Publications

151.

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

152.

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 disulfideSci. Rep. 11, 7076 (2021)

153.

Liu, J., Liu, Y., Yang, J., Zeng, X. C., and He, XDirectional 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)

154.

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 mutationChem. Biol. Drug Des. 98, 60-72 (2021)

155.

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

156.

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

157.

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 ratiosGreen Chem. 23, 3386-3391 (2021)

158.

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

159.

Liu, Y., Cong, Y., Zhang, C., Fang, B., Pan, Y., Li, Q., You, C., Gao, B., Zhang, J. Z. H., Zhu, T., and Zhang, LEngineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinementRSC Adv. 11, 12036-12042 (2021)

160.

Li, M. and Zhang, J. Z. H. Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipolesPhys. Chem. Chem. Phys. 23, 8926-8935 (2021)

161.

Schlick, T., Zhu, Q., Jain, S., and Yan, S. Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element. Biophys. J. 120, 1040-1053 (2021)

162.

Wang, J.-N., Liu, W., Li, P., Mo, Y., Hu, W., Zheng, J., Pan, X., Shao, Y., and Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 4. adaptive QM/MMJ. Chem. Theory Comput. 17, 1318-1325 (2021)

163.

Paz, A. S. P. and Glover, W. J. Diabatic many-body expansion: Development and application to charge-transfer reactionsJ. Chem. Theory Comput. 17, 1497-1511 (2021)

164.

Zhu, Q. and Schlick, T. A Fiedler vector scoring approach for novel RNA motif selectionJ. Phys. Chem. B. 125,1144-1155 (2021)

165.

Duan, L., Dong, S., Huang, K., Cong, Y., Luo, S., and Zhang, J. Z. H. Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax. Phys. Chem. Chem. Phys. 23, 2025-2037 (2021)

166.

Zeng, J., Zhang, L., Wang, H., and Zhu, T. Exploring the chemical space of linear alkane pyrolysis via deep potential GENeratorEnergy Fuels. 35, 762–769 (2021)

167.

Brian, D., Liu, Z., Dunietz, B. D., Geva, E., and Sun, X. Three-state harmonic models for photoinduced charge transfer. J. Chem. Phys. 154, 174105 (2021)

168.

Brian, D. and Sun, X. Linear-response and nonlinear-response formulations of the instantaneous Marcus theory for nonequilibrium photoinduced charge transferJ. Chem. Theory Comput. 17, 2065–2079 (2021)

169.

Chen, J., Li, N., Wang, X., Chen, J., Zhang, J. Z. H., and Zhu, T. Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulationsPhys. Chem. Chem. Phys. 23, 10636-10649 (2021)

170.

Wang, X, Yan, J., Zhang, H., Xu, Z., and Zhang, J. Z. H. An electrostatic energy-based charge model for molecular dynamics simulationJ. Chem. Phys. 154, 134107 (2021)

171.

Yin, Y., Chen, H., and Yuan, Q. Strain-induced bandgap engineering in C3N nanotubesChem. Phys. Lett. 768, 138390 (2021)

172.

Portillo-Ledesma, S., Tsao, L. H., Wagley, M., Lakadamyali, M., Cosma, M. P., and Schlick, T. Nucleosome clutches are regulated by chromatin internal parametersJ. Mol. Biol. 433, 166701 (2021)

173.

Lu, J., Xia, S., Lu, J., and Zhang, Y. Dataset construction to explore chemical space with 3D geometry and deep learningJ. Chem. Inf. Model. 61,1095-1104 (2021)

174.

Zhao, J., Blayney, A., Liu, X., Gandy, L., Jin, W., Yan, L., Ha, J.-H., Canning, A. J., Connelly, M., Yang, C., Liu, X., Xiao, Y., Cosgrove, M. S., Solmaz, S. R., Zhang, Y., Ban, D., Chen, J., Loh, S. N., and Wang, C. EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interactionNat. Commun. 12, 986 (2021)

175.

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study. Phys. Chem. Chem. Phys. 23, 12408-12420 (2021)

176.

Wang, T., Hu, Z., Nie, X., Huang, L., Hui, M., Sun, X., and Zhang, G. Thermochromic aggregation-induced dual phosphorescence via temperature-dependent sp3 -linked donor-acceptor electronic coupling. Nat. Commun. 12, 1364 (2021)

177.

Long, B., Wang, Y., Xia, Y., He, X., Bao, J. L., and Truhlar, D. G. Atmospheric kinetics: Bimolecular reactions of carbonyl oxide by a triple-level strategy. J. Am. Chem. Soc. 143, 8402–8413 (2021)

178.

Bao, J., He, X., and Zhang, J. Z. H. DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures. Chem. Inf. Model. 61, 2231–2240 (2021)

179.

Schlick, T. and Portillo-Ledesma, S. Biomolecular modeling thrives in the age of technology. Nat. Comput. Sci. 1, 321-331 (2021)

180.

Schlick, T. and Bishop, T. C. MGO on the go: Multiscale genome symposium-annual biophysical society meeting 2021. Biophys. Rev. 13, 309–310 (2021)

181.

Schlick, T., Portillo-Ledesma, S., Myers, C. G., Beljak, L., Chen, J., Dakhel, S., Darling, D., Ghosh, S., Hall, J., Jan, M., Liang, E., Saju, S., Vohr, M., Wu, C., Xu, Y., Xue, E. Biomolecular modeling and simulation: A prospering multidisciplinary field. Annu. Rev. Biophys. 50, 267-301 (2021)

182.

Gómez-García, P. A., Portillo-Ledesma, S., Neguembor, M. V., Pesaresi, M., Oweis, W., Rohrlich, T., Wieser, S., Meshorer, E., Schlick, T., Cosma, M. P., Lakadamyali, M. Mesoscale modeling and single-nucleosome tracking reveal remodeling of clutch folding and dynamics in stem cell differentiation. Cell Rep. 34, 108614 (2021)

183.

Yusufova, N., Kloetgen, A., Teater, M., Osunsade, A., Camarillo, J. M., Chin, C. R., Doane, A. S., Venters, B. J., Portillo-Ledesma, S., Conway, J., Phillip, J. M., Elemento, O., Scott, D. W., Béguelin, W., Licht, J. D., Kelleher, N. L., Staudt, L. M., Skoultchi, A. I., Keogh, M.-C., Apostolou, E., Mason, C. E., Imielinski, M., Schlick, T., David, Y., Tsirigos, A., Allis, C. D., Soshnev, A. A., Cesarman, E., and Melnick, A. M. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature. 589, 299-305 (2021)

184.

Wang, F., Hu, Z., Wang, X. B., Sun, Z., and Sun, H. Assessment of DFT methods for the prediction of detachment energies and electronic structures of complex and multiply charged anions. Comput. Theor. Chem. 1202, 113295 (2021)

185.

Han, Y., He, L., Qi, Y., Zhao, Y., Pan, Y., Fang, B., Li, S., Zhang, J. Z. H., and Zhang, L. Identification of three new compounds that directly target human serine hydroxymethyltransferase 2. Chem. Biol. Drug Des. 97, 221-230 (2021)

186.

Cao, L., Zeng, J., Xu, M., Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Fragment-based ab initio molecular dynamics simulation for combustion. Molecules. 26, 3120 (2021)

187.

Luo, S., Huang, K., Zhao, X., Cong, Y., Zhang, J. Z. H., and Duan, L. Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculationsNanoscale. 13, 8313-8332 (2021)

188.

Lv, Y., Luo, S., Huang, K., Wang, H., Dong, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy methodJ. Mol. Liq. 336, 116214 (2021)

189.

Zelovich, T. and Tuckerman, M. E. OH− and H3O+ Diffusion in model AEMs and PEMs at low hydration: Insights from ab initio molecular dynamicsMembranes. 11, 355 (2021)

190.

Zhu, X., Hu, C. T., Erriah, B., Vogt-Maranto, L., Yang, J., Yang, Y., Qiu, M., Fellah, N., Tuckerman, M. E., Ward, M. D., and Kahr, B. Imidacloprid crystal polymorphs for disease vector control and pollinator protection. J. Am. Chem. Soc. 143, 17144–17152 (2021)

191.

Brian, D. and Sun, X. Charge-transfer landscape manifesting the structure–rate relationship in the condensed phase via machine learningJ. Phys. Chem. B. 125, 13267–13278 (2021)

192.

Hu, Z., Brian, D., and Sun, X. Multi-state harmonic models with globally shared bath for nonadiabatic dynamics in the condensed phase. J. Chem. Phys. 155, 124105 (2021)

193.

Zhao, X., Luo, S., Huang, K., Xiong, D., Zhang, J. Z. H., and Duan, L. Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugsNanoscale. 13, 19218-19237 (2021)

194.

Li, M., Lu, W.C., and Zhang, J. Z.H. Introducing the effective polarizable bond (EPB) model in DNA simulationsChem. Phys. Lett. 785, 139160 (2021)

195.

Brian, D. and Sun, X. Generalized quantum master equation: A tutorial review and recent advances. Chin. J. Chem. Phys. 34, 497 (2021)

196.

Dong, G., Hu, Z., Sun, X., and Dong, H. Structural reconstruction of optically invisible state in a single molecule via scanning tunneling microscopeJ. Phys. Chem. Lett. 12, 10034–10039 (2021)

197.

Xu, M., Zhu, T., and Zhang, J. Z. H. Automated construction of neural network potential energy surface: The enhanced self-organizing incremental neural network deep potential method. J. Chem. Inf. Model. 61, 5425–5437 (2021)

198.

Paz, A. S., Baleeva, N. S., and Glover, W. J. Active orbital preservation for multiconfigurational self-consistent fieldJ. Chem. Phys. 155, 071103 (2021)

199.

 Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Computational insights into the binding mechanism of OxyS sRNA with chaperone protein HfqBiomolecules. 11, 1653 (2021)

200.

Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cellseLife. 10, e72062 (2021)

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