A Molecular Dynamics Study of the Role of Adatoms in SAMs of Methylthiolate on Au(111): A New Force Field Parameterized from Ab Initio Calculations

Abstract

Starting from ab initio calculations and using a force matching procedure, we have developed a new force field for molecular dynamics simulations of self-assembled monolayers of methylthiolate (MT) on Au(111) surfaces. This new force field is able to reproduce several observed features of SAMs of MT on Au(111) surface, such as the formation of gold vacancy islands and the (√3 × √3)R30 lattice. We have studied the dynamics of Au adatoms and monatomic vacancies on the Au(111) surface for the SAM of MT at room temperature. It is observed that monatomic vacancies coarsen to form large vacancy islands while the adatoms group to form clusters. Both results are in agreement with experiments. At elevated temperatures, Au adatoms that are lifted from the surface leave an atomic vacancy on it. The liquid-like diffusion of gold adatoms on the SAM surface occurs by hopping between pairs of methylthiolate to which the adatom is temporarily bound. Our findings indicate that structural models of the c(4 × 2) unit cell including adatoms and vacancies at room temperature need to be revisited.

Atomistic Simulations of Self-Assembled Monolayers on Octahedral and Cubic Gold Nanocrystals

“…We have tested two other interaction models proposed in the literature 19,41 . The models by Pool et al 43 yields the best average surface per thiol for Au(100) and Au(111) …”

“…These ligands form compact monolayers on the nanocrystal surface. These self-assembled monolayers (SAM) have been widely studied on flat gold surfaces in the literature [15][16][17][18][19][20] . On Au(111) thiolate headgroups form hexagonal overlayer structures, while on Au(100) a complex distorted hexagonal order denoted by c(2x8) is observed 21 .…”

A van der Waals DFT study of chain length dependence of alkanethiol adsorption on Au(111): physisorption vs. chemisorption

“…Hence, a very large number of experimental and theoretical studies have been carried out to clarify this issue most of which were addressing the questions of where the sulfur atom binds on the Au(111) surface and what are the factors that drive the formation of c(4×2) superlattice. 3,4,8,9,25,26 To this end early computational studies focused on C1 SAMs to determine sulfur binding site since it requires the minimum computational power. 8,25 However, as mentioned above, the chain-chain interactions has a significant effect in the film structure and computational results obtained for C1 SAMs cannot directly be extended to longer chain thiols.…”

Computer simulation and analysis of self-assembled alkylthiol monolayers on the surface of liquid mercury

“…As the reader shall see in Chap. 4, the number of Hg atoms that one has to simulate in this case appears to be exceedingly large, ∼ 3 × 10 5 , compared to several thousands of Au atoms, which were allowed to move in a few computer studies of SAMs on Au [32,37,42,43]. This is necessary in order to account for the pronounced surface layering of liquid mercury (as explained in Chap.…”

“…Computer simulation studies of the self-assembled alkylthiol monolayers on metals [28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] focus on the SAMs on crystalline surfaces (mostly Au) as well. Moreover, in the vast majority of the simulations only the structure of the densely packed monolayers of thiols standing tilted to the surface normal (i.e.…”