Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Norio Yoshida Last modified date:2019.04.27

Associate Professor / Faculty of Sciences / Department of Chemistry / Faculty of Sciences


Papers
1. Chen Yang, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano, 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, Journal of Physical Chemistry A, 123, 3344-3354, 2019.03.
2. Hiroko X. Kondo, Norio Yoshida, Matsuyuki Shirota, Kengo Kinoshita, Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2, Journal of Physical Chemistry B, 12, 10825-10833, 2018.12.
3. Ryo Fujiki, Yukako Kasai, Yuki Seno, Toru Matsui, Yasuteru Shigeta, Norio Yoshida, Haruyuki Nakano, 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, Physical Chemistry Chemical Physics, 20, 27272-27279, 2018.08.
4. Itaru Onishi, Shunya Sunaba, Norio Yoshida, Fumio Hirata, Masayuki Irisa, Role of Mg2+ ions in DNA hydrolysis by EcoRV, Studied by 3D-RISM and MD, Journal of Physical Chemistry B, 122, 9061-9075, 2018.09.
5. Cheng Cheng, Motoshi Kamiya, Mizuki Takemoto, Ryuichiro Ishitani, Osamu Nureki, Norio Yoshida, Shigehiko Hayashi, An Atomistic Model of a Precursor State of Light-Induced Channel Opening of Channelrhodopsin, Biophysical Journal, 115, 1281-1291, 2018.04.
6. Norio Yoshida, 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, Chemical Physics Letters, 2018.03, A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example..
7. Norio Yoshida, Masahiro Higashi, Hideyoshi Motoki, Shun Hirota, Theoretical Analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach, The Journal of Chemical Physics, Vol. 148,025102(7pp), 2018.01.
8. Ken-ichi Amano, Yasuyuki Yokota, Takashi Ichii, Norio Yoshida, Naoya Nishi, Seiji Katakura, Akihito Imanishi, Ken-ichi Fukui, Tetsuo Sakka, Relationship between Force Curve Measured by Atomic Force Microscopy in Ionic Liquid and its Density Distribution on a Substrate, Physical Chemistry Chemical Physics, 2017.06.
9. Yuichi Tanaka, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano, Solvatochromism and Preferential Solvation of Brooker’s Merocyanine in Water–Methanol Mixtures, Journal of Computational Chemistry, Vol. 38, pp. 2411-2419, 2017.06.
10. Nirun Ruankaew, Norio Yoshida, Yoshihiro Watanabe, Haruyuki Nakano, Saree Phongphanphanee, Size-dependent adsorption sites in a Prussian blue nanoparticle: A 3D-RISM study, Chemical Physics Letters, Vol. 684,
pp. 117-125, 2017.06.
11. Tanimoto Shoichi, Masahiro Higashi, Norio Yoshida, Haruyuki Nakano, The ion-dependence of carbohydrate binding of CBM36: An MD and 3D-RISM study, Journal of Physics: Condensed Matter, Vol. 28,344005(8pp), 2016.07.
12. Norio Yoshida, Yuki Seno, 中野 晴之, Theoretical analysis of complex formation of p-carboxybenzeneboronic acid with a monosaccharide, Journal of Molecular Liquids, 10.1016/j.molliq.2015.12.063 , 217, 93-98, 2016.04.
13. Jiraphorn Phanich, Thanyada Rungrotmongkol, Daniel Sindhikara, Saree Phongphanphanee, Norio Yoshida, Fumio Hirata, Nawee Kungwan, Supot Hannongbua, 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, Protein Science, 10.1002/pro.2718, 25, 147-158, 2016.01, The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. The binding affinity or the binding free energy of ligand to receptor was found to be deter- mined by a subtle balance of two major contributions that largely cancel out each other: the ligand-receptor interactions and the dehydration free energy. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated resi- due, is the main source of high-level oseltamivir resistance. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site..
14. Yuichi Tanaka, Norio Yoshida, 中野 晴之, Three-Dimensional Reference Interaction Site Model Self-Consistent Field Analysis of Solvent and Substituent Effects on the Absorption Spectra of Brooker’s Merocyanine, Journal of Computational Chemistry, 10.1002/jcc.23980 , 36, 1655-1663, 2015.05.
15. Yukako Kasai, Norio Yoshida, 中野 晴之, Theoretical Analysis of Co-Solvent Effect on the Proton Transfer Reaction of Glycine in a Water-Acetonitrile Mixture, Journal of Chemical Physics, 10.1063/1.4921432, 142, 204103, 2015.05.
16. Tomoka Furukawa-Hagiya, Norio Yoshida, Shutaro Chiba, Tomohiko Hayashi, Tadaomi Furuta, Yoshiro Sohma, Minoru Sakurai, Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter, CHEMICAL PHYSICS LETTERS, 10.1016/j.cplett.2014.10.038, 616, 165-170, 2014.11.
17. Norio Yoshida, Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4879795, 140, 21, 2014.06, The three-dimensional reference interaction site model (3D-RISM) method was efficiently imple- mented in the fragment molecular orbital (FMO) method. The method is referred to as the FMO/3D- RISM method, and allows us to treat electronic structure of the whole of a macromolecule, such as a protein, as well as the solvent distribution around a solute macromolecule. The formalism of the FMO/3D-RISM method, for the computationally available form and variational expressions, are proposed in detail. A major concern leading to the implementation of the method was decreasing the computational costs involved in calculating the electrostatic potential, because the electrostatic po- tential is calculated on numerous grid points in three-dimensional real space in the 3D-RISM method. In this article, we propose a procedure for decreasing the computational costs involved in calculating the electrostatic potential in the FMO method framework. The strategy involved in this procedure is to evaluate the electrostatic potential and the solvated Fock matrix in different manners, depending on the distance between the solute and the solvent. The electrostatic potential is evaluated directly in the vicinity of the solute molecule by integrating the molecular orbitals of monomer fragments of the solute molecule, whereas the electrostatic potential is described as the sum of multipole interactions when an analog of the fast multipole method is used. The efficiency of our method was demonstrated by applying it to a water trimer system and three biomolecular systems. The FMO/3D-RISM cal- culation can be performed within a reasonable computational time, retaining the accuracy of some physical properties..
18. Yukako Kasai, Norio Yoshida, Haruyuki Nakano, Theoretical analysis of salt effect on intramolecular proton transfer reaction of glycine in aqueous NaCl solution, Journal of Molecular Liquids, 10.1016/j.molliq.2014.02.013, 200, 32-37, 2014.12.
19. Saree Phongphanphanee, Norio Yoshida, Shigetoshi Oiki, Fumio Hirata, Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probe by 3D-RISM theory, Journal of Molecular Liquids, 2000, 52-58, 2014.02.
20. Yutaka Maruyama, Norio Yoshida, Hiroto Tadano, Daisuke Takahashi, Mitsuhisa Sato, Fumio Hirata, Massively Parallel Implementation of 3D-RISM Calculation with Volumetric 3D-FFT, Journal of Computational Chemistry, 35, 1347-1355, 2014.04.
21. Norio Yoshida, Masaru Matsugami, Fumio Hirata, Theoretical Characterization of the "Ridge" in the Supercritical Region in the Fluid Phase Diagram of Water, The Journal of Chemical Physics, 140, 104511, 2014.03.
22. Saree Phongphanphanee, Norio Yoshida, Shigetoshi Oiki, Fumio Hirata, Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory, Pure and Applied Chemistry, DOI 10.1515/pac-2014-5018, 86, 97-104, 2014.12.
23. Norio Yoshida, Hidetsugu Tanaka, Fumio Hirata, Theoretical Study of Salt Effects on Diels-Alder Reaction of Cyclopentadiene With Methyl Vinyl Ketone Using RISM-SCF Theory, Journal of Physical Chemistry B, 117, 14115-14121, 2013.10.
24. Katsura Nishiyama, Yasuhiro Watanabe, Norio Yoshida, Fumio Hirata, Solvent dependence of Stokes shift for organic solute–solvent systems: A comparative study by spectroscopy and reference interaction-site model–self-consistent-field theory, The Journal of Chemical Physics, 139, 094503, 2013.09.
25. Ryosuke Ishizuka, Norio Yoshida, Extended Molecular Ornstein-Zernike Integral Equation for Fully Anisotropic Solute Molecules: Formulation in a Rectangular Coordinate System, The Journal of Chemical Physics, http://dx.doi.org/10.1063/1.4819211], 139, 084119, 2013.08, An extended molecular Ornstein-Zernike (XMOZ) integral equation is formulated to calculate the spatial distribution of solvent around a solute of arbitrary shape and solid surfaces. The conventional MOZ theory employs spherical harmonic expansion technique to treat the molecular orientation of components of solution. Although the MOZ formalism is fully exact analytically, the truncation of the spherical harmonic expansion requires at a finite order for numerical calculation and causes the significant error for complex molecules. The XMOZ integral equation is the natural extension of the conventional MOZ theory to a rectangular coordinate system, which is free from the trunca- tion of spherical harmonic expansion with respect to solute orientation. In order to show its appli- cability, we applied the XMOZ theory to several systems using the hypernetted-chain (HNC) and Kovalenko-Hirata approximations. The quality of results obtained within our theory is discussed by comparison with values from the conventional MOZ theory, molecular dynamics simulation, and three-dimensional reference interaction site model theory. The spatial distributions of water around the complex of non-charged sphere and dumbbell were calculated. Using this system, the approxi- mation level of the XMOZ and other methods are discussed. To assess our theory, we also computed the excess chemical potentials for three realistic molecules (water, methane, and alanine dipeptide). We obtained the qualitatively reasonable results by using the XMOZ/HNC theory. The XMOZ the- ory covers a wide variety of applications in solution chemistry as a useful tool to calculate solvation thermodynamics..
26. Yuichi tanaka, Norio Yoshida, Haruyuki Nakano, Solvent effect on excited states of merocyanines: A theoretical study using the RISM–SCF method, Chemical Physics Letters, http://dx.doi.org/10.1016/j.cplett.2013.08.004, 583, 69-73, 2013.08.
27. Shinya Fujishige, Yukio Kawashima, Norio Yoshida, Haruyuki Nakano, Three-dimensional Reference Interaction Site Model Self-consistent Field Study of the Electronic Structure of [Cr(H2O)6]3+ in Aqueous Solution, Journal of Physical Chemistry A, dx.doi.org/10.1021/jp405876g , 117, 8314-8322, 2013.08.
28. Jooyeon Hong, Norio Yoshida, Song-Ho Chong, Chewook Lee, Sihyun Ham, Fumio Hirata, Elucidating the Molecular Origin of Hydrolysis Energy of Pyrophosphate in Water, Journal of Chemical Theory and Computation, 10.1021/ct300099e, 8, 2239-2246, 2012.07.
29. Ryosuke Ishizuka, Norio Yoshida, Application of efficient algorithm for solving six-dimensional molecular Ornstein-Zernike equation, The Journal of Chemical Physics, 136, 114106(6pages).
30. Daniel J. Sindhikara, Norio Yoshida, Fumio Hirata, Placevent: an algorithm for prediction of explicit solvent atom distribution -- application to HIV-1 protease and F-ATP synthase, Journal of Computational Chemistry, 10.1002/jcc.22984.
31. Yasuomi Kiyota, Norio Yoshida, Fumio Hirata*, A new approach for investigating the molecular recognition of protein: Toward structure-based drug-design based on the 3D-RISM theory, Journal of Chemical Theory and Computation, 7, 3803.
32. Saree Phongphanphanee, Norio Yoshida, Fumio Hirata*, Reply to Comment on Molecular Selectivity in Aquaporin Channels Studied by the 3D- RISM Theory, Journal of Physical Chemistry B, 115, 8367.
33. Daniel Sindhikara, Norio Yoshida, Mikio Kataoka, Fumio Hirata*, Solvent penetration in photoactive yellow protein R52Q mutant: a theoretical study, Journal of Molecular Liquids, 164, 120.
34. Yasuomi Kiyota, Norio Yoshida, Fumio Hirata*, Affinity of Small Ligands to Myoglobin Studied by the 3D-RISM Theory Journal of Molecular Liquids, Journal of Molecular Liquids, 159, 93.
35. Norio Yoshida, Yasuomi Kiyota, Fumio Hirata*, The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA, Journal of Molecular Liquids, 159, 83, 2011.03.
36. Saree Phongphanphanee, Thanyada Rungrotmongkol, Norio Yoshida, Supot Hannongbua, Fumio Hirata*, Proton transport through the Influenza A M2 channel: 3D-RISM Study, Journal of the American Chemical Society, 132, 9782.
37. Saree Phongphanphanee, Norio Yoshida, Fumio Hirata*, Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory, Journal of Physical Chemistry B, 114, 7967.
38. Yutaka Maruyama, Norio Yoshida, Fumio Hirata*, Revisiting the Salt-Induced Conformational Change of DNA with 3D-RISM Theory, Journal of Physical Chemistry B, 114, 6464.
39. Hidetsugu Tanaka, Norio Yoshida, Yasuhiro Ikuta, Yasuomi Kiyota, Fumio Hirata*, RISM-SCF Study of the Solvation Effect on a Nucleophilic Aromatic Substitution between 4-_uoronitrobenzen and azide anion, The International Journal of Liquid State Sciences, 2, 15.
40. Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata*, Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory, Journal of the American Chemical Society, Communication, 131, 3852.
41. Saree Phongphanphanee, Norio Yoshida, Fumio Hirata*, The Potential of Mean Force of Water and Ions in Aquaporin Channels Investigated by the 3D-RISM Method, Journal of Molecular Liquids, 147, 107.
42. Saree Phongphanphanee, Norio Yoshida, Fumio Hirata*, On the Proton Exclusion of Aquaporins: A Statistical Mechanics Study, Journal of the American Chemical Society, Communication, 130, 1540.
43. Norio Yoshida*, Tateki Ishida, Fumio Hirata*, 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, Journal of Physical Chemistry B, 112, 433.
44. Norio Yoshida*, Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method, Condensed Matter Physics, 10, 363.
45. Saree Phongphanphanee, Norio Yoshida, Fumio Hirata*, The statistical-mechanics study of equilibrium water distribution in aquaporin, Chemical Physics Letters, 449, 196.
46. Norio Yoshida, Saree Phongphanphanee, Fumio Hirata*, Selective ion-binding by lysozyme probed with the integral equation theory, Journal of Physical Chemistry B, 111, 4588.
47. Norio Yoshida, Saree Phongphanphanee, Yutaka Maruyama, Takashi Imai, Fumio Hirata*, Selective ion-binding by protein probed with the 3D-RISM theory, Journal of the American Chemical Society, Communication, 128, 12042, 2006.05.
48. Jin Yong Lee, Norio Yoshida, Fumio Hirata*, Conformational equilibrium of 1.2-dichloroethane in water: Comparison of PCM and RISM-SCF methods, Journal of Physical Chemistry B, 110, 16018.
49. Norio Yoshida, Ryosuke Ishizuka, Hirofumi Sato, Fumio Hirata*, Ab initio Theoretical Study of Temperature and Density Dependence of Molecular and Thermodynamic Properties of Water in the Entire Fluid Region, Journal of Physical Chemistry B, 110, 8451.
50. Norio Yoshida, Fumio Hirata*, A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions, Journal of Computational Chemistry, 27, 453.
51. Norio Yoshida, Shigeki Kato*, Molecular Ornstein-Zernike approach to the solvent effects on solute electronic structures in solution, The Journal of Chemical Physics, 113, 4974, 2000.09.
52. Katsura Nishiyama*, Yasuhiro Watanabe, Norio Yoshida, Fumio Hirata, Solvent Effects on Electronic Structures of Coumarin 153: Parallel Studies by Means of Spectroscopy and RISM-SCF Calculations, Journal of the Physical Society of Japan.
53. Norio Yoshida*, Molecular Ornstein-Zernike self-consistent-field approach to hydrated electron, Procedia Computer Science, 4, 1214.
54. Norio Yoshida, Saree Phongphanphanee, Fumio Hirata*, Selective ion binding by human lysozyme studied by the statistical mechanical integral equation theory, Lecture Series on Computer and Computational Sciences, 7, 799.