Publications

351.

Wang, T., Su, X., Zhang, X., Nie, X., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. Aggregation-induced dual-phosphorescence from organic molecules for non-doped light-emitting diodesAdv. Mater. 31, 1904273 (2019)

352.

Sun, X. Hybrid equilibrium-nonequilibrium molecular dynamics approach for two-dimensional solute-pump/solvent-probe spectroscopyJ. Chem. Phys. 151, 194507 (2019)

353.

Wang, M., Mei, Y., and Ryde, U. Host-guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. J. Chem. Theory Comput. 15, 2659-2671 (2019)

354.

Zhang, Y., Xia, K., Cao, Z., Gräter, F., and Xia, F. A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data. Phys. Chem. Chem. Phys. 21, 9720-9727 (2019)

355.

Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., and Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev. 119, 9478-9508 (2019)

356.

Han, Y., Liu, J., Huang, L., He, X., and Li, J. Predicting the phase diagram of solid carbon dioxide at high pressure from first principles. npj Quantum Materials. 4, 10 (2019)

357.

Zhang, L., Mei, D., Wu, Y., Shen, C., Hu, W., Zhang, L., Li, J., Wu, Y., and He, X. Syntheses, structures, optical properties, and electronic structures of Ba6Cu2GSn4S16 (G= Fe, Ni) and Sr6D2FeSn4S16 (D= Cu, Ag). J. Solid State Chem. 272, 69-77 (2019)

358.

Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., and Zhang, J. Z. H. Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Front Chem. 7, 540 (2019)

359.

Verma, P., Janesko, B. G., Wang, Y., He, X., Scalmani, G., Frisch, M. J., and Truhlar, D. G. M11plus: A range-separated hybrid meta functional with both local and rung-3.5 correlation terms and high across-the-board accuracy for chemical applications. J. Chem. Theory Comput. 15, 4804-4815 (2019)

360.

He, L., Bao, J., Yang, Y., Dong, S., Zhang, L., Qi, Y., and Zhang, J. Z. H. Study of SHMT2 inhibitors and their binding mechanism by computational alanine scanning. J. Chem. Inf. Model. 59, 3871-3878 (2019)

361.

Xu, M., Zhu, T., and Zhang, J. Z. H. Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential. J. Phys. Chem. A. 123, 6587-6595 (2019)

362.

Liu, J., Sun, H., Glover, W. J., and He, X. Prediction of excited-state properties of oligoacene crystals using fragment-based quantum mechanical method. J. Phys. Chem. A. 123, 5407-5417 (2019)

363.

Lu, J., Wang, C., and Zhang, Y. Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network. J. Chem. Theory Comput. 15, 4113-4121 (2019)

364.

Chen, J., Wang, X., Pang, L., Zhang, J. Z. H., and Zhu, T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 47, 6618-6631 (2019)

365.

Lu, Q., He, X., Hu, W., Chen, X., and Liu, J. Stability, vibrations, and diffusion of hydrogen gas in clathrate hydrates: Insights from ab initio calculations on condensed-phase crystalline structures. J. Phys. Chem. C. 123, 12052-12061 (2019)

366.

Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J., and Yu, X. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22. J. Biol. Chem. 294, 8653-8663 (2019)

367.

Cao, H., Wang, J., He, L., Qi, Y., and Zhang, J. Z. H. DeepDDG: Predicting the stability change of protein point mutations using neural networks. J. Chem. Inf. Model. 59, 1508-1514 (2019)

368.

Verma, P., Wang, Y., Ghosh, S., He, X., and Truhlar, D. G. Revised M11 exchange-correlation functional for electronic excitation energies and ground-state properties. J. Phys. Chem. A. 123, 2966-2990 (2019)

369.

Luo, H., Hao, X., Gong, Y., Zhou, J., He, X., and Li, J. Rational crystal polymorph design of olanzapine. Cryst. Growth Des. 19, 2388-2395 (2019)

370.

Sun, Z., Wang, X., Zhang, J. Z. H., and He, Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys. Chem. Chem. Phys. 21, 14923-14940 (2019)

371.

Tuckerman, M. E. Machine learning transforms how microstates are sampled. Science. 365, 982-983 (2019)

372.

Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. Z. H., and Duan, L. Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Phys. Chem. Chem. Phys. 21, 20951-20964 (2019)

373.

Zelovich, T., Vogt-Maranto, L., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Hydroxide ion diffusion in anion-exchange membranes at low hydration: Insights from ab initio molecular dynamics. Chem. Mater. 31, 5778-5787 (2019)

374.

Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., and Zhu, T. Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologiesJ. Biomol. Struct. Dyn. 1-15 (2019)

375.

Shtukenberg, A. G., Tan, M., Vogt-Maranto, L., Chan, E. J., Xu, W., Yang, J., Tuckerman, M. E., Hu, C. T., and Kahr, B. Melt crystallization for paracetamol polymorphism. Cryst. Growth Des. 19, 4070-4080 (2019)

376.

Li, P., Liu, F., Shao, Y., and Mei, Y. Computational insights into endo/exo selectivity of the Diels-Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level. J. Phys. Chem. B. 123, 5131-5138 (2019)

377.

Zhang, Z., Liu, X., Yan, K., Tuckerman, M. E., and Liu, J. Unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics. J. Phys. Chem. A. 123, 6056-6079 (2019)

378.

Liu, X., Zhao, Y., and Zhang, J. Z. H. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem. Phys. Lett. 735, 136771 (2019)

379.

Chen, J., Gao, H., Ding, T., Ji, L., Zhang, J. Z. H., Gao, G., and Xia, F. Mechanistic studies of CO2 cycloaddition reaction catalyzed by amine-functionalized ionic liquids. Front Chem. 7, 615 (2019)

380.

Duan, G., Ji, C., and Zhang, J. Z. H. A force consistent method for electrostatic energy calculation in fluctuating charge model. J. Chem. Phys. 151, 094105 (2019)

381.

Xu, M., Felker, P. M., Mamone, S., Horsewill, A. J., Rols, S., Whitby, R. J., and Bačić, Z. The endofullerene HF@C60: Inelastic neutron scattering spectra from quantum simulations and experiment, validity of the selection rule, and symmetry breakingJ. Phys. Chem. Lett. 10, 5365−5371 (2019)

382.

Felker, P. M., Lauvergnat, D., Scribano, Y., Benoit, D. M., and Bačić, Z. Intramolecular stretching vibrational states and frequency shifts of (H2)2 confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis setsThe Journal of Chemical Physics151, 124311 (2019)

383.

Wang, T., Su, X., Zhang, X., Huang, W., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. A combinatory approach towards the design of organic polymer luminescent materials. J. Mater. Chem. C. 7, 9917-9925 (2019)

384.

Mulvihill, E., Schubert, A., Sun, X., Dunietz, B. D., and Geva, E. A modified approach for simulating electronically nonadiabatic dynamics via the generalized quantum master equationJ. Chem. Phys. 150, 034101 (2019)

385.

L. Petingi and T. Schlick, "Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots'', In: I. Holmes, C. Martín-Vide, M. Vega-Rodríguez, Editors, Algorithms for Computational Biology (AlCoB 2019), Lec. Notes in Comp. Sci. (LNCS) 11488: 68-79 (2019) 

386.

Jung, J., Nishima, W., Daniels, M., Bascom, G., Kobayashi, C., Adedoyin, A., Wall. M., Lappala, A., Phillips, D., Fischer, W., Tung, C.-S., Schlick, T., Sugita, Y., and Sanbonmatsu,  K. Y. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulationsJ. Comp. Chem. 40, 1919-1930 (2019)

387.

Jain, S., Saju, S., Petingi, L., and Schlick, T. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structuresMethods. 162-163, 74-84 (2019)

388.

Portillo-Ledesma, S. and Schlick, T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modelingWIREs Comput. Mol. Sci. e1434 (2019)

389.

Felker, P. M. and  Bačić, Z. Weakly bound molecular dimers: Intramolecular vibrational fundamentals, overtones, and tunneling splittings from full-dimensional quantum calculations using compact contracted bases of intramolecular and low-energy rigid-monomer intermolecular eigenstatesJ. Chem. Phys. 151, 024305 (2019)

390.

Chen, J., Wang, X., Zhang, J. Z. H., and Zhu, T. Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor-CDK2 Association Probed by Interaction Entropy Method. ACS Omega. 3, 18052-18064 (2018)

391.

Zhao, P., Cao, H., Chen, Y., and Zhu, T. Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett. 728, 94-101 (2019)

392.

Perišić, O., Portillo-Ledesma, S, and Schlick, T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res. 47, 4948-4957 (2019)

393.

Sun, Z., Wang, X., and Zhang, J. Z. H. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem. Phys. Lett. 723, 1-10 (2019)

394.

Liu, W., Li, P., and Mei, Y. Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1. J. Mol. Model. 25, 187 (2019)

395.

Wang, X., Tu, X., Deng, B., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive steered MD for configurational sampling. J. Comput. Chem. 40, 1270-1289 (2019)

396.

Huang, D., Qi, Y., Song, J., and Zhang, J. Z. H. Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes. J. Comput. Chem. 40, 1045-1056 (2019)

397.

Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Influence of the protein environment on the electronic excitation of chromophores in the phycoerythrin 545 light-harvesting complex: A combined MD-QM/MM method with polarized protein-specific charge scheme. J. Phys. Chem. B. 123, 2040-2049 (2019)

398.

Chen, J., Pang, L., Wang, W., Wang, L., Zhang, J. Z. H., and Zhu, T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculationsJ. Biomol. Struct. Dyn. 1-15 (2019)

399.

Liu, W., Dai, X., Jih, J., Chan, K., Trang, P., Yu, X., Balogun, R., Mei, Y., Liu, F., Zhou, Z. H. Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development. PLOS Pathog. 15, e1007615 (2019)

400.

Yang, Y., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Computational analysis for residue-specific CDK2-inhibitor bindings. Chinese Journal of Chemical Physics. 32, 134-142 (2019)

Pages