Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

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Publications

2021

Fragment-based Ab Initio Molecular Dynamics Simulation for Combustion

Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang
Molecules, 2021, 26 (11), 3120.
DOI: 10.3390/molecules26113120

Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study

Chih-Hao Chin, Tong Zhu, John ZH Zhang
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D1CP00133G

Automatically Construct Neural Network Potentials for Molecular Dynamics Simulation of Zinc Proteins

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in Chemistry, 2021, 9, 385.
DOI: 10.3389/fchem.2021.692200

Extensive Evaluation of Force Fields for G-Quadruplexes

Na Li, Tong Zhu
ChemRxiv Preprint.
DOI: 10.26434/chemrxiv.14369897

Binding Mechanisms of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations

Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2021.
DOI: 10.1039/D0CP06438F

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement

Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John ZH Zhang, Tong Zhu, Lujia Zhang
RSC Advances, 2021, 11 (20), 12036–12042.
DOI: 10.1039/D1RA00352F

Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator

Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu
Energy & Fuels, 2021, 35 (1), 762–769.
DOI: 10.1021/acs.energyfuels.0c03211

2020

Pharmacological activation of the p53 pathway by a new compound CYZ2017 exerts anti-tumor effects

Yuqiao Han, Ziwei Ren, Yixin Wu, Yunzhong Chen, Zhenmei Cui, Tong Zhu, Mingliang Ma, Yijie Du, Suzhen Dong
Biochemical and Biophysical Research Communications, 2020, 533 (4), 1069–1075.
DOI: 10.1016/j.bbrc.2020.09.122

Ab Initio Molecular Dynamics Simulation of Zinc metalloproteins with Enhanced Self-Organizing Incremental High Dimensional Neural Network

Mingyuan Xu, Tong Zhu, John ZH Zhang
ChemRxiv, 2020.
DOI: 10.26434/chemrxiv.13207967

Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation

Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John ZH Zhang
Nature communications, 2020, 11 (1), 1–9.
DOI: 10.1038/s41467-020-19497-z

Design, synthesis, and structure activity relationship (SAR) studies of novel imidazo [1, 2-a] pyridine derivatives as Nek2 inhibitors

Haili Wang, Yunzhong Chen, Xiaofan Gu, Jianbei Xi, Ziwei Ren, Shuting Wang, Yanhong Duan, Hongyu Li, Tong Zhu, Yijie Du, Xiongwen Zhang, Mingliang Ma
Bioorganic & Medicinal Chemistry, 2020, 28 (23), 115775.
DOI: 10.1016/j.bmc.2020.115775

An Approach to Computing Solvent Reorganization Energy

Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu, John ZH Zhang
Journal of Chemical Theory and Computation, 2020, 16 (10), 6513–6519.
DOI: 10.1021/acs.jctc.0c00672

Reaction mechanism and product branching ratios of $\ce{OH + C2H3F}$ reaction: A theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng-Hui Zhang
Chinese Journal of Chemical Physics, 2020, 33 (2), 203–209.
DOI: 10.1063/1674-0068/cjcp2001016

An ab initio/RRKM study of the reaction mechanism and product branching ratios of $\ce{CH3OH+}$ and $\ce{CH3OH++}$ dissociation

Cuiyu Li, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Journal of Molecular Structure, 2020, 1217, 128410.
DOI: 10.1016/j.molstruc.2020.128410

Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling

Zhenmei Gao, Jingxiao Bao, Shuhua Shi, Xiongwen Zhang, Ya Gao, Tong Zhu
Chemical Physics Letters, 2020, 741, 137126.
DOI: 10.1016/j.cplett.2020.137126

Supramolecular prodrug nanovectors for active tumor targeting and combination immunotherapy of colorectal cancer

Xianli Hu, Bo Hou, Zhiai Xu, Madiha Saeed, Fang Sun, Zhenmei Gao, Yi Lai, Tong Zhu, Fan Zhang, Wen Zhang, Huaijun Yu
Advanced Science, 2020, 7 (8), 1903332.
DOI: 10.1002/advs.201903332

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Haisheng Ren, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2020, 22 (2), 683–691.
DOI: 10.1039/C9CP05091D

2019

Formation mechanism and spectroscopy of $\ce{C6H}$ radicals in extreme environments: a theoretical study

Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang
Physical Chemistry Chemical Physics, 2019, 21 (41), 23044–23055.
DOI: 10.1039/C9CP03662H

Nanoporous $\ce{Ni3P}$ Evolutionarily Structured onto a Ni Foam for Highly Selective Hydrogenation of Dimethyl Oxalate to Methyl Glycolate

Jian Zhu, Liqun Cao, Cuiyu Li, Guofeng Zhao, Tong Zhu, Wei Hu, Weidong Sun, Yong Lu
ACS applied materials & interfaces, 2019, 11 (41), 37635–37643.
DOI: 10.1021/acsami.9b11703

Understanding the selectivity of inhibitors toward PI4KIII$\alpha$ and PI4KIII$\beta$ based molecular modeling

Shuaizhen Tian, Jinzhe Zeng, Xiao Liu, Jianzhong Chen, John ZH Zhang, Tong Zhu
Physical Chemistry Chemical Physics, 2019, 21 (39), 22103–22112.
DOI: 10.1039/C9CP03598B

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

Jianzhong Chen, Baohua Yin, Laixue Pang, Wei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1624616

Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential

Mingyuan Xu, Tong Zhu, John ZH Zhang
The Journal of Physical Chemistry A, 2019, 123 (30), 6587–6595.
DOI: 10.1021/acs.jpca.9b04087

Self-assembly of metallo-nucleoside hydrogels for injectable materials that promote wound closure

Qian Tang, Taylor N Plank, Tong Zhu, Huizhen Yu, Zhilei Ge, Qian Li, Li Li, Jeffery T Davis, Hao Pei
ACS applied materials & interfaces, 2019, 11 (22), 19743–19750.
DOI: 10.1021/acsami.9b02265

Comparison of RP-3 pyrolysis reactions between surrogates and 45-component model by ReaxFF molecular dynamics simulations

Pei Zhao, Song Han, Xiaoxia Li, Tong Zhu, Xiaofang Tao, Li Guo
Energy & Fuels, 2019, 33 (8), 7176–7187.
DOI: 10.1021/acs.energyfuels.9b01321

Understanding Aldose Reductase-Inhibitors interactions with free energy simulation

Zhaoxi Sun, Xiaohui Wang, Qianqian Zhao, Tong Zhu
Journal of Molecular Graphics and Modelling, 2019, 91, 10–21.
DOI: 10.1016/j.jmgm.2019.05.011

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

Jianzhong Chen, Xingyu Wang, Laixue Pang, John ZH Zhang, Tong Zhu
Nucleic acids research, 2019, 47 (13), 6618–6631.
DOI: 10.1093/nar/gkz499

Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

Pei Zhao, Huali Cao, Yu Chen, Tong Zhu
Chemical Physics Letters, 2019, 728, 94–101.
DOI: 10.1016/j.cplett.2019.05.001

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John ZH Zhang, Tong Zhu
Journal of Biomolecular Structure and Dynamics, 2019.
DOI: 10.1080/07391102.2019.1591304

L-4, a well-tolerated and orally active inhibitor of Hedgehog pathway, exhibited potent anti-tumor effects against medulloblastoma in vitro and in vivo

Mingfei Zhu, Hong Wang, Chenglin Wang, Yanfen Fang, Tong Zhu, Weili Zhao, Xiaochun Dong, Xiongwen Zhang
Frontiers in pharmacology, 2019, 10, 89.
DOI: 10.3389/fphar.2019.00089

A fragment quantum mechanical method for metalloproteins

Mingyuan Xu, Xiao He, Tong Zhu, John ZH Zhang
Journal of chemical theory and computation, 2019, 15 (2), 1430–1439.
DOI: 10.1021/acs.jctc.8b00966

2018

Effect of substituents in different positions of aminothiazole hinge-binding scaffolds on inhibitor--CDK2 association probed by interaction entropy method

Jianzhong Chen, Xingyu Wang, John ZH Zhang, Tong Zhu
ACS Omega, 2018, 3 (12), 18052–18064.
DOI: 10.1021/acsomega.8b02354

Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations

Ya Gao, Tong Zhu, Chaomin Zhang, John ZH Zhang, Ye Mei
Chemical Physics Letters, 2018, 706, 594–600.
DOI: 10.1016/j.cplett.2018.07.014

Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method

Ya Gao, Tong Zhu, Jianzhong Chen
Chemical Physics Letters, 2018, 706, 400–408.
DOI: 10.1016/j.cplett.2018.06.040

Donor engineering for NIR-II molecular fluorophores with enhanced fluorescent performance

Qinglai Yang, Zhubin Hu, Shoujun Zhu, Rui Ma, Huilong Ma, Zhuoran Ma, Hao Wan, Tong Zhu, Zhengyan Jiang, Weiqiang Liu, Liying Jiao, Haitao Sun, Yongye Liang, Hongjie Dai
Journal of the American Chemical Society, 2018, 140 (5), 1715–1724.
DOI: 10.1021/jacs.7b10334

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Mingyuan Xu, Tong Zhu, John ZH Zhang
Frontiers in chemistry, 2018, 6, 189.
DOI: 10.3389/fchem.2018.00189

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein

Xianwei Wang, Yang Li, Ya Gao, Zejin Yang, Chenhui Lu, Tong Zhu
Scientific reports, 2018, 8 (1), 1–10.
DOI: 10.1038/s41598-018-23783-8

Automated fragmentation QM/MM calculation of NMR chemical shifts for protein-ligand complexes

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
Frontiers in chemistry, 2018, 6, 150.
DOI: 10.3389/fchem.2018.00150

2017

Structure-based design and synthesis of imidazo [1, 2-a] pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities

Jian-Bei Xi, Yan-Fen Fang, Brendan Frett, Meng-Li Zhu, Tong Zhu, Yan-Nan Kong, Feng-Jie Guan, Yun Zhao, Xiong-Wen Zhang, Hong-Yu Li, Ming-Liang Ma, Wenhao Hu
European journal of medicinal chemistry, 2017, 126, 1083–1106.
DOI: 10.1016/j.ejmech.2016.12.026

Optimization of convergence criteria for fragmentation methods

Zhaoxi Sun, Tong Zhu, Xiaohui Wang, Ye Mei, John ZH Zhang
Chemical Physics Letters, 2017, 687, 163–170.
DOI: 10.1016/j.cplett.2017.08.059

Origins of Protons in C--H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules

Zhoujie Luo, Ya Gao, Tong Zhu, John Zenghui Zhang, Fei Xia
The Journal of Physical Chemistry A, 2017, 121 (34), 6523–6529.
DOI: 10.1021/acs.jpca.7b06411

An electrochemical biosensor with dual signal outputs: toward simultaneous quantification of pH and $\ce{O2}$ in the brain upon ischemia and in a tumor during cancer starvation therapy

Li Liu, Fan Zhao, Wei Liu, Tong Zhu, John ZH Zhang, Chen Chen, Zhihui Dai, Huisheng Peng, Jun-Long Huang, Qin Hu, Wenbo Bu, Yang Tian
Angewandte Chemie International Edition, 2017, 56 (35), 10471–10475.
DOI: 10.1002/anie.201705615

Single biosensor for simultaneous quantification of glucose and pH in a rat brain of diabetic model using both current and potential outputs

Shuai Li, Anwei Zhu, Tong Zhu, John ZH Zhang, Yang Tian
Analytical chemistry, 2017, 89 (12), 6656–6662.
DOI: 10.1021/acs.analchem.7b00881

Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors

Changcheng Jing, Ziyan Li, Kaili Jia, Chen Chen, Xiao Liu, Beibei Wang, Wenhao Hu, Jia Li, Tong Zhu, Suzhen Dong
Archiv der Pharmazie, 2017, 350 (1), e1600173.
DOI: 10.1002/ardp.201600173

A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids

Minmin Huang, Zhoujie Luo, Tong Zhu, Jian Chen, John Zenghui Zhang, Fei Xia
RSC advances, 2017, 7 (81), 51521–51527.
DOI: 10.1039/C7RA09485J

A test of AMBER force fields in predicting the secondary structure of $\alpha$-helical and $\beta$-hairpin peptides

Ya Gao, Chaomin Zhang, Xianwei Wang, Tong Zhu
Chemical Physics Letters, 2017, 679, 112–118.
DOI: 10.1016/j.cplett.2017.04.074

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

Li L Duan, T Zhu, Yu C Li, Qing G Zhang, John ZH Zhang
Scientific reports, 2017, 7 (1), 1–14.
DOI: 10.1038/srep42223

Direct folding simulation of helical proteins using an effective polarizable bond force field

Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John ZH Zhang
Physical Chemistry Chemical Physics, 2017, 19 (23), 15273–15284.
DOI: 10.1039/C7CP02101A

Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction

Suzhen Dong, Yubing Lei, Shikun Jia, Lixin Gao, Jia Li, Tong Zhu, Shunying Liu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2017, 27 (4), 1105–1108.
DOI: 10.1016/j.bmcl.2016.11.055

2016

Predicted PAR1 inhibitors from multiple computational methods

Ying Wang, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Chemical Physics Letters, 2016, 659, 295–303.
DOI: 10.1016/j.cplett.2016.07.059

New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment

Fengping Lv, Chen Chen, Yang Tang, Jianhai Wei, Tong Zhu, Wenhao Hu
Bioorganic & medicinal chemistry letters, 2016, 26 (15), 3714–3718.
DOI: 10.1016/j.bmcl.2016.05.077

PBSA_E: A PBSA-Based Free Energy Estimator for Protein--Ligand Binding Affinity

Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang
Journal of chemical information and modeling, 2016, 56 (5), 854–861.
DOI: 10.1021/acs.jcim.6b00001

Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases

Wang Liu, Yu Lu, Xiaoping Chai, Xiao Liu, Tong Zhu, Xihan Wu, Yanfen Fang, Xuan Liu, Xiongwen Zhang
Journal of Experimental & Clinical Cancer Research, 2016, 35 (1), 1–15.
DOI: 10.1186/s13046-016-0464-2

A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach

Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He
RSC advances, 2016, 6 (110), 108590–108602.
DOI: 10.1039/C6RA22518G

Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity

Yanfen Fang, Yannan Kong, Jianbei Xi, Mengli Zhu, Tong Zhu, Tongtong Jiang, Brendan Frett, Wenhao Hu, Hong-yu Li, Mingliang Ma, others
Oncotarget, 2016, 7 (48), 79327.
DOI: 10.18632/oncotarget.12687

2015

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method

Tong Zhu, John ZH Zhang, Xiao He
Advance in Structural Bioinformatics, 2015, 49–70.
DOI: 10.1007/978-94-017-9245-5_5

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Jason Swails, Tong Zhu, Xiao He, David A Case
Journal of biomolecular NMR, 2015, 63 (2), 125–139.
DOI: 10.1007/s10858-015-9970-3

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John ZH Zhang
Journal of chemical information and modeling, 2015, 55 (9), 1903–1913.
DOI: 10.1021/acs.jcim.5b00173

2010-2014

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations

Tong Zhu, John ZH Zhang, Xiao He
Physical Chemistry Chemical Physics, 2014, 16 (34), 18163–18169.
DOI: 10.1039/C4CP02553A

Fragment Quantum Mechanical Calculation of Proteins and Its Applications

Xiao He, Tong Zhu, Xianwei Wang, Jinfeng Liu, John ZH Zhang
Accounts of chemical research, 2014, 47 (9), 2748–2757.
DOI: 10.1021/ar500077t

Electronic polarization stabilizes tertiary structure prediction of HP-36

Li L Duan, Tong Zhu, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2014, 20 (4), 1–19.
DOI: 10.1007/s00894-014-2195-7

Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-$\beta$-lactamase: experimental and computational study

Jiao Chen, Hui Chen, Tong Zhu, Dandan Zhou, Fang Zhang, Xingzhen Lao, Heng Zheng
Physical Chemistry Chemical Physics, 2014, 16 (14), 6709–6716.
DOI: 10.1039/C3CP55069A

Automated fragmentation QM/MM calculation of amide proton chemical shifts in proteins with explicit solvent model

Tong Zhu, John ZH Zhang, Xiao He
Journal of chemical theory and computation, 2013, 9 (4), 2104–2114.
DOI: 10.1021/ct300999w

A New Quantum Calibrated Force Field for Zinc–Protein Complex

Tong Zhu, Xudong Xiao, Changge Ji, John ZH Zhang
Journal of chemical theory and computation, 2013, 9 (3), 1788–1798.
DOI: 10.1021/ct301091z

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

Li L Duan, Tong Zhu, Ye Mei, Qing G Zhang, Bo Tang, John ZH Zhang
Journal of molecular modeling, 2013, 19 (6), 2605–2612.
DOI: 10.1007/s00894-013-1798-8

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

Tong Zhu, Xiao He, John ZH Zhang
Physical Chemistry Chemical Physics, 2012, 14 (21), 7837–7845.
DOI: 10.1039/C2CP23746F

Quasi-classical Trajectory Study of Reaction $\ce{O (^3P) + HCl (v= 2; j= 1, 6, 9) -> OH + Cl}$

Tong Zhu, Guo-Dong Hu, Qing-Gang Zhang
Chinese Physics Letters, 2010, 27 (3), 033102.
DOI: 10.1088/0256-307X/27/3/033102

Theoretical study of stereodynamics for reaction $\ce{O (^3P) + HCl}$

Tong Zhu, Guo-Dong Hu, Jian-Zhong Chen, Xin-Guo Liu, Qing-Gang Zhang
Chinese Physics B, 2010, 19 (8), 083402.
DOI: 10.1088/1674-1056/19/8/083402

Quasi-classical trajectory study of the reaction $\ce{O (^3P) + HCl -> OH + Cl}$ and $\ce{O (^3P) + DCl -> OD + Cl}$: Vector and scalar properties

Tong Zhu, Guodong Hu, Qinggang Zhang
Journal of Molecular Structure: THEOCHEM, 2010, 948 (1-3), 36–42.
DOI: 10.1016/j.theochem.2010.02.015

THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION $\ce{O (^3 P) + HCl -> OH + Cl}$ FOR THE $^3 A^{″}$ ELECTRONIC STATES

Huirong Liu, Xinguo Liu, Tong Zhu, Haizhu Sun, Qinggang Zhang
Journal of Theoretical and Computational Chemistry, 2010, 9 (06), 1033–1042.
DOI: 10.1142/S0219633610006183

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

Guo-Dong Hu, Tong Zhu, Shao-Long Zhang, Dunyou Wang, Qing-Gang Zhang
European journal of medicinal chemistry, 2010, 45 (1), 227–235.
DOI: 10.1016/j.ejmech.2009.09.048