Effect of conformational symmetry upon the formation of cysteine clusters on the Au(110)-(1 × 1) Surface: A first-principles study

Journal of Physical Chemistry C

Volumn 117, Issue 39, 2013, Pages 20351-20360

  Buimaga Iarinca, Luiza ^a   Morari, Cristian ^a  

^a NATIONAL INSTITUTE FOR RESEARCH AND DEVELOPMENT OF ISOTOPIC AND MOLECULAR TECHNOLOGIES   (Romania)

Author keywords

[No Author keywords available]

Indexed keywords

FIRST-PRINCIPLES STUDY; GEOMETRICAL MODELS; GOLD SURFACES; LONG CHAINS; NUCLEATION CENTER; PHYSICOCHEMICAL PROPERTY; RELATIVE POSITIONS; ROTATIONAL CONFORMERS;

NUCLEATION;

AMINO ACIDS;

EID: 84885133089     PISSN: 19327447     EISSN: 19327455     Source Type: Journal    
DOI: 10.1021/jp4072857     Document Type: Article

References (42)

1. Smith, R. K.; Lewis, P. A.; Weiss, P. S. Patterning Self-Assembled Monolayers Prog. Surf. Sci. 2004, 75, 1-68
2. Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M. Self-Assembled Monolayers of Thiolates on Metals as a Form of Nanotechnology Chem. Rev. 2005, 105, 1103-1169
3. Whitesides, G. M.; Kriebel, J. K.; Love, J. C. Molecular Engineering of Surfaces Using Self-Assembled Monolayers Sci. Prog. 2005, 88, 17-48
4. Ulman, A., Ed., Self-Assembled Monolayers of Thiols. Thin Films; Academic Press: San Diego, 1998; Vol. 24.
5. Nilsson, A.; Pettersson, L. G. M. Chemical Bonding on Surfaces Probed by X-ray Emission Spectroscopy and Density Functional Theory Surf. Sci. Rep. 2004, 55, 49-167
6. Ishii, H.; Sugiyama, K.; Eisuke, I.; Seki, K. Energy Level Alignment and Interfacial Electronic Structures at Organic/Metal and Organic/Organic Interfaces Adv. Mater. (Weinheim, Ger.) 1999, 11, 605-625
7. Heimel, G.; Romaner, L.; Brédas, J.-L.; Zojer, E. Band Lineup and Interface Energetics at Covalent Metal-Molecule Junctions: π-Conjugated Thiols on Gold Phys. Rev. Lett. 2006, 96, 196806
8. De Renzi, V.; Rousseau, R.; Marchetto, D.; Biagi, R.; Scandolo, S.; del Pennino, U. Metal Work-Function Changes Induced by Organic Adsorbates: a Combined Experimental and Theoretical Study Phys. Rev. Lett. 2005, 95, 046804
9. Rauls, E.; Blankenburg, S.; Schmidt, W. G. DFT Calculations of Adenine Adsorption on Coin Metal (110) Surfaces Surf. Sci. 2008, 602, 2170-2176
10. 3 Chem. Phys. 2002, 116, 10277-10286
11. Morari, C.; Rignanese, G. M.; Melinte, S. Electronic Properties of 1-4,dicyanobenze and 1-4,diisocyanidebenzen Molecules Contacted Between Two Platinum and Palladium Electrodes: A First-Principles Study Phys. Rev. B 2007, 76, 115428
12. Xue, Y.; Datta, S.; Ratner, M. A. Charge Transfer and Band Lineup in Molecular Electronic Devices: A Chemical and Numerical Interpretation J. Chem. Phys. 2001, 115, 4292-4300
13. Tonigold, K.; Gross, A. Adsorption of Small Aromatic Molecules on the (111) Surfaces of Noble Metals: A Density Functional Theory Study with Semiempirical Corrections for Dispersion Effects J. Chem. Phys. 2010, 132, 224701-224711
14. Kühnle, A.; Linderoth, T. R.; Besenbacher, F. Enantiospecific Adsorption of Cysteine at Chiral Kink Sites on Au(110)-(1 × 2) J. Am. Chem. Soc. 2006, 128, 1076-1077
15. Kühnle, A.; Linderoth, T. R.; Schunack, M.; Besenbacher, F. L-Cysteine Adsorption Structures on Au(111) Investigated by Scanning Tunneling Microscopy Under Ultra-High Vacuum Conditions Langmuir 2006, 22, 2156-2160
16. Mirkin, C. A; Letsinger, R. L.; Mucic, R. C.; Storhoff, J. J. A DNA-Based Method for Rationally Assembling Nanoparticles into Macroscopic Materials Nature (London) 1996, 382, 607-609
17. Plekan, O.; Feyer, V.; Ptasińska, S.; Tsud, N.; Cháb, V.; Matolín, V.; Prince, K. C. Photoemission Study of Thymidine Adsorbed on Au(111) and Cu(110) J. Phys. Chem. C 2010, 114, 15036-15041
18. Feyer, V.; Plekan, O.; Prince, K. C.; SÌutara, F.; Skála, T.; Cháb, V.; Matolín, V.; Stenuit, G.; Umari, P. Bonding at the organic/metal interface: Adenine to Cu(110) Phys. Rev. B 2009, 79, 155432
19. Kühnle, A.; Linderoth, T. R.; Hammer, B.; Besenbacher, F. Chiral Recognition in Dimerization of Adsorbed Cysteine Observed by Scanning Tunnelling Microscopy Nature (London) 2002, 415, 891-893
20. Kühnle, A.; Molina, L. M.; Linderoth, T. R.; Hammer, B.; Besenbacher, F. Growth of Unidirectional Molecular Rows of Cysteine on Au(110)-(1 × 2) Driven by Adsorbate-Induced Surface Rearrangements Phys. Rev. Lett. 2004, 93, 086101
21. Kühnle, A.; Linderoth, T. R.; Besenbacher, F. Self-Assembly of Monodispersed, Chiral Nanoclusters of Cysteine on the Au(110)-(1 × 2) Surface J. Am. Chem. Soc. 2003, 125, 14680-14681
22. Greber, T.; ŠljivancÌanin, Ž.; Schillinger, R.; Wider, J.; Hammer, B. Chiral Recognition of Organic Molecules by Atomic Kinks on Surfaces Phys. Rev. Lett. 2006, 96, 056103
23. Schillinger, R.; ŠljivancÌanin, Ž.; Hammer, B.; Greber, T. Probing Enantioselectivity with X-Ray Photoelectron Spectroscopy and Density Functional Theory Phys. Rev. Lett. 2007, 98, 136102
24. ŠljivancÌanin, Ž.; Gothelf, K.; Hammer, B. Density Functional Theory Study of Enantiospecific Adsorption at Chiral Surfaces J. Am. Chem. Soc. 2002, 124, 14789-14794
25. Di Felice, R.; Selloni, A.; Molinari, E. DFT Study of Cysteine Adsorption on Au(111) J. Phys. Chem. B 2003, 107, 1151-1156
26. Di Felice, R.; Selloni, A. Adsorption modes of cysteine on Au(111): thiolate, amino-thiolate, disulfide J. Chem. Phys. 2004, 120, 4906-4914
27. Höffling, B.; Ortmann, F.; Hannewald, K.; Bechstedt, F. Single Cysteine Adsorption on Au(110): A First-Principles Study Phys. Rev. B 2010, 81, 045407
28. Buimaga-Iarinca, L.; Calborean, A. Electronic Structure of the ll-Cysteine Dimers Adsorbed on Au(111): A Density Functional Theory Study Phys. Scr. 2012, 86, 035707
29. Wilke, J. J.; Lind, M. C.; Schaefer, H. F., III; Csaszar, A. G.; Allen, W. D. Conformers of Gaseous Cysteine J. Chem. Theory Comput. 2009, 5, 1511-1523
30. Graff, M.; Bukowska, J. Adsorption of Enantiomeric and Racemic Cysteine on a Silver Electrode-SERS Sensitivity to Chirality of Adsorbed Molecules J. Phys. Chem. B 2005, 109, 9567-9574
31. Ordejón, P.; Artacho, E.; Soler, J. M. Self-Consistent Order-N Density-Functional Calculations for Very Large Systems Phys. Rev. B 1996, 53, R10441-R10444
32. Soler, J. M.; Artacho, E.; Gale, J. D.; García, A.; Junquera, J.; Ordejón, P.; Sánchez-Portal, D. The Siesta Method for Ab Initio Order-N Materials Simulation J. Phys.: Condens. Matter 2002, 14, 2745-2779
33. 60 Phys. Rev. B 1992, 46, 1754-1765
34. Sankey, O. F.; Niklewski, D. J. Ab-initio Multicenter Tight-binding Model for Molecular-Dynamics Simulations and Other Applications in Covalent Systems Phys. Rev. B 1989, 40, 3979-3995
35. Huzinaga, S., Ed. Gaussian Basis Sets for Molecular Calculations; Elsevier: Berlin, 1984.
36. Bachelet, G. B.; Hamann, D. R.; Schluter, M. Pseudopotentials That Work: From H to Pu Phys. Rev. B 1982, 26, 4199-4228
37. Hammer, B.; Hansen, L. B.; Nø rskov, J. K. Improved Adsorption Energetics Within Density-Functional Theory Using Revised Perdew-Burke-Ernzerhof Functionals Phys. Rev. B 1999, 59, 7413-7421
38. Krüger, D.; Fuchs, H.; Rousseau, R.; Marx, D.; Parrinello, M. Pulling Monatomic Gold Wires with Single Molecules: An Ab Initio Simulation Phys. Rev. Lett. 2002, 89, 186402
39. Buimaga-Iarinca, L.; Morari, C. Adsorption of Cysteine Clusters on Au(110)-(1 × 1) Surface: A DFT Study RSC Adv. 2013, 3, 5036-5044
40. Bogdan, D.; Morari, C. Electronic Properties of DNA Nucleosides Adsorbed on a Au(100) Surface J. Phys. Chem. C 2012, 116, 7351-7359
41. n (n = 1, 2, 4) Organometallics 1996, 15, 2923-2931
42. Hirshfeld, F. L. Bonded-Atom Fragments for Describing Molecular Charge Densities Theor. Chim. Acta 1977, 44, 129-138