Publications

251.

Shen,  Z. and Glover, W. J. Flexible boundary layer using exchange for embedding theories. I. Theory and implementationJ. Chem. Phys. 155, 224112 (2021) 

252.

Shen, Z., Peng, S., and Glover, W. J. Flexible boundary layer using exchange for embedding theories. II. QM/MM dynamics of the hydrated electronJ. Chem. Phys. 155, 224113 (2021)

253.

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

254.

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 potentialJ. Phys. Chem. A 125, 10677–10685 (2021)

255.

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

256.

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

257.

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

258.

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 simulationsInt. J. Mol. Sci. 22, 13587 (2021)

259.

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 calculationJ. Biomol. Struct. Dyn. 1-9 (2021)

260.

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 proteaseJ. Biomol. Struct. Dyn. 1-9 (2021)

261.

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 calculationsChin. J. Chem. Phys. 34, 6 (2021)

262.

Liu, J., Yang, J., Zeng, X. C., Xantheas, S. S., Yagi, K., and He, X. Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21Nat. Commun. 12, 6141 (2021)

263.

Zha, J., Zhang, Y., Xia, K., Gräter, F., and Fei Xia. Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Front. Biosci. 7, 632122 (2020)

264.

Zhang, B., Ma, Y., Jin, X., Wang, Y., Suo, B., He, X., and Jin, Z. GridMol2. 0: Implementation and application of linear‐scale quantum mechanics methods and molecular visualization. Int. J. Quantum Chem. 120, e26402 (2020)

265.

Shan, J., Pan, X., Wang, X., Xiao, X., and Ji, C. FragRep: A web server for structure-based drug design by fragment replacement. J. Chem. Inf. Model. 60, 5900–5906 (2020)

266.

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 calculationsJ. Phys. Chem. A. 125, 980−989 (2021)

267.

Cendagorta, J. R., Shen, H., Bačić, Z., and Tuckerman, M. E. Enhanced sampling path integral methods using neural network potential energy surfaces with application to diffusion in hydrogen hydratesAdv. Theory Simul. 4, 2000258 (2020)

268.

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

269.

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

270.

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)

271.

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)

272.

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)

273.

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)

274.

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)

275.

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)

276.

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)

277.

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)

278.

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)

279.

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)

280.

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)

281.

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

282.

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)

283.

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)

284.

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 contentJ. Phys. Chem. C. 124, 16315–16323 (2020)

285.

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

286.

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 ethalineJ. Phys. Chem. B. 124, 5251–5264 (2020)

287.

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++ dissociationJ. Mol. Struct. 1217, 128410 (2020)

288.

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

289.

 Jin, X., Glover, W. J., and He, X. Fragment quantum mechanical method for excited states of proteins: Development and application to the green fluorescent proteinJ. Chem. Theory Comput. 16, 5174–5188 (2020)

290.

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)

291.

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)

292.

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)

293.

Felker, P. M. and Bačić, Z. H2O–CO and D2O–CO complexes: Intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculationsJ. Chem. Phys. 153, 074107 (2020)

294.

Felker, P. M. and Bačić, Z. Flexible water molecule in C60: Intramolecular vibrational frequencies and translation-rotation eigenstates from fully coupled nine-dimensional quantum calculations with small basis setsJ. Chem. Phys. 152, 014108 (2020)

295.

Xu, M., Felker, P. M., and Bačić, Z. Light molecules inside the nanocavities of fullerenes and clathrate hydrates: Inelastic neutron scattering spectra and the unexpected selection rule from rigorous quantum simulationsInt. Rev. Phys. Chem. 39, 425-463 (2020)

296.

Cendagorta, J. R., Tolpin, J., Schneider, E., Topper, R. Q., and Tuckerman, M. E. Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables. J. Phys. Chem. B. 124, 3647–3660 (2020)

297.

Fellah, N., Shtukenberg, A. G., Chan, E. J., Vogt-Maranto, L., Xu, W., Li, C., Tuckerman, M. E., Kahr, B., and Ward, M. D. Disorderly conduct of benzamide IV: Crystallographic and computational analysis of high entropy polymorphs of small molecules. Cryst. Growth Des. 20, 2670-2682 (2020)

298.

Hou, X., Sun, J., Ge, L., Liang, X., Li, K., Zhang, Y., and Fang, H. Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pocketsEur. J. Med. Chem. 190, 112131 (2020)

299.

Huang, K., Luo, S., Cong, Y., Zhong, S., Zhang, J. Z. H., and Duan, L. An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinityNanoscale. 12, 10737-10750 (2020)

300.

Li, C., Wang, B., Jia, X., and Zhang, J. Z. H. Efficient calculation of excess free energy of pure and mixed alcohol solutions. Chem. Phys. Lett. 749, 137397 (2020)

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