201. |
Shen, Z. and Glover, W. J. Flexible boundary layer using exchange for embedding theories. I. Theory and implementation. J. Chem. Phys. 155, 224112 (2021)
|
|
202. |
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 cells. eLife. 10, e72062 (2021)
|
|
203. |
Brian, D. and Sun, X. Charge-transfer landscape manifesting the structure–rate relationship in the condensed phase via machine learning. J. Phys. Chem. B. 125, 13267–13278 (2021)
|
|
204. |
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)
|
|
205. |
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 drugs. Nanoscale. 13, 19218-19237 (2021)
|
|
206. |
Li, M., Lu, W.C., and Zhang, J. Z.H. Introducing the effective polarizable bond (EPB) model in DNA simulations. Chem. Phys. Lett. 785, 139160 (2021)
|
|
207. |
Brian, D. and Sun, X. Generalized quantum master equation: A tutorial review and recent advances. Chin. J. Chem. Phys. 34, 497 (2021)
|
|
208. |
Dong, G., Hu, Z., Sun, X., and Dong, H. Structural reconstruction of optically invisible state in a single molecule via scanning tunneling microscope. J. Phys. Chem. Lett. 12, 10034–10039 (2021)
|
|
209. |
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)
|
|
210. |
Abreu, C. R. A. and Tuckerman, M. E. Multiple timescale molecular dynamics with very large time steps: avoidance of resonances. Eur. Phys. J. B. 94, 231 (2021)
|
|
211. |
Dai, D., Wang, X., Liu, Y., Yang, X.-L., Glaubitz, C., Denysenkov, V., He, X., Prisner, T., and Mao, J. Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water. Nat. Commun. 12, 6880 (2021)
|
|
212. |
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)
|
|
213. |
Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Computational insights into the binding mechanism of OxyS sRNA with chaperone protein Hfq. Biomolecules. 11, 1653 (2021)
|
|
214. |
Yang, C. and Zhang, Y. Lin_F9: A linear empirical scoring function for protein–ligand docking. J. Chem. Inf. Model. 61, 4630–4644 (2021)
|
|
215. |
Pan, X., Yang, J., Van, R., Epifanovsky, E., Ho, J., Huang, J., Pu, J., Mei, Y., Nam, K., and Shao, Y. Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions. J. Chem. Theory Comput. 17, 5745–5758 (2021)
|
|
216. |
Atsango, A. O., Tuckerman, M. E., and Markland, T. E. Characterizing and contrasting structural proton transport mechanisms in azole hydrogen bond networks using ab initio molecular dynamics. J. Phys. Chem. Lett. 12, 8749–8756 (2021)
|
|
217. |
Chan, E. J., Shtukenberg, A. G., Tuckerman, M. E., and Kahr, B. Crystal structure prediction as a tool for identifying components of disordered structures from powder diffraction: A case study of benzamide II. Cryst. Growth Des. 21, 5544–5557 (2021)
|
|
218. |
Hu, Z., Sun, Z., and Sun, H. Simulation of negative ion photoelectron spectroscopy using a nuclear ensemble approach: Implications from a nuclear vibration effect. J. Phys. Chem. A. 125, 6621–6628 (2021)
|
|
219. |
Li, N., Gao, Y., Qiu, F., and Zhu, T. Benchmark force fields for the molecular dynamic simulation of G-quadruplexes. Molecules. 26, 5379 (2021)
|
|
220. |
Rogal, J., & Tuckerman, M. E. (2021). Pathways in Classification Space: Machine Learning as a Route to Predicting Kinetics of Structural Transitions in Atomic Crystals. In Multiscale Dynamics Simulations (pp. 312-348).
|
|
221. |
Zhao, Y., Miao, Y., Zhi, F., Pan, Y., Zhang, J., Yang, X., Zhang, J. Z. H., and Zhang, L. Rational design of pepsin for enhanced thermostability via exploiting the guide of structural weakness on stability. Front. Phys. 9, 755253 (2021)
|
|
222. |
Wang, X., Li, X., He, X., and Zhang, J. Z. H. A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions. Phys. Chem. Chem. Phys. 23, 21001-21012 (2021)
|
|
223. |
Paz, A. S., Baleeva, N. S., and Glover, W. J. Active orbital preservation for multiconfigurational self-consistent field. J. Chem. Phys. 155, 071103 (2021)
|
|
224. |
Li, Z. and Zhang, J. Z. H. Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. Phys. Chem. Chem. Phys. 23, 13926-13933 (2021)
|
|
225. |
Zeng, J., Weng, J., Zhang, Y., Xia, F., Cui, Q., and Xu, X. Conformational features of Ras: Key hydrogen-bonding interactions of Gln61 in the intermediate state during GTP hydrolysis. J. Phys. Chem. B. 125, 8805–8813 (2021)
|
|
226. |
Huai, Z., Tong, Z., Mei, Y., and Mo, Y. Theoretical study of the spectral differences of the Fenna–Matthews–Olson protein from different species and their mutants. J. Phys. Chem. B. 125, 8313–8324 (2021)
|
|
227. |
Pan, X., Wang, H., Li, C., Zhang, J. Z. H., and Ji, C. MolGpka: A web server for small molecule pKa prediction using a graph-convolutional neural network. J. Chem. Inf. Model. 61, 3159–3165 (2021)
|
|
228. |
Kaplan, M., Wang, Y., Chreifi, G., Zhang, L., Chang, Y.-W., and Jensen, G. J. Programmed flagellar ejection in caulobacter crescentus leaves PL-subcomplexes. J. Mol. Biol. 433, 1670042 (2021)
|
|
229. |
Li, M., Lu, W.C., and Zhang, J. Z. H. Ultra-coarse-graining modeling of liquid water. J. Chem. Phys. 154, 224506 (2021)
|
|
230. |
Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., and Zhang, J. Z. H. Anchor-Locker binding mechanism of the coronavirus spike protein to human ACE2: Insights from computational analysis. J. Chem. Inf. Model. 61, 3529–3542 (2021)
|
|
231. |
Wen, W., Huang, D., Bao, J., Zhang, J. Z. H. Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning. Phys. Chem. Chem. Phys. 23, 15591-15600 (2021)
|
|
232. |
Felker, P. M., Liu, Y., Li, J., and Bačić, Z. DCl–H2O, HCl–D2O, and DCl–D2O dimers: Inter- and intramolecular vibrational states and frequency shifts from fully coupled quantum calculations on a full-dimensional neural network potential energy surface. J. Phys. Chem. A. 125, 6437–6449 (2021)
|
|
233. |
Tinnin, J., Aksu, H., Tong, Z., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials. J. Chem. Phys. 154, 214108 (2021)
|
|
234. |
Zhao, X., Zhang, P., Li, Y., Wu, S., Li, F., Wang, Y., Liang, S., He, X., Zeng, Y., and Liu, Z. Glucose–lipopeptide conjugates reveal the role of glucose modification position in complexation and the potential of malignant melanoma therapy. J. Med. Chem. 64, 11483–11495 (2021)
|
|
235. |
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)
|
|
236. |
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)
|
|
237. |
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)
|
|
238. |
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)
|
|
239. |
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 hydrates. Adv. Theory Simul. 4, 2000258 (2020)
|
|
240. |
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)
|
|
241. |
Shan, J. and Ji, C. MolOpt: A web server for drug design using bioisosteric transformation. Curr. Comput. Aided Drug Des. 16, 460 - 466 (2020)
|
|
242. |
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)
|
|
243. |
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)
|
|
244. |
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)
|
|
245. |
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)
|
|
246. |
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)
|
|
247. |
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)
|
|
248. |
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)
|
|
249. |
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)
|
|
250. |
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)
|
|