Citation: YIN Di, QIU Zongyang, LI Pai, LI Zhenyu. A Molecular Dynamics Study of Carbon Dimerization on Cu(111) Surface with Optimized DFTB Parameters[J]. Acta Physico-Chimica Sinica, ;2018, 34(10): 1116-1123. doi: 10.3866/PKU.WHXB201801151 shu

A Molecular Dynamics Study of Carbon Dimerization on Cu(111) Surface with Optimized DFTB Parameters

Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, P. R. China

Corresponding author: LI Zhenyu, zyli@mail.ustc.edu.cn
Received Date: 18 December 2017
Revised Date: 11 January 2018
Accepted Date: 11 January 2018
Available Online: 15 October 2018
Fund Project: the Special Program for Applied Research on Super Computation of the National Nature Science Foundation of China-Guangdong Joint Fund U1501501The project was supported by National Natural Science Foundation of China (21573201), the Ministry of Science and Technology of China (2016YFA0200604), and the Special Program for Applied Research on Super Computation of the National Nature Science Foundation of China-Guangdong Joint Fund (U1501501)the Ministry of Science and Technology of China 2016YFA0200604National Natural Science Foundation of China 21573201

Cu has been widely used as a substrate material for graphene growth. To understand the atomistic mechanism of growth, an efficient and accurate method for describing Cu-C interactions is necessary, which is the prerequisite of any possible large-scale molecular simulation studies. The semi-empirical density-functional tight-binding (DFTB) method has a solid basis from the density functional theory (DFT) and is believed to be a good tool for achieving a balance between efficiency and accuracy. However, existing DFTB parameters cannot provide a reasonable description of the Cu surface structure. At the same time, DFTB parameters for Cu-C interactions are not available. Therefore, it is highly desirable to develop a set of DFTB parameters that can describe the Cu-C system, especially for surface reactions. In this study, a parametrization for Cu-C systems within the self-consistent-charge DFTB (SCC-DFTB) framework is performed. One-center parameters, including on-site energy, Hubbard, and spin parameters, are obtained from DFT calculations on free atoms. Two-center parameters can be calculated based on atomic wavefunctions. The remaining repulsive potential is obtained as the best compromise to describe different kinds of systems. Test calculations on Cu surfaces and Cu-or C atom-adsorbed Cu surfaces indicate that the obtained parameters can generate reasonable geometric structures and energetics. Based on this parameter set, carbon dimerization on the Cu(111) surface has been investigated via molecular dynamics simulations. Since they are the feeding species for graphene growth, it is important to understand how carbon dimers are formed on the Cu surface. It is difficult to observe carbon dimerization in brute-force MD simulations even at high temperatures, because of the surface structure distortion. To study the dimerization mechanism, metadynamics simulations are performed. Our simulations suggest that carbon atoms will rotate around the bridging Cu atom after a bridging metal structure is formed, which eventually leads to the dimer formation. The free energy barrier for dimerization at 1300 K is about 0.9 eV. The results presented here provide useful insights for understanding graphene growth.
- Copper surface,
- Carbon dimer,
- DFTB,
- Molecular simulation
1. [1]
  Tetlow, H.; de Boer, J. P.; Ford, I.; Vvedensky, D.; Coraux, J.; Kantorovich, L. Phys. Rep. 2014, 542, 195. doi: 10.1016/j.physrep.2014.03.003 doi: 10.1016/j.physrep.2014.03.003
2. [2]
  Wu, P.; Zhang, W.; Li, Z.; Yang, J. Small 2014, 10, 2136. doi: 10.1002/smll.201303680 doi: 10.1002/smll.201303680
3. [3]
  Wu, P.; Zhang, Y.; Cui, P.; Li, Z. Y.; Yang, J. L.; Zhang, Z. Y. Phys. Rev. Lett. 2015, 114, 216102. doi: 10.1103/PhysRevLett. 114.216102 doi: 10.1103/PhysRevLett.114.216102
4. [4]
  Li, P.; Li, Z.; Yang, J. J. Phys. Chem. C 2017, 121, 25949. doi: 10.1021/acs.jpcc.7b09622 doi: 10.1021/acs.jpcc.7b09622
5. [5]
  Wu, P.; Zhang, W.; Li, Z.; Yang, J.; Hou, J. G. J. Chem. Phys. 2010, 133, 071101. doi:10.1063/1.3473045 doi: 10.1063/1.3473045
6. [6]
  Li, X.; Cai, W.; An, J.; Kim, S.; Nah, J.; Yang, D.; Piner, R.; Velamakanni, A.; Jung, I.; Tutuc, E. Science 2009, 324, 1312. doi: 10.1126/science.1171245 doi: 10.1126/science.1171245
7. [7]
  Henkelman, G.; Uberuaga, B. P.; Jónsson, H. J. Chem. Phys. 2000, 113, 9901. doi: 10.1063/1.1329672 doi: 10.1063/1.1329672
8. [8]
  Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 7260. doi: 10.1103/PhysRevB.58.7260 doi: 10.1103/PhysRevB.58.7260
9. [9]
  Frauenheim, T.; Seifert, G.; Elstner, M.; Hajnal, Z.; Jungnickel, G.; Porezag, D.; Suhai, S.; Scholz, R. Phys. Stat. Sol. (b) 2000, 217, 41. doi: 10.1002/(SICI)1521-3951(200001)217:1<41::AID-PSSB41>3.0.CO;2-V doi: 10.1002/(SICI)1521-3951(200001)217:1<41::AID-PSSB41>3.0.CO;2-V
10. [10]
  Porezag, D.; Frauenheim, T.; Kohler, T.; Seifert, G.; Kaschner, R. Phys. Rev. B 1995, 51, 12947. doi:10.1103/PhysRevB.51.12947 doi: 10.1103/PhysRevB.51.12947
11. [11]
  Elstner, M.; Frauenheim, T.; Kaxiras, E.; Seifert, G.; Suhai, S. Phys. Stat. Sol. (b) 2000, 217, 357. doi: 10.1002/(SICI)1521-3951(200001) 217:1<357::AID-PSSB357>3.0.CO;2-J doi: 10.1002/(SICI)1521-3951(200001)217:1<357::AID-PSSB357>3.0.CO;2-J
12. [12]
  Elstner, M. Theor. Chem. Acc. 2006, 116, 316. doi: 10.1007/s00214-005-0066-0 doi: 10.1007/s00214-005-0066-0
13. [13]
  Page, A. J.; Ohta, Y.; Irle, S.; Morokuma, K. Acc. Chem. Res. 2010, 43, 1375. doi: 10.1021/ar100064g doi: 10.1021/ar100064g
14. [14]
  Wang, Y.; Page, A. J.; Nishimoto, Y.; Qian, H.-J.; Morokuma, K.; Irle, S. J. Am. Chem. Soc. 2011, 133, 18837. doi: 10.1021/ja2064654 doi: 10.1021/ja2064654
15. [15]
  Li, H. -B.; Page, A. J.; Wang, Y.; Irle, S.; Morokuma, K. Chem. Comm. 2012, 48, 7937. doi: 10.1039/C2CC32995F doi: 10.1039/C2CC32995F
16. [16]
  Wahiduzzaman, M.; Oliveira, A. F.; Philipsen, P.; Zhechkov, L.; van Lenthe, E.; Witek, H. A.; Heine, T. J. Chem. Theory Compt. 2013, 9, 4006. doi: 10.1021/Ct4004959 doi: 10.1021/Ct4004959
17. [17]
  Oliveira, A. F.; Philipsen, P.; Heine, T. J. Chem. Theory Compt. 2015, 11, 5209. doi: 10.1021/ acs.jctc.5b00702 doi: 10.1021/acs.jctc.5b00702
18. [18]
  Slater-Koster files containing atomic parameters used in DFTB calculations. http://www.dftb.org/parameters/ (accessed Dec 1, 2017)
19. [19]
  Frenzel, J.; Oliveira, A. F.; Duarte, H. A.; Heine, T.; Seifert, G. Z. Anorg. Allg. Chem. 2005, 631, 1267. doi: 10.1002/zaac.200500051 doi: 10.1002/zaac.200500051
20. [20]
  Guimaraes, L.; Enyashin, A. N.; Frenzel, J.; Heine, T.; Duarte, H. A.; Seifert, G. ACS Nano 2007, 1, 362. doi:10.1021/nn700184k doi: 10.1021/nn700184k
21. [21]
  Koskinen, P.; Makinen, V. Comput. Mater. Sci. 2009, 47, 237. doi:/10.1016/j.commatsci.2009.07.013 doi: 10.1016/j.commatsci.2009.07.013
22. [22]
  Slater, J. C.; Koster, G. F. Phys. Rev. 1954, 94, 1498. doi: 10.1103/PhysRev.94.1498 doi: 10.1103/PhysRev.94.1498
23. [23]
  Gaus, M.; Cui, Q. A.; Elstner, M. J. Chem. Theory Compt. 2011, 7, 931. doi:10.1021/Ct100684s doi: 10.1021/Ct100684s
24. [24]
  Grundk tter-Stock, B.; Bezugly, V.; Kunstmann, J.; Cuniberti, G.; Frauenheim, T.; Niehaus, T. A. J. Chem. Theory Compt. 2012, 8, 1153. doi:10.1021/ct200722n doi: 10.1021/ct200722n
25. [25]
  Gaus, M.; Chou, C. -P.; Witek, H.; Elstner, M. J. Phys. Chem. A 2009, 113, 11866. doi:10.1021/jp902973m doi: 10.1021/jp902973m
26. [26]
  Bodrog, Z.; Aradi, B.; Frauenheim, T. J. Chem. Theory Compt. 2011, 7, 2654. doi:10.1021/ct200327s doi: 10.1021/ct200327s
27. [27]
  José, M. S.; Emilio, A.; Julian, D. G.; Alberto, G.; Javier, J.; Pablo, O.; Daniel, S. -P. J. Phys.: Condens. Matter 2002, 14, 2745. doi: 10.1088/0953-8984/14/11/302 doi: 10.1088/0953-8984/14/11/302
28. [28]
  Thomas, F.; Gotthard, S.; Marcus, E.; Thomas, N.; Christof, K.; Marc, A.; Michael, S.; Zoltán, H.; Aldo, Di, C.; Sándor, S. J. Phys.: Condens. Matter 2002, 14, 3015. doi: 10.1088/0953-8984/14/11/313 doi: 10.1088/0953-8984/14/11/313
29. [29]
  Aradi, B.; Hourahine, B.; Frauenheim, T. J. Phys. Chem. A 2007, 111, 5678. doi: 10.1021/jp070186p doi: 10.1021/jp070186p
30. [30]
  Kresse, G.; Furthmuller, J. Comput. Mater. Sci. 1996, 6, 15. doi: 10.1016/0927-0256(96)00008-0 doi: 10.1016/0927-0256(96)00008-0
31. [31]
  Kresse, G.; Furthmuller, J. Phys. Rev. B 1996, 54, 11169. doi:10.1103/PhysRevB.54.11169 doi: 10.1103/PhysRevB.54.11169
32. [32]
  Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865. doi:10.1103/PhysRevLett.77.3865 doi: 10.1103/PhysRevLett.77.3865
33. [33]
  Knaup, J. M.; Hourahine, B.; Frauenheim, T. J. Phys. Chem. A 2007, 111, 5637. doi:10.1021/jp0688097 doi: 10.1021/jp0688097
34. [34]
  Burdick, G. A. Phys. Rev. 1963, 129, 138. doi: 10.1103/PhysRev.129.138 doi: 10.1103/PhysRev.129.138
35. [35]
  Shin, H.; Kang, S.; Koo, J.; Lee, H.; Kim, J.; Kwon, Y. J. Chem. Phys. 2014, 140, 114702. doi: 10.1063/1.4867544 doi: 10.1063/1.4867544
36. [36]
  Van Wesep, R. G.; Chen, H.; Zhu, W.; Zhang, Z. J. Chem. Phys. 2011, 134, 171105. doi: 10.1063/1.3587239 doi: 10.1063/1.3587239
37. [37]
  Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2002, 99, 12562. doi: 10.1073/pnas.202427399 doi: 10.1073/pnas.202427399
1. [1]
  Huimin Gao , Zhuochen Yu , Xuze Zhang , Xiangkun Yu , Jiyuan Xing , Youliang Zhu , Hu-Jun Qian , Zhong-Yuan Lu . A mini review of the recent progress in coarse-grained simulation of polymer systems. Chinese Journal of Structural Chemistry, 2024, 43(5): 100266-100266. doi: 10.1016/j.cjsc.2024.100266
2. [2]
  Feng Zheng , Ruxun Yuan , Xiaogang Wang . “Research-Oriented” Comprehensive Experimental Design in Polymer Chemistry: the Case of Polyimide Aerogels. University Chemistry, 2024, 39(10): 210-218. doi: 10.12461/PKU.DXHX202404027
3. [3]
  Guoliang Liu , Zhiqiang Liu , Anmin Zheng . Modulation of zeolite surface realizes dynamic copper species redispersion. Chinese Journal of Structural Chemistry, 2024, 43(6): 100308-100308. doi: 10.1016/j.cjsc.2024.100308
4. [4]
  Zhenchun Yang , Bixiao Guo , Zhenyu Hu , Kun Wang , Jiahao Cui , Lina Li , Chun Hu , Yubao Zhao . Molecular engineering towards dual surface local polarization sites on poly(heptazine imide) framework for boosting H₂O₂ photo-production. Chinese Chemical Letters, 2024, 35(8): 109251-. doi: 10.1016/j.cclet.2023.109251
5. [5]
  Zhenyu Hu , Zhenchun Yang , Shiqi Zeng , Kun Wang , Lina Li , Chun Hu , Yubao Zhao . Cationic surface polarization centers on ionic carbon nitride for efficient solar-driven H₂O₂ production and pollutant abatement. Chinese Chemical Letters, 2024, 35(10): 109526-. doi: 10.1016/j.cclet.2024.109526
6. [6]
  Fang-Yuan Chen , Wen-Chao Geng , Kang Cai , Dong-Sheng Guo . Molecular recognition of cyclophanes in water. Chinese Chemical Letters, 2024, 35(5): 109161-. doi: 10.1016/j.cclet.2023.109161
7. [7]
  Shiyu Hou , Maolin Sun , Liming Cao , Chaoming Liang , Jiaxin Yang , Xinggui Zhou , Jinxing Ye , Ruihua Cheng . Computational fluid dynamics simulation and experimental study on mixing performance of a three-dimensional circular cyclone-type microreactor. Chinese Chemical Letters, 2024, 35(4): 108761-. doi: 10.1016/j.cclet.2023.108761
8. [8]
  Shaonan Tian , Yu Zhang , Qing Zeng , Junyu Zhong , Hui Liu , Lin Xu , Jun Yang . Core-shell gold-copper nanoparticles: Evolution of copper shells on gold cores at different gold/copper precursor ratios. Chinese Journal of Structural Chemistry, 2023, 42(11): 100160-100160. doi: 10.1016/j.cjsc.2023.100160
9. [9]
  Caihong Mao , Yanfeng He , Xiaohan Wang , Yan Cai , Xiaobo Hu . Synthesis and molecular recognition characteristics of a tetrapodal benzene cage. Chinese Chemical Letters, 2024, 35(8): 109362-. doi: 10.1016/j.cclet.2023.109362
10. [10]
  Cheng-Da Zhao , Huan Yao , Shi-Yao Li , Fangfang Du , Li-Li Wang , Liu-Pan Yang . Amide naphthotubes: Biomimetic macrocycles for selective molecular recognition. Chinese Chemical Letters, 2024, 35(4): 108879-. doi: 10.1016/j.cclet.2023.108879
11. [11]
  Zhiwei Zhong , Yanbin Huang , Wantai Yang . A simple photochemical method for surface fluorination using perfluoroketones. Chinese Chemical Letters, 2024, 35(5): 109339-. doi: 10.1016/j.cclet.2023.109339
12. [12]
  Yukai Tong , Zhijun Wu , Bo Zhou , Min Hu , Anpei Ye . Surface tension of single suspended aerosol microdroplets. Chinese Chemical Letters, 2024, 35(4): 109062-. doi: 10.1016/j.cclet.2023.109062
13. [13]
  Yu He , Hao Jiang , Shaoxuan Yuan , Jiayi Lu , Qiang Sun . On-surface photo-induced dechlorination. Chinese Chemical Letters, 2024, 35(9): 109807-. doi: 10.1016/j.cclet.2024.109807
14. [14]
  Zhimin Sun , Xin-Hui Guo , Yue Zhao , Qing-Yu Meng , Li-Juan Xing , He-Lue Sun . Dynamically switchable porphyrin-based molecular tweezer for on−off fullerene recognition. Chinese Chemical Letters, 2024, 35(6): 109162-. doi: 10.1016/j.cclet.2023.109162
15. [15]
  Li Lin , Song-Lin Tian , Zhen-Yu Hu , Yu Zhang , Li-Min Chang , Jia-Jun Wang , Wan-Qiang Liu , Qing-Shuang Wang , Fang Wang . Molecular crowding electrolytes for stabilizing Zn metal anode in rechargeable aqueous batteries. Chinese Chemical Letters, 2024, 35(7): 109802-. doi: 10.1016/j.cclet.2024.109802
16. [16]
  Minghao Hu , Tianci Xie , Yuqiang Hu , Longjie Li , Ting Wang , Tongbo Wu . Allosteric DNAzyme-based encoder for molecular information transfer. Chinese Chemical Letters, 2024, 35(7): 109232-. doi: 10.1016/j.cclet.2023.109232
17. [17]
  Chuan-Zhi Ni , Ruo-Ming Li , Fang-Qi Zhang , Qu-Ao-Wei Li , Yuan-Yuan Zhu , Jie Zeng , Shuang-Xi Gu . A chiral fluorescent probe for molecular recognition of basic amino acids in solutions and cells. Chinese Chemical Letters, 2024, 35(10): 109862-. doi: 10.1016/j.cclet.2024.109862
18. [18]
  Luyao Lu , Chen Zhu , Fei Li , Pu Wang , Xi Kang , Yong Pei , Manzhou Zhu . Ligand effects on geometric structures and catalytic activities of atomically precise copper nanoclusters. Chinese Journal of Structural Chemistry, 2024, 43(10): 100411-100411. doi: 10.1016/j.cjsc.2024.100411
19. [19]
  Daheng Wen , Weiwei Fang , Yongmei Liu , Tao Tu . Valorization of carbon dioxide with alcohols. Chinese Chemical Letters, 2024, 35(7): 109394-. doi: 10.1016/j.cclet.2023.109394
20. [20]
  Xianxu Chu , Lu Wang , Junru Li , Hui Xu . Surface chemical microenvironment engineering of catalysts by organic molecules for boosting electrocatalytic reaction. Chinese Chemical Letters, 2024, 35(8): 109105-. doi: 10.1016/j.cclet.2023.109105

Get Citation

PDF

XML

Metrics

PDF Downloads(10)
Abstract views(621)
HTML views(249)

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