Publications

Selected Publications

167 publications, 2010–2026.

  1. 2026

    1. Yueqian Sun, Shuwen Zhang, John ZH Zhang, Tong Zhu

      Machine learning driven ReaxFF optimization for combustion.

      Chinese Journal of Chemical Physics 39 (2) , 233–244

      2026
    2. Duo Zhang, Anyang Peng, Chun Cai, Wentao Li, Yuanchang Zhou, Jinzhe Zeng, Mingyu Guo, Chengqian Zhang, Bowen Li, Hong Jiang, Tong Zhu, Weile Jia, Linfeng Zhang, Han Wang

      A graph neural network for the era of large atomistic models.

      npj Computational Materials

      2026
    3. Tianyue Wang, Xujun Zhang, Langcheng Wang, Odin Zhang, Jike Wang, Ercheng Wang, Jialu Wu, Renling Hu, Jingxuan Ge, Shimeng Li, Qun Su, Jiajun Yu, Tingjun Hou, Tong Zhu, Chang-Yu Hsieh, Yu Kang

      AutoLoop is an autoregressive deep learning method for protein loop prediction with high accuracy.

      Cell Reports Physical Science 7 (1)

      2026
    4. Jiabin Yin, Jianqiang Feng, Zhenjia Gan, Bowen Li, Binju Wang, Tong Zhu, John ZH Zhang

      Mechanistic Insights into Nitrogenase-Catalyzed Nitrogen Fixation: A QM/MM Study.

      ACS Catalysis 16 (2) , 1224–1238

      2026
    5. Renjie Zhu, Tong Zhu, Ruibo Wu, Fei Xia

      Enhancing the Simulation Accuracy of Small Organic Molecules with an Optimized Lennard-Jones Coarse-Grained Model.

      2026
    6. Mingyuan Xu, Bowen Li, Zhaojia Dong, Pavlo O Dral, Tong Zhu, Hongming Chen

      SOT-RM: An equivariant shortcut and optimal transportation-based flow model for exploring chemical reaction mechanisms.

      2026
    7. Wan-sheng Ren, Jin Xiao, Yingfeng Zhang, Tong Zhu, John ZH Zhang

      A practical framework for rapid calculation of protein polarization energies with anisotropic atomic polarizabilities.

      The Journal of Chemical Physics 164 (5)

      2026
    8. Jin-En He, Mingjun Yang, Zhe-Ning Chen, Tong Zhu, Jun Chen

      Understanding the Adsorption and Desorption Dynamics for On-surface Systems.

      2026
    9. Xi Zhu, Jiarui Chang, Min Fang, Xinyu Wu, Zhixiang Yin, John ZH Zhang, Fenghua Qi, Tong Zhu, Ya Gao

      Comparative binding mechanisms of SND1 with MTDH and small-molecule inhibitors: insights from molecular dynamics simulations and free energy calculations.

      Physical Chemistry Chemical Physics 28 (16) , 10216–10229

      2026
    10. Mingwei Ding, Chen Huang, Yibo Hu, Yifan Li, Zitian Lu, Xingtai Yu, Duo Zhang, Wenxi Zhai, Tong Zhu, Qiangqiang Gu

      Automating computational chemistry workflows via OpenClaw and domain-specific skills.

      Journal of Chemical Theory and Computation

      2026
    11. Mingyuan Xu, Bowen Li, Zhaojia Dong, Yuxinxin Chen, Pavlo Dral, Tong Zhu, Hongming Chen

      SOT-RM: An equivariant shortcut and optimal transport-based flow model for exploring chemical reaction mechanisms.

      2026
    12. Wan-sheng Ren, Jin Xiao, Yingfeng Zhang, Tong Zhu, John ZH Zhang

      GMFCC-UMA: A Fragment-Based Machine Learning Framework for Scalable Ab Initio-Quality Protein Energies.

      Journal of Chemical Theory and Computation 22 (9) , 4822–4834

      2026
    13. Renling Hu, Jialu Wu, Qun Su, Shimeng Li, Yang Li, Tianyue Wang, Yu Kang, Tong Zhu, Chang-yu Hsieh, Tingjun Hou

      LamNet: an alchemical-path-aware graph neural network to accelerate binding free energy calculations for drug discovery and beyond.

      National Science Review 13 (3) , nwaf559

      2026
    14. Tong Zhu, Weinan E

      From artificial intelligence for science to autonomous chemical innovation: closing the loop in energy and chemical engineering.

      Clean Energy 10 (4) , 1–8

      2026
    15. Xilin Bai, Sixuan Mi, Qi’ang Gong, Jinghui Lu, Jiuzhong Yang, Yang Pan, Xiaohu Li, Zhenrong Sun, Tong Zhu, Ralf I Kaiser

      Experimental astrochemistry and machine learning unravel the formation of oxygen-bearing organic molecules in extraterrestrial ices.

      Communications Chemistry

      2026
    16. Dao Li, Xu Li, Jie Yun, Qizhao Liu, Shansong Gao, Haisheng Li, Tong Zhu, Rongheng Gou

      Automated Reaction Path Discovery for Coal Pyrolysis: Scalable Dataset Construction and Mechanistic Insights for Clean Energy Applications.

      Clean Energy , zkag036

      2026
    17. Shenggeng Lin, Hong Tan, Keyao Wang, Ruixuan Wang, Hongxia Wang, Tong Zhu, Yi Xiong

      RNARL: reinforcement learning-driven unified generative framework for multi-objective RNA codon design.

      Genome Biology

      2026
    18. Jin-En He, Mingjun Yang, Zhe-Ning Chen, Tong Zhu, Jun Chen

      Coverage-Dependent Free-Energy Bottlenecks in CO Adsorption and Desorption on Ru (0001).

      JACS Au

      2026
    19. Zhaojia Dong, Hanwen Zhang, Bowen Li, Sixuan Mi, Jiabin Yin, Jingbo Wang, Jianyi Ma, Tong Zhu

      Improvements in chemical reaction pathway exploration algorithms and dataset generation.

      Scientific Data 13 (1101)

      2026 doi:10.1038/s41597-026-07771-6
  2. 2025

    1. Manyi Yang, Duo Zhang, Xinyan Wang, BoWen Li, Linfeng Zhang, Weinan E, Tong Zhu, Han Wang

      Ab Initio Accuracy Neural Network Potential for Drug-Like Molecules.

      Research 8 , 0837

      2025
    2. Yuanqing Wang, Kenichiro Takaba, Michael S Chen, Marcus Wieder, Yuzhi Xu, Tong Zhu, John ZH Zhang, Arnav Nagle, Kuang Yu, Xinyan Wang

      On the design space between molecular mechanics and machine learning force fields.

      Applied Physics Reviews 12 (2)

      2025
    3. Yingfeng Zhang, Jin Xiao, Shunyu Wang, Tong Zhu, John ZH Zhang

      The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H--Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States.

      Journal of Chemical Theory and Computation 21 (7) , 3410–3425

      2025
    4. Jin Xiao, Yingfeng Zhang, Bowen Li, Shuwen Zhang, Ya Gao, Wei Chen, Han Wang, John ZH Zhang, Tong Zhu

      A Deep Learning-Augmented Density Functional Framework for Reaction Modeling with Chemical Accuracy.

      JACS Au 5 (8) , 3892

      2025
    5. Bowen Li, Jin Xiao, Ya Gao, John ZH Zhang, Tong Zhu

      Transition state searching accelerated by neural network potential.

      Journal of Chemical Information and Modeling 65 (5) , 2297–2303

      2025
    6. Xinyu Lu, Hao Ma, Hui Li, Jia Li, Yi Rong, Yuqiang Li, Tong Zhu, Guokun Liu, Bin Ren

      Vib2Mol: from vibrational spectra to molecular structures-a unified deep learning framework.

      arXiv preprint arXiv:2503.07014

      2025
    7. Mingyuan Xu, Bowen Li, Zhaojia Dong, Pavlo Dral, Tong Zhu, Hongming Chen

      ECTS: An ultra-fast diffusion model for exploring chemical reactions with equivariant consistency.

      2025
    8. Jiaying Gu, Jin Xiao, Xingyu Wu, Xi Zhu, Huimin Chen, John ZH Zhang, Tong Zhu, Ya Gao, Zhixiang Yin

      Interaction of magnesium ion and acetate anion in bulk water: Toward high-level machine learning potential.

      Chinese Journal of Chemical Physics 38 (1) , 95–101

      2025
    9. Hei Wun Kan, Xiao-Tian Li, Tong Zhu, Yuzhi Xu, John ZH Zhang

      Invariant-Potential-Driven Molecular Dynamics Unravels Formose Reaction Kinetics.

      2025
    10. Gehui Wang, Si Zhang, Can Wu, Tong Zhu, Xinbei Xu, Shuangshuang Ge, Haitao Sun, Zhenrong Sun, Jiaxin Wang, Yuemeng Ji

      Atmospheric sulfate aerosol formation enhanced by interfacial anions.

      PNAS nexus 4 (3) , pgaf058

      2025
    11. Xin Zhang, Junfeng Bai, Bowen Liu, Tong Zhu, Hao Zhao

      Real-fluid transport property computations based on the Boltzmann-weighted full-dimensional potential model.

      Applications in Energy and Combustion Science 23 , 100342

      2025
    12. Bowen Li, Sixuan Mi, Jin Xiao, Duo Zhang, Shuwen Zhang, John Zhang, Han Wang, Tong Zhu

      General reactive machine learning potentials for CHON elements.

      2025
    13. Yuzhi Xu, Daqian Bian, Cheng-Wei Ju, Fanyu Zhao, Pujun Xie, Yuanqing Wang, Wei Hu, Zhenrong Sun, John ZH Zhang, Tong Zhu

      Pretrained E (3)-equivariant message-passing neural networks with multi-level representations for organic molecule spectra prediction.

      npj Computational Materials 11 (1) , 203

      2025
    14. Xingyu Wu, Xi Zhu, Min Fang, Fenghua Qi, Zhixiang Yin, John ZH Zhang, Shihua Luo, Tong Zhu, Ya Gao

      Insights into Binding Mechanisms of Potential Inhibitors Targeting PCSK9 Protein via Molecular Dynamics Simulation and Free Energy Calculation.

      Molecules 30 (14) , 2962

      2025
    15. Jian Xue, Meng Li, Li Kang, Meiting Wang, Jiabin Yin, Donghui Sun, Yaqi Deng, Qinghua Wei, Jiemin Wong, Tong Zhu

      Identification of Nogo-B as a potential therapeutic target of osteosarcoma via stereochemically selective covalent probes.

      Cell Death \& Disease 16 (1) , 537

      2025
    16. Jin Xiao, Yingfeng Zhang, Bowen Li, Jinzhe Zeng, John ZH Zhang, Tong Zhu

      DeePaTB: A deep learning powerd semi-empirical quantum mechanical method.

      2025
    17. Tianqing Hu, Zihan Zou, Bo Li, Tong Zhu, Shaonan Gu, Jun Jiang, Yi Luo, Wei Hu

      Deep learning for bidirectional translation between molecular structures and vibrational spectra.

      Journal of the American Chemical Society 147 (31) , 27525–27536

      2025
    18. Jian Xue, Meng Li, Ying Wang, Donghui Sun, Shilong Hao, Zhuochao Liu, Weibin Zhang, Lei Li, Tong Zhu, Shunying Liu

      Identification of EEF1A2 as a potential therapy target of osteosarcoma using novel compound 8e.

      European Journal of Medicinal Chemistry , 118355

      2025
    19. Renjie Zhu, Yuwei Zhang, Tong Zhu, Fei Xia

      Coarse-Grained Simulation of Persistence Length and Twisting Dynamics of Micrometer-Scale Microtubules.

      The Journal of Physical Chemistry Letters 16 (29) , 7300–7306

      2025
    20. Xuwen Chen, Meng Li, Zongjing Hu, Donghui Sun, Yikai Xu, Wenwen Dong, Tong Zhu, Weibin Zhang, Shunying Liu

      Thiazolidinones as Potential PGK1 Inhibitors for Treatment of Osteosarcoma Growth and Metastasis.

      Journal of Medicinal Chemistry 68 (21) , 22216–22245

      2025
    21. Jiabin Yin, Jianqiang Feng, Zhenjia Gan, Bowen Li, Binju Wang, Lujia Zhang, Tong Zhu, John ZH Zhang

      QM/MM study of cytochrome P450 TxtE catalysis: Substrate reorganization enables selective aromatic nitration.

      The Journal of Chemical Physics 163 (16)

      2025
    22. Jianhan Liao, Xiaoxin Shi, Ya Gao, Xingyu Wang, Tong Zhu

      Application of Modern Intelligent Algorithms in Retrosynthesis Prediction.

      Communications in Computational Chemistry 7 (4) , 289–310

      2025
    23. Zizhu Tan, Chia-Heng Hsiung, Jiahui Feng, Yangye Zhang, Yihan Wan, Junlin Chen, Ke Sun, Peilong Lu, Jianyang Zang, Wenxing Yang, Ya Gao, Jiabin Yin, Tong Zhu, Yang Lu, Zijian Pan, Yilong Zou, Can Liao, Xiaosong Li, Yuxuan Ye, Yu Liu, Xin Zhang

      Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.

      Cell 188 (24) , 6987–7005

      2025
  3. 2024

    1. Jin Xiao, YiXiao Chen, LinFeng Zhang, Han Wang, Tong Zhu

      A machine learning-based high-precision density functional method for drug-like molecules.

      Artificial Intelligence Chemistry 2 (1) , 100037

      2024
    2. Jiayi Wei, Yueyang Sun, Heming Wang, Tong Zhu, Li Li, Ying Zhou, Quan Liu, Zhen Dai, Wenjuan Li, Taihua Yang

      Designer cellular spheroids with DNA origami for drug screening.

      Science advances 10 (29) , eado9880

      2024
    3. Haoqing Fu, Mengna Zhang, Jiancai Leng, Wei Hu, Tong Zhu, Yujin Zhang

      Predicting Two-Photon Absorption Spectra of Octupolar Molecules: A Deep-Learning Approach Based Exclusively on Molecular Structures.

      The Journal of Physical Chemistry A 128 (2) , 431–438

      2024
    4. Yaqi Deng, Zongjing Hu, Jian Xue, Jiabin Yin, Tong Zhu, Shunying Liu

      Visible-light-promoted $\alpha$-C (sp3)--H amination of ethers with azoles and amides.

      Organic Letters 26 (4) , 933–938

      2024
    5. Likun Wang, Na Li, Mengyao Cao, Yun Zhu, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei

      Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.

      Advanced Science 11 (42) , 2409880

      2024
    6. Jianhan Liao, Xiaoxin Shi, Tong Zhu

      Application of modern intelligent algorithms in retrosynthesis prediction.

      2024
    7. Bowen Li, Jin Xiao, Ya Gao, John Zhang, Tong Zhu

      Transition State Searching Accelerated by Deep Learning Potential.

      2024
    8. Jinhua Liu, Yaqi Deng, Jiabin Yin, Jian Ji, Cong Guan, Xuwen Chen, Xiang Wu, Tong Zhu, Shunying Liu

      A one-pot photocatalytic triazole-based linkerology for PROTACs.

      Cell Reports Physical Science 5 (8)

      2024
    9. Yaqi Deng, Jiabin Yin, Zongjing Hu, Jian Xue, Jian Ji, Tong Zhu, Shunying Liu

      Iodide ion-enabled highly regioselective $\alpha$-C (sp3)--H triazolization of ethers with N-sulfonyl-1, 2, 3-triazoles.

      New Journal of Chemistry 48 (34) , 15002–15007

      2024
    10. Jiajia Sun, Wei Lai, Jiayan Zhao, Jinhong Xue, Tong Zhu, Mingshu Xiao, Tiantian Man, Ying Wan, Hao Pei, Li Li

      Rapid identification of drug mechanisms with deep learning-based multichannel surface-enhanced Raman spectroscopy.

      ACS sensors 9 (8) , 4227–4235

      2024
    11. Yuzhi Xu, Daqian Bian, Cheng-Wei Ju, Fanyu Zhao, Pujun Xie, Yuanqing Wang, Wei Hu, Zhenrong Sun, John Zhang, Tong Zhu

      EnviroDetaNet: Pretrained E (3)-equivariant Message-Passing Neural Networks with Multi-Level Molecular Representations for Organic Molecule Spectra Prediction.

      2024
    12. Jian Xue, Hongtao Li, Ruyu Wang, Meiting Wang, Xixiang Chen, Yaqi Deng, Jiani Lu, Yexi Li, Yuheng Song, Jianrong Xu, Tong Zhu, Lili Chen, Shunying Liu

      Novel Alkynylamide-Based Nonpeptidic Allosteric Inhibitors for SARS-CoV-2 3-Chymotrypsin-like Protease.

      ACS Pharmacology \& Translational Science 7 (10) , 3170–3191

      2024
    13. Xuwen Chen, Hongtao Li, Meiting Wang, Donghui Sun, Jiani Lu, Tong Zhu, Hongzhuan Chen, Lili Chen, Shunying Liu

      Discovery of chalcone derivatives as bifunctional molecules with anti-SARS-CoV-2 and anti-inflammatory activities.

      Journal of Natural Products 87 (12) , 2680–2694

      2024
    14. Xiao-Tian Li, Sixuan Mi, Yuzhi Xu, Bo-Wen Li, Tong Zhu, John ZH Zhang

      Discovery of new synthetic routes of amino acids in prebiotic chemistry.

      JACS Au 4 (12) , 4757

      2024
    15. Han Wang, Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Jiameng Huang, Bowen Li, Yifan Shan, Jinzhe Zeng, Yuzhi Zhang, Siyuan Liu, Yifan Li, Junhan Chang, Xinyan Wang, Shuo Zhou, Jianchuan Liu, Xiaoshan Luo, Zhenyu Wang, Wanrun Jiang, Jing Wu, Yudi Yang, Jiyuan Yang, Manyi Yang, Fu-Qiang Gong, Linshuang Zhang, Mengchao Shi, Fu-Zhi Dai, Darrin York, Shi Liu, Tong Zhu, Zhicheng Zhong, Jian Lv, Jun Cheng, Weile Jia, Mohan Chen, Guolin Ke, Weinan E, Linfeng Zhang

      DPA-2: Towards a universal large atomic model for molecular and materials simulation.

      2024
    16. Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Anyang Peng, Jiameng Huang, Bowen Li, Yifan Shan, Jinzhe Zeng, Yuzhi Zhang, Siyuan Liu, Yifan Li, Junhan Chang, Xinyan Wang, Shuo Zhou, Jianchuan Liu, Xiaoshan Luo, Zhenyu Wang, Wanrun Jiang, Jing Wu, Yudi Yang, Jiyuan Yang, Manyi Yang, Fu-Qiang Gong, Linshuang Zhang, Mengchao Shi, Fu-Zhi Dai, Darrin M. York, Shi Liu, Tong Zhu, Zhicheng Zhong, Jian Lv, Jun Cheng, Weile Jia, Mohan Chen, Guolin Ke, Weinan E, Linfeng Zhang, Han Wang

      DPA-2: a large atomic model as a multi-task learner.

      npj computational materials 10 (1) , 293

      2024
    17. Qiuyue Nie, Chunxiao Sun, Shuai Liu, Qiang Li, Maria Zotova, Tong Zhu, Xue Gao

      Enzymatic ring contraction for the biosynthesis of sulfur-containing cyclopentachromone.

      Journal of the American Chemical Society 147 (1) , 548–556

      2024
    18. Jiajia Sun, Wei Lai, Jiayan Zhao, Jinhong Xue, Tong Zhu, Mingshu Xiao, Tiantian Man, Ying Wan, Hao Pei, Li Li

      Correction to “Rapid Identification of Drug Mechanisms with Deep Learning-Based Multichannel Surface-Enhanced Raman Spectroscopy”.

      ACS sensors 10 (1) , 574–574

      2024
    19. Manyi Yang, Duo Zhang, Xinyan Wang, Lingfeng Zhang, Tong Zhu, Han Wang

      Ab initio accuracy neural network potential for drug-like molecules.

      2024
  4. 2023

    1. Jinzhe Zeng, Liqun Cao, Tong Zhu

      Neural network potentials.

      Quantum Chemistry in the Age of Machine Learning , 279–294

      2023
    2. Chuchu Li, Yuqiao Han, Zhengyang Wang, Yanan Yu, Chen Wang, Ziwei Ren, Yanzhi Guo, Tong Zhu, XuWen Li, Suzhen Dong

      Function-oriented synthesis of Imidazo [1, 2-a] pyrazine and Imidazo [1, 2-b] pyridazine derivatives as potent PI3K/mTOR dual inhibitors.

      European Journal of Medicinal Chemistry 247 , 115030

      2023
    3. Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang

      Theoretical study of the absorption and emission spectrum and non-adiabatic excited state dynamics of gas-phase xanthone.

      Journal of the Chinese Chemical Society 70 (3) , 372–385

      2023
    4. Chen Wang, Ya Gao, Jiaying Gu, Huimin Chen, Zhixiang Yin, Hao Zhu, Tong Zhu

      Ensemble-based virtual screening of human PI4KIII$\alpha$ inhibitors toward the Hepatitis C virus.

      Chemical Physics Letters 815 , 140354

      2023
    5. Likun Wang, Jiayan Zhao, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei

      Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection.

      ChemPlusChem 88 (9) , e202300083

      2023
    6. Qi Zhang, Tong Zhu

      Interaction of divalent cations and amino acids in bulk water: Molecular simulations with neural network potentials.

      Chinese Journal of Chemical Physics 36 (2) , 162–168

      2023
    7. Cong Guan, Jiabin Yin, Jian Ji, Jinhua Liu, Xiang Wu, Tong Zhu, Shunying Liu

      Regioselectively Electrochemical Synthesis of N 2-Selective C--H Amination of Ethers with N-Tosyl 1, 2, 3-Triazole via Triazole Radical Cation.

      Organic Letters 25 (28) , 5383–5388

      2023
    8. Han Wang, Duo Zhang, Xinzijian Liu, Xiangyu Zhang, Chengqian Zhang, Chun Cai, Hangrui Bi, Yiming Du, Xuejian Qin, Jiameng Huang, Bowen Li, Yifan Shan, Jinzhe Zeng, Yuzhi Zhang, Siyuan Liu, Yifan Li, Junhan Chang, Xinyan Wang, Shuo Zhou, Jianchuan Liu, Xiaoshan Luo, Zhenyu Wang, Wanrun Jiang, Jing Wu, Yudi Yang, Jiyuan Yang, Manyi Yang, Fu-Qiang Gong, Linshuang Zhang, Mengchao Shi, Fu-Zhi Dai, Darrin York, Shi Liu, Tong Zhu, Zhicheng Zhong, Jian Lv, Jun Cheng, Weile Jia, Mohan Chen, Guolin Ke, Weinan E, Linfeng Zhang

      DPA-2: Towards a universal large atomic model for molecular and material simulation.

      arXiv e-prints , arXiv–2312

      2023
    9. Yanzhi Guo, Yuqiao Han, Ziyan Li, Jiali Ji, Tong Zhu, Yijie Du, Suzhen Dong

      A new inhibitor of human peptide deformylase suppresses cell proliferation and induces cell apoptosis and autophagy in cancers.

      Anti-Cancer Drugs 34 (4) , 483–494

      2023
    10. Xinyi Zhao, Raorao Yang, Zhi-Hui Zhang, Tong Zhu, Liang Zhang

      Theoretical investigation of the lack of chiral self-sorting behaviour of a molecular cinquefoil knot.

      Supramolecular Chemistry 34 (5-6) , 247–256

      2023
    11. Wei Hu, Tianqing Hu, Bo Li, Zihan Zou, Tong Zhu, Yujin Zhang, Jun Jiang, Yi Luo

      A Machine Learning Protocol to Directly Translate Molecular Infrared or Raman Spectra into Molecular Formula.

      2023
    12. Likun Wang, Jiayan Zhao, Xiewei Xiong, Li Li, Tong Zhu, Hao Pei

      Front Cover: Enzyme-Free Nucleic Acid Circuits for Fold-Change Detection (ChemPlusChem 9/2023)..

      ChemPlusChem 88 (9) , 1

      2023
  5. 2022

    1. Xiaoniu Fang, Ya Gao, Chen Wang, Huimin Chen, Tong Zhu

      Exploring the selective mechanism of inhibitors towards different subtypes of class I PI3K.

      Chemical Physics Letters 786 , 139174

      2022
    2. Shuangfei Gu, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang

      Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD3CH2F.

      Chinese Journal of Chemical Physics 35 (3) , 431–442

      2022
    3. Bo Wang, Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Darrin York, Tong Zhu, John Zhang

      Growth of polycyclic aromatic hydrocarbon and soot inception by in silico simulation.

      2022
    4. Liqun Cao, Jinzhe Zeng, Bo Wang, Tong Zhu, John ZH Zhang

      Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT.

      Physical Chemistry Chemical Physics 24 (19) , 11801–11811

      2022
    5. Xiewei Xiong, Tong Zhu, Yun Zhu, Mengyao Cao, Jin Xiao, Li Li, Fei Wang, Chunhai Fan, Hao Pei

      Molecular convolutional neural networks with DNA regulatory circuits.

      Nature Machine Intelligence 4 (7) , 625–635

      2022
    6. Ya Gao, Bo Wang, Shiyu Hu, Tong Zhu, John ZH Zhang

      An efficient method to predict protein thermostability in alanine mutation.

      Physical Chemistry Chemical Physics 24 (48) , 29629–29639

      2022
    7. Yaqi Deng, Rou Pi, Li Niu, Yun Zhao, Dan Ni, Longlong Song, Zi Li, Wangyujing Han, Qinghua Wei, Yuqiao Han, Tong Zhu, Zhengli Luo, Donghui Sun, Suzhen Dong, Shunying Liu

      Novel 2-phenyl-3-(Pyridin-2-yl) thiazolidin-4-one derivatives as potent inhibitors for proliferation of osteosarcoma cells in vitro and in vivo.

      European Journal of Medicinal Chemistry 228 , 114010

      2022
    8. Fanglong Zhao, Chunxiao Sun, Zhiwen Liu, Alan Cabrera, Mario Escobar, Shunyu Huang, Qichen Yuan, Qiuyue Nie, Kevin Lee Luo, Angela Lin, Jeffrey A. Vanegas, Tong Zhu, Isaac B. Hilton, Xue Gao

      Multiplex base-editing enables combinatorial epigenetic regulation for genome mining of fungal natural products.

      Journal of the American Chemical Society 145 (1) , 413

      2022
  6. 2021

    1. Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John ZH Zhang, Tong Zhu

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

      RSC advances 11 (20) , 12036–12042

      2021
    2. Mingyuan Xu, Tong Zhu, John ZH Zhang

      Automated construction of neural network potential energy surface: The enhanced self-organizing incremental neural network deep potential method.

      Journal of Chemical Information and Modeling 61 (11) , 5425–5437

      2021
    3. Na Li, Tong Zhu

      Extensive Evaluation of Force Fields for G-Quadruplexes.

      2021
    4. Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John ZH Zhang, Tong Zhu

      Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations.

      Physical Chemistry Chemical Physics 23 (17) , 10636–10649

      2021
    5. Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang

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

      Physical Chemistry Chemical Physics 23 (21) , 12408–12420

      2021
    6. Mingyuan Xu, Tong Zhu, John ZH Zhang

      Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteins.

      Frontiers in Chemistry 9 , 692200

      2021
    7. Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang

      Fragment-based ab initio molecular dynamics simulation for combustion.

      Molecules 26 (11) , 3120

      2021
    8. Zhiwen Liu, Fanglong Zhao, Boyang Zhao, Jie Yang, Joseph Ferrara, Banumathi Sankaran, B. V. Venkataram Prasad, Biki Bapi Kundu, George N. Phillips, Yang Gao, Liya Hu, Tong Zhu, Xue Gao

      Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins.

      Nature communications 12 (1) , 4158

      2021
    9. Na Li, Ya Gao, Feng Qiu, Tong Zhu

      Benchmark force fields for the molecular dynamic simulation of G-quadruplexes.

      Molecules 26 (17) , 5379

      2021
    10. Hao Pei, Xiewei Xiong, Tong Zhu, Yun Zhu, Mengyao Cao, Jin Xiao, Li Li, Fei Wang, Chunhai Fan

      Molecular convolutional neural networks with DNA regulatory circuits.

      2021
  7. 2020

    1. Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Haisheng Ren, John ZH Zhang, Tong Zhu

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

      Physical chemistry chemical physics 22 (2) , 683–691

      2020
    2. Jianzhong Chen, Laixue Pang, Wei Wang, Lifei Wang, John ZH Zhang, Tong Zhu

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

      Journal of Biomolecular Structure and Dynamics

      2020
    3. Baohua Yin, Laixue Pang, Wei Wang, John ZH Zhang, Tong Zhu

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

      Journal of Biomolecular Structure and Dynamics

      2020
    4. Zhenmei Gao, Jingxiao Bao, Shuhua Shi, Xiongwen Zhang, Ya Gao, Tong Zhu

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

      Chemical Physics Letters 741 , 137126

      2020
    5. Cuiyu Li, Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang

      An ab initio/RRKM study of the reaction mechanism and product branching ratios of CH3OH+ and CH3OH++ dissociation.

      Journal of Molecular Structure 1217 , 128410

      2020
    6. Chih-Hao Chin, Tong Zhu, John Zeng-Hui Zhang

      Reaction mechanism and product branching ratios of OH+ C2H3F reaction: A theoretical study.

      Chinese Journal of Chemical Physics 33 (2) , 203–209

      2020
    7. Chih-Hao Chin, Tong Zhu, John Zeng-Hui Zhang

      OH+ C_2H_3F 的反应机理及产物支化比反应的理论研究 (英文).

      Chinese Journal of Chemical Physics

      2020
    8. Linfeng Zhang, Han Wang, Tong Zhu

      Explore the Chemical.

      2020
    9. Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu

      Explore the Chemical Space of Linear Alkanes Pyrolysis via Deep Potential Generator.

      2020
    10. Bo Wang, Cuiyu Li, Jia Xiangyu, Tong Zhu, John ZH Zhang

      An Approach to Computing Solvent Reorganization Energy.

      Journal of Chemical Theory and Computation 16 (10) , 6513–6519

      2020
    11. Haili Wang, Yunzhong Chen, Xiaofan Gu, Jianbei Xi, Ziwei Ren, Shuting Wang, Yanhong Duan, Hongyu Li, Tong Zhu, Yijie Du

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

      Bioorganic \& Medicinal Chemistry 28 (23) , 115775

      2020
    12. Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John ZH Zhang

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

      Nature communications 11 (1) , 5713

      2020
    13. Mingyuan Xu, Tong Zhu, John ZH Zhang

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

      2020
    14. Yuqiao Han, Ziwei Ren, Yixin Wu, Yunzhong Chen, Zhenmei Cui, Tong Zhu, Mingliang Ma, Yijie Du, Suzhen Dong

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

      Biochemical and biophysical research communications 533 (4) , 1069–1075

      2020
    15. Jinzhe Zeng, Linfeng Zhang, Han Wang, Tong Zhu

      Exploring the chemical space of linear alkane pyrolysis via deep potential generator.

      Energy \& fuels 35 (1) , 762–769

      2020
    16. Ya’nan Yu, Yuqiao Han, Fupo Zhang, Zhenmei Gao, Tong Zhu, Suzhen Dong, Mingliang Ma

      Design, synthesis, and biological evaluation of imidazo [1, 2-a] pyridine derivatives as novel PI3K/mTOR dual inhibitors.

      Journal of Medicinal Chemistry 63 (6) , 3028–3046

      2020
  8. 2019

    1. Mingyuan Xu, Xiao He, Tong Zhu, John ZH Zhang

      A fragment quantum mechanical method for metalloproteins.

      Journal of chemical theory and computation 15 (2) , 1430–1439

      2019
    2. Mingfei Zhu, Hong Wang, Chenglin Wang, Yanfen Fang, Tong Zhu, Weili Zhao, Xiaochun Dong, Xiongwen Zhang

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

      Frontiers in Pharmacology 10 , 89

      2019
    3. Chih-Hao Chin, Tong Zhu, John ZH Zhang

      Theoretical investigations of photoionization efficiency of naphthalene.

      2019
    4. Tong Zhu, Chih-Hao Chin, John ZH Zhang

      Formation Mechanism of a Nonterrestrial C6H Radical: An Ab Initio/RRKM Study on the Reaction of Tetracarbon with Acetylene.

      2019
    5. Pei Zhao, Huali Cao, Yu Chen, Tong Zhu

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

      Chemical Physics Letters 728 , 94–101

      2019
    6. Zhaoxi Sun, Xiaohui Wang, Qianqian Zhao, Tong Zhu

      Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.

      Journal of Molecular Graphics and Modelling 91 , 10–21

      2019
    7. Jianzhong Chen, Xingyu Wang, Laixue Pang, John ZH Zhang, Tong Zhu

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

      Nucleic Acids Research 47 (13) , 6618–6631

      2019
    8. Mingyuan Xu, Tong Zhu, John ZH Zhang

      Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential.

      The Journal of Physical Chemistry A 123 (30) , 6587–6595

      2019
    9. Pei Zhao, Song Han, Xiaoxia Li, Tong Zhu, Xiaofang Tao, Li Guo

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

      Energy \& Fuels 33 (8) , 7176–7187

      2019
    10. Shuaizhen Tian, Jinzhe Zeng, Xiao Liu, Jianzhong Chen, John ZH Zhang, Tong Zhu

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

      Physical Chemistry Chemical Physics 21 (39) , 22103–22112

      2019
    11. Chih-Hao Chin, Tong Zhu, John Zeng Hui Zhang

      Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study.

      Physical Chemistry Chemical Physics 21 (41) , 23044–23055

      2019
    12. Jinzhe Zeng, Liqun Cao, Mingyuan Xu, Tong Zhu, John ZH Zhang

      Neural network based in silico simulation of combustion reactions.

      arXiv preprint arXiv:1911.12252

      2019
    13. Liqun Cao, Jinzhe Zeng, Mingyuan Xu, Chih-Hao Chin, Tong Zhu, John ZH Zhang

      Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation.

      2019
    14. Qian Tang, Taylor N Plank, Tong Zhu, Huizhen Yu, Zhilei Ge, Qian Li, Li Li, Jeffery T Davis, Hao Pei

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

      ACS applied materials \& interfaces 11 (22) , 19743–19750

      2019
  9. 2018

    1. Xianwei Wang, Yang Li, Ya Gao, Zejin Yang, Chenhui Lu, Tong Zhu

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

      Scientific reports 8 (1) , 5475

      2018
    2. Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He

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

      Frontiers in Chemistry 6 , 150

      2018
    3. Mingyuan Xu, Tong Zhu, John ZH Zhang

      A force balanced fragmentation method for ab initio molecular dynamic simulation of protein.

      Frontiers in Chemistry 6 , 189

      2018
    4. Ya Gao, Tong Zhu, Jianzhong Chen

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

      Chemical Physics Letters 706 , 400–408

      2018
    5. Ya Gao, Tong Zhu, Chaomin Zhang, John ZH Zhang, Ye Mei

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

      Chemical Physics Letters 706 , 594–600

      2018
    6. Jianzhong Chen, Xingyu Wang, John ZH Zhang, Tong Zhu

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

      ACS Omega 3 (12) , 18052–18064

      2018
    7. Xiaofan Jiang, Tong Zhu, Tatsuhiro Kodama, Nithin Raghunathan, Alina Alexeenko, Dimitrios Peroulis

      Multi-point wireless temperature sensing system for monitoring pharmaceutical lyophilization.

      Frontiers in chemistry 6 , 288

      2018
    8. Jinzhe Zeng, Liqun Cao, JZ Zhang, Chih-Hao Chin, Tong Zhu

      ReacNetGen: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations.

      2018
    9. X Jin, T Zhu

      Zhang JZH and He X (2018) Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

      Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems--Recent Developments and Advanced Applications , 15057

      2018
  10. 2017

    1. Changcheng Jing, Ziyan Li, Kaili Jia, Chen Chen, Xiao Liu, Beibei Wang, Wenhao Hu, Jia Li, Tong Zhu, Suzhen Dong

      Discovery of bisindole as a novel scaffold for protein tyrosine phosphatase 1B inhibitors.

      Archiv der Pharmazie 350 (1) , e1600173

      2017
    2. Li L Duan, T Zhu, Yu C Li, Qing G Zhang, John ZH Zhang

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

      Scientific Reports 7 (1) , 42223

      2017
    3. 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

      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.

      European Journal of Medicinal Chemistry 126 , 1083–1106

      2017
    4. Suzhen Dong, Yubing Lei, Shikun Jia, Lixin Gao, Jia Li, Tong Zhu, Shunying Liu, Wenhao Hu

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

      Bioorganic \& Medicinal Chemistry Letters 27 (4) , 1105–1108

      2017
    5. Ya Gao, Chaomin Zhang, Xianwei Wang, Tong Zhu

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

      Chemical Physics Letters 679 , 112–118

      2017
    6. Lili Duan, Tong Zhu, Changge Ji, Qinggang Zhang, John ZH Zhang

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

      Physical Chemistry Chemical Physics 19 (23) , 15273–15284

      2017
    7. Li Liu, Fan Zhao, Wei Liu, Tong Zhu, John ZH Zhang, Chen Chen, Zhihui Dai, Huisheng Peng, Jun-Long Huang, Qin Hu

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

      Angewandte Chemie 129 (35) , 10607–10611

      2017
    8. Shuai Li, Anwei Zhu, Tong Zhu, John ZH Zhang, Yang Tian

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

      Analytical Chemistry 89 (12) , 6656–6662

      2017
    9. Zhoujie Luo, Ya Gao, Tong Zhu, John Zenghui Zhang, Fei Xia

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

      The Journal of Physical Chemistry A 121 (34) , 6523–6529

      2017
    10. Jinfeng Liu, Tong Zhu, Xiao He, John ZH Zhang

      MFCC-Based Fragmentation Methods for Biomolecules.

      Fragmentation: Toward Accurate Calculations on Complex Molecular Systems , 323–348

      2017
    11. Zhaoxi Sun, Tong Zhu, Xiaohui Wang, Ye Mei, John ZH Zhang

      Optimization of convergence criteria for fragmentation methods.

      Chemical Physics Letters 687 , 163–170

      2017
    12. Meiling Zhang, Miaojun Zhu, Qin Hu, Chun Li, Zhenhua Zhu, Yingyong Hou, Jing Xu, Hailong Wang, Tong Zhu, Tom Tang

      Genome-wide microRNA expression profiling in malignant pleural effusion to identify a ten-microRNA signature..

      2017
    13. Minmin Huang, Zhoujie Luo, Tong Zhu, Jian Chen, John Zenghui Zhang, Fei Xia

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

      RSC advances 7 (81) , 51521–51527

      2017
  11. 2016

    1. Wang Liu, Yu Lu, Xiaoping Chai, Xiao Liu, Tong Zhu, Xihan Wu, Yanfen Fang, Xuan Liu, Xiongwen Zhang

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

      Journal of Experimental \& Clinical Cancer Research 35 (1) , 183

      2016
    2. Xiao Liu, Jinfeng Liu, Tong Zhu, Lujia Zhang, Xiao He, John ZH Zhang

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

      Journal of Chemical Information and Modeling 56 (5) , 854–861

      2016
    3. Xinsheng Jin, Tong Zhu, John ZH Zhang, Xiao He

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

      RSC advances 6 (110) , 108590–108602

      2016
    4. Yanfen Fang, Yannan Kong, Jianbei Xi, Mengli Zhu, Tong Zhu, Tongtong Jiang, Brendan Frett, Wenhao Hu, Hong-yu Li, Mingliang Ma

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

      Oncotarget 7 (48) , 79327

      2016
    5. Fengping Lv, Chen Chen, Yang Tang, Jianhai Wei, Tong Zhu, Wenhao Hu

      New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment.

      Bioorganic \& Medicinal Chemistry Letters 26 (15) , 3714–3718

      2016
  12. 2015

    1. Jason Swails, Tong Zhu, Xiao He, David A Case

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

      Journal of biomolecular NMR 63 (2) , 125–139

      2015
    2. Jinfeng Liu, Tong Zhu, Xianwei Wang, Xiao He, John ZH Zhang

      Quantum fragment based ab initio molecular dynamics for proteins.

      Journal of chemical theory and computation 11 (12) , 5897–5905

      2015
    3. Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John ZH Zhang

      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.

      Journal of chemical information and modeling 55 (9) , 1903–1913

      2015
    4. Tong Zhu, Xiao He, JZ Zhang

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

      Physical Chemistry Chemical Physics 17 (18) , 12367–12367

      2015
  13. 2014

    1. Xiao He, Tong Zhu, Xianwei Wang, Jinfeng Liu, John ZH Zhang

      Fragment quantum mechanical calculation of proteins and its applications.

      Accounts of chemical research 47 (9) , 2748–2757

      2014
    2. Tong Zhu, John ZH Zhang, Xiao He

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

      Physical Chemistry Chemical Physics 16 (34) , 18163–18169

      2014
    3. Li L Duan, Tong Zhu, Qing G Zhang, Bo Tang, John ZH Zhang

      Electronic polarization stabilizes tertiary structure prediction of HP-36.

      Journal of Molecular Modeling 20 (4) , 2195

      2014
    4. Tong Zhu, John ZH Zhang, Xiao He

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

      Advance in Structural Bioinformatics , 49–70

      2014
  14. 2013

    1. Tong Zhu, John ZH Zhang, Xiao He

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

      Journal of chemical theory and computation 9 (4) , 2104–2114

      2013
    2. Tong Zhu, Xudong Xiao, Changge Ji, John ZH Zhang

      A new quantum calibrated force field for zinc--protein complex.

      Journal of Chemical Theory and Computation 9 (3) , 1788–1798

      2013
    3. Li L Duan, Tong Zhu, Ye Mei, Qing G Zhang, Bo Tang, John ZH Zhang

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

      Journal of molecular modeling 19 (6) , 2605–2612

      2013
    4. Xudong Xiao, Tong Zhu, Chang G Ji, John ZH Zhang

      Development of an effective polarizable bond method for biomolecular simulation.

      The Journal of Physical Chemistry B 117 (48) , 14885–14893

      2013
  15. 2012

    1. Tong Zhu, Xiao He, John ZH Zhang

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

      Physical Chemistry Chemical Physics 14 (21) , 7837–7845

      2012
  16. 2010

    1. Guo-Dong Hu, Tong Zhu, Shao-Long Zhang, Dunyou Wang, Qing-Gang Zhang

      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.

      European journal of medicinal chemistry 45 (1) , 227–235

      2010
    2. Tong Zhu, Guodong Hu, Qinggang Zhang

      Quasi-classical trajectory study of the reaction O (3P)+ HCl→ OH+ Cl and O (3P)+ DCl→ OD+ Cl: Vector and scalar properties.

      Journal of Molecular Structure: THEOCHEM 948 (1-3) , 36–42

      2010
    3. Zhu Tong, Hu Guo-Dong, Chen Jian-Zhong, Liu Xin-Guo, Zhang Qing-Gang

      Theoretical study of stereodynamics for reaction O (3P)+ HCl.

      Chinese Physics B 19 (8) , 083402

      2010
    4. Huirong Liu, Xinguo Liu, Tong Zhu, Haizhu Sun, Qinggang Zhang

      THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O (3 P)+ HCl→ OH+ Cl FOR THE 3 A ″ELECTRONIC STATES.

      Journal of Theoretical and Computational Chemistry 9 (06) , 1033–1042

      2010
    5. Zhu Tong, Hu Guo-Dong, Zhang Qing-Gang

      Quasi-classical Trajectory Study of Reaction O (3 P)+ HCl (v= 2; j= 1, 6, 9)→ OH+ Cl.

      Chinese Physics Letters 27 (3) , 033102

      2010
    6. Zhu Tong, Hu Guo-Dong, Zhang Qing-Gang

      Quasi-classical Trajectory Study of Reaction O (P-3) plus HCl (v= 2; j= 1, 6, 9)-> OH plus Cl.

      CHINESE PHYSICS LETTERS 27 (3)

      2010