, S. Irle, K. Morokuma, “Optimisation of a Genetic
Algorithm for the Functionalisation of Fullerenes”, Journal of Chemical Theory and Computation, 8,1841 (2012).
(5) J. Kim, A. J. Page, S. Irle, K. Morokuma, “The Dynamics of Local Chirality during SWCNT Growth:Armchair versus Zigzag Nanotubes”, Journal of the American Chemical Society, 134, 9311 (2012).
(6) H.-B. Li, A. J. Page, Y. Wang, S. Irle, K. Morokuma, “Sub-Surface Nucleation of Graphene Precursors
near a Ni(111) Step-Edge”, ChemComm, In press.
(7) A. J. Page, T. Isomoto, J. Knaup, S. Irle, K. Morokuma, “Effects of Molecular Dynamics Thermostatson Non-Equilibrium Systems.”, Journal of Chemical Theory and Computation, Submitted.
(8) H.-B. Li, A. J. Page, S. Irle, K. Morokuma, “SWCNT Growth from Chiral Carbon Nanorings: Prediction of
Chirality and Diameter Influence on Growth Rates”, Journal of the American Chemical Society, In press.

3.

Presentations at Academic Conferences(1) “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).
(2) “Understanding Nanoscale Self-Assembly Processes Using QM/MD: Mechanisms of Carbon Nanotube
Nucleation and Growth”. (Talk) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, 2011 World
Congress of WATOC, Abstract Page OC098, Santiago de Compostela, Spain (2011).
(3) “Mechanisms of Carbon-Based Nanostructure Self-Assembly: Insights from Density-Functional TightBinding Molecular Dynamics”. (Talk) A. J. Page, K. R. S. Chandrakumar, S. Irle, K. Morokuma, 7thCongress of the International Society for Theoretical Chemical Physics, Abstract Page 6A2-2C, Tokyo,
Japan (2011).

4.
(1)Book Chapters“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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Miho HATANAKAFIFC Fellow, Fukui Kenichi Memorial Research Group 1

1.

Summary of the research of the year

(A) DFT study of the mechanism of NO reduction in bacterial nitric oxide reductase

Nitrous oxide reductase (NOR) is a key enzyme for the reduction of NO which is a
step in anaerobic respiration process.
2NO + 2H+ + 2e → N2O + H2O(1)This reaction is interesting because it contains N-N bond formation and N-O bondcleavage. Additionally, NOR has a key to clarify the evolutional history of acquirementof aerobic respiration, because NOR has the same ancestor as Cytochrom c Oxidase(CcO) which catalyzes the reduction of O2 in aerobic respiration. The overall structureof NOR is quite similar to that of CcO, though the structure of active site and proton
pathway are different. The most notable difference in active site between NOR and CcO
is that the active site of NOR has a heme-Fe and a non heme-Fe, so-called FeB, whilstthat of CcO has a heme-Fe and a non heme-Cu. Therefore, the role of two metal centers
could have a quite important key to clarify the evolutional change.
Although several mechanisms have been proposed in previous studies, such as thecis:FeB mechanism, the trans mechanism, and the cis:b3 mechanism, it is a highly
controversial issue. In this study, we performed density functional theory to understandthe enzymatic mechanism of NO reduction. An X-ray structure of cytochromec-dependent NOR (cNOR) from Pseudomonas aeruginosa (PDB code 3O0R) was used
as a starting point for our calculations.
As shown in Figure 1, we compare
the reaction energy profile for threemechanisms, and clarify that first NO
coordinates to heme-Fe and second
NO form a stable N-N bond with NO
coordinating to heme-Fe. The
formation of N-N bond between two
NO seems difficult, because it is wellknown that two neutral NO molecules
cannot form a stable bond in gas

Scheme 1. Possible reaction pathways for two
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phase. However, NO coordinating to heme-Fe
can coordinate to the second neutral NO
molecule without reaction barrier, because
NO in Cmp2 is partly reduced by heme-Fe,and has an anionic character.
After producing the five membered-ring
complex (Cmp7), one N-O bond has to becleaved to yield N2O (Cmp9). Then, theFigure 1. The reaction energy (in remaining oxygen atom coordinates to both
two Fe centers to form a -oxo complex
kcal/mol) for two NO addition(Cmp10). After the addition of two protons
and two electrons, and the subsequent dissociation of a water molecule, Cmp10 can
return to the starting point of this enzymatic cycle (Cmp1), as summarized in Path(a) in
Scheme 2. However, the barrier of N-O bond cleavage from Cmp7 is 27.9 kcal/mol,which is too large compared with the experimental barrier of 13.3 kcal/mol.
To find a favorable reaction path, protons and electrons adducts to Cmp7 are
examined, because two protons and two electrons which are needed for this reaction canbe added in any step of this reaction. Firstly, we focus on the NO cleavage mechanismof protonated Cmp7 (Cmp7p) as shown in Path(b) in Scheme 2. Surprisingly, the barrierof N-O bond cleavage fromseptet Cmp8p is only 11.1
kcal/mol, which is much lower
than that from the deprotonatedcomplex (Cmp7). However,combined with the energetics ofproton transfer from Glu211 tohyponitrite (N2O2), which isendothermic by 7.4 kcal/mol, thebarrier for N-O bond cleavage
from Cmp7p is 18.6kcal/mol
which is still larger than theexperimental barrier of 13.3
kcal/mol. In other words, aproton addition does not promote the Scheme 2. Possible reaction pathways for NO
N-O bond cleavage.
bond cleavage and N2O dissociation
Secondly, reduced Cmp7p, which－ 112 －

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Ⅳ 研究業績 (2011)means a proton and an electron adduct to Cmp7, is examined (Cmp7h) whose reaction
pathway is shown in Path (c) in Scheme 2. In this case, the proton transfer from Glu211
to hyponitrite is endothermic by 2.6kcal/mol and the barrier of subsequent N-O bondcleavage reaction is 8.4 kcal/mol. Therefore, the barrier of N-O bond cleavage fromsextet Cmp7h is 11.0 kcal/mol which is good agreement with the experimental barrierof 13.3 kcal/mol. To clarify the total barrier for NO bond cleavage, we need to estimate
the energetics of electron transfer from heme b ,which is another heme in cNOR and arelay point of electron transfer, to Cmp7p. Although, it is difficult to calculate accurate
absolute redox potentials because they depend on the surrounding environments,
relative redox potential values for the same model can be calculated with much higher
accuracy because the surroundings are the same. Therefore, we fit the parameter byusing electron affinity of Cmp10p in our model to adjust its electron affinity calculated
by Seigbahn et al. By using this parameter, energetics of electron transfer to Cmp7p canbe estimated which is exoergic by -5.4 kcal/mol. Therefore, on the basis of the results of
our DFT calculations, we propose an enzymatic reaction mechanism of NO reduction incNOR as shown in Scheme 3. It should be noted that our proposed mechanism is thesame as that of NO reduction in “heme Fe/ non heme CuB system” proposed by
Seigbahn and coworkers.

Scheme 3. Proposed mechanism for NO reduction in bacterial cNOR(B) Effect of protein environment on the NO reduction: An ONIOM study
As seen in the previous section, we found a reasonable pathway as seen in Scheme 3
and succeeded in explaining the experimental reaction barrier. Next, we recalculate theenergetics of this reaction pathway by using ONIOM (DFT:MM) method to examine
the effect of surrounding residues. We expected that the reaction barrier for the rate
determining step (N-O bond cleavage step: TS8h_9h) could be lowered by considering thesurrounding environment because the typical role of enzyme is to promote the reaction
by lowering the reaction barrier. However, the energetics from Cmp8h through Cmp10h
calculated by ONIOM-ME and ONIOM-EE methods are quite similar to that calculated
by DFT method, although there are differences of optimized geometries caused by the
restriction from surrounding protein. To clarify the effect of protein, we focus on the－ 113 －

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N-O bond cleavage step (Cmp8h→TS8h_9h) and examine the following effect, such as (i)electrostatic (ES) and van der Waals (vdW) interactions between QM and MM regionand (ii) deformation of QM region. Firstly, the effects of ES and vdW interactions are
examined. If these interactions between QM and MM in TS8_9h are smaller than those inCmp8h, the reaction barrier obtained by ONIOM must have a lower value than thatobtained by DFT in gas phase. To clarify how QM-MM interaction affects the value ofreaction barrier, we calculate difference of ES and vdW interaction energies, anddecompose them into contributions from eachresidue in the protein. However, the ES and vdWinteractions lower the barrier of N-O bondcleavage only by 2.8 kcal/mol, and -0.1 kcal/mol,
respectively, and only several residues near fromthe active site have the contributions. Both ES and
vdW effects do not affect the reaction barrier somuch, that means the mechanism of NO reduction
can be controlled by the several residues
coordinating to heme-Fe and non heme-FeB
directly. Lastly, we focus on the effect of
Figure 2. Geometry of TS8h_9h for NO
surrounding protein on the geometry of the active
bond cleavage calculated bysite, so-called the effect of deformation of QM
ONIOM-ME method
region. One of the notable differences ofgeometry between DFT (in gas phase) and ONIOM is that heme obtained by DFT has aplanar structure whilst heme obtained by ONIOM has a puckering structure because of
the geometric restrain from surroundings. In addition, we notice that intermediates
without bridged structures between heme Fe and non heme Fe dissociate only in gas
phase. Therefore, it can be said that the most important role of surrounding protein is tokeep a reasonable distance between upper part (non heme-FeB part) and lower part(heme-Fe part).

2. Original papers(1) Miho Hatanaka, Keiji Morokuma, “The Mechanism of the reduction of nitric oxide
in cytochrome c-dependent nitric oxide reductase (cNOR): A DFT study” Manuscript in
preparation.
3.

Presentation at academic conferences－ 114 －

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Ⅳ 研究業績 (2011)(1) Miho Hatanaka, Keiji Morokuma“Theoretical study of the reduction of nitric oxide in bacterial nitric oxide reductase”
52th Sanibel Symposium, St. Simons Island, Georgia, 2012/2/19(2) 畑中美穂・諸熊奎治「ヘム鉄・非ヘム鉄酵素を用いた NO 還元反応に関する理論的研究」
第５回分子科学討論会 2011 札幌

2011/9/20 1P111

4. Others(1) Miho Hatanaka, Keiji Morokuma“Theoretical study on the reduction of nitric oxide in bacterial nitric oxide reductase”
第 9 回京都大学福井謙一記念研究センターシンポジウム 福井謙一博士ノーベル賞受賞 30 周年記念

京都

2012/1/6 P50－ 115 －

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Xin LIJST Fellow, Fukui Kenichi Memorial Research Group 1(To 31 Dec. 2011)
1. Summary of the research of the year
Photodynamics and Isomerization Mechanisms of All-trans and 13-cis, 15-synRetinal Protonated Schiff Base in the light-adapted and dark-adapted
Bacteriorhodopsin
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 (Scheme1). In addition, there is a 40:60 mixture of all-trans (bRAT) and 13-cis, 15-syn (bR13C)
in the dark-adapted bR (see Scheme 1). bR13C can not release a proton but equilibrates
thermally with bRAT in the minute range. Photodynamics of all-trans and 13-cis,
15-syn retinal protonated Schiff base (RPSB) in bacteriorhodopsin and without anenvironment have been elucidated by nonadiabatic ONIOM(QM:MM) and QM
simulations. For both all-trans and 13-cis, 15-syn RPSB, bR protein favors the
C13=C14 bond-specific, ultrafast and unidirectional photoisomerization with a highquantum yield. The all-trans and 13-cis, 15-syn chromophore can be photoisomerized
to 13-cis, 15-anti and 13-trans, 15-syn (not 13-trans, 15-anti) RPSB, respectively.
Moreover, a thermal isomerization from 13-trans, 15-syn to 13-trans, 15-anti(all-trans) occurs by rotating the C15=N double bond. Therefore, there arelight-induced and thermal isomerizations from 13-cis, 15-syn (dark-adapted bR) to
all-trans RPSB (light-adapted bR). In addition, the thermal isomerizations between
several intermediates 13-cis, 15-syn (bR13C), 13-trans, 15-syn (K13C), all-trans (bRAT),
and 13-cis, 15-anti (KAT) in bR protein have been further investigated by the ONIOM(QM:MM) method. The key role of protein environment is discussed. The
isomerization mechanisms for the light-adapted and dark-adapted bR to their K states
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have been elucidated in the present work.
Scheme 1

Figure 1. Excited-state population for photoisomerization of 13-cis, 15-syn (upper)
and all-trans (lower) within and without bR protein.

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2. Original papers(1) 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).
(2) Xin Li, Lung Wa Chung, and Keiji Morokuma, “Modeling Photobiology Using
Quantum Mechanics (QM) and Quantum Mechanics/Molecular Mechanics (QM/MM)
Calculations,” In “Computational Methods for Large systems: Electronic Structure
Approaches for Biotechnology and Nanotechnology” Reimers, J. R. Eds. John Wiley& Sons, Inc., Hoboken, 2011, pp 397-433.
(3) Lung Wa Chung, Xin Li, Hajime Hirao, and Keiji Morokuma, “Comparative
Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in Heme and Non-Heme
Complexes”, J. Am. Chem. Soc. (Commun.) 133, 20076-20079 (2011).
(4) Abdel-Azeim, S.; Li, X.; Chung, L. W.; Morokuma, K. “Zinc-Homocysteine Displacementin Cobalamin-Dependent Methionine Synthase and its Role in Substrate Activation: DFT and
ONIOM Study”, J. Comput. Chem. 32, 3154-3167 (2011).

(5) Jiayun Pang, Xin Li, Keiji Morokuma, Nigel S. Scrutton, and Michael J. Sutcliffe,“Large-Scale Domain Conformational Change Is Coupled to the Activation of the
Co−C Bond in the B12-Dependent Enzyme Ornithine 4,5-Aminomutase: A
Computational Study” J. Am. Chem. Soc. 134, 2367-2377 (2012).
(6) 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, 2, 327-350 (2012).

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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1.

K. R. S. CHANDRAKUMAR
JST Fellow, Fukui kenichi Memorial Research Group 1(To 10 May 2011)
Summary of the research of the year 2012

Formation of Carbon Nanocapsule from Carbon Nanocone Aggregates around Nickel
Nanocluster: An Insight from Density Functional Tight-Binding based Molecular
Dynamics (DFTB-MD) Method
In our recent study, we have reported that interaction of nanohorns with the iron or
nickel catalyst at higher temperature leads to the formation of a new form of carbon
nanomaterials called as, nanooysters, a hollow graphene capsules containing metal particles
that resemble pearls in an oyster shell. The structure of the oyster consists primarily ofhexagons along with a few pentagons that are typically localized near the edges where thetwo cones are joined together. It may be noted that the formation of nanooysters has also been
experimentally characterized. Herein, we demonstrate the effect of the change indisclination (apex) angle (DA) or cone angle of the nanohorns is very significant in such hightemperature reactions. In particular, the nanohorns with DA-60 can lead to the formation of
nanooysters while the carbon nanocapsule-like structure is preferably formed from theaggregates of the nanohorns with DA-120. The structural transformation of carbon nanocone
into nanocapsules in the presence of iron and nickel nanoclusters as catalyst has been studied
using the recently developed density functional tight binding (DFTB) based molecular
dynamics simulation. In the present DFTB/MD simulations, we employed theself-consistent-charge DFTB (SCC-DFTB) method in combination with a finite electronic
temperature approach with Te=10000 K to evaluate the quantum chemical Born-Oppenheimer
potential on the fly. In the molecular dynamics simulations the velocity-Verlet integrator
was used with a time step of 1 fs, and the nuclear temperature was controlled by connecting
the Nose−Hoover chain thermostat to the degrees of freedom of the present model system.
We have annealed the initial starting structure at different temperatures 1500, 2000 and 2500
K for 10 ps, and ten such trajectories have been considered at the respective temperature for30-40ps. Thus, the investigation in this work is comprised of a total of 60 trajectories plus alarge number of less systematic supplementary simulations. As shown in Figure 1, Ourinitial structure comprise of the nanocone with definite length along with the iron nanoclusterof size Fe38 and Ni38.

Figure 1: Structures of the Carbon nanohorn with apex
angle 120, as well as the catalysts
Ni38 and Fe38.
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The nanohorn with DA-120 is structurally different from that of DA-60 and at the apex
region of the nanocone, DA-120 is characterized by the presence of 4m-ring instead of
5m-ring of DA-60. We initially optimized the iron and nickel nanoclusters of size 38 alongwith the nanohorn DA-120 with diameter 5 Å. The metal clusters are found to have the facecentered cubic structure with octahedron symmetry and the interaction of the cone is favoredwith the cluster at the face with 7-atom ring structure. The geometrical parameters alongwith the binding energy details are given in Table 1. Strikingly, it can be seen from Table 1
that the binding of strength of DA-120 is almost twice that of DA-60 with the iron or nickel
nanoclusters. In addition, the binding of strength of the nanocone with the iron cluster isobserved to be much stronger than nickel cluster.
Table 1: Binding energy and geometrical parameters of the nanocones (DA-60 and DA-120)
interacting with iron and nickel nanoclusters
Metal
Cluster (M)Cone-Metal-Cone (C-M-C)
M-C

C-C@5/4m

BE

DA60-Fe38
DA120-Fe38

2.281
2.205

1.434/1.498
1.544/1.547

-3.91
-6.03

DA60-Ni38
DA120-Ni38

2.387
2.334

1.425/1.463
1.486/1.584

-2.15
-3.59

In all the MD trajectories, the above optimized structure of the individual complexesof iron and nickel is considered to the initial structures with different random seed numbers.
Our initial results for iron complexes at 1500 and 2000 K reveal that part of the metal cluster
is covered by one cone and the other cone either covers the metal cluster or it is in thesuspended position. The apex part of the cone is always connected to the catalyst even at~15ps and the 4m-ring is found to be stable. At 2000k, some of the trajectories show thatthe 4m-ring at the apex region is destroyed and metal encapsulated complex structure isobserved. However, at 2500 K, only few trajectories exhibit the cone-cone interaction andmost of the structures are found to be very much similar to the encapsulated complex or
partially connected cone-cone types of structures even up to 30 ps. These results for theDA-120 are completely different from that of DA-60 wherein the structural transformation ofcone into nanooyster-like transformation is observed at temperatures range of 1500 -2500 K
within 6-8 ps. The reason for such differences may be due to the strong interaction of
DA-120 with the iron cluster, the flexibility or movement of the cones is restricted and hence,the cones remains to be intact with the catalysts. In some cases, the 4m-rings are destroyed
at the apex region and the resulting complex with such defect structure very strongly bound to
the Fe surface. The thermal energy supplied even at 2500 K is not sufficient to overcome
the interaction between the 4m-rings of the cones and the catalyst. However, at 3000 - 3500
K, the nanocones are decomposed into small carbon clusters and hence, the nanooyster-like－2－－ 120 －

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Ⅳ 研究業績 (2011)transformation is not observed for the case of iron.
Let us now discuss the nature of interactionof nickel nanoclusters with nanocones, DA-120.
More strikingly, the present results as shown in
Figure 2, demonstrate that the resultant product isneither nanooyster nor the complex obtained foriron case.
Herein, the observed product is
nanocapsule-like structure, comprising mostly
Figure 2: carbon Nanocapsule with
6m-rings around the capsule and 5m-rings at the
the Nickel Catalyst
regions where the cones are interconnected to eachother (interfacial region). This feature is very uniquely observed for the case of nickel
catalyst.
The snapshots for the formation of carbon nanocapsule are presented in Figure 3 andthe corresponding carbon polygonal ring formation dynamics is represented in figure 4. It
can be seen from figure 3 that the nanocones slowly move from the catalyst surface,maintaining the metal-cone interaction through the 4m-ring of the apex region of thenanocone. The cone-cone interaction initially begins with the bonding at the peripheral
regions of the cones and this process drives the formation of few polygonal carbon rings in
the time interval of 9-12 ps (as shown in figure 4). Once the two cones are intact with eachother, the contact of the cone with the catalyst becomes weak and the peripheral regions ofboth the cones are connected each other at 16 ps, this leading to the formation of carbon
nanocapsule.

Figure 3: The mechanism of the nickel catalyzed nanocapsule formation.
The numbers at each snapshot indicate the time in ps.
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Figure 4: Carbon polygonal ring formation dynamics for one of the trajectories at 1500
K, catalyzed by Ni38 cluster.

From the Figures 3 and 4, it is evident that initially, both the cones have to move forwardfrom the tip position to the edge and thereafter, both the cones are zipped together. The entire
process is leading to the formation new 5m and 6m-rings as it is shown in Fig. 4.
Considering the time scale, it can be mentioned that the flipping of the cones and theformation of the capsule-like structure takes place in the time range of 10-12 ps and 14-15ps,
respectively. In addition, our simulation results illustrate that the transformation process isfaster at 2500K compared to that of 1500K. It can be seen from Fig.4 that the nanocapsule
growth process and the increment in the number of new 5m and 6m-rings at 1500K is quite
sharp, indicating the growth process is quite fast with threshold time period. We have also
observed that the 3m and 7m-rings are not formed. More strikingly, the structure of the tube
is not changed after annealing the structure up to 34ps, which is also evident from the ringcount (From Fig. 4). Since the interaction strength of the nanocapsule with the nickel
cluster is found to be very weak, the nanocapsule is liberated from the catalyst surface.
The irregular shape of the capsule can be attributed due to the presence of 5m-rings. In
general, one 4m-ring is present at the capping region, which is surrounded by the five
6m-rings in the normal cones. However, the number of 5m-rings is increased to 8-10,
during the growth of the capsule along with few 6m-rings. This type of arrangement of therings causes the irregular types of structure. Since the nanocone has the zigzag as well asarmchair types of edges, the formation of 5m, 6m and 7m rings is expected when two cones
joins together especially at the interface region. These features are completely different
from the case of iron cluster-nanocone interaction.
On comparing DA-120 nanocone interaction with the iron/nickel-catalyzed reaction,
the mechanism of the formation of the nanocapsule structure is found to be profoundly
different from the DA-60. In the present case, the basic structure of the zigzag as well asarmchair types of edges are not destroyed at the peripheral region and hence, the mechanismof the formation of the nanocapsule has been explained in terms of the interface or bridge
region at the intra-molecular junctions of the two cones which can have the 5m-rings aroundthe tube. However, in case of nickel cluster-induced tube formation, the mechanism is not－4－－ 122 －

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Ⅳ 研究業績 (2011)very apparent from the trajectories. The zigzags as well as armchair types of edges are foundto have no role. Thus, although there are some similarities with the interaction of nanocones
DA60 with different catalysts, the interaction of the cones DA-120 with the iron and nickel
cluster is very different from each other.

2.

Original Papers
1. DNA Base-Gold Nano Cluster Complex as a Potential Catalyzing Agent: An
Attractive Route for CO Oxidation Process
Naresh K Jena, KRS Chandrakumar, and Swapan K Ghosh J. Phys. Chem. C, 2012
(In Press) DOI: 10.1021/jp304660
2. Water Molecule Encapsulated in Carbon Nanotube Model Systems: Effect ofConfinement and Curvature
Naresh K. Jena, Manoj K. Tripathy, Alok K. Samanta, K. R. S. Chandrakumar andSwapan K. Ghosh Theo. Chem. Acc. 131, 2012, 1205
3. High-Temperature Transformation of Fe-Decorated Single-Wall Carbon Nanohorns toNanooysters: A Combined Experimental and Theoretical Study (Communicated to
Nanoscale)3.

Presentations at Academic Conferences－5－－ 123 －

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Fengyi LIU
JST Fellow, Fukui kenichi Memorial Research Group 1
1. Summary of the research of the year
Ring-Opening and Ring-Closure Mechanism of Spiropyran-Merocyanine Photochromic Reaction
The photochromic reaction of Spiropyran-Merocyanine(SP-MC) photochromic reaction has been a hot but
challenging subject for theoretical chemists. Due to the dramatic changes of electronic structure during thering-open and ring-closure processes and highly flexible geometry of MC isomers, the potential energy
surfaces of SP-MC are complex. The efficient nonadiabatic path from excited- to ground state, including
crucial structures such as conical intersections and unusual intersystem crossing, have not been wellunderstood.

Figure 1. Spiropyran-Merocyanine photochromic reaction path and unsubstituted MC(H-MC), 6-NO2
MC(NO2-MC) and protonated MC(MCOH+).
Unsubstituted H-SP↔MC photoisomerization: We carried out CASPT2//CASSCF calculation to explore
the ground- and excited-state PESs of the model molecule. The SP-MC ring-opening reaction takes place in
two steps: (1) Photocleavage of C-O bond. Starting from the FC(S0-SP), the molecules follow two primary
reaction paths, S1-SP S1-TCC and S1-SPS1-CCC, both are barrierless downhill MEP. Along the S1-MEP,
the S0 and S1 curve intersect with each other and form extensive state-interacting regions (S1-S0 gaps <10
kcal/mol). The torsional modes around dihedral angle α, β and γ (See Figure 1 for definition) regulate thebranching 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, OBF, HT and BP can take place in MC
photoisomerization. Considering of their relative long life time (~10ps), low isomerization barriers andflexible reaction paths, all MC conformers can be generated from the CCC and TCC. Several type of MECIs
were located at the CASSCF level and are responsible to produce ground-state MC isomers.

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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) CI (S2/S1,β2) TS(β2,S1)  TCC(S1)  CI2S1/S0SP(S0). These results
agree with the experimental findings.
NO2-SP↔MC photoisomerization: The photochromic reaction for NO2-SP-MC is more complicated thanunsubstituted one, since the NO2- substituent has significant to the electronic state, especially inducing
charge-transfer process during C-O bond cleavage and formation.. The ring-opening mechanism for NO2-SP
was studied at the SA4-CASSCF(12,11) level with CASPT2 energy correction. NO2-SP molecule is initially
excited to S1 (ππ*) state, then the C-O bond cleavage take place along two paths (as shown in Figure 2).
During this process, two type of CIs, CI(S2/S1) and CI(S1/S0) play their roles to form MC products. The
experimentally undetectable excited-state intermediates, S1-CCC and S1-TCC were optimized and are locatedin the shallow well of the S1 PES. The NO2-SP* TCC reaction path is more favorable than NO2-SP*
CCC.

Figure 2. The Ring-openning reaction paths for NO2-SPMC.
NO2-SP↔MC acidichromic/photochromic reaction: Acidichromism stands for the phenomenon that the
protonated form and the conjugate base of some compounds have distinctly different absorption spectra. It
can occur in together with photochromism. In such cases, it is possible to take advantage them to constructinteresting molecular devices. The reaction scheme of acdio-/photochromic reaction of SP and MC areshown in Figure 3.

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Figure 3. Schematic SP-MC Acido- and photochromic reaction path.
In this scheme, how does the reaction take place between neutral NO2-SP and MCOH+ is not known; inaddition, the role of experimentally suggested side-reaction (C-N cleavage) is also to be understood.
Therefore, 4SA-CASSCF(12-in-11)/6-31G calculation were carried out to locate the C-O and C-N cleavage.
It is found the protonated MCOH+ isomers are more stable that protonated SP, which reverses the direction of
the SP-MC thermalchomism. Actually once the O15 in SP is attached by proton, the C-O bond dissociates
instantly to produce CCCOH+ or TCCOH+; then isomerization take place among the MCOH+ isomers. The
protonation/deprotonation of molecule only occur in MC form (rather than SP).
We also found the C-N cleavage in N-protonated SP(SP-NH+) as a competing side-equilibrium process,accounting for the unreactive “sink” reported by UV/vis spectroscopy experiment. The C-N dissociation on
S1 state is as low as ~6.5 kcal/mol so it take place easily though a CI between S1/S0 states (Figure 4).

Figure 4. SPNH+MA+ as an unreactive sink.

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2. Original papers(1) Fengyi LIU, Keiji MOROKUMA,“Computational Study on the Working Mechanism of a Stilbene Light-Driven Molecular
Rotary Motor: Sloped Minimal Energy Path and Unidirectional Nonadiabatic
Photoisomerization”,
J. Am. Chem. Soc., 2012, 134, 4864–4876.
(2) Fengyi LIU, Keiji MOROKUMA,"Ring-OpeningandPhotochromic Reaction:

Ring-Closure

MechanismoftheSpiropyran-Merocyanine

A CASSCF/CASPT2 Study”

manuscript in preparation.
3. Presentation at academic conferences(1) Fengy Liu and Keiji Morokuma, Poster on:"Theoretical study on the working mechanism of stilbene light-driven molecular rotary
motor",“7th Congress of the International Society for Theoretical Chemical Physics”, September
2-8, 2011, Tokyo, Japan.

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Hongyan XIAOJST Fellow, Fukui Kenichi Memorial Research Group 1
1. Summary of the research of the year
I. Fitting Global Ab Initio Potential Energy Surfaces for Low-lying Doublet States of NO3
Recently a joint experimental and theoretical work proved the exclusive excited-state roaming pathway
in the reaction NO3 → NO + O2 that eventually produced two different product channels (a) and (b).
NO 3  hv  NO ( 2   , v  0  1, low N )  O 2 ( 3  g , v  5  10) major channel(a ) NO ( 2   , v  0  1, high N )  O 2 ( 3  g , v  0  4) minor channel(b)

The theoretical studies predicted specific NO Λ doublet propensities, namely, orientations of the unpaired
electron with respect to the molecular rotation plane for the two product channels. The experimental studies
using the ion imaging technique via multiple rotational branches proved that the major product channel witha high O2 vibrational excitation produced a lower translational energy NO fragment in the A' Λ doublet state,while the minor product channel with a low O2 vibrational excitation produced a higher translational energy
NO fragment in the A'' Λ doublet state, confirming the theoretical predictions.
In order to fully support the theoretical conclusions derived from potential energy surface (PES)
characteristics and limited classical dynamics from dissociation transition states, it is highly desirable toperform classical and hopefully quantum dynamics calculations for complete evolution of the system fromphotoexcitation in the Franck-Condon region through succeeding nonadiabatic and dissociation processes tothe product. In order to make this possible it is essential to have full PESs of multiple electronic states
involved at a higher level than used in our previous reaction path characterization study. In particular, we areconcerned with a small active space (11e,8o) used in such a study, which might have resulted in some errors
in the very flat PESs in the roaming region as well as dissociation transition states.
In the present work, we develop such analytical global PESs for NO3 on the basis of multistate(MS)-CAS(17e,13o)PT2/aug-cc-pVTZ ab initio calculations. The fits are made on roughly 74000
MS-CAS(17e,13o)PT2/aug-cc-pVTZ calculations of electronic energies, where these PESs are invariant of
permutations of oxygen atoms (see below Fitting scheme). The surfaces describe two roaming pathways forNO3 → NO2-----O → NO + O2 involving different electronic states discovered in the photolysis of NO3[Xiao, H. Y. et al. J. Phys. Chem. Lett. 2011, 2, 934]. These pathways become accessible at excess energy of~210 kJ/mol above the ground state global minimum of NO3. The ab initio data below 360 kJ/mol are
reproduced very well by the fitted PESs with the fitting RMS errors of less than 5.5 kJ/mol for all the threestates. Moreover, key local minima and energy profiles along the roaming pathways on the fitted PESs arecompared with those on the ab initio PESs. In addition, potential contour maps in the roaming region are also
compared. These careful evaluations of the fitted PESs suggest that the present fitted PESs are well suited for
future dynamics calculations of this system.

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Ⅳ 研究業績 (2011)

Fitting scheme
Initial structures and electronic energies

6

6

6

6

6

6

V  C 0   C 1i q i    C 2 ij q i q j     C 3 ijk q i q j q ki 1

i 1 j 1

6

6

6

6

i  1 j  1k  1

66

 ...       ...  C Nijklm ... n q i q j q k q l q m ... q ni  1 j  1k  1l  1 m  1

n 1

refit
GRRM search on the fitted PES

Sampling points

Properties evaluated on the fitted PES

II. Theoretical Study of the Photodissociation Dynamic of Ketene
The photodissociation dynamics of ketene (H2CCO) has been paid close attention by experiments andtheories in the past several decades. At 193 nm the ketene photolysis has the following pathways:~
H 2CCO  h  CH 2 ( X 3 B1 )  CO
CH 2 (a~1 A1 )  CO~
CH 2 (b 1B1 )  CO~
H CCO( X 2 A)  H~
C 2O( X 3 Σ  )  H 2

(1)
(2)
(3)
( 4)
(5)

For the photochemical reactions of ketene in the near ultraviolet absorption region, the mechanism isvery clear that the ketene molecule in the ground state (S0) was first excited to the first excited singlet state(S1) via a UV laser (300~360 nm), and the excited ketene underwent nonadiabatic transition to lower
electronic states, i.e. S0 and the first triplet state (T1), the final leading to the C═C bond fission mainly
occurred on the S0 and T1 states, which are relative to pathway (2) and pathway (1), respectively. In thehigher excitation energy region (193~215 nm) within the banded S2‒S0 absorption system, although there
have been numerous experimental and theoretical reports, the photodissociation dynamics of ketene stillneed gain a further insight.
To be motivated by some experimental different conclusions and the fast development of the high level
theoretical calculation methods, we will do a systemic study on the photodissociation dynamics of ketene
considering the six lowest electronic states (S0, S1, S2, T1, T2 and T3), in order to explore the photodissociation
mechanism of ketene under the higher excitation energy.
We proposed the main photodissociation mechanism of ketene as follows (see Figure 1), after one photon
absorption to the S2 state, ketene can decay to the S2/S1/T2 intersection through S2-TS along the minimum
energy path on the S2 state. Since the internal conversion is usually more efficient than the intersystemcrossing from the S2/S1/T2 intersection, it may further be inactive to the S1 state. Due to a higher dissociation－ 129 －

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Ⅳ 研究業績 (2011)barrier (267.1 kJ/mol) on the S1 state, S1 will relax to the S0 state via S1/S0-MSX. Finally, ketene directly~
dissociates into CH ( a~1A )  CO( X 1  ) on the S state. The result supported the experimental ones. In201

addition, we assigned the correlative dissociation pathways.

S2 578.9
S2/T3-MSX1

S2-TS

550.4

~
HCCO( X 2 A )  H
440.2bCH2 (a~1 A1 )  CO

554.1
T3-GM

S2/S1-MSX(S2/T2-MSX)
431.3(434.5)
S1/T2 (T2/T1)

360.3a344.9(351.5)523.0

S1 366.6

T3/T2-MSX
528.7
S1-DC-TS

S2/S1-MSX(S2/T2-MSX)
431.3(434.5)

494.3

460.0aS1/T1-MSX2
313.7
S1-GM
227.2
T1-GM

~
CH2 (b 1B1 )  CO~

T1-DC-TS CH2 ( X 3 B1 )  CO

S1/T1-MSX1 S1/S0-MSX
250.9

293.8

248.1 S /T -MSX
0

1

206.1

180.4

S0-GM
0.0

Figure 1. The PESs for the processes of ketene photoexcitation and photolysis. a,bThe values are thedissociation energies in experiment.

III. Theoretical Study on Catalytic Enantioselective Mechanism of Passerini Reaction
The Passerini three-component reaction, which involves a carbonyl compound, a carboxylic acid and an
isocyanide, has been investigated intensively during the past two decades. Recently, Maeda S. and coworkers
used the artificial force induced reaction (AFIR) method to study on the mechanism of the Passerini reaction
systematically and proposed that the Passerini reaction is actually a four-component reaction via
four-component transition states (TSs) involved an extra carboxylic acid. Based on the previous study, we
will continue to explore the mechanism and enantioselectivity of the Passerini reaction in relation to catalyst.

1

2

3

Cat.

Figure 2. The structures of reactants and catalyst in the Passerini reaction.

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Ⅳ 研究業績 (2011)

In this study we chose the real system in experiment (Angew. Chem. Int. Ed. 2008, 47, 388) to search, asshown in Figure 2. In comparison with the Passerini reaction involving catalyst, we also considered no
catalyst reaction, that is to say only including reactants 1, 2 and 3. We used the ONIOM(M062X/6-31G:PM6)
method in the initial AFIR search, where the mixing order of different species is based on the experimental
procedure. Then, all the lower energy pathways were optimized by the ONIOM(M062X/6-31+G**:PM6)
method. We also considered the solvent effect using PCM model, where toluene is as a solvent.
The present ONIOM(M062X/6-31+G**:PM6) results show that in no catalyst system, the products areracemic adducts. In the generation chirality step, the difference of the energy barrier between TSs to produce
S-conformation and R-conformation is only 0.2 kJ/mol. For the involving catalyst system, we found eightTSs (4 S-conformation and 4 R-conformation) in the generation chirality step. In Figure 3, we take examples
for the structures of TSs. (Si-face attack is relative to R-conformation; Re-face attack is relative toS-conformation.) The difference of the energy barrier among TSs is about 1.8 kJ/mol. Although the results
are in agreement with the experimental ee value (S-conformation is major), the difference of the energy
barrier is too small. Therefore, we are carrying on the high level calculations to validate the present results.

Re-face

Si-face

Figure 3. The structures of transition state in the generation chirality step.

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).
(2) Michael P. Grubb, Michelle L. Warter, Hongyan Xiao, Satoshi Maeda, Keiji Morokuma
and Simon W. North.
“No straight path: roaming in both ground- and excited-state photolytic channels of NO3 →NO +O2”
Science 335, 1075-1078 (2012)(3) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma“Global Ab Initio Potential Energy Surfaces for Low-lying Doublet States of NO3”
Submitted.

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Ⅳ 研究業績 (2011)(4) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma“Multireference Theoretical Study of the Photodissociation Dynamics of Ketene”
Manuscript in preparation.
3. Presentation at academic conferences(1) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma (Poster)“A theoretical study on the photodissociation of HNO3 involving S2, S1 and S0 states”
7th Congress of the International Society for Theoretical Chemical Physics, Abstract page
3PP-47, Tokyo, Japan, September 2~8, 2011.
(2) Hongyan Xiao, Satoshi Maeda and Keiji Morokuma (Poster)“Multireference theoretical study of the photodissociation dynamics of ketene”
The 9th FIFC symposium, Kyoto, January 6, 2012.

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Ⅳ 研究業績 (2011)

Lina DINGJST Fellow, Fukui kenichi Memorial Research Group 1
1. Summary of the research of the year

Reaction Mechanism of Photo-induced Decarboxylation of the
Photoactivatable Green Fluorescent Protein:An ONIOM(QM:MM) Study

Green fluorescent protein (GFP) and its variants have played an important role inbiological imaging and analysis. Photoactivatable fluorescent proteins have attracted a plentyof scientific interests, since dramatic contrast by emission upon an irradiation makes them
particularly popular and important as optical markers.

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

Photo-induced transformation between the neutral form (responsible to the A band) andanion form (the B band) of the GFP chromophore is essential to fluorescent emission. As
shown in Scheme 1, an irreversible Type II and so-called Kolbe mechanism was proposed forthe wild-type (WT) GFP which accompanies the photo-induced decarboxylation of GLU222,
supported by X-ray crystallography and mass spectrometry. Due to the similarity to the wellknown thermal Kolbe reaction, the decarboxylation of GLU222 of GFP (or GLU219 of
PA-GFP) was proposed to occur because of the photo-induced oxidation of GLU; upon
photo-excitation one electron transfers from anionic GLU to the chromophore, followed bydecarboxylation of the neutral species. The reported order of the decarboxylation rate (254
nm > 280 nm > 476 nm) showed clearly that it was excitation-wavelength dependent.
Recently, X-ray crystal structures of native and photo-activated states of PA-GFP were also
reported. In addition, rate measurements for irreversible photoactivation in WT-GFP and
PA-GFP reveal similar kinetics.

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Very recently, Roy et al. reported QM/MM and MD study of the decarboxylation processof IrisFP; here however one electron was arbitrarily removed from the QM system.; Nakatsuji
and Krylov et al. have identified the critical CT states involved in the Kolbe mechanism
which were proposed to be accessible via either directly one-photon absorption, or a two-step
excitation via S1.

Scheme 1. Irreversible Type II Kolbe mechanism for the photo-decarboxylation.

Knowledge of potential energy surfaces (PESs) of the ground and excited states involved
is of great importance in understanding the reaction mechanism. In particular, it is a challenge
to characterize the nature of electronic structures involved and details of the decarboxylation
process. Here, we investigated the reaction mechanism of the irreversible photo-induced
decarboxylation of PA-GFP, which is still unclear and remains unresolved till now, by the
ONIOM(CASSCF:Amber) and ONIOM(CASPT2:Amber) methods.

Mechanisic study on the Photoisomerization in Polypyridyl mononuclear
ruthenium(II) aquo (PMRA) complexe

Polypyridyl mononuclear ruthenium(II) aquo (PMRA) complexes have considerable
attractions as competent water oxidation catalysts, since the typical feature was established
for a series of Ir complexes and polypyridyl ruthenium compounds. Relative to the higher
nuclearity systems, the mononuclear systems that generally easier synthesis and study bringthe important implications related to water oxidation catalysts. The proton-coupledelectron-transfer reactions associated with the water splitting bring comprehensive studies on
PMRA complexes because how electrons and protons are transferred is critical in developing
our understanding of important biological reactions such as respiration, nitrogen fixation, andphotosynthesis as well as energy conversion in artificial photosynthesis or fuel cells. Up to－ 134 －

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Ⅳ 研究業績 (2011)

now,

the

rare

photo-isomerization

reaction

has

been

surprisingly

observedincis-[Ru(bpy)2(OH2)2]2+ (bpy = 2,2-bipyridine) and trans-[Ru(tpy)(pynp)OH2]2+ by Meyer andYagi, respectively. In case of cis-[Ru(bpy)2(OH2)2]2+, the trans form appeared to be a
photo-stationary state and slowly reversed to the cis form. However, no evidence of aphotostationary

state

was

found

betweentrans-[Ru(tpy)(pynp)OH2]2+

(A)

and

cis-[Ru(tpy)(pynp)-OH2]2+ (A’) during 5-75 ℃. However, the forward process from trans- tocis- form can occur and the reverse cannot. The redox reactions and water oxidation catalyses
are significantly controlled by the photoisomerization.
As a possible mechanism proposed by Yagi, the photoisomerization process should takeplace as following: visible-light irradiation can generate metal-ligand charge transfer (3MLCT)
state which is followed by the thermally accessible metal-center (3MC) state, on which anaquo ligand dissociation could occur from A and a five-coordinate [Ru(tpy)(pynp)]2+
intermediate could be formed; a water molecule re-coordinates to the metal center of theintermediate from the opposite side of tpy plane to form A’ isomer. The Ru-O bond cleavage
could be involved since the consistence between the photoisomerization activationenergy(41.7 kJ mol-1) and the water exchange activation enthalpy (50.6-87.8 kJ mol-1) inruthenium aquo complexes. However, no clear information could explain why the forward
isomerization from A to A’ can occur but the reverse process cannot, despite two compoundswith similar UV-vis spectrum.
O2

tpy

N7
N6
N8
N4

Ru1

N5

tpy

py

O2

N4

N7

N6

Ru1

N3

N8
N3

np

N5

py

np

A
A’
Figure 1 The structures of A and A’ with labels on main atoms and group names
Theoretical

study

on

the

photo-isomerization

pathways

betweentrans-[Ru(tpy)(pynp)OH2]2+ and cis-[Ru(tpy)(pynp)-OH2]2+ would be interesting to clear thereason why two compounds with similar UV-vis spectrum have different reactivity. Also, theinvestigation study on the mechanism will be important for the new design of water splitting－ 135 －

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Ⅳ 研究業績 (2011)

catalysts since the redox and oxidate reactions are significantly controlled by thephotoisomerization.

2. Original Papers(1) Lina Ding, Lung Wa Chung, Keiji Morokuma“Reaction Mechanism of Photo-induced Decarboxylation of the Photoactivatable
Green Fluorescent Protein:An ONIOM(QM:MM) Study”
To be submitted(2) Lina Ding, Keiji Morokuma“Mechanisic study on the Photoisomerization in Polypyridyl mononuclear
ruthenium(II) aquo (PMRA) complexe”
In preparation

3. 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
(2) Lina Ding, Lung-Wa Chung, Keiji Morokuma. Theoretical Study on the
Photoisomerization of Mononuclear Ruthenium(II) Monoaquo Complex,
福井謙一博士ノーベル賞受賞 30 周年記念 京都, 2012, Jan.01－ 136 －

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Ⅳ 研究業績 (2011)

Hai-Bei LI
JST Fellow, Fukui Kenichi Memorial Research Group 1

1. Summary of the Research of the Year(A) SWCNT Growth from Chiral Carbon Nanorings: Prediction of Chirality andDiameter Influence on Growth Rates
Traditional CNT growth methods, such as carbon-arc, laser evaporation, and catalytic
chemical vapor deposition (CCVD) are incapable of in situ control of (n, m) chirality during
CNT synthesis, primarily due to the high temperatures employed. Recently proposed
bottom-up strategy based upon organic synthetic methods represents a more realistic approach
towards

chirality-controlled

SWCNT

growth.

While

the

relationshipbetween

cycloparaphenylenes (CPP) and the growth of armchair SWCNTs was at first a theoretical
hypothesis, organic species including CPPs have been synthesized by a number of groups. It
was originally imagined that chirality-controlled SWCNT growth could be achieved in thismanner using low temperature CVD in conjunction with, for example, acetylene. In thepresent work, we illustrated the catalyst-free, chirality-controlled growth of chiral and zigzag
single-walled carbon nanotubes (SWCNTs) from organic precursors using quantum chemical
simulations. Growth of (6,6), (4,3), (6,5), (6,1), (10,1) and (8,0) SWCNTs was induced byethynyl radical (C2H) addition to organic precursors. Figure 1 depicts the evolution of(6,6)-SWCNT growth following the simulation time. About 7.5-Å-long (6,6) SWCNT withalmost 5 belts is produced within 500 ps. The present QM/MD simulations have shown thatC2H radicals can facilitate the H abstraction, and act as sidewall growth agent, that is, thesuccessful growth of (6,6)-SWCNT is proposed by H-abstraction and C2H insertion
mechanism, as shown in Figure 1. Figure 2 shows the six-membered ring counting statistics
as a function of simulation times during (n,m)-SWCNT growth. All the simulations show astrong dependence of the SWCNT growth rate on the chiral angle. The SWCNT diameter
however does not influence the SWCNT growth rate under these conditions. This agreementwith a previously proposed screw-dislocation-like model of transition metal-catalyzed
SWCNT growth rates [F. Ding, et al. Proc. Natl. Acad. Sci. 2009, 106, 2506] indicates that the－ 137 －

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Ⅳ 研究業績 (2011)

SWCNT growth rate is an intrinsic property of the SWCNT edge itself. Conversely, using ab
initio simulation, we predict that the rate of SWCNT growth via Diels-Alder cycloaddition of
C2H2 is strongly influenced by the diameter of the SWCNT, which suggests that therelationship between the SWCNT’s diameter and its rate of growth depends explicitly on thegrowth conditions.

Figure 1. The snapshots of SCC-DFTB/MD simulations of (6,6)-SWCNT growth.

Figure 2. Six-membered ring counting statistics as a function of simulation times.

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Ⅳ 研究業績 (2011)(B) Sub-Surface Nucleation of Graphene Precursors near a Ni(111) Step-Edge
Graphene, a two-dimensional honeycomb lattice of sp2 bonded carbon atoms, has
attracted much attention due to its remarkable electronic, optical, and mechanical properties.
Despite a great number of experimental and theoretical investigations on graphene nucleationand growth, the precise, atomistic nucleation and growth mechanism of graphene remains the
topic of fierce debate. In the present work, graphene nucleation at a Ni(111) step-edge has
been modeled by means of quantum chemical molecular dynamics (QM/MD) simulations at
1,180 K. These simulations demonstrate for the first time the nucleation of a graphene island
precursor not on the Ni(111) surface, but in the Ni(111) subsurface. The mechanism ofgraphene nucleation observed in trajectory T1 is depicted in Figure 1. Nucleation occurs via
three stages: (a) sub-surface diffusion of carbon atoms leads to the formation of small carbon
chains; (b) coalescence of these chains leads to the formation of amorphous carbon clusters;(c) simultaneous sub-surface  surface precipitation, and amorphoussp2 conversion of the
carbon cluster. A sufficiently high local carbon concentration in the Ni(111) subsurface is anecessary prerequisite for graphene nucleation. These QM/MD simulations also shed light on
the precise role of the step-edge on the graphene nucleation process. After precipitation of thegraphene island precursor to the Ni(111) surface takes place, the step-edge defect provides
anchoring points, via dominant  C-Ni bonding. In contrast to common assumptions, thesesimulations demonstrate that the step-edge defect (and the Ni(111) surface in general) is ahighly malleable and mobile entity, capable of being deformed, or even destroyed, by theprecipitating carbon structure. While such deformation and destruction of the step-edge isobserved during the nucleation process, we demonstrate the Ni(111) step-edges ability to‘heal’ itself over longer periods of time.

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Ⅳ 研究業績 (2011)

Figure 1. QM/MD simulation showing sub-surface nucleation of a graphene precusor on
Ni(111) (trajectory T1). Cyan spheres represent C atoms; yellow/red spheres represent
non-step-edge/step-edge Ni atoms, respectively.

2. Original papers(1) H. B. Li, A. J. Page, S. Irle and K. Morokuma, “Theoretical Insights for Chirality-Controlled
SWCNT Growth from a Cycloparaphenylene Template”, ChemPhysChem, 13, 1479 (2012).

(2) H. B. Li, A. J. Page, Y. Wang, S. Irle and K. Morokuma, “Sub-Surface Nucleation ofGraphene

Precursors

near

a

Ni(111)

Step-

Edge”,

ChemComm,

Accepted.

DOI:10.1039/c2cc32995f.
(3) H. B. Li, A. J. Page, A. M. Mebel, S. Irle, and K. Morokuma, “SWCNT Growth from Chiral
Carbon Nanorings:

Prediction of Chirality and Diameter Influence on Growth Rates”,

Journal of the American Chemical Society, (Submitted).

(4) H. B. Li, A. J. Page, A. M. Mebel, S. Irle, and K. Morokuma, “Fullerene Formation from－ 140 －

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Ⅳ 研究業績 (2011)

Hydrocarbon Combustions: Quantum Chemical Molecular Dynamics Study”, Manuscript
in preparation.
(5) H. B. Li, S. Irle and K. Morokuma, “Growth Mechanism of Hexagonal-Shape PAH
Fragments in H-Rich Environment”, Manuscript in preparation.
(6) H. B. Li, A. J. Page, S. Irle and K. Morokuma, “Surface Nucleation of Graphene Precursors
under Lower Bulk Carbon Concentration”, Manuscript in preparation.

(7) H. B. Li, A. J. Page, S. Irle and K. Morokuma, “Dependence of the Catalyst-Free
Bottom-up Growth of Single-Walled Carbon Nanotube on Temperature”, 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)－ 141 －

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Ⅳ 研究業績 (2011)

Lung Wa CHUNG
JST Fellow, Fukui kenichi Memorial Research Group 1
1. Summary of the research of the year
1a. Reaction Mechanism of Biosynthesis of Antibiotic Fosfomycin in HppE. Hydroxypropylphosphonicacid epoxidase (HppE) is a novel non-heme enzyme, that has a unique active site and catalyzes epoxidationfrom (S)-hydroxypropylphosphonic acid (HPP) to give antibiotic fosfomycin (Scheme 1). Interestingly,
reaction can be changed to dehydrogenation or oxygenation, when (R)-HPP or (S)-hydroxybutylphosphonicacid (HBP) was used as the substrate. Ferryl-oxo and ferric-superoxo species have been proposed to be an
active oxidant for the key hydrogen atom transfer (HAT) step in HPPE. We have carried out
ONIOM(QM/MM) calculations to study reaction mechanisms of divergent reactions in HppE (Scheme 2).
We found that conformation of the substrate can influence the reaction site for HAT and thus change theproduct.
Scheme 1.

Scheme 2.

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Ⅳ 研究業績 (2011)

1b. Comparative Reactivity of Hydrogen Atom Transfer (HAT) with Important Metal-Oxo andFerric-Superoxo Species. Heme- and non-heme-containing oxygenases and oxidases play vital roles inmanyselectiveandefficientbiochemical

oxidations.

Severalspecies

includingferryl-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 or observed 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 of catalyzing 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! We theoretically and systematically compare reactivity ofseveral key ferric-superoxo and ferryl-oxo model complexes. Reactivity is found to correlate well withthermodynamic driving force and can increase with higher electrophilicity of the oxidant. Reactivity of theferric-superoxo oxidants generally is not “superior” to the ferryl-oxo ones. Compared to the high-spin
non-heme ferric-superoxo, the lower reactivity of low-spin heme ferric-superoxo, seldom utilized in nature,
can be attributed to lower electrophilicity and more pronounced quenching of anti-ferromagnetic coupling
between the ferric and superoxo parts (Scheme 3). On the basis of these results, I suggested that a cationic
heme-like ferric-superoxo could be a reactive oxidant.
Scheme 3.

In addition, I further generalized HAT mechanisms (Scheme 4), based on the comparative study on HAT
with important Fe-oxo species (heme, non-heme and synthetic model complexes). In general, there can be
two classes of HAT mechanisms via either ferryl-oxo or ferric-oxyl type transition state. For the former case,type of ET ( or ) can affect the reaction path ( or -pathway). The -pathway via -ET is generally morefavorable in many non-heme complexes. While the -pathway with stabilization of half-filled 3d orbital was
found to take place in HPPE, in which ferric-oxyl type (i.e. ligand-metal charge-transfer state) transition stateis involved.

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Ⅳ 研究業績 (2011)

Scheme 4.

1c. Reaction Mechanism of Hydrogenation of Carbon Dioxide Catalyzed by Ir-PNP Complex: A
PNP-ligated iridium(III) trihydride complex 1 was reported to give the highest catalytic activity forhydrogenation of carbon dioxide in aqueous KOH by Nozaki group. The catalytic hydrogenation can betuned to be a reversible process with the same catalyst at the expense of the activity, when triethanolamine
was used as a base. DFT calculations were performed to understand reaction mechanism of hydrogenation ofcarbon dioxide. Our calculations suggested two competing reaction pathways: either the deprotonative
dearomatization step or the hydrogenolysis step as the rate-determining step (Scheme 5). The results nicely
explain our experimental observations, dependence of both the strength of the base and hydrogen pressure.
Scheme 5.

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2. Original papers(1) 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. 2012, 2, 327.
(2) 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.
(3) 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
Comput. (Lett.) 2011, 7, 2694.
(4) 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, 133,
20076.
(5) Tanaka, R.; Yamashita, M.; Chung, L. W.; Morokuma, K.; Nozaki, K. “Hydrogenation of Carbon
Dioxide Catalyzed by Ir-PNP Complex: Reversibility and Reaction Mechanism” Organometallics
2011, 30, 6742.

3. Presentation at academic conferences(1) 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.
(2) 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 I
1. Summary of the research of the year
Towards understanding the HppE catalytic mechanism
The formation of fosfomycin [cis-(1R,2S)-epoxypropylphosphonic acid, an antibiotic in clinical use] iscatalyzed by the enzyme 2-hydroxypropylphosphonic acid epoxidase (HppE), which structure was defined
several years ago. Systematic experimental studies with S and R forms of 2-hydroxypropylphosphonic acid(Hpp) suggest that the reaction mechanism includes two main steps: (i) H abstraction from C1/C2 atom of
the substrate; and further (ii) formation of epoxide cycle after H-abstraction from C1 atom or formation of
keto-structure after H-abstraction fromC2 atom. The S-substrate results in
cis-epoxide as the sole product of thereaction, while only the keto-compound
is obtained from the R-substrate. Thus,
based on the experimental hypotheses
about the possible reaction pathways,(a)

we performed a DFT model study on
the catalytic conversion of both S and R
forms of Hpp, considering only the firstcoordination sphere of the iron cation(see Fig. 1a). The first step of
H-abstraction and formation of alkyl
radical is found to be the rate limiting
step of the process, requiring above
30 kcal/mol in the case of ferricsuperoxo active species . A decrease in(b)

the energy barriers for H abstraction is

Figure 1. (a) Structure of HppE and model applied in theobserved with ferryl-oxo active species.

theoretical

Furtherstudy.

(b)

Energydiagram(gas-phasesimulations,applying

calculations) for fosfomycin formation from S-Hpp in casetwo-layered ONIOM method, showof ferryl-superoxo active species. The schemes correspondthat the influence of the environment isto the structures of the reactant complex, the radial
intermediate and the product (I, III and V, respectively).

also

important

for

the

correct

understanding of the catalytic role of
HppE in the fosfomycin biosynthesis.

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Theoretical modeling of stereochemistry control of copper catalysts based on the chirality of DNA

Another interesting topic on which wehave been working is the theoreticalinvestigation of the detailed mechanismof organic reactions catalyzed by hybrid
Cu(II)L/DNA supramolecular catalysts
and the options for stereo-control of the
products. The idea to harness chiralbiomoleculesofnaturalorigininasymmetric organic synthesis is not a
Figure 2. Scope of Cu(II)L/DNA catalyzed reactions (R = Ph,
Me, p-MeOPh, p-ClPh, o-BrPh, 2-furanyl, cyclohexyl, etc.).

new one and proved to be quite aversatile one. In a series of experimental
studies Feringa and co-authros haveshown that such catalysts could be successfully applied in several types of reactions like Diels-Alder (DA),Friedel-Crafts (FC) and Michael addition (see Fig. 2). The DNA based catalysts combine the catalytic powerof the transition metal complexes and the chiral architecture of the biopolymer resulting in both efficiency
and high enantioselectivity of the reaction. Another important advantage of these catalytic systems is thatthey are water-soluble and do not require the usage of expensive and environment unfriendly organic
solvents; while, on the other hand, the DNA component is cheap, readily available and desired
oligo/polymers with designed nucleotide sequence and length could be prepared relatively easily.

Figure 3. (a) Scheme of the reaction of interest - DA addition of cyclopentadiene to α,β-unsaturated 2-acyl
imidazoles. (b) Scheme representing the local structure of the reactant complex consisting of Cu(II), L (L =bipyridine) and the dienophile reactant coordinated to the metal cation via the acyl oxygen and the pyridyl
nitrogen. (c) Examples for coordination modes of Cu(II)L complex to a double-stranded DNA oligomer.
Front and side view presented for minor groove coordination and two different complexes of intercalation
via L with reactant facing the major (left structure) or minor (right structure) groove. The structures on thisfigure are tentative, not theoretically optimized or experimentally observed ones.

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As we are mainly interested in DA and FC reactions for which Cu(II)-bpy complexes results in highest
stereoselectivity, we considered Cu(II)-bpy complex and two different DNA dodecamer fragments: the AT
rich d(CAAAAATTTTTG)2 and the CG rich one d(CGCGCGCGCGCG)2 and according to the experimental
data CG rich sequences (DNA2) perform best for the DA and FC reactions. In case of intermolecular
reactions (most common in the experimentally studies) the reactant molecule is α,β-unsaturated 2-acyl
imidazole structure as the 2-acyl imidazole moiety ensures stable coordination of the organic structure to theCu(II) ion (see Fig. 2 a & b).
Before studying the reaction mechanism of the catalyzed process and compare it with the referent reaction
without a catalyst or with only Cu(II) complex as Lewis acid catalyst, it was important to propose a suitablemodel of the supramolecular complex. The available experimental data are not sufficient or ambiguous todefine the structure of the supramolecular complex. A lot of other experimental studies (not connected withthe role of DNA as asymmetric microenvironment) have revealed that organic molecules and metal
complexes could interact with the DNA strand in two main modes: minor groove coordination orintercalation inbetween DNA base pairs (see Fig. 3c). It is possible that the metal complex including theligand and the reactant is coordinated in mixed mode with the ligand anchored between the DNA base pairs
and the reactant molecule nestling in the minor groove. In the search for a suitable structure we combined
dockingexperiments

andmolecular

dynamics (MD). The results from the MD
simulations show that both types ofinteractions result in formation of stablesupramolecular structures. In case of minor
groove coordination of the metal complex
with the ligand (bpy) nested in the groovethereactant

interactionis

exposedwithforfurther

dienophile(pentacyclodien) or nucleophile. However,such a structure of the complex catalyst
Figure 4. An example of minor groove coordination ofLCu(II)R complex to DNA1. The upper panel shows thewill hardly favor the formation of a specificstereoisomer, i.e. will not show stereo

results from the docking while in the lower panel of thespecificity. Intercalation results in slightly

structures resulting from the MD simulations are given.

morestablecomplexes

(by

ca.

8-10 kcal/mol) as in the obtained structures
the attack to one site of the reactant ishinter due to sterical constraints. Further simulations of the reaction mechanism on QMMM level will bebased on the most stable representatives.

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2. Original papers
Galina Petrova, Lung Wa Chung, Keiji Morokuma, DFT and ONIOM modeling of fosfomycin biosynthesis
catalyzed by HppE. In preparation.

3. Presentation at academic conferences
Galina Petrova, Lung Wa Chung, Keiji Morokuma (FIFC)“Towards understanding the HppE catalytic mechanism: theoretical modeling of fosfomycin biosynthesis”(Poster presentation)
9th FIFC Symposium, Kyoto, Japan (6 January 2012)－ 149 －

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Raman Kumar SINGH
JST Fellow, Fukui kenichi Memorial Research Group 1(To 31 Aug. 2011)
1. Summary of Research
The Reaction Pathway for C4H2 Polyyne Fusion Reactions: A Theoretical Investigation
The one dimensional (1D) carbon nanowire made of a long linear carbon chains inserted
inside a multiwalled carbon nanotube (MWCNT) has attracted a great deal of attention formany researchers to trap its optical and electronic properties for the advancement of
nanotechnology, material science and the basic research. The linear carbon chains canpossess either cumulenic or polyynic structure. Recently, Shinohara and his co-workers
succeeded in synthesising single(double)-wall carbon nanotubes encapsulating C10H2 polynne
molecules and found that a high-temperature fusion reaction occurs to form long linear
carbon chains inside the 1D nanospace of MWCNT. However, the reaction pathways for suchfusion reactions are still unknown and unexplored either experimentally or theoretically, as
far as we know. To address this issue, we have considered the minimal polyyne (C4H2) nanofusion reactions (Fig. 1) as a first step to investigate theoretically using density functional
theory.
; n≥2Figure 1: Schematic representation of nano-fusion reactions of polyyne in multiwalled carbon
nanotube .

In this work, our focus is to find the reaction pathway of C4H2 polyyne fusion reactions in gas
phase and then to see the effect of the single-wall carbon nanotube on the gas phase reaction
pathways systems.

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Figure 2: Open-shell singlet gas phase reaction pathway for C4H2 polyyne fusion reaction at
the UB3LYP/6-31g(d,p) level.

Figure 2 shows that the reactants convert into the final product via two intermediates andthree transition state (TS) structures in gas phase wherein all the intermediates and transition
states structures are open shell singlet. It implies that C4H2 fusion reaction follows open-shell
singlet reaction pathways. However, TS3 has very high barrier height in comparison to therest TS structures.
To see the effect of single-wall carbon nanotubes (SWNTs) on the gas phase reaction
pathways, a two layer ONIOM calculations (QM/MM) were performed in which (8,8)SWNT
of length 20 Å was treated by the Dreiding force field molecular mechanics method and thegas phase reaction pathways systems inside the single-wall carbon nanotube were taken underquantum mechanical methods (i.e. UB3LYP/6-13g(d,p) : open-shell singlet) treatment. The
optimized geometries are presented in figure 3. This figure shows that the hydrogenmolecules are not adsorbed by the wall of the nano-tube. However, the relative energy
profiles remained similar to the gas phase reaction pathways, as can be seen in the figure 4.

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Figure 3: Optimized geometries of the gas phase reaction pathway inside the (8,8) SWNT oflength 20 Å and diameter 10.77 Å at the ONIOM(UB3LYP/6-31g(d,p):Dreiding) level with
open-shell singlet.

Figure 4: Open-shell singlet reaction pathway for C4H2 polyyne fusion reaction with andwithout the (8,8) SWNT ( length 20 Å and diameter 10.77 Å).

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In summary, this study shows that C4H2 fusion reaction follows open-shell singlet reaction
pathways in gas phase as well as inside the SWNT. TS3 has the largest barrier height and thehydrogen molecules are not adsorbed by the wall of the nano-tube. These results also seem toindicate that these findings are not sufficient and needs to explore another reaction
mechanism. Since the present investigation was carried out a zero-kelvin temperature and thepolyyne nano-fusion reaction occurs at very high temperature and high vacuum. Therefore,
the role of temperature is crucial and the temperature dependent reaction pathways need to be
explored and investigated theoretically to capture the real essence of such polyyne nanofusion reaction.

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Travis HARRISJSPS Foreign Researcher, Fukui kenichi Memorial Research Group 1(From 21 Jan. 2012)
1. Summary of the research of the year
ONIOM Investigation of Iron Uptake by Ferritin
Ferritins are the major iron storage proteins of animals, plants, and microorganisms, which are criticalfor preventing toxic radical chemistry and oxidative damage. Animal ferritins are composed of a 12 nm
diameter protein shell (Figure 1a) surrounding an 8 nm cavity that can store up to 4500 iron atoms in theform of a hydrated iron oxide. This shell comprises 24 subunits, each structured as a 4-α-helix bundle (Figure1b). Catalytically active, H or M, and inactive, L, subunits occur in animals in various ratios withtissue-specific distributions. The catalytic centers of H and M subunits are dinuclear ferroxidase sites (Figure
1b and c) where Fe2+ is oxidized by O2,
proceeding through a spectroscopicallycharacterizedintermediate
di-ferricdi-ferrictoproductaperoxoμ-oxo/hydroxo(Fe-O-Fe)

withrelease of H2O2. The Fe-O-Fe dimers
move 20 Å through a channel in thesubunit, aggregating with subsequently
formed dimers to form tetramers andlarger multimers before entering thecavity near the four-fold symmetry axis

Figure 1. (A) Ferritin protein cage with four subunits in yellow
forming a four-fold symmetry axis (PDB 1MFR). (B) A single
subunit with iron indicated by purple spheres (PDB 3RBC).

(Figure 1a and b).
The general mechanism of iron storage by ferritin has been outlined by years of experimental studies,but many aspects remain uncertain, including the role of water and the protein environment in the ferroxidase
reaction, the peroxo coordination mode, and the protonation states of the intermediates and dimer products.
The purpose of the current research is to theoretically define the structures of all intermediates and productsin the reaction pathway through comparison with the available X-ray diffraction, EXAFS, Mössbauer, MCD,
and Raman data.
Initial coordinates of the Fe(II)- and Fe(III)-bound states were taken from crystallographic structures ofCu(II)- (PDB 3RE7, 2.8 Å) and Fe(III)-bound (PDB 3RBC, 2.7 Å) bullfrog M ferritin, respectively. Eachmodel was based on a single subunit containing ~3000 atoms. Structural optimizations were carried out forthe 9 Å region surrounding the Fe centers using ONIOM-ME(B3LYP:Amber) with SDD(f) for Fe and
6-31G* for others. The QM layer for representative models including capping H atoms are shown in Figure 2.
These models were also used in a separate series of QM-only calculations.

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Figure 2. QM models of (A) Fe(II)-bound and (B) Fe(III)-bound ferroxidase sites withcoordinates from crystallographic structures of Cu(II)-bound and Fe(III)-bound bullfrog
M ferritin, respectively.
The Cu(II)-bound crystal structure on which the Fe(II) model is based (Figure 2a) defines athree-coordinate A site and five-coordinate B site; however, interpretation of MCD data led to assignments ofa square pyramidal A site and trigonal bipyramidal B site. At 2.8 Å resolution the coordinates of watermolecules are highly uncertain; thus, we examined models with one or two waters added to the A site, as well
as models with and without the B-site water. Key structural parameters and Heisenberg exchange coupling
constants of the optimized models are presented in Table 1. Model R1 can be ruled out due to a large rotationof the Glu23 side chain to an anti coordination mode and tetrahedral geometry at FeA. The discrepancy in the
Glu23 side chain conformation is also described by the 81° change in the O1-O2-FeA-O3 dihedral angle (seelabels in Figure 2a) relative to that of the crystal structure (151°). To match the experimental 5-coordinate
geometry at FeA, Glu23 can be bidentate as in R2 and R3, or an additional H2OA can be present as in R4 andR5. The dihedral angles show that the Glu23 bidentate coordination mode (126 or 142°) is achieved with lessrotation than the syn monodentate mode (-165 or -157°), in which the uncoordinated Glu(O) is hydrogenbonding to a water ligand. On the other hand, it is this latter hydrogen bonding mode that is clearly present in
the oxidized crystal structure and thus less rearrangement would be required. A further consequence ofmonodentate coordination is that it allows FeA to move closer to FeB in models R4 and R5, as shown by theshorter Fe...Fe distances (4.48 and 4.23 Å). While the crystallographic Fe…Fe distance has a large error bar(4.3 ± 0.4 Å), in R2 it is likely too long (4.88 Å) for it to be a reasonable candidate, in addition to theinconsistent tetrahedral geometry at FeB. R5 is also disfavored by the 6-coordinate geometry at each Fe, due
to the H2OB migrating to a bridging position. R3 and R4 remain as the best models and neither is clearlyfavored. The Fe…Fe distances and J values are reasonable, but neither has the combination of trigonal
bipyramidal and square pyramidal geometry indicated by MCD. Forthcoming TD calculations will provide
another means to compare the models to the MCD results.

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Table 1. Composition, structural parameters and exchange coupling constants for ONIOM-optimized
Fe(II)-bound models
Glu23

O1-O2-FeA-O3

FeA

FeB
a

Fe…Fe

J

(Å)

(cm-1)

a

model

nH2OA

nH2OB

coordination(°)

geometry

R1

1

1

anti

70

Td

SP

4.71

-1.4

R2

1

0

bidentate

126

TB

Td

4.88

-0.8

R3

1

1

bidentate

142

TB

Td/TB

4.74

-0.6

R4

2

0

syn

-165

SP

SP

4.48

-0.9

R5

2

1

syn

-157

O

O

4.23

syn

Exp

151

SP/TB

geometry

TB/SP

4.3 ± 0.4

-0.9
b

-0.8

a

Td, tetrahedral; TB, trigonal bipyramidal; SP, square pyramidal; O, octahedral. b4.63 Å in the subunit used for these optimizations.

The Fe(III) products of the ferroxidase reaction have a much shorter Fe…Fe distance of 3.1 ± 0.1 Åin the crystal structure (see Figure 2b) that is consistent with the 2.99 Å EXAFS value. Based on thisdistance, a μ-oxo/hydroxo ligand must be present but hidden by the electron density of the Fe centers in the
crystal structure. The number and positions ofwater-derived ligands are again uncertain, and theone labeled O2-/OH-/H2O in Figure 2b isparticularly interesting as it may be a second

Table 2. Composition, Fe…Fe distances, isomer
shifts,doublets which were attributed to a mixture offour μ-oxo/hydroxo-bridged species. To identify
these products, ONIOM optimizations andMössbauer calculations were carried out formodels with various water-derived ligands, andrepresentative results are presented in Table 2.
The single μOH -bridged model, Ox1, has thelongest Fe…Fe distance of 3.50 Å, as the bridge
is insufficient to maintain the crystallographic

theexperimental

uncertainty.

Furtherof

ONIOM-

Fe…Fe

δ(FeA, FeB)ΔEQ(FeA, FeB)

model

ligands(Å)(mm/s)a(mm/s)a,b

Ox1

OH-

3.50

0.50, 0.50

0.43, 1.12

Ox2

O2-

3.35

0.51, 0.50

1.77, 1.43

-

Ox3

2OH

3.07

0.56, 0.51

0.49, 1.25

Ox4

O2-, OH-

2.88

0.55, 0.47

1.33, 0.94

c

1.95c

Exp2

0.55c

1.63c

Exp3

0.48c

1.17c

Exp4

0.52c

0.63c

3.1 ± 0.1

0.48aCalculated with B3LYP, Wachter’s basis set for Fe, cc-pVDZ for2-

the distance to 3.35 Å, which is still not within

splittings

bridging

Exp1-

models. The stronger μO ligand in Ox2 reduces

quadrupole

optimized Fe(III)-bound models

bridge. Mössbauer spectra show four quadrupole

distance of 3.05 Å in the subunit used for theandother atoms according to Bochevarov et. al. JCTC 2010, 6, 3735.
b

ONIOM-EE values. cParameters for four quadrupole doublets.

strengthening the bonds between the Fe sites, Ox3 has two μOH- ligands, resulting in a 3.07 Å distance thatis remarkably close to the initial 3.05 Å distance. The quadrupole splittings of Ox3 greatly differ between thetwo sites (0.49 and 1.25 mm/s), and match well with two of the experimental values, Exp4 (0.63 mm/s) andExp3 (1.17). The corresponding calculated isomer shifts are systematically 0.03–0.04 mm/s higher than theexperimental values if Exp4 is assigned to site A and Exp 3 to site B. Thus, the four experimental quadrupole－ 156 －

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doublets may represent four sites rather than four dimers. Replacing one of the μOH- bridges with μO2results in the shortest distance of all, 2.88 Å, which is not within the reported crystallographic error bar;
however, it is only 0.11 Å shorter than the EXAFS distance. The FeA and FeB isomer shifts (0.55 and 0.47mm/s) agree well with Exp2 (0.55 mm/s) and both Exp1 (0.48 mm/s) and Exp3 (0.48 mm/s), respectively.
The corresponding quadrupole splitting for FeA is 0.30 mm/s lower than that of Exp2, and similarly, FeB has
a quadrupole splitting 0.23 mm/s lower than that of Exp3. Overall, doubly bridged structures are strongly
favored over the singly bridged structures, and it is likely that both Ox3 and Ox4 are produced in the
ferroxidase reaction.
This work has identified the most probably structures of the Fe(II)- and Fe(III)-bound states of theferroxidase site, while eliminating many possible candidates. Ongoing TD-DFT calculations and anevaluation of the peroxo-intermediate will ensure that this is the most comprehensive theoretical study of theferroxidase reaction to date.

2. Original papers(1) Harris, T. V.; Szilagyi, R. K.,“Comparative Assessment of the Composition and Charge State of Nitrogenase
FeMo-Cofactor”
Inorg. Chem. 50(11), 4811-4824(2011).
3. Presentation at academic conferences(1) Harris, T, V.; Szilagyi, R. K.,“Density Functional Evaluation of the Composition, Charge, and Magnetic Structure of
Nitrogenase FeMo-Cofactor”
CPMD Meeting, Barcelona (P35), Sept. 5, 2011.
4. Book Chapters(1) Harris, T. V.; Szilagyi, R. K.,“Nitrogenase Structure and Function Relationships by Density Functional Theory”
In Nitrogen Fixation: Methods and Protocols; Ribbe, M. W. Ed.; Humana Press: New York,
2011; pp 267-292.
5. Others(1) Harris, T. V.
“Development of Density Functional Methods for Iron-Sulfur Clusters: Application to the
Elusive Structure of the Iron-Molybdenum Cofactor of Nitrogenase”
Dissertation, Montana State University, Nov. 2011.
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Ⅳ 研究業績 (2011)�方����� ���ー�� �年�の研究の��

配位不飽和金属部位へのガス分子吸着に関する理論研究を行った．

䛆ጞ䜑䛻䛇㻌
金属と有機配位子の多彩な組み合わせによって生み出される多孔性配位高分子と呼ばれる新規物質群が近年注目を集め，ガス吸着材，ガス分離材，触媒，センシング材等への応用が期待され，近年盛んに研究が展開されている．多孔性配位高分子は規則的に配列したナノメートルオーダーの細孔を有し，その細孔内にはオープンメタルサイトと呼ばれる配位不飽和な金属部位を有する構造が報告されている．ガス分子の吸着においてはそのオー
プンメタルサイトが相互作用部位として有効に働いている事が示唆されており，そのような部位における相互作用を明らかにすることは，選択的吸着や触媒反応などに有用であると考えられる．実際，赤外分光や核磁気共鳴分光法など様々な実験的手法でその相互作用の存在を示す報告がなされている．その一方で，その相互作用に対する理論的研究の展開
は発展途上であり，主に静電相互作用である事が示唆されつつあるが定量的な評価は行われていない．
そこで多孔性配位高分子の構成単位の一つである paddle-wheel 構造に注目した．
Paddle-wheel 構造は４つのカルボキシレート誘導体配位子と二個の金属イオンから構成
され，多くの多孔性配位高分子骨格中に見られる基本構造である．金属イオンとして Cuを対象とした．Cu は Zn と並んで多孔性配位高分子骨格の合成において最もよく用いられ－ 158 －

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Ⅳ 研究業績 (2011)ている金属の一つであり，本研究で多様な骨格に対する知見を与える事ができると考えられる．

䛆◊✲┠ⓗ䛸ィ⟬䛇
下の Figure 1 に，対象としたモデル構造を示した．二核の Cu と四つのカルボキシレー
ト誘導体からなる配位子によって構築された paddle-wheel 構造において，軸位（z 軸方向）のガス分子（L）に対してオープンメタルサイトが相互作用部位として働く．

Figure 1

ガス分子が存在しない構造およびガス分子が捕捉された構造を DFT 法で構造最適化を行い，その相互作用エネルギーを下式で評価した．相互作用エネルギーの評価の際にはBSSE 補正を行った．
Eb , L   ECu  L   ECu  2 EL  2

本研究目的は，この相互作用の性質を明らかにすることで細孔中におけるオープンメタル
サイトが果たす役割を明らかにすることである．

䛆◊✲⤖ᯝ䛇
Cu paddle-wheel 構造は，基底状態が open shell singlet であり，triplet 状態へ容易に励起し，その励起エネルギーは小さいことが知られている．そこで各々のスピン状態にお－ 159 －

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Ⅳ 研究業績 (2011)

ける相互作用エネルギーの違いについて検討を行ったが，その差はほとんどなかった．これはスピンが分布するのは Figure 1 において dx2-y2 軌道（x 軸と y 軸方向）であり，ガス分子が相互作用するのは z 軸方向（主に 4pz 軌道）であるため，スピン状態の違いが直接，ガス分子との相互作用エネルギーに影響を与えないためと考えられる．

Figure 2
以下は全て triplet 状態における計算結果を示す．ガス分子として L = MeNC, MeCN,
H2O, C2H4, C2H2, CO, CO2, N2, CH4, H2 に対してその相互作用のエネルギーを Table １にまとめた．
（Table １）各 L における相互作用エネルギー（Eb, L）と構造
Eb, L / kcalmol-1

L

SCS-MP2

Structure / ÅExptl.

r(Cu-Cu)r(Cu-L)

MeNC

17.2

2.650

2.174

MeCN

11.7

2.590

2.193

H2O

12.2

2.562

2.241

C2H4

7.8

2.568

2.574

C2H2

6.9

2.559

2.572

CO

5.8

2.573

2.267

CO2

4.3

2.507

2.429

N2

3.5

2.525

2.394

CH4

1.8

4. 3

2.500

2.737

H2

1.2

1. 6

2.508

2.221

7. 3

－ 160 －

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Ⅳ 研究業績 (2011)

相互作用のエネルギー評価は SCS-MP2 法によって行った．実験値が報告されている
C2H2, H2 については良い一致を示す一方で，CH4 については実験値と合っていない．これは参考としている実験値が，CH4 の吸着部位の周りには骨格の構成要素である芳香環が複数存在し，それら芳香環からなる細孔壁が構成するポテンシャル場によって捕捉された値となっているためである．つまり，今後はオープンメタルサイトとガス分子の相互作用だ
けでなく，細孔壁の効果を取り込んだ検討が必要である事が示唆される結果と言える．実際 Figure 1 のモデル構造においてカルボキシレート部分の置換基を R = H, Me, Ph で検討した場合も若干の相互作用エネルギーの違いが見られた．これは置換基による Cu の電荷の変化が影響しているためと考えられるが，今後は細孔中の環境を再現したモデル計算による検討も重要であることが示唆された．また，L = CO について，その電荷移動の評価を行った．その結果，CO 分子のσ軌道からの供与については 0.322 e と大きな供与が見られる一方で，CO 分子のπ*軌道への逆供与については 0.048 e とほとんど寄与が無いことが明らかとなった．実際，実験によっても赤外分光の CO 分子の伸縮振動の高波数シフトが見られており，その結果とも一致しており，その相互作用の性質としてこの電荷移動の寄与があることが明らかとなった．

Cu-Cu 金属間距離が，L との相互作用前（r(Cu-Cu) = 2.487 Å）に比べ長くなっている．
これは上で述べたようにガス分子が z 軸方向で相互作用するため，dz2 軌道との反発が大き
くなり Cu-Cu 間の反発も大きくなるためである．相互作用エネルギーが大きくなるにつれその距離の変化も大きくなっている．しかし，相互作用エネルギーが小さいガス分子については，その電荷移動はほとんど見られず，CO の場合とは異なる相互作用によって捕捉されるものと考えられる．そこで静電相互作用に注目した．静電相互作用による安定化エ
ネルギーを定量的に明らかにするためにエネルギー分割法による相互作用の解析を行った．

－ 161 －

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Ⅳ 研究業績 (2011)

その結果，ガス分子と Cu-paddle-wheel オープンメタルサイトにおける相互作用エネルギ
ーと静電相互作用による安定化エネルギーに比例関係の相関があることを見出した．つまり，オープンメタルサイトはこれまで示唆されてきたように静電相互作用によるガス分子捕捉を可能にする部位であるということを定量的に評価することに成功した．
これは多孔性配位高分子において選択的ガス分子の捕捉・放出のための設計する上で重要な知見をあたえるものである．

－ 162 －

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Ⅳ 研究業績 (2011)

2. 論�(1) Jose Alberto, Rodríguez-Velamzán, Miguel A. González, José A Real, MiguelCastro, M. Carmen Muñoz, Ana B. Gasper Ryo Ohtani, Masaaki Ohba, Ko Yoneda,
Yuh Hijikata, Nobuhiro Yanai, Motohiro Mizuno, Ando Hideo, and Susumu Kitagawa“A switchable molecular rotator: neutron spectroscopy study on a polymericspin-crossover compound”
J. Am. Chem. Soc., 134, 5083-5089 (2012)(2) Daiki Umeyama, Satoshi Horike, Munehiro Inukai, Yuh Hijikata, and Susumu
Kitagawa“Confinement of mobile histamine in coordination nanochannels for fast
proton transfer”
Angew. Chem. Int. Ed., 50, 11706-11709 (2011)(3) Nobuhiro Yanai, Koji Kitayama, Yuh Hijikata, Hiroshi Sato, Ryotaro Matsuda,
Yoshiki Kubota, Masaki Takata, Motohiro Mizuno, Takashi Uemura, and Susumu
Kitagawa“Reporting structural transformation of soft porous crystals for detectionof CO2”Nat. Mater., 10, 787-793 (2011)(4) Yuh Hijikata, Satoshi Horike, Daisuke Tanaka, Juergen Groll, Motohiro Mizuno,
Jungeun Kim, Masaki Takata, and Susumu Kitagawa“Differences of crystal structure and dynamics between soft porous
nanocrystal and bulk crystal”
Chem. Commun., 47, 7632-7634 (2011)
3. 学会��
(1) 土方 優，榊 茂好「配位不飽和 2 核銅(II)錯体とガス分子の相互作用に関する理論的研究」
錯体化学会第 61 回討論会 岡山 2011/9/17-19(2) 犬飼宗弘，堀毛悟史，梅山大樹，土方 優，北川 進「無加湿条件下でプロトン伝導性を示す多孔性金属錯体の合成と評価」
日本化学会第 92 春季年会 神奈川 2012/3/25-28(3) 梅山大樹，堀毛悟史，土方 優，犬飼宗弘，北川 進「規則性配位空間におけるヒスタミンの配列制御と高プロトン伝導」
錯体化学会第 61 回討論会 岡山 2011/9/17-19(4) 犬飼宗弘，堀毛悟史，梅山大樹，土方 優，北川 進「無加湿条件下でプロトン伝導性を示す多孔性金属錯体の合成と評価」
第 37 回固体イオニクス討論会 鳥取 2011/12/7-9－ 163 －

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Ⅳ 研究業績 (2011)(5) Yuh Hijikata and Shigeyoshi Sakaki“Theoretical Study of Interaction between Gas Molecule and Paddle-Wheel unitof MOF”
7th Congress of the International Society for Theoretical Chemical Physics,
Tokyo 2011/9/2-8(6) 杉本雅行，堀毛悟史，土方 優，北川 進「4,4'-スルホニル二安息香酸を用いた二次元骨格多孔性配位高分子のガス吸着特性」
錯体化学会第 61 回討論会 岡山 2011/9/17-19(7) 大谷 亮，犬飼宗弘，土方 優，越山友美，大場正昭，北川 進「膜親和性金属錯体の開発と脂質二重層膜の修飾」
錯体化学会第 61 回討論会 岡山 2011/9/17-19(8) 犬飼宗弘，堀毛悟史，梅山大樹，土方 優，北川 進「無加湿条件下でプロトン伝導性を示す多孔性金属錯体の合成」
錯体化学会第 61 回討論会 岡山 2011/9/17-19(9) 土方 優，榊 茂好「配位不飽和 2 核錯体と気体分子の相互作用に関する理論的研究」
第 5 回分子科学討論会 札幌 2011/9/20-23－ 164 －

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Ⅳ 研究業績 (2011)

�野 ��
特推研究フェロー
�� �年度の研究の要�
本年度は遷移金属錯体に対する溶媒和効果を中心に研究を行った。
���に�
遷移金属錯体の特徴として電子状態が複雑で大きな分極性を持つ点などが挙げられるが、溶媒中での反応性や分子的性質を調べる上で、d 軌道の方向性に基づき遷移金属錯体の周囲の溶媒配置を空間的に考慮する事は重要である。無数の溶媒分子から成る分子集団性を扱う必要性からも現状このような計算を行う為に有用な方法としては、周囲の溶媒分子を古典的な MM モデルで陽に表す
QM/MM 法、あるいは積分方程式により統計分布関数で表す 3D-RISM-SCF 法が主に挙げられる。
近年の計算機の向上から CP-MD などの計算の適用範囲も広がりつつあるものの、これらは QM/MM法と同様に溶媒群の箱サイズの点から解離反応などについては制限があり、3D-RISM-SCF 法による研究対象分野というものは、いまだ多く残されていると考える。
特に 1D-RISM-SCF 法では溶質の作る空孔領域を過大評価する点、また溶質周囲の静電ポテンシ
ャルを点電荷近似により評価する点で、かさ高く分極性が大きな系への適用の際に問題が起こる事がしばしばあった。後者の点については近年考案された 1D-RISM-SCF-SEDD 法でも解消されているが、3D-RISM-SCF 法はこの２点について解消する可能性も持ち、溶液内の遷移金属錯体の反応や分子的性質を調べる上で有用であると期待される。本研究では 3D-RISM-SCF 法における静電ポ
テンシャルの計算を行う上で、波動関数から直接計算を行う近接領域、溶質点電荷から近似計算を行う遠方領域、またスイッチング関数を用いて近接領域と遠方領域の静電ポテンシャルを滑らかに繋ぐ為のスイッチング領域の３つの領域に溶媒空間を分ける事で記述精度を保ちつつコスト削減を行った。この 3D-RISM-SCF 法を白金錯体へと適応した研究について、以下報告する。
�プラチン錯体の加水分解反応に関する研究�
シスプラチン、cis-PtCl2(NH3)2 は抗癌活性を持つ事が知られ、古くから多くの実験的、理論的研究が広く行われて来た。その抗癌活性は、癌細胞の DNA 塩基に付加し DNA 合成を阻害する事に由来し、加水分解反応はその前段階の重要な反応と目されている（Scheme 1）。
第一、第二加水分解においてプラチン
錯体はその電荷変化に示される通り、
電子状態および溶媒和構造の大きな変化を伴う。特にこのようなイオン性解
離は溶媒和エネルギーの定量的議論が難しい。本研究では 3D-RISM-SCF 法

Scheme 1 : シスプラチンの第一、第二加水分解を適用して、溶媒効果の解析を試みた。

－ 165 －

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Ⅳ 研究業績 (2011)

3D-RISM 法は平衡溶媒分布を解く際に必要な溶質まわりの静電ポテンシャルを波動関数から直接計算できる長所があり、Pt の孤立電子対が占める d 軌道の形等も反映できると期待した。また抗癌活性を持たない事が知られる trans-PtCl2(NH3)2 についても、同様に理論的検討を行った。
構造最適化計算は DFT 法により行い M06-2X を採用した。Pt の内殻電子は HW ECP で置き換え
た LANL2TZ(f)基底を、残る原子については 6-31++G**を用いた。更に精度の向上のため 6-31++G**を cc-pVTZ に置き換え、Cl と O 原子に aug-cc-pVTZ を用いて MP2 計算を行った。特に高精度な電子状態計算として CCSD(T)と MP2 による電子相関エネルギーを cc-pVDZ 基底レベルにて評価を行い、MP2 自由エネルギーを補正する事で CCSD(T)自由エネルギーを計算した。また溶質運動に対する熱力学補正（零点、熱、エントロピー補正）について以下のように行った。振動運動項は計算
コストの都合から PCM 法における調和振動数を用いて計算した。溶質分子の並進運動項については Whitesides らによる溶媒体積補正を利用して求めた。
例としてシスプラチンの加水分解反応の構造変化を図１に、またシス、トランスプラチンの自由エネルギー変化を図２に示した。

図１：シスプラチンの第一、第二加水分解反応における構造変化

図２：シス、トランスプラチンの加水分解反応における MP2 自由エネルギー変化
左：シスプラチン 右：トランスプラチン

赤：熱力学補正後

緑：熱力学補正前 括弧内：CCSD(T)これらの結果、第一加水分解における活性化自由エネルギーは、シス体で 20.8 kcal/mol、トランス体で 20.3 kcal/mol と見積もられ、第二加水分解においてシス体では障壁は変わらず 20.9 kcal/mol で－ 166 －

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Ⅳ 研究業績 (2011)

あるのに対し、トランス体では若干増加して 23.2 kcal/mol と見積もられた。この結果は実験値に適ったものであり、また得られた平衡定数 pK1 はシス体で 3.74、トランス体で 5.94、pK2 はシス体で6.90、トランス体で 9.69 であり、この値は実験値に比べて大きいものの、その大きさの順序は上手く実験結果の傾向を再現したものである。特に気相中での反応と比較して PAS1 から PS1 への解離
反応では 100 kcal/mol、また PAS2 から PS2 への解離反応では 200 kcal/mol もの大きな反応障壁の低下があり、加水分解反応が進むためには溶媒効果が必要不可欠である事が確かめられた。また第一加水分解において置換された Cl アニオンはその強い静電相互作用によって Pt 錯体の第一溶媒和圏に留まり易い傾向がある事を図２は示唆しており、Cl アニオンが解離せずに進んだ場合の第二加水分解反応についても調べた結果、活性化自由エネルギー自体は変化しない事が分かった。従って、
系の自由エネルギーの観点から、Cl アニオンは第二加水分解が進んだ後で第一溶媒和圏から離れる
方が反応経路として有利である点なども明らかにした。
【d8 平面４配位型金属錯体と水の相互作用に関する研究�
ｄ８平面４配位型金属錯体が正電荷を持つ場合、z 軸上の水分子は O 原子を中心金属へ向けた構造（O 配向）をとる事が実験、理論研究から示唆されている。[Pt(pyridine)4]Cl2・３H2O 結晶などが例に挙げられるが、これは水素結合が電子的に富んだ領域と正に誘起された部位の静電相互作用に由来するという一般的理解に反しない。一方、全体で中性電荷となる金属錯体の場合、過去のMP2 計算によれば、水分子の H 原子が電子不足のｄ８中心金属へ向いた構造（H 配向）がエネル
ギー的に優位であると予測されており、一般的理解とは逆方向の水素結合を意味する。この存在は近年、実際に trans-PtCl2(NH3)(N-glycine)・H2O 結晶における中性子散乱実験で立証された。
これらの実験、理論研究を踏まえて、本研究では正および中性電荷を示すｄ８平面４配位型金属
錯体のモデル系として、Pt2+を中心金属とした[Pt(NH3)4]2+と trans-PtCl2(NH3)(N-glycine)の錯体に対し、その z 軸上の水分子との相互作用について気相中での２つの配向の違いを明らかにした。
更にｄz2 軌道の影響を調べるため、電子分布の広がりの小さい Pd2+を中心金属とした系に対しても同様に、水分子の２つの配向における相互作用の違いを比較、検討した。
金属錯体と z 軸上の水１分子を QM 領域として扱い、水の２つの配向に関して次のように参照構造を決めた。O 配向では水の O 原子が z 軸上に存在するように、また H 配向では H 原子と O 原子が z 軸上に位置するように束縛条件を加えた上で、M06-2X 汎関数による DFT 計算を行い、構造を最適化した。Pt は６０個の内殻電子を、Pd は２８個の内殻電子を Hay-Wadt ECP に置き換え
た LANL2TZ(f)を基底関数に選び、残る原子は 6-31++G**基底を用いた。これにより得た金属錯体と水分子の内部座標は固定し、中心金属と水の O 間の距離を変化させる事で気相中のエネルギーおよび水溶媒中の自由エネルギーの振る舞いを調べた。基底関数は水の O と配位子の Cl に
aug-cc-pTVZ を、残る配位子に cc-pTVZ を用いて MP2 計算を行い、BSSE を補正した。
結果、Pt 錯体と水分子の相互作用系に対する H 配向と O 配向の参照構造を図３に示す。この参照構造に対して、H 配向における解離状態を基準０にとった気相中のエネルギー変化は図４の通り、水の２つの配向構造で大きく異なる結果を得た。まず正に帯電した tetra-ammine 錯体では O 配向の結合エネルギーが Pt で-12.2、Pd で-13.7 kcal/mol と H 配向に比べて非常に大きな安定化を持つ。一方、中性の glycine 錯体では H 配向の結合エネルギーが Pt で-4.2、Pd で -2.7 kcal/mol とO 配向より優位な構造となる事が示され、先の結晶構造で見られる水の配向性に一致する。また－ 167 －

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Pt、Pd 錯体での結合エネルギーを比較するため、H 配向と O 配向に対して中心金属と水の O 間距離が 3.1、3.4Åの構造を参照にし、エネルギー分割法を用いて表１の結果を得た。

図３：[Pt(NH3)4]2+ 及び trans-PtCl2(NH3)(N-glycine)錯体に対する水の配向性

図４：気相中における Pt 及び Pd 錯体と水のエネルギー変化
赤：H 配向１、緑：O 配向１、青：H 配向 2、紫：O 配向２。

エネルギー基準 0 は H 配向の解離状態。単位：kcal/mol

中心金属、
電荷に依らず、
総じて MP2 分散項(DISP)は H 配向の方が O 配向よりも約 4 kcal/molの安定化を引き起こしており、また tetra-ammine 錯体における O 配向の大きな結合エネルギ
ーは静電項(ES)に起因する事が分かった。Glycine 錯体の H 配向では分極項(POL)および電荷移動項(CT)の安定化も起こっているが、分散項による寄与が大半を占める。また Pd のｄz2 軌道がPt 錯体よりも広がりが小さい事により、交換反 表１：相互作用エネルギー成分
発項(EX+REP)の不安定化は小さいが、分数値

Pt-ammine 錯体

Pd-ammine 錯体

は予想に反し同程度であった。水溶媒中での自

H 配向

O 配向

H 配向

O 配向

ES

+3.7

-13.3

+6.4

-14.0

EX+REP

+5.9

+5.2

+3.6

+3.2

POL+CT

-3.1

-2.8

-2.7

-2.7

DISP

-4.2

-0.8

-3.7

+0.0

由エネルギー変化の比較を図５に示すが、気相中 tetra-ammine 錯体においてエネルギー的に不利であった H 配向は、大きな溶媒和自由エネ
ルギーの相対的安定化によって、Pt 錯体の第一
溶媒和圏の z 軸方向において同程度に起こり得Pt-glycine 錯体

るという結果が得られた。更に tetra-ammine

H 配向 1

O 配向 1

H 配向 1

O 配向 1

ES

-3.9

-3.8

-1.1

-4.3

EX+REP

+6.8

+6.0

+4.3

+3.8

POL+CT

-2.4

-1.3

-1.5

-1.0

DISP

-4.9

-1.3

-4.4

-0.6

錯体での H 配向の大きな溶媒和安定化の原因として、O 原子を向けた水溶媒分子が増加する領域を特定した結果、z 軸上の水分子の近傍における溶媒和構造の違いのみならず、NH3 配位子→金属への電荷移動により間接的に引き起こされる

Pd-glycine 錯体

NH3 配位子の周囲での溶媒和構造の違いというものも一因である事を明らかにした。

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図５：水溶媒中での Pt 及び Pd 錯体と水の自由エネルギー変化
赤：H 配向１、緑：O 配向１、青：H 配向 2、紫：O 配向２。

エネルギー基準 0 は H 配向の解離状態。単位：kcal/mol

2. 論�

3. 学会��
(1) 青野 信治・榊 茂好「プラチン錯体の加水分解反応における溶媒効果」
理論化学討論会 2011 岡山 2011/5/12 1P09
(2) Shinji Aono, Shigeyoshi Sakaki,“Solvation Effect on Hydrolysis of Platin Complex”
International Society for Theoretical Chemical Physics, Tokyo, 2011.9.04(4PP-42)(3) 青野 信治・榊 茂好「d8平面４配位型金属錯体と水の相互作用の理論的研究」
分子科学討論会2011

北海道

2011/9/20

1E21

4. �の�
(1) 青野 信治「４配位および６配位白金錯体における溶媒和効果：3D-RISM-SCF法によるアプローチ」
化学反応のポテンシャル曲面とダイナミックス 京都 2012/3/30－ 169 －

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�本��

特推研究フェロー
�� 今年度の研究の��
今年度は二つのテーマ 1. Au(I)-Cu(I)対を含む vapochromic 錯体の燐光の帰属と発光メカ
ニズムについて理論研究 2. 五配位 Ni(II)錯体の結晶中でのスピンクロスオーバー現象の理論的考察 を行った。
Au(I)-Cu(I)相互作用を含む多核金属錯体の発光メカニズムと金属�相互作用【������】ガスの吸着によって発光する vapochromic 錯体は、有害ガスの検知に用いることが出来る。ガスの種類によって発光ピークが異なる場合、有害ガスの特定にも応用可能である。d10-d10 対を持つ金属錯体はその弱い相互作用のため、ガス吸着による構造変化が大きく、発光ピークの領域が大きいケースが多い。
最近、Au(I)-Cu(I)対を含む三核錯体[Au(im(CH2Py)2)2(CuL2)2]3+ (Scheme 1. 1; L=MeCN, 2 ;L=MeOH)が合成され、MeOH、MeCN ガス雰囲気化で発光スペクトルのピークがそれぞれ462nm(青), 520nm(緑)と異なることが報告された[1]。Au(I)-Cu(I)対を持つ vaporchromic 錯体
は、この錯体が初めての合成例である。本研究では発光メカニズムと Au(I)-Cu(I)相互作用を調べることを目的に、DFT 法と SCS-MP2 法を用いて基底状態、励起状態の分子構造と燐光の帰属、Au-Cu 相互作用の評価を行い、MeOH、MeCN 雰囲気で燐光が異なる理由を解明した。
【計算�法】S0 と T1 状態について Au-Cu 距離を SCS-MP2 法で評価し、それ以外は B3PW91
汎関数を用いた DFT 計算で構造最適化した。基底関数は、Au と Cu 原子の内殻電子を
Stuttgart ECP で置き換え 2f 分極関数を加えたものを用い、その他の原子には 6-31G(d), O 原子には 6-31+G(d)を用いた(BSI)。S0-T1 励起エネルギーは、配位子に cc-pVDZ, O 原子に
aug-cc-pVDZ を用いて(BS II)、B3PW91 汎関数で評価した。

Scheme 1[結�と考察] SCS-MP2 で最適化した 1, 2 の Au-Cu 距離は実験値を良く再現した (1; cal.
4.631 Å, expl. 4.591 Å, 2; cal. 2.767 Å, expl. 2.792 Å)。錯体 1 の発光は Cu d  Py *遷移
(MLCT)と帰属され、錯体 2 の発光は Au-Cu 5d-3d antibonding MO から Au-Cu 6p-4sp
bonding MO への遷移と帰属された (Scheme 2)。1, 2 の S0-T1 遷移エネルギーは実験値と良く一致した (1: cal. 2.62 eV, expl. 2.68 eV, 2: cal. 2.40 eV, expl. 2.47 eV)。Scheme 2 に示すように、2 では S0-T1 遷移が anti-bonding MO  bonding MO 遷移であるため、1 に比べて emission
peak が red shift する。Au-Cu 相互作用は SCS-MP2 法で 0.89 kcal/mol と評価されたが (BSSE
補正後)、 Au-Au 相互作用(6-12 kcal/mol) と比較すると著しく小さい。Au-Cu 相互作用が弱く、NHC 分子が柔軟であるため、ガス分子の吸着により 1 と 2 の構造が容易に相互変換することが分かった。

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Ⅳ 研究業績 (2011)

Scheme 2[�考��] [1] Strasser, C. E. et al. J. Am. Chem. Soc. 2010,132, 10009.

五配位 Ni(II)錯体の結晶中でのスピンクロスオーバー現象の理論的考�【������】遷移金属錯体の結晶中でのスピンクロスオーバー現象は、工業的な応用が期 待 さ れ る 。 近 年 、 五 配 位 Ni(II) ス ピ ン ク ロ ス オ ー バ ー (SCO) 錯 体
TpPh,MeNi(S2CNMe2)[TpPh,Me=hydrotris(3-phenyl-5methyl-1-pyrazolyl)borate]が、結晶中で二つの独立な構造 Ni1, Ni2 を持ち (Scheme1, Fig1)、磁気的性質が異なることが、X 線構造と磁化率の測定によって明らかにされた。Ni1 の構造は 123K と 293K で大きな違いがないが、Ni2 では 123K と 293K で構造が大きく異なる。このことは SCO が Ni1 で起こ
らず、Ni2 で起きていることを示している。
本研究では、単量体の構造と電子状態、及び結晶化の影響を考慮した場合の違いを電子状態計算から議論し、分子性結晶中のスピンクロスオーバー現象の理由を説明する。
Ni1
Ni2

Ni2
Ni1

Fig.1 X-ray structure of TpPh,MeNi(S2CNMe2) in 123K

Scheme 1 TpPh,MeNi(S2CNMe2)【計算��】単量体の構造最適化を行い X 線構造と比較した。Ph, Me を H 原子に置換したモデル錯体で電子状態と一重項、三重項の相対安定性を議論した。結晶の効果を取り入れるため、周囲の置換基の位置を X 線構造で固定した構造最適化を行った。基底関数は BSI(Ni: SDD ECP plus 2f polarization functions, C, H, N, B, S: 6-31G(d)), BSII (Ni: C, H, N,
B, S: cc-pVDZ) を用い、構造最適化は B3PW91/BSI, 相対エネルギーは B3LYP*/BSII で計算した。
[結果と考�]単量体の構造と X 線構造を比較すると、Ni1 の 123K, 293K の構造は tripletの構造と良く一致した(Table 1)。Ni1 は低温から高温まで HS(high spin)を維持している。

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Ⅳ 研究業績 (2011)

Ni2 は 123K, 293K で構造が異なり SCO が起きていることが分かるが、計算結果との一致が悪く、結晶の効果が大きい。結晶化による影響で Ni2 の SCO が誘発されていることが示唆された。
Table 1. 単量体の最安定化構造と X 線構造との比較
expl.

calcd.

Ni1

Ni2

T (K)

123K

293K

123K

293K

singlettripletNi-N1 (Å)

2.038

2.048

2.401

2.149

2.927

2.069

Ni-N3 (Å)

2.111

2.111

2.003

2.083

1.929

2.128

Ni-N5 (Å)

2.048

2.058

1.972

2.046

1.913

2.063

Ni-S2 (Å)

2.34202.34352.25672.323

2.21912.3789Ni-S1 (Å)

2.40062.39292.27212.36142.22732.4357モデル錯体で singlet と triplet の構造を比較すると、triplet では Ni-Nax が singlet より短く、Ni-Neq と Ni-S が長い(Fig.2)。これは dz2(HOMO)から dxy(LUMO)への一電子励起により singlet と triplet の構造が変化するためである (Fig3)。
zyx

Fig.2 singlet and triplet structure of model complex

dz2(HOMO)

dxy(LUMO)

Fig.3

HOMO and LUMO and spin density of triplet

Fig.4

PES along Ni-Nax and Ni-S distancespin density of triplet－ 172 －

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Ⅳ 研究業績 (2011)

モデル錯体で Ni-Nax, Ni-S 距離の変化に対する singlet と triplet の potential energy
surface (PES) から、Ni-Nax が長く Ni-S 距離が短い構造では、singlet が triplet より安定であることが分かった(Fig4)。Ni2 の Ni-S の分子面は c 軸に対して平行、Ni1 の Ni-S は c軸に対して垂直であるため、結晶の c 軸方向の長さが短い場合(123K)、Ni2 の Ni-S が小さ
くなり triplet が不安定化することにより SCO が起きる。c 軸方向の短縮により、Ni2 のPh と Ni1 の五員環との距離が短くなるため、Ni-Nax の距離が大きくなり singlet が安定化する。モデル錯体の PES と低温高温の X 線構造の比較から Ni2 の SCO の原因を理解することが出来た。
��(1) Yumiko KATAOKA, Dharam PAUL, Hiroyuki MIYAKE, Tsuyoshi YAITA, Eisaku MIYOSHI,
Hirotoshi MORI, Shinya TSUKAMOTO, Hiroshi TATEWAKI, Satoshi SHINODA, andHoroshi TSUKUBE“Experimeltal and Theoretical Approaches Toward Anion-responsive
Tripode-Lanthanide Complexes: Mixed Donor Ligand Effects on Highly
Coordinated Complexation and Luminescence Sensing Profiles”
Chem. A. Eur. J., 14, 5258-5266 (2008).
(2) Shinya TSUKAMOTO, Hirotoshi MORI, Hiroshi TATEWAKI, and Eisaku MIYOSHI“CASSCF and CASPT2 calculations for lanthanide trihalides LnX3 using model
core potentials”
Chem. Phys. Lett., 474, 28-32 (2009).
(3) Shigeyoshi SAKAKI, Daisuke KAWAI, and Shinya TSUKAMOTO“Theoretical Study of Metallasilatranes; Bonding Nature and Prediction of
New Metallasilatrane”
Collection of Czechoslovak Chemical Communications, 76, 619-629 (2011).
(4) Shinya TSUKAMOTO and Shigeyoshi SAKAKI“Theoretical Study of Pt(PR3)2(AlCl3) (R=H, Me, Ph, or Cy) Including an
Unsupported Bond between Transition Metal and Non-Transition Metal Elements;
Geometry, Bond Strength, and Prediction”
J. Phys. Chem. A, 115, 8520-8527 (2011).
2. ������(1) Shinya Tsukamoto, Hirotoshi Mori, Hiroshi Tatewaki, and Eisaku Miyoshi“Ab initio study for lanthanide trihalide by means of relativistic model corepotentials”
WATOC 2008, Sydney, Australia (2008).
(2) Shinya Tsukamoto, Hirotoshi Mori, Hiroshi Tatewaki, and Eisaku Miyoshi“Ab initio study for lanthanide fluorides by means of relativistic model core

－ 173 －

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Ⅳ 研究業績 (2011)

potentials”
APCTCC 2009, Port Dickson, Malaysia (2009).
(3) Shinya Tsukamoto, Hirotoshi Mori, Hiroshi Tatewaki, and Eisaku Miyoshi“CASSCF and CASPT2 calculations for lanthanide trihalides LnX3 using model
core potentials” XIII-th ICQC, Helsinki, Finland (2009).
��2011 �
(1) 塚本 晋也, 榊 茂好
“Pt(PR3)2(AlCl3) (R=H, Me, Ph, Cy) の理論研究：構造、結合、及び M-Al を持つ錯体の理論予測” 第 14 回理論化学討論会 5 月 12-14 日、岡山大学、岡山市 1P19
(2) Shinya Tsukamoto, Shigeyoshi Sakaki“Theoretical study of luminescent vapochromic complexes including
AuCu2(NHC)2 core” International Society for Theoretical Chemical Physics(ISTCP-VII)
September 2-8, Waseda University, Tokyo (Japan) 3PP-48(3) 塚本 晋也, 榊 茂好
“Cu2Au 骨格を持つ 3 核錯体の理論的研究:分子依存性と Au-Cu 結合” 第 61 回 錯体化学討論会 9 月 17-19 日、岡山理科大学、岡山市 2Bb-16－ 174 －

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Milind Madhusudan DESHMUKHSPR Fellow, Fukui kenichi Memorial Research Group 2
1. Summary of the research carried out during April 2011 to April 2012.
Theoretical Study of Complex Systems involving Non-covalent Interactions:
Development of Computational Strategies and Application.
Non-covalent interactions plays dominant role in the structure and function of not
only the biomolecular systems but are also important in supramolecular assemblies andmaterial sciences. Accurate estimation of non-covalent interaction is extremely importantto get insights into structure and stability of these systems. However, evaluation ofintermolecular distance and binding energy (BE) of van der Waals complex/cluster at ab
initio level of theory is computationally demanding when many monomers are involved.
Starting from MP2 energy, we reached a two step evaluation method of BE of van der
Waals complex/cluster through reasonable approximations as given in equation 1;(1)
BE  BE(HF)  {BE(MP2 or MP2.5) - BE
(HF)}
MiMj

Mi-Mj

Mi-Mj

where HF represents the Hartree-Fock calculation, Mi, Mj etc. are interacting monomers,and MP2.5 represents the arithmetic mean of MP2 and MP3. The first term is the usual
binding energy of the complex/cluster evaluated at the HF level. The second term is thesum of the difference in two-body binding energy between the correlated and HF levelsof theory. This approximate evaluation methodology was applied to various van der
Waals complexes from S22 data set consisting of up-to-four monomers at MP2 andMP2.5 levels of theory. We found that this method is capable of providing precise
estimate of the binding energy. The nice correlation (Figure 1) between binding energy
estimated with present approximate equation and standard approach (BEref.; see equation2) was indeed encouraging.
(2)
BE ref .  E MP 2 (or MP 2.5) (M1, M 2, M3,....)   E MP 2 (or MP 2.5) ( Mi )MiFigure 1: Comparison of the binding energy estimated by standard approach (BEref.) withthat estimated by approximate eqs. 1
The maximum error of the BE is less than 1 kcal/mol and 1% in most cases except forseveral limited cases. The origins of error in these cases are discussed. Althoughmoderately large error was found in some limited cases, it is noted that the equation 1
was able to reproduce precisely the potential energy surface in such case too (see Figure1－ 175 －

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Ⅳ 研究業績 (2011)

1). The computation time with this approximate evaluation method decreases by about
half than the conventional method. For details see reference 1 from publication list.
The above developed strategy was extremely useful in of our study ofabsorption/adsorption of CO2 and CS2 into porous coordination polymers (PCPs). PCPs
recently attract much attention to the potential application to gas storage, gas separation,
catalysis, and nanospace engineering. The flexibility in use of variety of organic linkers
and/or metals leads to syntheses of many kinds of PCPs with required property. Amongthe desired properties of such compounds, selective uptake and storage of gas molecule
have been investigated well. Recently, optical and magnetic properties and their
responses to inclusion of a guest molecule have started to draw new attention in thechemistry of PCP. Recently the chemresponsive switching of spin-state was recently
shown to occur by gas absorption in the Hofmann-type three-dimensional PCP{FeII(Pz)[PtII(CN)4]}n (Pz=pyrazine). For instance, the absorption of such bulky
molecules as benzene, pyrazine, water, methanol etc. stabilizes the high spin state; notethat though water and methanol are not bulky, they forms bulky cluster in PCP. Of
particular interest is the absorption of CS2 molecule; despite of its small size, CS2
absorption induces the spin transition from the high-spin to the low-spin state. This is thereverse to the spin transition by bulky molecules. On the other hand, the absorption ofsimilar CO2 does not induce any spin transition. In this work, we theoreticallyinvestigated the interactions of CS2 and CO2 molecules with a realistic model consistingof a unit cell of the Hofmann-type PCP {Fe(Pz)[Pt(CN)4]}n as shown in Figure 2.

Side view
Top view
Figure 2: Realistic model (RM) of CS2-absorbed PCP; Fe (green), Pt (pink), N (blue), C(gray), and S (yellow).
The purposes of the present work are to find the binding sites of these gases in the
Hofmann-type PCP, to evaluate their binding energies, and to clarify the determining
factors for absorption site and absorption energies of these gases with the PCP. We
believe that the knowledge of such determining factors is indispensible to understanding
the gas absorption with PCP and finding a gas molecule which induces the spin transition
between high and low spin states.

2－ 176 －

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Ⅳ 研究業績 (2011)

The binding energy of gas molecule with framework was evaluated with ONIOM
scheme, as shown in Eq. 3.
High
High
Low
Low
(3)
BE ONIOM BE Low
RM
RM  BESM1  BESM1  BESM 2  BESM 2
where superscripts “High” and “Low” represents the high quality calculation and low
quality calculation, respectively and subscripts, “RM”, “SM1”, and “SM2” represents
realistic model, small model 1 and small model 2; See Figure 3 for details of small model
systems. The first term on the right hand side of Eq. 3 is the binding energy of gas
molecule with realistic model, RM. This is a “real low” component of the ONIOM
equation. The second term represents, binding energy of gas molecule with small modelSM1 and the third term represent binding energy of gas molecule with small model SM2.
The M06-2X level of theory was employed with cc-pVTZ basis sets for low quality
calculation and scaled MP2 methods21 were used with aug-cc-pVTZ basis sets for highquality calculation.



 



(b) Small model 2 (SM2)(a) Small model 1 (SM1)

Figure 3: Small models (a) SM1 and (b) SM2 representing the Pz and Pt interaction
sites respectively. These models were used in ONIOM calculations.
The binding energies of CS2 and CO2 are evaluated to be -17.3 kcal mol-1 and -4.0 kcal
mol-1, respectively at the ONIOM(MP2.5:M06-2X) level and -25.0 kcal mol-1 and -6.0
kcal mol-1 at ONIOM(MP2:M06-2X) level, indicating that CS2 strongly absorbs in PCP
but CO2 weakly. The absorption positions of these molecules are completely different
between CO2 and CS2; CO2 molecule exists between two Pt sites. To the contrary, one S
atom of CS2 exists between two Pz ligands and the other S atom is between two Pt sites.
See Figure 4 and Figure 5 for the corresponding potential energy surface of CS2 and CO2
absorption in Hofmann-type PCP, respectively.

Figure 4: Comparison of potential energy surface between M062X and ONIOM forabsorption of CS2 in PCP.

3

－ 177 －

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Ⅳ 研究業績 (2011)

Figure 5: Comparison of potential energy surface between M062X and ONIOM forabsorption of CO2 in PCP.
Note that only model systems are shown in Figure 4 and 5 for brevity and the potential
energy surfaces are scanned using ONIOM equation 3. The optimized position of CS2
agrees with experimentally reported X-ray structure. Based on energy decomposition
analysis and electrostatic potential of the PCP framework, it is concluded that both of thelarge binding energy and absorption position of CS2 arise from large dispersion
interaction between CS2 and Pz. The different absorption position of CO2 arises fromlarge electrostatic interactions between CO2 and Pt site, and small binding energy of CO2
comes from weak dispersion interaction with both Pz and Pt site.
2. Original Papers(1) Deshmukh Milind M. and Sakaki Shigeyoshi,"Two-step Evaluation of Potential Energy Surface and Binding Energy of van der
Waals Complexes"
J. Comput. Chem., 33, 617 (2012).
(2) Deshmukh Milind M. and Sakaki Shigeyoshi,"Binding energy of gas molecule with two pyrazine molecules as organic
linker in metal–organic framework: its theoretical evaluation and understanding ofdetermining factors"
Theor. Chem. Acc., 130, 475 (2011).
(3) Deshmukh Milind M.; Ohba Masaaki, Kitagawa Susumu, and Sakaki Shigeyoshi,"Absorption of CO2 and CS2 into Hofmann-type Porous Coordination Polymer:
Theoretical Study of Binding Energy, Absorption Position, and Understanding of
Determining Factors" (to be submitted). (2012).
3. Presentations at academic conferences(1) Deshmukh Milind M. and Sakaki Shigeyoshi,“Highly accurate approximate method for evaluation of binding energy of van der
Waals complexes”
The 9th Triennial Congress of the World Association of Theoretical andComputational Chemist (WATOC), Santiago-de-compostela, Spain, July 17, 2011.

4－ 178 －

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Ⅳ 研究業績 (2011)(2) Deshmukh Milind M. and Sakaki Shigeyoshi,“Dispersion Energy of van der Waals Complex; Approximate Evaluation with
Pair-wise Correlation Effect”
The 7th Congress of the International Society for Theoretical Chemical Physics(ISTCP-VII) at Waseda University, Tokyo, Japan on September 2-8, 2011.
(3) Deshmukh Milind M. and Sakaki Shigeyoshi,“Highly accurate approximate method for evaluation of binding energy of van der
Waals complexes”
The 14th Annual Meeting of Theoretical Chemistry Society, Okayama, Japan,
May 2011.
4. Others(1) Deshmukh Milind M. and Sakaki Shigeyoshi“Absorption of Gases into Metal Organic Framework: A theoretical investigation”
The 8th symposium of Fukui Institute for Fundamental Chemistry, Kyoto, Dec.3,
2010.
(2) Deshmukh Milind M. and Sakaki Shigeyoshi“Absorption of CO2, CS2 and OCS into Hofmann type Metal-organic
Framework: Binding Energy, Absorption Position and Determining Factors”
The 9th symposium of Fukui Institute for Fundamental Chemistry, Kyoto, Jan. 6,
2012

5－ 179 －

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Ⅳ 研究業績 (2011)

Guixiang ZENGSPR Fellow, Fukui kenichi Memorial Research Group 2
1. Summary of the research of the year
Theoretical Study of Noble Features in Oxidative Addition of B−Br σ−Bond of Bromoborane toM(PMe3)2 (M= Pt or Pd)
Formation processes of cis−boryl complex via oxidative additions of B−H, B−B, and B−E (E═Si,
Ge, or Sn) bonds to low−valent transition−metal complexes have been clarified theoretically. However,
the mechanism for trans-boryl complex produced by the oxidative addition of B−X (X═Cl, Br, or I)
bond to Pd(0) and Pt(0) complexes remains unclear yet, in which the cis−trans isomerization is
proposed to be involved. In general, the cis-trans isomerization occurs via spin conversion process, but
the cis-trans isomerization taking place on single potential surface has not been investigated well. Here,
we theoretically investigated the oxidative addition of the B−Br bond of bromoborane Br2B(OSiMe3)
to M(PMe3)2 (M ═ Pt or Pd) to explore possible reaction pathways and to clarify the process of thethermal cis−trans isomerization in the reaction presented in Eq. 1.

Geometry and frequency calculations were carried out by DFT method with triple-zeta quality
basis sets. The singlet−triplet energy difference was evaluated with DFT and MP2 to MP4(SDQ)
methods.
The first step is the coordination of Br2B(OSiMe3) with M(PMe3)2 (M ═ Pt or Pd) to form aprecursor complex. The next is the B−Br bond cleavage. In the Pt system, two reaction courses are
possible (Figure 1);

Figure 1. Oxidative addition of the B−Br bond to M(PMe3)2 (M ═ Pt or Pd). Ea (kcal/mol) is Gibbs
energy barrier in solvent (toluene),1－ 180 －

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Ⅳ 研究業績 (2011)

one is the nucleophilic attack pathway which directly affords the trans-product. The other one is the
stepwise reaction pathway which includes the cis−oxidative addition followed by the cis−transisomerization. The former reaction course is more favorable. In the Pd system, only the stepwise
pathway was found. Interestingly, the thermal cis−trans isomerization was found to occur on the
singlet potential energy surface due to the strong donation ability of the boryl group.
Theoretical Study on Transition−Metal Oxoboryl Complex: M−BO Bonding Nature, Mechanismof the Formation Reaction, and Prediction of New Oxoboryl Complex
The synthesis of B−O multiple−bonded compound has been very difficult for a long time. This is
surprising because B≡N triple−bonded compounds were synthesized and well characterized. One of
the reasons is that the B−O bond is highly polarized and easily undergoes oligomerization reaction toform B−O−B linkage rather than staying as B=O double or B≡O triple bond. In 2010, Braunschweig
et al made a breaktrhough. They synthesized a remarkably stable neutral platinum(II)−oxoboryl
complex PtBr(BO)(PCy3)2, as shown in Eq. 1.

In this work, we theoretically investigated the M-BO bond nature, mechanism of the formation
reaction, and make prediction of new oxoboryl complex with DFT method.
First, we make comparison of the Pt−BO bond with other Pt−L bond (L = CN¯, CO, and NO+) isinteresting. As shown in Table 1, the electron population on the LUMO of the [PtBr(PMe3)2]+ moiety
considerably increases in the order NO+ < CO < CN¯ << BO¯.

Consistent with this result, the electron

population on the HOMO (the lone pair orbital) of BO¯, CN¯, CO and NO+ decreases in the order
NO+ >> CO > CN¯ > BO¯. On the other hand, the electron populations on the π* orbitals increase in
the order BO¯ < CN¯ < CO << NO+.
weaker in the order BO−

These results indicate that the σ−donation ability becomes−>> CN > CO > NO+, but the dπ−electron accepting ability becomesstronger in the reverse order.
Second, the formation reaction of theoxoboryl

complex

PtBr(BO)(PMe3)2

roles. The electron−donating bulky phosphinewasligand is favorable for the reaction by enhancing
Bδ+−Br2δ− polarization,

explored. It occurs through a four−centerthetransition state (see Scheme 1), in which thetransition state, and more destabilizing the boryl

δ+

B −Br2δ−polarization and the Br2Si and thestabilizing

thecomplex (reactant) than the oxoboryl complex

O pπB pπ charge transfer interactions play key(product).
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Ⅳ 研究業績 (2011)

Scheme 1.

Table 1. Important Molecular Orbitals and Their Electron Populationsa of [MBr(PMe3)2]+ and L
Ligand in MBrL(PMe3)2 (L=BO¯, CN¯, CO, and NO+).
[MBr(PMe3)2]+

L

 2*

LUMO

HOMO

HOMO−1

5σ

 2*

Pt

1.174 e1.946 e1.972 e0.702 e0.068 e0.042 ePd

1.076 e1.975 e1.981 e0.853 e0.055 e0.034 eNi

0.999 e1.976 e1.985 e0.857 e0.053 e0.023 eIr

1.212 e1.977 e1.973 e0.596 e0.043 e0.035 eRh

1.190 e1.910 e1.979 e0.729 e0.040 e0.024 eCN¯

Pt

0.608 e1.961 e1.975 e1.481 e0.067 e0.057 eCOPt

0.413 e1.841 e1.881 e1.636 e0.210 e0.183 eNO+Pt

0.179 e1.497 e1.564 e1.860 e0.479 e0.530 e

L

BO¯

a

M

The electron population of each MO is presented here. In the unoccupied orbital, the population

increases from zero to the number here in the complex. In the doubly occupied orbital (HOMO,
HOMO−1, and 5σ), the population decreases from two to the number here in the complex.

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At last, MBrCl(BO)(CO)(PR3)2 (M=Ir and Rh) is predicted to be good candidate of stableoxoboryl complex based on the comparisons in the ∆G0‡ and ∆G0 values of the formation reaction, theM−BO bonding nature, and the M-BO interaction energy between MBrCl(BO)(CO)(PR3)2 and
PtBr(BO)(PR3)2.
2. Original Papers.
(1) Guixiang ZENG and Shigeyoshi SAKAKI“Noble Reaction Features of Bromoborane in Oxidative Addition of B−Br σ-Bond to[M(PMe3)2](M = Pt or Pd): Theoretical Study”

Inorg. Chem. 50, 5290–5297(2011)(2) Guixiang ZENG and Shigeyoshi SAKAKI“Theoretical Study on the Transition-Metal Oxoboryl Complex: M−BO Bonding Nature,
Mechanism of the Formation Reaction, and Prediction of a New Oxoboryl Complex”
Inorg. Chem. 51, 4597−4605 (2012)
3. Presentation at academic conferences(1) Guixiang Zeng and Shigeyoshi Sakaki“Noble Reaction Features of Bromoborane in Oxidative Addition of B−Br σ-Bond to[M(PMe3)2](M = Pt or Pd): Theoretical Study”
The 14th Symposium on theoretical chemistry (1P12), Okayama University, Okayama, May
12~14, 2011
(2) Guixiang Zeng and Shigeyoshi Sakaki“Noble Reaction Features of Bromoborane in Oxidative Addition of B−Br σ-Bond to[M(PMe3)2](M = Pt or Pd): Theoretical Study”
The 7th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
Waseda University, Tokyo, Japan, September 2-8, 2011.

4－ 183 －

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Nozomi TAKAGISPR Fellow, Fukui kenichi Memorial Research Group 2
1. Summary of the research of the year
A Theoretical Study of Dynamic Behavior of Hydrogen-bridged Bis(silylene)tungsten
Complexes
Hydrogen-bridged bis(silylene)tungsten complexes (1 – 3 in

R1

Scheme 1) are of considerable interest, because theseOC

Si

complexes are considered as a model of the transition state inW

H/D exchange of methane and silane by Cp2MR (M = Ln; R =to R4). Interestingly, only in 3 two different types of processes,

H
Si

OC
R3

H, CH3, SiH3). The variable temperature 1H NMR spectra show
dynamic behavior involving site-exchanges of substituents (R1R2

R4

1 : R1 = H, R2 = tBu, R3 = R4 = Me
2 : R1 = R3 = R4 = Me, R2 = tBu
3 : R1 = R3 = Me, R2 = R4 = tBu

Scheme 1

the cis/trans-exchange (Process I) and the trans/trans-exchange(Process II), were observed independently and simultaneously depending on the temperature,
though only Process I was observed in 1 and 2. I investigated the mechanism of the dynamic
behavior by density functional theory and post-Hartree-Fock calculations. The calculations indicatethat in the Process I the 1,3-Me migration occurs easier than the W=silylene rotation (Figure 1). In
W=Si Rotation+18.0[+17.0]1,3-Me Migraton

3-TS3b

+15.0[+13.9]3-Int2a3-Int1+11.0[+9.7]+10.5[+8.9]

Me
OC

+14.8
[+13.9]3-TS3a+15.8[+14.5]3-TS2b3-TS13-Int2bMe+13.3[+11.6]
3-Int3a3-TS4a3-TS4a+14.8[+13.6]3-TS53-Int4+11.5[+10.1]+10.7[+9.0]+9.7[+7.3]

tBu

Me
OC

H

tBu
Si

W

Si

OC

+17.9
[+17.1]3-Int3b+11.4[+9.4]

SiW

0.0

3-TS2a+24.1[+24.0]

tBu

H
Si

OC
tBu

Me

-1.6
[-1.3]
trans-3cis-3

Figure 1. Energy profile for cis/trans-exchange process (Process I) of 3 calculated at the B3PW91 and the
SCS-MP2 level. (in kcal/mol).

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Ⅳ 研究業績 (2011)

2.454Å
2.537Å
1.720Å
Si

W

Si

1.653Å

2.513Å

3-TS
2.519Å

+11.3[+12.0]Si
W1.696Å

2.479Å

Si
W

1.693Å

Mea
OC

2.521Å

tBua
SiW

0.0 kcal/mol

H

OC

tBub
Si

W

Si
tBub

trans-3

Meb
OC

OC
Meb

H
Si

tBua

0.0
Mea

trans-3'

Figure 2. Energy profile for trans/trans-exchange process (Process II) of 3 calculated at the B3PW91 and the
SCS-MP2 level. (in kcal/mol).

the Process II, the hydrogen-bridged bis(silylene) unit rotates with the smaller activation barrier
than that of Process I (Figure 2). This result agrees well the experimental fact that the Process II
takes place at lower temperature (ΔG≠298 = 12.3kcal/mol) than the Process I. The details of thereaction features as well as the characteristic bonding features of the three-center interaction of
Si-H-Si, the W-Si double bonding nature, and the rather short Si-Si distance were also investigated.
A Theoretical Study of Unusual Y-Shaped Three-coordinate Pt Complex: Pt(0) σ-Disilane
Complex or Pt(II) Disilyl Complex?
The unusual Y-shaped structure of the recently reported three-coordinate Pt complex
Pt[NHC(Dip)2](SiMe2Ph)2 (NHC = N-heterocyclic carbene; Dip = 2,6-diisopropylphenyl) was
considered a snapshot of the reductive
elimination of disilane. A density functional
theory study indicates that this structure arises
from

the

strongtrans-influence

of

N

N
C

the

139.8°

2.126Å

extremely σ-donating carbene and silyl ligands.

Pt

Though this complex can be understood to be

80.3°

Si

a Pt(II) disilyl complex bearing a distorted

2.345Å
Si

3.025Å

geometry due to the Jahn-Teller effect, its 195Pt

Si-Pt-C-N = 27.3°

NMR chemical shift is considerably different

Figure 3. Optimized structure of Pt[NHC(Dip)2](SiMe3)2
at the B3PW91 level.

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Ⅳ 研究業績 (2011)

5dz2

from those of Pt(II) complexes but close toPt[NHC(Dip)2]

those of typical Pt(0) complexes. Its

5dyz

6pz

+

Si···Si bonding interaction is 50% of the
donation(0.607e)

usual energy of a Si-Si single bond. Theinteraction between the Pt center and the

back-donation(0.307e)disilane(SiMe2Ph)2 moiety can be understood in

-antibonding MO

-bonding MO

Scheme 2

terms of donation and back-donationinteractions of the Si-Si σ-bonding and σ*-antibonding molecular orbitals with the Pt center. Thus,
we conclude that this is likely a Pt(0) σ-disilane complex and thus a snapshot after a considerable
amount of the charge transfer from the two silyl groups to the Pt center has occurred. Phenyl anion(Ph-) and [R-Ar]- [R-Ar = 2,6-(2,6-iPr2C6H3)2C6H3] as well as the divalent carbon(0) ligand
C(NHC)2 also provide similar unusual Y-shaped structures. Three-coordinate digermyl, diboryl, andsilyl-boryl complexes of Pt and a disilyl complex of Pd are theoretically predicted to have similar
unusual Y-shaped structures when a strongly donating ligand coordinates to the metal center. In a
trigonal-bipyramidal Ir disilyl complex Ir(SiR3)2(NHC)(PH3)2, the equatorial plane has a similar
unusual Y-shaped structure. These results suggest that various snapshots can be shown for the
reductive eliminations of the Ge-Ge, B-B, and B-Si σ-bonds (Figure 4).
N138.4°
SiC

Pt

139.6°
139.2°
81.2°

2.112Å

2.133Å

2.308Å
83.3°

2.318ÅSi(A) [Pt(Ph)(SiMe3)2]-Pt 2.323Å
85.2°

Si

3.144Å

Si

Si-Pt-C-C = 83.3°(C) Pt[C(NHC)2](SiMe3)2(B) [Pt(R-Ar)(SiMe3)2]-

N

N

N

C

C

C

Pt

Pt

153.5° Pt 135.7°

2.064Å

2.086Å
141.6°
141.4°
2.436Å
2.436Å
76.9°
GeN

Si-Pt-C-C = 73.3°

N

N

C
C

2.319Å

Si

Si-Pt-C-C = 72.4°

3.067Å

N

3.017Å

C

137.4° 2.119Å

Pt

Si

Si-Pt-C-C = 89.9°

Ge-Pt-C-N = 19.8°

N

C

N

3.031Å

Ge

Si-Pt-C-N = 19.9°(D) Pt[NHC(Dip)2](GeMe3)2

148.6°

2.024Å
62.7°

2.082Å

2.381Å

B
B B-Pt-C-N = 0.0°
O O2.107ÅO O

Si 2.550Å

Si-Pt-C-N = 21.4°(E) Pt[NHC(Dip)2](BO2C2H2)2

70.8° B

1.988ÅO

B-Pt-C-N = 16.0°(F) Pt[NHC(Dip)2](SiMe3)(BO2C2H2)

Figure 4. Various snapshots for reductive elimination of Si-Si, Ge-Ge, B-B, and B-Si bonds calculated at theB3PW91 level.

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Ⅳ 研究業績 (2011)

2. Original papers(1) "Bonding Situation in "Early-Late" Transition Metal Complexes Cl3M-M'(PCl3)4 (M = Ti,
Zr, Hf; M' = Co, Rh, Ir) - Theoretical Study for a Ligand Fine Tuning of M-M’ Bonds -"N. Takagi, A. Krapp, G. Frenking, Z. Anorg. Alleg. Chem. 637, 1728-1735 (2011).
(2) "Carbodiphosphorane-Analogues E(PPh3)2 with E = C - Pb. A Theoretical Study with
implications for ligand design"
N. Takagi, R. Tonner, and G. Frenking, Chem. Eur. J., 18, 1772-1780 (2012).
(3) "Synthesis of Kinetically Stabilized 1,2-Dihydrodisilenes"
T. Agou, Y. Sugiyama, T. Sasamori, H. Sakai, Y. Furukawa, N. Takagi, J. D. Guo, S.
Nagase, D. Hashizume, N. Tokitoh, J. Am. Chem. Soc., 134, 4120-4122 (2012).
(4) "A Theoretical Study of Unusual Y-Shaped Three-coordinate Pt Complex: Pt(0) σ-Disilane
Complex or Pt(II) Disilyl Complex?"
N. Takagi, S. Sakaki, J. Am. Chem. Soc., in press.
3. Presentation at academic conferences(1) "Characteristic Fluxional Behavior and Bonding Nature of Hydrogen-bridged Bis(silylene)
Complexes"
N. Takagi, Y. Odagiri, H. Hashimoto, H. Tobita, S. Sakaki, The 7th Congress of theInternational Society for Theoretical Chemical Physics (ISTCP-VII), Tokyo, September 2 –8, 2011.
(2) "A theoretical study of dynamic behavior of hydrogen-bridged bis(silylene)tungsten
complexes"
N. Takagi, Y. Odagiri, H. Hashimoto, H. Tobita, S. Sakaki, The 61st Japan Society of
Coordination Chemistry Symposium, Okayama, September, 17 – 19, 2011.
(3) "Characteristic Fluxional Behavior and Bonding Nature of Hydrogen-bridged Bis(silylene)
Complexes"
N. Takagi, Y. Odagiri, H. Hashimoto, H. Tobita, S. Sakaki, The 9th Fukui Institute for
Fundamental Chemistry Symposium, Kyoto, January 6, 2012.

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Ⅳ 研究業績 (2011)

Masayuki NAKAGAKISPR Fellow, Fukui kenichi Memorial Research Group 2
1. Summary of the research of the year
Theoretical Study of Inverted Sandwich Type Complexes of N2
β-diketiminate ligands make low-valent and low-coordinate transition metal complexes and form theinversed sandwich type complexes (ISTCs). Especially, ISTCs bridged by dinitrogen molecule areinteresting for its spin states and coordination mode of N2. The (μ-N2)[Fe(DDP)]2 (DDPH =2-{(2,6-diisopropyl-phenyl)imino}pent-2-ene, which is refer to “nacnac” in several works) was reported bySmith et al. and the coordination mode of N2 is η1-end-on. On the other hand, (μ-N2)[Cr(DDP)]2 wasreported by Tsai et. al. and the coordination mode of N2 is η2-end-on mode (Scheme 1). The effective
magnetic moment μeff of (μ-η2:η2-N2)[Cr(DDP)]2 at 293 K is 3.9 μB, which suggests antiferromagnetic
coupling between the Cr atoms, though the values of (μ-η1:η1-N2)[Fe(DDP)]2 is 7.9 μB, which seems toferromagnetic coupling between two metal atoms.
In this study, we investigated the electronic structure of the dinitrogen bridged ISTCs of chromium(I),manganese(I), and iron(I) and clarify the differences between these complexes.
Scheme 1 (μ-N2)[M(AIP)]2 (M= Cr, Mn, Fe; DDP: R=Me, R’=2,6-iPr2C6H3; AIP: R=H, R’=H)

We replaced the DDP ligands with AIP (AIPH = 1-amino-3-imino-prop-1-ene; Scheme 1) for brevity. The
validity of using the model complex was confirmed in our previous study of benzene complex. Geometry
optimizations were carried out for each spin states by the complete active space self-consistent field(CASSCF) method. The active space consists of the d-orbitals of two metals and two π* orbitals ofdinitrogen molecule. The second-order perturbation theory with a CASSCF reference function (CASPT2)
calculations were carried out at CASSCF optimized structures. CASCI calculations with the orbitals werecarried out to obtain the occupation number and spin density of each localized orbitals
The relative energies of various spin states of (μ-N2)[M(AIP)]2 (M=Cr, Mn, Fe) with η1-end-on andη2-side-on coordination modes of N2 are listed in Table 1. In the (μ-N2)[Cr(DDP)]2, the singlet state is themost stable spin state, though the stability is similar to each other among singlet to nonet. Under the
Boltzmann distribution at 293K, the effective magnetic moment estimated by CASPT2 is μeff = 2.7 μB, which－ 188 －

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Ⅳ 研究業績 (2011)is close to the experimental value (3.9 μB). In the (μ-N2)[Fe(AIP)]2, the septet state with η1-end-on is themost stable, which agree with the experimental result. In the (μ-N2)[Mn(AIP)]2, nonet state with η2-side-on isslightly more stable than that with η1-end-on mode. Compare to the case of Cr complex, the energy
differences of spin states are large, that is, strong high-spin coupling.
Table 1 Relative energies (kcal/mol) with end-on and side-on modes of (μ-N2)[M(AIP)]2 (M=Cr, Mn, Fe)calculated by CASPT2 method.
(μ-N2)[Cr(AIP)]2 (μ-N2)[Mn(AIP)]2 (μ-N2)[Fe(AIP)]2
η1-endη2-side11tet

η1-endη2-side

23.2

11.6

η1-endη2-side

9tet

22.5

4.0

0.2

0.0

28.9

14.8

7tet

17.8

2.6

5.2

5.0

0.0

3.6

5tet

13.2

1.4

9.6

9.4

7.4

9.8

3let

10.1

0.5

13.8

13.9

14.0

15.6

1let

8.4

0.0

18.4

18.7

21.8

22.0

Molecular orbital (MO) interaction diagram of (μ-η2:η2-N2)[Cr(AIP)]2 is shown in Scheme 2. The righthand is the orbital diagram of Cr(AIP) moiety and left hand is N2 π* orbitals. The energy destabilization of
Cr dyz orbital is large because of the overlap with the lone pair orbital of AIP ligand. The CASSCF(10,12)
natural orbitals of (μ-η2:η2-N2)[Cr(AIP)]2, which correspond to the optimized orbitals in Scheme 2, areshown in Figure 1. Number in parentheses represents occupation number in the singlet state. The π-bondorbital (φ1), which consists of two Cr dyz orbitals and N2 π*z orbital, is very stable and almost doubly
occupied. Though the Cr dxy orbital belong to same symmetry with N2 π*x orbital, the δ(dxy)-bond between
N2 and two Cr(AIP) is not confirmed. The other 8 electrons of active space singly occupy in dz2, dxy, dx2-y2
and dxz orbitals (φ2-φ9). Generally, high spin state is more favorable than low spin state when orbital energies
are similar. However, the dxy orbital in b1g (φ2) is stabilized by unoccupied π*x orbital and dxz orbital in b2u(φ9) is destabilized by occupied πx orbital. Because the energy levels of degenerate d-orbitals split by theseinteractions, two electrons in paired d-orbitals prefer open-shell singlet. In fact, the occupation number of φ2
is 1.02 and the one of φ9 is 0.94.
Scheme 2 MO diagram of (μ-η2:η2-N2)[Cr(AIP)]2－ 189 －

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Ⅳ 研究業績 (2011)

φ1(1.96)φ2(1.02)φ3(1.00)

φ4(1.00)

φ5(1.06)

φ6(1.01)φ7(0.97)φ8(0.99)φ9(0.94)

φ10(0.02)

φ11(0.01)

φ12(0.01)

2

2

Figure 1. CASSCF orbitals of (μ-η :η -N2)[Cr(AIP)]2.
The MO diagram of (μ-η1:η1-N2)[Fe(AIP)]2 are shown in Scheme 3. In the isolate Fe(AIP), the A1 state
which has doubly occupied dx2-y2 and dz2 orbitals is ground state, though the B2 state which has doubly
occupied dxz and dy2 orbitals is only 0.6 kcal/mol higher at CASSCF level. At the η1-end-on mode, bonding
orbital is formed by Fe dxz orbitals and N2 π*x orbital. The CASSCF(10,10) natural orbitals of(μ-η1:η1-N2)[Fe(AIP)]2, which correspond to the optimized orbitals in Scheme 3, are shown in Figure 2 withthe occupation numbers of the septet state in parentheses. To avoid the convergence problem, the dx2 orbitals
were excluded from the active space and taken as core orbitals. There are two bonding orbitals, π(dyz)-bondand π(dxz)-bond, and they are doubly occupied in main electron configuration. Two dz2-y2, dxy orbitals andnon-bonding dxz, dyz orbitals are singly occupied and it takes high-spin coupling.
The electronic structure of (μ-η2:η2-N2)[Mn(AIP)]2 is similar to that of (μ-η1:η1-N2)[Fe(AIP)]2. By theforming of ISTC, the Mn dyz and dxy orbitals form π(dyz)-bond and δ(dxy)-bond with the two N2 π* orbitals
instead of π(dxz)-bond because of difference of coordination mode.
Scheme 3 MO diagram of (μ-η1:η1-N2)[Fe(AIP)]2－ 190 －

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Ⅳ 研究業績 (2011)

φ1(1.55)φ2(1.45)φ3(1.00)

φ6(1.00)

φ7(1.00)

φ8(1.00)
1φ4(1.00)

φ5(1.00)

φ9(0.55)

φ10(0.45)

1

Figure 2. CASSCF orbitals of (μ-η :η -N2)[Fe(AIP)]2
Different from the π-bond of (μ-N2)[Cr(AIP)]2, the occupation numbers of anti-bonding orbitals are large in(μ-N2)[Mn(AIP)]2 and (μ-N2)[Fe(AIP)]2. Table 2 shows the main electron configurations of 9B2u state of(μ-η2:η2-N2)[Mn(AIP)]2 and 7B1g state of (μ-η1:η1-N2)[Fe(AIP)]2 in CASSCF wavefunction. In fact, bothstates have several important configurations. In 7B1g state, the second reading terms are single or double
excitation from bonding orbital to anti-bonding orbital. In 9B2u state, configurations which have excitationfrom bonding orbital to anti-bonding orbital of δ(dxy)-bond are more dominant. This multi-reference
character results from the spin polarization of bonding orbitals. In (μ-N2)[Mn(AIP)]2 and (μ-N2)[Fe(AIP)]2,
the non-bonding orbitals, which consist of the same d-orbitals as bonding one, are singly occupied, though
the non-bonding dyz orbital is vacant in (μ-N2)[Cr(AIP)]2. The exchange integral between bonding andnon-bonding orbital is clearly larger than the others. So the spin polarization, α-electron polarizes to metalside and β-electron polarizes to N2 side, occurs to stabilize by the exchange interaction.
Table 4 Main electron configurations of CASSCF wavefunction. Orbital index correspond to Figure 5 and 6
State

Configuration
φ1

φ2 φ 3

Coefficient
φ4 φ 5φ6 φ7

φ8 φ 9

φ10

φ11

φ12

(μ-η2:η2-N2)[Mn(AIP)]2
9

B2u

2

α

α

α

α

α

α

α

α

α

β

0

0.6135

β

α

α

α

α

α

α

α

α

α

β

α

−0.5363

2

2

α

α

α

α

α

α

α

α

0

0

0.3108

α

2

α

α

α

α

α

α

α

α

0

β

−0.1912

0

α

α

α

α

α

α

α

α

α

β

2

−0.1839(μ-η1:η1-N2)[Fe(AIP)]2
7

B1g

2

2

α

α

α

α

α

α

0

0

0.5804

2

α

α

α

α

α

α

α

β

0

0.3707

α

2

α

α

α

α

α

α

0

β

0.3236

2

0

α

α

α

α

α

α

2

0

−0.2284

0

2

α

α

α

α

α

α

0

2

−0.2096

α

α

α

α

α

α

α

α

β

β

0.1861－ 191 －

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Ⅳ 研究業績 (2011)

The spin polarization can be recognized by localized orbital description. Table 3 shows the main electron
configurations of CASCI wavefunction with the localized molecular orbitals under C2v symmetry. In this setof orbitals, the 9B2u state of (μ-η2:η2-N2)[Mn(AIP)]2 and the 7B1g state of (μ-η1:η1-N2)[Fe(AIP)]2 could be
mainly expressed by one configuration. In the configuration, β-electrons occupy the N2 π* orbitals though the
α-electrons occupy the d-orbitals of M(AIP), which can be regarded as three-center three-electron (3c-3e)
bond.
Table 3 Main electron configurations of CAS-CI wavefunction with the localized molecular orbitals underC2v symmetry. Parentheses represent double occupied (core) orbitals.
State

Configuration

Coefficient
M2(AIP)

M1(AIP)dx2-y2

dz2

dxy

N2

dxz

dyz

dx2-y2

dz2

dxy

dxz

dyz

π*z

π*x

(μ-η2:η2-N2)[Mn(AIP)]2
9

B2u

α

α

α

α

α

α

α

α

α

α

β

β

0.8136

α

α

α

α

α

α

α

α

α

β

α

β

−0.1799

α

α

α

α

β

α

α

α

α

α

α

β

0.1799(μ-η1:η1-N2)[Fe(AIP)]2
7

B1g

(2)

α

α

α

α

(2)

α

α

α

α

β

β

0.7744

(2)

α

α

α

α

(2)

α

α

α

β

α

β

−0.1769

(2)

α

α

α

β

(2)

α

α

α

α

α

β

−0.1769

Summary
In the (μ-N2)[Cr(AIP)]2, the spin states of two Cr atoms take weak low-spin coupling and the open-shell
singlet is the most stable state, though the spin states are near degenerated among singlet to nonet. The
π-bond orbital, which consists of dyz orbitals of two Cr atoms and π*z orbital of N2, is very stable and almost
doubly occupied. The degenerated d-orbitals of two Cr(AIP)s split because the dxy orbital in b1g is stabilized
by unoccupied π*x orbital and dxz orbital in b2u is destabilized by occupied πx orbital. Because of the energy
splitting, eight single occupied d-electrons prefer the open-shell singlet.
In the (μ-N2)[Mn(AIP)]2 and (μ-N2)[Fe(AIP)]2, the spin states of two metal atoms take strong high-spin
coupling, nonet and septet states are most stable states, respectively. They form two bond between N2 andtwo M(AIP) moieties; π(dyz)-bond and π(dxz)-bond in η2-side-on and π(dyz)-bond and π(dxz)-bond in
η1-end-on. The single occupation of non-bonding orbitals cause the spin polarization of bonding orbitals,
α-electron localizes to metal side moieties and β-electron localizes to N2 side, and the high-spin state isfavorable.
In the (μ-N2)[Cr(AIP)]2, η2-side-on coordination mode of N2 is obviously stable than η1-end-on mode
because of the favorable orbital overlap between Cr dyz and N2 πx* orbitals to form the π-bond. In the(μ-N2)[Mn(AIP)]2 and (μ-N2)[Fe(AIP)]2, the stabilities of two coordination modes are comparable, because
the advantage of the π(dxz)-bond compared to the δ(dxy)-bond and destabilization of π(dyz)-bond cancel out.

－ 192 －

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2. Presentation at academic conferences(1) Masayuki Nakagaki, Yusaku I. Kurokawa, and Shigeyoshi Sakaki“Theoretical Study of Inverted Sandwich Type Dinuclear Complexes of ethylene anddinitrogen molecules”
7th Congress of the International Society for Theoretical Chemical Physics Tokyo (Waseda
Univ.) 2011/9/3 3PP-52(2) 中垣 雅之、黒川 悠索、榊 茂好「クロム(I)-エチレン及び窒素分子の逆サンドイッチ型錯体及び類似錯体の電子構造に関する理論的研究」
第５回分子科学討論会 2011 札幌 札幌 2011/9/22 3P129
3. Others(1) 中垣 雅之、黒川 悠索、榊 茂好「クロム(I)及び鉄(I)-窒素分子の逆サンドイッチ型錯体の電子構造に関する理論的研究」
第9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 2012/1/6(2) 中垣 雅之、黒川 悠索、榊 茂好「クロム(I)及び鉄(I)-N2錯体の理論的研究 ―異常なスピン多重度とその起源―」
第１回協定講座シンポジウム「計算アルゴリズムと化学・生物学の融合」神戸（神戸大学）2012/2/17.

－ 193 －

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Terutaka YOSHIZAWASPR Fellow, Fukui kenichi Memorial Research Group 2
1. Summary of the research of the year
NMR shielding constants of CuX, AgX, and AuX (X = F, Cl, Br, and I) investigated by density
functional theory based on the Douglas–Kroll–Hess Hamiltonian
Introduction
NMR shielding constants of heavy metal elements are of considerable interest in molecularscience and theoretical chemistry, because those shielding constants reflect characteristic electronic
structure, in particular, relativistic effects in the system including heavy elements. Actually, David andRestrepo recently reported that the paramagnetic term of the Au nuclear magnetic resonance (NMR)
shielding constant of AuF molecule is more than three times as large as those of AuCl, AuBr, and AuI.
They discussed that this result arises from spin-orbit (SO) effect enhanced by the highelectronegativity of F atom. Since their report, the relation between the SO effect and theelectronegativity attracts a lot of interests, because the SO effect does not seem to directly relate toelectronegativity. However, the mechanism of the relation has not been elucidated yet.
In the present study, we combined the DFT method with the second-order DKH (DKH2)
one-electron Hamiltonian and applied it to the calculation of the NMR shielding constant. Then, weapplied this method to the NMR shielding constant of the metal in CuX, AgX, and AuX (X = F, Cl, Br,
and I), investigated relativistic effects on the NMR shielding constant, and discussed the reasons why
the electronegativity of halogen influences the NMR shielding constant.
Results and discussion
Cu, Ag, and Au shielding constants of MX (M = Cu, Ag, or Au; X = F, Cl, Br, or I)
NMR shielding constants of metal center are summarized in Table 1 The Cu shielding constant of
CuI agrees well with the experimental value in the HF, B3LYP, and BP86 calculations.
In the Ag chemical shift, AgNO3 in aqueous solution was experimentally taken as a reference. In
general, it is difficult to calculate the shielding constant with solvation structure. Hence, we employed
here the chemical shift relative to that of AgF. The HF-calculated δ(Ag) value is considerably negativein AgCl, AgBr, and AgI, which does not agree with the experimentally reported increasing order of
δ(Ag); AgF < AgCl < AgBr < AgI. The B3LYP- and BP86-calculated δ(Ag) values are negative at
AgCl but increase in the order AgF < AgBr < AgI. These results indicate that the DKH2-B3LYP and1－ 194 －

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Ⅳ 研究業績 (2011)

DKH2-BP86 methods are better than the DKH2-HF method.
The DKH2-HF-calculated Au shielding constant decreases in the order AuF >> AuCl > AuBr ~AuI, which agrees with the decreasing order of 4c-HF-calculated values. However, it is noted that the
DKH2-HF method overestimates the Au shielding constant by about 1000 ppm, compared to the
4c-HF method. The similar overestimation was reported also in the ZORA-DFT-calculated Hgshielding constant of HgX2, compared to the 4c-DFT value. These overestimations would be due toinsufficiency of the higher order relativistic correction terms of the DKH Hamiltonian. Though the
DKH2-DFT-calculated Au shielding constant of AuF is somewhat smaller and those of AuBr and AuI
are somewhat larger than the 4c-HF values, the same trend of the Au shielding constant is observed, as
will be discussed below.
As reported by David and Restrepo, the Au shielding constant of AuF is extremely larger thanthat of the other AuX in our DKH2-DFT and DKH2-HF calculations. However, the Cu and Ag
shielding constants of CuF and AgF, respectively, are not very large; see Table 1 All these results
indicate that the large Au shielding constant in AuF is characteristic and its reason is of considerable
interest from the viewpoint of the relativistic effects, as follows: The Au shielding constants of AuF
calculated by the scalar relativistic DKH2-B3LYP method is the smallest; 6926 ppm, 8658 ppm, 9186
ppm, and 9753 ppm for AuF, AuCl, AuBr, and AuI, respectively. This result clearly indicates that thescalar relativistic effect is not responsible for this characteristic feature and the SO effect plays animportant role for the very large Au shielding constant of AuF.

Contributions of diamagnetic, paramagnetic, spin-dipolar, and Fermi contact terms to metal shielding
constant of MX2－ 195 －

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Ⅳ 研究業績 (2011)

To elucidate the reason why the Au
shielding constant is much larger in AuF
than in AuCl, AuBr, and AuI unlike the Ag
and Cu shielding constants of AgF and CuF,
we decomposed the metal shielding constantinto the diamagnetic, paramagnetic, and thesum of SD and FC terms, as shown in Figure
1. In all of CuX, AgX, and AuX, thediamagnetic term little depends on the kindof X. In CuX, on the other hand, when goingfrom CuF to CuCl, the paramagnetic term
considerably increases but the SD+FC term
considerably decreases. The decrease in the
SD+FC term largely cancels the increase in
the paramagnetic term, leading to themoderate increase in the Cu shielding
constant. When going from CuCl to CuI, theparamagnetic term moderately increases but
the SD+FC term little changes. As a result,
the Cu shielding constant monotonously
increases when going from CuF to CuI. In
AgX, the paramagnetic term little changes
when going from AgF to AgI. This is against
the general trend that the paramagnetic termof metal halide depends on the halide. In the
Ga shielding constant of GaX4– and the In
Figure 1. Diamagnetic, paramagnetic, and sum of

one of InX4–, however, the paramagnetic

spin-dipolar and Fermi contact terms of MX (M = Cu,

term little changes when going from X = ClAg, or Au; X = F, Cl, Br, or I) calculated by theto I like AgX, (while the diamagnetic term

DKH2-BP86 method.

largely changes). This means that the little

dependence of paramagnetic term on halide in AgX is not surprising; the reason must be discussed in anear future. The SD+FC term moderately decreases when going from AgF to AgCl but thenmoderately increases when going from AgCl to AgI. As a result of these changes, the Ag shielding
constant of AgF becomes moderately smaller than those of AgBr and AgI. In AuX, the paramagnetic3－ 196 －

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Ⅳ 研究業績 (2011)

term considerably increases but the SD+FC term extremely decreases, when going from AuF to AuCl.
When going from AuCl to AuI, both terms moderately increase. Based on these results, it is concluded
that the extremely large Au shielding constant in AuF arises from the extremely large SD+FC term in
AuF. Thus, the next issue to be investigated is the reason why the SD+FC term is very large in AuF.
Reason why SD+FC term is very large in AuF.
We evaluated how much each transition between the occupied and virtual orbitals contributes tothe paramagnetic term of CuX and AuX. In CuF, the HOMO → LUMO transition contributes the mostto the paramagnetic term. In AuF, the HOMO–1 → LUMO transition contributes the most. Both of the
HOMO of CuF and the HOMO–1 of AuF mainly consist of the metal dπ orbital into which the F pπ
orbital mixes in an anti-bonding way, as shown in Figure 2. The LUMO mainly consists of metal s anddσ orbital with which halogen pσ orbital overlaps in an anti-bonding way. These two MOs are named(dπ–pπ) and (s+dσ–pσ), respectively, hereafter. On the other hand, the contribution of this transition isvery small in the other MCl, MBr, and MI. More important is that this contribution decreases verymuch by about 3000 ppm when going from AuF to AuCl and by about 1000 ppm when going fromCuF to CuCl. The HOMO-LUMO (or HOMO–1-LUMO) energy gap is not different very much; it is1.82 eV, 1.92 eV, 1.85 eV, and 1.72 eV for CuF, CuCl, CuBr, and CuI, respectively, and 1.79 eV, 1.83
eV, 1.63 eV, and 1.42 eV for AuF, AuCl, AuBr, and AuI, respectively. These results suggest that not thedenominator of Eq. (1) but the numerator is responsible for the large negative paramagnetic term ofAuF:
Occ Vir

 tuPara  
i

a

(0,1)
(1,0)
i ht(1,0) a a hu(0,1)
i,SF i  i hu ,SF  a  a ht.
a  i(1)

As shown in Figure 2, the metal d-orbital component of the HOMO (or HOMO–1) is considerablylarger than the F p-orbital component only in CuF and AuF. Moreover, the contributions of the metald-orbital component is dominant in the HOMO (or HOMO–1)-LUMO contribution. The mixing (oroverlap) between the metal d-orbitals of the HOMO (or HOMO–1) and of the LUMO is essential for
the Cu and Au shielding constants. Actually, the metal part of the LUMO for CuF and AuF is thelargest in CuX and AuX, respectively. On the other hand, the Ag d-orbital component is smaller thanthe F p-orbital one in the HOMO (dπ–pπ) of AgF, like the other halides. Therefore, the large
paramagnetic terms of CuF and AuF are attributed to the large metal d-orbital component of the
HOMO or HOMO–1 (dπ–pπ), respectively.
The d component of the dπ–pπ MO mainly depends on the relative energies of M dπ and X pπ
orbitals; if the X pπ is at a lower energy than the M dπ, the M dπ component is larger than the X pπ
component, as schematically shown in scheme 1. The 4d orbital of Ag is at considerably low energy,
4－ 197 －

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Ⅳ 研究業績 (2011)

as well known. As a result, the 4d component of Ag is considerably smaller than the F pπ orbital in thedπ–pπ MO of AgF. On the other hand, the d orbitals of Cu and Au are at higher energy than the F pπ
orbital, which leads to the large dπ component in the dπ–pπ MO. When going from MF to MCl, thehalogen pπ orbital energy rises in energy, and hence the dπ orbital component decreases in the dπ–pπ
MO of MCl.
References[1] J. David, A. Restrepo, Phys. Rev. A
2007, 76, 052511.
[2] L. Bizzocchi, B. M. Giuliano, J.-U.
Grabow, J. Mol. Struct. 2007, 833, 175.
[3] H. Looser, D. Brinkmann, J. Magn.
Reson. 1985, 64, 76.
2. Original papers
T.

Yoshizawa,

S.

Sakaki“NMR

shielding constants of CuX, AgX, andAuX (X = F, Cl, Br, and I) investigatedby density functional theory based on
the Douglas–Kroll–Hess Hamiltonian”
in preparation.
3.

Presentation

atacademic

conferences
T.

Yoshizawa,

calculations

S.

of

Sakaki“NMR

transition

metal

complexes containing M ≡ P triplebond”

International

TheoreticalSociety

ChemicalforPhysics(ISTCP-VII), 3PP-57, September 2-8,
2011,

WasedaUniversity,

Tokyo(Japan).

5－ 198 －

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Ⅳ 研究業績 (2011)中���

特推研究フェロー
（平成 23 年 5 月 10 日まで）1� 今年度の研究の要�
今年度はパラジウム表面吸着 CO 分子の価電子励起スペクトルについて研究を行った。
䛆ጞ䜑䛻䛇㻌 金属表面に吸着した分子は、金属表面との相互作用により孤立分子とは全く異なった性質を持つようになり、例えば不均一触媒の開始反応の推進力となるため、反応機構を議論する上で非常に重要なステップである。しかしながら、金属表面のような反無限系を高精度かつ効率的に取り扱う理論的手法はほとんど提案されていない。
我々のグループではこれまで、クラスターモデルを基に有効ポテンシャルを用いて金属バルクの効果を取り込むことで金属表面の計算を行う手法の開発を行ってきた。本手法はクラスターモデルを用いているため、従来の高精度電子状態理論への応用が極めて簡単に行えることが最大の利点である。
本研究では、最も典型的な表面化学吸着現象として知られるパラジウム(111)表面への CO 分子の化学吸着に着目し、吸着 CO 分子の内殻イオン化スペクトルと価電子励起スペクトルを高精度励起状態計算手法の 1 つである SAC-CI 法を用いて計算し実験スペクトルとの比較を行った。
内殻イオン化スペクトルについては昨年度すでに検討を行っていたので、今年度は価電子励起ス
ペクトルについて検討を行った。
䛆᭷ຠ䝫䝔䞁䝅䝱䝹䛾సᡂ䛇ポテンシャルの作成はパラジウム 43 原子からなる参照クラスターに対して、中心 10 原子からなるモデルクラスターの表面軌道の軌道エネルギーを再現するように決定した（図・1）。ポテンシャル作成は密度汎関数法を用いて行い、基底関数は Cristiansen の(541/541/211)基底および内殻 28 電子を有効内殻ポテンシャルで置き換えたものを使用した。

Pd10

Pd43

図・1

参照クラスター(Pd43)とモデルクラスター(Pd10)－ 199 －

fukui2011_02.indb 199

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Ⅳ 研究業績 (2011)䛆䝟䝷䝆䜴䝮⾲㠃྾╔ 㻯㻻 ศᏊ䛾౯㟁Ꮚບ㉳䝇䝨䜽䝖䝹䛇以上のように作成した有効ポテンシャルを用いて、パラジウム(111)表面吸着 CO 分子の価電子励起スペクトルを SAC-CI 法を用いて計算した。
計算は Pd10CO クラスターモデルを用いて行い、CO の基底関数には Ahlrich の TZV を使用した。
表・1 に従来のクラスターモデルおよび有効ポテンシャルを用いた結果についてまとめた。

表・1

SAC-CI 法によるパラジウム(111)表面吸着 CO 分子の価電子励起スペクトルの計算結果
Pd10CO without EP

Pd10CO with EP∆EEx / eV

Osc. stln.

Assign∆EEx / eV

Osc. stln.

AssignS1

8.27

0.0005

d*←1π

7.78

0.0000

d*←1π

S2

8.49

0.0004

s*←1π

7.91

0.0003

d*←1π

S3

8.79

0.0057

s*←5σ

8.54

0.0006

s*←1π

S4

8.86

0.0058

s*←1π

8.97

0.0015

s*←5σ

S5

9.32

0.0005Ryd←1π9.10

0.0037

s*←1π

S6

9.62

0.0020

Ryd←5σ9.34

0.0015Ryd←1π実験や過去の計算研究から、吸着 CO 分子の価電子励起(2π*←1π)は 8.0 – 9.0 eV 付近に観測されると予測されている。しかしながら、本研究ではその付近に CO の価電子励起に由来する状態は観測されず、パラジウム表面への電荷移動型の励起状態が観測された。そこで、今後の予備検討として、CIS 法を用いて基底状態から 14 eV までのおよそ 1600 状態を計算したが、CO 分子の価電子励起由来のピークは観測できず、さらに高エネルギー領域に存在するか、もしくは電荷移動型の励起と混合している可能性が考えられる。今後は、SAC-CI 法を用いてさらに高エネルギー領域まで計算を行う予定である。

－ 200 －

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2. ��(1) Naoki NAKATANI, Yutaka HITOMI, and Shigeyoshi SAKAKI,“Multistate CASPT2 Study of Native Iron(III)-Dependent Catechol Dioxygenase
and Its Functional Models: Electronic Structure and Ligand-to-Metal Charge
Transfer Excitation”
J. Phys. Chem. B 115, 4781-4789(2011).

－ 201 －

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Ⅳ 研究業績 (2011)

Toru MATSUIVisiting Scholar, JSPS Fellow (Osaka University)
1. Summary of the research of the year
(A) DNA Scission Reaction by Metallo-Bleomycin: Similarities and Differences between Feand Co- Bleomycin
DNA scission reactions by Fe- and Co-bleomycins (BLMs, the model is shown in Scheme A-1)
were theoretically investigated with the density functional theory (DFT) method. The geometry oftransition states is similar between Fe- and Co-BLMs. In this study, we theoretically investigatedthe DNA scission reaction on the basis of the idea that DNA can be nicked by the ·OH radical via
O-O homolysis. We reproduced the computed reaction barrier in Fe-BLM proposed by Decker et al.
and estimated that the reaction barrier of DNA scission is too high in the case of Co-BLM.
Especially in the case of Co-BLM, the triplet state is more stable than the open-shell singlet in thetransition state. When we run the IRC calculation from the transition state in triplet state, we obtain
the different geometry from the original ground state. From these results, we found that the DNA
scission reaction by Co-BLM can occur in the triplet state and that there exist two triplet states as
the excited state of Co-BLM. To obtain the whole image of photo-excited states of Co-BLM, we
computed singlet and triplet excited states by using TD-DFT. Figure A-1 shows the results ofcomputed UV-Vis spectrum of Co-BLM. This UV-Vis spectrum agrees well with the experimental
data. When the excitation energy is small, the electronic state changes from the closed-shell singlet
to the lowest excited triplet (T1) state via S9 state which corresponds to the small peak found in
UV-Vis spectrum. After reaching T1-opt geometry, this reaction occurs thermally through the crosspoint. From the result of potential energy surface, it is found that 22.1 kcal/mol more energy isneeded to pass the cross point from the T1-opt geometry.

Scheme A-1: Two models used in this study. (a) large model which contains a peptide part and DNA
backbone. (b) small model which removes the peptide and DNA backbone－ 202 －

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Ⅳ 研究業績 (2011)

Figure A-1: (a) Computed (left) and observed UV-Vis spectra (right, Taken from Chang and Meares,
Biochemistry, 1984, 23, 2268, Figure 5.) (b) Scatter plot of relative energy (in eV) from S0 state andthe subtracted electron densities of important excited state from S0 state.

Figure A-2: Summary for the photo-induced reaction in Co(III)-BLM.
When the excitation energy is large enough, the electronic state changes to the Tr state via triplet
states T9, T6 and singlet state S25 corresponding to the peak in UV-Vis spectrum. This excitationenergy is so large that the reaction could occur spontaneously. The whole reaction diagram is shownin Figure A-2.
The difference of reactivity in DNA scission reaction between Fe-BLM and Co-BLM can beunderstood by using small model. When we devide the bond scission energy into several terms, it isfound that the bond energy of metal-ooxygen bond mainly contributes to the difference.

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Figure A-3: (a) Potential energy surface for O-O in each metal. Co(T) has two local minima and across point between two electronic states. (b) The distance between metal and O atom in each
optimized geometry in small model.
Next, we focused on the O-OH bond in HOO-M(III)-BLM with the 1D-potential energy surfaces
for the bond length r(Oa－Ob). We draw the 1D- potential energy surface as shown in Figure A-3a.
When O-O bond is 1.80 Å, the T1 state is 5 kcal/mol more stable than Tr, whereas Tr is 4 kcal/mol
more stable in O-O bond is 1.90 Å. Therefore, there exists a cross point between T1 and Tr statearound O-O: 1.80-1.90 Å. Within the single reference calculation, we cannot obtain the relative
energy of cross point. After the cross point, we can obtain a local minimum of HOO-Co(III)-BLM(minimum of Tr state).
Figure A-3b shows the change of the distance between the metal and Oa atom. The distance
between Fe and Oa decreases as the value r(Oa－Ob) becomes larger, whereas the distance between
Co and Oa does not strongly depend on the value r(Oa－Ob).
The difference in metal-oxygen bond energy can be explained by the difference in occupation
number of d-electron. Fe-OOH species can use the energy from d-π bond to decrease the energy for
O-O cleavage. On the other hand, Co-OOH species cannot take the advantage and needs much moreenergy for the dissociation.
(B) A Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials

The standard hydrogen electrode (SHE) potential in aqueous solution was evaluated with newcomputational procedure which provides the Gibbs energy of a proton in aqueous solution from theexperimental pKa value and the Gibbs energy change by deprotonation reactions of several neutral
alcohol molecules as shown in Figure B-1. Table B-1 lists the Gibbs energy of a proton and SHE
potential obtained by our new computational schemes. The most reliable Gibbs energy of a proton
is measured by Tissander et al. When we employ ab initio calculation method such as HF andpost-HF calculations, the computed energy almost reproduces this value, whereas DFT tends tounderestimate the G(H+, aq) by 4-7 kcal/mol.

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Figure B-1: The reference molecule and its observed pKa.
Table B-1: Computed Gibbs energy of H2(gas), Gibbs energy of proton and SHE potential in eachcomputational method.
B3LYP/6-31G*
B3LYP/6-31+G*
B3LYP
BHandHLYPc
BLYPLC-BLYc
M06
HF/CBS
MP2/CBS
MP3
MP4(DQ)
MP4(SDQ)
CCSD
CCSD(T) d
G3MP2
G3
G3B3
Exp.

H2(gas)/ a.u.

H+(aq)/a.u.

SHE / V

-1.176 831-1.176 929-1.180 489-1.170 182-1.170 171-1.159 827-1.171 108-1.134 578-1.168 626-1.175 017-1.176 600-1.176 646-1.177 276-1.177 276-1.181 772-1.178 832-1.179 145-0.407 78b-0.404 371-0.413 945-0.417 645-0.404 263-0.415 463-0.402 285-0.427 640-0.422 656-0.422 550-0.426 358-0.425 964-0.424 967-0.422 578-0.423 967-0.422 997-0.423 041-0.423 739e

4.88
4.99
4.80
4.54
4.87
4.44
5.00
3.80
4.40
4.49
4.41
4.42
4.45
4.52
4.54
4.53
4.53
4.44

When we employ MP3, and MP4(DQ), G(H+, aq) are somewhat overestimated. The basis set
effect on the Gibbs energy of a proton first examined at the B3LYP level. As shown in Table B-1,
the inclusion of diffuse function such as 6-31+G* considerably changes the Gibbs energy. Because－ 205 －

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Ⅳ 研究業績 (2011)

the Gibbs energy moderately changes when going to 6-31++G** from 6-31+G*, we employed
6-31++G** hereafter. Most of DFT methods overestimate the SHE potential. The overestimationin DFT calculation comes from the underestimation of energy of G(H+, aq) as discussed in theprevious section. This overestimation corresponds to the 0.17-0.30 V compared with previously
reported theoretical values. As the ratio of HF exchange increases in the hybrid functional, thecomputed SHE potential becomes closer to the experimental value; see B3LYP, BHandHLYP, andBLYP calculations in Table B-1. The importance of HF exchange is also seen in
LC-BLYP-calculated values which better agrees with the experimental value than BLYP-calculated
value. The HF/CBS method considerably underestimates the SHE potential as shown in Table B-1.
Judging from the result that the HF-calculated Gibbs energy of a proton is almost the same as that
calculated by the other method, the error arises from the energy of H2 in gas phase. It is likely thatthe lack of the correlation energy in the HF method is a plausible reason. Most of post-HF methods
reproduce the experimental SHE potential. CCSD(T)-calculated SHE potential slightly
overestimates the IUPAC value of 4.44 V. G3, G3MP2, and G3B3 methods also provide amoderately different SHE potential from the other post-HF methods.
This scheme also reproduces well the redox potential of several typical reactions within almost 0.1
V. B3LYP also gives excellent redox potential of the same reaction with almost the same accuracy
with our new computational scheme. This computational scheme will be applicable to computemany redox potentials.

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2. Original papers(1) Toru MATSUI, Takeshi BABA, Katsumasa KAMIYA, Yasuteru SHIGETA"'An accurate density functional theory based estimation of pKa value of polar residues
combined with experimental data: from amino acids to minimal proteins"
Physical Chemistry Chemical Physics,14, pp. 4181-4187 (2012).
(2) Toru MATSUI, Hideaki MIYACHI, Takeshi BABA, Yasuteru SHIGETA
A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils
Bridge Formation”
The Journal of Physical Chemistry A, 115, 8524-8531 (2011).
(3) Katsumasa KAMIYA, Toru MATSUI, Takashi SUGIMURA, and Yasuteru SHIGETA"Theoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered
Ketene-Olefin [2+2] Cycloaddition"
The Journal of Physical Chemistry A, 116, 1168-1175 (2012).
(4) Yasuyuki. NAKANISHI, Toru MATSUI, Yasutaka KITAGAWA, Yasuteru SHIGETA, Toru
SAITO, Yusuke KATAOKA, Takashi KAWAKAMI, Mitsutaka OKUMURA, and Kizashi
YAMAGUCHI“Electron Conductivity in Modified Models of Artificial Metal-DNA Using Green's
Function-Based Scattering Theory”
Bulletin of Chemical Society of Japan, 84, 366-375 (2011)(5) Takeshi BABA, Katsumasa KAMIYA, Toru MATSUI, Naoki SHIBATA, Yoshiki
HIGUCHI, Tatsuya KOBAYASHI, Seiji NEGORO, Yasuteru SHIGETA“Molecular dynamics studies on mutational structures of a nylon-6 byproduct-degrading
enzyme”
Chemical Physics Letters, 507, 157-161 (2011).

3．

List of review articles(1) T. Matsui, H. Miyachi and Y. Shigeta “Theoretical Studies on metal-containing artificial
DNA bases”, Progress in Theoretical Chemistry and Physics, Springer, 22, pp. 434-460.

4.

List of books(1) T. Matsui, H. Miyachi, Y. Shigeta and K. Hirao (2012) “Metal-Assisted Proton Transfer in
Guanine-Cytosine Pair: An Approach from Quantum Chemistry”, in Some Applications of
Quantum Mechanics, ISBN 978-953-51-0059-1, edited by Mohammad Reza Pahlavani ,InTech, p. 167-188.

5.

Presentation at academic conferences－ 207 －

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Ⅳ 研究業績 (2011)(1) (Poster) T. Matsui, H. Miyachi and Y. Shigeta, “Electronic structure and UV absorption
spectra of metal-mediate DNA: an approach from theoretical chemistry”, The Seventh
Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII),
4PP-68, Tokyo September 2-8, 2011.
(2) (口頭) 松井 亨，馬場 剛史，安田 奈都美，神谷 克政，北河 康隆，重田 育照，奥村 光隆
"タンパク質内アミノ酸側鎖の酸解離定数の新規算出法と応用", 第5回分子科学総合
討論会, 1B02, 北海道大学，札幌市, 2011年 9月(3) (口頭) 松井 亨，馬場 剛史，安田 奈都美，神谷 克政，北河 康隆，重田 育照，奥村 光隆
"官能基の類似性を利用した酸解離定数の新規算出法と応用", 第92回日本化学会春季年会, 3A4-48, 慶應義塾大学，横浜市, 2012年 3月－ 208 －

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Wilfredo Credo CHUNG
FIFC Fellow(To 30 Sept. 2011)
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 11 and 9
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 (2011)

evolution of theactivedihedralangles(=C10-C11=C12-C13=
or
11
and
=C8-C9=C10-C11=
or 9, 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 11 in addition to rapid change in 11 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 9 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 9 or 11. 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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Ⅳ 研究業績 (2011)

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

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.

Rh and isoRh chromophores.
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 9 and 11
at the time of
hopping
areplotted (comparewith Figure 11,
reference 9 and
Figure10,reference 10). All
Rh trajectories gothough only one
MECI region withclockwise-twistedand9counterclockwisetwisted
11 Figure 4. Diagram of the twist angles of -C11=C12- (11) and -C9=C10- (9) 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,
CI=minimum energy conical intersection.
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Ⅳ 研究業績 (2011)

towards the formation of bathoRh and the regeneration of the reactant. The relaxation of the excitedstate of isoRh, on the other hand, goes through two MECI regions. Most of trajectories from isoRhgo through the MECI region with 9 ~ -90° and clockwise-twisted 11, 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) (ave=233 fs) than that through CI(isoRh->9,11-dicisRh) (ave=188 fs). The
difference is revealed in the dissimilarity in the twist speed of 9 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
F. Boll, Am. J. Med. Sci. 1878, 151, 190.
F. D. Collins, R. A. Morton, Biochem. J. 1950, 47, 18.
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.
1
2
3
4
5

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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 Papers
1. W. C. Chung, S. Nanbu and T. Ishida, QM/MM Trajectory Surface Hopping Approach to
Photoisomerization of Rhodopsin and Isorhodopsin: The Origin of Faster and More Efficient
Isomerization for Rhodopsin, J. Phys. Chem. B, 2012, 116 (28), 8009–8023.
2. W. C. Chung, S. Nanbu and T. Ishida, A Nonadiabatic Ab Initio Dynamics Study on
Rhodopsin and Its Analog Isorhodopsin: Chemical Dynamics Reasons behind Selection of
Rhodopsin by Life, Chemistry Letters 2011, 40, 1395-1397.
3. W. C. Chung and T. Ishida, An MD simulation of the decoy action of Epstein–Barr virus
LMP1 protein mimicking the CD40 interaction with TRAF3, Theoretical Chemistry
Accounts 2011, 130, 401-410.
3. Presentation at academic conferences
1. W. C. Chung, S. Nanbu and T. Ishida Nonadiabatic ab initio dynamics of rhodopsin andisorhodopsin: a QM/MM trajectory surface hopping (TSH) approach based on the
Zhu-Nakamura theory 14th Asian Chemical Congress, Bangkok, Thailand, September 5 – 11,
2011 (Poster).
2. W. C. Chung, S. Nanbu and T. Ishida Nonadiabatic ab initio dynamics of rhodopsin andisorhodopsin: a QM/MM trajectory surface hopping (TSH) approach based on the
Zhu-Nakamura theory 27th Symposium on Chemical Kinetics and Dynamics, June 8-10, 2011,
Tokyo, Japan (Poster).

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Takafumi IWAKIFIFC Fellow
1. Summary of the research of the year
Confinement Effect of Folding Transition for Semiflexible and Flexible Polymer Chains
Living organism is constituted by lots of biopolymers, which are confined in a tiny cell. For example,
DNA in vivo is usually 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, the effect ofconfinement to the structure and behavior of polymeric molecules has not been well understood.
To get insight into this problem,
we performed a Langevin dynamics
simulation of a simplified model
polymer confined in a spherical cavity.
In

Fig.

1,

typicalsnapshotsofpolymeric chain undergoing a folding
transition under confined and freeconditions are shown. It is known thatfolding transition of a flexible polymer
is a continuous transition, and thefolded structure is in a liquid-like oramorphous state. On the other hand, asemiflexible

polymerundergoesadiscontinuous transition, and the folded
structure is in an ordered state. Fromthe present simulation study, we foundthat the confinement effect shifts thetransition

point

in

the

opposite

direction between a flexible polymer
and a semiflexible polymer. That is to

Figure 1: Snapshots of the folding transition of linear
polymer chains. (a) A flexible polymer in a free solution.
(b) A confined flexible polymer. (c) A semiflexible polymer
in a free solution. (d) A confined semiflexible polymer.

say, for a flexible polymer, the confinement retards the transition, and, for a semiflexible polymer, it
promotes the transition. This fact comes from the difference of an essential mechanism to determine thetransition points between the two cases. For a flexible polymer, the transition occurs continuously so that thetransition point is defined as compared with the ideal chain as a reference state. In this case, an excluded
volume of an actual polymer is the origin of the retardation of the transition. For a semiflexible chain, thetransition occurs abruptly with a great change of a volume of a chain expansion. In this case, conformational
entropy of a swelling state is the reason of the promotion of the transition. We successfully explained this－ 214 －

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qualitative difference of the confinement effect by a simple scaling argument.

Study of DNA Double Strand Breaking Produced by Ionizing Radiations
DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus
there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes
that lead to their production have not yet been clearly understood, and there is no established theory that canaccount for the statistics of their production, in particular, the number of DSBs per base pair per unit Gy, here
denoted by P1, which is the most important parameter for evaluating the degree of risk posed by DSBs.
Using the single-molecule observation method with giant DNA molecules (166 kbp), we evaluate the number
of DSBs caused by -ray irradiation. We found that, in the dependence of P1 to the DNA concentration, there
are two characteristic regions. In a low DNA concentration region, P1 is nearly constant to the DNA
concentration. On the other hand, P1 is nearly inversely proportional to the DNA concentration above acertain threshold DNA concentration. We calculate the probability to occur double strand breaking on thebasis of a simple model, which well accounts for the marked profile of P1 over all measured region. Basedon this argument, we show that it is necessary to consider the characteristics of giant DNA molecules assemiflexible polymers to interpret the intrinsic mechanism of DSBs. This work is now submitted to ascientific journal.

Numerical Fluid Dynamics Study ofa Heated Oil Droplet on Air-Water
Interface
A centimeter-sized droplet of liquidparaffin on water can be accelerated by a laser
irradiation. In this scale of experiments, theorigin of the migration force is attributable to
the Marangoni effect: a surface force arisingfrom a local difference of surface tensions. For
example, as shown in Fig. 2, irradiation of thelaser induces flows outside and inside thedroplet by thermal Marangoni effect, which inturn influences a temperature distribution of
the heated droplet. In actual experiments, wefound that the presence/absence of surfactant(SDS) changes the migration direction to the
opposite side. Since this system has a low
symmetry, we performed a CFD simulation to
analyze an essential mechanism of this change

Figure 2: Flow pattern and temperature
distribution of a paraffin droplet on pure water
heated by a laser irradiation.

－ 215 －

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Ⅳ 研究業績 (2011)

in the acceleration direction.
Here, we performed a numerical simulation of thermal fluid on an irregular lattice with a finite volume
method. Several causes were assumed for the above-mentioned effect of SDS. For example, the differencein the shape of the droplet might have induced a different flow mode inside the droplet. Nonlinear effect of
the hydrodynamics might have promoted the appearance of the different modes in similar experimental
systems. These expectations were, however, denied by a sequence of simulations. We found that the
migration direction changes due to the temperature coefficients of surface tensions changed by thepresence/absence of SDS. The Marangoni effect on an oil droplet on an air-water interface caused by local
heating induces two types of actions on the droplet. One is the viscous friction force from an external flow
induced by caterpillar-like action of the droplet surface. This force always accelerates the droplet toapproach a heating spot. The other is the Young force arising from a dynamical breaking of a surface
tension balance in a periphery of the droplet. This force is determined by the weight of the temperature
coefficient of surface tension in each of interfaces. When the magnitude relation of the temperature
coefficients between air-water interface and oil surfaces reverses, the Young force changes its direction.
Thus, we simulated a thermal flow for two typical sets of temperature coefficients of surface tensions.
Consequently, we obtained flow patterns and temperature distributions very similar to experimentallyobtained ones in the presence/absence of SDS, respectively, which rationalize that the above-mentioned
mechanism is applicable to the interpretation of the experimentally observed effect of SDS. This work is
now submitted to a scientific journal.

Study of the Dynamical Mechanism of the Self-Organization of the Tooth Germ
In the development process of the tooth germ, the enamel knot is formed simultaneously with theepithelial invagination. The epithelial invagination is considered as the buckling of the growing surface layerof the tooth germ. However, the mechanism of the formation of the enamel knot is not understood well interms of both physics and molecular biology. In order to solve this problem from the perspective of physics,
we performed Brownian dynamics simulations of a coarse-grained toy model of cell population. In thesimulations, we found that according to the proliferation rates of the surface layer and the interior of thedental epithelial, the buckling formation undergoes several courses. In particular, when the proliferation rateof the surface layer is considerably larger than that of the interior, the bending is not uniform, and the pluralbuds are formed similarly to the actual development process. This fact suggests that the formation of theenamel knot is governed by a rather simple mechanical process. To get a further insight, we calculate the“free energy of time course” of the buckling process of elastic continuous segment for the several given
paths, and found that the shrinking speed of the end-to-end distance determines the favored type of buckling.
In fact, when this speed is faster, buckling along with a growth of plural peaks is more favored. This wellcorresponds to the simulation result and also the actual development process. We are now writing themanuscript of these results, which is to be submitted to a scientific journal.

－ 216 －

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2. Original papers(1) S. N. Watanabe, T. Iwaki, M. I. Kohira, N. Magome, and K. Yoshikawa,“Negative photophoresis of smoke particles observed under microgravity”
Chem. Phys. Lett. 511, 447-451(2011).
(2) Y. Higuchi, K. Yoshikawa, and T. Iwaki“Stiffness causes opposite trend on the folding transition of a single polymer chain in aconfined space”
Physical Review E, 84, 021924 (5 pages) (2011).
3. Presentation at academic conferences(1) T. Iwaki, “Transportation of a micro droplet by light irradiation: The influence of an advection and the
Marangoni effect.” (invited), Optics in the Life Science Congress, Monterey, USA (April 4-6, 2011)(2) 岩城 貴史、“液滴の温度マランゴニ対流の数値シミュレーション”、 日本物理学会 2011年秋季大会、Toyama, Sep. 22, 2011

(3) 岩城 貴史、“液滴の温度マランゴニ対流の数値シミュレーション II”、 日本物理学会第67 回年次大会、Nishinomiya, March 25, 2012

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 abiological cell””), Kenichi Yoshikawa and Takafumi Iwaki, パリティ (parity), vol. 26, No. 05, pp.
13-21 (issued on Apr. 25, 2011)－ 217 －

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Natsuhiko YOSHINAGAFIFC Fellow(To 15 Dec. 2011)
Assitant Professor, WPI-AIMR, Tohoku University
1. Summary of the research of the year (3-5 pages, includes appropriate figures and tables)
Spontaneous motion of a droplet coupled with a chemical wave
Spatiotemporal patterns are widely seen in living systems; target, spiral, stripe, and dot patterns havebeen observed at various scales from the interior of a cell to a swarm of cells. Most of studies have focusedon patterns at larger scales, which can be successfully reproduced using reaction diffusion dynamics. In
contrast, it is only recently that internal patterns in a single cell have been visualized. These patterns are
expected to relate to cellular functions; examples include calcium ions for signal transduction, Min proteinsfor cell division, and actin cytoskeltons for mechanical properties. Although pattern formation in a cell is
expected to be analyzed in the framework of a reaction-diffusion system, as demonstrated in in vitro
experiments, sufficient understanding of the connection between pattern formation and cellular function islacking. In this paper we focus motility, as a typical aspect of cellular functions, arising from internal
patterns. Several artificial systems imitating cell motility have been proposed as self-propelled particles.
Although no external force is exerted on the particles (a force-free condition), the motion is induced by theasymmetric distribution of an electric field, concentration of chemicals, temperature, and so on. These
asymmetric distributions are either a priori embedded in the asymmetry of the surface properties of theself-propelled objects or a posteriori created by nonlinear effects; motion itself destabilizes a symmetric
distribution, for instance, through advective flow. In both cases, however, most studies have focused on
motion under steady distributions.
In order to understand the dynamic features of cell motility, a system connecting the dynamic patternwith motion is desirable. In fact, experimental and numerical evidence of chemo-mechanical coupling insuch systems has been demonstrated. In this work we propose a theoretical framework for a chemical system
exhibiting self-organized patterns, leading to spontaneous motion. We consider that the Marangoni effect issuitable for this purpose as it has been shown to drive an object under force-free conditions by aninhomogeneous interfacial tension arising from a gradient in the chemical concentration. In our system, theenergy supply and consumption can generate a pattern in a droplet through nonlinear chemical kinetics andthe pattern at the interface of the droplet creates inhomogeneous interfacial tension. This generates a flow
surrounding the droplet, resulting in motion.

Rigidity Sensing Explained by Active Matter Theory
Living cells respond to mechanical as well as biochemical cues. Rigidity sensing designates the web of－ 218 －

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Ⅳ 研究業績 (2011)

complex mechanisms whereby a cell will adapt, as a function of the elastic modulus of its environment,
diverse aspects of its phenotype, including motility, gene expression, proliferation, and fate after
differentiation. The traction forces that a cell exerts on a flat, elastic plate depend in a nontrivial way on theextracellular stiffness, being roughly proportional to the elastic modulus in a softer environment andsaturating to a finite value for stiffer substrates. Similar force-rigidity data are obtained whether forces aremeasured locally or globally for both integrin-mediated and cadherin-mediated adhesion, and even when the
traction forces are exerted by assemblies of cells in a monolayer epithelium. Single-cell rheology assays
show that cells respond to sudden changes in substrate rigidity too rapidly to be detected at the dataacquisition rate. These observations call for a simple, generic explanation that is valid for short timescales
where cell signaling cannot operate.
It is found that the magnitude of traction forces exerted by living animal cells on their environmentis a monotonically increasing and approximately sigmoidal function of the stiffness of the external medium.
We rationalize this observation using active matter theory, and propose that adaptation to substrate rigidity
results from an interplay between passive elasticity and active contractility.

Fig. 1: Schematic representation of the model

Self-propelled motion of a fluid droplet under chemical reaction
Self-propelled motion of particles has attracted much attention recently from the viewpoint of
nonlinear physics far from equilibrium. There are several experiments of self-propulsion of droplets in fluids.
It has been shown that the Belousov-Zhabotinsky reaction composed in a fluid droplet triggers a spontaneous
motion of a droplet. Computer simulations of convective droplet motion and nano-dimer motors driven bychemical reactions have also been carried out. There are theoretical studies of droplet motion due to aninterfacial tension gradient along the droplet surface. However, these theories are concerned only with thesteady velocity of a droplet. As a related theoretical study, the mesoscopic description of the thermo-capillaryeffect has been formulated. A transition between a motionless and migrating droplet driven by chemical
reactions has been studied in a system where a droplet is on a solid substrate.
We study self-propelled dynamics of a droplet due to a Marangoni effect and chemical reactions
in a binary fluid with a dilute third component of chemical product which affects the interfacial energy of adroplet. The equation for the migration velocity of the center of mass of a droplet is derived in the limit of an
infinitesimally thin interface. We found that there is a bifurcation from a motionless state to a propagatingstate of droplet by changing the strength of the Marangoni effect.

－ 219 －

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Fig. 2: Translational motion of a droplet. The droplet is migrating to the right under the non-uniform
distribution of the c component indicated by the small dots.

2. Original papers(1) Shunsuke Yabunaka, Takao Ohta, and Natsuhiko Yoshinaga“Self-propelled motion of a fluid droplet under chemical reaction”
J. Chem. Phys. 136, 074904 (2012).
(2) Hiroyuki Kitahata, Natsuhiko Yoshinaga, Ken H. Nagai, and Yutaka Sumino" Spontaneous motion of a droplet coupled with a chemical wave""
Phys. Rev. E. Rapid Communications 84, 015101 (2011).
selected by PRE Kaleidoscope Images: July 2011(3) Philippe Marcq, Natsuhiko Yoshinaga, and Jacques Prost“Rigidity sensing explained by active matter theory”
Biophys. J. 101, L33-L35 (2011).
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”
Regional Bio-Soft Matter Workshop: Non-equilibrium statistical Physics in Bio-Soft
Systems, Taipei, Taiwan, (27-29 Oct., 2011)(2) Natsuhiko Yoshinaga, Ken Nagai, and Yutaka Sumino, and Hiroyuki Kitahata“Self-propulsion of a drop driven by Marangoni flow”
Workshop: Collective Dynamics and Pattern Formation in Active Matter Systems, Dresden,
Germany, (29 Aug. - 16 Sep., 2011)(3) Natsuhiko Yoshinaga, Jean-Francois Joanny, Jacques Prost, and Philippe Marcq“Polarity Patterns of Stress Fiber ”
7th International Conference on Biological Physics 2011, UCSB, USA, (22-24 June, 2011)
4. Others－ 220 －

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Ⅳ 研究業績 (2011)���行

�ンターフ�ロー（平成 23 年 10 月 1 日から）
1. 今年度の研究の要�
今年度は時間依存密度汎関数理論を用いて、光化学反応において重要な役割を果たしている円錐
交差の解析を行った。

䛆ጞ䜑䛻䛇

円錐交差は、電子励起状態からの非常に速い無輻射遷移を説明する非常に重要な機構である。電子状態計算による円錐交差の解析には、静的および動的な電子相関をバランスよく記述する手法が要求される。円錐交差の領域では複数のポテンシャルエネルギー面が縮退しているため、様々な電子配置(静的電子相関)を考慮する必要がある。また動的電子相関の有無により、円錐交差の近傍における分子の構造やポテンシャルエネルギー面の形状は定性的に異なる。動的電子相関の寄与は電子状態によって異なるため、円錐交差の探索過程でこの効果を無視するわけにはいかない。動的電子相関の取り扱いに優れた方法として、線形応答に基づく時間依存密度汎関数(LR-TDDFT) 法が知られている。しかし LR-TDDFT 法では、単純なエチレン分子でさえ正しい円錐交差の構造を与えることが出来ない[1]。これは、静的電子相関の取り扱いが不十分であるためである。スピン反転励起に基づく LR-TDDFT (SFDFT) 法[2]は、部分的にではあるが静的電子相関を取り入れることができる。SFDFT 法を用いることでエチレンの円錐交差が正しく記述できることを、私は過去に報告した[3]。得られた計算結果は、波動関数に基づく高精度の ab initio 計算を非常によく再現した。これ
は、円錐交差を解析する手段として LR-TDDFT 法の可能性を示している。

䛆䝇䝏䝹䝧䞁ศᏊ䛾ග໬Ꮫ䛇㻌

SFDFT 法は、波動関数に基づく計算に比べて計算コストが小さく、電子相関もあらわに考慮されている。その特性を生かし、スチルベン分子の計算に適用し、励起状態のポテンシャル面を解析した。スチルベンは、エチレンの水素原子をベンゼン環で置き換えた化合物であり、過去のエチレンの研究の自然な拡張である。また、スチルベンの光異性化の反応機構を理解することは、光駆動分子モーターやフォトクロミック材料など、材料科学の分野における分子設計で重要な知見を与える。

－ 221 －

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Ⅳ 研究業績 (2011)

図 1 に示したのは、ねじれたスチルベンにおける円錐交差およびエネルギー極小点の構造である。２つの構造の主な違いは、ベンゼン環の回転

80°

86°

27°

5°

によるものである。円錐交差の構造は、エチレンのそれと非常によく似ており、スチルベンの二重結合もエチレンのそれで定性的に理解できることがわかる。一方、エチレンと異なり、エネルギ

図１ ねじれたスチルベン分子の構造:

ー極小点が存在することを示した。エチレンでは、

円錐交差(左)、エネルギー極小点(右)円錐交差が同時に励起状態のポテンシャル面のエネルギー最小点になる。最近の実験結果[4,5]によると、ねじれたスチルベンにおいて、この極小点の存在(phantom state)が示唆されており、本研究における計算結果は、それを支持するものである。
また、本研究ではもう一つ別の円錐交差の構造を指摘した(図２)。

1.96 Å

2.10 Å

スチルベンの光化学反応では、シス‐トランス異性化のほかに環化した生成物(DHP)を得る。今回明図２ シス‐スチルベンの構造: 円錐構造(左)、DHP(右)らかにした円錐交差の構造はDHP に似ており、環化反応のメカニズムに関与していることが推定される。
これらをふまえ、基底状態および励起状態のポテンシャル面において重要な構造を同定し、まとめたものが図３である。トランス体は光励起された後、反応障壁を超えてねじれた構造をとる。そこから、円錐交差から基底状態へ戻るあるいは励起状態でシス体を生成する。一方シス体の場合、ねじれた構造の円錐交差を経て基底状態、あるいはもう一つの円錐交差から DHP を生成する２つの経路が考えられる。将来的には、非断熱分子動力学を用いて、シス‐トランス光異性化および環化反応のメカニズムを明らかにしたいと考えている。

4.45(S1)trans (S0/S1)pyr(S1)cis?
4.06 4.16/4.18
4.08(S1)pyr
4.05

trans

(S1)DHP
3.72

4.75(S0/S1)coop
3.87/3.89
2.60

3.07

(S0)trans
0.00

4.99

(S0)DHP
1.75
0.35

1.04

(S0)cis
0.21
cis

DHP

図３ スチルベン分子のポテンシャル面のまとめ (単位: eV)－ 222 －

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Ⅳ 研究業績 (2011)䛆⁐፹ຠᯝ䜢⪃៖䛧䛯෇㗹஺ᕪ䛾グ㏙䛇

溶液内分子の電子励起状態を理解するためには、量子力学に基づく溶質分子の記述と溶質‐溶媒間の相互作用の表現を両立させる必要がある。しかし、実験で取り扱われている分子はサイズが大きく、従来の波動関数に基づく計算手法では計算コストが莫大なものになる。私は、LR-TDDFT 法とプログラムパッケージ GAMESS に実装されている電子分極を考慮した溶媒モデル(EFP)を組み合わせ、その解析的エネルギー微分を導入した[6]。これは，励起状態における分子動力学シミュレー
ションを低コストで実現し、動的過程を解析する手法として重要な寄与である。
この方法を拡張し、上で述べたように円錐交差の解析に優れた SFDFT 法に適用した。そして、
SFDFT/EFP 法の解析的エネルギー微分を実装した。同時に、円錐交差の探索プログラムを導入し、溶液内分子の円錐交差を記述できるようにした。開発した方法を緑色蛍光タンパク質(GFP)の発色団 (HBI)に適用した。GFP の発色団は、水溶液中で蛍光が著しく減少することが知られている。これは、円錐交差を介した速い緩和過程が存在するためであるといわれている。
図４に示したのは、緑色蛍光タンパク質(GFP)の発色団の水和クラスターにおける円錐交差の構造の一例である。溶液内では、
C=C 周りのねじれ角が 104 度
から 90 度に減少し、C=C のimidazolinone 環に対する面外角が 30 度からほぼ 0 度の平面
となった。
図４

溶媒効果により、ポテンシ

GFP 発色団の水和クラスターの円錐交差ャルエネルギー面も、定性的に異なる描像となった。表１

Geometry

State

Gas

+1 water+1 water +50 EFPに示したように、溶媒和クラ

S0

S0

0.00

0.00

0.00

*

3.94

3.85

3.88

S0

2.46

2.49

N/A

*

2.89

2.71

N/A

3.022

2.744

2.128

3.022

2.744

2.128

スターでは*状態の極小点が存在せず、直接、円錐交差(*)twiにいたる反応経路であることが示唆される。これは、GFP(S0/*)CI

水溶液では蛍光が抑制され、非常に速い緩和を起こすこ

表１

GFP 発色団のエネルギー (単位: eV)とと対応している。
本研究では、ポテンシャルエネルギー面に基づく解析を行った。すなわち、限られた数の溶媒和構造を発生させ、それを初期条件として円錐交差などの構造を求めた。しかし、溶液系では溶媒分子の自由度が非常に大きいため、自由エネルギーに基づいた議論のほうが便利である。例えば、－ 223 －

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Ⅳ 研究業績 (2011)

QM/MM 法や積分方程式による円錐交差の記述法[7,8]が提案されている。これらを SFDFT 法と組み合わせることで、溶液内における円錐交差の議論が行うことが可能になると期待している。

����[1] B. G. Levine, C. Ko, J. Quenneville, and T. J. Martínez, Mol. Phys. 104, 1039-1051(2006).
[2] N. Minezawa and M. S. Gordon, J. Phys. Chem. A 113, 12749-12753 (2009).
[3] Y. Shao, M. Head-Gordon, and A. I. Krylov, J. Chem. Phys. 118, 4807-4818 (2003).
[4] W. Fuss, C. Kosmidis, W. E. Schmid, and S. A. Trushin, Chem. Phys. Lett. 385, 423-430 (2004).
[5] S. A. Kovalenko, A. L. Dobryakov, I. Ioffe, and N. P. Ernsting, Chem. Phys. Lett. 493 255-258(2010).
[6] N. Minezawa, N. de Silva, F. Zahariev, and M. S. Gordon, J. Chem. Phys. 134, 054111 [12 pages](2011).
[7] G. Cui and W. Yang, J. Chem. Phys. 134, 204115 [12 pages] (2011).
[8] S. Yamazaki and S. Kato, J. Chem. Phys. 123, 114510 [13 pages] (2005).

�� 論�(1) N. Minezawa and M. S. Gordon, “Photoisomerization of stilbene: A spin-flip density functional
theory approach”, J. Phys. Chem. A 115, 7901-7911 (2011).
(2) A. Defusco, N. Minezawa, L. V. Slipchenko, F. Zahariev, and M. S. Gordon, “Modeling solvent
effects on electronic excited states”, J. Phys. Chem. Lett. 2, 2184-2192 (2011).
(3) N. Minezawa and M. S. Gordon, “Optimizing conical intersections of solvated molecules: The
combined spin-flip density functional theory/effective fragment potential method”, J. Chem. Phys.,
accepted.

�� �の�
(1) 嶺澤 範行「SFDFT法による緑色蛍光タンパク質発色団のポテンシャル面の理論的研究」
第９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2012/01/06(2) 嶺澤 範行「時間依存密度汎関数理論による非断熱過程の解析」
化学反応のポテンシャル曲面とダイナミックス

京都（京都大学）

2012/03/30－ 224 －

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Ⅳ 研究業績 (2011)

Kunkun GUO
FIFC Fellow(From 1 Mar. 2012)

1. Summary of the research of the year
Vesicle shapes encapsulated by two aqueous phase systems
Liquid ordered domains enriched in sphingolipids and cholesterol, known as lipid rafts, have received
widespread attention from the cell biology and membrane biophysics during the last decade because they are
believed to play a key role in several important cellular functions, including membrane sorting andtrafficking, signal transduction, and cell polarization.
The interior of living cells is crowded with macromolecules and organelles. The weight fractions ofproteins, RNAs, and polysaccharides in the interior of living cells are on the order of 20-30 %. In such a
concentrated environment, local phase separation may occur, involving local composition differences andmicrocompartments, e.g. cell functioning and the performance of cytoplasmic proteins. As a simplistic modelof the cytoplasmic medium, the solutions of the water-soluble macromolecules polyethylene glycol (PEG)
and dextran would undergo phase separation with the concentrations of the polymers increasing. Dynamic
microcompartmentation of macromolecules between the enclosed phases are found to resemble similar
partitioning behavior as proposed in cytoplasm of living cells. Interesting phenomena associated with thephase separation processes, such as wetting transition, vesicle budding, fission of vesicles, and the formationof membrane nanotubes, are observed in the recent experiments.
Here, we theoretically consider such a system that a vesicle membrane which is consisted of two
components is encapsulated by aqueous two-phase polymer, see Fig. 1. The
system is assumed to be homogeneous with the same density ρ0.

The twocomponents of the vesicle are assumed to be locally incompressible, and thatthe total amounts of amphiphiles A and B on the vesicle membrane areconserved during evolution. The local bending modulus of the membrane, κ,
is determined by the local concentration of amphiphiles ϕA and ϕB, where
ϕA+ϕB=1, as well as their bending modulus, κA and κB . The local bending
modulus obeys with a linear relationship that is κ=κAϕA+κBϕB=κ0+ζϕm,
where ϕm=ϕA-ϕB, κ0=(κA+κB)/2 and ζ=(κA-κB)/2. Similarly, the local
Fig.

1:

The

schematic

illustration of the system that a
two-component

vesicleindicated by the contour is
encapsulated by aqueous twophases α and β.

spontaneous curvature cm is also known as composition-dependent and canbe expressed as cm=cAϕA+cBϕB=c0+εϕm with the average spontaneous
curvature given by c0=(cA+cB)/2 and the difference of the spontaneous
curvatures between the two components given by ε=cA-cB. nα polymer α withchain length Nα and nβ polymer β with chain length Nβ dispersed in a goodsolution S are encapsulated inside the vesicle membrane with volume－ 225 －

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Ⅳ 研究業績 (2011)

fraction ϕα=nαNα/(ρ0Vm), ϕβ=nβNβ/(ρ0Vm), respectively. The small solution molecules S can be freely
penetrate into the membrane which is dependent on the chemical potential across the membrane, but the twokinds of polymer can not penetrate into the membrane and are always located inside the membrane.
Therefore, the volume fraction of polymer α and polymer β will be changed along with the vesicle volume.
At the same time, the solvents can be assumed as the background of such a compound system and then its
effects can be neglected. Therefore, the free energy of such a system corresponding to the membrane and thecomponents inside the membrane can be written as
βF =

1
1
√
[ b(∇φm ) 2 + f (φm ) + (κ 0 + ζφm )(2H + c0 + φm ) 2 ] gdudv +∆ P dV
2
2
1
1
+
dr [
φα (r ) ln φα (r ) +φβ (r ) ln φβ (r ) + χ α β φα (r )φβ (r ) + χ A α φA (r )φα (r )NαNβ+ χ A β φA (r )φβ (r ) + χ B α φB (r )φα (r ) + χ B β φB (r )φβ (r ) + w(r )(φα (r ) + φβ (r ))]The free energy function βFm which is related to the membrane can be written based upon the discrete
space and given byN

βF m =
k= 1

1b(φm (k) − φm (k − 1)) 2 |τ (k)| +
2

N

+
k= 1
N

+
k= 1

f (φm (k))
k= 1

|τ (k)| + |τ (k + 1)|
2

1
P(κ 0 + ζφm (k))(2H (k) + c0 + φm (k )) 2 ](|τ (k )| + |τ (k + 1)|) +42|τ (k)| + |τ (k + 1)|
χ A α φA (k )φα (k)+2Nχ B α φB (k)φα (k )

+

N

k= 1

|τ (k)| + |τ (k + 1)|
+
2

N

k= N

r (k)n (k)|τ (k)|k= 1

χ A β φA (k )φβ (k)|τ (k)| + |τ (k + 1)|2χ B β φB (k )φβ (k )|τ (k )| + |τ (k + 1)|
2

k= 1
N

k= 1

Likewise, the free energy βFin of three components inside the vesicle can be written as

Another two parameters, ψ and η, are therefore introduced and defined as follows,ψ(r ) = φα (r ) − φβ (r ) , η = φα (r ) + φβ (r ) .

Then, the model free energy βFin for the mixtures inside the vesicle in terms of ψ is written as
βF i n { ψ} =dr [f ψ (ψ) + f i n t (ψ, m )] +Dψ2

dr (∇ψ(r )) 2

The kinetic equations which describe the evolution of the order parameter ψ inside the vesicle and thephase separation coupled with vesicle deformation can be solved using the simplest dissipative models andare written as the Time-dependent Ginzburg-Landau equations and given by,－ 226 －

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Ⅳ 研究業績 (2011)

N

δ[βF m +∂r (k)
k − 1 γ(k)|τ |]= −Lr∂tδr (k)= − L r [A (k)n (k) + B (k)|τ (k)|τ ]|τ (k)| + |τ (k + 1)| − 1
2∂φm (k)δβF m |τ (k)| + |τ (k + 1)| − 1= − L φ m ∇2∂t
δφm (k)2

The initial vesicle shape encapsulated aqueous two-phasesystems are randomly generated. The initial positions of thevesicle and distributions of the order parameters, ψ and ϕm,
are inserted into right hand of the above equations. Then, thepositions of the vesicle and distributions of these orderparameters in the next time step are obtained. This procedurecan be iterated until the unchanged shape and the stable
distributions of these order parameters have both beenreached.
The vesicle shape encapsulated by two aqueous phasesystems at the final simulation step is presented in Figure 2.
Fig. 2: the vesicle shape encapsulatedby two aqueous phase systems,
membrane indicated by red and bluelines, the phase encapsulated by vesicle
indicated two phase colored by whiteand black.

After simulations, the shape of vesicle is not a sphere, andbecome shape deformations. The polymer systems also separate
from homogeneous phase into two aqueous phases. However,the system of the vesicle shape encapsulated by two aqueous
phase systems still do not explain all experimental results, but
we would like to provide deep insights into the experiment infurther work.

2. Original papers(1) Kunkun Guo, Jianfeng Li“Exploration of the shapes of double-walled vesicle with a confined inner membrane”
J. Phys. Condens. Matter 23 (2011) 285103 (12pp).
3. Presentation at academic conferences
4. Others(1) Kunkun Guo“Actin polymerization and depolymerization via Brownian dynamics simulations”
Seminar in Prof. Yoshikawa group, Kyoto, March, 2012

－ 227 －

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Ⅳ 研究業績 (2011)��
分子�学��所励������(���グループ所�)1� �年�の��の��
GFPc-X-CFPc モデルペプチドにおけるアミノ酸経�励起エネルギー移動[1]【���】�
生化学分野の実験において、GFP(緑蛍光蛋白質)とその色素変異ファミリーの間の励起エネルギ
ー移動(EET)が、近年、分子の会合を測る蛍光プローブとして使われている。EET プロセスは主にFRET(蛍光共鳴エネルギー移動)機構によって起こるが、それとは別に蛋白質が介在する超交換相互作用の寄与が存在している。この寄与は通常 FRET の項と比べて小さいが、まれに相対的に無視できないほど大きいこともある。量子化学的手法を元に、GFPc(GFP 色素)と CFPc(シアン蛍光蛋白質色素)間の励起エネルギー移動について、架橋するブリッジのアミノ酸残基の種類による超交換相
互作用項の大きさの依存性を調べた。GFPc-X-CFPc 系では、Through-residue X の項の違いで超交換相互作用項全体の大きさが制御されることがわかった。

【�法】
以前開発した EET 電子カップリング
計算法および EET トンネル移動経路決定法[2]を GFPc-ブリッジ-CFPc のモデ
ルシステムに適用して、この系の電子
カップリングに対する蛋白質の寄与、
特にアミノ酸の種類に拠る違いを調べた。GFPc と CFPc を両端に持ち、間にアミノ酸 X を持つ、GFPc-X-CFPc ペ
図 1. GFPc-X-CFPc モデル。

プチドモデル系を作り、GFPc と CFPcの間の励起エネルギー移動の電子カップリングを計算し、その間接項の寄与の成分を調べた。その結果得られたアミノ酸 X に対する依存性について報告する。X には Ala, His, Phe, Trp, Tyr, Val のうち一つが入る。電子カップリング
計算の前に、X 以外の部分については X=Ala として B3LYP/6-31G*で構造最適化してあり、そのあとX のみを再び構造最適化している。その最適化構造を図１に示す。以降の計算では CIS/D95 を用いている。計算手順としては、まず参照分子として GFPc (両端に CH3 を含む)、CFPc (両端に CH3 を含む)および、X (側鎖及びα炭素を含む)の３つを用いた MOD 法[3]により、それぞれのフラグメン
トに局在化した分子軌道を作り、残りのペプチド部分を Pipek-Mezey 法で局在化するというハイブ
リッド局在化法[4]を行いてモデル全域における局在化分子軌道を得た。この結果得られる、分子
軌道は GFPc-pep1-X-pep2-CFPc の 5 か所のフラグメントに局在化する（図１）。これらの局在分子－ 228 －

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Ⅳ 研究業績 (2011)

軌道から作られる Slater determinant を基底として、EET トンネル経路を計算し、そのアミノ酸ごとの違いを調べた。電子トンネル経路の計算にはグリーン関数法を用いており、トンネルエネルギ
ーは CFPc と GFPc のそれぞれの第一励起エネルギーの平均値を用いた(4.12eV=0.1515au)。

【結果】
まず、計算された結果から、この系では直接項の寄与が特に大きいことがわかり、そのため、ここで考えているような系ではドナー、アクセプター状態に直接関与しないブリッジアミノ酸のミューテーションは全体のカップリングにはあまり寄与しないことがわかる。一方で、超交換項についてはアミノ酸の種類に依存して大きく変動することがわかった。そこで、それぞれのアミノ酸Ｘに関して、超交換項に主要な寄与を与える Exciton タイプの Slater determinant を通る EET 経路の寄与を計算し、結果をペプチドボンド経由の経路の結果と合わせて表１に示す。A->B は A にある
exciton が B に移る経路であることを表す。アミノ酸の種類を変えることに拠り、X 経由経路の寄与だけが主に変動していることがわかる。超交換相互作用の項の中では、ペプチドの寄与とアミノ酸残基の寄与は競合しており、アミノ酸の種類によってその大小が入れ替わりうる。表 1 では X はアミノ酸残基の第一励起エネルギーとトンネリングエネルギーの差ΔE が大きい順に並んでおり、X
経由経路の寄与の大きさとΔE に依存関係があるのがわかる。このほかに、ドナー、アクセプターとアミノ酸残基の間の相互作用もいくらか関係している。今回のモデルについては主成分である直接項に対してペプチド項は正、残基項は負の位相を持って計算されているので、有効な残基の場合ほど全体の電子カップリングは小さくなっているが、このようなケースでも、ちゃんと個別の寄与の大小を議論できるのが我々の解析方法の特色である。

表 1. 局在 Exciton 経由 EET トンネル経路の寄与

X

CFPc->X/ X->GFPc

CFPc->pep1/ pep1->GFPc

CFPc->pep2/ pep2->GFPc

Ala-7.32/ -6.63-13.3/ -13.5-8.77/ -8.50

Val-3.11/ -2.76-12.8/ -12.6-8.71/ -8.43

His

14.7/ 14.7

-13.6/ -13.3-9.33/ -8.79

Phe

27.5/ 28.5

-13.1/ -13.2-8.20/ -8.48

Trp

35.9/ 36.9

-13.3/ -13.8-8.09/ -8.53

Tyr

35.2/ 36.4

-12.8/ -12.8-8.40/ -8.76[1] T. Kawatsu, J. Hasegawa, Int. J. Quantum Chem. published online: 23 FEB 2012.
[2] T. Kawatsu, J. Hasegawa, K. Matsuda, J. Phys. Chem. A 115, 10814-10822(2011).
[3] K. Toyota, M. Ehara, H. Nakatsuji, Chem. Phys. Lett. 356, 1-6(2002).
[4] J. Hasegawa, T. Kawatsu, K. Toyota, K. Matsuda, Chem. Phys. Lett. 508, 171-176(2011).

－ 229 －

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Ⅳ 研究業績 (2011)

2. 論�(1) Tsutomu Kawatsu, and Jun-Ya Hasegawa, “Excitation energy transfer in
GFP-X-CFP model peptides (X = amino acids): Direct Versus through-bridgeenergy transfers,” Int. J. Quantum Chem. published online: 23 FEB 2012.
(2) Tsutomu Kawatsu, Jun-ya Hasegawa, and Kenji Matsuda, “Bridge-mediatedexcitation energy transfer pathways through protein media: a Slater
determinant-based electronic coupling calculation combined with localized
molecular orbitals,” J. Phys. Chem. A 115(39), 10814-10822(2011).
(3) Jun-ya Hasegawa, Tsutomu Kawatsu, Kazuo Toyota, and Kenji Matsuda,“Chemical-intuition based LMO transformation simplifies excited-state wave
functions of peptides,” Chem. Phys. Lett. 508, 171-176(2011).
3. 学会��
(1) 河津励、長谷川淳也、松田建児「Super-exchange 機構励起エネルギー移動におけるブリッジの寄与」
第 5 回分子科学討論会 札幌 2011/9/21 2P113(2) Tsutomu Kawatsu, Jun-ya Hasegawa, Kenji Matsuda“Bridge-mediated electronic coupling between two excited states, calculatingbased on the localized Slater determinant”
The 7th Congress of the International Society for Theoretical Chemical Physics(ISTCP-VII), Tokyo, 2011.9.3 3B3-8C(3) 河津励、長谷川淳也、松田建児
局所化分子軌道法を用いた励起エネルギー移動経路の探索
第14回理論化学討論会 岡山 2011/5/14 3B4b
4. �の�
(1) 河津励、長谷川淳也「GFP-X-CFPモデルペプチドにおけるアミノ酸経由励起エネルギー移動」
第９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 2012/1/6 P40(2) 河津励、長谷川 淳也「励起エネルギー移動における超交換項の寄与」
第２回計算物質科学イニシアティブ（CMSI）研究会 仙台 2012/1/30 P11(3) 河津励、長谷川淳也「GFP model励起エネルギー移動におけるペプチドの寄与」
スーパーコンピュータワークショップ2012 岡崎 2012/1/24(4) 河津励「ブリッジを経由する励起エネルギー移動の計算」
CMSI 若手技術交流会 ［第三回］東京 2011/11/25(5) 河津励、長谷川淳也、松田建児「励起エネルギー移動におけるペプチドブリッジの寄与」
計算分子科学研究拠点(TCCI) 第２回研究会 神戸 2012/8/12－ 230 －

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Ⅴ 資料 (2011)

外国人共同研究者受入れ状況（平成 23 年度）

氏名

受入れ身分

受入れ期間

所属機関・職

University of

外国人

平成23年3月19日～

共同研究者

平成23年4月16日

Burger, Steven K.

外国人

平成23年4月11日～

McMaster University

共同研究者

平成23年5月26日（カナダ）・研究員

Sivakumar

外国人

平成24年2月29日～

Emory University

共同研究者

平成24年3月21日（アメリカ）・研究員

Jiayun Pang

Sekharan

受入れ教員

Manchester

諸熊奎治（イギリス）・研究員

諸熊奎治

諸熊奎治

研究内容

複雑分子系のシミュレーション

複雑分子系のシミュレーション

複雑分子系のシミュレーション－ 231 －

05 shiryo.indd 231

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Ⅴ 資料 (2011)

海外渡航一覧（平成 23 年度）

職

名

氏

名

期間（自）

期間（至）

目

的

地

特定研究員

Alister Page

2011.4.8

2011.4.14

アメリカ合衆国

特定研究員

岩城

貴史

2011.4.3

2011.4.8

アメリカ合衆国

特定助教

前田

理

2011.4.17

2011.4.20

中華人民共和国研究員（学術研究奨励）諸熊奎治

2011.5.14

2011.6.8

アメリカ合衆国研究員（学術研究奨励）諸熊奎治

2011.6.23

2011.6.30

チェコ

研究員（学術研究奨励）諸熊奎治

2011.7.15

2011.7.24

スペイン研究員（学術研究奨励）榊茂好2011.5.17

2011.5.26

チェコ

研究員（学術研究奨励）榊茂好2011.5.31

2011.6.3

シンガポール

特定研究員

義永

那津人

2011.6.21

2011.6.26

アメリカ合衆国

准教授

石田

俊正

2011.7.15

2011.7.30

スペイン

特定研究員

Alister Page

2011.7.11

2011.7.26

スペイン

Li Xin2011.7.13

2011.7.24

スペイン

2011.7.17

2011.7.25

スペイン

2011.7.15

2011.7.24

スペイン

産学官連携研究員
研究員（学術研究奨励）
研究員（科学研究）榊茂好

DESHMUKH,
Milind Madhusudan

特定助教

前田

理

2011.7.16

2011.7.25

スペイン研究員（学術研究奨励）諸熊奎治

2011.8.11

2011.8.18

中国

研究員（学術研究奨励）榊茂好2011.8.17

2011.8.19

中国

2011.8.16

2011.8.21

フィリピン共和国
ドイツ

研究員（学術研究奨励）

Wilfredo C. Chung

特定研究員

義永

那津人

2011.8.27

2011.9.28

研究員（学術研究奨励）諸熊奎治

2011.9.2

2011.9.9

タイ

2011.9.4

2011.9.9

タイ

研究員（学術研究奨励）

Wilfredo C. Chung

フランス

研究員（学術研究奨励）榊茂好2011.9.2

2011.9.8

タイ

研究員（学術研究奨励）榊茂好2011.10.2

2011.10.10

ギリシャ

研究員（学術研究奨励）諸熊奎治

2011.10.7

2011.10.31

アメリカ合衆国

特定研究員

義永

那津人

2011.10.26

2011.10.30

台湾

研究員（学術研究奨励）諸熊奎治

2011.12.8

2011.12.15

ニュージーランド

研究員（学術研究奨励）諸熊奎治

2012.1.8

2012.1.21

アメリカ合衆国

特定研究員

畑中

美穂

2012.2.18

2012.2.27

アメリカ合衆国研究員（学術研究奨励）諸熊奎治

2012.3.25

2012.3.28

シンガポール－ 232 －

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Ⅴ 資料 (2011)

研究業績一覧（2011 年度）№

Authors

長谷川

Title

JournalVolume(Number),first page to last
page

year

淳也

1

J. Hasegawa, T. Kawatsu, K.
Toyoya, and K. Matsuda

Chemical-intuition based LMO
transformation simplifies excited-state
wave functions of peptides

Chem. Phys.
Letters508(1-3),
171-176

2011

2

Y. Kitagawa, K. Matsuda,
and J. Hasegawa

Theoretical Study of the Excited Statesof the Photosynthetic Reaction Centerin Photosystem II: Electronic Structure,
Interactions, and Their Origin

Biophys. Chem.

159(2-3),
227-236

2011

3

T. Kawatsu, K. Matsuda, and
J. Hasegawa

Bridge-Mediated Excitation Energy
Transfer Pathways through Protein Media:
a Slater Determinant-Based Electronic
Coupling Calculation Combined with
Localized Molecular Orbitals

J. Phys. Chem. A

115(39),10814-10822

2011

4

J. Hasegawa and K. Matsuda

Theoretical study of the excited states andthe redox potentials of unusually distorted
β-trifluoromethylporphycene

Theoret. Chem.
Acc.

130(2-3),
175-1852011

5

J. Hasegawa, K. Fujimoto,and H. Nakatsuji

Color tuning in photo-functional proteins

ChemPhysChem

12(17),
3106-3115

2011

6

Y. Yamamoto, J. Hasegawa,and Y. Ito

Kinetic investigation on carbamate
formation from the reaction of carbon
dioxide with amino acids in homogeneous
aqueous solution

J. Phys. Org.
Chem.

25(3),
239-247

2012

7

T. Sakano, J. Hasegawa,K. Higashiguchi, and K.
MatsudaChronological Change from FaceOn to Edge-On Ordering of Zinc
Tetraphenylporphyrin at PhenyloctaneHOPG Interface

Chem. Asian J.

7(2),394-399

2012

8

T. Kawatsu and J. Hasegawa

Excitation Energy Transfer in GFP-XCFP Model Peptides (X=amino acids):
direct vs. through-bridge energy transfers

Intern. J.
Quantum. Chem.

In Press

2012

9

J. Hasegawa, K. Fujimoto,and H. Nakatsuji

Color tuning in human cone visual
pigments: the role of the protein
environment

Progress in
Theoretical
Physics andChemistryIn Press

2012

10

T. Kawatsu, K. Matsuda, and
J. Hasegawa

Singlet Excitation Energy Transfer
Mediated by Local Exciton Bridges

J. Phys. Chem. C

Accepted201211

Hideo Ando, Yoshihide
Nakao, Hirofumi Sato,
Masaaki Ohba, Susumu
Kitagawa, Shigeyoshi Sakaki

Theoretical study on high-spin to low-spintransition of {Fe(pyrazine)[Pt(CN)4]}:
Guest-induced entropy decrease

Chem. Phys.
Lett.

511, 399-404

2011

12

Yusaku I. Kurokawa,
Yoshihide Nakao, andShigeyoshi Sakaki

Theoretical Study of Inverted SandwichType Complexes of 4d Transition Metal
Elements: Interesting Similarities to andDifferences from 3d Transition Metal
Complexes

J. Phys. Chem. A

116, 2292–2299

2012

中尾

嘉秀

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Volume(Number),first page to last
page

year

J. Am. Chem.
Soc.

134,
1825–1839

2012

Oscillator strength of symmetry-forbidden
d-d absorption of octahedral transition
metal complex: theoretical evaluation.

Inorg. Chem.

51,
2785-2792

2012

15

Suhara, Masanori; Ozaki,
Hiroyuki; Endo, Osamu;
Ishida, Toshimasa; Katagiri,
Hideki; Egawa, Toru;
Katouda, Michio

Changes in the Electronic Structures of aSingle Sheet of Sashlike Polydiacetylene
Atomic Sash upon Structural
Transformations

J. Phys. Chem. C

115(19),9518-9525

2011

16

Wilfredo Credo Chung andToshimasa Ishida

An MD simulation of the decoy actionof Epstein-Barr virus LMP1 protein
mimicking the CD40 interaction with
TRAF3

Theo. Chem.
Acc.

130(2),
401-4102011

17

Jun-ichi Aihara, Rika Sekine
and Toshimasa Ishida

Electronic and Magnetic Characteristics
of Polycyclic Aromatic Hydrocarbons
with Factorizable Kekule Structure Count

J. Phys. Chem. A

115(33),9314-9321

2011

18

Wilfredo Credo Chung,
Shinkoh Nanbu, andToshimasa Ishida

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

Chem. Lett.

40(12),
1395-1397

2011

19

Hidekazu Ikeno, Teruyasu
Mizoguchi, Yukinori
Koyama, Zenpachi Ogumi,
YasuharuUchimoto, and Isao
Tanaka,Theoretical Fingerprints of Transition
Metal L2,3 XANES/ELNES for Lithium
Transition Metal Oxides by ab Initio
Multiplet Calculations

J. Phys. Chem. C

115,11871-11879

2011

20

S. Ootsuki, H. Ikeno, Y.
Umeda, H. Moriwake, A.
Kuwabara, O. Kido, S. Ueda,
I. Tanaka, Y. Fujikawa, and T.
Mizoguch

Ab-initio multiplet calculation of oxygen
vacancy effect on Ti-L2,3 electron energy
loss near edge structures of BaTiO3

99,2331092011№

Authors

Title

13

Yoshihiro Matano, Kazuaki
Matsumoto, Hironobu
Hayashi, Yoshihide
Nakao, Tatu Kumpulainen,
Vladimir Chukharev,
Nikolai V. Tkachenko,
Helge Lemmetyinen, Soji
Shimizu, Nagao Kobayashi,
Daisuke Sakamaki, Akihiro
Ito, Kazuyoshi Tanaka, andHiroshi Imahori

Effects of Carbon–Metal–Carbon
Linkages on the Optical, Photophysical,
and Electrochemical Properties of
Phosphametallacycle-Linked Coplanar
Porphyrin Dimers

14

Ken Saito, Yoshinori Eishiro,
Yoshihide Nakao, Hirofumi
Sato, Shigeyoshi Sakaki

石田

池野

諸熊

Journal

俊正

豪一

奎治

21

Z. Ke, S. Abe, T. Ueno and K.
MorokumaRh-catalyzed Polymerization of
Phenylacetylene: Theoretical Study of
the Reaction Mechanism, Regioselectivity
and Stereoregularity

J. Am. Chem.
Soc.

133,
7926–7941

2011

22

H. Hirao, F. Li, L. Que, Jr.,and K. Morokuma

Theoretical Study of the Mechanismof Oxoiron(IV) Formation from H2O2
and a Nonheme Iron(II) Complex: O–O
Cleavage Involving Proton-Coupled
Electron Transfer

Inorg. Chem.

50,
6637-6648

2011

23

H.-J. Qian, A. van Duin, K.
Morokuma and S. Irle

Reactive Molecular Dynamics Simulationof Fullerene Combustion Synthesis:
ReaxFF vs DFTB Potentials

J. Chem. Theo.
Comp.

7,
2040-2048

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Ⅴ 資料 (2011)

Volume(Number),first page to last
page

year

ACS Chem. Bio.

6,775-780.

2011

Finding Reaction Pathways of Type A +B → X: Toward Systematic Prediction of
Reaction Mechanisms,

J. Chem. Theo.
Comp.

7,
2335-2345.

2011

X. Li, L. W. Chung, and K.
Morokuma

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

J. Chem. Theo.
Comp.

7,
2694-2698.

2011

27

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

Thermal Annealing of SiC Nanoparticles
Induces SWNT Nucleation: Evidence for a
Catalyst-Independent VSS Mechanism

PhysChemChem
Phys

13,
15673-15680.

2011

28

H. Hirao and K. Morokuma

ONIOM(DFT:MM) Study of
2-Hydroxyethylphosphonate Dioxygenase:
What Determines the Destinies ofDifferent Substrates?

J. Am. Chem.
Soc.

133,
14550-14553.

2011

29

S. Abdel-Azeim, X. Li, L. W.
Chung and K. Morokuma

Zinc–Homocysteine Displacement in
Cobalamin-Dependent Methionine
Synthase and its Role in the Substrate
Activation: DFT, ONIOM, and QM/MM
Molecular Dynamics Studies

J. Comp. Chem.

32,3154-3167.

2011

30

W. Zhang, Y. Tang, M. Lei,
K. Morokuma, and D. G.
Musaev

Ditantalum dinitrogen complex: Reactionof H2 molecule with “end-on-bridged”[TaIV]2(μ-η1:η1-N2) and bis(μ-nitrido)[TaIV]2(μ-N)2 complexes. Inorg. Chem.

50,
9881-9490.

2011

31

J. Kim, S. Irle and K.
Morokuma

Determination of Local Chirality of
Irregular Single-Walled Carbon Nanotube
Based on Individual Hexagons

Phys. Rev. Lett.

107,
175505/1-5.

2011

32

Y. Wang, A. J. Page, Y.
Nishimoto, H.-J. Qian, K.
Morokuma and S. Irle

Template Effect in the Competition
Between Haeckelite and Graphene Growthon Ni(111): Quantum Chemical Molecular
Dynamics Simulations

J. Am. Chem.
Soc.

133, 18837–
18842.

2011

33

S. Sekharan and K.
Morokuma

Why 11-Retinal? Why Not 7-, 9- or 13-inthe Eye?

J. Am. Chem.
Soc.

133, 1905219055.

2011

34

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

Hot giant fullerenes eject capture C2
molecules. QM/MD simulations withconstant density

J. Phys. Chem. C

115,
22707-2271.

2011

35

Y. Okamoto, F. Kawamura,.Y.
Ohta, A. J. Page, S. Irle and K.
Morokuma

SCC- DFTB/MD Simulation of Transition
Metal Catalyst Particle Melting andCarbide Formation

J. Comp. Theo.
Nanosci.

8,
1755-1763.

2011

36

K. Ando and K. Morokuma

DFT and ONIOM Study on the Alkylationof the Lithium Enolate in Solution:
Microsolvation Cluster Models for
CH2=CHOLi + CH3Cl + (THF)0-6

Theo. Chem.
Acct.

130,
323-331.

2011

37

L. W. Chung, X. Li, H. Hirao
and K. Morokuma

Comparative Reactivity of FerricSuperoxo and Ferryl-Oxo Species in Hemeand non-Heme Complexes.

J. Am. Chem.
Soc.

133,
20076–20079.

2011

38

R. Tanaka, M. Yamashita, L.
W. Chung, K. Morokuma, and
K. Nozaki

Mechanistic Studies on the Reversible
Hydrogenation of Carbon Dioxide
Catalyzed by an Ir-PNP complex,
Organometallics, 30, 6742–6750 (2011).

Organometallics

30,
6742–6750.

2011

39

H. M. Nguyen, H. Hirao, U. V.
Dang, K. Morokuma

Computational Studies of Bacterial
Resistance to b-Lactam Antibiotics:
Mechanism of Covalent Inhibition of thePenicillin-Binding Protein 2a (PBP2a)

J. Chem. Inf.
Model.

51,
3226-3234..

2011

№

Authors

Title

Journal24

A. Altun, K. Morokuma andS. Yokoyama

H-bond network around retinal regulates
the evolution of ultraviolet and violet
vision25

S. Maeda and K. Morokuma

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Ⅴ 資料 (2011)

Volume(Number),first page to last
page

year

Mater. Express1,
343–349.

2011

Quantum Mechanical/Molecular
Mechanical Structure, Enantioselectivity
and Spectroscopy of Hydroxyretinals andInsights into the Evolution of Color Vision
in Small White Butterflies

J. Phys. Chem. B

115,15380-15388.

2011

Y. Matsuda, K. Hoki, S.
Maeda, K. Hanaue, K. Ohta,
K. Morokuma, N. Mikami,
and A. Fujii

Experimental and theoretical investigationsof isomerization reactions of ionized
acetone and its dimer

Phys. Chem.
Chem. Phys.

14,712-719.

2012

43

Y. Nishimoto, Z. Wang, K.
Morokuma, and S. Irle

Molecular and electronic structures ofendohedral fullerenes, Sc2C2@C3v-C82
and Sc2@C3v-C82: Benchmark for SCCDFTB and proposal of new inner cluster
structures

Phys. Status
Solidi B

249,
324-334.

2012

44

J. Pang, X. Li, K. Morokuma,
N. S. Scrutton, and M. J.
Sutcliffe

Large-scale Domain Conformational
Change Is Coupled to the Activation of
the Co-C bond in the B12-Dependent
Enzyme Ornithine 4,5-Aminomutase: A
Computational Study

J. Am. Chem.
Soc.

134,
2367-2377.

2012

45

S. Maeda and K. Morokuma

Toward Predicting Full Catalytic Cycles
Using Automatic Reaction Path Search
Method: A Case Study on HCo(CO)3Catalyzed Hydroformylation

J. Chem. Theo.
Comp.

8,
380-385.

2012

46

M. P. Grubb, M. L. Warter,
H.-Y. Xiao, S. Maeda, K.
Morokuma, S. W. North

No Straight Path: Multistate Roaming as
the Only Route for the NO3 → NO + O2
Reaction

Science335,
1075-1078.

2012

47

F. Liu, and K. Morokuma

A Computational Study on the Working
Mechanism of Stilbene Light-Driven
Molecular Rotary Motor: Sloped
Minimal Energy Path and Unidirectional
Nonadiabatic Isomerization

J. Am. Chem.
Soc.

134,
4864-4876.

2012

48

H.-B. Li, A. J. Page, S. Irle,
and K. Morokuma

Theoretical Insights into ChiralityControlled SWCNT Growth from a
Cycloparaphenylene Template

ChemPhysChem

13,1479-1485.

2012

榊

茂好

49

Hirofumi Sato,Chisa
Kikumori, Shigeyoshi Sakaki

Solvation structure of coronene-transition
metal complex: a RISM-SCF study

Phys. Chem.
Chem.. Phys.

13 (1):
309-3132011

50

Naoki Nakatani, Yutaka
Hitomi, and Shigeyoshi
Sakaki

Multi-State CASPT2 Study of
Native Iron(III)-dependent Catechol
Dioxygenase and Its Functional Models:Electronic Structure and Ligand-to-Metal
Charge-Transfer Excitation

J. Phys. Chem. B

115,
4781–4789

2011

51

Atsushi Ishikawa andShigeyoshi Sakaki,

Theoretical Study of Photoinduced
Epoxidation of Olefins Catalyzed by
Ruthenium Porphyrin

J. Phys. Chem. A

115,
4774–4785

2011

52

Shigeyoshi Sakaki,
Daisuke Kawai, and Shinya
Tsukamoto

Theoretical Study of Metallasilatranes;
Bonding Nature and Prediction of New
Metallasilatrane

Collect. Czech.
Chem. Commun.

76 (No. 5).
619–629

2011

53

Atsuhi Ikeda, Yoshihide
Nakao, Hirofumi Sato,
Shigeyoshi Sakaki,

A resonance theory consistent with
Mulliken-population concept

Chem. Phys.
Lett.

505,
4-6

2011

№

Authors

Title

Journal40

J. M. Knaup. K. Morokuma
and S. Irle

A simulation of possible carbon nanotubes
slitting in a CMOS compatible way

41

S. Sekharan, S. Yokoyama,.
K. Morokuma

42－ 236 －

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Ⅴ 資料 (2011)

Volume(Number),first page to last
page

year

Inorg. Chem.

50,
5290-5297

2011

Shinya Tsukamoto andShigeyoshi Sakaki

Theoretical Study of Pt(PR 3)2(AlCl3)(R=H, Me, Ph, or Cy) Including an
Unsupported Bond between Transition
Metal and Non-Transition Metal
Elements; Geometry,Bond Strength, andPrediction

J. Phys. Chem. A

115, (30),8520-8527

2011

56

Daisuke Yokogawa, Kohei
Ono, Hirofumi Sato,
Shigeyoshi Sakaki

Theoretical study on aquation reactionof cis-platin complex: RISM-SCFSEDD, a hybrid aproach of accuratequantum chemical method and statisticalmechanics

Dalton Trans.

40 (42),11125-11130

2011

57

Hideo Ando, Yoshihide
Nakao, Hirofumi Sato,
Masaaki Ohba, Susumu
Kitagawa, Shigeyoshi Sakaki

Theoretical Study on High-Spin to
Low-Spin Transition of {Fe(pyrazine)[Pt(CN)4]}: Guest-Induced Entropy
Decrease

Chem. Phys.
Lett.

511(4-6),
399-404

2011

58

Shibata, Naoto, Hirofumi
Sato, Shigeyoshi Sakaki, Yuji
SugitaTheoretical Study of Magnesium Fluoride
in Aqueous Solution

J. Phys. Chem. B

115 (3-5),10553-10559

2011

59

Hiroyuki Sakaba, Hiroyuki
Oike, Masaaki Kawai,
Masato , Takami, Chizuko
Kabuto, Mausumi Ray,
Yoshihide Nakao, Hirofumi
Sato, and Shigeyoshi Sakaki

Synthesis, Structure, and Bonding Natureof Ethynediyl-Bridged Bis(silylene)
Dinuclear Complexes of Tungsten and
Molybdenum

Organometalics

30(17)
4515-4531

2011

60

Kazuhide Ichikawa, Ayumu
Wagatsuma, Yusaku I.
Kurokawa, Shigeyoshi
Sakaki, Akitomo Tachibana

Inverted-sandwich-type and openlantern-type dinuclear transition metal
complexes: theoretical study of chemicalbonds by electronic stress tensor

Theor. Chem.
Acc.

130 (2-3)
237-250

2011

Milind Deshmukh,
Shigeyoshi Sakaki

Binding energy of gas molecule withtwo pyrazine molecules as organic
linker in meal-organic framework: its
theoretical evaluation and understandingof determining factors

Theor. Chem.
Acc.

130 (2-3)
475-482

2011№

Authors

54

Guixiang Zeng andShigeyoshi Sakaki

Noble Reaction Features of Bromoboranein Oxidative Addition of B−Br σ−Bondto M(PMe3)2 (M= Pt or Pd): Theoretical
Study

55

61

前田

Title

Journal理

62

S. Maeda, K. Morokuma

Finding Reaction Pathways of Type A +B → X: Toward Systematic Prediction of
Reaction Mechanisms

J. Chem. Theory
Comput.

7,2335-2345

2011

63

N. S. Shuman, T. M. Miller, J.
F. Friedman, A. A. Viggiano,
S. Maeda, K. Morokuma

Temperature Dependences of Rate
Coefficients for Electron Catalyzed
Mutual Neutralization

J. Chem. Phys.

135,024204(8 pages)

2011

64

S. Maeda, K. Ohno, K.
Morokuma

Exploring Multiple Potential Energy
Surfaces: Photochemistry of Small
Carbonyl Compounds

Adv. Phys. Chem.

2012,268124(13 pages)

2011

65

Y. Matsuda, K. Hoki, S.
Maeda, K.-i. Hanaue, K.
Ohta, K. Morokuma, N.
Mikami, A. Fujii

Experimental and Theoretical
Investigations of Isomerization Reactionsof Ionized Acetone and Its Dimer

Phys. Chem.
Chem. Phys.

14,712-719

2012

66

S. Maeda, K. Morokuma

Toward Predicting Full Catalytic Cycle
Using Automatic Reaction Path Search
Method: A Case Study on HCo(CO)3Catalyzed Hydroformylation

J. Chem. Theory
Comput.

8,
380-3852012－ 237 －

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Ⅴ 資料 (2011)№

Authors

Title

JournalVolume(Number),first page to last
page

year

67

P. S. Krstic, J. P. Allain,
A. Allouche, J. Jakowski,
J. Dadras, C. N. Taylor, Z.
Yang, K. Morokuma, S.
Maeda

Dynamics of Deuterium Retention andSputtering of Li–C–O Surfaces

Fusion Eng. Des.

[doi:10.1016/
j.fusengdes.
2011.07.009]

2012

68

M. P. Grubb, M. L. Warter,
H. Xiao, S. Maeda, K.
Morokuma, S. W. North

No Straight Path: Roaming in Both
Ground- and Excited-State Photolytic
Channels of NO3 → NO + O2

Science335,
1075-1078

2012

Zhuofeng Ke
69

Ke, Zhuofeng, Abe, S., Ueno,
T., & Morokuma, Keiji*

Rh-catalyzed Polymerization of
Phenylacetylene: Theoretical Studies of
the Reaction Mechanism, Regioselectivity
and Stereoregularity

J. Am. Chem.
Soc.

133 (20),7926-7941

2011

70

Liu, Y., Ke, Zhuofeng, Liu,
Shuwen, Chen, Wen-Hua,
Jiang, Shibo; Jiang, Zhi-Hong

An Amphiphilic Conjugate Approach
toward the Design and Synthesis of
Betulinic Acid–Polyphenol Conjugates as
Inhibitors of the HIV-1 gp41 Fusion Core
Formation

ChemMedChem

6 (9),
1654-1664

2011

71

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 aConcerted Mechanism

J. Am. Chem.
Soc.

133 (9),2904–2915

2011

Determination of Local Chirality
in Irregular Single-Walled Carbon
Nanotubes Based on Individual Hexagons

Phys. Rev. Lett.

107(17),175505

2011

2011

Joonghan Kim
72

Joonghan Kim, Stephan Irle,
and Keiji Morokuma

Alister Page
73

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

SWNT Nucleation from Carbon-Coated
SiO2 Nanoparticles via a Vapor-SolidSolid Mechanism

J. Am. Chem.
Soc.

133(3),
621-628

74

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

Chem. Phys.
Lett.

508(4-6),
235-241

75

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

J. Comp. Theor.
Nanoscience8(9),1755-1763

76

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

Thermal Annealing of SiC Nanoparticles
Induces SWNT Nucleation: Evidence fora Catalyst Independent SWNT Nucleation
Mechanism

Phys. Chem.
Chem. Phys.

13(34),
15673-15680

77

Y. Wang, A. J. Page, Y.
Nishimoto, H.-J. Qian, S. Irle,
K. Morokuma

Haeckelite Islands in Graphene Nucleation
on Ni(111): Density Functional Tight
Binding MD Simulations

J. Am. Chem.
Soc.

133(46),
18837-18842

78

H.-B. Li, A. J. Page, S. Irle, K.
Morokuma

Theoretical Insights into ChiralityControlled SWCNT Growth from a
Cycloparaphenylene Template

ChemPhysChem

13(6),
1479-1485

79

M. A. Addicoat, A. J. Page,
Z. Brain, L. Flack, S. Irle, K.
Morokuma

Optimisation of a Genetic Algorithm for
the Functionalisation of Fullerenes

J. Chem. Theor.
Comp.

8(5),
1841-1851

80

J. Kim, A. J. Page, S. Irle, K.
Morokuma

The Dynamics of Local Chirality during
SWCNT Growth: Armchair versus Zigzag
Nanotubes

J. Am. Chem.
Soc.

134(22),9311-9319－ 238 －

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Ⅴ 資料 (2011)

Title

JournalVolume(Number),first page to lastpage№

Authors81

H.-B. Li, A. J. Page, Y. Wang,
S. Irle, K. Morokuma

Sub-Surface Nucleation of Graphene
Precursors near a Ni(111) Step-Edge

Chem. Comm.

In press

82

A. J. Page, T. Isomoto, J.
Knaup, S. Irle, K. Morokuma

Effects of Molecular Dynamics
Thermostats on Non-Equilibrium Systems

J. Chem. Theor.
Comp.

Submitted

83

H.-B. Li, A. J. Page, S. Irle, K.
Morokuma

SWCNT Growth from Chiral Carbon
Nanorings: Prediction of Chirality andDiameter Influence on Growth Rates

J. Am. Chem.
Soc.

Submitted

year

Xin Li84

Xin Li, Lung Wa Chung, andKeiji Morokuma

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

J. Chem. Theory
Comput. (Lett.)

7,2694–2698

2011

85

Lung Wa Chung, Xin Li,
Hajime Hirao and Keiji
MorokumaComparative Reactivity of FerricSuperoxo and Ferryl-Oxo Species in
Heme and Non-Heme Complexes

J. Am. Chem.
Soc.

133 (50),
20076–20079

2011

86

Safwat Abdel-Azeim, Xin
Li, Lung Wa Chung, Keiji
MorokumaZinc–Homocysteine binding incobalamin-dependent methionine
synthase and its role in the substrateactivation: DFT, ONIOM, and QM/MM
molecular dynamics studies

J. Comput.
Chem.

32 (15),3154-3167

2011

87

Lung Wa Chung, Hajime
Hirao, Xin Li and Keiji
Morokuma

The ONIOM method: its foundation
and applications to metalloenzymes andphotobiology

WIREs Comput.
Mol. Sci.

2 (2),
327–350201288

Jiayun Pang, Xin Li, Keiji
Morokuma, Nigel S. Scrutton,
and Michael J. Sutcliffe

Large-Scale Domain Conformational
Change Is Coupled to the Activation of
the Co−C Bond in the B12-Dependent
Enzyme Ornithine 4,5-Aminomutase: A
Computational Study

J. Am. Chem.
Soc.

134,
2367-2377

2012

K.R.S. Chandrakumar
89

Naresh K Jena, KRS
Chandrakumar, and Swapan
K GhoshDNA Base-Gold Nano Cluster Complex
as a Potential Catalyzing Agent: An
Attractive Route for CO Oxidation
ProcessJ. Phys. Chem C.

In Press

2012

90

Naresh K. Jena, Manoj K.
Tripathy, Alok K. Samanta,
K. R. S. Chandrakumar andSwapan K. Ghosh

Water Molecule Encapsulated in Carbon
Nanotube Model Systems: Effect ofConfinement and Curvature

Theo. Chem.
Acc.

131,
1205-1211

2012

Computational Study on the Working
Mechanism of a Stilbene Light-Driven
Molecular Rotary Motor: Sloped
Minimal Energy Path and Unidirectional
Nonadiabatic Photoisomerization

J. Am. Chem.
Soc.

134,
4864–4876

2012

Fengyi Liu

91

Fengyi Liu and Keiji
Morokuma

Hongyan Xiao
92

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

93

Michael P. Grubb, Michelle
L. Warter, Hongyan Xiao,
Satoshi Maeda, Keiji
Morokuma and Simon W.
North

No Straight Path: Roaming in Both
Ground- and Excited-state Photolytic
Channels of NO3 → NO +O2

Science335,
1075-1078

2012－ 239 －

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Ⅴ 資料 (2011)№

Authors

Title

JournalVolume(Number),first page to last
page

year

Haibei Li
94

Hai-Bei Li, Aister. J. Page,
Sthephan. Irle and K.
Morokuma,

Theoretical Insights for ChiralityControlled SWCNT Growth from a
Cycloparaphenylene Template

ChemPhysChem

13,1479-1485,
2012.

2012

95

Hai-Bei Li, Aister. J. Page,
Ying Wang, Sthephan. Irle
and K. Morokuma

Sub-Surface Nucleation of Graphene
Precursors near a Ni(111) Step- Edge

ChemComm

accepted,
DOI:10.1039/
c2cc32995f

2012

96

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

Pd-Catalyzed Copolymerization of
Methyl Acrylate with Carbon Monoxide:
Structures, Properties and Mechanistic
Aspects toward Ligand Design

J. Am. Chem.
Soc.

133 (17),6761–6779

2011

97

Safwat Abdel-Azeim, Xin
Li, Lung Wa Chung, Keiji
MorokumaZinc–Homocysteine binding incobalamin-dependent methionine
synthase and its role in the substrateactivation: DFT, ONIOM, and QM/MM
molecular dynamics studies

J. Comput.
Chem.

32 (15),3154-3167

2011

98

Xin Li, Lung Wa Chung and
Keiji Morokuma

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

J. Chem. Theory
Comput.

7 (9),
2694–2698

2011

99

Lung Wa Chung, Xin Li,
Hajime Hirao and Keiji
MorokumaComparative Reactivity of FerricSuperoxo and Ferryl-Oxo Species in Heme
and Non-Heme Complexes

J. Am. Chem.
Soc.

133 (50),
20076–20079

2011

100

Ryo Tanaka, Makoto
Yamashita, Lung Wa Chung,
Keiji Morokuma and Kyoko
Nozaki

Mechanistic Studies on the Reversible
Hydrogenation of Carbon Dioxide
Catalyzed by an Ir-PNP Complex

Organometallics

30 (24),6742–6750

2011

101

Lung Wa Chung, Hajime
Hirao, Xin Li and Keiji
Morokuma

The ONIOM method: its foundation
and applications to metalloenzymes andphotobiology

WIREs Comput.
Mol. Sci.

2 (2),
327–350

2012

102

G. V. Vayssilov, Y. Lykhach,
A. Migani, T. Staudt, G. P.
Petrova, N. Tsud, T. Skála, A.
Bruix, F. Illas, K. C. Prince,
V. Matolín, K. M. Neyman, J.
LibudaSupport nanostructure boosts oxygen
transfer to catalytically active platinum
nanoparticles

Nat. Mater.

10 (4),
310-3152011

103

G. P. Petrova, G. V. Vayssilov,
B. Galabov

Enhanced reactivity of carbonylcompounds on MgO surface: A
computational study

J. Mol. Catal. A

342-343,
67-73

2011

104

K. Chakarova, G. Petrova,
M. Dimitrov, L. Dimitrov, G.
Vayssilov, T. Tsoncheva, K.
Hadjiivanov

Coordination state of Cu+ ions in Cu-[Al]MCM-41

Appl. Catal. B

106 (1-2),
186-194

2011

105

M. A. Rangelov, G. P.
Petrova, V. M. Yomtova, G. V.
Vayssilov

Determination of the optimal positionof adjacent proton-donor centers for theactivation or inhibition of peptide bondformation - A computational model study

J. Mol. Graph.
Model.

30,
10-14

2011

106

G. P. Petrova, G. V. Vayssilov,
N. RöschInteraction of ethene and ethyne with bareand hydrogenated Ir4 clusters. A density
functional study

Catal. Sci. Tech.

1 (6),
958-970

2011

Lung Wa Chung

Galina Petrova－ 240 －

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Ⅴ 資料 (2011)

Volume(Number),first page to last
page

year

Phys. Chem.
Chem. Phys.

14 (17),5879-5890

2012

An Examination of Density Functionals
on Aldol,Mannich and α-Aminoxylation
Reactions Enthalpy Calculations

Theor. Chem.
Acc.

130 (2-3),
153-160

2011

Comparative Assessment of theComposition and Charge State of
Nitrogenase FeMo-Cofactor.

Inorg. Chem.

50(11),
4811-4824

2011

110

Yuh Hijikata, Satoshi Horike,
Daisuke Tanaka, Juergen
Groll, Motohiro Mizuno,
Jungeun Kim, Masaki Takata,and Susumu Kitagawa

Differences of crystal structure anddynamics between soft porous nanocrystal
and bulk crystal

Chem. Commun.

47,
7632-7634

2011

111

Nobuhiro Yanai, Koji
Kitayama, Yuh Hijikata,
Hiroshi Sato, Ryotaro
Matsuda, Yoshiki Kubota,
Masaki Takata, Motohiro
Mizuno, Takashi Uemura,and Susumu Kitagawa

Reporting structural transformation ofsoft porous crystals for detection of CO2

Nat. Mater.

10,787-793

2011

112

Daiki Umeyama, Satoshi
Horike, Munehiro Inukai,
Yuh Hijikata, and Susumu
Kitagawa

Confinement of mobile histamine incoordination nanochannels for fast protontransfer

Angew. Chem.
Int. Ed.

50,
11706-11709

2011

113

Jose Alberto RodríguezVelamazán, Miguel A.
González, José Antonio Real,
Miguel Castro, M. Carmen
Muñoz, Ana Belén Gaspar
Ryo Ohtani, Masaaki Ohba,
Ko Yoneda, Yuh Hijikata,Nobuhiro Yanai, Motohiro
Mizuno, Ando Hideo, andSusumu Kitagawa

A switchable molecular rotator: neutron
spectroscopy study on a polymeric spincrossover compound

J. Am. Chem.
Soc.

134,
5083-5089

2012

Solution reaction space Hamiltonianbased on an electrostatic potential
representation of solvent dynamics

J. Chem. Phys.

Vol.134
1441082011

Shigeyoshi Sakaki,
Daisuke Kawai, and Shinya
Tsukamoto

Theoretical Study of Metallasilatranes;
Bonding Nature and Prediction of New
Metallasilatrane.

Collection ofCzechoslovak
ChemicalCommunications

76,
619-6292011

Shinya Tsukamoto andShigeyoshi Sakaki

Theoretical Study of Pt(PR3)2(AlCl3)(R=H, Me, Ph, or Cy) Including an
Unsupported Bond between Transition
Metal and Non-Transition Metal
Elements; Geometry, Bond Strength, andPrediction.

J. Phys. Chem. A,

115,
8520-8527

2011№

Authors

Title

107

G. V. Vayssilov, G. P. Petrova,
E. A. I. Shor, V. A. Nasluzov,
A. M. Shor, P. S. Petkov, N.
Rösch

Reverse hydrogen spillover on andhydrogenation of supported metal clusters:
Insights from computational model studies

JournalRaman Kumar Singh108

Raman K. Singh, Takao
Tsuneda and Kimihiko Hirao

Travis Harris
109

土方

青野
114

塚本
115

116

Travis V. Harris, Robert K.
Szilagyi

優信治
S. Aono, T. Yamamoto, S.
Kato

晋也

－ 241 －

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Ⅴ 資料 (2011)№

Authors

Title

JournalVolume(Number),first page to last
page

year

Milind Deshmukh
117

Deshmukh Milind M. and
Sakaki Shigeyoshi

Two-step Evaluation of Potential Energy
Surface and Binding Energy of van der
Waals Complexes

J. Comput.
Chem.

33,
617-628

2012

118

Jayshree K. Khedkar, Milind
M. Deshmukh, Shridhar R.
Gadre, and Shridhar P. Gejji

Hydrogen bond energies and cooperativity
in substituted calix[n]arenes (n=4, 5)

J. Phys. Chem. A

116,3739-3744

2012

119

Deshmukh Milind M. and
Sakaki Shigeyoshi

Binding energy of gas molecule withtwo pyrazine molecules as organic
linker in metal–organic framework: its
theoretical evaluation and understandingof determining factors

Theor. Chem.
Acc.

130,
475-482

2011

120

Deshmukh Milind M.;
Bartolotti Libero Jr. andGadre Shridhar R.

Intramolecular Hydrogen Bond Energy andCooperative Interactions in Alpha-, Beta-,
and Gamma-Cyclodextrin Conformers

J. Comput. Chem.

32,
2996 - 3004

2011

會

桂香

121

Guixiang Zeng andShigeyoshi Sakaki

Noble Reaction Features of Bromoboranein Oxidative Addition of B−Br σ−Bond
to [M(PMe3)2] (M= Pt or Pd): Theoretical
Study

Inorg. Chem

50(11),
5290-5297

2011

122

Guixiang Zeng andShigeyoshi Sakaki

Theoretical Study on the Transition-Metal
Oxoboryl Complex: M−BO Bonding
Nature, Mechanism of the Formation
Reaction, and Prediction of a New
Oxoboryl Complex

Inorg. Chem

51(8),
4597-4605

2012

123

N. Takagi, A. Krapp, G.
Frenking

Bonding Situation in "Early-Late"
Transition Metal Complexes Cl3MM'(PCl3)4 (M = Ti, Zr, Hf; M' = Co, Rh,Ir) - Theoretical Study for a Ligand Fine
Tuning of M-M’ Bonds -Z. Anorg. Alleg.
Chem.

637,
1728-1735

2011

124

N. Takagi, R. Tonner, G.
Frenking

Carbodiphosphorane-Analogues E(PPh3)2
with E = C - Pb. A Theoretical Study with
implications for ligand design

Chem. Eur. J.

18,
1772-1780

2012

125

T. Agou, Y. Sugiyama,
T. Sasamori, H. Sakai,
Y. Furukawa, N. Takagi,
J. D. Guo, S. Nagase, D.
Hashizume, N. Tokitoh

Synthesis of Kinetically Stabilized
1,2-Dihydrodisilenes

J. Am. Chem.
Soc.

134,
4120-4122

2012

N. Takagi, S. Sakaki

A Theoretical Study of Unusual Y-Shaped
Three-coordinate Pt Complex: Pt(0)σ-Disilane Complex or Pt(II) Disilyl
Complex?

J. Am. Chem.
Soc.

in press

2012

NMR shielding constants of CuX,
AgX, and AuX (X = F, Cl, Br, and I)
investigated by density functional theory
based on the Douglas–Kroll–Hess
Hamiltonian

in preparation

髙木

126

吉澤

127

望

輝高

T. Yoshizawa, S. Sakaki－ 242 －

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Ⅴ 資料 (2011)

Volume(Number),first page to last
page

year

J. Phys. Chem. B

115,4781-4789

2011

Molecular dynamics studies on mutational
structures of a nylon-6 byproductdegrading enzyme

Chem. Phys.
Lett.

507,
157-161

2011

130

Y. Nakanishi, T. Matsui,
Y. Kitagawa, Y. Shigeta,
T. Saito, Y. Kataoka, T.
Kawakami, M. Okumura andK. Yamaguchi

Electron Conductivity in Modified Modelsof Artificial Metal-DNA Using Green's
Function-Based Scattering Theory

Bull. Chem. Soc.
Japan

84,
366-375

2011

131

T. Matsui, H. Miyachi, T.
Baba and Y. Shigeta

A Theoretical Study on Reaction Schemeof Silver (I) Containing 5-Substituted
Uracils Bridge Formation

J. Phys. Chem. A

115,
8504-8511

2011

132

K. Kamiya, T. Matsui, T.
Sugimura and Y. Shigeta

Theoretical Insight into Stereoselective
Reaction Mechanisms of 2,4-PentanediolTethered Ketene-Olefin [2+2]Cycloaddition

J. Phys. Chem. A

116,1168-1175

2012

133

T. Matsui, T. Baba, K.
Kamiya and Y. Shigeta

An accurate density functional theory
based estimation of pKa value of polar
residues combined with experimental
data: from amino acids to minimal
proteins

Phys. Chem.
Chem. Phys.

12,4181-4187

2012

134

Wilfredo Credo Chung,
Shinkoh Nanbu, Toshimasa
IshidaQM/MM Trajectory Surface Hopping
Approach to Photoisomerization of
Rhodopsin and Isorhodopsin: The Origin
of Faster and More Efficient Isomerization
for Rhodopsin

J. Phys. Chem. B

116 (28),
8009–8023.

2012

135

Wilfredo Credo Chung,
Shinkoh Nanbu, Toshimasa
IshidaA Nonadiabatic Ab Initio Dynamics
Study on Rhodopsin and Its Analog
Isorhodopsin: Chemical Dynamics
Reasons behind Selection of Rhodopsin
by Life

Chemistry
Letters40,
1395-1397

2011

136

‑Wilfredo Credo Chung,Toshimasa Ishida

An MD simulation of the decoy actionof Epstein–Barr virus LMP1 protein
mimicking the CD40 interaction with
TRAF3

Theoretical
Chemistry
Accounts

130,
401-410

2011

№

Title

JournalMultistate CASPT2 Study of Native
Iron(III)-Dependent Catechol
Dioxygenase and Its Functional Models:Electronic Structure and Ligand-to-Metal
Charge-Transfer Excitation

129

T. Baba, K. Kamiya, T.
Matsui, N. Shibata, Y.
Higuchi, T. Kobayashi, S.
Negoro and Y. Shigeta

中谷

128

松井

Authors

直樹
Naoki Nakatani, Yutaka
Hitomi, and Shigeyoshi
Sakaki亨

Wilfredo Credo Chung

岩城

貴史

137

S. N. Watanabe, T. Iwaki, M.
I. Kohira, N. Magome, and K.
Yoshikawa

Negative photophoresis of smoke particles
observed under microgravity

Chem. Phys.
Lett.

511,
447-451

2011

138

Y. Higuchi, K. Yoshikawa,and T. Iwaki

Stiffness causes opposite trend on thefolding transition of a single polymer
chain in a confined space

PhysicalReview E

84,021924 (1-5)

2011－ 243 －

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Ⅴ 資料 (2011)№

義永

Authors

Title

JournalVolume(Number),first page to last
page

year

那津人

139

Shunsuke Yabunaka,
Takao Ohta, and Natsuhiko
Yoshinaga

Self-propelled motion of a fluid droplet
under chemical reaction

J. Chem. Phys.

136,074904

2012

140

Philippe Marcq, Natsuhiko
Yoshinaga, and Jacques Prost

Rigidity sensing explained by active
matter theory

Biophys. J.

101,
L33-L35

2011

141

Hiroyuki Kitahata, Natsuhiko
Yoshinaga, Ken H. Nagai,
and Yutaka Sumino

Spontaneous motion of a droplet coupledwith a chemical wave

Phys. Rev.
E Rapid
Communications

84,
015101

2011

嶺澤

範行

142

Noriyuki Minezawa andMark S Gordon

Photoisomerization of Stilbene: A SpinFlip Density Functional Theory ApproachJ. Phys. Chem. A

115(27),7901-7911

2011

143

Albert DeFusco, Noriyuki
Minezawa, Lyudmila
V Slipchenko, Federico
Zahariev, and Mark S Gordon

Modeling Solvent Effects on Electronic
Excited States

J. Phys. Chem.
Lett.

2(17),
2184-2192

2011

Kunkun Guo
144

Kunkun Guo, Wenjia Xiao,
and Dong Qiu

Polymerization of actin filaments coupledwith adenosine triphosphate hydrolysis:
Brownian dynamics and theoreticalanalysisJ. Chem. Phys.

135(10),105101(1)105101(6)

2011

145

Kunkun Guo, Jianfeng Li

Exploration of the shapes of doublewalled vesicles with a confined inner
membrane

J. Phys.:Condens. Matter

23,
285103 (12pp)

2011

河津

励

146

Tsutomu Kawatsu, and Junya Hasegawa

Excitation energy transfer in GFP-X-CFP
model peptides (X = amino acids): Direct
Versus through-bridge energy transfersInt. J. QuantumChem.

publishedonline2012

147

Tsutomu Kawatsu, Junya Hasegawa, and Kenji
MatsudaBridge-mediated excitation energy
transfer pathways through protein media:
a Slater determinant-based electronic
coupling calculation combined withlocalized molecular orbitals

J. Phys. Chem. A

115(39), 1081410822

2011

148

Jun-ya Hasegawa, Tsutomu
Kawatsu, Kazuo Toyota, andKenji Matsuda

Chemical-intuition based LMO
transformation simplifies excited-state
wave functions of peptides

Chem. Phys.
Lett.

508, 171-176

2011－ 244 －

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Ⅴ 資料 (2011)－ 245 －

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Ⅴ 資料 (2011)

Fukui International Symposium for
Theoretical Chemistry (FISTC)
Place:

Fukui Institute for Fundamental Chemistry, Kyoto University

Schedule:

Wednesday, August 31, 1300: opening, lectures and banquet
Thursday, September 1, 2011, 900: lectures; 1700: closing
Banquet: Aug. 31 PM 7:00-9:00

Organizers: Keiji Morokuma and Shigeyoshi Sakaki
Fukui Institute for Fundamental Chemistry of Kyoto University is planning to organize
International Symposium for Theoretical and Computational Chemistry for August 31 to September
1, 2011 at Kyoto. Fukui Institute was built by late Professor Kenichi Fukui at 1985 after he retired
from Kyoto University to continue his research with young colleagues. After he has passed away,
the Institute has become a part of Kyoto University.
In this symposium, we would like to invite excellent theoretical and computational chemists
from abroad and Japan including young researchers, to provide high quality lectures about new
methods, new targets for molecular science and new theoretical and computational results, and todeepen contact and enhance cooperative works between Japan and other countries. In this small
symposium we hope to provide ample time for open and personal discussion. Another important
purpose is to encourage excellent young theoretical and computational chemists. They are
performing excellent works but they do not have many chances to present their oral talks ininternational conferences. In this symposium, we will provide such opportunities to young researchers.
We hope that many people join to this international symposium at Fukui Institute for
Fundamental Chemistry. We believe that you will have good chances to listen excellent talks andto enjoy direct discussion with excellent speakers.

Speakers (Alphabetical)
Marcus Elstner (Karlsruhe)
Gernot Frenking (Marburg)
Jurgen Gauss (Mainz)
Jyunya Hasegawa (Kyoto)
Shigehiko Hayashi (Kyoto)
So Hirata (Illinois)
Toshimasa Ishida (Kyoto)－ 246 －

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Ⅴ 資料 (2011)

Kwang S. Kim (Pohan)
Kazuo Kitaura (Kyoto)
Shuhua Li (Nanjing)
Satoshi Maeda (Kyoto)
Masayoshi Nakano (Toyonaka)
Yoshihide Nakao (Kyoto)
Josef Noga (Blatislaba)
Yu-ki Ohtsuka (Okazaki-Kobe)
Kiyoshi Yagi (Osaka)
Shusuke Yamanaka (Toyonaka)
Koichi Yamashita (Tokyo)
Kazunari Yoshizawa (Fukuoka)

Program (temporary)
Wednesday, August 3
13:00-13:10

Opening

13:10-13:40

Koichi Yamashita(Tokyo)

13:40-14:20

Kwang S. Kim(Pohan)

14:20-15:00			
15:00-15:20

Masayoshi Nakano(Toyonaka)

15:20-16:00

Josef Noga(Bulatislava)

16:00-16:40

Kiyoshi Yagi(Osaka)

16:40-17:00

Break

17:00-17:20

Toshimasa Ishida(Kyoto)

17:20-17:40

Shusuke Yamanaka, Keita Kanda,		Toru Saito,Yasutaka Kitagawa,		

Takashi Kawakami,Masahiro Ehara,		Mitsutaka Okumura,Haruki Nakamura,		Kizashi Yamaguchi(Toyonaka)

17:40-18:00

Yuhki Ohtsuka, Seiichiro Ten-no,		Shigeru Nagase(Okazaki-Kobe)

18:00-18:20

Satoshi Maeda(Kyoto)

18:20-18:40

Yoshihide Nakao(Kyoto)

19:00-21:00			

Thursday, September 1
9:00-9:40

Kazunari Yoshizawa(Fukuoka)

9:40-10:20

Gernot Frenking(Marburg)－ 247 －

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Ⅴ 資料 (2011)

10:20-10:40

Break

10:20-11:00

Shigehiko Hayashi (Kyoto)

11:00-11:40

Marcus Elstner(Karlsruhe)

11:40-12:20

Junya Hasegawa(Kyoto)

12:20-14:00

Lunch

14:00-14:40

Kazuo Kitaura (Kyoto)

14:40-15:20

Shuhua Li(Nangin)

15:20-15:40

Break

15:40-16:20

Jurgen Gauss(Mainz)

16:20-17:00

So Hirata(Illinois)

17:00-17:10			

Registration
Please send e-mail to the office of Fukui Institute with the information described below:
Your Name:
Affiliation(Company/Intitute/University):
Address:
E-mail Address:
Banquet (¥5,000): Yes or No(The payment will be accepted at the conference desk)
Send the above information to; higashida@adm.t.kyoto-u.ac.jp－ 248 －

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Ⅴ 資料 (2011)－ 249 －

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Ⅴ 資料 (2011)－ 250 －

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Ⅴ 資料 (2011)－ 251 －

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Ⅴ 資料 (2011)

第 9回

京
都
大
学

10:00−10:45［榊司会榊］榊田中榊榊義榊榊榊榊榊榊榊榊榊榊榊榊榊榊副榊榊榊榊長榊［榊開式の辞榊］
榊田中榊功
榊榊榊榊榊榊榊榊榊榊榊榊榊長榊［榊挨拶榊］
榊江﨑榊信芳榊京都大学榊理事・副学長榊小森榊悟
榊京都大学榊工学榊榊科長榊
テ榊プカット
ご見学
講演会（3階大会議室）［榊司会榊］榊太田榊隆夫榊榊榊榊榊榊榊榊榊榊榊榊榊榊副榊榊榊榊長榊

玉尾 皓平（理化学研究所 基幹研究所 所長）「深化・拡大を続ける有機元素化学：実験と理論の連携の舞台」11:00−12:00− 昼食 −［榊司会榊］榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊榊

諸熊 奎治（福井謙一記念研究センター リサーチリーダー）「化学反応の理論研究 : フロンティア理論から現在，未来へ」 13:30−14:15
平尾 公彦（理化学研究所 計算科学研究機構 機構長）
「コンピュータと福井先生」

14:15−15:00− コーヒーブレイク −15:30−17:20

ポスターセッション（3 階大会議室）

17:30−19:00

懇親会（1階多目的ルーム）

平成24年

1月6日

会場：京都大学 福井謙一記念研究センター
京都大学福井謙一記念研究センター〒606-8103 京都市左京区高野西開町34-4
問合せ先：長谷川榊淳也榊／榊E-mail : hasegawa@fukui.kyoto-u.ac.jp
事務室榊／榊Tel : 075-711-7708
Fax : 075-781-4757

Tel : 075-711-7867

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1. Ab initio MO ÜBňĮıŕh¥Rď:ċą#©ÊtGQ¾pĐâŗĎHďCÌfŘĝ īahĭëUĭaÉuĭÀíĭĆÀæºĭćēÁĝ

2. CAM-B3LYP ďĕėĭęŏŕŐĞĴœÂIĐ!ÉĞĺŐģŕÀªŗĎHďCÌfŘĝ ĬMćĝ ¡ĭĆÀĝ æºĭćĝ ēÁĭY@ĝ /ĝ

3. PCM ď:ċąÊtÀª^ĐâŗĎHďCÌf[1]ĭĎHď½[2]Ř Ĭ [1]ĭĆÀ æº[1]ĭ P2[2]ĭć ēÁ[1] ĒH[1]ĭMć ¡[1]ĭa

h[1]ř

4. Comparative Study of Diradical Characters and Third-Order Nonlinear Optical
Properties of Linear/Cyclic Acenes versus Phenylenes(Osaka Univ.) ĬShabbir Muhammad, Takuya Minami, Hitoshi Fukui, Kyohei Yoneda, Shu Minamide,
Ryohei Kishi, Yasuteru Shigeta, Masayoshi Nakano

5. lÕ$áËç»zjãCGQ~äfď:ċąéH£ π TB«ĐèBÖ¤YĎ©ÊtďĊāČĐÄ§ĞĎHďCÌfğĝīë

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hĭĆÀæºĭćēÁĝ

6. Broken-Symmetry TDDFT ÜBňĮıŕh¥Rďĕėâ{ÛëB«Đ°S0+Į
ŅĤĶŐĐÄ§ŗĎHďCÌfŘĝ īaÉuĭahĭÀíĭĆÀæºĭćēÁĝ

7. ęœĲķĳĶuÑĘmĈė3½SĥŎłĝœĸĻłőŕĤĐâ{YĎ©ÊtďäĈėÄ§ŗHĎHQHQďCÌfQËÔÒŘĝ īÝÀhĭĝ a hĭĆÀæºĭćēÁĝhĭçĭ."Ñĭëåĭ_ÀHsĭ_ä

8. Polyacene Ăĕđ Dicyclopenta-fused acene ďĂĆėâ{Yŕ·îiYŕé°SDYĐäĐ§ŗĎHďCÌf[1]ĭFacultés Universitaires Notre-Dame de la Paix[2]Ř īç[1]ĭÝÀ
Raphaël Carion[2], Benoît Champagne[2]ĭćēÁ[1]h[1]ĭ

9. ŅœıįœŘC60 êĐè¸¤#!É[ďHĈėÂètĐ"qŗĎHďCÌfĭUniversité de BordeauxŘ Ĭ.|ĭCastet FrédéricĭëåĭćēÁ
-2－ 254 －05 shiryo.indd 254

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Ⅴ 資料 (2011)10. ŅœıőĻĭęįœĐâ{YďäĈėÄ§ŗĎHďCÌfŘ Ĭëĝ åĭ.ĝ |ĭaĝhĭĆÀĝ æºĭćĝ ēÁ

11. ÄĎEïďĕėİĶőœÂIĐé°SDYďĊāČĐ§ñ(ĎHďCÌfŝ1Şĭ¿áËŏňĵľļĲņőĶŖŝ2Şĭ=Õx'HR,RÞŝ3Ş) Ĭ."Ñŝ1ŞĭċÀû3ŝ2ŞĭIÀ³ ŝ2ŞĭÝÀ hŝ1Şĭa hŝ1ŞĭĆÀæºŝ1ŞĭćēÁŝ1ŞĭWU Tsun-Chengŝ3ŞĭWU Yao-Tingŝ3Şĭ§H­ăŝ1Şĭ¶¨Öpŝ1ŞĭyĄãŝ1Ş

12. sÖ¤ÝLàĐĭŎĭġŐYďHĈėØB"qĐÄ§ñ(ĎHďCÌf) ĬĒHĭ_ÀHsĭÐ

13. y Ni >sàĐ

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IYŗĎHď½[1]ĭĎHďCÌf[2]Ř Ĭ-¬oĐ[1]ĭ[1]ĭĆÀæº[2]ĭTÀKąâ[1]ĭ
ÂŔSV[1]ĭeøú[1]ĭ _Ñ[1]ĭ MĐ[1]14. Self-diffusion in crystalline silicon: A Car-Parrinello molecular dynamics study(Hďf[1]ĭIPCMS[2]ĭĎHCÌf[3]) Ĭ\®[1]ĭMauro Boero[2]ĭĆÀæº[3]ĭ{_µ[1]15. First-layer initial oxidation process of a Si(100) surface: A Car-Parrinello molecular dynamics
investigation of the atomic-scale mechanism(Hďf[1]ĭIPCMS[2]ĭĎHCÌf[3]) Ĭ\®[1]ĭMauro Boero[2]ĭĆÀæº[3]ĭ{_µ[1]16. Ä§ď:ċąĸěŒœĠŏĩňŕ¾Ù¬ďHĈėęŉĻÚ"qďĊāČĐ§( nÈÕHď¾6[1]ĭÙ¯Hď½[2]ĭĎHď½[3]ĭ nÈÕHQďfQ[4]ĭĎHďCÌf
[5]) ĬėF%2[1]ĭÏö[2]ĭ[3]ĭò3[4]ĭĆÀæº[5]17. ħŐĐ¦Í¤ďĂĆė(Đ"qH½) ĬÎþĭê¥

18. ďĂĆėłĝĻŕŐÂIĐèBŔńŒĶœ¤#*W(

Hď½) ĬÓA°ĭ_¥s

19. P8; QM/MM ÀªďĂĆėè¸Î(Đ2ìĘ¾ĈėÀª^ĐâHď½) ĬĀ ³2ĭ_ ¥s

20. @Y α-Amylase ĐÙ¬Yď)ēĈuÑcĖĄĐTďäĈėÄ§(Hď½) Ĭ\ĝ ø±ĭĝ Ćq

21. >ÛtBĘ/Ĕ RESP Ęāĉ QM/MM ´ĞĺŐģŕÀª
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22. Theoretical Analysis of Chalcone Isomerase Catalyzed Reaction(

Hď½[1]ĭ#OÒQËÔz[2]) Ĭ:Àĝ ě[1]ĭĝ ēH[2]ĭĝ Ćq[1]ĭ(ëĝ Ć¡[1]-3－ 255 －05 shiryo.indd 255

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Ⅴ 資料 (2011)

23. MS-CASPT2 ĘWćĉŁŏĭœĐÊðÐ±1Ó¥ĐÄ§(Hďŕ½[1]ĭļľœŉĳŖńH[2]) Ĭć+/[1]ĭ[2]ĭĆq[1]ĭ(ëĆ¡[1]

24. ®kįőœĐè¸¤#ĎĽœķuÑ: Pê DFT čĐ Charge Decomposition(Hŕď) Ĭ¤!

25. Atoms-in-Molecules Analysis of Dipole Moment Enhancement in Hydrogen-Bonded
Molecular Crystal 5-Bromo-9-hydroxyphenalenoneŗH½Ř ĬH·H¡ĭTëä3

26. Thermally Induced Synthesis and Properties of Low-Bandgap Conjugated Polymers
Containing Isothianaphthene Dimer SubunitsŗąHQHQďfQËÔÒŘ Ĭl¹hĭ_7ĭć9/ĭ\ćĭD/

27. ĴőĦŏĳĤ
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28. Reentrant Volume Phase Transition of Cross-linked Poly(N-isopropylacrylamide) Gels
in Mixed Hydrogen-Bonding Solvents(Kyoto Univ.) ĬHiroyuki Kojima, Tsuyoshi Koga, and Fumihiko Tanaka

29. }¬®-ÊB«ďĂĆėőĠŒĭŕĐBxu(ąHQHQďĝ fQËÔÒĝ Ę#O,Q[) ĬĘ¢ĝ PIă

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32. Palladium-Catalyzed Asymmetric Reactions Using Polymer-Based Chiral Phosphine
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Ⅴ 資料 (2011)

36. VÜ¬ļěķŒĢĬęľıěĶĐ X °0+ĮŅĤĶŐĐ©'Àª( Hďf[1]ĭHĎmÕHďf[2]ĭ5Hďf[3]) ĬÀĝ Ñ[1]ĭñĝ g[1]ĭÀĝ '[1]ĭ
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Hf[1]ř5Hf[2]Ř Ĭĝ ¤p[1]ř©ĝ s[2]řÀĝ '[1]38. 2D lattice liquid models - 2 y³Đv9(Hf) ĬÊĝ sĘĭbĝ Đ³ĭö0ĝ øsĭ_ĝ Ĉ

39. (ÌÔĘāĉBÌÔĐJ7$ŚőĲĸŕŐ¹ÈĐ!É[ĒĐW(HÐĽ[1]ĭÏyHwE[2]) ĬČöeµ[1]ĭë7U[2]ĭ¬²)[1]

40. GFP-X-CFP ŋĵŐŅńĲķďĂĆėęŉĻÚ­!ÉĞĺŐģŕ¤#(HÐ

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41. ©'B#DďĕėĪŕŋĤŒŉĳĤß(II)àďäĈėÄ§
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Hďf[2]) Ĭ] ;Ñ[1]ĭ× í:Ē[2]ĭë 8[2]42. A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and its Analog Isorhodopsin(HÐĽ[1]ĭH½f[2]) Wilfredo C. Chung[1]ĭ.Ąĝ P[2]ĭĬÊÀĝ ¤[1]

43. Ö¤ÝLÚ$ďĂĆė X °(HÐ

44. őŕīŕ
(HÐ|¶YĐ©'ÀªĽ) Ĭ«ć ÷ďĕėňŎœĩĹ"qĐfĬŉŌőŕĬōœĽ) Ĭ`Bĝ ø2

45. SFDFT ďĕė GFP ¶5ĐÄ§
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HÐ

ĽœľŖ) Ĭd¸ÛìNÂÉ*WďĕėmxÝL¿A*WxuĐ´#¾pĎ( HÃÇĽœľŖ[1]ĭ HÐ ôËÔĽ[2]ĭĲŎŐ―H,Q[3])Ĭ$Àĝ ½[1,2]ĭ ó»ĝ L­[2,3]47. Multireference theoretical study of the photodissociation dynamics of keteneŗHÐĽŘ ĬHongyan Xiao, Satoshi Maeda, Keiji Morokuma

48. Catalytic Mechanism in Artificial Metalloenzyme: QM/MM Study of Phenylacetylene
Polymerization by Rhodium Complex Encapsulated in apo-Ferritin(FIFC, Kyoto University[1], iCeMS, Kyoto University, [2]) ĬZhuofeng Ke[1], Satoshi Abe[2],Takafumi Ueno[2], and Keiji Morokuma[1]-5－ 257 －05 shiryo.indd 257

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Ⅴ 資料 (2011)

49. The Dynamics of Local Chirality during SWCNT Growth: A QM/MD Investigation(Fukui Institute for Fundamental Chemistry[1], Department of Chemistry, Graduate School of Science,
Nagoya University[2], Cherry L. Emerson Center for Scientific Computation and Department ofChemistry, Emory University[3]) ĬJoonghan Kim[1], Alister J. Page[1], Stephan Irle[2], and Keiji
Morokuma[1,3]50. Theoretical study on the reduction of nitric oxide in bacterial nitric oxide reductase(FIFC[1], Emory Univ.[2]) ○Miho Hatanaka[1], Keiji Morokuma[1,2]

51. Photochemistry and Photophysics behind Light-Driven Molecular Rotary Motor(FIFC, Kyoto Univ.) ĬFengyi Liu, Keiji Morokuma
52. Comparative Reactivity of Ferric-Superoxo and Ferryl-Oxo Species in Heme and
Non-Heme Complexes(FIFC) ĬLung Wa Chung, Xin Li and Keiji Morokuma

53. Chirality-controlled SWCNT growth from hydrocarbon templates(FIFC) ĬHai-Bei Li, Alister J. Page, Stephan Irle, and Morokuma Keiji

54. Chirality Controlled SWCNT Growth from an Organic Template: The Role of the C2HRadical(FIFC) ĬAlister J. Page, Haibei Li, Stephan Irle, Keiji Morokuma

55. Theoretical study on the photoisomerization of Mononuclear Ruthenium(II) Monoaquo
Complex(FIFC) ĬLina Ding, Lung Wa Chung, Keiji Morokuma

56. Towards understanding the HppE catalytic mechanism: theoretical modeling offosfomycin biosynthesis(FIFC) ĬGalina Petrova, Lung Wa Chung, Keiji Morokuma

57. ÝL-ŃőĠňěĬœĐ DNA dxuďäĈėÄ§
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59. PêřØ9ÝLàĎ}ĐĐÄ§ŗHÐĽŘ ĬĔć ­ĭ éN

60. ÝLØí1ĪěĶĒĐ|B0ďäĈėÄ§ŗHÐôËÔĽŘĝ Ĭ>ĝ ĭĝ éN-6－ 258 －05 shiryo.indd 258

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Ⅴ 資料 (2011)

61. Theoretical study of Absorption of CO2, CS2 and OCS into Hoffman type Metal Organic
Framework: Binding Energy Evaluation, Absorption Position and Understanding of
Determining Factors(FIFC [1], Grad. School of Sciences, Kyushu Univ.[2], Grad. School. of Eng. Kyoto Univ.[3])ĬMilind Deshmukh [1], Masaaki Ohba [2], Kitagawa sususmi [3], Shigeyoshi Sakaki [1]62. ĤŒŊ(I))đÞ(I)-¨¬BĐÏĪœķěĳĲ9àĐèBuÑďäĈėÄ§(HÐôËÔĽœľŖ[1]ĭQCRI[2]) ĬA ē[1]ĭĚe và[2]ĭ éN[1]63. }¬rwćĉŀĮŖĬŏőœŗıœĥĮĴœàĐ#`#ďäĈėÄ§( HÐ Ľ[1]ĭ-Hď½[2]) ĬĘ[1]ĭ\Àv[2]ĭ¢O[2]ĭĕÀ/W[2]ĭ
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Ⅴ 資料 (2011)

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Ⅴ 資料 (2011)

第9回
福井センターセ��ーThe 9th FIFC Seminar
2012年3月16日(金)14:00-17:00

京都大学福井謙一記念研究センター 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,, KyotoyUniv. on March,, 16(Fri.),( ), 2012))

14:00～15:00 Shinkoh NANBU (Sophia Univ., Tokyo)“Nonadiabatic
Nonadiabatic dynamics in photochemical processes
processes"

15:00～15:30 Yoshihide NAKAO (FIFC)“Theoretical Study of Physical Properties in First-Row
Transition Metal Complexes”
C”
Coffee break

16:00～17:00 Shoji TAKADA (Kyoto Univ.)“Coarse-grained molecular simulations of large
biomolecules: From theory to applications”
多数の方のご来場を歓迎いたします
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理系インスパイアー講義�����年������
畑中フェローが、北摂三田高校にて開催された「理系インスパイアー講義」に出講し、分子科学シミュレーションの面白さを伝えました。クイズを交えた楽しい講義が行われました。
科学技術フェスタin Kyoto 2011 ���2�年12�1��1���
榊リサーチリーダーが、国立京都国際会館にて開催された「科学技術フェスタ in Kyoto 2011」に出展しました。コンピュータを使う化学の研究について、特に、金属などに現れるｄ電子、ｄ軌道の面白さを伝えました。

京都大学アカデミックデイ �����年������
諸熊リサーチリーダーが、「京都大学アカデミックデイ」に出展し、理論化学のおもしろさを伝えました。

ウォークイン サイエンス �����年���������
諸熊グループのオフィスアシスタントの三木さん、堀さん、延山さんが、理学研究科・社会交流室が主催する「ウォークイン サイエンス」に出展し、 Zest御池 河原町広場にて理論化学のデモンストレーションをしました。

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京都大学福井謙一記念研究センター

年報

2011

2012 年 12 月発行
発行人

田 中 一 義編

石 田 俊 正者

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

株式会社 エヌジーピー（京都市右京区太秦森ヶ東町 21-10）（無断転載を禁ず）

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