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
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