Citation: Yujie Tang, Mo Zheng, Chunxing Ren, Xiaoxia Li, Li Guo. Visualized Reaction Tracking and Physical Property Analysis for a Picked 3D Area in a Reactive Molecular Dynamics Simulation System[J]. Acta Physico-Chimica Sinica, ;2021, 37(10): 200303. doi: 10.3866/PKU.WHXB202003037 shu

Visualized Reaction Tracking and Physical Property Analysis for a Picked 3D Area in a Reactive Molecular Dynamics Simulation System

Yujie Tang ^{1, 2, 3} ,
Mo Zheng ^{1, 3} ,
Chunxing Ren ^{1, 2, 3} ,
Xiaoxia Li ^{1, 2, 3,,} ,
Li Guo ^{1, 2, 3}

1.
State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
2.
School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
3.
Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China

Corresponding author: Xiaoxia Li, xxia@ipe.ac.cn
Received Date: 16 March 2020
Revised Date: 7 April 2020
Accepted Date: 10 April 2020
Available Online: 14 April 2020
Fund Project: the National Key Research and Development Plan of China 2016YFB0600302National Natural Science Foundation of China 91641102National Natural Science Foundation of China 91434105National Natural Science Foundation of China 21606231

Recently, the application of ReaxFF based reactive molecular dynamics simulation (ReaxFF MD) in complex processes of pyrolysis, oxidation and catalysis has attracted considerable attention. The analysis of the simulation results of these processes is challenging owing to the complex chemical reactions involved, coupled with their dynamic physical properties. VARxMD is a leading tool for the chemical reaction analysis and visualization of ReaxFF MD simulations, which allows the automated analysis of reaction sites to get overall reaction lists, evolution trends of reactants and products, and reaction networks of specified reactants and products. The visualization of the reaction details and dynamic evolution profiles are readily available for each reactant and product. Additionally, the detailed reaction sites of bond breaking and formation are available in 2D chemical structure diagrams and 3D structure views; for specified reactions, they are categorized on the basis of the chemical structures of the bonding sites or function groups in the reacting species. However, the current VARxMD code mainly focuses on global chemical reaction information in the simulation system of the ReaxFF MD, and is incapable of locally tracking the chemical reaction and physical properties in a 3D picked zone. This work extends the VARxMD from global analysis to a focused 3D zone picked interactively from the 3D visualization modules of VARxMD, as well as physical property analysis to complement reaction analysis. The analysis of reactions and physical properties can be implemented in three steps: picking and drawing a 3D zone, identifying molecules in the picked zone, and analyzing the reactions and physical properties of the picked molecules. A 3D zone can be picked by specifying the geometric parameters or drawing on a screen using a mouse. The picking of a cuboid or sphere was implemented using the VTK 3D view libraries by specifying geometric parameters. The interactive 3D zone picking was implemented using a combination of observer and command patterns in the VTK visualization paradigm. The chemical reaction tracking and dynamic radial distribution function (RDF) of the 3D picked zone was efficiently implemented by inheriting data obtained from the global analysis of VARxMD. The reaction tracking between coal particles in coal pyrolysis simulation and dynamic structure characterization of carbon rich cluster formation in the thermal decomposition of an energetic material are presented as application examples. The obtained detailed reactions between the coal particles and comparison of the reaction between the locally and globally picked areas in the cuboid are helpful in understanding the role of micro pores in coal particles. The carbon to carbon RDF analysis and comparison of the spherical region picked for the layered molecular clusters in the pyrolysis system of the TNT crystal model with the standard RDF of the 5-layer graphene demonstrate the extended VARxMD as a chemical structure characteristic tool for detecting the dynamic formation profile of carbon rich clusters in the pyrolysis of TNT. The extended capability of VARxMD for a 3D picked zone of a ReaxFF MD simulation system can be useful for interfacial reaction analysis in a catalysis system, hot spot formation analysis in the detonation of energetic material systems, and particularly the pyrolysis or oxidation processes of coal, biomass, polymers, hydrocarbon fuels, and energetic materials.
- ReaxFF MD,
- Regional reaction tracking,
- Physical property,
- Visualization
1. [1]
  van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. J. Phys. Chem. A 2001, 105, 9396. doi: 10.1021/jp004368u doi: 10.1021/jp004368u
2. [2]
  https://lammps.sandia.gov/ (accessed Apr. 8, 2020).
3. [3]
  https://www.scm.com/product/reaxff/ (accessed Apr. 8, 2020).
4. [4]
  https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/ / (accessed Apr. 8, 2020).
5. [5]
  Carter Edwards, H.; Trott, C. R.; Sunderland, D. J. Parallel Distrib. Comput 2014, 74, 3202. doi: 10.1016/j.jpdc.2014.07.003 doi: 10.1016/j.jpdc.2014.07.003
6. [6]
  Dontgen, M.; Przybylski-Freund, M. D.; Kroger, L. C.; Kopp, W. A.; Ismail, A. E.; Leonhard, K. J. Chem. Theory Comput 2015, 11, 2517. doi: 10.1021/acs.jctc.5b00201 doi: 10.1021/acs.jctc.5b00201
7. [7]
  https://www.scienomics.com/analyze/ (accessed Apr. 8, 2020).
8. [8]
  Zeng, J.; Cao, L.; Chin, C. -H.; Ren, H.; Zhang, J. Z.; Zhu, T. Phys. Chem. Chem. Phys 2020, 22, 683. doi: 10.1039/C9CP05091D doi: 10.1039/C9CP05091D
9. [9]
  Wu, Y.; Sun, H.; Wu, L.; Deetz, J. D. J. Comput. Chem. 2019, 40, 1586. doi: 10.1002/jcc.2580 doi: 10.1002/jcc.2580
10. [10]
  Zheng, M.; Li, X.; Guo, L. J. Mol. Graph. Model. 2013, 41, 1. doi: 10.1016/j.jmgm.2013.02.001 doi: 10.1016/j.jmgm.2013.02.001
11. [11]
  Liu, J.; Li, X.; Guo, L.; Zheng, M.; Han, J.; Yuan, X.; Nie, F.; Liu, X. J. Mol. Graph. Model. 2014, 53, 13. doi: 10.1016/j.jmgm.2014.07.002 doi: 10.1016/j.jmgm.2014.07.002
12. [12]
  Liu, J.; Li, X.; Guo, L.; Zheng, M.; Han, J; Yuan, X; Nie, F.; Liu, X. Comp. App. Chem. 2014, 31, 641. doi: 10.11719/com.app.chem20140601
13. [13]
  Han, J.; Li, X.; Guo, L.; Zheng, M.; Qiao, X.; Liu, X.; Gao, M.; Zhang, T.; Han, S. Comp. App. Chem. 2015, 32, 519. doi: 10.11719/com.app.chem20150502
14. [14]
  He, Q.; Ren, C; Li, X; Guo, L.; Zhang, T.; Gao, M.; Han, S. Comp. App. Chem 2019, 36, 299. doi: 10.16866/j.com.app.chem201904001
15. [15]
  Zhang, T.; Li, X.; Guo, L.; Guo, X. Energy Fuels 2019, 33, 11210. doi: 10.1021/acs.energyfuels.9b02843 doi: 10.1021/acs.energyfuels.9b02843
16. [16]
  Zhao, P.; Han, S.; Li, X.; Zhu, T.; Tao, X.; Guo, L. Energy Fuels 2019, 33, 7176. doi: 10.1021/acs.energyfuels.9b01321 doi: 10.1021/acs.energyfuels.9b01321
17. [17]
  Zheng, M.; Li, X.; Wang, M.; Guo, L. Fuel 2019, 253, 910. doi: 10.1016/j.fuel.2019.05.085 doi: 10.1016/j.fuel.2019.05.085
18. [18]
  Ren, C.; Li, X.; Guo, L. J. Chem. Inf. Model. 2019, 59, 2079. doi: 10.1021/acs.jcim.8b00952 doi: 10.1021/acs.jcim.8b00952
19. [19]
  Schroeder, W.; Martin, K.; Lorensen, B. The Visualization Toolkit: An Object-Oriented Approach to 3d Graphics, 4th ed.; Kitware, Inc.: Clifton Park, NY, USA, 2018; pp. 35-80.
20. [20]
  Zheng, M.; Li, X.; Liu, J.; Wang, Z.; Gong, X.; Guo, L.; Song, W. Energy Fuels 2014, 28, 522. doi: 10.1021/ef402140n doi: 10.1021/ef402140n
21. [21]
  Zheng, M.; Li, X.; Guo, L. Fuel 2018, 233, 867. doi: 10.1016/j.fuel.2018.06.133 doi: 10.1016/j.fuel.2018.06.133
22. [22]
  Gao, M.; Li, X.; Guo, L. Fuel Process. Technol 2018, 178, 197. doi: 10.1016/j.fuproc.2018.05.011 doi: 10.1016/j.fuproc.2018.05.011
23. [23]
  Shi, L. Study on the Cleavage of Covalent Bonds in Coal Pyrolysis from Various Temperature Stages. Ph. D. Dissertation, Beijing University of Chemical Technology: Beijing, 2014.
24. [24]
  Furman, D.; Kosloff, R.; Dubnikova, F.; Zybin, S. V.; Goddard, W. A.; Rom, N.; Hirshberg, B.; Zeiri, Y. J. Am. Chem. Soc. 2014, 136, 4192. doi: 10.1021/ja410020f doi: 10.1021/ja410020f
25. [25]
  Rom, N.; Hirshberg, B.; Zeiri, Y.; Furman, D.; Zybin, S. V.; Goddard, W. A.; Kosloff, R. J. Phys. Chem. C 2013, 117, 21043. doi: 10.1021/jp404907b doi: 10.1021/jp404907b
26. [26]
  Strachan, A.; van Duin, A. C. T.; Chakraborty, D.; Dasgupta, S.; Goddard, W. A. Phys. Rev. Lett 2003, 91, 098301. doi: 10.1103/PhysRevLett.91.098301 doi: 10.1103/PhysRevLett.91.098301
27. [27]
  An, Q.; Goddard, W. A.; Zybin, S. V.; Jaramillo-Botero, A.; Zhou, T. J. Phys. Chem. C 2013, 117, 26551. doi: 10.1021/jp404753v doi: 10.1021/jp404753v
28. [28]
  Guo, D.; An, Q.; Goddard, W. A.; Zybin, S. V.; Huang, F. J. Phys. Chem. C 2014, 118, 30202. doi: 10.1021/jp5093527 doi: 10.1021/jp5093527
29. [29]
  Greiner, N. R.; Phillips, D. S.; Johnson, J. D.; Volk, F. Nature 1988, 333, 440. doi: 10.1038/333440a0 doi: 10.1038/333440a0
30. [30]
  Mochalin, V. N.; Shenderova, O.; Ho, D.; Gogotsi, Y. Nat. Nanotechnol. 2012, 7, 11. doi: 10.1038/nnano.2011.209 doi: 10.1038/nnano.2011.209
1. [1]
  Ruming Yuan , Laiying Zhang , Xiaoming Xu , Pingping Wu , Gang Fu . Application of Mathematica in Visualizing Physical Chemistry Formulas. University Chemistry, 2024, 39(8): 375-382. doi: 10.3866/PKU.DXHX202401030
2. [2]
  Yanxin Wang , Hongjuan Wang , Yuren Shi , Yunxia Yang . Application of Python for Visualizing in Structural Chemistry Teaching. University Chemistry, 2024, 39(3): 108-117. doi: 10.3866/PKU.DXHX202306005
3. [3]
  Hongyun Liu , Jiarun Li , Xinyi Li , Zhe Liu , Jiaxuan Li , Cong Xiao . Course Ideological and Political Design of a Comprehensive Chemistry Experiment: Constructing a Visual Molecular Logic System Based on Intelligent Hydrogel Film Electrodes. University Chemistry, 2024, 39(2): 227-233. doi: 10.3866/PKU.DXHX202309070
4. [4]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
5. [5]
  Zhenli Sun , Ning Wang , Kexin Lin , Qin Dai , Yufei Zhou , Dandan Cao , Yanfeng Dang . Visual Analysis of Hotspots and Development Trends in Analytical Chemistry Education Reform. University Chemistry, 2024, 39(11): 57-64. doi: 10.12461/PKU.DXHX202403095
6. [6]
  Shiyan Cheng , Yonghong Ruan , Lei Gong , Yumei Lin . Research Advances in Friedel-Crafts Alkylation Reaction. University Chemistry, 2024, 39(10): 408-415. doi: 10.12461/PKU.DXHX202403024
7. [7]
  Haiying Wei , Daqing Yang , Mingtao Run , Guoyan Huo . Examination and Analysis on Rationality of Experimental Design: Based on Reaction of Potassium Permanganate with Potassium Bormide. University Chemistry, 2024, 39(10): 283-288. doi: 10.12461/PKU.DXHX202404068
8. [8]
  Feiya Cao , Qixin Wang , Pu Li , Zhirong Xing , Ziyu Song , Heng Zhang , Zhibin Zhou , Wenfang Feng . Magnesium-Ion Conducting Electrolyte Based on Grignard Reaction: Synthesis and Properties. University Chemistry, 2024, 39(3): 359-368. doi: 10.3866/PKU.DXHX202308094
9. [9]
  Jinyao Du , Xingchao Zang , Ningning Xu , Yongjun Liu , Weisi Guo . Electrochemical Thiocyanation of 4-Bromoethylbenzene. University Chemistry, 2024, 39(6): 312-317. doi: 10.3866/PKU.DXHX202310039
10. [10]
  Xu Liu , Chengfang Liu , Jie Huang , Xiangchun Li , Wenyong Lai . Research on the Application of Diversified Teaching Models in the Teaching of Physical Chemistry. University Chemistry, 2024, 39(8): 112-118. doi: 10.3866/PKU.DXHX202402021
11. [11]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
12. [12]
  Danqing Wu , Jiajun Liu , Tianyu Li , Dazhen Xu , Zhiwei Miao . Research Progress on the Simultaneous Construction of C—O and C—X Bonds via 1,2-Difunctionalization of Olefins through Radical Pathways. University Chemistry, 2024, 39(11): 146-157. doi: 10.12461/PKU.DXHX202403087
13. [13]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
14. [14]
  Ji Qi , Jianan Zhu , Yanxu Zhang , Jiahao Yang , Chunting Zhang . Visible Color Change of Copper (II) Complexes in Reversible SCSC Transformation: The Effect of Structure on Color. University Chemistry, 2024, 39(3): 43-57. doi: 10.3866/PKU.DXHX202307050
15. [15]
  Hongsheng Tang , Yonghe Zhang , Dexiang Wang , Xiaohui Ning , Tianlong Zhang , Yan Li , Hua Li . A Wonderful Journey through the Kingdom of Hazardous Chemicals. University Chemistry, 2024, 39(9): 196-202. doi: 10.12461/PKU.DXHX202403098
16. [16]
  Wentao Lin , Wenfeng Wang , Yaofeng Yuan , Chunfa Xu . Concerted Nucleophilic Aromatic Substitution Reactions. University Chemistry, 2024, 39(6): 226-230. doi: 10.3866/PKU.DXHX202310095
17. [17]
  Zitong Chen , Zipei Su , Jiangfeng Qian . Aromatic Alkali Metal Reagents: Structures, Properties and Applications. University Chemistry, 2024, 39(8): 149-162. doi: 10.3866/PKU.DXHX202311054
18. [18]
  Xuan Zhou , Yi Fan , Zhuoqi Jiang , Zhipeng Li , Guowen Yuan , Laiying Zhang , Xu Hou . Liquid Gating Mechanism and Basic Properties Characterization: a New Experimental Design for Interface and Surface Properties in the Chemistry “101 Plan”. University Chemistry, 2024, 39(10): 113-120. doi: 10.12461/PKU.DXHX202407111
19. [19]
  Heng Zhang . Determination of All Rate Constants in the Enzyme Catalyzed Reactions Based on Michaelis-Menten Mechanism. University Chemistry, 2024, 39(4): 395-400. doi: 10.3866/PKU.DXHX202310047
20. [20]
  Yuting Zhang , Zhiqian Wang . Methods and Case Studies for In-Depth Learning of the Aldol Reaction Based on Its Reversible Nature. University Chemistry, 2024, 39(7): 377-380. doi: 10.3866/PKU.DXHX202311037

Get Citation

PDF

XML

Metrics

PDF Downloads(9)
Abstract views(314)
HTML views(25)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142