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

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

采用优化的DFTB参数对铜(111)表面碳二聚化的分子动力学研究

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中国科学技术大学合肥微尺度物质科学国家研究中心，合肥 230026

通讯作者: 李震宇, zyli@mail.ustc.edu.cn

基金项目:
国家自然科学基金-广东联合基金(第二期)超级计算科学应用研究专项 U1501501

国家自然科学基金(21573201), 科学技术部(2016YFA0200604)及国家自然科学基金-广东联合基金(第二期)超级计算科学应用研究专项(U1501501)资助

科学技术部 2016YFA0200604

国家自然科学基金 21573201

摘要: 针对铜表面化学反应，我们发展了一套铜-碳体系的密度泛函紧束缚(DFTB)参数。测试结果表明这套参数可以很好的描述吸附铜或碳原子前后铜表面的几何结构和能量。基于这套参数，我们对Cu(111)表面的碳二聚化过程进行了分子模拟研究。即使在高温下，直接的分子动力学模拟也很难观察到碳二聚体的形成。这是因为高温下铜表面显著的结构弛豫一定程度上阻止了二聚化。为了研究高温下铜表面碳二聚化的机理，我们进行了赝动力学模拟。发现在二聚化的过程中，碳原子形成C-Cu-C桥状结构以后，会绕中间Cu原子转动，最后形成碳二聚体。1300 K下碳二聚化的自由能垒约0.9 eV。

关键词:

铜表面
/ 碳二聚体
/ DFTB
/ 分子模拟

English

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
Accepted Date: 11 January 2018
Revised Date: 11 January 2018
Available Online: 15 October 2018
Fund Project:

The 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)

Abstract: 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.

Key words:

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
2. [2]
  Wu, P.; Zhang, W.; Li, Z.; Yang, J. Small 2014, 10, 2136. 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
4. [4]
  Li, P.; Li, Z.; Yang, J. J. Phys. Chem. C 2017, 121, 25949. 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
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
7. [7]
  Henkelman, G.; Uberuaga, B. P.; Jónsson, H. J. Chem. Phys. 2000, 113, 9901. 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
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
10. [10]
  Porezag, D.; Frauenheim, T.; Kohler, T.; Seifert, G.; Kaschner, R. Phys. Rev. B 1995, 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
12. [12]
  Elstner, M. Theor. Chem. Acc. 2006, 116, 316. 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
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
15. [15]
  Li, H. -B.; Page, A. J.; Wang, Y.; Irle, S.; Morokuma, K. Chem. Comm. 2012, 48, 7937. 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
17. [17]
  Oliveira, A. F.; Philipsen, P.; Heine, T. J. Chem. Theory Compt. 2015, 11, 5209. 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
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
21. [21]
  Koskinen, P.; Makinen, V. Comput. Mater. Sci. 2009, 47, 237. 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
23. [23]
  Gaus, M.; Cui, Q. A.; Elstner, M. J. Chem. Theory Compt. 2011, 7, 931. 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
25. [25]
  Gaus, M.; Chou, C. -P.; Witek, H.; Elstner, M. J. Phys. Chem. A 2009, 113, 11866. doi: 10.1021/jp902973m
26. [26]
  Bodrog, Z.; Aradi, B.; Frauenheim, T. J. Chem. Theory Compt. 2011, 7, 2654. 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
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
29. [29]
  Aradi, B.; Hourahine, B.; Frauenheim, T. J. Phys. Chem. A 2007, 111, 5678. doi: 10.1021/jp070186p
30. [30]
  Kresse, G.; Furthmuller, J. Comput. Mater. Sci. 1996, 6, 15. 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
32. [32]
  Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 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
34. [34]
  Burdick, G. A. Phys. Rev. 1963, 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
36. [36]
  Van Wesep, R. G.; Chen, H.; Zhu, W.; Zhang, Z. J. Chem. Phys. 2011, 134, 171105. doi: 10.1063/1.3587239
37. [37]
  Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2002, 99, 12562. doi: 10.1073/pnas.202427399

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1.
沈阳化工大学材料科学与工程学院沈阳 110142

采用优化的DFTB参数对铜(111)表面碳二聚化的分子动力学研究

通讯作者: 李震宇, zyli@mail.ustc.edu.cn

English

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

Corresponding author: LI Zhenyu, zyli@mail.ustc.edu.cn

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通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

采用优化的DFTB参数对铜(111)表面碳二聚化的分子动力学研究

通讯作者: 李震宇, zyli@mail.ustc.edu.cn

English

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

Corresponding author: LI Zhenyu, zyli@mail.ustc.edu.cn

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

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