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南部 伸孝

ナンブ シンコウ  (Nambu Shinkoh)

基本情報

所属
上智大学 理工学部物質生命理工学科 教授
学位
博士（理学）(慶應義塾大学)
連絡先
shinkoh.nanbusophia.ac.jp
通称等の別名
Shinkoh NANBU
研究者番号
00249955
J-GLOBAL ID
200901062366264730
researchmap会員ID
1000144738

1988年4月-1994年3月
慶應義塾大学理工学部化学科，岩田末廣教授の指導のもと，電子励起状態の研究とともに核の運動に関する理論的研究を実施。
1994年4月-1997年3月
分子研理論研究系分子基礎理論第二，中村宏樹教授および，カナダのWaterloo大学，F. O. Goodman教授とともに共同研究を行い，非断熱遷移に特有な現象を利用した分子スイッチの可能性について提案。
1995年9月-2002年3月
計算科学研究センター，青柳睦前助教授（現在は，九州大学　情報基盤センター教授）とともに分子の高振動励起状態の研究を実施。
1999年6月-1999年12月
米国イリノイ州アルゴンヌ国立研究所にて訪問研究員として従事し，理論化学部門Stephen K. Gray教授のもと，多原子分子への応用が可能である遷移状態波束動力学計算の開発を実施。
1994年4月-現在
素反応過程の研究を中心に電子励起状態と反応動力学の研究を実施。特に，多自由度系への新展開を目指しプログラム開発を実施。一方，スーパーコンピュータの能力を活用し，機能分子，タンパク質の機能及び生理活性分子の探索を実施。

2015年-2016年　上智大学大学院　理工学研究科　理工学専攻　化学領域主任
2012年-2013年　上智大学大学院　学務委員会委員（理工委員）
2010年-2012年　上智大学大学院　理工学研究科　理工学専攻　化学領域主任
2012年 　上智大学　理工学部　推進委員
2012年-　上智大学　地球環境研究所員

(研究テーマ)
非断熱現象を利用した物質の機能発現と反応制御
分子高次系機能解明のための分子科学　－先端計測法の開拓による素過程的理解
光に応答する生体分子の非断熱動力学シミュレーション
温暖化関連ガス循環解析のアイソトポマーによる高精度化の研究（サブテーマ）理論計算によるアイソトポマー分別係数の決定
生体調整ペプチドの科学的基盤構築
アイソトポマーの計測・解析技術開発による物質循環解析
Photo-chemical reaction in condensed phase
生体分子の構造と光応答の相関に対する非断熱遷移動力学法によるアプローチ

(共同・受託研究希望テーマ)
フォトクロミック現象の理論的解明と応用

研究キーワード

 11

研究分野

 3

経歴

 4

学歴

 3

受賞

 2

論文

 134
  • Yuanzhe Li, Sebastian Oscar Danielache, Yoshiaki Endo, shinkoh Nanbu, Yuichiro Ueno
    2024年3月25日  査読有り
    <p id="p1">High-resolution and high-precision spectrum data presents a challengingmeasurement. We report newly measured ultraviolet absorptioncross-sections of 32SO2, 33SO2, 34SO2, and 36SO2 for the - band over thewavelength range 240 to 320 nm at a resolution of 0.4 cm−1. Theresolution is improved by 20 times compared to a previous study(Danielache et al., 2012). A least absolute deviation linear regressionmethod was applied to calculate the cross-sections and spectral errorsfrom a set of measurements recorded at a wide range of pressure toensure optimal signal-to-noise ratio at all wavelengths. Based on thisanalysis, error bars on the measured cross-sections ranged between 3 and10%. The overall features of measured cross-sections, such as peakpositions of isotopologues, are consistent with previous studies. Weprovide improved spectral data for studying sulfur mass-independentfraction (S-MIF) signatures in SO2 photoexcitation. Our spectralmeasurements predict that SO2 photoexcitation produces 33E = −0.8±0.2‰and 36E = −4.0±0.4‰, whose magnitudes are smaller than those reported byDanielache et al. (2012).</p>
  • Nana Iwasa, Shinkoh Nanbu
    Chemical Physics Letters 838 141088-141088 2024年3月  査読有り責任著者
  • Karolis Sarka, Shinkoh Nanbu
    ACS Earth and Space Chemistry 7(12) 2374-2381 2023年12月11日  査読有り責任著者
  • 冬月世馬, 藤原綾香, 南部伸孝
    日本地球化学会年会要旨集 70 2023年12月1日  査読有り
  • Nozomi Tomioka, Shinkoh Nanbu, Tomoyo Misawa-Suzuki, Hirotaka Nagao
    RSC Advances 11 36644-36650 2021年11月  査読有り
  • Miho Motoyama, Thu‐Hong Doan, Paulina Hibner‐Kulicka, Ryo Otake, Malgorzata Lukarska, Jean‐Francois Lohier, Kota Ozawa, Shinkoh Nanbu, Carole Alayrac, Yumiko Suzuki, Bernhard Witulski
    Chemistry – An Asian Journal 2021年6月22日  査読有り
  • Manabu Nakazono, Shinkoh Nanbu, Takeyuki Akita, Kenji Hamase
    Journal of Oleo Science 70(11) 1677-1684 2021年  査読有り
    Methyl groups were introduced on the acridine moiety in chemiluminescent acridinium esters that have electron-withdrawing groups (trifluoromethyl, cyano, nitro, ethoxycarbonyl) at the 4-position on the phenyl ester. The introduction of methyl groups at the 2-, 2, 7-, and 2, 3, 6, 7-positions on the acridine moiety shifted the optimal pH that gave relatively strong chemiluminescence intensity from neutral conditions to alkaline conditions. 4-(Ethoxycarbonyl)phenyl 2, 3, 6, 7, 10-pentamethyl-10λ4-acridine-9- carboxylate, trifluoromethanesulfonate salt showed long-lasting chemiluminescence under alkaline conditions. Acridinium esters to determine hydrogen peroxide concentration at pH 7-10 were newly developed.
  • Manabu Nakazono, Shinkoh Nanbu, Takeyuki Akita, Kenji Hamase
    Journal of Photochemistry & Photobiology, A: Chemistry 403 112851-10 pages 2020年8月24日  査読有り
  • Tianlong Jiang, Kenta Moriwaki, Osamu Kobayashi, Kazuya Ishimura, Sebastian O. Danielache, Shinkoh Nanbu
    Journal of Computational Chemistry 41(11) 1116-1123 2020年1月26日  査読有り責任著者
  • Tomoyo Misawa-Suzuki, Takashi Watanabe, Mariko Okamura, Shinkoh Nanbu, Hirotaka Nagao
    Inorganic Chemistry 59(1) 612-622 2020年1月6日  査読有り
  • Tianlong Jiang, Tamao Saito, Shinkoh Nanbu
    Bulletin of the Chemical Society of Japan 92 1436-1443 2019年8月8日  査読有り責任著者
  • Manabu Nakazono, Shinkoh Nanbu, Takeyuki Akita, Kenji Hamase
    Dyes and Pigments 170 107628-6 pages 2019年6月12日  査読有り
  • Karolis Sarka, Shinkoh Nanbu
    The Journal of Physical Chemistry A 123 3697-3702 2019年4月10日  査読有り責任著者
  • Karolis Sarka, Sebastian O. Danielache, Alexey Kondorskiy, Shinkoh Nanbu
    Chemical Physics 516 108-115 2019年1月4日  査読有り責任著者
  • Karolis Sarka, Sebastian O. Danielache, Alexey Kondorskiy, Shinkoh Nanbu
    Chemical Physics 508 61 2018年5月31日  査読有り責任著者
    This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Authors because of a large amount of errors caused by incorrect interpretation of the potential energy curve boundaries by the data processing functions in their close-coupling algorithm, producing incorrect wavefunctions for the continuum region in the absorption spectrum. The spectrum calculated using the incorrect wavefunctions introduced periodic fluctuation in the absorption cross-section seen in the original article, which results in erroneous isotopic fractionation values. The updated spectra calculated after fixing the issues features a smooth continuum band, removing all false artifacts from isotopic effect analysis, producing significantly different results from the ones in this original article. The authors will submit the corrected data in a new article.
  • Manabu Nakazono, Shinkoh Nanbu
    Luminescence 33(2) 345-348 2018年3月1日  査読有り
    Enhancement effect on the chemiluminescence of acridinium ester derivatives under neutral conditions was investigated. Additions of phenols did not enhance the chemiluminescence intensities of acridinium ester derivatives in the presence of horseradish peroxidase and hydrogen peroxide. Additions of cetyltrimethylammonium bromide apparently enhanced the chemiluminescence intensities of phenyl 10-methyl-10λ4-acridine-9-carboxylate derivatives with electron-withdrawing groups at the 4-position of the phenyl group. In particular, the chemiluminescence intensity of 4-(trifluoromethyl)phenyl 10-methyl-10λ4-acridine-9-carboxylate trifluoromethanesulfonate salt was 5.5 times stronger in the presence of cetyltrimethylammonium bromide than in its absence at pH 7. The chemiluminescence intensity of 3,4-dicyano-phenyl 10-methyl-10λ4-acridine-9-carboxylate trifluoromethanesulfonate salt was 46 times stronger in the presence of cetyltrimethylammonium bromide at pH 7 than in its absence at pH 10.
  • Yuka Sumoge, Shinkoh Nanbu, Hirotaka Nagao
    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY 23(23) 2998-3007 2017年6月  査読有り
    The reactions of azide ions coordinated to ruthenium(II) centers bearing two 2,2-bipyridine (bpy) ligands, that is, [Ru-II(N-3)(2)(bpy)(2)] (1), [Ru-II(N-3)(NH=CHR1)(bpy)(2)](+) (2; R-1 = CH3, C2H5), and [Ru-II(N-3)(NCCH3)(bpy)(2)](+) (3), with haloalkanes (CRRRX)-R-1-R-2-X-3 (R-1 = H, CH3, C2H5, R-2 = H, CH3, R-3 = H, CH3, X = I, Br) afforded imine (NH=(CRR2)-R-1) and ammine (NH3) ligands with dinitrogen evolution. The formation of these nitrogen-containing moieties depended on both the reaction solvent and the alkyl group of the haloalkane. Four types of imine complexes, [(RuL)-L-II(NH=(CRR2)-R-1)(bpy)(2)](n+) [L = N-3(-) (2), I- (4), NH=CHR1 (5), and CH3CN (6)], were synthesized and characterized. The oxidation reactions of the imine complexes 5 and 6 followed by electron- and proton-transfer reactions to give nitrile complexes were studied by electrochemical measurements. These results revealed new strategies for the synthesis of N-C bonds and nitrogen-containing compounds through the reactions of azido and related ligands.
  • Karolis Sarka, Sebastian O. Danielache, Alexey Kondorskiy, Shinkoh Nanbu
    CHEMICAL PHYSICS 488 36-42 2017年5月  査読有り責任著者
    The electronic structures of triplet S-2 ground and excited states are studied by ab initio molecular orbital and configuration interaction calculation. Potential energy curves correlated with S(P-3) + S(P-3) and S(P-3) + S(D-1) at the dissociation limit are evaluated, and electronic terms for a total of 11 states are assigned. Transition dipole moments, as a function of internuclear distance, are determined for two allowed transitions to 1(3) IIu and 1(3)Sigma(-)(u) excited states. Furthermore, the total absorption cross-sections are computed to estimate isotope-fractionation constants, epsilon, for four most common isotopologues: (SS)-S-32-S-32, (SS)-S-32-S-33, (SS)-S-32-S-34, and (SS)-S-32-S-36 by quantum close-coupling (R-matrix) expansion approach. Zero-point energy based constants epsilon(ZPE) are estimated as well to compare with the obtained isotope effects. Three-isotope plots are shown to express mass-independent fractionation effect; large isotopic effects were found on 365 and S-33 in 230-240 nm range, and only on S-36 in 240-267 nm range. (C) 2017 Elsevier B.V. All rights reserved.
  • Ayumi Ohta, Osamu Kobayashi, Sebastian O. Danielache, Shinkoh Nanbu
    CHEMICAL PHYSICS 485 45-59 2017年3月  査読有り責任著者
    The ultra-fast photoisomerization reactions between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) in both hexane and ethanol solvents were revealed by nonadiabatic ab initio molecular dynamics (AI-MD) with a particle-mesh Ewald summation method and our Own N-layered Integrated molecular Orbital and molecular Mechanics model (PME-ONIOM) scheme. Zhu-Nakamura version trajectory surface hopping method (ZN-TSH) was employed to treat the ultra-fast nonadiabatic decaying process. The results for hexane and ethanol simulations reasonably agree with experimental data. The high nonpolar-nonpolar affinity between CHD and the solvent was observed in hexane solvent, which definitely affected the excited state lifetimes, the product branching ratio of CHD:HT, and solute (CHD) dynamics. In ethanol solvent, however, the CHD solute was isomerized in the solvent cage caused by the first solvation shell. The photochemical dynamics in ethanol solvent results in the similar property to the process appeared in vacuo (isolated CHD dynamics). (C)2017 Elsevier B.V. All rights reserved.
  • Manabu Nakazono, Yuji Oshikawa, Mizuho Nakamura, Hidehiro Kubota, Shinkoh Nanbu
    JOURNAL OF ORGANIC CHEMISTRY 82(5) 2450-2461 2017年3月  査読有り
    Various novel acridinium ester derivatives having phenyl and biphenyl moieties were synthesized, and their optimal chemiluminescence conditions were investigated. Several strongly chemiluminescent acridinium esters under neutral conditions were found, and then these derivatives were used to detect hydrogen peroxide and glucose. Acridinium esters having strong electron-withdrawing groups such as cyano, methoxycarbonyl, and nitro at the 4-position of the phenyl moiety in phenyl 10-methyl-10 lambda(4)-acridine-9-carboxylate trifluoromethanesulfonate salt showed strong chemiluminescence intensities. The chemiluminescence intensity of 3,4-dicyanophenyl 10-methyl-10 lambda(4)-acridine-9-carboxylate trifluoromethanesulfonate salt was approximately 100 times stronger than that of phenyl 10-methyl-10 lambda(4)-acridine-9-carboxylate trifluoromethanesulfonate salt at pH 7. The linear calibration ranges of hydrogen peroxide and glucose were 0.05-10 mM and 10-2000 mu M using 3,4-(dimethoxycarbonyl)phenyl 10-methyl-10 lambda(4)acridine-9-carboxylate trifluoromethanesulfonate salt at pH 7 and pH 7.5, respectively. The proposed chemiluminescence reaction mechanism of acridinium ester via a dioxetanone structure was evaluated via quantum chemical calculation on density functional theory. The proposed mechanism was composed of the nucleophilic addition reaction of hydroperoxide anion, dioxetanone ring formation, and nonadiabatic transition due to spin orbit coupling around the transition state (TS) to the triplet state (T-1) following the decomposition pathway. The TS which appeared in the thermal decomposition would be a rate determining step for all three processes.
  • Tomoyo Suzuki, Yutaka Suzuki, Tatsuya Kawamoto, Ryo Miyamoto, Shinkoh Nanbu, Hirotaka Nagao
    INORGANIC CHEMISTRY 55(14) 6830-6832 2016年7月  査読有り
    Dinuclear ruthenium complexes in a mixed valence state of Ru-III-Ru-IV, having a doubly oxido-bridged and acetato(-) or nitrato-capped framework, [{Ru-III,Ru-IV ebpma)}(2)(mu-O)(2),(mu-L)](PF6)(2) [ebpma = ethylbis (2-pyridylmethyl) amine; L = CH3COO- (1), NO3- (2)1 were synthesized. In aqueous solutions, the diruthenium complex 1 showed multiple redox processes accompanied by proton transfers depending on the pH. The protonated complex of 1, which is described as was obtained.
  • Hiroki Nakamura, Shinkoh Nanbu, Yoshiaki Teranishi, Ayumi Ohta
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18(17) 11972-11985 2016年5月  査読有り
    Various quantum mechanical effects such as nonadiabatic transitions, quantum mechanical tunneling and coherence play crucial roles in a variety of chemical and biological systems. In this paper, we propose a method to incorporate tunneling effects into the molecular dynamics (MD) method, which is purely based on classical mechanics. Caustics, which define the boundary between classically allowed and forbidden regions, are detected along classical trajectories and the optimal tunneling path with minimum action is determined by starting from each appropriate caustic. The real phase associated with tunneling can also be estimated. Numerical demonstration with use of a simple collinear chemical reaction O + HCl -&gt; OH + Cl is presented in order to help the reader to well comprehend the method proposed here. Generalization to the on-the-fly ab initio version is rather straightforward. By treating the nonadiabatic transitions at conical intersections by the Zhu-Nakamura theory, new semiclassical MD methods can be developed.
  • Hiroki Nakamura, Shinkoh Nanbu, Yoshiaki Teranishi, Ayumi Ohta
    Physical Chemistry Chemical Physics 18 11972-11985 2016年3月21日  査読有り
  • Osamu Kobayashi, Shinkoh Nanbu
    CHEMICAL PHYSICS 461 47-57 2015年11月  査読有り
    We extended a particle mesh Ewald (PME) summation method to the ONIOM (our Own N-layered Integrated molecular Orbitals and molecular Mechanics) scheme (PME-ONIOM) to validate the simulation in solution. This took the form of a nonadiabatic ab initio molecular dynamics (MD) simulation in which the Zhu-Nakamura trajectory surface hopping (ZN-TSH) method was performed for the photoisomerization of a (Z)-penta-2,4-dieniminium cation (protonated Schiff base, PSB3) electronically excited to the S-1 state in a methanol solution. We also calculated a nonadiabatic ab initio MD simulation with only minimum image convention (MI-ONIOM). The lifetime determined by PME-ONIOM-MD was 3.483 ps. The MI-ONIOM-MD lifetime of 0.4642 ps was much shorter than those of PME-ONIOM-MD and the experimentally determined excited state lifetime. The difference eminently illustrated the accurate treatment of the long-range solvation effect, which destines the electronically excited PSB3 for staying in S-1 at the pico-second or the femto-second time scale. (C) 2015 Elsevier B.V. All rights reserved.
  • Alexey D. Kondorskiy, Shinkoh Nanbu
    The Journal of Chemical Physics 143 114103-16 pages 2015年9月16日  査読有り
  • Alexey D. Kondorskiy, Shinkoh Nanbu
    JOURNAL OF CHEMICAL PHYSICS 143(11) 2015年9月  査読有り
    We present an approach, which allows to employ the adiabatic wave packet propagation technique and semiclassical theory to treat the nonadiabatic processes by using trajectory hopping. The approach developed generates a bunch of hopping trajectories and gives all additional information to incorporate the effect of nonadiabatic coupling into the wave packet dynamics. This provides an interface between a general adiabatic frozen Gaussian wave packet propagation method and the trajectory surface hopping technique. The basic idea suggested in [A. D. Kondorskiy and H. Nakamura, J. Chem. Phys. 120, 8937 (2004)] is revisited and complemented in the present work by the elaboration of efficient numerical algorithms. We combine our approach with the adiabatic Herman-Kluk frozen Gaussian approximation. The efficiency and accuracy of the resulting method is demonstrated by applying it to popular benchmark model systems including three Tully's models and 24D model of pyrazine. It is shown that photoabsorption spectrum is successfully reproduced by using a few hundreds of trajectories. We employ the compact finite difference Hessian update scheme to consider feasibility of the ab initio "on-the-fly" simulations. It is found that this technique allows us to obtain the reliable final results using several Hessian matrix calculations per trajectory. (C) 2015 AIP Publishing LLC.
  • Ayumi Ohta, Osamu Kobayashi, Sebastian O. Danielache, Shinkoh Nanbu
    CHEMICAL PHYSICS 459 45-53 2015年9月  査読有り
    The photoisomerization process between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) has been studied by nonadiabatic ab initio molecular dynamics based on trajectory surface-hopping approach with a full-dimensional reaction model. The quantum chemical calculations were treated at MS-MR-CASPT2 level for 8 electrons in 8 orbitals with the cc-pVDZ basis set. The Zhu-Nakamura formula was employed to evaluate nonadiabatic transition probabilities. S-1 and S-2 states were included in the photoisomerization dynamics. Lifetimes and CHD: HT branching ratios were computationally estimated on the basis of statistical analysis of multiple executed trajectories. The analysis of trajectories suggested that the nonadiabatic transitions at the S-0/S-1 and S-1/S-2 conical intersections (CoIn) are correlated to the Kekule-type vibration and the C3-C4-C5 bending motion, respectively. The one-sided branching ratio was obtained by excitations to the S-2 state; 70:30. The critical branching process was found to be dominated by the location of CoIn in potential energy hypersurface of the excited state. (C) 2015 Elsevier B.V. All rights reserved.
  • Tomoko Akama, Osamu Kobayashi, Shinkoh Nanbu
    The Journal of Chemical Physics 142 204104-6 pages 2015年5月27日  査読有り
  • Tomoko Akama, Osamu Kobayashi, Shinkoh Nanbu
    JOURNAL OF CHEMICAL PHYSICS 142(20) 2015年5月  査読有り
    The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrdinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function. Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost. (C) 2015 AIP Publishing LLC.
  • Tatsuhiro Murakami, Ayumi Ohta, Tomoya Suzuki, Kumiko Ikeda, Sebastian O. Danielache, Shinkoh Nanbu
    CHEMICAL PHYSICS 452 17-24 2015年5月  査読有り
    Photodissociation dynamics of sulfuric acid after excitation to the first and second excited states (S-1 and S-2) were studied by an on-the-fly ab initio molecular dynamics simulations based on the Zhu-Nakamura version of the trajectory surface hopping (ZN-TSH). Forces acting on the nuclear motion were computed on-the-fly by CASSCF method with Dunning's augmented cc-pVDZ basis set. It was newly found that the parent molecule dissociated into two reaction-channels (i) HSO4(1(2)A'') + H(S-2) by S-1-excitation, and (ii) HSO4(2(2)A'') + H(S-2) by S-2-excitation. The direct dissociation dynamics yield products different from the SO2 + 2OH fragments often presented in the literature. Both channels result in the same product and differs only in the electronic state of the HSO4 fragment. The trajectories running on S-2 do not hop with S-0 and a nonadiabatic transition happens at the S-2-S-1 conical intersection located at a longer OH bond-length than the S-1-S-0 intersection producing an electronic excited state (2(2)A'') of HSO4 product. (C) 2015 Elsevier B.V. All rights reserved.
  • Noriyuki Suzuki, Takao Yoshitani, Shota Inoue, Daisuke Hashizume, Hajime Yoshida, Meguru Tezuka, Keisuke Ida, Sayoko Nagashima, Teiji Chihara, Osamu Kobayashi, Shinkoh Nanbu, Yoshiro Masuyama
    ORGANOMETALLICS 33(19) 5220-5230 2014年10月  査読有り
    Zirconium complexes of some [5]cumulene derivatives were studied for their variable coordination modes and haptotropic shifts. Some [5]cumulene compounds reacted with zirconocene(II) species to afford 1-zirconacyclopent-3-yne complexes that have five-membered cycloalkyne structures. Only a few [5]cumulene compounds afforded eta(2)-coordinated complexes in the presence of neutral ligands such as trimethylphosphine and tert-butyl isocyanide. Interconversion between the five-membered structure and the eta(2)-complex was observed. Investigation of [5]cumulene derivatives of various cycloalkylidene moieties indicated that the eta(2)-complex was preferred when the [5]cumulene has bulkier substituents. A [5]cumulene with 2,2,6,6-tetramethylcyclohexylidene groups much preferred the 1-zirconacyclopent-3-yne structure to eta(2)-coordination. In sharp contrast, the eta(2)-coordinated complex was favored for a [5]cumulene with 2,2,7,7-tetramethylcycloheptylidene groups in the presence of PMe3. Small differences in steric environments caused totally different reactivity in [5]cumulene complexes. DFT calculations on the formation enthalpy were consistent with the experimental results, although that cannot fully rationalize the difference.
  • 村上 龍大, Danielache Sebastian O, 南部 伸孝
    日本地球化学会年会要旨集 61(3P17) 2014年9月  査読有り
  • Manabu Nakazono, Konen Obayashi, Yuji Oshikawa, Kazushi Tani, Genki Suenaga, Yukio Ando, Shinkoh Nanbu, Ryoichi Kuwano
    JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 289 39-46 2014年9月  査読有り
    Various unsymmetric indolylmaleimides were synthesized. Their photophysical properties and affinities for amyloid fibrils were evaluated. Some unsymmetric indolylmaleimides have large Stokes shifts of more than 120 nm, fluorescence emission maxima wavelengths of more than 550 nm and different emissions under UV irradiation at 365 nm. From the results of histopathologic methods using stains, 3-(1H-indol-3-yl)-1-methyl-4-phenyl-1H-pyrrole-2,5-dione has high selectivity for amyloid fibrils in senile systemic amyloidosis. (C) 2014 Elsevier B.V. All rights reserved.
  • 赤間知子, 佐藤紀穂, 南部伸孝
    Journal of Computer Chemistry, Japan 13(3) 184-186 2014年9月1日  査読有り
    The real-time propagation (RT) of time-dependent Hartree-Fock (TDHF) method and time-dependent density functional theory (TDDFT) have been applied to describing electron dynamics. However, RT-TDHF/TDDFT calculations are computationally demanding. We have developed and implemented RT-TDHF/TDDFT based on the three-term recurrence relation (3TRR) to accelerate time-evolution procedure. 3TRR achieved an efficient time-evolution of electron dynamics.
  • Hiroya Kano, Daichi Tanoue, Hiroaki Shimaoka, Kohei Katano, Takeshi Hashimoto, Hideyuki Kunugita, Shinkoh Nanbu, Takashi Hayashita, Kazuhiro Ema
    ANALYTICAL SCIENCES 30(6) 643-648 2014年6月  査読有り
    An inclusion complex consisting of a boronic acid fluorophore (C1-APB) and beta-cyclodextrin (beta-CyD) acts as a supramolecular sugar sensor whose response mechanism is based on photoinduced electron transfer (PET) from the excited pyrene to the boronic acid. We have investigated the PET process in C1-APB/CyD complexes by using time-resolved photoluminescence (TRPL) measurements at room temperature, and have succeeded in estimating the electron-transfer time to be about 1 ns. We have also studied the effects of CyDs on the PET process by comparing two kinds of CyDs (alpha-CyD, beta-CyD) under different water-dimethylsulfoxide (DMSO) concentration conditions. We found that the CyDs interacting with the boronic acid moiety completely inhibits PET quenching and increases the monomer fluorescence intensity.
  • Sebastian O. Danielache, Suzuki Tomoya, Alexey Kondorsky, Ikuo Tokue, Shinkoh Nanbu
    The Journal of Chemical Physics 140(4) 044319-11pages 2014年1月29日  査読有り
  • Sebastian O. Danielache, Suzuki Tomoya, Alexey Kondorsky, Ikuo Tokue, Shinkoh Nanbu
    JOURNAL OF CHEMICAL PHYSICS 140(4) 2014年1月  査読有り
    Ultraviolet absorption cross sections of the main and substituted sulfur monoxide (SO) isotopologues were calculated using R-Matrix expansion technique. Energies, transition dipole moments, and nonadiabatic coupling matrix elements were calculated at MRCI/AV6Z level. The calculated absorption cross section of (SO)-S-32-O-16 was compared with experimental spectrum; the spectral feature and the absolute value of photoabsorption cross sections are in good agreement. Our calculation predicts a long lived photoexcited SO* species which causes large non-mass dependent isotopic effects depending on the excitation energy in the ultraviolet region. (C) 2014 AIP Publishing LLC.
  • Hiroya Kano, Daichi Tanoue, Hiroaki Shimaoka, Kohei Katano, Takeshi Hashimoto, Hideyuki Kunugita, Shinkoh Nanbu, Takashi Hayashita, Kazuhiro Ema
    Analytical Sciences 30(6) 643-648 2014年  査読有り
    An inclusion complex consisting of a boronic acid fluorophore (C1-APB) and β-cyclodextrin (β-CyD) acts as a supramolecular sugar sensor whose response mechanism is based on photoinduced electron transfer (PET) from the excited pyrene to the boronic acid. We have investigated the PET process in C1-APB/CyD complexes by using time-resolved photoluminescence (TRPL) measurements at room temperature, and have succeeded in estimating the electron-transfer time to be about 1 ns. We have also studied the effects of CyDs on the PET process by comparing two kinds of CyDs (α-CyD, β-CyD) under different water-dimethyisulfoxide (DMSO) concentration conditions. We found that the CyDs interacting with the boronic acid moiety completely inhibits PET quenching and increases the monomer fluorescence intensity. © 2014 The Japan Society for Analytical Chemistry.
  • SEBASTIAN O, DANIELACHE, TOMOYA SUZUKI, SHINKOH NANBU
    MINERALOGICAL MAGAZINE 77(5) 942 2013年7月  
  • J. A. Schmidt, M. S. Johnson, S. Hattori, N. Yoshida, S. Nanbu, R. Schinke
    ATMOSPHERIC CHEMISTRY AND PHYSICS 13(3) 1511-1520 2013年  査読有り
    The isotopic fractionation in OCS photolysis is studied theoretically from first principles. UV absorption cross sections for OCS, (OCS)-S-33, (OCS)-S-34, (OCS)-S-36 and (OCS)-C-13 are calculated using the time-depedent quantum mechanical formalism and a recently developed ab-initio description of the photodissociation of OCS which takes into account the lowest four singlet and lowest four triplet electronic states. The calculated isotopic fractionations as a function of wavelength are in good agreement with recent measurements by Hattori et al. (2011) and indicate that photolysis leads to only a small enrichment of S-34 in the remaining OCS. The photodissociation dynamics provide strong evidence that the photolysis quantum yield is unity at all wavelengths for atmospheric UV excitation, for all isotopologues. A simple stratospheric model is constructed taking into account the main sink reactions of OCS and it is found that overall stratospheric removal slightly favors light OCS in constrast to the findings of Leung et al. (2002). These results show, based on isotopic considerations, that OCS is an acceptable source of background stratosperic sulfate aerosol in agreement with a recent model study of Bruhl et al. (2012). The C-13 isotopic fractionation due to photolysis of OCS in the upper stratosphere is significant and will leave a clear signal in the remaining OCS making it a candidate for tracing using the ACE-FTS and MIPAS data sets.
  • Sebastian O. Danielache, Shohei Hattori, Matthew S. Johnson, Yuichiro Ueno, Shinkoh Nanbu, Naohiro Yoshida
    JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES 117(D24) 2012年12月19日  査読有り
  • Zilong Zheng, Yi Zhao, Shinkoh Nanbu
    JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 11(6) 1311-1322 2012年12月  査読有り
    Ab initio method is used to figure out the structures and photo-physical processes of 2-aryl substituted indoles, 2-phenylindole (2PI), 2-naphthylindole (2NI), and 2-anthracenylindole (2AI), synthesized experimentally with strong uorescence. The results show that the photo-absorption and uorescence measured experimentally correspond to the monovalent anions deprotonated in the indole NH end, other than the neutral compounds. During the photochemical reaction, the angles between the planes of the indole and 2-aryl substituted moieties keep unchanged, but the photo-induced intramolecular charge transfer can immediately occur in the anions. Furthermore, the photo-physical processes after photoexcitation are analyzed by using a linear reaction coordinate.
  • Sebastian O. Danielache, Shohei Hattori, Matthew S. Johnson, Yuichiro Ueno, Shinkoh Nanbu, Naohiro Yoshida
    JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES 117 2012年12月  査読有り
    We report measurements of the ultraviolet absorption cross-sections of (SO2)-S-32, (SO2)-S-33, (SO2)-S-34 and (SO2)-S-36 recorded from 250 to 320 nm at 293 K with a resolution of 8 cm(-1). This is the first reported measurement of the (SO2)-S-36 cross-section. This work improves earlier measurements of the (SO2)-S-32, (SO2)-S-33 and (SO2)-S-34 cross-sections and is in good agreement concerning fine structure and peak widths, with localized differences at the peak maxima when isotope effects are taken into account. SO2 samples were produced in an identical process via combustion of isotopically enriched S-0, eliminating effects due to variation in oxygen isotopic composition. Peak positions for the rare isotopologues are red shifted relative to the (SO2)-S-32 isotopologue. Starting at the origin the shift increases linearly through the band. A linear shift model based on the spectrum of (SO2)-S-32 was used to estimate the cross-sections of (SO2)-S-33,34,36; the average of the wavelength resolved absolute difference between the modeled and experimental spectra is 77.4, 107 and 139 parts per thousand respectively. While the peak-to-valley amplitude of (SO2)-S-36 tends to be smaller than the other isotopologues throughout the spectrum, integrated band intensities for all isotopologues are conserved to within 4% relative to (SO2)-S-32. The cross-sections were used in a photochemical model to obtain fractionation constants to compare with photochemical chamber experiments. We conclude that planetary atmospheres will exhibit isotopic fractionation from both photoexcitation and photodissociation, and that experiments in the literature have isotopic imprints arising from both the (BB1)-B-1-X(1)A(1) and the (CB1)-B-1-X(1)A(1) bands. Citation: Danielache, S. O., S. Hattori, M. S. Johnson, Y. Ueno, S. Nanbu, and N. Yoshida (2012), Photoabsorption cross-section measurements of S-32, S-33, S-34, and S-36 sulfur dioxide for the (BB1)-B-1-X(1)A(1) absorption band, J. Geophys. Res., 117, D24301, doi: 10.1029/2012JD017464.
  • Wilfredo Credo Chung, Shinkoh Nanbu, Toshimasa Ishida
    Journal of Physical Chemistry B 116(28) 8009-8023 2012年7月19日  査読有り
    The photoinduced cis-trans isomerization dynamics of rhodopsin and isorhodopsin are studied using a newly developed hybrid QM/MM trajectory surface hopping MD scheme based on the Zhu-Nakamura theory for nonadiabatic transitions. Rhodopsin and isorhodopsin have 11-cis and 9-cis forms of retinal as chromophore and the two proteins are isomerized to bathorhodopsin enclosing the all-trans form. The simulation reproduced faster and more efficient isomerization in rhodopsin than in isorhodopsin. In the excited state, rhodopsin shows a straightforward dynamics, whereas isorhodopsin dynamics is rather complicated and in a back-and-forth manner. The latter complicated dynamics would be mainly due to a narrow space near the active dihedral angle =C8-C9=C10-C11= (ø9) created by Thr 118 and Tyr 268 in opsin. Rhodopsin gives bathorhodopsin only while isorhodopsin yields a byproduct. The rigorous selectivity in rhodopsin would be another reason why rhodopsin is selected biologically. Comparison with our previous opsin-free investigations reveals that opsin tends to confine the twist of the active dihedral to only one direction and funnels transitions into the vicinity of minimum energy conical intersections (MECI). The twist-confinement totally blocks simultaneous twisting of ø9 and ø11 (=C10-C11=C12-C13=) and enhances the quantum yields. The opposite rotation of ø9 and ø11 ("wring-a-wet-towel" motion) takes place upon photoexcitation, which also does without opsin. The wring-a-wet-towel motion is dynamically enhanced in comparison with the one expected from locations of the MECI. The present simulation reveals that the Weiss-Warshel model for cis-trans photoisomerization is not applicable for rhodopsin because the branching ratio after transition is crucial. © 2012 American Chemical Society.
  • Wilfredo Credo Chung, Shinkoh Nanbu, Toshimasa Ishida
    JOURNAL OF PHYSICAL CHEMISTRY B 116(28) 8009-8023 2012年7月  査読有り
    The photoinduced cis-trans isomerization dynamics of rhodopsin and isorhodopsin are studied using a newly developed hybrid QM/MM trajectory surface hopping MD scheme based on the Zhu-Nakamura theory for nonadiabatic transitions. Rhodopsin and isorhodopsin have 11-cis and 9-cis forms of retinal as chromophore and the two proteins are isomerized to bathorhodopsin enclosing the all-trans form. The simulation reproduced faster and more efficient isomerization in rhodopsin than in isorhodopsin. In the excited state, rhodopsin shows a straightforward dynamics, whereas isorhodopsin dynamics is rather complicated and in a back-and-forth manner. The latter complicated dynamics would be mainly due to a narrow space near the active dihedral angle = C8-C9 = C10-C11 =(phi(9)) created by Thr 118 and Tyr 268 in opsin. Rhodopsin gives bathorhodopsin only while isorhodopsin yields a byproduct. The rigorous selectivity in rhodopsin would be another reason why rhodopsin is selected biologically. Comparison with our previous opsin-free investigations reveals that opsin tends to confine the twist of the active dihedral to only one direction and funnels transitions into the vicinity of minimum energy conical intersections (MECI). The twist-confinement totally blocks simultaneous twisting of phi(9) and phi(11) (= C10-C11 = C12-C13 =) and enhances the quantum yields. The opposite rotation of phi(9) and phi(11) ("wring-a-wet-towel" motion) takes place upon photoexcitation, which also does without opsin. The wring-a-wet-towel motion is dynamically enhanced in comparison with the one expected from locations of the MECI. The present simulation reveals that the Weiss-Warshel model for cis-trans photoisomerization is not applicable for rhodopsin because the branching ratio after transition is crucial.
  • Tatsuhiro Murakami, Manabu Nakazono, Alexey Kondorskiy, Toshimasa Ishida, Shinkoh Nanbu
    Physical Chemistry Chemical Physics 14(32) 11546-11555 2012年6月26日  査読有り
  • Hong Zhang, Qiao Sun, Zhen Li, Shinkoh Nanbu, Sean S. Smith
    COMPUTATIONAL AND THEORETICAL CHEMISTRY 990 185-193 2012年6月  査読有り
    In this paper we perform high level complete active space self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) calculations to generate three-dimensional potential energy surfaces for the proton chain transfer in the green fluorescent protein (GFP) based on a minimal quantum mechanical cluster model. Both the electronic ground state and the first excited state are considered within an approximate rigid model. We focus on the energetic terms of the proton transfers in this paper, and the exact quantum dynamics simulations for proton transfer on the ground and excited states will be reported later. Our results from MRCI quantum mechanical calculations are contrasted with those of other computational studies using both CASPT2 method and OFT method, and are compared with the experimental findings for GFP in the full protein environment. (C) 2012 Elsevier B.V. All rights reserved.
  • ZiLong Zheng, Yi Zhao, Shinkoh Nanbu
    Journal of Theoretical and Computational Chemistry 11(6) 1311-1322 2012年5月27日  査読有り
  • Sebastian O. Danielache, Shohei Hattori, Matthew S. Johnson, Yuichiro Ueno, Shinkoh Nanbu, Naohiro Yoshida
    Journal of Geophysical Research Atmospheres 117(24) 2012年  査読有り
    We report measurements of the ultraviolet absorption cross-sections of 32SO2, 33SO2, 34SO 2 and 36SO2 recorded from 250 to 320 nm at 293 K with a resolution of 8 cm-1. This is the first reported measurement of the 36SO2 cross-section. This work improves earlier measurements of the 32SO2, 33SO2 and 34SO2 cross-sections and is in good agreement concerning fine structure and peak widths, with localized differences at the peak maxima when isotope effects are taken into account. SO2 samples were produced in an identical process via combustion of isotopically enriched S 0, eliminating effects due to variation in oxygen isotopic composition. Peak positions for the rare isotopologues are red shifted relative to the 32SO2 isotopologue. Starting at the origin the shift increases linearly through the band. A linear shift model based on the spectrum of 32SO2 was used to estimate the cross-sections of 33,34,36SO2; the average of the wavelength resolved absolute difference between the modeled and experimental spectra is 77.4, 107 and 139 ‰ respectively. While the peak-to-valley amplitude of 36SO2 tends to be smaller than the other isotopologues throughout the spectrum, integrated band intensities for all isotopologues are conserved to within 4% relative to 32SO2. The cross-sections were used in a photochemical model to obtain fractionation constants to compare with photochemical chamber experiments. We conclude that planetary atmospheres will exhibit isotopic fractionation from both photoexcitation and photodissociation, and that experiments in the literature have isotopic imprints arising from both the B1B1-X 1A1 and the C1B1-X1A 1 bands. © 2012. American Geophysical Union. All Rights Reserved.
  • ZiLong Zheng, Yi Zhao, Manabu Nakazono, Shinkoh Nanbu
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14(9) 3017-3024 2012年  査読有り
    Photo-physical properties of bromo-indolylmaleimide (IM-Br), indole-succinimide (IS), and their anions were theoretically investigated compared with the previous theoretical result for indolylmaleimide (IM) [Phys. Chem. Chem. Phys., 2010, 12, 9783]. The energies for the electronic excited states as well as the ground states were computed for these molecules using the multi-reference perturbation calculations based on the second order Rayleigh-Schrodinger perturbation theory (CASPT2) at the cc-pVDZ basis set level. The electron-accepting or electron-donating effect caused by bromine-substitution was discussed in the intra-molecular charge transfer (ICT) mechanism. The order of natural orbitals of the bromine-substituted monovalent anion with a deprotonated indole NH group (I(-)M-Br) was found to be rearranged by the effect of electron-donation, which leads to pseudo-crossing of the potential energy cures of the S-1 and S-2 states. The large stokes shift observed for I(-)M-Br was due to pseudo-crossing. Meanwhile, IM and IM-Br show abnormal deprotonation, which is explained by the charge distribution on the indole and maleimide moieties. Finally, the monovalent anions I(-)M-Br and I(-)M by a deprotonation of the indole NH end and the neutral IS were proposed to be the most feasible candidates corresponding to the experimental spectra in solution.

MISC

 9
  • 杉山数馬, 吉永竜平, 橋本剛, 南部伸孝, 早下隆士, 欅田英之, 江馬一弘
    応用物理学会春季学術講演会講演予稿集(CD-ROM) 67th 2020年  
  • 羽根田涼, 杉山数馬, 藤澤真友子, 欅田英之, 江馬一弘, 橋本剛, 早下隆士, 南部伸孝
    分子科学討論会講演プログラム&要旨(Web) 12th 2018年  
  • Toshimasa Ishida, Shinkoh Nanbu, Hiroki Nakamura
    INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY 36(2) 229-285 2017年  査読有り招待有り
    It is now confirmed that the Zhu-Nakamura (ZN) theory of nonadiabatic transition is useful to investigate various nonadiabatic chemical dynamics. The theory, being one-dimensional, presents a whole set of analytical formulas that enables us to treat the dynamics efficiently. It is also quite significant that classically forbidden transitions can be dealt with analytically. The theory can be combined with the trajectory surface hopping (TSH) method (ZN-TSH) and is demonstrated to be useful to clarify the dynamics of not only simple tri-atomic reactions but also large chemical systems. The whole set of analytical formulas directly applicable to practical systems is summarised and the applications to polyatomic systems are illustrated. Examples of polyatomic molecules are H2SO4, NH3, indolylmaleimide, cyclohexadiene (CHD), and retinal. The Fortran code for the whole set of ZN formulas is provided in Appendix for the convenience of a reader who is interested in using them. The ZN-TSH method can be combined with the QM/MM method to clarify reaction dynamics in the surrounding environment. This is named as ZN-QM/MM-TSH. The particle-mesh Ewald (PME) method can also be combined with ZN-TSH to clarify reaction dynamics in solutions. This is named as ZN-PME-TSH. Formulations of these methods are presented together with practical applications. Examples treated by ZN-QM/MMTSH are photoisomerization dynamics of retinal chromophore embedded in the protein environment. The differences in the isomerization mechanisms between rhodopsin and isorhodopsin are made clear. The faster and more efficient isomerization of rhodopsin compared to isorhodopsin is nicely reproduced. Examples of reactions in solutions are photoisomerizations of retinal and CHD. The experimentally observed long life time of the excited state of retinal is reproduced and is found to be due to the long-range solvation effect. The solvent dependent branching ratios of CHD: hexatriene (HT) are clarified for the ethanol and hexane solvents by the ZN-PME-TSH method. Both ZN-QM/MM-TSH and ZN-PME-TSH are thus demonstrated to be promising methods to deal with a wide range of nonadiabatic dynamics in large chemical and biological systems.
  • 赤間 知子, 小林 理, 南部 伸孝, 武次 徹也
    ケモインフォマティクス討論会予稿集 2016 P10 2016年  
    時間依存Schr&amp;ouml;dinger方程式やその近似式は、実時間発展により超高速現象である電子ダイナミクスを記述できる。しかし、これらの時間微分方程式を解くための時間発展の計算は、高いコストを要することが多く、これまで適用が限られていた。一方、核波束ダイナミクスの分野では、Chebyshev多項式の3項間漸化式を用いて時間発展を行う実核波束発展法が開発され、計算コストの大幅な削減に成功している。そこで本研究では、実核波束発展法を参考に、効率的な時間発展法として3項間漸化式(3TRR)法を開発した。3TRR法では、演算子変換の導入によって導かれる3項間漸化式を用いて、変換されたエネルギー・時間軸上で効率的に計算を行う。元のエネルギーと時間を得るのに必要な逆変換の式の導出も行った。3TRR法を、電子ダイナミクスを記述するRT-TDHF/TDDFT計算に適用し、計算の効率化を目指した。
  • Shinkoh Nanbu, Toshimasa Ishida, Hiroki Nakamura
    CHEMICAL SCIENCE 1(6) 663-674 2010年  査読有り招待有り筆頭著者責任著者
    A variety of chemical phenomena are governed by non-adiabatic transitions at conical intersections of potential energy surfaces, if not directly, but indirectly in the midst of the processes. In other words, the non-adiabatic transition makes one of the most significant key mechanisms in chemical dynamics. Since the basic analytical theory is now available to treat the transitions, it is possible to comprehend the dynamics of realistic chemical and biological systems with the effects of transitions taken into account properly. Another important quantum mechanical effect of tunneling can also be taken into account. Furthermore, it becomes feasible to control chemical dynamics by controlling the non-adiabatic transitions at conical intersections, and also to develop new molecular functions by using peculiar properties of non-adiabatic transitions. These may be realized, if we apply appropriately designed laser fields. This perspective review article explains the above mentioned ideas based on the authors&apos; recent activities. The non-adiabatic chemical dynamics is expected to open a new dimension of chemistry.
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