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Xiao He - Publications

Affiliations: 
2006-2010 Chemistry University of Florida, Gainesville, Gainesville, FL, United States 
 2011-2012 Chemistry University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
 2012- State Key Laboratory for Precision Spectroscopy East China Normal University, Shanghai, Shanghai Shi, China 
Website:
http://faculty.ecnu.edu.cn/s/3005/t/31597/main.jspy
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Year Citation  Score
2022 Liu Y, Zhang C, Liu Z, Truhlar DG, Wang Y, He X. Supervised learning of a chemistry functional with damped dispersion. Nature Computational Science. 3: 48-58. PMID 38177952 DOI: 10.1038/s43588-022-00371-5  0.38
2022 Zhang C, Verma P, Wang J, Liu Y, He X, Wang Y, Truhlar DG, Liu Z. Performance of Screened-Exchange Functionals for Band Gaps and Lattice Constants of Crystals. Journal of Chemical Theory and Computation. PMID 36520598 DOI: 10.1021/acs.jctc.2c00822  0.363
2021 Long B, Wang Y, Xia Y, He X, Bao JL, Truhlar DG. Atmospheric Kinetics: Bimolecular Reactions of Carbonyl Oxide by a Triple-Level Strategy. Journal of the American Chemical Society. PMID 34029069 DOI: 10.1021/jacs.1c02029  0.34
2021 Hao X, Liu J, Ali I, Luo H, Han Y, Hu W, Liu J, He X, Li J. Ab initio determination of crystal stability of di-p-tolyl disulfide. Scientific Reports. 11: 7076. PMID 33782489 DOI: 10.1038/s41598-021-86519-1  0.519
2020 Jin X, Glover WJ, He X. Fragment Quantum Mechanical Method for Excited States of Proteins: Development and Application to the Green Fluorescent Protein. Journal of Chemical Theory and Computation. PMID 32551640 DOI: 10.1021/Acs.Jctc.9B00980  0.363
2020 Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Physical Chemistry Chemical Physics : Pccp. PMID 32459230 DOI: 10.1039/D0Cp01095B  0.422
2020 Huang L, Han Y, Liu J, He X, Li J. Ab Initio Prediction of the Phase Transition for Solid Ammonia at High Pressures. Scientific Reports. 10: 7546. PMID 32372007 DOI: 10.1038/S41598-020-64030-3  0.592
2020 Wang Z, Han Y, Li J, He X. Combining the Fragmentation Approach and Neural Network Potential Energy Surfaces of Fragments for Accurate Calculation of Protein Energy. The Journal of Physical Chemistry. B. PMID 32208716 DOI: 10.1021/Acs.Jpcb.0C01370  0.562
2020 Li H, Zhang W, Liu J, Jin X, Gu X, Zeng XC, He X. Quantitative Prediction of Aggregation-Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra. Angewandte Chemie (International Ed. in English). PMID 32167638 DOI: 10.1002/Anie.202003326  0.345
2020 Liu J, He X. QM Implementation in Drug Design: Does It Really Help? Methods in Molecular Biology (Clifton, N.J.). 2114: 19-35. PMID 32016884 DOI: 10.1007/978-1-0716-0282-9_2  0.336
2020 Xu J, Liu J, Liu J, Hu W, He X, Li J. Phase Transition of Ice at High Pressures and Low Temperatures. Molecules (Basel, Switzerland). 25. PMID 31979295 DOI: 10.3390/Molecules25030486  0.533
2020 Wang Y, Verma P, Zhang L, Li Y, Liu Z, Truhlar DG, He X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proceedings of the National Academy of Sciences of the United States of America. PMID 31953258 DOI: 10.1073/Pnas.1913699117  0.451
2020 Huang L, Han Y, He X, Li J. Ab initio-enabled phase transition prediction of solid carbon dioxide at ultra-high temperatures Rsc Advances. 10: 236-243. DOI: 10.1039/C9Ra06478H  0.565
2019 Huang L, Han Y, He X, Li J. Ab initio-enabled phase transition prediction of solid carbon dioxide at ultra-high temperatures. Rsc Advances. 10: 236-243. PMID 35492555 DOI: 10.1039/c9ra06478h  0.511
2019 Mao J, Aladin V, Jin X, Leeder AJ, Brown LJ, Brown RCD, He X, Corzilius B, Glaubitz C. Exploring Protein Structures by DNP-Enhanced Methyl Solid-State NMR Spectroscopy. Journal of the American Chemical Society. PMID 31756090 DOI: 10.1021/Jacs.9B11195  0.317
2019 Verma P, Janesko BG, Wang Y, He X, Scalmani G, Frisch MJ, Truhlar DG. 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. Journal of Chemical Theory and Computation. PMID 31381338 DOI: 10.1021/Acs.Jctc.9B00411  0.425
2019 Liu J, Sun H, He X. Prediction of Excited-State Properties of Oligoacene Crystals Using Fragment-Based Quantum Mechanical Method. The Journal of Physical Chemistry. A. PMID 31187994 DOI: 10.1021/Acs.Jpca.8B12552  0.381
2019 Verma P, Wang Y, Ghosh S, He X, Truhlar DG. Revised M11 Exchange-Correlation Functional for Electronic Excitation Energies and Ground-State Properties. The Journal of Physical Chemistry. A. PMID 30707029 DOI: 10.1021/Acs.Jpca.8B11499  0.446
2019 Xu M, He X, Zhu T, Zhang JZH. A Fragment Quantum Mechanical Method for Metalloproteins. Journal of Chemical Theory and Computation. PMID 30620584 DOI: 10.1021/Acs.Jctc.8B00966  0.401
2019 Lu Q, He X, Hu W, Chen X, Liu J. Stability, Vibrations, and Diffusion of Hydrogen Gas in Clathrate Hydrates: Insights from Ab Initio Calculations on Condensed-Phase Crystalline Structures Journal of Physical Chemistry C. 123: 12052-12061. DOI: 10.1021/Acs.Jpcc.8B11586  0.368
2019 Luo H, Hao X, Gong Y, Zhou J, He X, Li J. Rational Crystal Polymorph Design of Olanzapine Crystal Growth & Design. 19: 2388-2395. DOI: 10.1021/Acs.Cgd.9B00068  0.546
2019 Zhang L, Mei D, Wu Y, Shen C, Hu W, Zhang L, Li J, Wu Y, He X. Syntheses, structures, optical properties, and electronic structures of Ba6Cu2GSn4S16 (G = Fe, Ni) and Sr6D2FeSn4S16 (D = Cu, Ag) Journal of Solid State Chemistry. 272: 69-77. DOI: 10.1016/J.Jssc.2019.01.024  0.454
2019 Chen S, Ding X, Sun C, Cui H, Watts A, He X, Zhao X. Dynamic Coupling of the Aromatic Rotamer Conformation with the Bacteriorhodopsin Photocycle as Revealed by the Chemical Shift Assisted QM/MM Calculations Biophysical Journal. 116: 208a. DOI: 10.1016/J.Bpj.2018.11.1147  0.317
2018 Wang X, He X. An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules (Basel, Switzerland). 23. PMID 30241317 DOI: 10.3390/Molecules23102410  0.309
2018 Wang Y, Verma P, Jin X, Truhlar DG, He X. Revised M06 density functional for main-group and transition-metal chemistry. Proceedings of the National Academy of Sciences of the United States of America. PMID 30237285 DOI: 10.1073/Pnas.1810421115  0.442
2018 Jin X, Zhu T, Zhang JZH, He X. Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Frontiers in Chemistry. 6: 150. PMID 29868556 DOI: 10.3389/Fchem.2018.00150  0.366
2018 Wang Y, Liu J, Li J, He X. Fragment-based quantum mechanical calculation of protein-protein binding affinities. Journal of Computational Chemistry. PMID 29707784 DOI: 10.1002/Jcc.25236  0.533
2018 Liu J, He X, Zhang JZH, Qi LW. Hydrogen-bond structure dynamics in bulk water: insights from simulations with coupled cluster theory. Chemical Science. 9: 2065-2073. PMID 29675248 DOI: 10.1039/C7Sc04205A  0.342
2018 Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. Journal of the American Chemical Society. PMID 29308643 DOI: 10.1021/Jacs.7B08569  0.327
2017 Wang Y, Wang X, Truhlar DG, He X. How Well Can the M06 Suite of Functionals Describe the Electron Densities of Ne, Ne6+ and Ne8+? Journal of Chemical Theory and Computation. PMID 29111721 DOI: 10.1021/Acs.Jctc.7B00865  0.45
2017 Bao JL, Wang Y, He X, Gagliardi L, Truhlar DG. Multiconfiguration Pair-Density Functional Theory is Free from Delocalization Error. The Journal of Physical Chemistry Letters. PMID 29090926 DOI: 10.1021/Acs.Jpclett.7B02705  0.429
2017 Wang Y, Jin X, Yu HS, Truhlar DG, He X. Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics. Proceedings of the National Academy of Sciences of the United States of America. PMID 28739954 DOI: 10.1073/Pnas.1705670114  0.392
2017 Liu J, He X. Accurate prediction of energetic properties of ionic liquid clusters using a fragment-based quantum mechanical method. Physical Chemistry Chemical Physics : Pccp. PMID 28737802 DOI: 10.1039/C7Cp03356G  0.337
2017 Liu J, He X, Zhang JZH. Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures. Physical Chemistry Chemical Physics : Pccp. PMID 28440370 DOI: 10.1039/C7Cp00667E  0.327
2017 Jin X, Zhang JZ, He X. Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method. The Journal of Physical Chemistry. A. PMID 28264557 DOI: 10.1021/Acs.Jpca.7B00859  0.373
2017 Wang X, Zhang JZH, He X. Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin Chinese Journal of Chemical Physics. 30: 705-716. DOI: 10.1063/1674-0068/30/Cjcp1709169  0.334
2016 Yu HS, He X, Li SL, Truhlar DG. MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions. Chemical Science. 7: 5032-5051. PMID 30155154 DOI: 10.1039/C6Sc00705H  0.496
2016 Yu HS, He X, Li SL, Truhlar DG. Correction: MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions. Chemical Science. 7: 6278-6279. PMID 30124670 DOI: 10.1039/c6sc90044e  0.316
2016 Liu X, Liu J, Zhu T, Zhang L, He X, Zhang JZ. PBSA_E: A PBSA based free energy estimator for protein-ligand binding affinity. Journal of Chemical Information and Modeling. PMID 27088302 DOI: 10.1021/Acs.Jcim.6B00001  0.32
2016 Yu HS, He X, Truhlar DG. MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids. Journal of Chemical Theory and Computation. PMID 26722866 DOI: 10.1021/Acs.Jctc.5B01082  0.499
2016 Yu HS, He X, Li SL, Truhlar DG. MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions Chemical Science. 7: 5032-5051. DOI: 10.1039/c6sc00705h  0.422
2016 Jin X, Zhu T, Zhang JZH, He X. A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach Rsc Advances. 6: 108590-108602. DOI: 10.1039/C6Ra22518G  0.304
2016 Wang Y, Liu J, Zhu T, Zhang L, He X, Zhang JZH. Predicted PAR1 inhibitors from multiple computational methods Chemical Physics Letters. 659: 295-303. DOI: 10.1016/J.Cplett.2016.07.059  0.365
2016 Li Y, Zhang S, Zhang JZH, He X. Assessing the performance of popular QM methods for calculation of conformational energies of trialanine Chemical Physics Letters. 652: 136-141. DOI: 10.1016/J.Cplett.2016.04.037  0.402
2015 Liu J, Zhang JZ, He X. Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins. Physical Chemistry Chemical Physics : Pccp. PMID 26686896 DOI: 10.1039/C5Cp05693D  0.375
2015 Liu J, Zhu T, Wang X, He X, Zhang JZ. Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. Journal of Chemical Theory and Computation. 11: 5897-5905. PMID 26642993 DOI: 10.1021/Acs.Jctc.5B00558  0.36
2015 Wang X, Zhang JZ, He X. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase. The Journal of Chemical Physics. 143: 184111. PMID 26567650 DOI: 10.1063/1.4935176  0.325
2015 Swails J, Zhu T, He X, Case DA. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. Journal of Biomolecular Nmr. 63: 125-39. PMID 26232926 DOI: 10.1007/S10858-015-9970-3  0.359
2015 Zhu T, He X, Zhang JZ. Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Physical Chemistry Chemical Physics : Pccp. 17: 12367. PMID 25897947 DOI: 10.1039/C5Cp90063H  0.372
2015 Yu HS, Zhang W, Verma P, He X, Truhlar DG. Nonseparable exchange-correlation functional for molecules, including homogeneous catalysis involving transition metals. Physical Chemistry Chemical Physics : Pccp. 17: 12146-60. PMID 25877230 DOI: 10.1039/C5Cp01425E  0.465
2015 Zhu T, Zhang JZ, He X. Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method. Advances in Experimental Medicine and Biology. 827: 49-70. PMID 25387959 DOI: 10.1007/978-94-017-9245-5_5  0.398
2014 Zhu T, Zhang JZ, He X. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Physical Chemistry Chemical Physics : Pccp. 16: 18163-9. PMID 25052367 DOI: 10.1039/C4Cp02553A  0.37
2014 He X, Zhu T, Wang X, Liu J, Zhang JZ. Fragment quantum mechanical calculation of proteins and its applications. Accounts of Chemical Research. 47: 2748-57. PMID 24851673 DOI: 10.1021/Ar500077T  0.427
2014 Hirata S, Gilliard K, He X, Li J, Sode O. Ab initio molecular crystal structures, spectra, and phase diagrams. Accounts of Chemical Research. 47: 2721-30. PMID 24754304 DOI: 10.1021/Ar500041M  0.679
2014 Zhang L, Gao B, Yuan Z, He X, Yuan YA, Zhang JZ, Wei D. Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way. Biochimica Et Biophysica Acta. 1844: 1183-92. PMID 24602769 DOI: 10.1016/J.Bbapap.2014.02.021  0.307
2014 He X, Ryu S, Hirata S. Finite-temperature second-order many-body perturbation and Hartree-Fock theories for one-dimensional solids: an application to Peierls and charge-density-wave transitions in conjugated polymers. The Journal of Chemical Physics. 140: 024702. PMID 24437897 DOI: 10.1063/1.4859257  0.526
2014 Hirata S, He X, Hermes MR, Willow SY. Second-order many-body perturbation theory: an eternal frontier. The Journal of Physical Chemistry. A. 118: 655-72. PMID 24328153 DOI: 10.1021/Jp410587B  0.536
2013 Wang B, He X, Merz KM. Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone. Journal of Chemical Theory and Computation. 9: 4653-9. PMID 26589175 DOI: 10.1021/Ct400631B  0.348
2013 Zhu T, Zhang JZ, He X. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. Journal of Chemical Theory and Computation. 9: 2104-14. PMID 26583557 DOI: 10.1021/Ct300999W  0.402
2013 Jia X, Wang X, Liu J, Zhang JZ, Mei Y, He X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. The Journal of Chemical Physics. 139: 214104. PMID 24320361 DOI: 10.1063/1.4833678  0.389
2013 Li Y, Gao Y, Zhang X, Wang X, Mou L, Duan L, He X, Mei Y, Zhang JZ. A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. Journal of Molecular Modeling. 19: 3647-57. PMID 23765039 DOI: 10.1007/S00894-013-1879-8  0.342
2013 Hirata S, He X. On the Kohn-Luttinger conundrum. The Journal of Chemical Physics. 138: 204112. PMID 23742459 DOI: 10.1063/1.4807496  0.516
2013 Liu J, He X, Zhang JZ. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. Journal of Chemical Information and Modeling. 53: 1306-14. PMID 23651068 DOI: 10.1021/Ci400067C  0.314
2013 Wang X, He X, Zhang JZ. Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field. The Journal of Physical Chemistry. A. 117: 6015-23. PMID 23517423 DOI: 10.1021/Jp312063H  0.316
2013 Wang X, Liu J, Zhang JZ, He X. Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. The Journal of Physical Chemistry. A. 117: 7149-61. PMID 23452268 DOI: 10.1021/Jp400779T  0.422
2012 He X, Sode O, Xantheas SS, Hirata S. Second-order many-body perturbation study of ice Ih. The Journal of Chemical Physics. 137: 204505. PMID 23206017 DOI: 10.1063/1.4767898  0.76
2012 Zhu T, He X, Zhang JZ. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Physical Chemistry Chemical Physics : Pccp. 14: 7837-45. PMID 22314755 DOI: 10.1039/C2Cp23746F  0.384
2011 Faver JC, Benson ML, He X, Roberts BP, Wang B, Marshall MS, Kennedy MR, Sherrill CD, Merz KM. Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes. Journal of Chemical Theory and Computation. 7: 790-797. PMID 21666841 DOI: 10.1021/Ct100563B  0.33
2011 Faver JC, Benson ML, He X, Roberts BP, Wang B, Marshall MS, Sherrill CD, Merz KM. The energy computation paradox and ab initio protein folding. Plos One. 6: e18868. PMID 21541343 DOI: 10.1371/Journal.Pone.0018868  0.337
2010 He X, Merz KM. Divide and conquer hartree-fock calculations on proteins Journal of Chemical Theory and Computation. 6: 405-411. PMID 20401160 DOI: 10.1021/Ct9006635  0.339
2009 He X, Fusti-Molnar L, Merz KM. Accurate benchmark calculations on the gas-phase basicities of small molecules. Journal of Physical Chemistry A. 113: 10096-10103. PMID 19694482 DOI: 10.1021/Jp904423R  0.38
2009 Molnar LF, He X, Wang B, Merz KM. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. The Journal of Chemical Physics. 131: 065102. PMID 19691412 DOI: 10.1063/1.3173809  0.361
2009 He X, Wang B, Merz KM. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. Journal of Physical Chemistry B. 113: 10380-10388. PMID 19575540 DOI: 10.1021/Jp901992P  0.381
2009 Li X, He X, Wang B, Merz K. Conformational variability of benzamidinium-based inhibitors. Journal of the American Chemical Society. 131: 7742-54. PMID 19435349 DOI: 10.1021/Ja9010833  0.337
2009 He X, Fusti-Molnar L, Cui G, Merz KM. Importance of dispersion and electron correlation in ab initio protein folding. The Journal of Physical Chemistry. B. 113: 5290-300. PMID 19320454 DOI: 10.1021/Jp8106952  0.371
2006 He X, Zhang JZ. The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy. The Journal of Chemical Physics. 124: 184703. PMID 16709127 DOI: 10.1063/1.2194535  0.395
2005 He X, Mei Y, Xiang Y, Zhang DW, Zhang JZ. Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins. 61: 423-32. PMID 16114038 DOI: 10.1002/Prot.20578  0.326
2005 He X, Zhang JZ. A new method for direct calculation of total energy of protein. The Journal of Chemical Physics. 122: 31103. PMID 15740185 DOI: 10.1063/1.1849132  0.39
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