Publications

2025

High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
K. Yagi, K. Gunst, T. Shiozaki, and Y. Sugita
J. Chem. Theory Comput. 21 4016-4029 (2025).
Fermi resonance in the radiative vibrational cooling dynamics of N2⁢O+
S. Harayama, S. Kuma, N. Kimura, K. C. Chartkunchand, M. Baba, T. Murakami, T. Takayanagi, K. Yagi, T. Yamaguchi, Y. Nakano and T. Azuma
Phys. Rev. A, 111, 032803 (2025).
Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
Y.-K. Lei, K. Yagi, and Y. Sugita
J. Chem. Theory Comput. 21, 2695-2711 (2025).
Gold(I)-Catalyzed [2 + 2] and [3 + 2] Cycloadditions of 1,1-Difluoroallenes with Aldehydes: Switchable Syntheses of Fluorinated Oxetanes and Furans
D. Miyazaki, K. Kudo, Y. Fujiki, N. Watanabe, T. Matsui, J. Ichikawa, and K. Fuchibe
Org. Lett. 27 3807-3812 (2025).

非調和性と環境を考慮した生体分子の振動計算
八木清, 杉田有治
生物物理 64, 205-208 (2024).
Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
H. Otaki, S. Ishiuchi, M. Fujii, Y. Sugita and K. Yagi
Phys. Chem. Chem. Phys. 26, 9906-9914 (2024).
Suzuki-Miyaura cross-coupling reaction catalyzed by [R₃Si-IPr]Pd complexes: a computational study
T. Matsui, J. Fujiwara, N. Fukaya and V. Ya. Lee
Mendeleev Commun. 34, 1-5 (2024).
Assessment of the Applicability of the LFC/3D-RISM-SCF Scheme for pK_a Prediction in Methanol Solutions
R. Fujiki, T. Matsui, Y. Shigeta, N. Yoshida, H. Nakano
Chemistry Letters, 53, upad09 (2024).