Publications

Jia, X., Ge, H., and Mei, Y. Free energy change estimation: The divide and conquer MBAR method. J. Comput. Chem. 42, 1204-1211 (2021)

Ding, T., Zha, J., Zhang, D., Zhang, J., Yuan, H., Xia, F, and Gao, G. CO₂ atmosphere enables efficient catalytic hydration of ethylene oxide by ionic liquids/organic bases at low water/epoxide ratios. Green Chem. 23, 3386-3391 (2021)

Abreu, C. R. A. and Tuckerman, M. E. Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics. Mol. Phys. e1923848 (2021)

Sun, Z., Gong, Z., Xia, F., and He, X. Ion dynamics and selectivity of Na_v channels from molecular dynamics simulation. Chem. Phys. 548, 111245 (2021)

Shao, G., Bao, J., Pan, X., He, X., Qi, Y., and Zhang, J. Z. H. Analysis of the binding modes of the first- and second-generation antiandrogens with respect to F876L mutation. Chem. Biol. Drug Des. 98, 60-72 (2021)

Liu, J., Liu, Y., Yang, J., Zeng, X. C., and He, X. Directional proton transfer in the reaction of the simplest criegee intermediate with water involving the formation of transient H₃O+. J. Phys. Chem. Lett. 12, 3379-3386 (2021)

Hao, X., Liu, J., Ali, I., Luo, H., Han, Y., Hu, W., Liu, J., He, X. and Li, J. Ab initio determination of crystal stability of di-p-tolyl disulfide. Sci. Rep. 11, 7076 (2021)

Shi, M., Jin, X., Wan, Z., and He, X. Automated fragmentation quantum mechanical calculation of ¹³C and ¹H chemical shifts in molecular crystals. J. Chem. Phys. 154, 064502 (2021)

Zhang, L., Zheng, J., Ma, M., Zhao, Y., Song, J., Chen, X., Cao, W., He, X., Xue, C., and Tang, Q. Drug-guided screening for pancreatic lipase inhibitors in functional foods. Food Funct. 12, 4644-4653 (2021)

Chen, R., Miao, Y., Hao, X., Gao, B., Ma, M., Zhang, J. Z. H., Wang, R., Li, S., He, X., and Zhang, L. Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation. Food Sci. Nutr. 9, 2943-2953 (2021)

Shao, G., Bao, J., Pan, X., He, X., Qi, Y., and Zhang, J. Z. Computational analysis of residue-specific binding free energies of androgen receptor to ligands. Front. Biosci. 8, 646524 (2021)

Sun, Z. and Zhang, J. Z. H. Thermodynamic insights of base flipping in TNA duplex: Force fields, salt concentrations, and free-energy simulation methods. CCS Chem. 3, 1026-1039 (2021)

Hong, R. S., Chan, E. J., Vogt-Maranto, L., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. Insights into the polymorphic structures and enantiotropic layer-slip transition in paracetamol form III from enhanced molecular dynamics. Cryst. Growth Des. 21, 886-896 (2021)

Zelovich, T., Winey, K. I., and Tuckerman, M. E. Hydronium ion diffusion in model proton exchange membranes at low hydration: Insights from ab initio molecular dynamics. J. Mater. Chem. A. 9, 2448-2458 (2021)

Liu, Y., Li, J., Felker, P. M., and Bačić, Z. HCl–H₂O dimer: An accurate full-dimensional potential energy surface and fully coupled quantum calculations of intra- and intermolecular vibrational states and frequency shifts. Phys. Chem. Chem. Phys. 23, 7101–7114 (2021)

Tian, S., Ji, C., and Zhang, J. Z. H. Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization. J. Biomol. Struct. Dyn. 39, 1588-1599 (2021)

Felker, P. M. and Bačić, Z. Intra- and intermolecular rovibrational states of HCl-H₂O and DCl-H₂O dimers from full-dimensional and fully coupled quantum calculations. Chin. J. Chem. Phys. 34, 6 (2021)

Zheng, L., Chen, Y., Bao, J., He, L., Dong, S., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of SARS-CoV-2 main protease. J. Biomol. Struct. Dyn. 1-9 (2021)

Xia, W., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation. J. Biomol. Struct. Dyn. 1-9 (2021)

Felker, P. M. and Bačić, Z. HDO−CO complex: D‑bonded and H‑bonded isomers and intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculations. J. Phys. Chem. A. 125, 980−989 (2021)

Chen, S., Ding, X., Sun, C., Watts, A., He, X., and Zhao, X. Dynamic coupling of tyrosine 185 with the bacteriorhodopsin photocycle, as revealed by chemical shifts, assisted AF-QM/MM calculations and molecular dynamic simulations. Int. J. Mol. Sci. 22, 13587 (2021)

Wu, D., Hu, Z., Li, J., and Sun, X. Forecasting nonadiabatic dynamics using hybrid convolutional neural network/long short-term memory network. J. Chem. Phys. 155, 224104 (2021)

Liu, J. and He, X. Ab initio molecular dynamics simulation of liquid water with fragment- based quantum mechanical approach under periodic boundary conditions. Chin. J. Chem. Phys. 34, 761-768 (2021)

Shen, C., Wang, X., and He, X. Fragment-based quantum mechanical calculation of excited-state properties of fluorescent RNAs. Front. Chem. 9, 801062 (2021)

Xue, Y., Wang, J.-N., Hu, W., Zheng, J., Li, Y., Pan, X., Mo, Y., Shao, Y., Wang, L., and Mei, Y. Affordable ab initio path integral for thermodynamic properties via molecular dynamics simulations using semiempirical reference potential. J. Phys. Chem. A 125, 10677–10685 (2021)

Schlick, T. From butterflies to bits: A sweeping vision for the code of life. Biophys. Rep. 1, 100010 (2021)

Song, H., Vogt-Maranto, L., Wiscons, R., Matzger, A. J., and Tuckerman, M. E. Generating cocrystal polymorphs with information entropy driven by molecular dynamics-based enhanced sampling. J. Phys. Chem. Lett. 11, 9751–9758 (2020)

Hu, W., Li, P., Wang, J.-N., Xue, Y., Mo, Y., Zheng, J., Pan, X., Shao, Y., Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 3. Gaussian smoothing on density-of-states. J. Chem. Theory Comput. 16, 6814–6822 (2020)

Burnham, C. J., Futera, Z., Bačić, Z., and English, N. J. Hydrogen intramolecular stretch redshift in the electrostatic environment of type II clathrate hydrates from Schrödinger equation treatment. Appl. Sci. 10, 8504 (2020)

Zeng, J., Cao, L., Xu, M., Zhu, T., and Zhang. J. Z. H. Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat. Commun. 11, 5713 (2020)

Li, M., Lu, W.C., and Zhang, J. Z. H. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys. Chem. Chem. Phys. 22, 26289-26298 (2020)

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study. Chin. J. Chem. Phys. 33, 203 (2020)

Du, J., Li, W., Liu, B., Zhang, Y., Yu, J., Hou, X., and Fang, H. An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators.  Bioorg. Med. Chem. 28, 115607 (2020)

Zhang, Y., Cao, Z., Zhang, J. Z. H., and Xia, F. Double-well ultra-coarse-grained model to describe protein conformational transitions. J. Chem. Theory Comput. 16, 6678–6689 (2020)

Shan, J. and Ji, C. MolOpt: A web server for drug design using bioisosteric transformation. Curr. Comput. Aided Drug Des. 16, 460 - 466 (2020)

Wang, B., Li, C., Jia, X., Zhu, T., and Zhang, J. Z. H. An approach to computing solvent reorganization energy. J. Chem. Theory Comput. 16, 6513–6519 (2020)

Han, J., Zhang, P., Aksu, H., Maiti, B., Sun, X., Geva, E., Dunietz, B. D., and Cheung, M. S. On the interplay between electronic structure and polarizable force fields when calculating solution-phase charge-transfer rates. J. Chem. Theory Comput. 16, 6481–6490 (2020)

Hu, Z., Tong, Z., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Photoinduced charge transfer dynamics in the carotenoid–porphyrin–C₆₀ triad via the linearized semiclassical nonequilibrium Fermi’s golden rule. J. Phys. Chem. B. 124, 9579–9591 (2020)

Zha, J., Ding, T., Chen, J., Wang, R., Gao, G., and Xia, F. Reaction mechanism of CO₂ and styrene oxide catalyzed by ionic liquids: A combined DFT calculation and experimental study. J. Phys. Chem. A. 124, 7991–7998 (2020)

Bao, J., He, X., and Zhang, J. Z. H. Development of a new scoring function for virtual screening: APBScore. J. Chem. Inf. Model. 60, 6355–6365 (2020)

Abreu, C. R. A. and Tuckerman, M. E. Molecular dynamics with very large time steps for the calculation of solvation free energies. J. Chem. Theory Comput. 16, 7314–7327 (2020)

Bogojeski, M., Vogt-Maranto, L., Tuckerman, M. E., Müller, K.-R., and Burke, K. Quantum chemical accuracy from density functional approximations via machine learning. Nat. Commun. 11, 5223 (2020)

Li, C., Chin, C.-H., Zhu, T., Zhang, J. Z. H. An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH₃OH⁺ and CH₃OH⁺⁺ dissociation. J. Mol. Struct. 1217, 128410 (2020)

Zhang, Y., Poe, D., Heroux, L., Squire, H., Doherty, B. W., Long, Z., Dadmun, M., Gurkan, B., Tuckerman, M. E., and Maginn, E. J. Liquid structure and transport properties of the deep eutectic solvent ethaline. J. Phys. Chem. B. 124, 5251–5264 (2020)

Zelovich, T. and Tuckerman, M. E. Water layering affects hydroxide diffusion in functionalized nanoconfined environments. J. Phys. Chem. Lett. 11, 5087–5091 (2020)

Luo, X., Liu, H., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of quaternary ammonium-tethered triblock copolymers: Effects of the degree of functionalization and styrene content. J. Phys. Chem. C. 124, 16315–16323 (2020)

Long, Z., Atsango, J. A., Napoli, J. A., Markland, T. E., and Tuckerman, M. E. Elucidating the proton transport pathways in liquid imidazole with first-principles molecular dynamics. J. Phys. Chem. Lett. 11, 6156–6163 (2020)

Tong, Z., Videla, P. E., Jung, K. A., Batista, V. S., and Sun, X. Two-dimensional Raman spectroscopy of Lennard-Jones liquids via ring-polymer molecular dynamics. J. Chem. Phys. 153, 034117 (2020)

Tong, Z., Gao, X., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Charge transfer rate constants for the carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation. J. Chem. Phys. 153, 044105 (2020)

Curchod, B. F. E., Glover, W. J., and Martínez, T. J. SSAIMS—stochastic-selection ab initio multiple spawning for efficient nonadiabatic molecular dynamics. J. Phys. Chem. A. 124, 6133–6143 (2020)