Publication

Peer Reviewed Paper

1. R. Fujiki, T. Matsui, Y. Shigeta, H. Nakano, N. Yoshida*, "Assessment of the Applicability of the LFC/3D-RISM-SCF Scheme for pKa Prediction in Methanol Solutions", Chemistry Letters, accepted.

2. K. Terayama, Y. Osaki, T. Fujita, R. Tamura, M. Naito, K. Tsuda*, T. Matsui* and M. Sumita*, “Koopmans’ Theorem-Compliant Long-range Corrected (KTLC) Density Functional Mediated by Black-box Optimization and Data-Driven Prediction for Organic Molecules”, Journal of Chemical Theory and Computation, 19, 6770-6781 (2023).

3. S. Onozawa, Y. Nishimura, T. Matsui*, "A Theoretical Study on Rate Constants of Excited State Proton Transfer Reaction in Anthracene-Urea Derivative ", Bulletin of the Chemical Society of Japan, 96. 215-222 (2023). (Selected Paper)

4. Y. Kanamaru, T. Matsui*, "Factor analysis of error in oxidation potential calculation: A machine learning study", Journal of Computational Chemistry, 43, 1504-1512 (2022). 

5. H. Izawa*, F. Yasufuku, T. Nokami, S. Ifuku, H. Saimoto, T. Matsui, K. Morihashi, and M. Sumita "Unique Photophysical Properties of 1,8-Naphthalimide Derivatives: Generation of Semi-stable Radical Anion Species by Photo-Induced Electron Transfer from a Carboxy Group", ACS Omega, 6, 13456–13465 (2021). Open Access

6. T. Takahashi, T. Matsui, K. Hengphasatporn, Y. Shigeta*,  "A Practical Prediction of LogPo/w through Semiempirical Electronic Structure Calculations with Dielectric Continuum Model", Bulletin of the Chemical Society of Japan, 94, 1807-1814 (2021).

7. S. Onozawa, T. Matsui*, Y. Nishimura, and K. Morihashi (2020) "アントラセン-ウレア誘導体の励起状態プロトン移動における蛍光挙動に関する解析" (in Japanese), Journal of Computer Chemistry, Japan, 18, 254-256. (2020) Open Access 

8. K. Hayasaka, T. Shibata, A. Sugahara, A. Momotake, T. Matsui, S. Neya, T. Ishizuka, Y. Xu, Y. Yamamoto*, "Characterization of Structure and Catalytic Activity of a Complex between Heme and an All Parallel-stranded Tetrameric G-quadruplex Formed from DNA/RNA Chimera Sequence d(TTA)r(GGG)dT", Bulletin of the Chemical Society of Japan, 93, 621-629 (2020).

9. K. Hengphasatporn, T. Matsui, Y. Shigeta*, "Estimation of Acid Dissociation Constants (pKa) of N-containing Heterocycles in DMSO and Transferability of Gibbs Free Energy in Different Solvent Conditions," Chemistry Letters, 49, 307-310 (2020).

10. T. Matsui*, J.-W. Song*, "A Density Functional Theory-Based Scheme to Compute the Redox Potential of a Transition Metal Complex: Applications to Heme Compound", Molecules, 24, 819-831 (2019). Open Access

11. R. Fujiki, Y. Kasai, Y. Seno, T. Matsui, Y. Shigeta, N. Yoshida* and H. 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). 

12. T. Matsui*, K. Yamamoto, T. Fujita, and K. Morihashi, "Molecular Dynamics and Quantum Chemical Approach for the Estimation of an Intramolecular Hydrogen Bond Strength in Okadaic Acid",  The Journal of Physical Chemistry B, 122, 7233-7242 (2018).

13. I. Kurniawan*, K. Kawaguchi, M. Shoji, T. Matsui, Y. Shigeta, and H. Nagao, "A Theoretical Study on Redox Potential and pKa of [2Fe-2S] Cluster Model from Iron-Sulfur Proteins", Bulletin of the Chemical Society of Japan, 91, 1451-1456 (2018) (Selected Paper).

14. T. Fujita,  T. Matsui*, M. Sumita, Y. Imamura, and K. Morihashi, "Theoretical study on naphthobischalcogenadiazole conjugated polymer systems and C61 derivative as organic photovoltaic semiconductors", Chemical Physics Letters, 693, 188-193. (2018). 

15. T. Matsui*, Y. Shigeta, and K. Morihashi, "Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups",Journal of Chemical Theory and Computation, 13, 4791-4803 (2017).

16. Y. Kitagawa*, M. Asaoka, Y. Natori, K. Miyagi, R. Teramoto, T. Matsui, Y. Shigeta, M. Okumura, M. Nakano, "Theoretical study on relationship between spin structure and electron conductivity of one-dimensional tri-nickel(II) complex" , Polyhedron, 136, 125-131 (2017).

17. T. Oshiyama*, N. Yasukawa, H. Kita, T. Matsui, M. Sumita and K. Morihashi*, "A Theoretical Guideline for Designing Effective Host Materials Based on 4, 4-bis (9-carbazolyl)-1, 1-biphenyl Derivatives for Blue Phosphorescent Devices", Bulletin of the Chemical Society of Japan, 90, 195-204 (2017).

18. K. Aikawa*, T. Matsui and K. Morihashi, "Theoretical Estimation of Effect of Conjugation Length and Side Chain in Charge Recombination Process in Poly (para-phenylenevinylene)", Chemistry Letters, 45, 628-630 (2016).

19. T. Matsui, Y. Imamura, I. Osaka, K. Takimiya and  T. Nakajima*, " Analyses of Thiophene-Based Donor-Acceptor Semiconducting Polymers toward Designing Optical and Conductive Properties: A Theoretical Perspective", The Journal of Physical Chemistry C, 120, 8305-8314 (2016). 

20. N. Takagi, K. Ishimura,M. Matsui, R. Fukuda, T. Matsui, T. Nakajima, M. Ehara and S. Sakaki*, "How can we understand Au8 cores and entangled ligands of selenolate-and thiolate-protected gold nanoclusters Au24 (ER) 20 and Au20 (ER) 16 (E= Se, S; R= Ph, Me)? A theoretical study", Journal of the American Chemical Society, 137, 8593-8602 (2015). 

21. Y. Kitagawa, M. Asaoka, K.  Miyagi, T.  Matsui, M. Nihei, H.  Oshio,M. Okumura and M. Nakano, "DFT and TD-DFT studies of electronic structures and one-electron excitation states of a cyanide-bridged molecular square complex",  Inorganic Chemistry Frontiers, 2, 771-779 (2015).

22. S. Maekawa, T. Matsui, K. Hirao, and Y. Shigeta*, “Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Towards Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase”, The Journal of Physical Chemistry B, 119, 5392-5403 (2015). 

23. T. Matsui*, Y. Kitagawa, M. Okumura, and Y. Shigeta*, "Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH", The Journal of Physical Chemistry A, 119, 369-376 (2015).

24. K. Kamiya*, T. Baba, M. Boero, T. Matsui, S. Negoro, and Y. Shigeta,"Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds", The Journal of Physical Chemistry Letters, 5, 1210-1216 (2014). 

25. T. Baba, T. Matsui*, K. Kamiya, M. Nakano, and Y. Shigeta*, “A density functional study on pKa of small polyprotic molecule”, International Journal of Quantum Chemistry, 114, 1128-1134 (2014). 

26. T. Matsui*, Y. Kitagawa, Y. Shigeta, and M. Okumura, “A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counter Ion: General Theory and Applications“, Journal of Chemical Theory and Computation, 9, 2974-2980 (2013). 

27. Y. Kitagawa*, T. Matsui, Y. Nakanishi, Y. Shigeta, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical studies of electronic structures, magnetic properties and electron conductivities of one-dimensional Nin (n = 3, 5, 7) complexes”, Dalton Transaction, 42, 16200-16208 (2013). 

28. Y. Kitagawa*, T. Matsui, N. Yasuda, H. Hatake, T. Kawakami, S. Yamanaka, M. Nihei, M. Okumura, H. Oshio and K. Yamaguchi “DFT calculations of effective exchange integrals at the complete basis set limit on oxo-vanadium ring complex”, Polyhedron, 66, 97-101 (2013). 

29. Y. Kitagawa,* N. Yasuda, H. Hatake, T. Saito, Y. Kataoka, T. Matsui, T. Kawakami, S. Yamanaka, M. Okumura and K. Yamaguchi, “Combination of approximate spin-projection and spin-restricted calculations based on ONIOM method for geometry optimization of large biradical systems”, International Journal of Quantum Chemistry, 113, 290-295 (2013). 

30. T. Matsui*, Y. Kitagawa, M. Okumura, Y. Shigeta and S. Sakaki*, "Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials", Journal of Computational Chemistry, 34, 21-26 (2013). 

31. T. Sugimura*, E. Mitani, T. Tei, T. Okuyama, K. Kamiya, T. Matsui and Y. Shigeta, “Temperature Independent Stereoselectivity in Intramolecular Cycloaddition of Ketene Generated from Diazoester in Solution and in Vapor Phase: How Entropy Term Governs the Selectivity”, Bulletin of the Chemical Society of Japan, 85, 504-510 (2012). 

32. K. Kamiya*, T. Matsui, T. Sugimura and Y. Shigeta, “Theoretical Insight into Stereoselective Reaction Mechanisms of 2,4-Pentanediol-Tethered Ketene-Olefin [2+2] Cycloaddition”, The Journal Physical Chemistry A, 116, 1168-1175 (2012). 

33. T. Matsui*, T. Baba, K. Kamiya and Y. Shigeta, “An accurate density functional theory based estimation of pKa values of polar residues combined with experimental data: from amino acids to minimal proteins”, Physical Chemistry Chemical Physics, 14, 4181-4187 (2012). 

34. T. Matsui*, H. Miyachi, T. Baba and Y. Shigeta, “A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation”, The Journal of Physical Chemistry A, 115, 8504-8510 (2011). 

35. Y. Nakanishi*, T. Matsui, Y. Kitagawa, Y. Shigeta, T. Saito, Y. Kataoka, T. Kawakami, M. Okumura and K. Yamaguchi, “Electron Conductivity in Modified Models of Artificial Metal-DNA Using Green's Function-Based Scattering Theory”, Bulletin of the Chemical Society of Japan, 84, 366-375 (2011) (Selected Paper). 

36. T. Baba, K. Kamiya, T. Matsui, N. Shibata, Y. Higuchi, T. Kobayashi, S. Negoro* and Y. Shigeta*, “Molecular dynamics studies on mutational structures of a nylon-6 byproduct-degrading enzyme”, Chemical Physics Letters, 507, 157-161 (2011). 

37. T. Matsui*, A. Oshiyama and Y. Shigeta, “A Simple Scheme for pKa of 5-substituted Uracils”, Chemical Physics Letters, 502, 238-242 (2011). 

38. Y. Kataoka*, T. Saito, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical Study on Electronic Configurations and Nature of Chemical Bonds of Dirhodium Tetraaceteto Complex [Rh2(CH3COO)4L2] (L=H2O, Free): Broken Symmetry Approach”, Bulletin of the Chemical Society of Japan, 83, 1481-1488 (2010). 

39. Y. Kitagawa*, T. Saito, Y. Nakanishi, Y. Kataoka, T. Matsui, T. Kawakami, M. Okumura and K. Yamaguchi, “Development of Approximately Spin Projected Energy Derivatives for Biradical Systems”, International Journal of Quantum Chemistry, 110, 3053-3060 (2010). 

40. T. Saito*, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical studies of the effect of orientation of ligands and spin contamination error on the chemical bonding in the FeO2 core in oxymyoglobin”, Journal of Molecular Structure (THEOCHEM), 954, 98-104 (2010). 

41. T. Saito*, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura and K. Yamaguchi, “Which hybrid GGA DFT is suitable for Cu2O2 systems if the spin contamination error is removed?”, Chemical Physics, 368, 1-6 (2010) (Selected Paper). 

42. Y. Nakanishi*, T. Matsui, Y. Shigeta, Y. Kitagawa, T. Saito, Y. Kataoka, T. Kawakami, M. Okumura and K. Yamaguchi, “Sequence dependent proton-transfer reaction in stacked GC pair III: The Influence of Proton Transfer to Conductivity“, International Journal of Quantum Chemistry, 110, 2221-2230 (2010). 

43. H. Miyachi*, T. Matsui, Y. Shigeta, K. Yamashita and K. Hirao, “Possibility of multi-conformational structure of mismatch DNA nucleobase in the presence of silver(I) ions”, Chemical Physics Letters, 495, 125-130 (2010). 

44. H. Miyachi*, T. Matsui, Y. Shigeta and K. Hirao, “Effects of mercury(II) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(II)-thymine nucleobase pairs”, Physical Chemistry Chemical Physics, 12, 909-917 (2010). 

45. Y. Kitagawa*, T. Saito, Y. Nakanishi, Y. Kataoka, T. Matsui, T. Kawakami, M. Okumura and K. Yamaguchi, “Spin Contamination Error in Optimized Geometry of Singlet Carbene ((1)A(1)) by Broken-Symmetry Method”, The Journal of Physical Chemistry A, 113, 15041-15046 (2009). 

46. T. Saito*, S. Nishihara, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura and K. Yamaguchi, “Transition state optimization based on approximate spin-projection (AP) method”, Chemical Physics Letters, 483, 168-171 (2009). 

47. T. Saito*, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical Studies on Chemical Bonding Between Cu(II) and Oxygen Molecule in Type 3 Copper Proteins”, International Journal of Quantum Chemistry, 109, 3649-3658 (2009). 

48. Y. Nakanishi*, Y. Kitagawa, T. Saito, Y. Kataoka, T. Matsui, T. Kawakami, M. Okumura and K. Yamaguchi, “Estimation of Effective Exchange Integral Value of Polyradical Systems Based on the Band Calculation”, International Journal of Quantum Chemistry, 109, 3632-3640 (2009). 

49. T. Matsui*, H. Miyachi, Y. Nakanishi, Y. Shigeta, T. Sato, Y. Kitagawa, M. Okumura and K. Hirao, “Theoretical Studies on Sulfur and Metal Cation (Cu(II), Ni(II), Pd(II), and Pt(II))-Containing Artificial DNA”, The Journal of Physical Chemistry B, 113, 12790-12795 (2009). 

50. T. Matsui*, T. Sato, Y. Shigeta and K. Hirao, "Sequence dependent proton-transfer reaction in stacked GC pair II: The origin of stabilities of proton-transfer products", Chemical Physics Letters, 478, 238-242 (2009). 

51. T. Matsui*, T. Sato and Y. Shigeta, "Sequence dependent proton-transfer reaction in stacked GC pair I: The possibilities of proton-transfer reaction", International Journal of Quantum Chemistry, 109, 2168-2177 (2009). 

52. Y. Nakanishi*, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobases”, Polyhedron, 28, 1945-1950 (2009) 

53.  Y. Nakanishi*, Y. Kitagawa, Y. Shigeta, T. Saito, T. Matsui, H. Miyachi, T. Kawakami, M. Okumura and K. Yamaguchi, “Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobases”, Polyhedron, 28, 1714-1717 (2009) 

54. T. Matsui, H. Miyachi, T. Sato, Y. Shigeta and K. Hirao*, "Structural origin of Copper ion containing artificial DNA", The Journal of Physical Chemistry B, 112, 16960-16965 (2008). 

55. Y. Shigeta*, H. Miyachi, T. Matsui and K. Hirao, “Dynamical quantum isotope effects on multiple proton transfer reactions”, Bulletin of the Chemical Society of Japan, 81, 1230-1240 (2008). 

56. T. Matsui, Y. Shigeta and K. Hirao*, "Multiple proton-transfer reactions in guanine-cytosine pairs by the coordination of Pt complex", The Journal of Physical Chemistry B, 111, 1176-1181 (2007). 

57. T. Matsui*, Y. Shigeta and K. Hirao, "The influence of Pt complex between guanine-cytosine pair", Chemical Physics Letters, 433, 331-334 (2006).

Review and Books

1. R.Fujiki, T.Matsui, Y.Shigeta, H. Nakano, N. Yoshida (2021), "Recent Developments of Computational Methods for pKa Prediction Based on Electronic Structure Theory with Solvation Models."  J, 4, pp. 849-864. 

2. T. Matsui, A. Kiyan, M. Shoji, and Y. Shigeta (2016) "プロトンの水和自由エネルギー: 酸解離定数および標準水素電極電位の高精度計算"(in Japanese), Journal of Computer Chemistry, Japan, 15, pp. 184-191. 

3. T. Matsui, H. Miyachi, Y. Shigeta and K. Hirao (2012) “Metal-Assisted Proton Transfer in Guanine-Cytosine Pair: An Approach from Quantum Chemistry”, in Some Applications of Quantum Mechanics, ISBN 978-953-51-0059-1, edited by Mohammad Reza Pahlavani , InTech, pp. 167-188. 

4. T. Matsui, H. Miyachi and Y. Shigeta (2011) “Theoretical Studies on metal-containing artificial DNA bases”, Progress in Theoretical Chemistry and Physics, Springer, 22, pp. 434-460.

5.  Y. Shigeta, H. Miyachi, T. Matsui, N. Yokoyama and K. Hirao (2009) “Quantum Theory in terms of Cumulant Variables”, Progress in Theoretical Chemistry and Physics, Springer, 20, pp. 3-36.