Publications

Xu, M., Zhu, T., and Zhang, J. Z. H. A force balanced fragmentation method for ab initio molecular dynamic simulation of protein. Front. Chem. 6, 189 (2018)

Gao, Y., Zhu T., Zhang, C. M., Zhang, J. Z. H., and Mei, Y. Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations. Chem. Phys. Lett. 706, 594-600 (2018)

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)

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)

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)

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 ₂ and epoxides under atmospheric pressure. Molecular Catalysis. 446, 124-130 (2018)

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)

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)

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)

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)

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

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)

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)

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)

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)

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

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 functions. J. Chem. Phys. 148, 102340 (2018)

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

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)

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

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)

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)

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@C₆₀. Phys. Chem. Chem. Phys., 19, 31274-31283 (2017)

Liu, W., Jia, X., Wang, M., Li, P., Wang, X., Hu, W., Zheng, J., and Mei, Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-L-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv. 7, 38570 (2017)

Huang, J., Mei, Y., König, G., Simmonett, A. C., Pickard IV, F. C., Wu, Q., Wang, L.-P., MacKerell Jr., A. D., Brooks, B. R., and Shao, Y. An estimation of hybrid quantum mechanical molecular mechanical polarization energies for small molecules using polarizable force-field approaches. J. Chem. Theory Comput. 13, 679-695 (2017)

Wang, Y., Jin, X., Yu, H. S., Truhlar, D. G., and He, X. Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics. Proc. Natl. Acad. Sci. U.S.A. 114, 8487-8492 (2017)

Li, M. and Zhang, J. Z. H. Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins. Phys. Chem. Chem. Phys. 19, 7410-7419 (2017)

Liu, J., He, X., and Zhang, J. Z. H. Structure of liquid water – a dynamical mixture of tetrahedral and ‘ring-and-chain’ like structures. Phys. Chem. Chem. Phys. 19, 11931-11936 (2017)

Sun, Z. X., Wang, X. H., and Zhang, J. Z. H. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation. Phys. Chem. Chem. Phys. 19, 15005 (2017)

Yan, Y., Wang, W., Sun, Z., Zhang, J. Z. H., and Ji, C. Protein–ligand empirical interaction components for virtual screening. J. Chem. Inf. Model. 57, 1793–1806 (2017)

Duan, L., Zhu, T., Ji, C., Zhang, Q., and Zhang, J. Z. H. Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys. Chem. Chem. Phys. 19, 15273-15284 (2017)

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)

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 level. J. Chem. Inf. Model. 57, 2476-2489 (2017)

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)

Luo, Z., Gao, Y., Zhu, T., Zhang, J. Z. H., and Xia, F. Origins of protons in C−H bond insertion products of phenols: Proton-self-sufficient function via water molecules.  J. Phys. Chem. A. 121, 6523-6529 (2017)

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)

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)

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)

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)

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

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)

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

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)

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)

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)

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 energy. Chin. J. Chem. Phys. 30, 789−799 (2017)

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)

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

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 myoglobin. Chin. J. Chem. Phys. 30, 705-716 (2017)

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)