Academic papers since the 1990s

1. S. Nakagawa, K. Kimura, Y. Okamoto, "Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA", J. Phys. Chem. B, 126, 10646-10661 (2022).

2. S. Nakagawa, O. Weingart, C. M. Marian, "Dual Photochemical Reaction Pathway in Flavin-Based Photoreceptor LOV Domain: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation", J. Phys. Chem. B, 121, 9583-9596 (2017).

3. C. M. Marian, S. Nakagawa, V. Rai-Constapel, B. Karasulu, W. Thiel, "Photophysics of Flavin Derivatives Absorbing in the Blue-Green Region: Thioflavins As Potential Cofactors of Photoswitches", J. Phys. Chem. B, 118, 1743-1753 (2014).

4. S. Nakagawa, P. Mark, H. Ågren, "Recipe of Polarized One-electron Potential Optimization for Development of Polarizable Force Fields", J. Chem. Theory Comput., 3, 1947-1959 (2007).

5. S. Nakagawa, "Polarizable Model Potential Function for Nucleic Acid Bases ", J. Comput. Chem., 1538-1550 (2007).

6. 中西浩一郎、岡崎進、中川節子　 "II-６．分子動力学法 "、 季刊化学総説　高精度分子設計と新素材開発、No.46 pp.135-147 (2000). 日本化学会編、学会出版センター.

7. S. Nakagawa, "Polarizable Model Potential Function for Ion-Methanol Systems ", J. Phys. Chem. A, 104, 5281-5290 (2000).

8. K. Maekawa, S. Ishikawa, H. Ishida, S. Nakagawa, K. Ohkubo, and T. Yamabe, "A molecular dynamics study of the stereoselective interaction between an enantiomeric amino-acid ester and an L-histidine-containing catalyst in the bilayer membrane ", Molecular Engineering 8, 9-24 (1998).

9. S. Nakagawa, "Transferability in multicenter polarizabilities of alkanes and alcohols derived from ab initio polarized one-electron potentials", Chem. Phys. Letters 278, 272-277 (1997).

10. S. Nakagawa, "Anisotropic contribution in multicenter polarizabilities and first hyperpolarizabilities. Ab initio MP2 calculations of acetylene, ethylene, ethane and benzene", Chem. Phys. Letters 246, 256-262 (1995).

11. K. Ueda, H. Ochiai, A. Imamura, and S. Nakagawa, "An investigation of the conformation of b-carrageenan by molecular mechanics and molecular dynamics simulations", Bull. Chem. Soc. Jpn., 68, 95-106 (1995).

12. 上田一義、落合洋、今村詮、中川節子、 "カラギーナン構成二糖の水溶液中における形態に関する分子力学および分子動力学による検討", 高分子論文集, 51, 400-408 (1994).

13. S. Nakagawa, H. -A. Yu, M. Karplus, and H. Umeyama, "Active site dynamics of acyl-chymotrypsin", PROTEINS: Structure, Function, and Genetics, 16, 172-194 (1993).

14. S. Nakagawa and N. Kosugi, "Polarized one-electron potentials fitted by multicenter polarizabilities and hyperpolarizabilities. Ab initio SCF-CI calculation of water", Chem. Phys. Letters, 210, 180-186 (1993).

15. Y. Shiratori and S. Nakagawa, "Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A₂", J. comput. Chem., 12, 717-730 (1991).

16. H. Kubodera, S. Nakagawa, and H. Umeyama, "Ab initio study on the transition state of acylation step of trypsin catalysis", J. Pharmacobio-Dyn., 13, 212-223 (1990).

17. 中川節子　 "セリンプロテアーゼの分子動力学 "、 生物物理、30巻 7-13 (1990)、 日本生物物理学会.

18. S. Nishikawa, J. Adiwinata, H. Morioka, T. Fujimura, T. Tanaka, S. Uesugi, T. Hakoshima, K. Tomita, S. Nakagawa, and M. Ikehara, "A thermoresistant mutant of ribonuclease T1 having three disulfide bonds", Protein Engineering, 3, 443-448 (1990).

19. Y. Shiratori, S. Nakagawa, H. Hori, K. Murakami, and H. Umeyama, "Protein modeling of human prorenin using the molecular dynamics method", J. Mol. Graphics, 8, 163-167 (1990).

20. Y. Tanaka, Y. Shiratori, and S. Nakagawa, "Theoretical studies of pK_a's for organic compounds in aqueous solution", Chem. Phys. Letters, 169, 513-518 (1990).

21. S. Kimura, T. Tanaka, I. Shimada, Y. Shiratori, S. Nakagawa, H. Nakamura, F. Inagaki, and Y. Ota, "Deletion of D-helix in bovine pancreatic phospholipase A₂", Agric. Biol. Chem., 54, 633-639 (1990).