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2020

Development of a solvent-polarizable three-dimensional reference interaction-site model theory

Yoshida, N. & Yamaguchi, T., Mar 21 2020, In : Journal of Chemical Physics. 152, 11, 114108.

Research output: Contribution to journalArticle

2019

Distinct ionic adsorption sites in defective Prussian blue: A 3D-RISM study

Ruankaew, N., Yoshida, N., Watanabe, Y., Nakayama, A., Nakano, H. & Phongphanphanee, S., Jan 1 2019, In : Physical Chemistry Chemical Physics. 21, 40, p. 22569-22576 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory

Tanimoto, S., Yoshida, N., Yamaguchi, T., Ten-No, S. L. & Nakano, H., Sep 23 2019, In : Journal of Chemical Information and Modeling. 59, 9, p. 3770-3781 12 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Effects of water addition on a catalytic fluorination of dienamine

Kuraoku, D., Yonamine, T., Koja, G., Yoshida, N., Arimitsu, S. & Higashi, M., Sep 21 2019, In : Molecules. 24, 19, 3428.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Implementation of state-averaged MCSCF method to RISM- and 3D-RISM-SCF schemes

okamoto, D., Watanabe, Y., Yoshida, N. & Nakano, H., Sep 2019, In : Chemical Physics Letters. 730, p. 179-185 7 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

β-sheet elasticity of peptide self-assembly mimic, PSAM, with a grafted sequence characterized by comprehensive analyses of isomorphous crystals

Fujiwara, H., Hongo, K., Hori, Y., Yoshida, N. & Makabe, K., Sep 15 2019, In : Journal of Molecular Liquids. 290, 111161.

Research output: Contribution to journalArticle

2018

A computational scheme of p: K a values based on the three-dimensional reference interaction site model self-consistent field theory coupled with the linear fitting correction scheme

Fujiki, R., Kasai, Y., Seno, Y., Matsui, T., Shigeta, Y., Yoshida, N. & Nakano, H., Jan 1 2018, In : Physical Chemistry Chemical Physics. 20, 43, p. 27272-27279 8 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin

Cheng, C., Kamiya, M., Takemoto, M., Ishitani, R., Nureki, O., Yoshida, N. & Hayashi, S., Oct 2 2018, In : Biophysical Journal. 115, 7, p. 1281-1291 11 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
1 Citation (Scopus)

Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2

Kondo, H. X., Yoshida, N., Shirota, M. & Kinoshita, K., Dec 6 2018, In : Journal of Physical Chemistry B. 122, 48, p. 10825-10833 9 p.

Research output: Contribution to journalArticle

Role of Mg2+ Ions in DNA Hydrolysis by EcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics

Onishi, I., Sunaba, S., Yoshida, N., Hirata, F. & Irisa, M., Oct 4 2018, In : Journal of Physical Chemistry B. 122, 39, p. 9061-9075 15 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

Yoshida, N., Higashi, M., Motoki, H. & Hirota, S., Jan 14 2018, In : Journal of Chemical Physics. 148, 2, 025102.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2017

A relationship between the force curve measured by atomic force microscopy in an ionic liquid and its density distribution on a substrate

Amano, K. I., Yokota, Y., Ichii, T., Yoshida, N., Nishi, N., Katakura, S., Imanishi, A., Fukui, K. I. & Sakka, T., Jan 1 2017, In : Physical Chemistry Chemical Physics. 19, 45, p. 30504-30512 9 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Size-dependent adsorption sites in a Prussian blue nanoparticle: A 3D-RISM study

Ruankaew, N., Yoshida, N., Watanabe, Y., Nakano, H. & Phongphanphanee, S., Jan 1 2017, In : Chemical Physics Letters. 684, p. 117-125 9 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Solvatochromism and preferential solvation of Brooker's merocyanine in water–methanol mixtures

Tanaka, Y., Kawashima, Y., Yoshida, N. & Nakano, H., Oct 30 2017, In : Journal of Computational Chemistry. 38, 28, p. 2411-2419 9 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
2016

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

Phanich, J., Rungrotmongkol, T., Sindhikara, D., Phongphanphanee, S., Yoshida, N., Hirata, F., Kungwan, N. & Hannongbua, S., Jan 1 2016, In : Protein Science. 25, 1, p. 147-158 12 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

The ion dependence of carbohydrate binding of CBM36: An MD and 3D-RISM study

Tanimoto, S., Higashi, M., Yoshida, N. & Nakano, H., Jul 1 2016, In : Journal of Physics Condensed Matter. 28, 34, 344005.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Theoretical analysis of complex formation of p-carboxybenzeneboronic acid with a monosaccharide

Seno, Y., Yoshida, N. & Nakano, H., May 1 2016, In : Journal of Molecular Liquids. 217, p. 93-98 6 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2015

Solvation theory of biological molecules

Yoshida, N., Jan 1 2015, In : Seibutsu-kogaku Kaishi. 93, 8, p. 481-486 6 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)
3 Citations (Scopus)
2014

Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probed by 3D-RISM theory

Phongphanphanee, S., Yoshida, N., Oiki, S. & Hirata, F., Dec 2014, In : Journal of Molecular Liquids. 200, PA, p. 52-58 7 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)
19 Citations (Scopus)

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT

Maruyama, Y., Yoshida, N., Tadano, H., Takahashi, D., Sato, M. & Hirata, F., Jul 5 2014, In : Journal of Computational Chemistry. 35, 18, p. 1347-1355 9 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Probing "ambivalent" snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory

Phongphanphanee, S., Yoshida, N., Oiki, S. & Hirata, F., Feb 1 2014, In : Pure and Applied Chemistry. 86, 2, p. 97-104 8 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)
4 Citations (Scopus)

Theoretical characterization of the "ridge" in the supercritical region in the fluid phase diagram of water

Matsugami, M., Yoshida, N. & Hirata, F., Mar 14 2014, In : Journal of Chemical Physics. 140, 10, 104511.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter

Furukawa-Hagiya, T., Yoshida, N., Chiba, S., Hayashi, T., Furuta, T., Sohma, Y. & Sakurai, M., Nov 25 2014, In : Chemical Physics Letters. 616-617, p. 165-170 6 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)
2013
16 Citations (Scopus)
5 Citations (Scopus)

Solvent effect on excited states of merocyanines: A theoretical study using the RISM-SCF method

Tanaka, Y., Yoshida, N. & Nakano, H., Jan 1 2013, In : Chemical Physics Letters. 583, p. 69-73 5 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Theoretical study of salt effects on the diels-alder reaction of cyclopentadiene with methyl vinyl ketone using RISM-SCF theory

Yoshida, N., Tanaka, H. & Hirata, F., Nov 14 2013, In : Journal of Physical Chemistry B. 117, 45, p. 14115-14121 7 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Three-dimensional reference interaction site model self-consistent field study of the electronic structure of [Cr(H2O)6] 3+ in aqueous solution

Fujishige, S., Kawashima, Y., Yoshida, N. & Nakano, H., Aug 29 2013, In : Journal of Physical Chemistry A. 117, 34, p. 8314-8322 9 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)
2012

Application of efficient algorithm for solving six-dimensional molecular Ornstein-Zernike equation

Ishizuka, R. & Yoshida, N., Mar 21 2012, In : Journal of Chemical Physics. 136, 11, 114106.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Elucidating the molecular origin of hydrolysis energy of pyrophosphate in water

Hong, J., Yoshida, N., Chong, S. H., Lee, C., Ham, S. & Hirata, F., Jul 10 2012, In : Journal of Chemical Theory and Computation. 8, 7, p. 2239-2246 8 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Placevent: An algorithm for prediction of explicit solvent atom distribution-Application to HIV-1 protease and F-ATP synthase

Sindhikara, D. J., Yoshida, N. & Hirata, F., Jul 5 2012, In : Journal of Computational Chemistry. 33, 18, p. 1536-1543 8 p.

Research output: Contribution to journalArticle

66 Citations (Scopus)

Solvent effects on electronic structures of coumarin 153: Parallel studies by means of spectroscopy and RISM-SCF calculations

Nishiyama, K., Watanabe, Y., Yoshida, N. & Hirata, F., Jan 1 2012, In : journal of the physical society of japan. 81, SUPPL. A, SA016.

Research output: Contribution to journalArticle

3 Citations (Scopus)
2011

Affinity of small ligands to myoglobin studied by the 3D-RISM theory

Kiyota, Y., Yoshida, N. & Hirata, F., Feb 15 2011, In : Journal of Molecular Liquids. 159, 1, p. 93-98 6 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)
33 Citations (Scopus)

Electrolytes in biomolecular systems studied with the 3D-RISM/RISM theory

Maruyama, Y., Yoshida, N. & Hirata, F., Dec 1 2011, In : Interdisciplinary Sciences: Computational Life Sciences. 3, 4, p. 290-307 18 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Solvent penetration in photoactive yellow protein R52Q mutant: A theoretical study

Sindhikara, D. J., Yoshida, N., Kataoka, M. & Hirata, F., Nov 1 2011, In : Journal of Molecular Liquids. 164, 1-2, p. 120-122 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA

Yoshida, N., Kiyota, Y. & Hirata, F., Feb 15 2011, In : Journal of Molecular Liquids. 159, 1, p. 83-92 10 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)
2010

Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory

Phongphanphanee, S., Yoshida, N. & Hirata, F., Jun 17 2010, In : Journal of Physical Chemistry B. 114, 23, p. 7967-7973 7 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Proton transport through the influenza A M2 channel: Three-dimensional reference interaction site model study

Phongphanphanee, S., Rungrotmongkol, T., Yoshida, N., Hannongbua, S. & Hirata, F., Jul 21 2010, In : Journal of the American Chemical Society. 132, 28, p. 9782-9788 7 p.

Research output: Contribution to journalArticle

37 Citations (Scopus)

Revisiting the salt-induced conformational change of DNA with 3D-RISM theory

Maruyama, Y., Yoshida, N. & Hirata, F., May 20 2010, In : Journal of Physical Chemistry B. 114, 19, p. 6464-6471 8 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)
2009

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids

Yoshida, N., Imai, T., Phongphanphanee, S., Kovalenko, A. & Hirata, F., Jan 29 2009, In : Journal of Physical Chemistry B. 113, 4, p. 873-886 14 p.

Research output: Contribution to journalArticle

96 Citations (Scopus)

Theoretical study of CO escaping pathway in myoglobin with the 3D-RISM teory

Kiyota, Y., Hiraoka, R., Yoshida, N., Maruyama, Y., Imai, T. & Hirata, F., Mar 25 2009, In : Journal of the American Chemical Society. 131, 11, p. 3852-3853 2 p.

Research output: Contribution to journalArticle

53 Citations (Scopus)

The potential of mean force of water and ions in aquaporin channels investigated by the 3D-RISM method

Phongphanphanee, S., Yoshida, N. & Hirata, F., Jul 20 2009, In : Journal of Molecular Liquids. 147, 1-2, p. 107-111 5 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)