Diffusion of 1,4-butanedithiol onAu(100)−(1×1): A DFT-based master-equation approach

Abstract

The functionalization of metal surfaces via thiol-bonded molecules and the assembly of nanodevices on the surfaces should profit from a detailed atomistic understanding of the binding and diffusion properties. These differ substantially from the in-depth investigated situation of single adatoms. We report density-functional calculations for the elementary diffusion steps of 1,4-butanedithiol radicals ͑BDTRs͒ adsorbed on a Au͑100͒-͑1 ϫ 1͒ surface. The elementary diffusion steps are then combined into a description of the diffusion mechanism on long-time scales by integrating a master equation. The two S-Au bonds cause a multivalley potential-energy surface, which implies a complex diffusion mechanism. We identify the effect of the geometry constraints imposed by the ͑CH 2 ͒ 4 backbone on binding and diffusion. To this purpose we compare to the diffusion of a single SCH 3 radical on the same Au͑100͒-͑1 ϫ 1͒ surface. Altogether, the motion of the BDTR is walkinglike with the S-atoms crossing bridge sites of the Au surface one after the other. The lowest density-functional theory-Perdew and Wang 91 energy barrier for translation is 0.35 eV while the energy barrier for rotation comes out larger, 0.43 eV. As a result of this difference there will be correlations between subsequent diffusive displacements of the molecule. The isotropic diffusion constant on long-time scales is computed and the numerical results follow an Arrhenius law.

The Role of a Double Molecular Anchor on the Mobility and Self‐Assembly of Thiols on Au(111): The Case of Mercaptobenzoic Acid

“…STM and electrochemical data reveal that the surfacec overage of 2-MBA on Au(111)i sn either time-nor concentration-dependent, in contrastt ow hat occurs for 4-MBA, which presents ap hase transition from the (4 p 3) structure (q = 0.25, a = 468)t oac (4 2) lattice (q = 0.33, a = 308) [16,21] The most direct way to accomplisht his task is by hopping the Au atom between these sites. [32,33,34] The optimized geometries in each site are very similarina ll cases but it is important to outline that the sulfur atom in sites 2a nd 3a re ; that is, av alue that is highert han for aromatic thiols bearingo nly the thiolate anchort og old, which exhibit small activation energies for translation (0.15-0.19 eV).…”

Extending first principle plasma-surface simulations to experimentally relevant scales

“…Another approach developed by the present authors [30,31] uses a selective acceleration of some relevant processes and also achieved speed-ups exceeding a factor 10 9 . Another direction of developments does not aim at accelerating the ab initio simulations but to extend them to longer times by a suitable combination with analytical models [32,33]. These methods will be called below Dynamical freeze out of dominant modes (DFDM).…”

“…Franke and Pehlke performed extensive density functional theory (DFT) simulations of the diffusion of a 1,4butaneditiol molecule on a gold surface [33]. They found the local adsorption energy minima of the molecule and then applied the nudged elastic band (NEB) approach [49] to compute the transition rates between them.…”

“…Here, we are not concerned with the details of the associated diffusion hops, Ref. [33]-but focus on the coarse graining idea.…”

“…Here, ∆E a→b is the energy barrier for the transition between states a and b which is computed using DFT, and ν 0 is the attempt frequency which is of the order of 10 12 s −1 [33]. The authors of this reference consider two stages of the evolution: the initial stage, corresponding to stage I in table 1, and the asymptotic hydrodynamic state, corresponding to stage III.…”