研究業績

原著論文・総説


    2024
  1. "C-H Bond dissociation enthalpy prediction with machine learning reinforced semi-empirical quantum mechanical calculations"
    Kaneko, Miki; Takano, Yu; Saito, Toru*
    Chem. Lett. 2024, 53, upae016.

    2. 2023
  2. "Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model"
    Kanematsu, Yusuke*; Kondo, Hiroko X.; Takano, Yu*
    Int. J. Mol. Sci. 2023, 24, 17172.

  3. "Semi-empirical and machine learning-based prediction of site of metabolisms mediated by aldehyde oxidase"
    Shiotake, Yuto; Takano, Yu; Saito, Toru*
    Chem. Phys. Lett. 2023, 833, 140942.

  4. "Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme"
    Fujikawa, Hinako; Kondo, Hiroko X.; Kanematsu, Yusuke; Takano, Yu*
    Chem. Lett. 2023, 52, 503-507

  5. "Unraveling Binding Mechanism and Stability of Urease Inhibitors: A QM/MM MD Study"
    Suenaga, Shunya; Takano, Yu; Saito, Toru*
    Molecules 2023, 28, 2697

  6. "Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix"
    Kondo, Hiroko X.*; Nakamura, Haruki; Takano, Yu*
    Chem. Phys. Lett. 2023, 815, 140361


  7. "開殻電子状態を有する生体高分子の分子シミュレーション"
    齋藤徹
    アンサンブル 2023, 25, 13-18.


  8. "Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals"
    Ang, Artoni Kevin R.*; Umena, Yasufumi; Sato-Tomita, Ayana; Shibayama, Naoya; Happo, Naohisa; Marumi, Riho; Yamamoto, Yuta; Kimura, Koji; Kawamura, Naomi; Takano, Yu; Matsushita, Tomohiro; Sasaki, Yuji C.; Shen, Jian-Ren; Hayashi, Kouichi
    J. Synchrotron Rad. 2023, 30, 368-378

  9. "Quantum chemical studies on hydrogen bonds in helical secondary structures"
    Takano, Yu*; Kondo, Hiroko X.; Nakamura, Haruki
    Biophys. Rev. 2022, 14, 1369-1378.

  10. "Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network"
    Kondo, Hiroko X.*; Iizuka, Hiroyuki; Masumoto, Gen; Kabaya, Yuichi; Kanematsu, Yusuke; Takano, Yu*
    Biomolecules 2023, 13, 137.

    11. 2022
  11. "Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations"
    Nakayoshi, Tomoki*; Ohnishi, Yusuke; Tanaka, Hideaki; Kurisu, Genji; Kondo, Hiroko X.; Takano, Yu*
    Int. J. Mol. Sci. 2022, 23, 15913.

  12. "Structures and mechanisms of actin ATP hydrolysis"
    Kanematsu, Yusuke*; Narita, Akihiro; Oda, Toshiro; Koike, Ryotaro; Takano, Yu; Moritsugu, Kei; Fujiwara, Ikuko; Tanaka, Kotaro; Komatsu, Hideyuki; Nagae, Takayuki; Watanabe, Nobuhisa; Iwasa, Mitsusada; Maeda, Yuichiro*; Takeda, Shuichi*
    Proc. Natl. Acad. Sci. USA 2022, 119, e2122641119.

  13. "Effects of Light-emitting Diode Irradiation Pattern on the Anthocyanin Content of Broccoli Sprouts in a Plant Factory for the Production of Functional Foods"
    Kohda, Jiro*; Sasaki, Rio; Suzuki, Rikuto; Kugimiya, Akimitsu; Nakano, Yasuhisa; Takano, Yu
    Jpn. J. Food. Eng. 2022, 23, 71-83.

  14. "Conformational Preference of Flavonols and Its Effect on the Chemical Properties Involved in Radical Scavenging Activity"
    Kondo, Hiroko X.*; Takano, Yu*
    Chemistry 2022, 4, 1123-1135.

  15. "Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network"
    Kondo, Hiroko X.*; Iizuka, Hiroyuki; Masumoto, Gen; Kabaya, Yuichi; Kanematsu, Yusuke*; Takano, Yu*
    Biomolcules 2022, 12, 1172.

  16. "Depolarizing Effects in Hydrogen Bond Energy in 310-Helices Revealed by Quantum Chemical Analysis"
    Kondo, Hiroko X.*; Nakamura, Haruki; Takano, Yu*
    Int. J. Mol. Sci. 2022, 23, 9032.

  17. "Singlet O2 Oxidation of the Radical Cation versus the Dehydrogenated Neutral Radical of 9-Methylguanine in a Watson-Crick Base Pair. Consequences of Structural Context"
    Moe, May Myat; Saito, Toru; Tsai, Midas.; Liu, Jianbo*
    J. Phys. Chem. B 2022, 126, 5458-5472.

  18. "Structure of Heme-binding Pocket in Heme Protein is Generally Rigid and can be Predicted by AlphaFold2"
    Kondo, Hiroko X.*; Kanematsu, Yusuke; Takano, Yu*
    Chem. Lett. 2022, 51, 704-708.

  19. "Evaluation of an Appropriate Standard Hydrogen Electrode Potential for Computing Redox Potentials of Catechins with Density Functional Theory"
    Duan, Lian; Takano, Yu*; Shigeta, Yasuteru*
    Chem. Lett. 2022, 51, 673-677.

  20. "Predicting reaction mechanisms for the threonine-residue stereoinversion catalyzed by a dihydrogen phosphate ion"
    Nakayoshi, Tomoki; Kato, Koichi; Kurimoto, Eiji; Takano, Yu; Oda, Akifumi*
    ACS Omega 2022, 7, 18306-18314.

  21. "QM/MM molecular dynamics simulations revealed catalytic mechanism of urease"
    Saito, Toru*; Takano, Yu
    J. Phys. Chem. B 2022, 126, 2087-2097.


  22. "Global analysis of heme proteins to elucidate the correlation between heme distortion and heme-binding pocket"
    Kondo, Hiroko X.*; Fujii, Masanori; Tanioka, Takuma; Kanematsu, Yusuke; Yoshida, Takashi; Takano, Yu*
    J. Chem. Inf. Model. 2022, 62, 775-784.

  23. "Development of a one-step analysis method for several amino acids using a microfluidic paper-based analytical device"
    Kugimiya, Akimitsu*; Wakimoto, Sho; Kohda, Jiro; Nakano, Yasuhisa; Takano, Yu
    Sci. Rep. 2022, 12, 3427.

  24. "Analysis of fluctuation in the heme-binding pocket and heme distortion in hemoglobin and myoglobin"
    Kondo, Hiroko X.*; Takano, Yu
    Life 2022, 12, 210.

  25. "Singlet O2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments"
    Benny, Jonathan.; Saito, Toru*; Moe, May Myat; Liu, Jianbo*
    J. Phys. Chem. A 2022, 126, 68-79.

    26. 2021
  26. "第一原理計算によるカテキンの酸化還元電位の理論予測"
    Duan, Lian; Takano, Yu*; Shigeta, Yasuteru*
    J. Comput. Chem. Jpn. 2021, 20, 137-139.

  27. "Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography"
    Nomura, Takashi; Kimura, Tetsunari; Kanematsu, Yusuke; Yamada, Daichi; Yamashita, Keitaro; Hirata, Kunio; Ueno, Go; Murakami, Hironori; Hisano, Tamao; Yamagiwa, Raika; Takeda, Hanae; Gopalasingam, Chai; Kousaka, Ryota; Ynagisawa, Sachiko; Shoji, Osami; Kumasaka, Takashi; Yamamoto, Masaki; Takano, Yu; Sugimoto, Hiroshi; Tosha, Takehiko*; Kubo, Minoru*; Shiro, Yoshitsugu*
    Proc. Natl. Acad. Sci. USA 2021, 118, e2101481118.

  28. "Spin‐projected QM/MM free energy simulations for oxidation reaction of guanine in B-DNA by singlet oxygen"
    Saito, Tohru*; Takano, Yu
    ChemPhysChem 2021, 22, 561-568.

    29. 2020
  29. "PyDISH: Database and analysis tools for heme porphyrin distortion in heme proteins"
    Kondo, Hiroko X.*; Kanematsu, Yusuke*; Masumoto, Gen; Takano, Yu*
    Database: The Journal of Biological Databases and Curation 2020, 2020, baaa066.

  30. "Quantitative assessment of reparameterized PM6 (rPM6) for hydrogen abstraction reactions"
    Saito, Toru*; Kambara, Hiroki; Takano, Yu
    Mol. Phys. 2020, 118, e1700313.

  31. "Microfluidic paper-based analytical device for histidine determination"
    Kugimiya, Akimitsu*; Fujikawa, Akane; Jiang, Xiao; Fan, Z. Hugh; Nishida, Toshikazu; Kohda, Jiro; Nakano, Yasuhisa; Takano, Yu
    Appl. Biochem. Biotech. 2020, 192, 812-821.

    32. 2019
  32. "Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in an anti-HIV neutralizing antibody PG16"
    Kondo Hiroko X.*; Kiribayashi, Ryo , Kuroda, Daisuke*; Saito, Toru; Kohda, Jiro; Kugimiya Akimitsu; Nakano, Yasuhisa; Tsumoto, Kohei; Takano, Yu*
    Sci. Rep. 2019, 9, 19840.

  33. "Hydrogen bond energies in alpha-helical peptides revealed by precise DFT calculations and molecular tailoring approach"
    Kondo, Hiroko X.*; Nakamura, Haruki; Takano, Yu*
    J. Comput. Chem. 2019, 40, 2043-2052.

  34. "Singlet-Triplet Energy Gaps in Binuclear Copper Complexes and Organic Diradicals by Approximate Spin Projected Spin-unrestricted Coupled Cluster Method"
    Saito, Toru*; Takano, Yu
    Chem. Lett. 2019, 48, 1441-1444.

    35. 2018
  35. "Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results"
    Saito, Toru*; Fujiwara, Manami; Takano, Yu
    Molecules 2018, 23, 3332.

  36. "UNO DMRG CAS CI calculations of binuclear manganese complex Mn(IV)2O2(NHCHCO2)4: Scope and applicability of Heisenberg model"
    Kawakami, Takashi; Miyagawa, Koichi; Sharma, Sandeep; Saito, Toru*; Shoji, Mitsuo; Yamada, Satoru; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima, Takahito; Yamaguchi, Kizashi
    J. Comput. Chem. 2018, 40, 333-341.

  37. "Transition State Search Using rPM6: Iron- and Manganese-catalyzed Oxidation Reactions as a Test Case"
    Saito, Toru*; Takano, Yu
    Bulletin of the Chemical Society of Japan 2018, 91, 1377-1389.

  38. "Zn2+-binding to the voltage-gated proton channel Hv1/VSOP"
    Iwaki, Masayo; Takeshita, Kohei; Kondo, Hiroko X.; Okamura, Yasushi; Takano, Yu; Nakagawa, Atsushi; Kandori, Hideki*
    J. Phys. Chem. B 2018, 122, 9076-9080.

  39. "Statistical and quantum-chemical analysis of heme porphyrin distortion effect in heme proteins: differences between oxidoreductases and oxygen carrier proteins"
    Kanematsu, Yusuke*;Imada, Yasuhiro; Kondo, Hiroko X.; Takano, Yu*
    Chem. Phys. Lett. 2018, 710, 108-112.

  40. "近似スピン射影法の開発と多核遷移金属錯体の電子状態・分子構造・物性解明への展開"
    北河康隆、齋藤徹、山口兆
    Bulletin of Japan Society of Coordination Chemistr 2018, 71, 57-68.

  41. "Approximate spin projection for broken-symmetry method and its application"
    in Symmetry (Group Theory) and Mathematical Treatment in Chemistry, Takashiro Akitsu, ed, (Chapter 7)
    Kitagawa, Yasutaka; Saito, Toru ; Yamaguchi, Kizashi
    IntechOpen 2018, 121-139.

  42. "A Bis(μ-oxido)dinickel(III) Complex with a Triplet Ground State"
    Morimoto, Yuma*; Takagi, Yusaku; Saito, Toru ; Ohta, Takehiro; Ogura, Takashi; Tohnai, Norimitsu; Nakano, Motohiro; Itoh Shinobu*
    Angew. Chem. Int. Ed. 2018, 57, 7640-7643.

  43. "Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials"
    Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada
    J. Phys. Soc. Jpn. 2018, 87, 061013.

  44. "The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs"
    Katsura, Yukako; Kondo, Hiroko X.; Ryan, Janelle; Harley, Vincent; Satta, Yoko
    BMC Evol. Biol. 2018, 18, 3.

  45. "rPM6 parameters for phosphorous and sulphur-containing open-shell molecules"
    Saito, Toru*; Takano, Yu
    Mol. Phys. 2018, 116, 602-610.

  46. "Strong Hydrogen-Bonds at the interface between Proton-Donating and Accepting Self-Assembled Monolayers on Au(111)"
    Kato Hiroyuki; Yoshimoto, Shinya; Ueda, Akira; Yamamoto, Susumu; Kanematsu, Yusuke; Tachikawa, Masanori; Mori, Hatsumi; Yoshinobu, Jun; Matsuda, Iwao
    Langmuir 2018, 34, 2189-2197.

  47. "Density functional study of porphyrin distortion effects on redox potential of heme"
    Imada, Yasuhiro; Nakamura, Haruki; Takano, Yu*
    J. Comput. Chem. 2018, 39(3), 143-150.


    48. 2017
  48. "Capturing an initial intermediate during enzymatic reaction of P450nor using time-resolved XFEL crystallography and caged-substrate"
    Tosha, Takehiko; Nomura, Takashi; Nishida, Takuma; Saeki, Naoya; Okubayashi, Kouta; Yamagiwa, Raika; Sugahara, Michihiro; Nakane, Takanori; Yamashita, Keitaro; Hirata, Kunio; Ueno, Go; Kimura, Tetsunari; Hisano, Tamao; Muramoto, Kazumasa; Sawai, Hitomi; Takeda, Hnae; Mizobata, Eiichi; Yamashita, Ayumi; Kanematsu, Yusuke; Takano, Yu; Nango, Eriko; Tanaka, Rie; Nureki, Osamu; Ikemoto, Yuka; Murakami, Nironori; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Yamamoto, Masaki; Ago, Hideo; Iwata, So; Sugimoto, Hiroshi*; Shiro, Yoshitsugu*; Kubo, Minoru*
    Nat. Comm. 2017, 8, 1585.

  49. "Theoretical Study of Magnetic Interaction in Pyrazole-bridged Dinuclear Cu(II) Complex"
    Miyagi, Koji; Kitagawa, Yasutaka*; Asaoka, Mizuki; Teramoto, Rena; Natori, Yoshiki; Saito, Toru; Nakano, Masayoshi*
    Polyhedron 2017, 136, 132-135.

  50. "Density functional study of the magneto-structural correlations of manganese complexes, [Mn2O2Hn(salpn)2]+(2-n) (n=0-2) from the viewpoint of the protonation modes of the bridging oxygen anions"
    Miyagawa, Koichi; Komi, Kyohei; Ohnari, Jinta; Maruyama, Tomohiro; Yamanaka, Shusuke*; Saito, Toru; Kawakami, Takashi; Yamaguchi, Kizashi; Okumura, Mitsutaka
    Polyhedron 2017, 136, 102-109.

  51. "Assessment of Semi-empirical Molecular Orbital Calculations for Describing Magnetic Interactions"
    Saito, Toru*; Kitagawa, Yasutaka; Kawakami, Takashi; Yamanaka, Shusuke; Okumura, Mitsutaka; Takano, Yu
    Polyhedron 2017, 136, 52-57.

  52. "Quantum Mechanics Study on Synthetic Models of Copper-containing Quercetin 2,4-Dioxygenase"
    Numata, Takahiro; Saito, Toru*; Kawakami, Takashi; Yamanaka, Shusuke; Okumura, Mitsutaka
    Polyhedron 2017, 136, 45-51.

  53. "rPM6 Parameters for Manganese and Application to Transition State Search for Oxidation Reactions of Cyclohexane by Manganese(IV)-Oxo Species"
    Saito, Toru*; Takano, Yu
    Chem. Lett. 2017, 46, 1567-1569.

  54. "Full-valence density matrix renormalization group calculations on meta-benzyne, based on unrestricted natural orbitals Revisit of seamless continuation from broken-symmetry to symmetry-adapted models for diradicals"
    Kawakami, Takashi*; Saito, Toru; Sharma Sandeep; Yamanaka, Shusuke; Yamada, Satoru; Nakajima Takahito; Okumura, Mitsutaka; Yamaguchi, Kizashi*
    Mol. Phys. 2017, 115, 2267-2284.

  55. "UNO DMRG CI Calculations of Effective Exchange Integrals for m-Phenylene-bis-methylene Spin Clusters"
    Kawakami, Takashi*; Sano, Shinsuke; Saito, Toru; Sharma Sandeep; Shoji, Mitsuo; Yamada, Satoru; Takano, Yu; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima Takahito; Yamaguchi, Kizashi*
    Mol. Phys. 2017, 115, 2154-2167.

  56. "Heterogeneous catalase-like activity of gold(I)?cobalt(III) metallosupramolecular ionic crystals"
    Yamada, Mihoko; Yoshinari, Nobuto; Kuwamura, Naoto; Saito, Toru; Okada, Satoshi; Maddala, Sai Prakash; Harano, Koji; Nakamura, Eiichi; Yamagami, Kohei; Yamanaka, Keisuke; Sekiyama, Akira; Suenobu, Tomoyoshi; Yamada, Yusuke; Konno, Takumi*
    Chem. Sci. 2017, 8, 2671-2676.

  57. "Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding"
    Hadara, Ryuhei*; Takano, Yu; Shigeta, Yasuteru
    J. Comput. Chem. 2017, 38, 790-797.


  58. "Applicability of Density Functional Tight Binding Method with Dispersion Correction to Investigate the Adsorption of Porphyrin/Porphycene Metal Complexes on Graphene"
    Kanematsu, Yusuke*; Gohara, Kazutoshi; Yamada, Hiroko ; Takano, Yu*
    Chem. Lett. 2017, 46, 51-52.

    59. 2016
  59. "医療分野を担う情報処理技術者の育成 －広島市立大学情報科学部医用情報科学科の学生実験－"
    福田浩士，中野靖久，藤原久志，香田次郎，常盤達司
    日本神経回路学会誌 2016, 23, 146-152.

  60. "Reparameterization of PM6 applied to organic diradical molecules"
    Saito, Toru*; Kitagawa, Yasutaka; Takano, Yu
    J. Phys. Chem. A 2016, 120, 8750?8760.

  61. "Recycling of biodiesel fuel wastewater for use as a liquid fertilizer for hydroponics"
    Kohda, Jiro*; Nakano, Yasuhisa; Kugimiya, Akimitsu; Takano, Yu; Yano, Takuo
    J. Mater. Cycles Waste Manag. 2017, 19, 999-1007.

  62. "Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile."
    Kanematsu, Yusuke*; Tachikawa, Masanori; Takano, Yu*
    J. Comput. Chem. 2016, 37, 2140-2145.
    Front cover of J. Comput. Chem.


  63. "Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations."
    Kamiya, Narutoshi*; Mashimo, Tadaaki; Takano, Yu; Kon, Takahide; Kurisu, Genji; Nakamura, Haruki
    Protein Eng. Des. Sel. 2016, 29, 317-326.

  64. "TaBoo SeArch algorithm with a modified inverse histogram for reproducing biologically relevant rare events of proteins."
    Harada, Ryuhei*; Takano, Yu*; Shigeta Yasuteru*
    J. Chem. Theory Comput. 2016, 12, 2436-2445.

  65. "QM/MM study of hydrolysis of arginine catalysed by arginase."
    Saito Toru*; Kawakami, Takashi; Yamanaka, Shusuke; Okumura, Mitsutaka
    Mol. Phys. 2016, 114, 431-439.

  66. "Nearsightedness-related indices of finite systems based on linear response function:one dimensional cases."
    Mitsuta, Yuki; Yamanaka, Shusuke*; Saito, Toru; Kawakami, Takashi; Yamaguchi, Kizashi; Okumura, Mitsutaka; Nakamura, Haruki
    Mol. Phys. 2016, 114, 380-388.

  67. "Structural basis for the membrane association of ankyrin G via palmitoylation."
    Fujiwara, Yuichiro*; Kondo, Hiroko X.; Shirota, Matsuyuki; Kobayashi Megumi; Takeshita, Kohei; Nakagawa, Atsushi; Okamura Yasushi; Kinoshita Kengo*
    Sci. Rep. 2016, 6, 23981(1-11).

  68. "Flow analysis of amino acids by using a newly developed aminoacyl-tRNA synthetase?immobilized, small reactor column?based assay."
    Kugimiya, Akimitsu*; Konishi, Hidenori; Fukada, Rie
    Appl. Biochem. Biotech. 2016, 178, 924-931.

  69. "Development of massive multi-level molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions."
    Takano, Yu*; Nakata, Kazuto; Yonezawa, Yasushige; Nakamura, Haruki
    J. Comput. Chem. 2016, 37, 1125-1132.

  70. "Direct interaction between the voltage-sensors produces coorperative sustained deactivation in voltage-gated H+ channel dimers."
    Okuda, Hiroko; Yonezawa, Yasushige; Takano, Yu; Okamura, Yasushi; Fujiwara, Yuichiro*
    J. Biol. Chem. 2016, 291, 5935?5947.

  71. "Density functional study of molecular interactions in secondary structures of proteins."
    Takano, Yu*; Kusaka, Ayumi; Nakamura, Haruki
    Biophysics and Physicobiology 2016, 13, 27-35.

    72. 2015
  72. "Chemiluminescence detection of serine, proline, glycine, asparagine, leucine, and histidine by using corresponding aminoacyl-tRNA synthetases as recognition elements."
    Kugimiya, Akimitsu*; Fukada, Rie
    Appl. Biochem. Biotech. 2015, 176, 1195-1202.

  73. "Efficient conformational sampling of proteins based on a multi-dimensional inverse histogram: An application to folding of chignolin in explicit solvent."
    Harada, Ryuhei*; Takano, Yu*; Shigeta, Yasuteru*
    Chem. Phys. Lett. 2015, 630, 68-75.

  74. "Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini-protein, chignolin."
    Harada, Ryuhei*; Takano, Yu*; Shigeta, Yasuteru*
    J. Comput. Chem. 2015, 36, 763-772.

  75. "Protein folding pathways extracted by OFLOOD: Outlier FLOODing method."
    Harada, Ryuhei*; Nakamura, Tomotake; Takano, Yu; Shigeta, Yasuteru*
    J. Comput. Chem. 2015, 36, 97-102.