Publication List

Original papers

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 (5 pages).
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 (14 pages)
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 (7 pages).
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 (17 pages).
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 (6 pages).
7. "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, 71– 83 (11 pages).
8. "Prediction of protein function from tertiary structure of the active site in heme proteins by convolutional neural network."
  Kondo, Hiroko, X.*; Iizuka, Hiroyuki; Matsumoto, Gen; Kabaya, Yuichi; Kanematsu, Yusuke; Takano, Yu*
  Biomolecules 2023, 13, 137 (15 pages).
9. "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 2023, 2023, baaa066 (11 pages).
10. "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 (13 pages).
11. "Structures and mechanisms of the actin ATP hydrolysis."
  Kanematsu, Yusuke*; Narita, Akihiro; Oda, Toshiro; Koike, Ryotaro; Ota, Motonari; Takano, Yu; Moritsugu, Kei; Fujiwara, Ikuko; Tanaka, Kotaro; Komatsu, Hideyuki; Nagae, Takayuki; Watanabe, Nobuhisa; Iwasa, Mitsusada; Maéda, Yuichiro*; Takeda Shuichi*
  Proc. Natl. Acad. Sci. USA 2022, 119, e2122641119 (12 pages).
  Press release (in Japanese)
12. "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.
13. "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.
14. "Elucidation of the correlation between the heme distortion and the tertiary structure of heme-binding pocket by convolutional neural network."
  Kondo, Hiroko, X.*; Iizuka, Hiroyuki; Matsumoto, Gen; Kabaya, Yuichi; Kanematsu, Yusuke*; Takano, Yu*
  Biomolecules 2022, 12, 1172 (16 pages).
  Editor's choice of Biomolecules
15. "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 (15 pages).
16. "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.
17. "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.
18. "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.
19. "QM/MM molecular dynamics simulations revealed catalytic mechanism of urease."
  Saito, Toru*; Takano, Yu
  J. Phys. Chem. B 2022, 126, 2087–2097.
  Supplementary cover of J. Phys. Chem. B
20. "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.
21. "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 (8 pages).
22. "Analysis of fluctuation in the heme-binding pocket and heme distortion in hemoglobin and myoglobin."
  Kondo, Hiroko X.*; Takano, Yu
  Life 2022, 12, 210 (15 pages).
23. "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.
24. "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; Yanagisawa, 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 (5 pages).
25. "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.
26. "Quantitative assessment of reparameterized PM6 (rPM6) for hydrogen abstraction reactions."
  Saito, Toru*; Kambara, Hiroki; Takano, Yu
  Mol. Phys. 2020, 118, e1700313 (6 pages).
27. "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.
28. "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 (9 pages).
29. "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.
30. "Hydrogen bond energies in &alpha-helical peptides revealed by precise DFT calculations and molecular tailoring approach."
  Kondo, Hiroko X.; Kusaka, Ayumi; Kitakawa, Colin K.; Onari, Jinta; Yamanaka, Shusuke; Nakamura, Haruki; Takano, Yu*
  J. Comput. Chem. 2019, 40, 2043-2052.
31. "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 (7 pages).
32. "Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP."
  Iwaki, Masayo;, Takeshita, Kohei; Kondo, Hiroko X.; Kinoshita, Kengo; Okamura, Yasushi; Takano, Yu; Nakagawa, Atsushi; Kandori, Hideki*
  J. Phys. Chem. B 2018, 122, 9076-9080.
33. "Transition state search using rPM6: iron- and manganese-catalyzed oxidation reactions as a test case."
  Saito, Toru*; Takano, Yu
  Bull. Chem. Soc. Jpn. 2018, 91, 1377-1389.
34. "Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins."
  Kanematsu, Yusuke*; Kondo, Hiroko X.; Imada, Yasuhiro; Takano, Yu*
  Chem. Phys. Lett. 2018, 710, 108-112.
35. "rPM6 parameters for phosphorous and sulphur-containing open-shell molecules."
  Saito, Toru*; Takano, Yu
  Mol. Phys. 2018, 116, 602-610.
36. "Density functional study of porphyrin distortion effects on redox potential of heme."
  Imada, Yasuhiro; Nakamura, Haruki; Takano, Yu*
  J. Comput. Chem. 2018, 39, 139-142.
37. "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, Hanae; Mizohata, Eiichi; Yamashita, Ayumi; Kanematsu, Yusuke; Takano, Yu; Nango, Eriko; Tanaka, Rie; Nureki, Osamu; Shoji, Osami; Ikemoto, Yuka; Murakami, Hironori; Owada, Shigeki; Tono, Kensuke; Yabashi, Makina; Yamamoto, Masaki; Ago, Hideo; Iwata, So; Sugimoto, Hiroshi*; Shiro, Yoshitsugu*; Kubo, Minoru*
  Nat. Commun. 2017, 8, 1585.
  Press release (in Japanese)
38. "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.
39. "rPM6 parameters for manganese and application to transition state search for oxidation reactions of cyclohexene by manganese(IV)-oxo species."
  Saito, Toru*; Takano, Yu
  Chem. Lett. 2017, 46, 1567-1569.
40. "UNO DMRG CASCI 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.
41. "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.
42. "Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding"
  Harada, Ryuhei*; Takano, Yu*; Shigeta, Yasuteru*
  J. Comput. Chem. 2017, 38, 790-797.
  Front cover of J. Comput. Chem.
43. "Applicability of density functional tight binding method with dispersion correction to investigate the adsorption of porhyrin/porphycene metal complexes on graphene."
  Kanematsu, Yusuke*; Gohara, Kazutoshi; Yamada, Hiroko; Takano, Yu*
  Chem. Lett. 2017, 46, 51-52.
44. "Reparameterization of PM6 applied to organic diradical molecules."
  Saito, Tohru*; Kitagawa, Yasutaka; Takano, Yu
  J. Phys. Chem. A 2016, 120, 8750-8760.
45. "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.
46. "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.
47. "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.
48. "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.
49. "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.
50. "Density functional study of molecular interactions in secondary structures of proteins."
  Takano, Yu*; Kusaka, Ayumi; Nakamura, Haruki
  Biophysics and Physicobiology 2016, 13, 27-35.
51. "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.
52. "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.
53. "Protein folding pathways extracted by OFLOOD: Outlier FLOODing method."
  Harada, Ryuhei*; Nakamura, Tomotake; Takano, Yu; Shigeta, Yasuteru*
  J. Comput. Chem. 2015, 36, 97-102.
54. "NMR characterization of the interaction of the endonuclease domain of MutL with divalent metal ions and ATP."
  Mizushima, Ryota; Kim, Ju Yaen; Suetake, Isao; Tanaka, Hiroaki; Takai, Tomoyo; Kamiya, Narutoshi; Takano, Yu; Mishima, Yuichi; Tajima, Shoji; Goto, Yuji; Fukui, Kenji; Lee, Young-Ho*
  PLoS One 2014, 9, e98554 (13 pages).
55. "Mg2+-dependent Interactions of ATP with the cystathionine-β-Synthase (CBS) domains of a magnesium transporter."
  Hirata, Yusuke; Funato, Yosuke; Takano, Yu; Miki, Hiroaki*
  J. Biol. Chem. 2014, 289, 14731-14739.
56. "Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins."
  Harada, Ryuhei*; Takano, Yu*; Shigeta, Yasuteru*
  J. Chem. Phys. 2014, 140, 125103 (7 pages).
57. "H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin."
  Okamoto, Yasunori; Onoda, Akira*; Sugimoto, Hiroshi; Takano, Yu; Hirota, Shun; Kurtz, Donald; Shiro, Yoshitsugu; Hayashi, Takashi*
  Chem. Comm. 2014, 50, 3421-3423.
  Front cover of Chem. Comm.
58. "Density functional study of the phosphodiester hydrolysis of RNA in RNA/DNA hybrid by RNase H."
  Kita, Makoto; Nakamura, Haruki; Takano, Yu*
  Mol. Phys. 2014, 112, 355-364.
59. "Molecular dynamics simulations accelerated by GPU for biological macromolecules with a non-Ewald scheme for electrostatic interactions."
  Mashimo, Tadaaki; Fukunishi, Yoshifumi; Kamiya, Narutoshi; Takano, Yu; Fukuda, Ikuo; Nakamura, Haruki*
  J. Chem. Theory Comp. 2013, 9, 5599-5609.
60. "Crystal structure, exogenous ligand binding and redox properties of an engineered diiron active site in a bacterial hemerythrin."
  Okamoto, Yasunori; Onoda, Akira*; Sugimoto, Hiroshi; Takano, Yu; Hirota, Shun; Kurtz, Donald; Shiro, Yoshitsugu; Hayashi, Takashi*
  Inorg. Chem. 2013, 52, 13014-13020.
61. "Quantum chemical study of conformational preferences in intermediates and transition states of the hydrolysis of dimethyl phosphate."
  Takano, Yu*; Kita, Makoto; Nakamura, Haruki
  J. Phys. Conf. Ser. 2013, 454, 012058.
62. "Evaluations of the conformational search accuracy of CAMDAS using experimental three-dimensional structures of protein-ligand complexes."
  Oda, Akifumi*; Yamaotsu, Noriyuki; Hirono, Shuichi; Takano, Yu; Fukuyoshi Shuichi; Nakagaki, Ryoichi; Takahashi, Ohgi
  J. Phys. Conf. Ser. 2013, 454, 012028.
63. "Theoretical studies of effect of protein environment on electronic structures and chemical indices of the active site of oxygenated and deoxygenated hemerythrin."
  Takano, Yu*; Yamaguchi, Kizashi; Nakamura, Haruki
  Int. J. Quantum Chem. 2013, 113, 497-503.
64. "Density functional studies of the structural variety of the Cu2S2 core of the CuA site."
  Takano, Yu*; Okuyama, Orio; Shigeta, Yasuteru; Nakamura, Haruki
  Int. J. Quantum Chem. 2012, 112, 3756-3762.
  Inside cover of Int. J. Quantum Chem.
65. "Creation of a binuclear purple copper site within a de novo coiled-coil protein."
  Shiga, Daigo; Funahashi, Yasuhiro; Masuda, Hideki; Kikuchi, Akihiro; Noda, Masanori; Uchiyama, Susumu; Fukui, Kiichi; Kanaori, Kenji; Tajima, Kunihiro; Takano, Yu;, Nakamura, Haruki; Kamei, Misato; Tanaka, Toshiki*
  Biochemistry 2012, 51, 7901-7907.
66. "Coordination effects on the electronic structure of the CuA site of cytochrome c oxidase."
  Koizumi, Kenichi; Shigeta, Yasuteru; Okuyama, Orio; Nakamura, Haruki; Takano, Yu*
  Chem. Phys. Lett. 2012, 531, 197-201.
67. "Possible mechanisms of water splitting reaction based on proton and electron release pathways revealed for CaMn4O5 cluster of PSII refined to 1.9 Å X-ray resolution.&quot
  Saito, Toru; Yamanaka, Shusuke*; Kanda, Keita; Isobe, Hiroshi; Takano, Yu; Shigeta, Yasuteru; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Okumura, Mitsutaka; Shoji, Mitsuo; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Int. J. Quantum Chem. 2012, 112, 253-276.
68. "Electronic structures of the Cu2S2 core of the CuA site in cytochrome c oxidase and nitrous oxide reductase.&quot
  Takano, Yu*; Shigeta, Yasuteru; Koizumi, Kenichi; Nakamura, Haruki
  Int. J. Quantum Chem. 2012, 112, 208-218.
69. "Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water."
  Ikebe, Jinzen; Umezawa, Koji; Kamiya, Narutoshi; Sugihara, Takanori; Yonezawa, Yasushige; Takano, Yu; Nakamura, Haruki; Higo, Junichi*
  J. Comput. Chem. 2011, 32, 1286-1297.
70. "Electronic structures of the [4Fe-4S] cluster in dark-operative protochlorophyllide oxidoreductase (DPOR)."
  Takano, Yu*; Yonezawa, Yasushige; Fujita, Yuichi; Kurisu, Genji; Nakamura, Haruki
  Chem. Phys. Lett. 2011, 503, 296-300.
71. "Theoretical studies on electronic structure and magnetic properties of mixed-valence uteroferrin active site."
  Koizumi, Kenichi*; Shoji, Mitsuo; Yamaguchi, Kizashi; Nakamura, Haruki; Takano, Yu
  Int. J. Quantum Chem. 2011, 111, 702-710.
72. "Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold."
  Shiga, Daigo; Nakane, Daisuke; Inomata, Tomohiko; Funahashi, Yasuhiro; Masuda, Hideki; Kikuchi, Akihiro; Oda, Masayuki; Noda, Masanori; Uchiyama, Susumu; Fukui, Kiichi; Kanaori, Kenji; Tajima, Kunihiko; Takano, Yu; Nakamura, Haruki; Tanaka, Toshiki*
  J. Am. Chem. Soc. 2010, 132, 18191-18198.
73. "Electronic structures of heme a of cytochrome c oxidase in the redox states. -Roles of propionate and formyl groups in electron transfer-"
  Takano, Yu*; Nakamura Haruki
  J. Comput. Chem. 2010 31 954-962.
74. "Density functional study of roles of porphyrin ring in electronic structures of heme."
  Takano, Yu*; Nakamura Haruki
  Int. J. Quantum Chem. 2009, 109, 3585-3591.
75. "Design of the distorted coordination structure of Cu2+ in a de novo designed protein.
  Shiga, Daigo; Nakane, Daisuke; Inomata, Tomohiko; Masuda, Hideki; Oda, Masayuki; Takano, Yu; Nakamura, Haruki; Mizuno, Toshihisa; Tanaka, Toshiki*
  Biopolymers 2009, 91 907-916.
76. "Theoretical studies of the magnetic couplings and the chemical indices of the biomimetic models of oxyhemocyanin and oxytyrosinase."
  Takano, Yu*; Koizumi, Kenichi; Nakamura, Haruki
  Inorganica Chim Acta 2009, 362, 4578-4584.
  (the special issue dedicated to Jerry Trofimenko)
77. "Membrane attachment facilitates ligand access to active site in monoamine oxidase A."
  Apostolov, Rossen; Yonezawa, Yasushige; Standley, Daron M.; Kikugawa, Gota; Takano, Yu; Nakamura, Haruki*
  Biochemistry 2009, 48, 5864-5873.
78. "Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase. -The origin of stronger antiferromagnetic couplings than other purple acid phosphatase-"
  Koizumi, Kenichi*; Yamaguchi, Kizashi; Nakamura, Haruki; Takano, Yu
  J. Phys. Chem. A 2009, 113, 5099-5104.
79. "Theoretical investigation of the electronic asymmetry of the special pair cation radical in the photosynthetic type-II reaction center."
  Yamasaki, Hideki*; Takano, Yu; Nakamura, Haruki
  J. Phys. Chem. B 2008 112, 13923-13933.
80. "Unexpected substantial stability of cyclopropanecarboxylate esters to acid and base hydrolytic conditions and implication for the design of prodrugs."
  Bender, David M.; Peterson, Jeffrey; McCarthy, James R.*; Gunaydin, Hakan; Takano, Yu; Houk, K. N.*
  Org. Lett. 2008, 10, 509-511.
81. "Theoretical studies on electronic structures and chemical indices of the active site in oxygenated and deoxygenated hemerythrin."
  Takano, Yu*; Isobe, Hiroshi; Yamaguchi, Kizashi
  Bull. Chem. Soc. Jpn. 2008, 81, 91-102.
  Selected paper of Bull. Chem. Soc. Jpn.
82. "Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of the protein environment and structural asymmetry."
  Yamasaki, Hideki; Nakamura, Haruki; Takano, Yu*
  Chem. Phys. Lett. 2007, 107, 324-329.
83. "Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species."
  Shoji, Mitsuo; Isobe, Hiroshi; Takano, Yu; Kitagawa, Yasutaka; Yamanaka, Shusuke; Okumura, Mitsutaka; Yamaguchi, Kizashi*
  Int. J. Quantum Chem. 2007, 107, 3250-3265.
84. "Hybrid density functional study of ligand coordination effects on the magnetic couplings and the dioxygen binding of the models of hemocyanin."
  Takano, Yu*; Yamaguchi, Kizashi
  Int. J. Quantum Chem. 2007, 107, 3103-3119.
85. "Quantum mechanical study of the proton transfer via a peptide bond in the novel pathway of proton translocation of cytochrome c oxidase."
  Takano, Yu*; Nakamura, Haruki
  Chem. Phys. Lett. 2006 430, 149-155.
86. "Theoretical study on the magnetic interactions of active site in hemerythrin."
  Shoji, Mitsuo; Hamamoto, Tomohiro*; Koizumi, Kenichi; Isobe, Hiroshi; Kitagawa, Yasutaka; Takano, Yu; Yamanaka, Shusuke; Okumura, Mitsutaka; Yamaguchi, Kizashi
  Polyhedron 2005, 24, 2701-2707.
87. "Mechanistic insights in charge transfer induced luminescence of 1,2-dioxetanones with substituents of low oxidation potentials."
  Isobe, Hiroshi*; Takano, Yu; Okumura, Mitsutaka; Kuramitsu, Seiki; Yamaguchi, Kizashi*
  J. Am. Chem. Soc. 2005 127 8667-8679.
88. "Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules."
  Takano, Yu; Houk, K. N.*
  J. Chem. Theory Comput. 2005, 1, 70-77.
  Most-cited article of J. Chem. Theory Comput. in 2005
89. "Conformational preferences in the transition states and tetrahedral intermediates of transacylations. Relationships to enzyme-bound conformations of phosphonate inhibitors of lipases and esterases."
  Takano, Yu; Houk, K. N.*
  J. Phys. Chem. A 2004, 108, 11740-11751.
90. "Spin and pseudo spins in theoretical chemistry. A unified view of superposed and entangled quantum systems."
  Yamaguchi, Kizashi; Nakano, Masayoshi; Nagao, Hidemi; Okumura Mitsutaka; Yamanaka, Syusuke; Kawakami, Takashi; Yamaki, Daisuke; Nishino, Masamichi; Shigeta, Yasuteru; Kitagawa, Yasutaka; Takano, Yu; Takahata, Masahiro; Takeda, Ryo
  Bull. Korean Chem. Soc. 2003, 24, 864-880
91. "Theoretical calculations of effective exchange integrals by spin projected and unprojected broken-symmetry methods. I: Cluster models of K2NiF4-type solids."
  Onishi, Taku; Yamaki, Daisuke; Yamaguchi, Kizashi*; Takano, Yu
  J. Chem. Phys. 2003, 118, 9747-9761.
92. "Theoretical studies on contributions of SOMO–SOMO and other couplings to the magnetic interaction in radical clusters."
  Takeda, Ryo*; Takano, Yu; Kitagawa, Yasutaka; Kawakami, Takashi; Yamashita, Yoshifumi; Matsuoka, Fumitake; Yamaguchi, Kizashi
  Synthetic Metal 2003 133-134 593-595.
93. "Systematic comparisons between broken-symmetry and symmetry-adapted approaches to transition states by chemical indices. A case study of the Diels–Alder reactions."
  Isobe, Hiroshi*; Takano, Yu; Kitagawa, Yasutaka; Kawakami, Takashi; Yamanaka, Syusuke; Yamaguchi, Kizashi; Houk, K. N.
  J. Phys. Chem. A 2003, 107, 682-694.
94. "Hybrid DFT studies on the magnetic interaction and weak covalent-bonding for phenalenyl radical dimeric pair.&qout;
  Takano, Yu*; Taniguchi, Takeshi; Isobe, Hiroshi; Kubo, Takashi; Morita, Yasushi; Yamamoto, Kagetoshi; Takui, Takeji; Nakasuji, Kazuhiro; Yamaguchi, Kizashi*
  J. Am. Chem. Soc. 2002, 124, 11122-11130.
95. "Effective exchange integrals, effective bond order, unpaired electron density and information entropy for a phenalenyl radical dimeric pair."
  Takano, Yu*; Taniguchi, Takeshi; Isobe, Hiroshi; Kubo, Takashi; Morita, Yasushi; Yamamoto, Kagetoshi; Takui, Takeji; Nakasuji, Kazuhiro; Yamaguchi, Kizashi
  Chem. Phys. Lett. 2002, 358, 17-23.
96. "Analytical and ab initio studies of effective exchange interactions, polyradical charcter, unpaired electron density and information entropy in radical clusters (R)N: Allyl radical cluster (N = 2–10) and hydrogen radical cluster."
  Yamaguchi, Kizashi*; Kawakami, Takashi; Takano, Yu; Kitagawa, Yasutaka; Yamashita, Yoshifumi; Fujita, Harunori
  Int. J. Quantum Chem. 2002, 90, 370-385.
97. "Theoretical studies of magnetic interactions in Mn(II)(hfac)2{di(4-pyridyl)phenylcarbene} and Cu(II)(hfac)2{di(4-pyridyl)phenylcarbene}.&qout;
  Takano, Yu*; Kitagawa, Yasutaka; Onishi, Taku; Yoshioka, Yasunori; Yamaguchi, Kizashi*; Koga, Noboru*; Iwamura, Hiizu
  J. Am. Chem. Soc. 2002, 124, 450-461.
98. "Theoretical investigation of magnetic parameters in two dimensional sheets of pure organic BEDT-TTF and BETS molecules by using ab initio MO and DFT methods."
  Kawakami, Takashi*; Taniguchi, Takeshi; Kitagawa, Yasutaka; Takano, Yu; Nagao, Hidemi; Yamaguchi, Kizashi
  Mol. Phys. 2002, 100, 2641-2652.
99. "Extended Hartree–Fock (EHF) theory of chemical reactions VI. Hybrid DFT and post-Hartree–Fock approaches for concerted and nonconcerted transition structures of the Diels-Alder reaction."
  Isobe, Hiroshi*; Takano, Yu; Kitagawa, Yasutaka; Kawakami, Takashi; Yamanaka, Shusuke; Yamaguchi, Kizashi; Houk, K. N.
  Mol. Phys. 2002, 100, 717-727.
100. "EHF theory of chemical reactions V. The nature of manganese-oxygen bonds in photosystem II by hybrid density functional (DFT) and coupled-cluster (CC) methods."
  Isobe, Hiroshi*; Soda, Tomohisa; Kitagawa, Yasutaka; Takano, Yu; Kawakami, Takashi; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Int. J. Quantum Chem. 2001, 85, 34-43.
101. "Theoretical study of the magnetic interaction for M–O–M type metal oxides. Comparison of broken-symmetry approaches."
  Onishi, Taku*; Takano, Yu; Kitagawa, Yasutaka; Kawakami, Takashi; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Polyhedron 2001, 20, 1177-1184.
102. "Theoretical studies on the magnetic and reversible dioxygen binding of the active site in hemocyanin."
  Takano, Yu*; Kubo, Shigehiro; Onishi, Taku; Isobe, Hiroshi; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Chem. Phys. Lett. 2001, 335, 395-403.
103. "Density functional study of intramolecular ferromagnetic interaction through m-phenylene coupling unit (II): Examination of functional dependency."
  Mitani, Masaki; Yamaki, Daisuke; Takano, Yu; Kitagawa, Yasutaka; Yoshioka, Yasunori; Yamaguchi, Kizashi*
  J. Chem. Phys. 2000, 113, 10486-10504.
104. "Density functional study of intramolecular ferromagnetic interaction through m-phenylene coupling unit (I): UBLYP, UB3LYP and UHF calculation."
  Mitani, Masaki; Mori, Hiroki; Takano, Yu; Yamaki, Daisuke; Yoshioka, Yasunori; Yamaguchi, Kizashi*
  J. Chem. Phys. 2000, 113, 4035-4051.
105. "Density functional and post Hartree–Fock studies on the effective exchange interaction of d-π-p and d-π-d conjugated systems involving m-phenylene bridge."
  Takano, Yu*; Onishi, Taku; Kitagawa, Yasutaka; Soda, Tomohisa; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Int. J. Quantum Chem. 2000, 80, 681-691.
106. "Ab initio computation of effective exchange integrals for H–H, H–He–H and Mn2O2 complex. Comparison of broken-symmetry approaches."
  Soda, Tomohisa*; Kitagawa, Yasutaka; Onishi, Taku; Takano, Yu; Shigeta, Yasuteru; Nagao, Hidemi; Yoshioka, Yasunori; Yamaguchi, Kizashi
  Chem. Phys. Lett. 2000, 319, 223-230.
107. "Experimental and theoretical studies on the selectivity of GGG triplets toward one-electron oxidation in B-form DNA."
  Yoshioka, Yasunori*; Kitagawa, Yasutaka; Takano, Yu; Yamaguchi, Kizashi*; Nakamura, Takashi; Saito, Isao*
  J. Am. Chem. Soc. 1999, 121, 8712-8719.
108. "Density functional study of intramolecular ferromagnetic interaction through m-phenylene coupling unit (III): Possibility of high-spin polymer."
  Mitani, Masaki*; Takano, Yu; Yoshioka, Yasunori; Yamaguchi, Kizashi
  J. Chem. Phys. 1999, 111, 1309-1324.
109. "Theoretical Studies of the effective exchange interactions and photoinduced magnetism in manganese and copper di(4-pyridyl)carbene complexes."
  Takano, Yu; Soda, Tomohisa; Kitagawa, Yasutaka; Yoshioka, Yasunori*; Yamaguchi, Kizashi
  Chem. Phys. Lett. 1999, 301, 309-316.
110. "Theoretical studies of decomposition reactions of dioxetane, dioxetanone, and related species. CT induced luminescence mechanism revisited."
  Takano, Yu; Tsunesada, Tsunaki; Isobe, Hiroshi; Yoshioka, Yasunori; Yamaguchi, Kizashi*; Saito, Isao*
  Bull. Chem. Soc. Jpn. 1999, 72, 213-225.
111. "Symmetry and broken symmetries in MO descriptions of unstable molecules II. Alignment, frustration and tunneling of spins in mesoscopic molecular magnets."
  Yamaguchi, Kizashi*; Yamanaka, Syusuke; Nishino, Masamichi; Takano, Yu; Kitagawa, Yasutaka; Nagao, Hidemi; Yoshioka, Yasunori
  Theor. Chem. Acc. 1999, 102, 328-345.
112. "Electronic structures of organometallic conjugated systems. Possibilities of molecular magnets, magnetic conductors and spin-mediated superconductors composed of metallocene units.
  Okamura, Taka-aki; Takano, Yu; Yoshioka, Yasunori; Ueyama, Norikazu; Nakamura, Akira; Yamaguchi, Kizashi*
  J. Organomet. Chem. 1998, 569, 177-187.
113. "Theoretical study of electronic structures of one-dimensional magnetic clusters composed of doublet lithium and copper atoms."
  Kawakami, Takashi; Yamanaka, Syusuke; Takano, Yu; Yoshioka, Yasunori*; Yamaguchi, Kizashi
  J. Mol. Struct. (Theochem) 1998, 451, 89-107.
114. "Ab initio size-consistent calculations of effective exchange interactions in mesoscopic magnetic clusters composed of triplet methylenes and quartet nitrogen atoms."
  Kawakami, Takashi; Yamanaka, Syusuke; Takano, Yu; Yoshioka, Yasunori; Yamaguchi, Kizashi*
  Bull. Chem. Soc. Jpn. 1998, 71, 2097-2108.
115. "Hubbard and Heisenberg models for four-site four-electron systems. Group-theoretical interrelationships and applications to multinuclear transition-metal clusters." Yoshioka, Yasunori*; Kubo, Shigehiro; Kiribayashi, Shinji; Takano, Yu; Yamaguchi, Kizashi*
  Bull. Chem. Soc. Jpn. 1998, 71, 573-588.

総説・解説

"Quantum chemical studies on hydrogen bonds in helical secondary structures"
Takano, Yu*; Kondo, Hiroko X.; Nakamura, Haruki
Biophys. Rev. 2022, 14, 1369-1378.
"Computational study of distortion effect of Fe-porphyrin found as a biological active site"
Takano, Yu*; Kondo, Hiroko X.; Kanematsu, Yusuke; Imada, Yasuhiro
Jpn. J. Appl. Phys. 2020, 59, 010502.
"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.
"Simple, yet powerful methodologies for conformational sampling of proteins."
Ryuhei Harada*, Yu Takano, Takeshi Baba, Yasuteru Shigeta*
Phys. Chem. Chem. Phys. 2015, 17, 6155-6173.
"タンパク質計算科学の進展."
鷹野優*・中村春木
パリティ 2014, 29, 63-64.
"非エバルト法に基づくGPUで加速されたG蛋白質共役型受容体の分子動力学計算."
真下忠彰・福西快文・神谷成敏・鷹野優・福田育夫・中村春木*
TSUBAME e-Science Journal 2013, 10, 8-12.
"暗所作動型プロトクロロフィリド還元酵素(DPOR)中の特異な[4Fe-4S]クラスターの電子構造と機能への影響."
鷹野優*
アンサンブル 2012, 14, 145-149.
"暗所作動型プロトクロロフィリド還元酵素中の特異な[4Fe-4S]クラスターの電子構造."
鷹野優*
生物物理 2011, 51, 232-233.
"Protein Data Bank Japan (PDBj)."
鷹野優*
化学と工業 2010, 63, 149.
"基礎からはじめる段階式蛋白質設計 −蛋白質構築原理を演繹的に探る−."
鷹野優*
蛋白質・酵素・化学 2009, 54, 1210-1210.
"光合成反応中心スペシャルペアの電子非対称性の構造的起源 −量子化学計算とバイオインフォマティクスによるアプローチ–."
山崎秀樹*・鷹野優・中村春木
生物物理 2009, 49, 84-85.
"オーダーメイドの酵素ができた！ −コンピュータを使って天然にない酵素をデザインする−."
鷹野優*
化学 2009, 64, 60-61.
"手をつなぐと、酵素反応も進む −酵素反応に対する新しいパラダイム−."
鷹野優
蛋白質・酵素・化学 2005, 50, 1453-1454.

Books (Chapter)

"Molecular Dynamics."
Takano, Yu; Ohkubo, Takahiro; Watanabe, Satoshi
Hyperordered Structures in Materials –Disorder in Order and Order within Disorder– (edited by Koichi Hayashi)
Chapter 9 Springer 2024 pp. 217–247.
"計算化学によるヘムタンパク質の機能解析と予測"
重田育照・下山絋充・神谷克政・鷹野優
ヘムタンパク質の科学 (城宜嗣・青野重利・齋藤正男編)
第1編第5章第7節 NTS 2022 日本 pp.233–242.
"有機デバイス・バイオ材料"
久保園芳博・佐々木裕次・鷹野優・山田容子
機能構造化学入門 3D活性サイトと物質デザイン (大門寛・佐々木裕次編)
8章丸善出版 2016 日本 pp. 139-161.
"第一原理電子状態計算法と分子動力学法"
森川良忠・鷹野優
機能構造化学入門 3D活性サイトと物質デザイン (大門寛・佐々木裕次編)
5章丸善出版 2016 日本 pp. 83-109.
"光化学系II"
鷹野優*
「見てわかる構造生命科学」ー生命科学研究へのタンパク質構造の利用ー (中村春木編)
Structure-16 化学同人 2014 日本 pp. 311-321.
"鉄ー硫黄タンパク質"
鷹野優*
「見てわかる構造生命科学」ー生命科学研究へのタンパク質構造の利用ー (中村春木編)
Structure-2 化学同人 2014 日本 pp. 107-122.
"Density functional study of the origin of the strongly delocalized electronic structure of the CuA site in cytochrome c oxidase."
Takano, Yu*; Okuyama, Orio; Shigeta, Yasuteru; Nakamura, Haruki
Progress in Theoretical Chemistry and Physics (edited by Kiyoshi Nishikawa, Jean Maruani, Erkki J. Brändas, Gerardo Delgado-Barrio, and Piotr Piecuch)
Chapter 30 Springer 2013 pp. 513-524.
"Validation of quantum chemical calculations for sulfonamide geometrical parameters."
Oda, Akifumi; Takano, Yu*; Takahashi, Ohgi
Progress in Theoretical Chemistry and Physics (edited by Kiyoshi Nishikawa, Jean Maruani, Erkki J. Brändas, Gerardo Delgado-Barrio, and Piotr Piecuch)
Chapter 17 Springer 2013 pp. 331-344.
"Chemical indices of the biomimetic models of oxyhemocyanin and oxytyrosinase."
Takano, Yu*; Yamaguchi, Kizashi; Nakamura, Haruki
Biomimetic Based Applications (editted by Anne George)
Chapter 8 INTECH 2011 Croatia pp. 123-140.
"多核遷移金属酵素・タンパク質."
鷹野優*・吉岡泰規
物性量子化学 (山口兆・吉岡泰規・中野雅由・長尾秀実・奥村光隆編)
第9章講談社サイエンティフィク 2004 日本 pp. 166-183.

Proceedings

"A theoretical approach to a novel pathway of proton translocation of cytochrome c oxidase."
Takano, Yu*; Nakamura, Haruki
AIP Conf. Proc. 2008, 1046, 60-63.
"Theoretical studies on magnetic interaction of M-π conjugated systems via pyrimidine coupler."
Takano, Yu; Isobe, Hiroshi; Kawakami, Takashi; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2002, 379, 531-536.
"Theoretical studies on electronic states of hole-doped copper oxides."
Onishi, Taku; Takano, Yu; Yamaki, Daisuke; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2002, 379, 507-512.
"Theoretical study on the magnetic interaction for manganese oxides."
Onishi, Taku; Takano, Yu; Kitagawa, Yasutaka; Kawakami, Takashi; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2002, 376, 335-340.
"Theoretical studies on magnetic interaction of Mn-π conjugated systems."
Takano, Yu; Soda, Tomohisa; Kitagawa, Yasutaka; Onishi, Taku; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2000, 343, 291-296.
"Theoretical studies on magnetic interaction of di-μ-oxo bridged manganese dimers."
Soda, Tomohisa; Kitagawa, Yasutaka; Onishi, Taku; Takano, Yu; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2000, 343, 157-162.
"Theoretical study on necessary conditions for reversible photoinduced magnetization: cobalt-iron cyanide system."
Nishino, Masamichi; Kitagawa, Yasutaka; Onishi, Taku; Soda, Tomohisa; Takano, Yu; Nagao, Hidemi; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2000, 343, 151-156.
"Theoretical studies on magnetic interactions of dichromium tetraacetate by using hybrid density functional theory."
Kitagawa, Yasutaka; Soda, Tomohisa; Onishi, Taku; Takano, Yu; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2000, 343, 145-150.
"Theoretical studies of the antiferromagnetic model clusters for K2MX4 type solids."
Onishi, Taku; Soda, Tomohisa; Kitagawa, Yasutaka; Takano, Yu; Yamaki, Daisuke; Takamizawa, Satoshi; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 2000, 343, 133-138.
"Ab initio crystal orbital study of ferromagnetic interaction of spins in polymer comprising phenylenevinylene."
Mitani, Masaki; Takano, Yu; Yamaki, Daisuke; Yoshioka, Yasunori; Yamaguchi, Kizashi*
Mol. Cryst. Liq. Cryst. 1999, 335, 613-622.