2024

(67) “Retrosynthesis Zero: Self-Improving Global Synthesis Planning Using Reinforcement Learning”
Jiasheng Guo^#, Chenning Yu^#, Kenan Li^#,$1, Yijian Zhang, Guoqiang Wang, Shuhua Li*, & Hao Dong*
J. Chem. Theory Comput., 2024, XX, 1.

(66) “Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production”
Yuqin Yang^#, Xiaoyu Wang^#, Xialian Wu^#, Shuyi Guo, Haokun Yang, Junxia Lu*, & Hao Dong*
J. Am. Chem. Soc., 2024, XX, 1.

(65) “Simulating chemical reactions promoted by self-assembled peptides with catalytic properties”
Yuqin Yang^#, Xiaoyu Wang^#, Hao Dong*
In Methods Enzymol., Academic Press, 2024.

(64) 
Biophys. Rep., 2024, 10, 1.

(63) “Individual dynamics and local heterogeneity provide a microscopic view of the epidemic spreading”
Youyuan Zhu, Ruizhe Shen, Hao Dong*, & Wei Wang*
Chin. Phys. B, 2024, 33, 058301.

2023

(62) “Accurate Modeling of Aqueous Chemistry at Nano-/micro-scale”
Jun Huo, Yijian Zhang, Kaiyu Zhang, Pei Liu, Benkun Hong, Hao Dong*, & Shuhua Li*
Sci. Sin. Chim., 2023, 53, 93.

(61) “Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids”
Yang Ge, Xueping Wang, Qiang Zhu, Yuqin Yang, Hao Dong, & Jing Ma*
J. Chem. Theory Comput., 2023, 19, 6718.

(60) “Microscopic Mechanism of Proton Transfer in Pure Water under Ambient Conditions”
Jun Huo, Jianghao Chen, Pei Liu, Benkun Hong, Jian Zhang, Hao Dong*, & Shuhua Li*
J. Chem. Theory Comput., 2023, 19, 4243. (Supplementary cover art)

(59) “A New Polymodal Gating Model of the Proton-activated Chloride Channel”
Piao Zhao^#, Cheng Tang^#,*, Yuqin Yang^#, Zhen Xiao, Samantha Perez-Miller, Heng Zhang, Guoqing Luo, Hao Liu, Yaqi Li, Qingyi Liao, Fan Yang, Hao Dong*, Rajesh Khanna*, & Zhonghua Liu*
PLoS Biol., 2023, 21, e3002309.

(58) “Research on Li⁺/Na⁺ Selectivity of NASICON-Type Solid-State Ion Conductors by First-Principles Calculations”
Menghang Zhang, Hui Pan, Yigang Wang, Jingui Yang, Hao Dong*, Ping He*, & Haoshen Zhou
Energy & Fuels, 2023, 37, 10663.

(57) “Spatial Heterogeneity and Infection Patterns on Epidemic Transmission Disclosed by a Combined Contact-dependent Dynamics and Compartmental Model”
Youyuan Zhu, Ruizhe Shen, Hao Dong*, & Wei Wang*
PLoS ONE, 2023, 18, e0286558. 

(56) “Redox-Stabilized Sn/SnO₂ Nanostructures for Efficient and Stable CO₂ Electroreduction to Formate”
Haoyang Jiang^#, Ziqi Fan^#, Mingzhe Zhang^#, Shuyi Guo^#, Le Li, Xiaohan Yu, Zhaoyang Liu, Wei Wang, Hao Dong*, Miao Zhong*
ChemElectroChem, 2023, 10, e202201164. (Cover art)

(55) “Collective Motions of Fish Originate from Balanced Local Perceptual Interactions and Individual Stochastics”
Mingjie Jiang^#, Anyu Zhou^#, Runping Chen, Yuqin Yang, Hao Dong*, & Wei Wang*
Phy. Rev. E 2023, 107, 024411.

(54) “Synergistic Regulation of Intermolecular Interactions to Control Chiral Structures for Chiral Recognition”
Weilin Chen, Lulu Fu, Zhiqiang Zhu, Jingyan Liu, Linxiu Cheng, Zhou Xu, Hao Dong*, Jing Ma, Yibao Li*, & Xiaolin Fan*
Chin. Chem. Lett. 2023, 34, 107713.

2022

(53) “A Bottom-up Design Strategy for Controllable Self-assembly Based on the Isotropic Double-well Potential”
Youyuan Zhu, Yijun Bai, Hao Dong*, & Wei Wang*
Phys. Chem. Chem. Phys. 2022, 24, 9467.

(52) “Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study”
Hongwei Chen^#, Changchang Lv^#, Lin Guo*, Ming Ma, Xiangfeng Li, Zhengyi Lan, Jun Huo, Hao Dong, Xiangdong Zhu, Qiang Zhu, Yuming Gu, Ziteng Liu, Jianjun Liu, Hangrong Chen, Xuefeng Guo*, & Jing Ma*
ACS Appl. Mater. Interfaces 2022, 14, 4836.

(51) “An Electrostatic-variable Coarse-grained Model for Predicting Enthalpy of Vaporization, Surface Tension, Diffusivity, Conductivity, and Dielectric Constant of Aqueous Ionic Liquid”
Yang Ge^#, Qiang Zhu^#, Yunzhi Li, Hao Dong*, & Jing Ma*
J. Mol. Liq. 2022, 346, 118230.

(50) “Global Fold Switching of RafH Protein: Diverse Structures with a Conserved Pathway”
Yiqiao Wang^#, Luyuan Zhao^#, Xuejie Zhou, Jian Zhang, Jun Jiang*, & Hao Dong*
J. Phys. Chem. B 2022, 16, 2979. (Supplementary cover art)

2021

(49) “Mutants only Partially Represent the Characteristics of the CRAC Channel Gating”
Jun Huo, Benzhuo Lu, & Hao Dong*
Chin. J. Chem. Phys. 2021, 34, 915.

(48) “Machine Learning on Properties of Multiscale Multisource Hydroxyapatite Nanoparticles Datasets with Different Morphologies and Sizes”
Ziteng Liu, Yinghuan Shi, Hongwei Chen, Tiexin Qin, Xuejie Zhou, Jun Huo, Hao Dong, Xiao Yang, Xiangdong Zhu, Xuening Chen, Li Zhang, Mingli Yang, Yang Gao*, & Jing Ma*
npj Comput. Mater. 2021, 7, 142.

(47) “Stable, Active CO2 Reduction to Formate via Redox-modulated Stabilization of Active Sites”
Le Li^#, Adnan Ozden^#, Shuyi Guo, F. Pelayo Garcı́a de Arquer, Chuanhao Wang, Mingzhe Zhang, Jin Zhang, Haoyang Jiang, Wei Wang, Hao Dong*, David Sinton, Edward H Sargent*, & Miao Zhong*
Nature Commun. 2021, 12, 5223. (Featured in a Nature Communications Editors’ Highlights webpage)

(46) “Two-dimensional Mo-based Compounds for the Li-O2 Batteries: Catalytic Performance and Electronic Structure Studies”
Xiaowei Mu^#, Chao Xia^#, Bin Gao, Shuyi Guo, Xueping Zhang, Jianping He, Hao Dong*, Ping He*, & Haoshen Zhou
Energy Storage Mater. 2021, 41, 650.

(45) “Self-assembled Peptide Nano-superstructure towards Enzyme Mimicking Hydrolysis”
Yu Chen^#, Yuqin Yang^#, Asuka A. Orrn^#, Pandeeswar Makam, Boris Redko, Elvira Haimov, Yannan Wang, Linda J. W. Shimon, Sigal Rencus-Lazar, Meiting Ju, Phanourios Tamamis*, Hao Dong*, & Ehud Gazit*
Angew. Chem. Int. Ed. 2021, 60, 17164.
MS online on NJU’s 119th Anniversary!

(44) “Effects of Cholesterol on the Partitioning of a Drug Molecule in Lipid Bilayers”
Yuqin Yang, Hao Dong*, & Huan-Xiang Zhou*
J. Phys. Chem. B 2021, 125, 5338.

(43) “Structures of wild-type and H451N mutant human lymphocyte potassium channel KV1.3”
Sanling Liu^#, Yue Zhao^#, Hao Dong^#,*, Liang Xiao, Yong Zhang, Yuqin Yang, Seow Theng Ong, K. George Chandy, Longhua Zhang*, & Changlin Tian*
Cell Discov. 2021, 7, 39.

(42) “Computation-driven synthesis of pentothal sodium”
Jitian Chen^#,$2, Tianyu Du^#,$2, Liuzhou Gao, Zhongjing Chai^$2, & Hao Dong*
Int. J. Quantum Chem. 2021, 121, e26624.

(41) “The morphology of hydroxyapatite nanoparticles regulates cargo recognition in clathrin-mediated endocytosis”
Cheng Zhu^#, Xuejie Zhou^#, Ziteng Liu, Hongwei Chen, Hongfeng Wu, Xiao Yang, Xiangdong Zhu, Jing Ma*, & Hao Dong*
Front. Mol. Biosci. 2021, 8, 627051.

(40) “Structures and Spectroscopic Properties of Large Molecules and Condensed-Phase Systems Predicted by Generalized Energy-Based Fragmentation Approach”
Wei Li, Hao Dong, Jing Ma, Shuhua Li*
Acc. Chem. Res. 2021, 54, 169.

2020

(39) “Gating and Regulation of the CRAC Channel: Recent Progress from Experiments and Molecular Modeling”
Jun Huo, Hao Dong*
Biopolymers 2020, 111, e23392. (Cover art)

(38) “A Two-ended DAta-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein”
Yigao Yuan^$1, Qiang Zhu, Ruiheng Song^$1, Jing Ma, & Hao Dong*
J. Chem. Theory Comput. 2020, 16, 4631–4640. (Supplementary cover art)

(37) “Accurate and Efficient Prediction of NMR Parameters of Condensed–Phase Systems with the Generalized Energy–Based Fragmentation Method”
Dongbo Zhao, Xiaolin Shen, Zheng Cheng, Wei Li, Hao Dong*, & Shuhua Li*
J. Chem. Theory Comput. 2020. 16, 2995–3005

(36) “Scorpion Toxin Inhibits the Voltage‐gated Proton Channel Using a Zn2+‐like Long‐range Conformational Coupling Mechanism”
Dongfang Tang^#, Yuqin Yang^#, Zhen Xiao, Jiahui Xu, Qiuchu Yang, Han Dai, Songping Liang, Cheng Tang*, Hao Dong*, & Zhonghua Liu*
Br. J. Pharmacol. 2020, 177, 2351-2364.

2019

(35) “Achieving Rich-Mixed-Valence Polysulfides/Carbon Nanotube Films Toward Ultrahigh Volume Energy Density and Largely Deformable Pseudocapacitors”
Weijie Song, Gengjie Wang, Dongbo Zhao, Yuewei Zhou^$2, Yuying Ding, Changbin Tan, Shaochun Tang*, Hao Dong*, & Xiangkang Meng*
ACS Appl. Mater. Interfaces 2019, 11, 25271.

(34) “Towards a model for activation of Orai channel”
Hao Dong^#,*, Yiming Zhang^#, Ruiheng Song^$1, Jingjie Xu, Yigao Yuan^$1, Jindou Liu, Jia Li, Sisi Zheng, Tiantian Liu, Benzhuo Lu*, Youjun Wang*, & Michael L. Klein*
iScience 2019, 16, 356.

(33) “In Situ Imaging Facet-induced Spatial Heterogeneity of Electrocatalytic Reaction Activity at Sub-Particle Level via Electrochemiluminescence Microscopy”
Ying Chen, Dongbo Zhao, Jiaju Fu, Xiaodan Gou, Dechen Jiang*, Hao Dong*, & Jun-Jie Zhu*
Anal. Chem. 2019, 91, 6829.

(32) “Equilibria between the K+ Binding and Cation Vacancy Conformations of Potassium Channels”
Yao He, Bo Zhang, Hao Dong*, Penglin Xu, Xiaoying Cai, Ting Zhou, Mu Yu, Jun Liang, Xiao Zheng*, & Changlin Tian*
Prot. & Cell 2019, 10, 533.

(31) “A Data-driven Accelerated Sampling Method for Searching Functional States of Proteins”
Qiang Zhu, Yigao Yuan^$1, Jing Ma*, & Hao Dong*
Adv. Theory Simul. 2019, 2, 1800171.

(30) “Principles Governing Catalytic Activity of Self-assembled Short Peptides”
Ruiheng Song^#,$1, Xialian Wu^#, Bin Xue, Yuqin Yang, Wenmao Huang, Guixiang Zeng, Jian Wang, Wenfei Li, Yi Cao, Wei Wang*, Junxia Lu*, & Hao Dong*
J. Am. Chem. Soc. 2019, 141, 223.

2018

(29) “Identification of Molecular Determinants that Govern Distinct STIM2 Activation Dynamics”
Sisi Zheng, Guolin Ma, Lian He, Tian Zhang, Jia Li, Xiaoman Yuan, Nhung T. Nguyen, Yun Huang, Xiaoyan Zhang, Ping Gao, Robert Nwokonko, Donald L. Gill, Hao Dong, Yubin Zhou*, & Youjun Wang*
PLoS Biol. 2018, 16, e2006898.

(28) “THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides”
Fang Wang, Dongbo Zhao, Hao Dong, Ling Jiang, Lin Huang, Yunfei Liu*, & Shuhua Li
Spectrochim. Acta. A 2018, 200, 195.

(27) “Reduction of Isoxazoles including Sulfamethoxazole by Aqueous FeII –Tiron Complex: Impact of Structures”
Yiling Chen, Hao Dong, Huichun Zhang*
Chem. Eng. J. 2018, 352, 501.

2017

(26) “Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane”
Qiang Zhu, Yilin Lu^$1, Xibing He, Tao Liu^$1, Hongwei Chen, Fang Wang, Dong Zheng, Hao Dong*, & Jing Ma*
Sci. Rep. 2017, 7, 17749.

(25) “Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers”
Dongbo Zhao, Ling Yang, Yigao Yuan^$1, Hanchen Wang^$1, Hao Dong*, & Shuhua Li*
J. Phys. Chem. B 2017, 121, 10064.

(24) “Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method”
Dongbo Zhao, Ruiheng Song^$1, Wei Li, Jing Ma, Hao Dong*, & Shuhua Li*
J. Chem. Theory Comput. 2017, 13, 5231. (cover art)

(23) “Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study”
Fang Wang, Dongbo Zhao, Hao Dong, Ling Jiang, Yunfei Liu*, & Shuhua Li*
Spectrochim. Acta. A 2017, 179, 255.

2016

(22) “Experimental and Computational Evidence for the Reduction Mechanisms of Aromatic N-oxides by Aqueous FeII–Tiron Complex”
Yiling Chen, Hao Dong, Huichun Zhang*
Environ. Sci. Technol. 2016, 50, 249.

2015

(21) “Understanding the Boron-Nitrogen Interaction and Its Possible Implications in Drug Design”
Hao Dong*, Wei Li, Jianwei Sun, Shuhua Li, & Michael L. Klein
J. Phys. Chem. B 2015, 119, 14393.

2014

(20) “Proton Release from the Histidine-tetrad in the M2 Channel of the Influenza A Virus”
Hao Dong, Giacomo Fiorin, William F. DeGrado, & Michael L. Klein*
J. Phys. Chem. B 2014, 118, 12644.
Accepted on Christa’s 100-day birthday!

(19) “Counterion-assisted Cation Transport in a Biological Calcium Channel”
Hao Dong, Michael L. Klein*, Giacomo Fiorin
J. Phys. Chem. B 2014, 118, 9668.

2013

(18) “Pore Waters Regulate Ion Permeation in a Calcium Release-activated Calcium Channel”
Hao Dong*, Giacomo Fiorin, Vincenzo Carnevale, Werner Treptow, & Michael L. Klein*
Proc. Natl. Acad. Sci. USA 2013, 110, 17332.

(17) “Exploring Histidine Conformations in the M2 Channel Lumen of the Influenza A Virus at Neutral pH via Molecular Simulations”
Hao Dong^#, Giacomo Fiorin^#, William F. DeGrado, Michael L. Klein*
J. Phys. Chem. Lett. 2013, 4, 3067.

(16) “Ab initio Calculations and Validation of the pH-dependent Structures of the His37-Trp41 Quartet, the Heart of Acid Activation and Proton Conductance in the M2 Protein of Influenza A Virus”
Hao Dong^#, Myunggi Yi^#, Timothy A. Cross, Huan-Xiang Zhou*
Chem. Sci. 2013, 4, 2776.

2012

(15) “Size Matters in Activation/Inhibition of Ligand-gated Ion Channels”
Juan Du, Hao Dong, Huan-Xiang Zhou*
Trends Pharmacol. Sci. 2012, 33, 482.

(14) “Glycines: Role in alpha-Helical Membrane Protein Structures and a Potential Indicator for Native Conformation”
Hao Dong, Mukesh Sharma, Huan-Xiang Zhou, & Timothy A. Cross*
Biochemistry 2012, 51, 4779.
Highlighted on Biochemistry Home Page

(13) “Gating Mechanism of a P2X4 Receptor Developed from Normal Mode Analysis and Molecular Dynamics Simulations”
Juan Du, Hao Dong, Huan-Xiang Zhou*
Proc. Natl. Acad. Sci. USA 2012, 109, 4140.

(12) “M2 Protein from Influenza A: from Multiple Structures to Biophysical and Functional Insights”
Timothy A. Cross*, Hao Dong, Mukesh Sharma, David D. Busath, & Huan-Xiang Zhou
Curr. Opin. Virol. 2012, 2, 128.

2011

(11) “Atomistic Mechanism for the Activation and Desensitization of an AMPA-Subtype Glutamate Receptor”
Hao Dong, Huan-Xiang Zhou*
Nature Commun. 2011, 2, 354.
Accepted on Daniel’s 60-day birthday!

2010

(10) “Insight into the Mechanism of the Influenza A Proton Channel from a Structure in a Lipid Bilayer”
Mukesh Sharma, Myunggi Yi, Hao Dong, Huajun Qin, Emily Peterson, David D. Busath, Huan-Xiang Zhou*, & Timothy A. Cross*
Science 2010, 330, 509.

(9) “Effects of Macromolecular Crowding on Protein Conformational Changes”
Hao Dong, Sanbo Qin, Huan-Xiang Zhou*
PLoS Comput. Biol. 2010, 6, e1000833.

(8) “A Computational Study towards Understanding the Mechanism of Phosphodiester Cleavage by Two Mononuclear Zn(II) Complexes”
Hao Dong
Phys. Chem. Chem. Phys. 2010, 12, 10434.

Before 2010

(7) “Understanding the Role of Intra- and Intermolecular Interactions in the Formation of Single- and Double-Helical Structures of Aromatic Oligoamides: A Computational Study”
Hao Dong, Shugui Hua, Shuhua Li*
J. Phys. Chem. A 2009, 113, 1335.

(6) “Unprecedented Immunosuppressive Polyketides from Daldinia eschscholzii, a Mantis-Associated Fungus”
Yinglao Zhang, Huiming Ge, Wei Zhao, Hao Dong, Qiang Xu, Shuhua Li, Jing Li, Jie Zhang, Yongchun Song, & Renxiang Tan*
Angew. Chem. Int. Ed. 2008, 47, 1.

(5) “Temperature Controlled Reversible Change of the Coordination Modes of the Highly Symmetrical Multitopic Ligand To Construct Coordination Assemblies: Experimental and Theoretical Studies”
Bo Zheng, Hao Dong, Junfeng Bai*, Yizhi Li, Shuhua Li*, & Manfred Scheer*
J. Am. Chem. Soc. 2008, 130, 7778.

(4) “Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach”
Wei Li, Hao Dong, & Shuhua Li*
in Progress in Theoretical Chemistry and Physics. Springer-Verlag, Berlin Heidelberg, 2008, 18, 289.

(3) “A Smart Supramolecular Hydrogel: pH-Modulated Reversibly Viscoelastic Properties”
Naien Shi, Hao Dong, Gui Yin, Zheng Xu*, Shuhua Li*
Adv. Funct. Mater. 2007, 17, 1837.

(2) “Estimation on the Individual Hydrogen-Bond Strength in Molecules with Multiple Hydrogen Bonds”
Hao Dong, Weijie Hua, Shuhua Li*
J. Phys. Chem. A 2007, 111, 2941.
One of the Most-Accessed Articles, April-June, 2007

(1) “Theoretical Study toward Understanding the Catalytic Mechanism of Pyruvate Decarboxylase.”
Jianyi Wang, Hao Dong, Shuhua Li*
J. Phys. Chem. B 2005, 109, 18664.