|
51. |
Long, Z. and Tuckerman, M. E. Hydroxide diffusion in functionalized cylindrical nanopores as idealized models of anion exchange membrane environments: An ab initio molecular dynamics study. J. Phys. Chem. C 127, 2792–2804 (2023)
|
|
|
52. |
Jiang, G., Hu, Z., Bai, L., Zhong, C., Lu, S., Han, B., Sun, Z., Zhu, S., Liang, Y., and Sun, H. Origins of near-infrared-II emission tail and fluorescence enhancement of the albumin-chaperoned cyanine dyes from a multiscale computational study. J. Mater. Chem. C (2023)
|
|
|
53. |
Li, F., Zhang, Y., Xia, F., and Xu, X. Development of multiscale ultra-coarse-grained models for the SARS-CoV-2 virion from cryo-electron microscopy data. Phys. Chem. Chem. Phys. 25, 12882-12890 (2023)
|
|
|
54. |
Zhu, X., Liu, X., Xia, F., and Liu, L. Theoretical study on the copper-catalyzed ortho-selective C-H functionalization of naphthols with α-phenyl-α-diazoesters. Molecules 28, 1767 (2023)
|
|
|
55. |
Kilgour, M., Rogal, J., and Tuckerman, M. Geometric deep learning for molecular crystal structure prediction. J. Chem. Theory Comput. (2023)
|
|
|
56. |
Zelovich, T., Dekel, D. R., and Tuckerman, M. E. Functional groups in anion exchange membranes: Insights from Ab initio molecular dynamics. J. Membr. Sci. 678, 121638 (2023)
|
|
|
57. |
Mao, A., Chen, C., Portillo-Ledesma, S., and Schlick, T. Effect of single-residue mutations on CTCF binding to DNA: Insights from molecular dynamics simulations. Int. J. Mol. Sci. 24, 6395 (2023)
|
|
|
58. |
Yan, S., Zhu, Q., Hohl, J., Dong, A., and Schlick, T. Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability. Proc. Natl. Acad. Sci. U.S.A. 120, e2221324120 (2023)
|
|
|
59. |
Song, L., Xiong, L., Ni, D., Chen, W., Ji, J., Xue, J., Chen, X., Wu, X., He, X., and Liu, S. One-pot construction of β-selective quinolines with γ-quaternary carbon from vinylquinolines with active ylides via Pd/Sc/Brønsted acid co-catalysis. ACS Catal. 13, 6509–6517 (2023)
|
|
|
60. |
Liu, X., Zheng, L., Qin, C., Cong, Y., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: III. Force-field comparison, three-trajectory realization and further dielectric augmentation. Molecules 28, 2767 (2023)
|
|
|
61. |
Pan, X., Zhao, F., Zhang, Y., Wang, X., Xiao, X., Zhang, J. Z. H., and Ji, C. MolTaut: A tool for the rapid generation of favorable tautomer in aqueous solution. J. Chem. Inf. Model. 63, 1833–1840 (2023)
|
|
|
62. |
Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Binding of berberine derivates to G-quadruplex: insight from a computational study. Phys. Chem. Chem. Phys. 25, 10741-10748 (2023)
|
|
|
63. |
Ma, M., Feng, Y., Miao, Y., Shen, Q., Tang, S., Dong, J., Zhang, J. Z. H., and Zhang, L. Revealing the sequence characteristics and molecular mechanisms of ACE inhibitory peptides by comprehensive characterization of 160,000 tetrapeptides. Foods 12, 1573 (2023)
|
|
|
64. |
Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone. J. Chin. Chem. Soc. 70, 372-385 (2023)
|
|
|
65. |
Liu, J. and He, X. Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems. WIREs Comput Mol Sci. 13, e1650 (2023)
|
|
|
66. |
Ma, M., Cong, Y., Zhang, J. Z. H., and Zhang, L. Rational design of a highly specific prolyl endopeptidase to activate the antihypertensive effect of peptides. ChemBioChem 24, e202200691 (2023)
|
|
|
67. |
Zhang, H., Saravanan, K. M., and Zhang, J. Z. H. DeepBindGCN: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction. Molecules 28, 4691 (2023)
|
|
|
68. |
Paz, A. S. P. and Glover, W. J. Efficient analytical gradients of property-based diabatic states: Geometry optimizations for localized holes. J. Chem. Phys. 158, 204107 (2023)
|
|
|
69. |
Zhang, Q. and Zhu, T. Interaction of divalent cations and amino acids in bulk water: Molecular simulations with neural network potentials. Chin. J. Chem. Phys. 36, 162 (2023)
|
|
|
70. |
Felker, P. M. and Bačić, Z. HF trimer: 12D fully coupled quantum calculations of HF-stretch excited intramolecular and intermolecular vibrational states using contracted bases of intramolecular and intermolecular eigenstates. J. Chem. Phys. 158, 234109 (2023)
|
|
|
71. |
Zhang, J., Cong, Y., Duan, L., and Zhang, J. Z. H. Combined antibodies evusheld against the SARS-CoV-2 Omicron variants BA.1.1 and BA.5: Immune escape mechanism from molecular simulation. J. Chem. Inf. Model. 63, 5297–5308 (2023)
|
|
|
72. |
Li, C., Zhang, A., Wang, L., Zuo, J., Zhu, C., Xu, J., Wang, M., and Zhang, J. Z. H. Development of a polynomial scoring function P3-Score for improved scoring and ranking powers. Chem. Phys. Lett. 824, 140547 (2023)
|
|
|
73. |
Jin, P., Wang, J.-N., Wang, X., Jia, M., Pan, H., Mei, Y., and Chen, J. Tracking the early stage of triplet-induced photodamage in a DNA dimer and oligomer containing 5-methylcytosine. J. Phys. Chem. B 127, 6878–6886 (2023)
|
|
|
74. |
Jiang, Y., Hu, Z., Yang, Y., and Peng, P., Zhong, C., Sun, H., Sun, Z., and Wang, X.-B. Beyond duality: Rationalizing repulsive coulomb barriers in host–guest cyclodextrin–dodecaborate complexes. J. Phys. Chem. Lett. 14, 6736–6742 (2023)
|
|
|
75. |
Naleem, N., Abreu, C. R. A., Warmuz, K., Tong, M., Kirmizialtin, S., and Tuckerman, M. E. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions. J. Chem. Phys. 159, 034102 (2023)
|
|
|
76. |
Bajpai, S., Petkov, B. K., Tong, M., Abreu, C. R. A., Nair, N. N., and Tuckerman, M. E. An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package. J. Comput. Chem. 44, 2166-2183 (2023)
|
|
|
77. |
Wang, X., Wang, Y., Guo, M., Wang, X., Li, Y., and Zhang, J. Z. H. Assessment of an electrostatic energy-based charge model for modeling the electrostatic interactions in water solvent. J. Chem. Theory Comput. (2023)
|
|
|
78. |
Xia, S., Chen, E., and Zhang, Y. Integrated molecular modeling and machine learning for drug design. J. Chem. Theory Comput. 19, 7478–7495 (2023)
|
|
|
79. |
Tang, X., Wang, J., Zhang, J., Miao, Y., Zhao, Y., Gao, B., and Zhang, L. Rational design of lipase MAS1 for the long-chain substrate affinity. Journal of East China University of Science and Technology, 49, 529-535 (2023)
|
|
|
80. |
Zha, J. and Xia, F. Developing hybrid all-atom and ultra-coarse-grained models to investigate taxol-binding and dynein interactions on microtubules. J. Chem. Theory Comput. 19, 5621–5632 (2023)
|
|
|
81. |
Li, Z., Portillo-Ledesma, S., and Schlick, T. Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data. Curr. Opin. Cell Biol. 83, 102209 (2023)
|
|
|
82. |
Guo, J., Xue, Y., Zhao, C., Zhao, J., Gao, Z., Mei, Y., and Song, Y.-Y. Integrated separation-electrochemical detection device based on wood column for online identification of enantiomer. Nano Res. (2023)
|
|
|
83. |
Li, Y., Yang, J., and He, X. Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surface. Nanoscale Adv. 5, 5322-5331 (2023)
|
|
|
84. |
Jiang, Y., Wan, Z., He, X., and Yang, J. Fine-tuning electrolyte concentration and metal–organic framework surface toward actuating fast Zn2+ dehydration for aqueous Zn-ion batteries. Angew. Chem. 62, e202307274 (2023)
|
|
|
85. |
Zhang, J., Kriebel, C. N., Wan, Z., Shi, M., Glaubitz, C., and He, X. Automated fragmentation quantum mechanical calculation of 15N and 13C chemical shifts in a membrane protein. J. Chem. Theory Comput. 19, 7405–7422 (2023)
|
|
|
86. |
Yu, L., He, X., Fang, X., Liu, L., and Liu, J. Deep learning with geometry-enhanced molecular representation for augmentation of large-scale docking-based virtual screening. J. Chem. Inf. Model. 63, 6501–6514 (2023)
|
|
|
87. |
Vindel-Zandbergen, P., Kȩdziera, D., Żółtowski, M., Kłos, J., Żuchowski, P., Felker, P. M., Lique, F., and Bačić, Z. H2O–HCN complex: A new potential energy surface and intermolecular rovibrational states from rigorous quantum calculations. J. Chem. Phys. 159, 174302 (2023)
|
|
|
88. |
Liu, Z., Hu, H., and Sun, X. Multistate reaction coordinate model for charge and energy transfer dynamics in the condensed phase. J. Chem. Theory Comput. 19, 7151–7170 (2023)
|
|
|
89. |
Yang, Y., Lyu, X., Cong, Y., Miao, T., Fang, B., Zhang, C., Shen, Q., Matthews, M., Fisher, A. J., Zhang, J. Z. H., Zhang, L., and Yang, R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int. J. Biol. Macromol. 253, 127093 (2023)
|
|
|
90. |
Duan, L., Tang, B., Luo, S., Xiong, D., Wang, Q., Xu, X., and Zhang, J. Z. H. Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease. Cell. Mol. Life Sci. 80, 313 (2023)
|
|
|
91. |
Liu, X., Zheng, L., Qin, C., Li, Y., Zhang, J. Z. H., and Sun, Z. Screening power of end-point free-energy calculations in cucurbituril host–guest systems. J. Chem. Inf. Model. 63, 6938–6946 (2023)
|
|
|
92. |
Zhao, C., Yang, G., Zhang, S., He, X., Zhong, Y., and Gao, X. Enhanced breathing effect of nanoporous UIO-66-DABA metal–organic frameworks with coordination defects for high selectivity and rapid adsorption of Hg(II). ACS Appl. Nano Mater. 6, 18372–18380 (2023)
|
|
|
93. |
Li, Z. and Schlick, T. Hi-BDiSCO: Folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res. gkad1121 (2023)
|
|
|
94. |
Li, Y., Wang, Y., Zhang, R. M., He, X., and Xu, X. Comprehensive theoretical study on four typical intramolecular hydrogen shift reactions of peroxy radicals: Multireference character, recommended model chemistry, and kinetics. J. Chem. Theory Comput. 19, 3284–3302 (2023)
|
|
|
95. |
Pan, X., Snyder, R., Wang, J.-N., Lander, C., Wickizer, C., Van, R., Chesney, A., Xue, Y., Mao, Y., Mei, Y., Pu, J., and Shao, Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models. J. Comput. Chem. (2023)
|
|
|
96. |
Xiong, Y., Zeng, J., Xia, F., Cui, Q., Deng, X., and Xu, X. Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process. J. Comput. Chem. 43, 906-916 (2022)
|
|
|
97. |
Lu, J. and Zhang, Y. Unified deep learning model for multitask reaction predictions with explanation. J. Chem. Inf. Model. 62, 1376–1387 (2022)
|
|
|
98. |
Zelovich, T., Simari, C., Nicotera, I., Dekel, D. R., and Tuckerman, M. E. The impact of carbonation on hydroxide diffusion in nano-confined anion exchange membranes. J. Mater. Chem. A. 10, 11137-11149 (2022)
|
|
|
99. |
Xu, J., Xue, Y., Jian, X., Zhao, Y., Dai, Z., Xu, J., … Mei, Y., and Song, Y. Y. Understanding of chiral site-dependent enantioselective identification on plasmon-free semiconductor based SERS substrate. Chem. Sci. (2022)
|
|
|
100. |
Pan, X., Wang, H., Zhang, Y., Wang. X., Li, C., Ji, C., and Zhang, J. Z. H. AA-score: A new scoring function based on amino acid-specific interaction for molecular docking. J. Chem. Inf. Model. 62, 2499–2509 (2022)
|
|
