Publications

451.

Wang, J., Cao, H., Zhang, J. Z. H., and Qi, Y. Computational protein design with deep learning neural networks. Sci. Rep. 8, 6349 (2018)

452.

Li, Y., Zhang, Y., Großerüschkamp, F., Stephan, S., Cui, Q., Kötting, C., Xia, F., and Gerwert, K. Specific substates of Ras to interact with GAPs and effectors: Revealed by theoretical simulations and FTIR experiments. J. Phys. Chem. Lett. 9, 1312-1317 (2018)

453.

Liu, X., Peng, L., Zhou, Y., Zhang, Y, and Zhang, J. Z. H. Computational alanine scanning with interaction entropy for protein–ligand binding free energies. J. Chem. Theory Comput. 14, 1772-1780 (2018)

454.

Qiu, L., Yan, Y., Sun, Z., Song, J., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning in protein–protein binding. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1342 (2018)

455.

Liu, J., Swails, J., Zhang, J. Z. H., He, X., and Roitberg, A. E. A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease. J. Am. Chem. Soc. 140, 1639–1648 (2018)

456.

Ji, L., Luo, Z., Zhang, Y., Wang, R., Ji, Y., Xia, F., Gao, G. Imidazolium ionic liquids/organic bases: Efficient intermolecular synergistic catalysts for the cycloaddition of  CO and epoxides under atmospheric pressure. Molecular Catalysis. 446, 124-130 (2018)

457.

Wang, P., Liu, L., Luo, Z., Zhou, Q., Lu, Y., Xia, F., and Liu, Y. Combination of transition metal Rh-catalysis and tautomeric catalysis through a bi-functional ligand for one-pot tandem methoxycarbonylation-aminolysis of olefins towards primary amides. J. Catal. 361, 230-237 (2018)

458.

Bačić, Z., Xu, M., and Felker, P. M. Coupled translation-rotation dynamics of H2 and H2O inside C60: Rigorous quantum treatment. Adv. Chem. Phys. 163, 195-216 (2018)

459.

Wang, X., Tu, X., Zhang, J. Z. H., and Sun, Z. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys. Chem. Chem. Phys. 20, 2009-2021 (2018)

460.

Powers, A., Scribano, Y., Lauvergnat, D., Mebe, E., Benoit, D. M., and Bačić, Z. The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates. J. Chem. Phys. 148, 144304 (2018)

461.

Gao, B., Jiang, S., Wang, L., Zhang, L., Wei, D. Energy and conformation determine the enantioselectivity of enzyme. Biochem. Eng. J. 129, 106-112 (2018)

462.

Jin, X., Zhu, T., Zhang, J. Z. H., and He, X. Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes. Front. Chem. 6, 150 (2018)

463.

Tuckerman M. and Ceperley, D. Preface: Special topic on nuclear quantum effectsJ. Chem. Phys. 148, 102001 (2018) 

464.

Chen, P.-Y., and Tuckerman, M. E. Molecular dynamics based enhanced sampling of collective variables with very large time stepsJ. Chem. Phys. 148, 024106 (2018)

465.

Cendagorta, J. R., Bačić, Z., and Tuckerman, M. E. An open-chain imaginary-time path-integral sampling approach to the calculation of approximate symmetrized quantum time correlation functionsJ. Chem. Phys. 148, 102340 (2018)

466.

Liu, J., He, X., Zhang, J. Z. H., and Qi, L.-W. Hydrogen-bond structure dynamics in bulk water: Insights from ab initio simulations with coupled cluster theory. Chem. Sci. 9, 2065-2073 (2018)

467.

Song, J., Qiu, L., and Zhang, J. Z. H. An efficient method for computing excess free energy of liquidScience China Chemistry, 61, 135-140 (2018)  

468.

Glover, W. J., Mori, T., Schuurman, M. S., Boguslavskiy, A. E., Schalk, O., Stolow, A., and Martínez, T. J. Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations. J. Chem. Phys. 148, 164303 (2018)

469.

Hagras, M. A. and Glover, W. J. Polarizable embedding for excited-state reactions: Dynamically weighted polarizable QM/MM. J. Chem. Theory Comput. 14, 2137-2144 (2018)

470.

Felker, P. M. and Bačić, Z. Accurate quantum calculations of translation-rotation eigenstates in electric-dipole-coupled H 2 O@C 60 assemblies. Chem. Phys. Lett. 683, 172-178 (2017)

471.

Jiang, M., Zhang, L., Wang, F., Zhang, J., Liu, G., Gao, B., and Wei, D. Novel application of magnetic protein: Convenient one-step purification and immobilization of proteins. Sci. Rep. 7, 13329 (2017)

472.

Wang, Y., Wang, X., Truhlar, D. G., and He, X. How well can the M06 suite of functionals describe the electron densities of Ne, Ne6+, and Ne8+? J. Chem. Theory Comput. 13, 6068-6077 (2017)

473.

Wang, X., Zhang, J. Z. H., and He, X. Ab initio quantum mechanics/molecular mechanics molecular dynamics simulation of CO in the heme distal pocket of myoglobinChin. J. Chem. Phys. 30, 705-716 (2017)

474.

Zhang, Y. and He, X. Reaction mechanisms of CO oxidation on cationic, neutral, and anionic X-O-Cu (X = Au, Ag) clustersChem. Phys. Lett. 686, 116-123 (2017)

475.

Wang, Y., Liu, J., Zhang, L., He, X., Zhang, J. Z. H. Computational search for aflatoxin binding proteins. Chem. Phys. Lett. 685, 1-8 (2017)

476.

Li, P., Jia, X., Wang, M., and Mei, Y. Comparison of accuracy and convergence rate between equilibrium and nonequilibrium alchemical transformations for calculation of relative binding free energyChin. J. Chem. Phys. 30, 789−799 (2017)

477.

Huang, M., Luo, Z., Zhu, T., Chen, J., Zhang, J. Z., and Xia, F. A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquidsRSC Adv. 7, 51521-51527 (2017) 

478.

Sun, Z., Wang, X., and Zhang, J. Z. H. Protonation-dependent base flipping in the catalytic triad of a small RNAChem. Phys. Lett. 684, 239-244 (2017)

479.

Sun, Z., Zhu, T., Wang, X., Mei, Y., and Zhang, J. Z. H. Optimization of convergence criteria for fragmentation methodsChem. Phys. Lett. 687, 163-170 (2017)

480.

Liu, F., Yang, Z., Yu, Y., Mei, Y., and Houk, K. N. Bimodal Evans–Polanyi relationships in dioxirane oxidations of sp3 C–H: Non-perfect synchronization in generation of delocalized radical intermediatesJ. Am. Chem. Soc. 139, 16650-16656 (2017)

481.

Jain, S. and Schlick, T. F-RAG: Generating atomic coordinates from RNA graphs by fragment assembly. J. Mol. Biol. 429, 3587-3605 (2017)

482.

Rao, S. S. P., Huang, S. C., Brian, G. S. H., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K. R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., Huang, X., Shamim, M. S., Shin, J., Turner, D., Ye, Z., Omer, A. D., Robinson, J. T., Schlick, T., Bernstein, B. E., Casellas, R., Lander, E. S., and Aiden, E. L. Cohesin loss eliminates all loop domains. Cell. 171, 305-320.e24 (2017)

483.

Felker, P.M., Vlček, V., Hietanen, I., Fitzgerald, S., Neuhauser, D. and Bačić, Z.Explaining the symmetry breaking observed in the endofullerenes H2@C60, HF@C60, and H2O@C60Phys. Chem. Chem. Phys., 19, 31274-31283 (2017)

484.

Schneider, E., Dai, L., Topper, R. Q., Drechsel-Grau, C., and Tuckerman, M. E. Stochastic neural network approach for learning high-dimensional free energy surfaces. Phys. Rev. Lett. 119, 150601 (2017)

485.

Wang, M., Li, P., Jia, X., Liu, W., Shao, Yi., Hu, W., Zheng, J., Brooks, B. R., and Mei, Y. Efficient strategy for the calculation of solvation free energies in water and chloroform at the quantum mechanical/molecular mechanical levelJ. Chem. Inf. Model. 57, 2476-2489 (2017)

486.

Brockherde, F., Vogt, L., Li, L., Tuckerman, M. E., Burke, K., and Müller, K. R. Bypassing the Kohn-Sham equations with machine learning. Nat. Commun. 8, 872 (2017)

487.

Dupuis, R., Benoit, M., Tuckerman, M. E., and Méheut, M. Importance of a fully anharmonic treatment of equilibrium isotope fractionation properties of dissolved ionic species as evidenced by Li+ (aq). Acc. Chem. Res. 50, 1597-1605 (2017)

488.

Shtukenberg, A. G., Zhu, Q., Carter, D. J., Vogt, L., Hoja, J., Schneider, E., Song, H., Pokroy, B., Polishchuk, I., Tkatchenko, A., Oganov, A. R., Rohl, A. L., Tuckerman, M. E., and Kahr, B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.  Chem. Sci. 8, 4926-4940 (2017)

489.

Sepehr, F., Liu, H., Luo, X., Bae, C., Tuckerman, M. E., Hickner, M. A., and Paddison, S. J. Mesoscale simulations of anion exchange membranes based on quaternary ammonium tethered triblock copolymers. Macromolecules. 50, 4397-4405 (2017)

490.

Bascom, G. D., Kim, T., and Schlick, T. Kilobase pair chromatin fiber contacts promoted by living-system-like DNA linker length distributions and nucleosome depletion. J. Phys. Chem. B. 121, 3882-3894 (2017)

491.

Bascom, G. and Schlick, T. Linking chromatin fibers to gene folding by hierarchical looping. Biophys. J. 112, 434-445 (2017)

492.

Rooklin, D. W., Modell, A. E., Li, H., Berdan, V., Arora, P. S., and Zhang, Y.  Targeting unoccupied surfaces on protein-protein interfacesJ. Am. Chem. Soc. 139, 15560-15563 (2017)

493.

Mu, H., Geacintov, N. E., Min, J. H., Zhang, Y., and Broyde, S. Nucleotide excision repair lesion-recognition protein Rad4 captures a pre-flipped partner base in a benzo[a]pyrene-derived DNA lesion: How structure impacts the binding pathway. Chem. Res. Toxicol. 30, 1344-1354 (2017)

494.

Zho, C. C., Farr, E. P., Glover, W. J., and Schwartz, B. J. Temperature dependence of the hydrated electron’s excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models. J. Chem. Phys. 147, 074503 (2017)

495.

Jin, X., Zhang, J. Z. H., and He, X. Full QM calculation of RNA energy using electrostatically embedded generalized molecular fractionation with conjugate caps method. J. Phys. Chem. A. 121, 2503–2514 (2017)

496.

Yan, Y., Yang, M., Ji, C., and Zhang, J. Z. H. Interaction entropy for computational alanine scanning. J. Chem. Inf. Model. 57, 1112-1122, (2017)

497.

Liu, J., Qi L., Zhang, J. Z. H., and He, X. Fragment quantum mechanical method for large-sized ion-water clusters. J. Chem. Theory Comput. 13, 2021-2034 (2017)

498.

Sun, Z., Yan, Y. N., Yang, M., and Zhang, J. Z. H. Interaction entropy for protein-protein bindingJ. Chem. Phys. 146, 124124 (2017)

499.

Gao, Y., Zhang, C., Zhang, J. Z. H., and Mei, Y. Evaluation of the coupled two-dimensional main chain torsional potential in modeling intrinsically disordered proteins. J. Chem. Inf. Model. 57, 267-274 (2017)

500.

Li, M. and Zhang, J. Z. H. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models. J. Chem. Phys. 146, 065101 (2017)

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