Dehydrogenation of aromatic molecules under a scanning tunneling microscope: Pathways and inelastic spectroscopy simulations

Journal of the American Chemical Society

Volumn 129, Issue 14, 2007, Pages 4298-4305

  Lesnard, Hervé ^a   Bocquet, Marie Laure ^a   Lorente, Nicolás ^b  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ PAUL SABATIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; COMPUTER SIMULATION; DEHYDROGENATION; DENSITY FUNCTIONAL THEORY; PYRIDINE; SCANNING TUNNELING MICROSCOPY;

ADIABATIC PATHWAYS; AROMATIC MOLECULES; INELASTIC SPECTROSCOPY SIMULATIONS;

MOLECULAR STRUCTURE;

AROMATIC COMPOUND; BENZENE; BENZENE DERIVATIVE; COPPER; PYRIDINE;

ADSORPTION; ARTICLE; CHEMICAL BOND; COMPARATIVE STUDY; CONFORMATION; DEHYDROGENATION; DENSITY FUNCTIONAL THEORY; REACTION ANALYSIS; SCANNING TUNNELING MICROSCOPY; SIMULATION; SPECTROSCOPY; SURFACE PROPERTY; THEORETICAL STUDY;

EID: 34247123733     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja067442g     Document Type: Article

References (47)

1. Lee, H. J.; Ho, W. Science 1999, 286, 1719-1722.
2. Komeda, T.; Kim, Y.; Kawai, M.; Persson, B. N. J.; Ueba, H. Science 2002, 295, 2055-2058.
3. Pascual, J. I.; Lorente, N.; Song, Z.; Conrad, H.; Rust, H.-P. Nature 2003, 423, 525-528.
4. Sloan, P. A.; Palmer, R. E. Nature 2005, 434, 367-371.
5. Stipe, B. C.; Rezaei, M. A.; Ho, W. Science 1998, 280, 1732-1735.
6. Lauhon, L. J.; Ho, W. Phys. Rev. Lett. 2000, 84, 1527-1530.
7. Lauhon, L. J.; Ho, W. Rev. Sci. Instrum. A 2001, 72, 216-223.
8. Kim, Y.; Komeda, T.; Kawai, M. Phys. Rev. Lett. 2002, 89, 126104.
9. Lorente, N.; Persson, M. Phys. Rev. Lett. 2000, 85, 2997-3000.
10. Lorente, N.; Persson, M.; Lauhon, L. J.; Ho, W. Phys. Rev. Lett. 2001, 86, 2593-2596.
11. Bocquet, M.-L.; Lesnard, H.; Lorente, N. Phys. Rev. Lett. 2006, 96, 096101.
12. Bocquet, M.-L.; Loffreda, D. J. Am. Chem. Soc. 2005, 127, 17207-17215.
13. Lauhon, L. J.; Ho, W. J. Phys. Chem. A 2000, 104, 2463-2467.
14. Komeda, T.; Kim, Y.; Sainoo, Y.; Kawai, M. J. Chem. Phys. 2004, 120, 5347-5352.
15. Lee, J.-G.; Ahner, J.; Yates, J. T. J. Chem. Phys. 2001, 114, 1414-1419.
16. Mate, C.; Somorjai, G.; Tom, H.; Zhu, X.; Shen, Y. J. Chem. Phys. 1988, 88, 441-450.
17. Giessel, T.; Schaff, O.; Lindsay, R.; Baumgärtel, P.; Polcik, M.; Bradshaw, A.; Koebbel, A.; McCabe, T.; Bridge, M.; Lloyd, D. R.; Woodruff, D. P. J. Chem. Phys. 1999, 110, 9666-9672.
18. Dougherty, D.; Lee, J.; Yates, J. J. Phys. Chem. B 2006, 110, 11991-11996.
19. Hahn, J. R.; Ho, W. J. Chem. Phys. 2006, 124, 204708.
20. Weinelt, M.; Wassdahl, N.; Wiell, T.; Karis, O.; Hasselström, J.; Bennich, P.; Nilsson, A.; Stöhr, J.; Samant, M. Phys. Rev. B 1998, 58, 7351-7360.
21. Doering, M.; Rust, H.-P.; Briner, B.; Bradshaw, A. Surf. Sci. 1998, 410, L736-L740.
22. Pascual, J. I.; Jackiw, J.; Song, Z.; Weiss, P.; Conrad, H.; Rust, H.-P. Surf. Sci. 2002, 502-503, 1-6.
23. Bilić, A.; Reimers, J.; Hush, N. J. Phys. Chem. B 2002, 106, 6740-6747.
24. Morin, C.; Simon, D.; Sautet, P. J. Phys. Chem. B 2003, 107, 2995-3002.
25. Kresse, G.; Fürthmuller, J. Comput. Mater. Sci. 1996, 6, 15.
26. Kresse, G.; Joubert, D. Phys. Rev. B 1999, 59, 1758-1775.
27. Henkelman, G.; Uberuaga, B.; Jonsson, H. J. Chem. Phys. 2000, 113, 9901-9904.
28. It should be noted that the pathway minimization procedure is performed at the gamma point only. However, all intermediate or transition states described in the figures result from further geometry optimization with the finer (4 x 4 x 1) k-point grid.
29. A mode frequency is a measure of the curvature of the PES. In the case of an imaginary frequency, the PES has turned from concave to convex revealing the appearance of a saddle point and hence characterizing the TS. The larger the modulus of the imaginary frequency, the steeper the descent along the reaction coordinate.
30. Meng, S.; Wang, E.; Frischkorn, C.; Wolf, M.; Gao, S. Chem. Phys. Lett. 2005, 402, 384-388.
31. Hoffmann, R. Rev. Mod. Phys. 1988, 60, 601-628.
32. Tersoff, J.; Hamman, D. R. Phys. Rev. Lett. 1983, 50, 1998-2001.
33. Lorente, N. Appl. Phys. A 2004, 78, 799-806.
34. Lorente, N.; Hedouin, M. F. G.; Palmer, R. E.; Persson, M. Phys. Rev. B 2003, 68, 155401.
35. Both calculations have been performed in two different implementations of DFT (VASP [ref 25] here, DACAPO [ref 36] in ref 34), and despite performing the calculations in the same numerical conditions there is a sizable energy difference probably stemming from the actual implementation of DFT in each code [ref 36].
36. http://dcwww.fysik.dtu.dk/campos/Dacapo/download.html.
37. In particular the VASP calculations used PAW while the DACAPO ones were performed with ultrasoft pseudopotentials; see ref 26 and references there in.
38. Bilić, A.; Reimers, J. R.; Hush, N. S.; Hoft, R. C.; Ford, M. J. J. Chem. Theory Comput. 2006, 2, 1093-1105.
39. Xi, M.; Yang, M. X.; Jo, S. K.; Bent, B. E.; Stevens, P. J. Chem. Phys. 1994, 101, 9122-9131.
40. Lukes, S.; Vollmex, S.; Witte, G.; Wöll, G. J. Chem. Phys. 2001, 114, 10123-10130.
41. Lomas, J. R.; Baddeley, C. J.; Tikhov, M. S.; Lambert, R. M.; Langmuir 1995, 11, 3048-3053.
42. Wan, L.-J.; Wang, C.; Bai, C.-I.; Osawa, M. J. Phys. Chem. B 2001, 105, 8399-8402.
43. The separating H rather lies in a pseudo-bridge position than in a strict on top position.
44. Loffreda, D.; Delbecq, F.; Vigné, F.; Sautet, P. J. Am. Chem. Soc. 2006, 128, 1316-1323.
45. Erwin, K. M.; DeTuri, V. F. J. Phys.Chem. A 2002, 106, 9947-9956.
46. One word of caution should be said whenever using energy values of the electronic structure obtained from Kohn and Sham orbitals of a DFT calculation: typically electronic energies are undervalued, so the above orbitals are probably further away from the Fermi level than the peaks depicted in Figure 4.
47. Lorente, N.; Rurali, R.; Tang, H. J. Phys.: Condens. Matter 2005, 17, S1049-S1075.