Publication

Reviewed Publications

• Original Research Papers

  • "Redesign of a thioflavin-T-binding protein with a flat β-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity"
    Yuina Miura, Sae Namioka, Atsushi Iwai, Norio Yoshida, Hiroyuki Konno, Youhei Sohma, O Motomu Kanai, Koki Makabe
    Int. J. Biol. Macromol., (2024) 269, 131992. (DOI: 10.1016/j.ijbiomac.2024.131992)

  • "RISMiCal: a software package to perform fast rism/3d-rism calculations"
    Yutaka Maruyama, Norio Yoshida
    J. Comput. Chem., (2024) 45, 1470-1482 (DOI: 10.1002/jcc.27340)

  • "Solvent distribution effects on quantum chemical calculations with quantum computers"
    Yuichiro Yoshida, Wataru Mizukami, Norio Yoshida
    J. Chem. Theory Comput., (2024) 20 1952-1972 (DOI: 10.1021/acs.jctc.3c01189)

  • "Assessment of the Applicability of the LFC/3D-RISM-SCF Scheme for pKa Prediction in Methanol Solutions"
    Ryo Fujiki,Toru Matsui, Yasuteru Shigeta, Norio Yoshida, Haruyuki Nakano
    Chem. Lett.,  (2024) 53, upad009 (DOI: 10.1093/chemle/upad009)

  • "Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory "
    Tsuyoshi Yamaguchi, Song-Ho Chong, and Norio Yoshida
    J. Chem. Phys., (2023) 159, 245101 (DOI: 10.1063/5.0185157 )

  • "Selective molecular recognition of amino acids and their derivatives by cucurbiturils in aqueous solution: an MD/3D-RISM study"
    Natthiti Chiangraeng, Haruyuki Nakano, Piyarat Nimmanpipug, and Norio Yoshida
    J. Mol. Liquids, (2023) 385, 122503 (DOI: 10.1016/j.molliq.2023.122503)

  • "Effects of intramolecular chain conformation on the hydration and miscibility of polyethylene glycol in water studied by means of polymer reference interaction site model theory"
    Tsuyoshi Yamaguchi, Song-Ho Chong, Norio Yoshida
    J. Chem. Phys., (2023) 159,  044901 (DOI: 10.1063/5.0159130)

  • "Tuning the ATP-ATP and ATP-disordered protein interactions in high ATP concentration by altering water models"
    Toshifumi Mori, Norio Yoshida
    J. Chem. Phys., (2023) 159, 035102 (DOI: https://doi.org/10.1063/5.0158046 )

  • "A method for protein structure sampling under three-dimensional reference interaction site model solvation based on hybrid Monte Carlo framework"
    Norio Yoshida, Tsuyoshi Yamaguchi
    J. Mol. Liquids, (2023) 385, 122418 (DOI: 10.1016/j.molliq.2023.122418)

  • "Effects of angular momentum and thermostat on molecular dynamics simulation of single-chain conformation in an implicit solvent"
    Tsuyoshi Yamaguchi, Song-Ho Chong, Norio Yoshida
    J. Mol. Liquids, (2023) 385, 122311 (DOI: 10.1016/j.molliq.2023.122311)

  • "Theoretical Analysis of the Role of Water in Ligand Binding to Cucurbit[n]uril of Different Sizes"
    Natthiti Chiangraeng, Haruyuki Nakano, Piyarat Nimmanpipug, and Norio Yoshida
    J. Phys. Chem. B. (2023) 127, 3651-3662 (DOI: 10.1021/acs.jpcb.3c00343)

  • "Phase equilibrium of three-component liquid systems composed of water, alcohol and sodium chloride studied by the reference interaction-site model integral equation theory"
    Tsuyoshi Yamaguchi, Song-Ho Chong, Norio Yoshida
    J. Chem. Phys., (2023) 158, 084502 (DOI: 10.1063/5.0142256) 

  • "Study of phase equilibria and thermodynamic properties of liquid mixtures using the integral equations theory: Application to water and alcohol mixtures"
    Tsuyoshi Yamaguchi, Song-Ho Chong, Norio Yoshida
    J. Chem. Phys., (2022) 157, 234502 (DOI: 10.1063/5.0131475 ) 

  • "Solvent effects in four-component relativistic electronic structure theory based on the reference interaction-site model"
    Kodai Kanemaru, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano
    J. Comput. Chem., (2022) 44, 5-14 ( DOI: doi.org/10.1002/jcc.27009 )

  • "Computational Analysis of the SARS-CoV-2 RBD–ACE2-Binding Process Based on MD and the 3D-RISM Theory"
    Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano
    J. Chem. Info. Model. (2022) 62, 2889-2898 (DOI: doi.org/10.1021/acs.jcim.2c00192 )

  • "Implementation of solvent polarization in three-dimensional reference interaction-site model self-consistent field theory"
    Norio Yoshida, Tsuyoshi Yamaguchi, Haruyuki Nakano
    Chem. Phys. Lett., (2022) 797, 139579, (DOI: 10.1016/j.cplett.2022.139579)

  • "Modeling the interaction of SARS-CoV-2 binding to the ACE2 receptor via molecular theory of solvation,"
    Alexander E. Kobryn, Yutaka Maruyama, Carlos A. Velazquez-Martinez, Norio Yoshida, Sergey Gusarov
    New J. Chem., (2021) 45, 15448-15457 (doi.org/10.1039/D1NJ02015C)

  • "Temperature-Responsive Morphology Formation of PS-b-PI copolymer: A Dissipative Particle Dynamics Simulation Study"
    Natthiti Chiangraeng, Ukrit Keyen, Norio Yoshida and Piyarat Nimmanpipug
    Soft Matter, (2021) 17, 6248-6258  (doi.org/10.1039/D1SM00152C)

  • "A computational method to simulate global conformational changes of proteins induced by cosolvent"
    Shoichi Tanimoto, Koichi Tamura, Shigehiko Hayashi, Norio Yoshida, Haruyuki Nakano
    J. Comput. Chem., (2021) 42, 552-563 (doi.org/10.1002/jcc.26481 )

  • "Solvation dynamics in electronically polarizable solvents: Theoretical treatment using solvent-polarizable three-dimensional reference interaction-site model theory combined with time-dependent density functional theory"
    Tsuyoshi Yamaguchi, Norio Yoshida
    J. Chem. Phys., (2021) 154, 044504 (doi.org/10.1063/5.0036289 )

  • "Nonequilibrium free-energy profile of charge-transfer reaction in polarizable solvent studied using solvent-polarizable three-dimensional reference interaction-site model theory"
    Tsuyoshi Yamaguchi, Norio Yoshida
    J. Chem. Phys., (2020) 153, 034502 (doi.org/10.1063/5.0013083)

• "Residue-Specific Binding Mechanisms of Thioflavin T to a Surface of Flat β-Sheets within a Peptide Self-Assembly Mimic"
  Sae Namioka, Norio Yoshida, Hiroyuki Konno, and Koki Makabe
  Biochemistry, (2020) 59, 2782-2787 (doi.org/10.1021/acs.biochem.0c00280)

• "Development of a solvent-polarizable three-dimensional reference interaction-site model theory "
  Norio Yoshida, Tsuyoshi Yamaguchi
  J. Chem. Phys., (2020) 152, 114108 (doi.org/10.1063/5.0004173) 

• "Distinct ionic adsorption sites in defective Prussian blue: a 3D-RISM study"
  Nirun Ruankaew, Norio Yoshida, Yoshihiro Watanabe, Akira Nakayama, Haruyuki Nakano, Saree Phongphanphanee
  Phys. Chem. Chem. Phys., (2019) 21, 22569-22576 (DOI: 10.1039/C9CP04355A )

• "Effects of Water Addition on a Catalytic Fluorination of Dienamine"
  Daiki Kuraoku, Tsunaki Yonamine, Genta Koja, Norio Yoshida, Satoru Arimitsu, Masahiro Higashi
  Molecules (2019) 24, 3428(1-8) ( DOI: 10.3390/molecules24193428 )

• "Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory"
  Shoichi Tanimoto, Norio Yoshida, Tsuyoshi Yamaguchi, Seiichiro Ten-no, Haruyuki Nakano
  J. Chem. Info. Model (2019) 59, 3770-3781 ( DOI: 10.1021/acs.jcim.9b00330)

• "Relation Between Anharmonicity of Free Energy Profile and Spectroscopy in Solvation Dynamics: Differences in Spectral Broadening and Peak Shift in Transient Hole-Burning Spectroscopy Studied by Equilibrium Molecular Dynamics Simulation"
  Tsuyoshi Yamaguchi, Norio Yoshida, Katsura Nishiyama
  J. Phys. Chem. B. (2019) 123, 7036-7042 ( DOI: 10.1021/acs.jpcb.9b04711 )

• "β-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals"
  Hideki Fujiwara, Kenta Hongo, Yuki Hori, Norio Yoshida, Koki Makabe
  J. Mol. Liquids, (2019) 290, 111161. ( DOI: 10.1016/j.molliq.2019.111161)

• "Implementation of state-averaged MCSCF method to RISM- and 3D-RISM-SCF "
  Daisuke Okamoto, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano
  Chem. Phys. Lett., (2019) 730, 179-185. (DOI: 10.1016/j.cplett.2019.05.051)

• "Three-Dimensional Reference Interaction Site Model Self-Consistent-Field Study on the Coordination Structure and Excitation Spectra of Cu(II)–Water Complexes in Aqueous Solution"
  Chen Yang, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano
  J. Phys. Chem. A, (2019) 123, 3344-3354. (DOI: 10.1021/acs.jpca.9b01364)

• "Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2"
  Hiroko X. Kondo, Norio Yoshida, Matsuyuki Shirota, Kengo Kinoshita
  J. Phys. Chem. B. (2018) 122, 10825-10833. (DOI: 10.1021/acs.jpcb.8b09446)

• "A computational scheme of pKa values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme"
  Ryo Fujiki, Yukako Kasai, Yuki Seno, Toru Matsui, Yasuteru Shigeta, Norio Yoshida, Haruyuki Nakano
  Phys. Chem. Chem. Phys., (2018) 20, 27272-27279. (DOI: 10.1039/C8CP04354J)

• "Role of Mg2+ ions in DNA hydrolysis by EcoRV, Studied by 3D-Rerefence interaction site model and molecular dynamics"
  Itaru Onishi, Shunya Sunaba, Norio Yoshida, Fumio Hirata, Masayuki Irisa
  J. Phys. Chem. B. (2018) 122, 9061-9075 (DOI: 10.1021/acs.jpcb.7b12555)

• "An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin"
  Cheng Cheng, Motoshi Kamiya, Mizuki Takemoto, Ryuichiro Ishitani, Osamu Nureki, Norio Yoshida, Shigehiko Hayashi
  Biophys. J., (2018) 115, 1281-1291. (DOI: 10.1016/j.bpj.2018.08.024)

• "A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method"
  Norio Yoshida
  Chem. Phys. Lett., (2018) 699, 22-27 (DOI: 10.1016/j.cplett.2018.03.034)

• "Theoretical Analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach "
  Norio Yoshida, Masahiro Higashi, Hideyoshi Motoki, Shun Hirota
  J. Chem. Phys., (2018) 148, 025102 (DOI: 10.1063/1.5009785)

• "A relationship between the force curve measured by atomic force microscopy in an ionic liquid and its density distribution on a substrate"
  Ken-ichi Amano, Yasuyuki Yokota, Takashi Ichii, Norio Yoshida, Naoya  Nishi, Seiji Katakura, Akihito Imanishi, Ken-ichi Fukui, Tetsuo Sakka
  Phys. Chem. Chem. Phys., (2017) 19, 30504-30512 (DOI:10.1039/C7CP06948K)

• "Solvatochromism and Preferential Solvation of Brooker’s Merocyanine in Water–Methanol Mixtures"
  Yuichi Tanaka, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano
  J. Comput. Chem., 38, (2017) 2411-2419 (DOI:10.1002/jcc.24902 )

• "Size-dependent adsorption sites in a Prussian blue nanoparticle: A 3D-RISM study"
  Nirun Ruankaew, Norio Yoshida, Yoshihiro Watanabe, Haruyuki Nakano, Saree Phongphanphanee
  Chem. Phys. Lett., 684, (2017) 117-125 (DOI: 10.1016/j.cplett.2017.06.053 )

• "The ion-dependence of carbohydrate binding of CBM36: An MD and 3D-RISM study"
  Shoichi Tanimoto, Masahiro Higashi, Norio Yoshida, Haruyuki Nakano
  J. Phys. Condens. Matter,  28, (2016) 344005(8pp) (DOI:10.1088/0953-8984/28/34/344005)

• "Theoretical analysis of complex formation of p-carboxybenzeneboronic acid with a monosaccharide"
  Yuki Seno, Norio Yoshida, Haruyuki Nakano
  J. Mol. Liquids,  217, (2016) 93-98 (DOI:10.1016/j.molliq.2015.12.063 )

• "A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase"
  Jiraphorn Phanich, Thanyada Rungrotmongkol, Daniel Sindhikara, Saree Phongphanphanee, Norio Yoshida, Fumio Hirata, Nawee Kungwan and Supot Hannongbua
  Protein Science, 25, (2016) 147-158 (DOI:10.1002/pro.2718)

• "Three-Dimensional Reference Interaction Site Model Self-Consistent Field Analysis of Solvent and Substituent Effects on the Absorption Spectra of Brooker’s Merocyanine"
  Yuichi Tanaka, Norio Yoshida, Haruyuki Nakano
  J. Comput. Chem., 36,  (2015) 1655-1663 ( DOI:10.1002/jcc.23980 )

• "Theoretical Analysis of Co-Solvent Effect on the Proton Transfer Reaction of Glycine in a Water-Acetonitrile Mixture "
  Yukako Kasai, Norio Yoshida, Haruyuki Nakano
  J. Chem. Phys., 142, (2015) 204103 (9pages) (DOI: 10.1063/1.4921432)

• "Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter"
  Tomoka Furukawa-Hagiya, Norio Yoshida, Shuntaro Chiba, Tomohiko Hayashi, Tadaomi Furuta, Yoshiro Sohma, Minoru Sakurai
  Chem. Phys. Lett., 616-617, (2014) 165-170 (DOI: 10.1016/j.cplett.2014.10.038)

• "Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method"
  Norio Yoshida
  J. Chem. Phys., 140, (2014) 214118 (13pages) (DOI: 10.1063/1.4879795)

• "Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probe by 3D-RISM theory"
  Saree Phongphanphanee, Norio Yoshida (equal contribution with the 1st author), Shigetoshi Oiki, Fumio Hirata
  J. Mol. Liquids,  200, (2014) 52-58. (DOI: 10.1016/j.molliq.2014.03.050)

• "Theoretical analysis of salt effect on intramolecular proton transfer reaction of glycine in NaCl aqueous solution"
  Yukako Kasai, Norio Yoshida, Haruyuki Nakano
  J. Mol. Liquids, 200, (2014) 32-37. (DOI:10.1016/j.molliq.2014.02.013)

• "Massively Parallel Implementation of 3D-RISM Calculation with Volumetric 3D-FFT"
  Yutaka Maruyama, Norio Yoshida, Hiroto Tadano, Daisuke Takahashi, Mitsuhisa Sato, Fumio Hirata
  J. Comput. Chem., 35 (2014) 1347-1355. (DOI:10.1002/jcc.23619)

• "Theoretical Characterization of the “Ridge” in the Supercritical Region in the Fluid Phase Diagram of Water"
  Masaru Matsugami, Norio Yoshida, Fumio Hirata
  J. Chem. Phys., 140, (2014) 104511 (6pages), (DOI:10.1063/1.4867974)

• "Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory"
  Saree Phongphanphanee, Norio Yoshida (equal contribution with the 1st author), Shigetoshi Oiki, Fumio Hirata
  Pure and Applied Chem., 86, (2014) 97-104, (DOI: 10.1515/pac-2014-5018)

• "Theoretical Study of Salt Effects on Diels-Alder Reaction of Cyclopentadiene With Methyl Vinyl Ketone Using RISM-SCF Theory"
  Norio Yoshida, Hidetsugu Tanaka, Fumio Hirata
  J. Phys. Chem. B, 117, (2013) 14115-14121, (DOI: 10.1021/jp4091552)

• "Solvent dependence of Stokes shift for organic solute-solvent systems: A comparative study by spectroscopy and reference interation-site model-self-consistent-field theory"
  Katsura Nishiyama, Yasuhiro Watanabe, Norio Yoshida, Fumio Hirata
  J. Chem. Phys., 139, (2013) 094503 (11pages), (DOI: 10.1063/1.4819268)

• "Solvent effect on excited states of merocyanines: A theoretical study using the RISM-SCF method"
  Yuichi Tanaka, Norio Yoshida, Haruyuki Nakano
  Chem. Phys. Lett., 583, (2013), 69-73, (DOI: 10.1016/j.cplett.2013.08.004)

• "Three-dimensional Reference Interaction Site Model Self-consistent Field Study of the Electronic Structure of [Cr(H2O)6]3+ in Aqueous Solution"
  Shinya Fujishige, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano
  J. Phys. Chem. A, 117, (2013) 8314-8322, (DOI: 10.1021/jp405876g)

• "Extended Molecular Ornstein-Zernike Integral Equation for Fully Anisotropic Solute Molecules: Formulation in a Rectangular Coordinate System"
  Ryosuke Ishizuka, Norio Yoshida
  J. Chem. Phys., 139, (2013) 084119 (10pages), (DOI: 10.1063/1.4819211)

• "Elucidating the Molecular Origin of Hydrolysis Energy of Pyrophosphate in Water"
  Jooyeon Hong, Norio Yoshida, Song-Ho Chong, Chewook Lee, Sihyun Ham, Fumio Hirata
  J. Chem. Theory Comput., 8, (2012) 2239-2246, (DOI: 10.1021/ct300099e)

• "Placevent: an algorithm for prediction of explicit solvent atom distribution -- application to HIV-1 protease and F-ATP synthase"
  Daniel Sindhikara, Norio Yoshida, Fumio Hirata
  J. Comput. Chem., 33, (2012) 1536-1543, (DOI: 10.1002/jcc.22984)

• "Application of efficient algorithm for solving six-dimensional molecular Ornstein-Zernike equation"
  Ryosuke Ishizuka,  Norio Yoshida
  J. Chem. Phys., 136, (2012) 114106(6pages), (DOI: 10.1063/1.3693623)

• Erratum "Application of efficient algorithm for solving six-dimensional molecular Ornstein-Zernike equation"
  Ryosuke Ishizuka, Norio Yoshida
  J. Chem. Phys., 141, (2014) 149907(2pages), (DOI: 10.1063/1.4898146)

• "A new approach for investigating the molecular recognition of protein: Toward structure-based drug-design based on the 3D-RISM theory"
  Yasuomi Kiyota, Norio Yoshida, Fumio Hirata
  J. Chem. Theory Comput., 7, (2011) 3803-3815, (DOI: 10.1021/ct200358h)

• Reply to Comment "Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory"
  Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
  J. Phys. Chem. B, 115, (2011) 8367-8369, (DOI: 10.1021/jp203661z)

• "Solvent penetration in photoactive yellow protein R52Q mutant: a theoretical study"
  Daniel Sindhikara, Norio Yoshida, Mikio Kataoka, Fumio Hirata
  J. Mol. Liquids, 164, (2011) 120-122, (DOI: 10.1016/j.molliq.2011.04.007)

• "Affinity of Small Ligands to Myoglobin Studied by the 3D-RISM Theory"
  Yasuomi Kiyota, Norio Yoshida, Fumio Hirata
  J. Mol. Liquids, 159, (2011) 93-98, (DOI: 10.1016/j.molliq.2010.07.016)

• "The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA"
  Norio Yoshida, Yasuomi Kiyota, Fumio Hirata
  J. Mol. Liquids, 159, (2011) 83-92, (DOI: 10.1016/j.molliq.2010.04.019)

• "Proton transport through the Influenza A M2 channel: 3D-RISM Study"
  Saree Phongphanphanee, Thanyada Rungrotmongkol, Norio Yoshida, Supot Hannongbua, Fumio Hirata
  J. Am. Chem. Soc., 132, (2010), 9782-9788, (DOI: 10.1021/ja1027293)

• "Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory"
  Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
  J. Phys. Chem. B,, 114, (2010), 7967-7973, (DOI: 10.1021/jp101936y)

• "Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory"
  Yutaka Maruyama, Norio Yoshida, Fumio Hirata
  J. Phys. Chem. B,, 114, (2010), 6464-6471, (DOI: 10.1021/jp912141u)

• "Theoretical Study of CO escaping pathway in Myoglobin with the 3D-RISM Theory"
  Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata
  J. Am. Chem. Soc. (communication) , 131, (2009), 3852-3853, (DOI: 10.1021/ja900332e)  

• "RISM-SCF Study of the Solvation Effect on A Nucleophilic Aromatic Substitution between 4-fluoronitrobenzen and azide anion"
  Hidetsugu Tanaka, Norio Yoshida, Yasuhiro Ikuta, Yasuomi Kiyota and Fumio Hirata
  Int. J. Liq. State Sciences, 2, (2010), 15-24, Invited 

• "The Potential of Mean Force of Water and Ions in Aquaporin Channels Investigated by the 3D-RISM Method"
  Saree Phongphanphanee, Norio Yoshida and Fumio Hirata
  J. Mol. Liquids, 147, (2009), 107-111, (DOI: 10.1016/j.molliq.2008.07.003) 

• "On the Proton Exclusion of Aquaporins: A Statistical Mechanics Study"
  Saree Phongphanphanee, Norio Yoshida and Fumio Hirata
  J. Am. Chem. Soc. (Communication), 130, (2008), 1540-1541, (DOI: 10.1021/ja077087) 

• "Theoretical Study of Temperature and Solvent Dependence of the Free Energy Surface of the Intramolecular Electron Transfer Based on the RISM-SCF Theory; Application to 1,3-Dinitrobenzene Radical Anion in Acetonitrile and Methanol"
  Norio Yoshida, Tateki Ishida and Fumio Hirata
  J. Phys. Chem. B, 112, (2008) 433-440, (DOI: 10.1021/jp076219i) 

• "The statistical-mechanics study of equilibrium water distribution in the aquaporin"
  Saree Phongphanphanee, Norio Yoshida and Fumio Hirata
  Chem. Phys. Lett., 449, (2007), 196-201, (DOI: 10.1016/j.cplett.2007.10.046)

• "Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method"
  Norio Yoshida
  Cond. Matt. Phys., 10, (2007), 363-372, (DOI: 10.5488/CMP.10.3.363)

• "Selective Ion-Binding by Protein Probed with the Statistical Mechanical Integral Equation Theory"
  Norio Yoshida, Saree Phongphanphanee and Fumio Hirata
  J. Phys. Chem. B, 111, (2007), 4588-4595, (DOI: 10.1021/jp0685535)

• "Selective ion-binding by protein probed with the 3D-RISM theory"
  Norio Yoshida, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai and Fumio Hirata
  J. Am. Chem. Soc. (Communication), 128, (2006), 12042-12043, (DOI: 10.1021/ja0633262)

• "Conformational equilibrium of 1,2-dichloroethane in water: Comparison of PCM and RISM-SCF methods"
  Jin Yong Lee, Norio Yoshida and Fumio Hirata
  J. Phys. Chem. B, 110, (2006), 16018-16025, (DOI: 10.1021/jp0606762)

• "Ab initio Theoretical Study of Temperature and Density Dependence of Molecular and Thermodynamic Properties of Water in the Entire Fluid Region: Autoionization Process"
  Norio Yoshida, Ryosuke Ishizuka, Hirofumi Sato and Fumio Hirata
  J. Phys. Chem. B, 110, (2006), 8451-8458, (DOI: 10.1021/jp0568834)

• "A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions"
  Norio Yoshida and Fumio Hirata
  J. Comput. Chem., 27, (2006), 453-462, (DOI: 10.1002/jcc.20356)

• "Molecular Ornstein-Zernike approach to the solvent effects on solute electronic structures in solution"
  Norio Yoshida and Shigeki Kato
  J. Chem. Phys., 113, (2000), 4974-4984, (DOI: 10.1063/1.1289465)

• Proceedings

  • "Application of the reference interaction site model self- consistent field method based on the Dirac–Hartree–Fock wave function to a chemical reaction"
    Kodai Kanemaru, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano
    IOP Conf. Series: Materials Science and Engineerging, 1280 (2023),0122002 (DOI: 10.1088/1757-899X/1280/1/012002) 

  • "Influence of the charge on the thioflavin-T fluorescence upon binding to the  beta-sheet surface"
    Sae Namioka, Norio Yoshida, Hiroyuki Konno, Koki Makabe
    The 57th Japanese Peptide Symposium, 15-16 

  • "The Reference Interaction Site Model Integrated Calculator (RISMiCal) program package for nano- and biomaterials design"
    Norio Yoshida
    IOP Conf. Series: Materials Science and Engineerging, 773 (2020),012062 (DOI: 10.1088/1757-899X/773/1/012062) 

• "Applicability of density functional and wave function theories combined with the three-dimensional reference interaction site model self-consistent field method to the d–d transitions of a transition metal aqua complex"
  Chen Yang, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano
  IOP Conf. Series: Materials Science and Engineerging, 773 (2020),012061 (DOI: 10.1088/1757-899X/773/1/012061) 

• "A 3D-RISM study of water and potassium ion adsorption in Montmorillonite nanoclay"
  Nirun Ruankaew, A. Kristinawati,  Norio Yoshida, Saree Phongphanphanee
  IOP Conf. Series: Materials Science and Engineerging, 773 (2020),012060 (DOI: 10.1088/1757-899X/773/1/012060) 

• "Solvated lithium ions in defective Prussian blue"
  Nirun Ruankaew, Norio Yoshida, Saree Phongphanphanee
  IOP Conf. Series: Materials Science and Engineerging, 526 (2019),012032 (DOI: 10.1088/1757-899X/526/1/012032) 

• "Solvent Effects on Electronic Structures of Coumarin 153: Parallel Studies by Means of Spectroscopy and RISM-SCF Calculations"
  Katsura Nishiyama, Y. Watanabe, Norio Yoshida, Fumio Hirata
  J. Phys. Soc. Jpn., 81 (2012), SA016(8pages), (DOI: 10.1143/JPSJS.81SA.SA016) 

• "Molecular Ornstein-Zernike self-consistent-field approach to hydrated electron"
  Norio Yoshida
  Procedia Computer Science, 4 (2011) 1214-1221, (DOI: http://dx.doi.org/10.1063/1.1289465)

• "超並列クラスタにおける３D-RISMへのVolumetric並列三次元FFTの適用と性能評価"
  多田野寛人、高橋大介、佐藤三久、吉田紀生、丸山豊、平田文男
  情報処理学会研究報告, 122 (2009) 1234-1239

• "Selective ion binding by human lysozyme studied by the statistical mechanical integral equation theory"
  Norio Yoshida, Saree Phongphanphanee and Fumio Hirata
  Lecture Series on Computer and Computational Sciences, 7, (2006), 799-802

• Books/Chapters

  • "A Statistical Mechanics Study of the Adsorption Sites of Alkali Ions in Prussian Blue", in: K. Nishiyama, T. Yamaguchi, T. Takamuku, N. Yoshida (Eds.), Molecular Basics of Liquids and Liquid-Based Materials, pp. 17-37 (Springer Singapore, Singapore, 2021)
    Nirun Ruankaew, Norio Yoshida, Saree Phongphanphanee

  • "Multiscale Solvation Theory for Nano- and Biomolecules", in: K. Nishiyama, T. Yamaguchi, T. Takamuku, N. Yoshida (Eds.), Molecular Basics of Liquids and Liquid-Based Materials, pp. 17-37 (Springer Singapore, Singapore, 2021)
    Norio Yoshida, Hirofumi Sato

  • "Self-consistent treatment of solvation structure with electronic structure based on 3D-RISM theory", in Mochizuki, Tanaka, and Fukuzawa (Ed.) "Recent advances of the fragment molecular orbital method - Enhanced performance and applicability", Chapter 27, (Springer Science Japan, 2021)
      Norio Yoshida

• "Molecular Aspects of Solvation Investigated using Statistical Mechanics", in Leszczynski (Ed.) "Handbook of Computational Chemistry", 2nd edn (Springer Science, 2016)
  Norio Yoshida, Katsura Nishiyama

• Review articles

  • "Recent Developments of Computational Methods for pKa Prediction Based on Electronic Structure Theory with Solvation Models"
    Ryo Fujiki, Toru Matsui, Yasuteru Shigeta, Haruyuki Nakano, Norio Yoshida
    J  4, (2021) 849-864 ( doi.org/10.3390/j4040058 ) 

  • "Structure and Properties of Supercritical Water: Experimental and Theoretical Characterizations"
    Norio Yoshida, Masaru Matsugami, Yuichi Harano, Keiko Nishikawa, Fumio Hirata
    J  4, (2021) 698-726 (doi.org/10.3390/j4040049)

  • "Molecular recognition and self-organization in life phenomena studied by a statistical mechanics of molecular liquids, the RISM/3D-RISM theory"
    Masatake Sugita, Itaru Onishi, Masayuki Irisa, Norio Yoshida, Fumio Hirata
    Molecules  26, (2021) 271 (1-29) (doi.org/10.3390/molecules26020271)

  • “Biophysics at Kyushu University,”
    Ryo Akiyama, Masahiko Annaka, Daisuke Kohda, Hiroyuki Kubota, Yusuke Maeda, Nobuaki Matsumori, Daisuke Mizuno, Norio Yoshida
    Biophysical Reviews, Vol. 12, pp. 245-247 (2020) 

  • "シトクロムcの多量体形成に関する理論的研究"
    根木秀佳, 吉田紀生, 廣田俊, 東雅大
    J. Comput. Chem. Jpn., 17, (2018) 8-13 (DOI: 10.2477/jccj.2018-0006)

• "Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids"
  Norio Yoshida
  J. Chem. Info. Model., 57, (2017) 2646-2656 (DOI:10.1021/acs.jcim.7b00389)

• 続・生物工学基礎講座 バイオよもやま話「生体分子の溶媒和理論」
  吉田紀生
  生物工学会誌，8, (2015) 481-486

• "液体の統計力学理論によるチャネルタンパクの透過現象解析"
  吉田紀生
  膜, 39, (2014) 379-384 

• "生体分子と水：液体の積分方程式理論によるアプローチ"
  吉田紀生
  アンサンブル, 15, (2013) 42-48 

• "液体の積分方程式理論と電子状態理論のハイブリッドによる溶液内分子の電子状態理論"
  吉田紀生
  アンサンブル, 14, (2012) 12-18 

• "Statistical Mechanics Theory of Molecular Recognition and Pharmaceutical Design"
  Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai, Fumio Hirata
  International Review in Physical Chemistry, 30, (2011), 445-478, (DOI: 10.1080/0144235X.2011.648755) 

• "分子認識の統計力学と生体機能”"
  吉田紀生, 丸山豊, Saree Phongphanphanee, 清田泰臣, 平田文男
  生物物理, 51 (2011),222-225

• "Molecular Recognition Explored by a Statistical-Mechanics Theory of Liquids"
  Saree Phongphanphanee, Norio Yoshida, Fumio Hirata
  Current Pharmaceutical Design, 17 (2011), 1740-1757, (DOI: 10.2174/138161211796355100) 

• "Electrolytes in Biomolecular Systems Studied with the 3D-RISM/RISM Theory"
  Yutaka Maruyama, Norio Yoshida, Fumio Hirata
  Inter disciplinary Sciences: Computational Life Sciences, 3 (2011), 290-307, (DOI: 10.1007/s12539-011-0104-7)

• "Molecular Recognition in Biomolecules Studied by Statistical Mechanical Integral-Equation Theory of Liquids"
  Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko and Fumio Hirata
  J. Phys. Chem. B, feature article, 113, (2009), 873-886, (DOI: 10.1021/jp807068k) 

• "RISM理論による溶液内分子の電子状態理論"
  吉田紀生
  アンサンブル, Vol.8, No.3, (2006), 16-20 

• Others

  • "くるくるパネル"
    吉田紀生
    マイコンBASICマガジン, (Oct. 1989), 170-171 

  • "キントン"
    吉田紀生
    マイコン別冊 X1プログラム大全集II マイコンBASICマガジンDELUXE, (May. 1988), 120-121

Non Reviewed Publications

• Books/Chapters

  • "Statistical mechanical integral equation approach to reveal the solvation effect on hydrolysis free energy of ATP and its analogue", in M. Suzuki (Ed.) "The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery", Chapter 5 (Springer Science, 2018)
    Norio Yoshida, Fumio Hirata

• "Theory of Molecular Recognition and Structural Fluctuation of Biomolecules", in Terazima et al.(Ed.) "Molecular Science of Fluctuations Toward Biological Functions", Chapter 8 (Springer Science, 2016)
  Fumio Hirata, Norio Yoshida, Bongsoo Kim

• 第10節 "液体の統計力学理論による分子認識・会合過程に関する研究”，第8章・非平衡界面での諸現象，「材料表面の親水・親油の評価と制御設計」，株式会社テクノシステム(2016)
  宮田竜彦，吉田紀生

• "水と生体分子のハーモニー", 巨大分子系の計算化学 超大型計算機時代の理論化学の新展開 15章, 日本化学会 編 (2012)
  吉田紀生，丸山豊，清田泰臣，平田文男，今井隆志

• "分子認識とイオンチャネルの統計力学理論", Medical Bio 10月別冊 揺らぎと生体機能, 寺嶋正秀 監修 (2010)
  平田文男、吉田紀生, Saree Phongphanphanee

• Statistical-mechanics theory of molecular recognition: water and other molecules recognized by protein, in Bihan and Fukuyama(Ed.): "Water, the forgotten biological molecule.", Chapter 4, (Pan Stanford Publishing, 2010)
  Norio Yoshida, Yasuomi Kiyota, Saree Phongphanphanee, Takashi Imai and Fumio Hirata

• Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids, in Feig(Ed.):"Modeling Solvent Environments.", Chapter 2, (Wiley-VCH, 2009)
  Norio Yoshida, Yasuomi Kiyota, Yasuhiro Ikuta, Takashi Imai and Fumio Hirata

• A Statistical Mechanics Theory of Molecular Recognition, in Terazima(Ed.) "Water and Biomolecules - Physical Chemistry of Life Phenomena.", Chapter 10, (Springer Science, 2008)
  Takashi Imai, Norio Yoshida, Andriy Kovalenko and Fumio Hirata

• Review articles

  • 特集「理論･計算による生体分子の機能解明」 "液体の積分方程式理論による生体分子機能解析手法"
    吉田紀生
    化学と工業，Vol. 74-8, (2021) 588-590

  • 特集 水チャネル「水チャネル蛋白質の動作機構に関する理論的研究 」
    Saree Phongphanphanee, 吉田紀生, 平田文男
    脳神経内科(neurology), Vol. 95, (2021) 615-627 

  • 量子化学スクール解説記事：「溶液内分子の量子化学計算手法」
    吉田紀生
    理論化学会誌フロンティア，Vol. 3, (2021) 81-85

  • 飛翔する若手研究者「液体の積分方程式理論による生体分子の分子認識解析」
    吉田紀生
    化学と工業，Vol. 66, (2013) 1004-1005