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

doi:10.3866/PKU.WHXB201801151

物理化学学报 >> 2018, Vol. 34 >> Issue (10): 1116-1123.doi: 10.3866/PKU.WHXB201801151

所属专题：材料科学的分子模拟

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

殷迪,邱宗仰,李湃,李震宇*()

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

收稿日期:2017-12-18 发布日期:2018-04-13
通讯作者: 李震宇 E-mail:zyli@mail.ustc.edu.cn
基金资助:
国家自然科学基金(21573201);科学技术部(2016YFA0200604);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)

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

Di YIN,Zongyang QIU,Pai LI,Zhenyu LI*()

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

Received:2017-12-18 Published:2018-04-13
Contact: Zhenyu LI E-mail:zyli@mail.ustc.edu.cn
Supported by:
National Natural Science Foundation of China(21573201);the Ministry of Science and Technology of China(2016YFA0200604);the Special Program for Applied Research on Super Computation of the National Nature Science Foundation of China-Guangdong Joint Fund(U1501501)

摘要/Abstract

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

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: Copper surface, Carbon dimer, DFTB, Molecular simulation

殷迪,邱宗仰,李湃,李震宇. 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[J]. 物理化学学报, 2018, 34(10), 1116-1123. doi: 10.3866/PKU.WHXB201801151

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

链接本文: https://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201801151

https://www.whxb.pku.edu.cn/CN/Y2018/V34/I10/1116

参考文献

1	Tetlow H. ; de Boer J. P. ; Ford I. ; Vvedensky D. ; Coraux J. ; Kantorovich L. Phys. Rep. 2014, 542, 195.
2	Wu P. ; Zhang W. ; Li Z. ; Yang J. Small 2014, 10, 2136.
3	Wu P. ; Zhang Y. ; Cui P. ; Li Z. Y. ; Yang J. L. ; Zhang Z. Y. Phys. Rev. Lett. 2015, 114, 216102.
4	Li P. ; Li Z. ; Yang J. J. Phys. Chem. C 2017, 121, 25949.
5	Wu P. ; Zhang W. ; Li Z. ; Yang J. ; Hou J. G. J. Chem. Phys. 2010, 133, 071101.
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.
7	Henkelman G. ; Uberuaga B. P. ; Jónsson H. J. Chem. Phys. 2000, 113, 9901.
8	Elstner M. ; Porezag D. ; Jungnickel G. ; Elsner J. ; Haugk M. ; Frauenheim T. ; Suhai S. ; Seifert G. Phys. Rev. B 1998, 58, 7260.
9	Frauenheim T. ; Seifert G. ; Elstner M. ; Hajnal Z. ; Jungnickel G. ; Porezag D. ; Suhai S. ; Scholz R. Phys. Stat. Sol. (b) 2000, 217, 41.
10	Porezag D. ; Frauenheim T. ; Kohler T. ; Seifert G. ; Kaschner R. Phys. Rev. B 1995, 51, 12947.
11	Elstner M. ; Frauenheim T. ; Kaxiras E. ; Seifert G. ; Suhai S. Phys. Stat. Sol. (b) 2000, 217, 357.
12	Elstner M. Theor. Chem. Acc. 2006, 116, 316.
13	Page A. J. ; Ohta Y. ; Irle S. ; Morokuma K. Acc. Chem. Res. 2010, 43, 1375.
14	Wang Y. ; Page A. J. ; Nishimoto Y. ; Qian H. -J. ; Morokuma K. ; Irle S. J. Am. Chem. Soc. 2011, 133, 18837.
15	Li H. -B. ; Page A. J. ; Wang Y. ; Irle S. ; Morokuma K. Chem. Comm. 2012, 48, 7937.
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.
17	Oliveira A. F. ; Philipsen P. ; Heine T. J. Chem. Theory Compt. 2015, 11, 5209.
18	Slater-Koster files containing atomic parameters used in DFTB calculations. http://www.dftb.org/parameters/ (accessed Dec 1, 2017)
19	Frenzel J. ; Oliveira A. F. ; Duarte H. A. ; Heine T. ; Seifert G. Z. Anorg. Allg. Chem. 2005, 631, 1267.
20	Guimaraes L. ; Enyashin A. N. ; Frenzel J. ; Heine T. ; Duarte H. A. ; Seifert G. ACS Nano 2007, 1, 362.
21	Koskinen P. ; Makinen V. Comput. Mater. Sci. 2009, 47, 237.
22	Slater J. C. ; Koster G. F. Phys. Rev. 1954, 94, 1498.
23	Gaus M. ; Cui Q. A. ; Elstner M. J. Chem. Theory Compt. 2011, 7, 931.
24	Grundk tter-Stock B. ; Bezugly V. ; Kunstmann J. ; Cuniberti G. ; Frauenheim T. ; Niehaus T. A. J. Chem. Theory Compt. 2012, 8, 1153.
25	Gaus M. ; Chou C. -P. ; Witek H. ; Elstner M. J. Phys. Chem. A 2009, 113, 11866.
26	Bodrog Z. ; Aradi B. ; Frauenheim T. J. Chem. Theory Compt. 2011, 7, 2654.
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.
28	Thomas F. ; Gotthard S. ; Marcus E. ; Thomas N. ; Christof K. ; Marc A. ; Michael S. ; Zoltán H. ; Aldo Di, C. ; Di C. ; Sándor S. J. Phys.: Condens. Matter 2002, 14, 3015.
29	Aradi B. ; Hourahine B. ; Frauenheim T. J. Phys. Chem. A 2007, 111, 5678.
30	Kresse G. ; Furthmuller J. Comput. Mater. Sci. 1996, 6, 15.
31	Kresse G. ; Furthmuller J. Phys. Rev. B 1996, 54, 11169.
32	Perdew J. P. ; Burke K. ; Ernzerhof M. Phys. Rev. Lett. 1996, 77, 3865.
33	Knaup J. M. ; Hourahine B. ; Frauenheim T. J. Phys. Chem. A 2007, 111, 5637.
34	Burdick G. A. Phys. Rev. 1963, 129, 138.
35	Shin H. ; Kang S. ; Koo J. ; Lee H. ; Kim J. ; Kwon Y. J. Chem. Phys. 2014, 140, 114702.
36	Van Wesep R. G. ; Chen H. ; Zhu W. ; Zhang Z. J. Chem. Phys. 2011, 134, 171105.
37	Laio A. ; Parrinello M. Proc. Natl. Acad. Sci. USA 2002, 99, 12562.

[1]	吴选军,李磊,彭亮,王叶彤,蔡卫权. 嵌入配位不饱和金属位对多孔芳香骨架材料储氢性能的影响[J]. 物理化学学报, 2018, 34(3): 286 -295 .
[2]	李爱静,谢炜,王明,徐四川. 多巴胺在其第三受体蛋白结构中的分子通道上传输动力学[J]. 物理化学学报, 2017, 33(5): 927 -940 .
[3]	王漪,贾南方,齐胜利,田国峰,武德珍. 1, 8-萘酰亚胺衍生物的合成、表征及电存储性能[J]. 物理化学学报, 2017, 33(11): 2227 -2236 .
[4]	刘晓龙,李晓霞,韩嵩,乔显杰,钟北京,郭力. RP-3高温氧化初始阶段反应机理的ReaxFF MD模拟[J]. 物理化学学报, 2016, 32(6): 1424 -1433 .
[5]	崔大超,任卫同,李文飞,王炜. 腺苷酸激酶催化循环后期Mg²⁺转移的分子动力学模拟[J]. 物理化学学报, 2016, 32(2): 429 -435 .
[6]	徐诗文,林东强,姚善泾. 布洛芬与人血白蛋白位点II动态结合过程的分子模拟:一种结合途径分析[J]. 物理化学学报, 2016, 32(11): 2811 -2818 .
[7]	鲁相,陈循,汪亚顺,谭源源,高木子源. 气体在无定型聚异戊二烯中扩散的分子动力学模拟[J]. 物理化学学报, 2016, 32(10): 2523 -2530 .
[8]	赵梦尧,杨雪平,杨晓宁. 石墨烯狭缝受限孔道中水分子的分子动力学模拟[J]. 物理化学学报, 2015, 31(8): 1489 -1498 .
[9]	吴选军, 赵鹏, 方继敏, 王杰, 刘保顺, 蔡卫权. 新型掺杂多孔芳香骨架材料的储氢性能模拟[J]. 物理化学学报, 2014, 30(11): 2043 -2054 .
[10]	何文英, 姚小军, 华英杰, 黄国雷, 吴秀丽, 李小宝, 韩长日, 宋小平. 考拉维酸对人血清白蛋白结构的影响[J]. 物理化学学报, 2014, 30(11): 2142 -2148 .
[11]	卞富永, 张继伟, 王丹, 徐四川. 甲基多巴透过POPC磷脂双层膜过程的分子动力学模拟[J]. 物理化学学报, 2014, 30(10): 1947 -1956 .
[12]	刘媛, 龙梅, 谢孟峡. 白杨素与不同构型人血清白蛋白的作用机制[J]. 物理化学学报, 2013, 29(12): 2647 -2654 .
[13]	黄永棋, 康雪, 夏斌, 刘志荣. M^pro-C蛋白三维结构域交换的机理: 来自分子模拟的线索[J]. 物理化学学报, 2012, 28(10): 2411 -2417 .
[14]	梅拥军, 韩一秀, 周洪, 姚林, 江波. 疏水缔合聚丙烯酸与蠕虫状胶束的协同作用[J]. 物理化学学报, 2012, 28(07): 1751 -1756 .
[15]	孙德林, 周健. 耗散粒子动力学模拟Nafion膜和PVA/Nafion共混膜的介观结构[J]. 物理化学学报, 2012, 28(04): 909 -916 .

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

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

RichHTML

PDF

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

Metrics

推荐阅读 0