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ISSN 1000-6818CN 11-1892/O6CODEN WHXUEU
Acta Phys Chim Sin >> 2016,Vol.32>> Issue(11)>> 2693-2708     doi: 10.3866/PKU.WHXB201608121         中文摘要
QSAR, Molecular Docking and Molecular Dynamics of 3C-like Protease Inhibitors
LIN Feng1, FU Xin-Mei2, WANG Chao1, JIANG Si-Yu1, WANG Jing-Hui1, ZHANG Shu-Wei1, YANG Ling3, LI Yan1
1 School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning Province, P. R. China;
2 State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, Liaoning Province, P. R. China;
3 Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning Province, P. R. China
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3C-like protease is an extremely important protease involved in the multiplicative process of coronaviruses, including the deadlyMiddle East respiratory syndrome coronavirus (MERS-CoV). 3C-like protease has become a hot research topic in the field of coronavirology. For the first time, a set of ligand-and receptorbased three-dimensional quantitative structure-activity relationships (3D-QSAR) models were carried out via comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to explore the structure-activity correlation of 43 peptidomimetic inhibitors of the 3C-like protease of the bat coronavirus HKU4 (HKU4-CoV), which belongs to the same 2c lineage as MERS-CoV and shows high sequence similarity with MERS-CoV. Based on the ligand-based alignment, an optimal CoMSIAmodel (yielded by steric, electrostatic, H-bond donor and H-bond acceptor fields) was obtained with good predictive power of Q2=0.522, R2 ncv=0.996 and R2 pre=0.904 (Q2:cross-validated correlation coefficient, R2 ncv:non-cross-validated correlation coefficient, R2 pre:predicted correlation coefficient for the test set of compounds). Molecular docking and molecular dynamics simulations were performed according to this model to further determine the interaction mechanism between ligands and the receptor. The experimental results show:(1) based on the optimal CoMSIAmodel, the 3D contour maps vividly illustrate that the molecular biological activity is influenced by the steric, electrostatic, H-bond donor and H-bond acceptor interactions of molecular groups. (2) Based on the docking analysis, hydrophobicity, crystal water, His166 andGlu169 have important roles in the ligands and receptor binding process. (3) Molecular dynamics (MD) simulations were carried out for further verification of the reliability of the docking model, and provide two new key residues, Ser24 and Gln192, which have two strong hydrogen bonds with the ligands. Some new compounds were obtained based on the modeling that are potential peptidomimetic inhibitors of 3C-like protease. These results help establish the binding mechanism between 3C-like protease and peptidomimetic inhibitors, and provide a valuable reference for future anti-MERS-CoV drug design.



Keywords: MERS-CoV   3C-like protease   Peptidomimetic inhibitor   3D-QSAR   Molecular docking   Molecular dynamics  
Received: 2016-05-31 Accepted: 2016-08-09 Publication Date (Web): 2016-08-12
Corresponding Authors: FU Xin-Mei, LI Yan Email: fuxinmei@dlut.edu.cn;yanli@dlut.edu.cn

Fund: The project was supported by the National Natural Science Foundation of China (11201049).

Cite this article: LIN Feng, FU Xin-Mei, WANG Chao, JIANG Si-Yu, WANG Jing-Hui, ZHANG Shu-Wei, YANG Ling, LI Yan. QSAR, Molecular Docking and Molecular Dynamics of 3C-like Protease Inhibitors[J]. Acta Phys. -Chim. Sin., 2016,32 (11): 2693-2708.    doi: 10.3866/PKU.WHXB201608121

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48. ZHANG Ji-Wei, BIAN Fu-Yong, SHI Guo-Jun, XU Si-Chuan.Molecular Dynamics Simulation of Dopamine Diffusion within and Permeation through POPC Phospholipid Bilayer Membrane[J]. Acta Phys. -Chim. Sin., 2014,30(1): 183-193
49. SHAN Sheng-Sheng, YAN Chao, XU Liang.Dihedral Dynamics Analyses of the Polymorphic Properties of Zn2+-Bound Amyloid β40 (Aβ40) and β42 (Aβ42)[J]. Acta Phys. -Chim. Sin., 2013,29(12): 2630-2638
50. WANG You-Juan, ZHAO Dong-Bo, RONG Chun-Ying, LIU Shu-Bin.Towards Understanding the Origin and Nature of the Conformational Stability of Water Clusters:a Density Functional Theory and Quantum Molecular Dynamics Study[J]. Acta Phys. -Chim. Sin., 2013,29(10): 2173-2179
51. SUN Wei, ZHANG Jin-Jiang, ZHAO Jian-Wei.Molecular Dynamics Simulation of a Nanosized Device[J]. Acta Phys. -Chim. Sin., 2013,29(09): 1931-1936
52. ZHANG Ning, LI Wei-Zhong, CHEN Cong, ZUO Jian-Guo.Evaluation of the Application of Hydrogen Bonding Criteria to DMSO Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2013,29(09): 1891-1899
53. GE Zhen-Peng, SHI Yan-Chao, LI Xiao-Yi.Effects of Orthogonal Electric Field on Water Flux through a Carbon Nanotube[J]. Acta Phys. -Chim. Sin., 2013,29(08): 1655-1660
54. ZHANG Li, CHEN Lang, WANG Chen, WU Jun-Ying.Molecular Dynamics Study of the Effect of H2O on the Thermal Decomposition of α Phase CL-20[J]. Acta Phys. -Chim. Sin., 2013,29(06): 1145-1153
55. BAI Shu, LI Hao, ZHANG Lin.Standing Orientation of Lysozymes Induced by Electrostatically Repulsive Surface[J]. Acta Phys. -Chim. Sin., 2013,29(04): 849-857
56. SUN Wei-Qi, ZHANG Ji-Long, ZHENG Qing-Chuan, SUN Zhi-Wei, ZHANG Hong-Xing.Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II[J]. Acta Phys. -Chim. Sin., 2013,29(04): 843-848
57. SONG Fenhong, LIU Chao, ZHOU Xuan.Molecular Dynamics Simulation of Heterogeneous Nucleation of Argon Vapor onto a Spherical Solid Particle[J]. Acta Phys. -Chim. Sin., 2013,29(04): 715-722
58. SHI Ji-Pei, ZHAO Juan, YANG Fan, WANG Jian-Ping.Femtosecond Two-Dimensional Infrared Spectroscopy of N-Ethypropionamide[J]. Acta Phys. -Chim. Sin., 2013,29(04): 695-700
59. LIU Yong-Li, LIU Huan, LI Wei, ZHAO Qian, QI Yang.Effect of Substrate Temperature on the Growth and Microstructure of ZnO Film[J]. Acta Phys. -Chim. Sin., 2013,29(03): 631-638
60. WU Yong-Quan, SHEN Tong, LU Xiu-Ming, ZHANG Ning, LAI Li-Shan, GAO Shuai.Solidification of Liquid Fe with Embedded Homogeneous Solid Fe Nanoparticles from Molecular Dynamics Simulations[J]. Acta Phys. -Chim. Sin., 2013,29(02): 245-249
61. KANG Cong-Min, ZHAO Xu-Hao, WANG Xin-Yu, CHENG Jia-Gao, LÜ Ying-Tao.QSAR and Molecular Docking on Five-Membered Heterocyclopyrimidines as Thymidylate Synthase Inhibitors[J]. Acta Phys. -Chim. Sin., 2013,29(02): 431-438
62. YANG Li-Jun, LIU Qian, YUAN Wen-Bin, YANG Sheng-Yong.Molecular Dynamics Simulations of Interactional Mechanism and Binding Energy Calculations between Kinase ABL and Small Molecules Binding at Myristoyl Pocket[J]. Acta Phys. -Chim. Sin., 2013,29(02): 423-430
63. BAI Shu, ZHOU Rong, LIU Fu-Feng.Rational Design of Affinity Ligand for the Oriented Immobilization of Trypsin[J]. Acta Phys. -Chim. Sin., 2013,29(02): 439-448
64. WANG Xiao-Juan, LI Zhi-Yi, LIU Zhi-Jun.Molecular Dynamics Simulations on Hydrolysis of Zinc Acetate in Supercritical Water[J]. Acta Phys. -Chim. Sin., 2013,29(01): 23-29
65. GE Song, CHEN Min.Effects of Surface Charge and Electric Field on the Interfacial Thermal Resistance at Liquid/Solid Interfaces[J]. Acta Phys. -Chim. Sin., 2012,28(12): 2939-2943
66. DONG Xiao-Yan, DU Wen-Jie, LIU Fu-Feng.Molecular Dynamics Simulation and Binding Free Energy Calculation of the Conformational Transition of Amyloid Peptide 42 Inhibited by Peptide Inhibitors[J]. Acta Phys. -Chim. Sin., 2012,28(11): 2735-2744
67. ZHOU Ting-Ting, SHI Yi-Ding, HUANG Feng-Lei.Thermal Decomposition Mechanism of β-HMX under High Pressures via ReaxFF Reactive Molecular Dynamics Simulations[J]. Acta Phys. -Chim. Sin., 2012,28(11): 2605-2615
68. WANG Ding, TIAN Guo-Cai.Simulation Study of the Effect ofMethanol on the Structure and Properties of 1-Butyl-3-methylimidazolium Tetrafluoroborate Ionic Liquid[J]. Acta Phys. -Chim. Sin., 2012,28(11): 2558-2566
69. HUANG Yang-Yu, YANG Xiu-Feng, LI Hao-Tian, JI Xiao-Feng, CHENG Hong-Li, ZHAO Yun-Jie, GUO Da-Chuan, LI Lin, LIU Shi-Yong.Protein-RNA Interaction Interface Prediction and Design[J]. Acta Phys. -Chim. Sin., 2012,28(10): 2390-2400
70. LUO Fang, GAO Jian, CHENG Yuan-Hua, CUI Wei, JI Ming-Juan.Interaction Mechanisms of Inhibitors of Glucoamylase by Molecular Dynamics Simulations and Free Energy Calculations[J]. Acta Phys. -Chim. Sin., 2012,28(09): 2191-2201
71. WANG Yan-Hong, CHEN Yu-Juan, BAO Ling, LANG Xue-Mei, FAN Shuan-Shi.Molecular Dynamics Simulation of CH4 Hydrate Decomposition in the Presence of Poly(2-ethyl-2-oxazoline)[J]. Acta Phys. -Chim. Sin., 2012,28(07): 1683-1690
72. XU Zhao-Ying, ZHAO Li-Ling, CAO Zan-Xia, WANG Ji-Hua.Effects of the Residue Mutations on the Segment of P53-DNA Binding Region Based on Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2012,28(07): 1665-1675
73. ZHANG Jin-Li, HE Zheng-Hua, HAN You, LI Wei, WU Jiang-Jie-Xing, GAN Zhong-Xue, GU Jun-Jie.Nucleation and Growth of Na2CO3 Clusters in Supercritical Water Using Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2012,28(07): 1691-1700
74. QIAO Kang, ZENG Ling-Xiao, JIN Hong-Wei, LIU Zhen-Ming, ZHANG Liang-Ren.QSAR Analysis of Human Adenosine A3 Receptor Antagonists[J]. Acta Phys. -Chim. Sin., 2012,28(06): 1509-1519
75. LAI Li-Shan, WU Yong-Quan, SHEN Tong, ZHANG Ning, GAO Shuai.Molecular Dynamics Simulation of Induced Solidification Process of Pure Liquid Fe by Al2O3 Nanoparticles[J]. Acta Phys. -Chim. Sin., 2012,28(06): 1347-1354
76. HU Yan-Bao, PENG Jing-Bo, GU Shuo, PEI Jian-Feng, ZOU Zhong-Mei.Molecular Docking in Xin-Ke-Shu Preparation's Multi-Target Effect on Coronary Heart Disease[J]. Acta Phys. -Chim. Sin., 2012,28(05): 1257-1264
77. LÜ Yong-Jun, CHEN Min.Molecular Transport through Finite-Length Carbon Nanotubes[J]. Acta Phys. -Chim. Sin., 2012,28(05): 1070-1076
78. GAO Yu-Fei, MENG Qing-Yuan, ZHANG Lu, LIU Jia-Qiu, JING Yu-Hang.Molecular Dynamics Simulation of Thermal Transport Properties for Boron Nitride Nanotubes[J]. Acta Phys. -Chim. Sin., 2012,28(05): 1077-1084
79. ZHANG Xia, ZHANG Qiang, ZHAO Dong-Xia.Quasi-Elastic Neutron Scattering Spectroscopy of the 1-Propanol/Water Solution by Molecular Dynamics Simulations[J]. Acta Phys. -Chim. Sin., 2012,28(05): 1037-1044
80. WANG Cun-Xin, CHANG Shan, GONG Xin-Qi, YANG Feng, LI Chun-Hua, CHEN Wei-Zu.Progress in the Scoring Functions of Protein-Protein Docking[J]. Acta Phys. -Chim. Sin., 2012,28(04): 751-758
81. LI Hai-Lan, JIA Yu-Xiang, HU Yang-Dong.Molecular Dynamics Simulation of the Desalination of Sea Water by a Forward Osmosis Membrane Containing Charged Carbon Nanotubes[J]. Acta Phys. -Chim. Sin., 2012,28(03): 573-577
82. LIU Zhen, LIU Gou-Sheng, YU Jian-Guo.Effect of Primary Alkylamine Adsorption on Muscovite Hydrophobicity[J]. Acta Phys. -Chim. Sin., 2012,28(01): 201-207
83. ZHANG Xia, ZHANG Qiang, ZHAO Dong-Xia.Hydrogen Bond Lifetime Definitions and the Relaxation Mechanism in Water Solutions[J]. Acta Phys. -Chim. Sin., 2011,27(11): 2547-2552
84. JIN Yi, WANG Yue, BIAN Fu-Yong, SHI Qiang, GE Mao-Fa, WANG Shu, ZHANG Xing-Kang, XU Si-Chuan.Three-Dimensional Structure of Dopamine 3-Subtype Receptor with the Active Site Residues for the Binding of Dopamine[J]. Acta Phys. -Chim. Sin., 2011,27(10): 2432-2446
85. LI Hong-Jian, LI An-Yang, TANG Hong, DOU Yu-Sheng.Molecular Dynamics Simulation of Effect of a Femtosecond Laser on the Photofragmentation Reaction Mechanism of C60[J]. Acta Phys. -Chim. Sin., 2011,27(09): 2072-2078
86. BAO Jian-Zhang, FENG Xin-Tian, YU Jian-Guo.GPU Triggered Revolution in Computational Chemistry[J]. Acta Phys. -Chim. Sin., 2011,27(09): 2019-2026
87. SHEN Tao, DU Feng-Pei, LIU Ting, YAO Guang-Wei, WU Zheng, FANG Meng-Meng, XU Xiao-Jie, LU Hui-Zhe.Molecular Simulation of the Interaction between Imidazole Glycerol Phosphate Dehydrase and Nitrogen-Containing Heterocyclic Phosphate Inhibitors[J]. Acta Phys. -Chim. Sin., 2011,27(08): 1831-1838
88. XU Pei-Jun, TANG Yuan-Yuan, ZHANG Jing, ZHANG Zhi-Bo, WANG Kun, SHAO Ying, SHEN Hu-Jun, MAO Ying-Chen.Molecular Dynamics Simulation of Organic Solvents Based on the Coarse-Grained Model[J]. Acta Phys. -Chim. Sin., 2011,27(08): 1839-1846
89. LI Miao-Miao, SHEN Rui-Qi, LI Feng-Sheng.Molecular Dynamics Simulation of Binding Energies, Mechanical Properties and Energetic Performance of the RDX/BAMO Propellant[J]. Acta Phys. -Chim. Sin., 2011,27(06): 1379-1385
90. LIU Yun-Hong, GAO Ya-Jun, WANG Fen-Ying, ZHU Tie-Min, ZHAO Jian-Wei.Molecular Dynamics Simulation of the Influence of Crystal Orientation on the Formation Probability of Silver Monoatomic Chains during Stretching[J]. Acta Phys. -Chim. Sin., 2011,27(06): 1341-1345
91. CHEN Cong, LI Wei-Zhong, SONG Yong-Chen, WENG Lin-Dong.Structure and Kinetics of Hydrogen Bonds in Aqueous Glucose Solutions[J]. Acta Phys. -Chim. Sin., 2011,27(06): 1372-1378
92. LIU Zhen-Hai, SHANG Ya-Zhuo, HUANG Yong-Min, PENG Chang-Jun, LIU Hong-Lai.Disassembly of Polyelectrolyte/Surfactants Complex Induced by Macroions[J]. Acta Phys. -Chim. Sin., 2011,27(05): 1135-1142
93. LIAO Rui-Jin, ZHU Meng-Zhao, ZHOU Xin, YANG Li-Jun, YAN Jia-Ming, SUN Cai-Xin.Molecular Dynamics Simulation of the Diffusion Behavior of Water Molecules in Oil and Cellulose Composite Media[J]. Acta Phys. -Chim. Sin., 2011,27(04): 815-824
94. HU Song-Qing, YU Li-Jun, YAN You-Guo, ZHANG Jun, REN Zhen-Jia, TI Yang.Experimental and Theoretical Study of the Synergistic Inhibitive Effect of SDBS and HA[J]. Acta Phys. -Chim. Sin., 2011,27(02): 275-280
95. JIA Yu-Xiang, LI Yan, HU Yang-Dong.Behavior of Carbon Nanotube Membranes as Channels of Salt and Water in Forward Osmosis Process[J]. Acta Phys. -Chim. Sin., 2011,27(01): 228-232
96. LIU Xiao-Yu, LI Chun, TIAN Wen-Yu, CHEN Tao, WANG Lu-Hua, ZHENG Zhong, ZHU Jian-Bo, SUN Mao, LIU Chun-Li.Molecular Dynamics Modeling of Uranyl Ion Adsorption onto the Basal Surfaces of Kaolinite[J]. Acta Phys. -Chim. Sin., 2011,27(01): 59-64
97. SUN Hao, JIANG Yong-Jun, YU Qing-Sen, GAO Hui.Molecular Dynamics Simulations on the Role of Structural Mg2+ Ions in Phosphoryl Transfer Catalyzed by GSK-3β[J]. Acta Phys. -Chim. Sin., 2011,27(01): 207-212
98. QIAO Gui-Min, REN Zhen-Jia, ZHANG Jun, HU Song-Qing, YAN You-Guo, TI Yang.Molecular Dynamics Simulation of Corrosive Medium Diffusion in Corrosion Inhibitor Membrane[J]. Acta Phys. -Chim. Sin., 2010,26(11): 3041-3046
99. LIU Yan-Yan, CHEN Pan-Ke, LUO Jian-Hui, ZHOU Ge, JIANG Bo.Molecular Simulation of Dilute Polyacrylamide Solutions[J]. Acta Phys. -Chim. Sin., 2010,26(11): 2907-2914
100. KE Yan-Rong, JIN Hong-Wei, LIU Zhen-Ming, ZHANG Liang-Ren.Homology Modeling and Structure Validation of the Adenosine A1 Receptor[J]. Acta Phys. -Chim. Sin., 2010,26(10): 2833-2839
101. ZHU Su-Hua, YAN Liu-Ming, JI Xiao-Bo, SHAO Chang-Le, LU Wen-Cong.Electroosmotic Drag of Water in Hydrated Potassium Perfluorosulfonated Polymer Membrane in External Electric Fields[J]. Acta Phys. -Chim. Sin., 2010,26(10): 2659-2665
102. LIU Fu-Feng, JI Luo, DONG Xiao-Yan.Effects ofMolecular Volume and Fractional Polar Surface Area of Osmolytes on the Thermal Stability of Chymotrypsin Inhibitor 2[J]. Acta Phys. -Chim. Sin., 2010,26(10): 2813-2820
103. WU Li-Xia, YU Feng, LIU Jing, DAI Jing-Hua, ZHOU Xiao-Guo, LIU Shi-Lin.Ab initioMolecular Dynamics Investigation on the Production Channels for the Reaction of O- with CH3F[J]. Acta Phys. -Chim. Sin., 2010,26(09): 2331-2336
104. LIU Fu-Feng, DONG Xiao-Yan, SUN Yan.Molecular Dynamics Simulation of the Conformational Transition of Amyloid Peptide 42 Inhibited by Trehalose[J]. Acta Phys. -Chim. Sin., 2010,26(06): 1643-1650
105. DING Yuan-Fa, ZHANG Yue, ZHANG Da-Hai, LI Zhong-Ping.Atomic Charge Transfer and Ensemble Selection inMolecular Dynamics Simulation of Vitreous Silica[J]. Acta Phys. -Chim. Sin., 2010,26(06): 1651-1656
106. ZHANG Yuan, CHEN Ya-Dong, YOU Qi-Dong, ZOU Li-Yun, YANG Yan.Homology Modeling and Molecular Docking Studies on the Selectivity of HDAC1/HDAC8[J]. Acta Phys. -Chim. Sin., 2010,26(06): 1676-1686
107. ZHANG Jun, YU Wei-Zhao, YAN You-Guo, YU Li-Jun, REN Zhen-Jia.Molecular Dynamics Simulation of the Adsorption Behavior of Imidazoline Corrosion Inhibitors on a Fe(001) Surface[J]. Acta Phys. -Chim. Sin., 2010,26(05): 1385-1390
108. DING Wei, LIU Guo-Yu, YU Tao, QU Guang-Miao, CHENG Jie-Cheng, WU Jun-Zheng.Molecular Dynamics Simulations and Free Energy Perturbation Calculations of Alkyl Aryl Sulfonate[J]. Acta Phys. -Chim. Sin., 2010,26(03): 727-734
109. ZHENG Chun-Song, XU Xiao-Jie, LIU Xian-Xiang, YE Hong-Zhi.Computational Pharmacology of Jingzhi Tougu Xiaotong Granule in Preventing and Treating Osteoarthritis[J]. Acta Phys. -Chim. Sin., 2010,26(03): 775-783
110. XIAO Hong-Yan, ZHEN Zhen, SUN Huan-Quan, CAO Xu-Long, LI Zhen-Quan, SONG Xin-Wang, CUI Xiao-Hong, LIU Xin-Hou.Molecular Dynamics Simulation of Anionic Surfactant at the Water/n-Alkane Interface[J]. Acta Phys. -Chim. Sin., 2010,26(02): 422-428
111. LI Bo, LIU Ming, HU Wen-Xiang.Molecular Docking and Molecular Dynamics Simulations of Fentanyl Analogs Binding to μ-Opioid Receptors[J]. Acta Phys. -Chim. Sin., 2010,26(01): 206-214
112. XIE Hui, LIU Chao.Effects of Surface Wettability on Bubbles in Nanochannels[J]. Acta Phys. -Chim. Sin., 2009,25(12): 2537-2542
113. GAO Ting-Hong, LIU Rang-Su, ZHOU Li-Li, TIAN Ze-An, XIE Quan.Formation Properties of Cluster Structures during the Rapid Solidification of Liquid Ca7Mg3 Alloy[J]. Acta Phys. -Chim. Sin., 2009,25(10): 2093-2100
114. LIU Tao, SUN Mao-Tang, DONG Xiao-Wu, REN Xin, YANG Xin, DU Li-Lin, HU Yong-Zhou.Structure-Based Drug Design, Synthesis and Antitumor Activities of Novel CDK7 Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(10): 2107-2112
115. ZHAO Jian-Wei, WANG Fen-Ying, JIANG Lu-Yun, YIN Xing, LIU Yun-Hong.Breaking Behavior of a Bicrystal Copper Nanowire Studied Using a Fourier Transformation Method[J]. Acta Phys. -Chim. Sin., 2009,25(09): 1835-1840
116. FU Yi-Zheng, LIU Ya-Qing, LAN Yan-Hua.Molecular Dynamics Simulation on Compatibility of Hydroxyl-Terminated Polybutadiene/Plasticizer Blends[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1267-1272
117. TAO Chang-Gui, FENG Hai-Jun, ZHOU Jian, LV Ling-Hong, LU Xiao-Hua.Molecular Simulation of Oxygen Adsorption and Diffusion in Polypropylene[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1373-1378
118. JIANG Yu-Ren, XU Hui, CHEN Fang-Jun, MA Guan-Jun.Molecular Docking of the Acetylcholinesterase Inhibitor Corydaline and Virtual Screening of Open Ring Derivatives[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1379-1384
119. ZHAO Jian-Wei, LIU Hong-Mei, NI Wen-Bin, GUO Yan, YIN Xing.Electron Transfer Studied at theMolecular Level[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1472-1480
120. LV Wen, LV Wei, NIU Yan, LEI Xiao-Ping.HomologyModeling andMolecular Docking on Muscarinic M1 Receptor[J]. Acta Phys. -Chim. Sin., 2009,25(07): 1259-1266
121. NIU Ji-Nan, QIANG Ying-Huai.Molecular Dynamics Simulation on Structure of Water Molecules in a Kaolinite-Water System[J]. Acta Phys. -Chim. Sin., 2009,25(06): 1167-1172
122. SONG Qi-Sheng, GUO Xin-Li, YUAN Shi-Ling, LIU Cheng-Bu.Molecular Dynamics Simulation of Sodium Dodecyl Benzene Sulfonate Aggregation on Silica Surface[J]. Acta Phys. -Chim. Sin., 2009,25(06): 1053-1058
123. XIE Hui, LIU Chao, LIU Bin-Wu.Molecular Dynamics Simulation of Gas Mixture Flow in Nanochannel[J]. Acta Phys. -Chim. Sin., 2009,25(05): 994-998
124. WEI Zhuo, ZHANG Huai, CUI Wei, JI Ming-Juan.Molecular Docking and 3D-QSAR on Maleimide Derivatives as Glycogen Synthase Kinase-3β Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(05): 890-896
125. SUN Hao, JIANG Yong-Jun, YU Qing-Sen, ZOU Jian-Wei.Molecular Dynamics Simulation of Significant Roles of Structural Water Molecules in Glycogen Synthase Kinase-3β[J]. Acta Phys. -Chim. Sin., 2009,25(04): 635-639
126. SUN Ni-Yue, LU Tao, CHEN Ya-Dong, HAO Lan-Hu, XU Yan, LI Rui-Jun.3D-QSAR and Molecular Docking Study on Selectivity of Indolocarbazole Series as Cyclin-Dependent Kinase Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(04): 645-654
127. CAI Kai-Cong, WANG Jian-Ping.Molecular Dynamical Structures of Glycolaldehyde[J]. Acta Phys. -Chim. Sin., 2009,25(04): 677-683
128. WU Xiao-Min, ZU Yuan-Gang, YANG Zhi-Wei, FU Yu-Jie, ZHOU Li-Jun, YANG Gang.Temperature-Controlled Molecular Dynamics Studies on the Folding Mechanism of the Tubulin Active Peptides[J]. Acta Phys. -Chim. Sin., 2009,25(04): 773-782
129. CHEN Xin-Yuan, LV Yang, LI Shen-Min.Molecular Dynamics Simulations on the Stability of (3+1) Mixed-Type Hybrid G-quadruplex in Human Telomere[J]. Acta Phys. -Chim. Sin., 2009,25(04): 783-791
130. CUI Wei, ZHANG Huai, JI Ming-Juan.Molecular Dynamics Simulations and Free Energy Calculations of a Novel Series of Protein Tyrosine Phosphatase 1B Difluoromethylenephosphonic Acid Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(04): 668-676
131. ZHAO Yong-Shan, ZHENG Qing-Chuan, ZHANG Hong-Xing, CHU Hui-Ying, SUN Chia-Chung.Homology Modeling of Human Serine Racemase and Its Molecular Docking with Peptide Inhibitors[J]. Acta Phys. -Chim. Sin., 2009,25(03): 417-422
132. HOU Ji-Xuan, SI Li-Ming.Optimization Theory for Neighbor List Algorithmin Fluid System Simulation[J]. Acta Phys. -Chim. Sin., 2009,25(03): 430-434
133. WAN Li-Hua, YA Ke-Feng, LI Xiao-Sen, FAN Shuan-Shi.Molecular Dynamics Simulation of Methane Hydrate Dissociation Process in the Presence of Thermodynamic Inhibitor[J]. Acta Phys. -Chim. Sin., 2009,25(03): 486-494
134. CHEN Cong, LI Wei-Zhong.Molecular Dynamics Simulation of Hydrogen Bonding Characteristics in Aqueous Glycerol Solutions[J]. Acta Phys. -Chim. Sin., 2009,25(03): 507-512
135. XI Hai-Tao; GAO Ya-Jun; SUN Xiao-Qiang; YIN Kai-Liang; CHEN Cheng-Lung.Binding Energy of the Electron Acceptor Cyclobis (Paraquat-Phenylene) Tetracationic Cyclophane and Electron Donating Phenyl Ether Derivatives[J]. Acta Phys. -Chim. Sin., 2009,25(02): 377-381
136. PAN Guo-Xiang; NI Zhe-Ming; WANG Fang; WANG Jian-Guo; LI Xiao-Nian.Molecular Dynamics Simulation on Structure, Hydrogen-Bond and Hydration Properties of Diflunisal Intercalated Layered Double Hydroxides[J]. Acta Phys. -Chim. Sin., 2009,25(02): 223-228
137. LI Xiang-Fu; CHEN Hong-Shan; MENG Fan-Shun; LIU Bai-Xing.Melting Behavior of (AgI)n Clusters by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2009,25(01): 103-106
138. LI Zhen-Quan; GUO Xin-Li; WANG Hong-Yan; LI Qing-Hua; YUAN Shi-Ling; XU Gui-Ying; LIU Cheng-Bu.Molecular Dynamics Simulation of Anionic Surfactant Aggregation at the Oil/Water Interface[J]. Acta Phys. -Chim. Sin., 2009,25(01): 6-12
139. FU Yi-Zheng; LIU Ya-Qing; MEI Lin-Yu; LAN Yan-Hua.Molecular Dynamics Simulation on Binding Energies and Mechanical Properties of HTPB and Different Crystal Faces of Al[J]. Acta Phys. -Chim. Sin., 2009,25(01): 187-190
140. LI Jun, FENG Jie, LI Wen-Ying, CHANG Hai-Zhou, XIE Ke-Chang.Determining Influences of the Aggregative State of Deoxidized Coal on Its Extraction by Molecular Mechanics and Molecular Dynamics Analysis[J]. Acta Phys. -Chim. Sin., 2008,24(12): 2297-2303
141. CHEN Ying; WANG Xiu-Ying; ZHAO Jun-Qing.Molecular Dynamics Simulation on Melting of Metal Cluster with Small Size[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2042-2046
142. YANG Zhen; YANG Xiao-Ning; XU Zhi-Jun.Molecular Dynamics Simulation of Structure and Dynamics Properties of Water Near an Au Nanoparticle[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2047-2052
143. YANG Xiao-Feng; QIN Zhang-Feng; WANG Jian-Guo.A Random Walk Model for Molecular Anisotropic Diffusion in Siliceous β-Zeolites[J]. Acta Phys. -Chim. Sin., 2008,24(11): 2128-2132
144. JIANG Yu-Ren; QIN Wei.3D-QSAR Analysis on Benzoxazinone Derivatives[J]. Acta Phys. -Chim. Sin., 2008,24(10): 1859-1863
145. XU Zhi-Guang; XU Xuan; YUAN Chuan-Neng.Molecular Docking on Taxotere Binding to αβ-Tubulin[J]. Acta Phys. -Chim. Sin., 2008,24(10): 1839-1844
146. HU Jian-Ping; KE Guo-Tao; CHANG Shan; CHEN Wei-Zu; WANG Cun-Xin.Conformational Change of HIV-1 Viral DNA after Binding with Integrase[J]. Acta Phys. -Chim. Sin., 2008,24(10): 1803-1810
147. MAO Rong-Rong; LV Yang; ZHOU Li-Chuan; LI Qin-Ning; LI Shen-Min.Molecular Dynamics Simulation of the Vibrational Energy Relaxation of I2 in Nano-confined Argon Solution[J]. Acta Phys. -Chim. Sin., 2008,24(08): 1451-1458
148. SHEN Qiu-Chan; LIANG Wan-Chun; HU Xing-Bang; LI Hao-Ran.Molecular Dynamics Simulation for Formamide Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1169-1174
149. ZHANG Jun; ZHAO Wei-Min; GUO Wen-Yue; WANG Yong; LI Zhong-Pu.Theoretical Evaluation of Corrosion Inhibition Performance of Benzimidazole Corrosion Inhibitors[J]. Acta Phys. -Chim. Sin., 2008,24(07): 1239-1244
150. CUI Bao-Qiu; GONG Li-Dong; ZHAO Dong-Xia.Molecular Dynamics Simulation of Microperoxidase in Aqueous Solution in Terms of the ABEEM/MM Method[J]. Acta Phys. -Chim. Sin., 2008,24(06): 1035-1040
151. DING Yuan-Fa; ZHANG Yue; ZHANG Fan-Wei; ZHANG Da-Hai; LI Zhong-Ping.Interatomic Potentials of Silica Glass for Molecular Dynamics Simulation at High Temperature[J]. Acta Phys. -Chim. Sin., 2008,24(05): 788-792
152. GENG Chun-Yu; DING Li-Ying; HAN Qing-Zhen; WEN Hao.Influence of Gas Molecule on Stability of Methane Hydrate[J]. Acta Phys. -Chim. Sin., 2008,24(04): 595-600
153. ZHANG Rong; TAN Zai-You; ZHENG Dun-Sheng; LUO San-Lai; LI Hao-Ran.Molecular Dynamics Simulations on the Special System of TFE Aqueous Solution[J]. Acta Phys. -Chim. Sin., 2008,24(03): 428-432
154. YAN Hui; YUAN Shi-Ling; LIU Cheng-Bu.Radical Chain Reaction of Alkene Molecule on H-terminated Si(100)-2×1 Surface[J]. Acta Phys. -Chim. Sin., 2008,24(01): 8-12
155. LI Shu; LIU Lei; CAO Zhen; WANG Ji-Qiang; YAN Tian-Ying.Molecular Dynamics Simulation on a Eutectic Systemof LiTFSI/Urea[J]. Acta Phys. -Chim. Sin., 2007,23(07): 983-986
156. Yuan Jian-Hui; Cheng Yu-Min.Effects of the Grafted Carboxyl on the Elastic Properties of Single-walled Carbon Nanotubes[J]. Acta Phys. -Chim. Sin., 2007,23(06): 889-894
157. YUAN Wei; LI He-Xian; WANG Ying; YANG Hai-Long; WANG Guo-Chang.Computer Simulation on Intermolecular Interaction of N-(1-naphthyl)-succinimide[J]. Acta Phys. -Chim. Sin., 2007,23(05): 630-634
158. PENG Chuan-Xiao; WANG Li; ZHANG Yan-Ning.Amorphization of Ni Nanowires Induced by Strain Rate[J]. Acta Phys. -Chim. Sin., 2007,23(04): 517-520
159. WANG Hai-Long;WANG Xiu-Xi;WANG Yu;LIANG Hai-Yi .Molecular Dynamics Simulations of Low Index Surfaces Melting Behaviors for Metal Cu[J]. Acta Phys. -Chim. Sin., 2006,22(11): 1367-1371
160. NA Ping;ZHANG Fan;LI Yan-Ni.Molecular Dynamics Simulation of Na-montmorillonite and Na/Mg-montmorillonite Hydrates[J]. Acta Phys. -Chim. Sin., 2006,22(09): 1137-1142
161. ZHOU Zhen;YAN Tian-Ying;GAO Xue-Ping.Simulation and Design for Energy Storage Materials[J]. Acta Phys. -Chim. Sin., 2006,22(09): 1168-1174
162. YE Ya-Jing;ZHANG Li-Tong;CHENG Lai-Fei;XU Yong-Dong.Structure Characteristic of Amorphous BCN System by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2006,22(07): 878-882
163. HOU Huai-Yu;CHEN Guo-Liang;CHEN Guang.Molecular Dynamics Simulation of the Structure Transformation before and after Ni Melting[J]. Acta Phys. -Chim. Sin., 2006,22(07): 771-776
164. QIAO Ying-xin; ZHOU Jia-ju.A 3D-QSAR Study with Energy of Molecular Orbitals on N-Aminoidazoles[J]. Acta Phys. -Chim. Sin., 2006,22(02): 209-214
165. ZHANG Shu-guang; SHI Wen-yan; LEI Wu; XIA Ming-zhu; WANG Feng-yun.Molecular Dynamics Simulation of Interaction between Calcite Crystal and Water-soluble Polymers[J]. Acta Phys. -Chim. Sin., 2005,21(11): 1198-1204
166. LIU Chun-li; LI Chun-hua; CHEN Wei-zu; WANG Cun-xin.Study on Interaction between HIV-1 Integrase and Its Dicaffeoyl Inhibitors through Molecular Modeling Approach[J]. Acta Phys. -Chim. Sin., 2005,21(11): 1229-1234
167. LIU Zhen-ming; LI Bo; LAI Lu-hua.Functional Classification of Phospholipase A2 Family[J]. Acta Phys. -Chim. Sin., 2005,21(10): 1143-1145
168. WU Xiao-ping; LIU Zhi-ping; WANG Wen-chuan.Molecular Dynamics Simulation of Gas Solubility in Room Temperature Ionic Liquids[J]. Acta Phys. -Chim. Sin., 2005,21(10): 1138-1142
169. WU Xiao-ping; LIU Zhi-ping.Computer Simulation Study of the Mixtures of Room Temperature Ionic Liquid [bmim][BF4] and Water[J]. Acta Phys. -Chim. Sin., 2005,21(09): 1036-1041
170. FANG Mei-juan; LUO Shu-na; WANG He-qing; LIU Wan-yun; ZHAO Yu-fen.The Effect of Phosphoryl Oxygen on the Intermolecular Action of Alanine and Lysozyme[J]. Acta Phys. -Chim. Sin., 2005,21(09): 1042-1045
171. LIU Hai-chun; ZOU Jian-wei; ZHANG Bing; ZHUANG Shu-lin; JIANG Yong-jun; YU Qing-sen.Homology Modeling of p-Hydroxymandelate Synthase and Its Molecular Docking with Substrate[J]. Acta Phys. -Chim. Sin., 2005,21(08): 852-856
172. LI Xu-Dong; HOU Ting-Jun; Xu Xiao-Jie.Comparative Studies of 14 Binding Free Energies Scoring Functions[J]. Acta Phys. -Chim. Sin., 2005,21(05): 504-507
173. ZHANG Ai-Long; LIU Rang-Su; LIANG Jia; ZHENG Cai-Xing.A Simulation Study for Effects of Cooling Rate on Evolution of Microstructures during Solidification Process of Liquid Metal Ni[J]. Acta Phys. -Chim. Sin., 2005,21(04): 347-353
174. HUANG Yu-Cheng; HU Ying-Jie; XIAO Ji-Jun; YIN Kai-Liang; XIAO He-Ming.Molecular Dynamics Simulation of Binding Energy of TATB- based PBX[J]. Acta Phys. -Chim. Sin., 2005,21(04): 425-429
175. QIN Xing; ZHANG Bing-Jian; ZHANG Hui; HU Wen-Xuan.Diffusivity of Liquid Mixture Confined in Silicate Pore by Molecular Dynamic Simulation[J]. Acta Phys. -Chim. Sin., 2005,21(03): 315-318
176. LIU Bing; LU Ai-Jun; LIAO Chen-Zhong; LIU Hai-Bo; ZHOU Jia-Ju.3D-QSAR of Sulfonamide Hydroxamic Acid HDAC Inhibitors[J]. Acta Phys. -Chim. Sin., 2005,21(03): 333-337
177. ZHANG Tao;GU Ting-Kun;QI Yuan-Hua.Evolvement on the Microstructure of Molten Compound AuCu3 in Rapid Cooling[J]. Acta Phys. -Chim. Sin., 2005,21(02): 173-176
178. LIU Ying-Chun;WANG Qi;LÜ Ling-Hong;ZHANG Lian-Zhong.Structural and Diffusion Properties of Water in Hydrophobic Micropores by Molecular Simulation[J]. Acta Phys. -Chim. Sin., 2005,21(01): 63-68
179. Wang Bao-Lei;Ma Ning;Wang Jian-Guo;Ma Yi;Li Zheng-Ming;Li Yong-Hong.3D-QSAR Analysis of New Sulfonylureas Related to Their Herbicidal Activity[J]. Acta Phys. -Chim. Sin., 2004,20(06): 577-581
180. Yin Kai-Liang;Xu Duan-Jun;Xia Qing;Ye Ya-Jing;Wu Guo-Ying;Chen Cheng-Lung.Molecular Dynamics Simulation on Solidification Process of n-hexadecane Systems[J]. Acta Phys. -Chim. Sin., 2004,20(03): 302-305
181. Liu Xin;Meng Chang-Gong;Liu Chang-Hou.Melting and Superheating of Ag at High Heating Rate[J]. Acta Phys. -Chim. Sin., 2004,20(03): 280-284
182. Shao Jun;Xu Hua;Lu Wen-Cong;Chen Nian-Yi.Transport Property Anomalies under High Pressure in Molten Na2O-SiO2 Binary System Studied by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2004,20(03): 237-239
183. Ding Jun-Jie;Ding Xiao-Qin;Zhao Li-Feng;Chen Ji-Sheng.Three Dimensional Quantitative Structure-activity Relationship of Dihydropyridine Derivatives[J]. Acta Phys. -Chim. Sin., 2003,19(12): 1108-1113
184. Qin Xu-Bo;Zhang Yan-Ning;Lu Jian-Lin.The Ability of Glass Formation Dominated by the Mismatch in Atomic Size[J]. Acta Phys. -Chim. Sin., 2003,19(12): 1163-1166
185. Bai Yu-Lin;Chen Xiang-Rong;Yang Xiang-Dong;Lu Peng-Fei.Structures of Small Sulfur Clusters Sn(n=2~8) from Langevin Molecular Dynamics Methods[J]. Acta Phys. -Chim. Sin., 2003,19(12): 1102-1107
186. Yu Yong-Hui;Li Chun-Hua;Lu Ben-Zhuo;Chen Wei-Zu;Wang Cun-Xin.A New Method to Select the Near-native Conformations from the Docked Structures[J]. Acta Phys. -Chim. Sin., 2003,19(08): 757-761
187. Zhang Tao;Zhang Xiao-Ru;Wu Ai-Ling;Guan Li;Xu Chang-Ye.Molecular Dynamics Simulations of the Heating and Melting Processes of Metal Cu[J]. Acta Phys. -Chim. Sin., 2003,19(08): 709-713
188. Liu Xin;Meng Chang-Gong;Liu Chang-Hou.Heating Rate Induced Melting and Superheating of Pb[J]. Acta Phys. -Chim. Sin., 2003,19(08): 681-685
189. Zhang Hui;Zhang Bing-Jian;Liang Shi-Qiang;Lu Ying-Hong;Hu Wen-Xuan.Shear Viscosity of Simple Fluids in Porous Media: Molecular Dynamic Simulations and Correlation Models[J]. Acta Phys. -Chim. Sin., 2003,19(04): 352-355
190. Peng Tao;Pei Jian-Feng;Zhou Jia-Ju.Three-dimensional Quantitative Structure-Activity Relationship Study of Tyrosine Kinase Inhibitors[J]. Acta Phys. -Chim. Sin., 2003,19(02): 163-166
191. Zhou Guo-Rong;Wu You-Shi;Zhang Chuan-Jiang;Zhao Fang.Molecular Dynamics Simulations of the Effect of Icosahedral Quasicrystal on the Formation of Amorphous[J]. Acta Phys. -Chim. Sin., 2003,19(01): 13-16
192. Zhang Yan-Ning;Wang Li;Bian Xiu-Fang.Melting of Au Nanoclusters by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2003,19(01): 35-39
193. Zhu Li-Li;Xu Xiao-Jie.3D-QSAR Analyses of Melatonin Antagonists[J]. Acta Phys. -Chim. Sin., 2002,18(12): 1087-1092
194. Zou Xia-Juan;Lai Lu-Hua;Jin Gui-Yu;Huang Gui-Qin.Studies on the 3D-QSAR of Novel 1-aryl-1,4-dihydro-3-acylhydrazinocarbonyl-6-methyl- 4-pyridazinones[J]. Acta Phys. -Chim. Sin., 2002,18(06): 513-516
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196. Wang Li;Yi Su;Bian XiuFang.Atom Clusters in Liquid and Amorphous of Ni3Al Alloy[J]. Acta Phys. -Chim. Sin., 2002,18(04): 297-301
197. Zhou Jian;Zhu Yu;Wang Wen-Chuan;Lu Xiao-Hua;Wang Yan-Ru;Shi Jun.Molecular Dynamics Study of Supercritical Aqueous Sodium Chloride Solutions[J]. Acta Phys. -Chim. Sin., 2002,18(03): 207-212
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199. Xu Hua;Shao Jun.Molecular Dynamics Simulation of Fast Li Conduction in Fluoroborate Glasses[J]. Acta Phys. -Chim. Sin., 2002,18(01): 10-13
200. Wang Li, Bian Xiu-Fang, Li Hui.Liquid-Solid Transition and Crystal Growth of Metal Cu by Molecular Dynamics Simulation[J]. Acta Phys. -Chim. Sin., 2000,16(09): 825-829
201. Hou Ting-Jun, Zhu Li-Zhi, Xu Xiao-Jie, Ji Ming-Juan, Ye Xue-Qi.Diffusion of Benzene in MCM-22 Zeolite:A Molecular Dynamics Study[J]. Acta Phys. -Chim. Sin., 2000,16(08): 701-707
202. Xu Hua, Shao Jun.Molecular Dynamics Simulation of the Phase Transition of α-berlinite under High Pressure[J]. Acta Phys. -Chim. Sin., 2000,16(06): 512-516
203. Hou Ting-Jun, An Yu, Ru Bing-Gen, Xu Xiao-Jie.Theoretic Studies of Dynamics Stability to Three Kinds of Metallothioneins[J]. Acta Phys. -Chim. Sin., 2000,16(03): 221-225
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206. Yang Guang-Fu, Liu Hua-Yin, Yang Xiu-Feng, Yang Hua-Zheng.CoMFA Studies on Herbicidal 1,2,4-Triazolo[1,5-a]pyrimidine-2-Sulfonanilides[J]. Acta Phys. -Chim. Sin., 1999,15(02): 190-192
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213. Gu Jian-De,Tian An-Min,Yan Guo-Sen.Molecular Dynamics Simulations for the Spectra of N2 and O2 Aqueous Solutions[J]. Acta Phys. -Chim. Sin., 1995,11(08): 719-723
214. Wang Jun-Mei,Hu Zhao-Lin,Ye Xue-Qi.Conformational Analysis of Leu-enkephalin by Molecular Dyanmics Method[J]. Acta Phys. -Chim. Sin., 1995,11(08): 673-677
215. Luo Zhao-Wen,Deng Qiao-Lin,Lai Lu-Hua,Xu Xiao-Jia,Tang You-Qi.Molecular Dynamic Study on Phospholipase A2 and its Complex[J]. Acta Phys. -Chim. Sin., 1995,11(07): 622-626
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217. Huang Shi-Ping, Liu Hong-Lin, Ma Yan-Hui, Tang Bo, Chen Nian-Yi.Molecular Dynamics Simulation of ZnCl2 Melts[J]. Acta Phys. -Chim. Sin., 1995,11(01): 71-73
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219. Huang Shi-Ping, Ma Yan-Hui, Tang Bo, Xu Hua, Chen Nian-Yi.Molecular Dynamics Study of NaCl-NaBr Melt[J]. Acta Phys. -Chim. Sin., 1994,10(11): 1045-1048
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