An Effective Pseudopotential for Modeling Gold Surface Slabs for Ab Initio Simulations

Abstract

Dedicated to Professor Michele Parrinello on the occasion of his 60th birthday.Self-assembled monolayers (SAMs) of sulfur-containing organic molecules on bulk gold surfaces are among some of the currently most-studied molecule/metal interfaces, with potential applications ranging from nanolithography [1] and molecular electronics [2] to biosensors. [3] As such, there has been an intense effort on the part of the atomistic-simulations community to model the structures, energetics and spectroscopic properties of these materials. [4][5][6][7][8][9][10][11][12] However, there is still much debate in the literature regarding the nature of the thiolatemetal interaction [13] as well as the nature of the adsorption sites of the thiols [14,15] and possible low-temperature superstructures.[16] With the notable exception of ref.[17], where ab initio molecular dynamics (AIMD) simulations have been performed to model the pulling of a single thiolate from a Au surface, there has been little attention paid to the role of finitetemperature effects in these materials by the ab initio electronic-structure community. This is despite the fact that gold is known to be a very dynamical element that exhibits exceptional diffusivity and mobility. Though it is possible to model the dynamical behavior of Au via effective interatomic potentials, [18] there currently is no reliable interatomic potential to model the molecule-metal interaction. In principle, AIMD would be a valuable tool to address these issues, but its applicability is severely limited by its computational cost, both in terms of the required large system sizes [7] and simulation times. Specifically, the modeling of a bulk Au surface requires slab models of 4-6 atomic layers in thickness [9] with each Au atom having a minimal number of 11 e À . As a result even a simple calculation providing the equivalent surface area to adsorb only four thiolate molecules requires around 600-1000 valence electrons. The current article is aimed at addressing this issue by employing an effective 1 e À valence-electron pseudopotential to emulate the behavior of the bulk gold substrate. The idea follows from the consideration that d electrons [a] Prof.

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

“…The adsorption energy with respect to the clean Au(111) surface, and the geometries of various relaxed structures are tabulated in Table . The results obtained for the hollow, bridge and ontop sites compare very well with previous DFT results at finite electronic temperature. ,, …”

“…The results obtained for the hollow, bridge and ontop sites compare very well with previous DFT results at finite electronic temperature. 20,54,55 When adatoms or vacancies are included on the surface, there is an increase of the adsorption energy. Our force field does not reproduce the energetic stability of the MT−Au−MT motif found in other studies.…”

Structure of aCH3SMonolayer on Au(111) Solved by the Interplay between Molecular Dynamics Calculations and Diffraction Measurements

“…Car-Parrinello MD simulations [22] were conducted, using the CPMD code [23], to generate 10 ps trajectories after 4 ps of equilibration; Nosé-Hoover thermostat chains on both electrons and nuclei are employed to enforce adiabaticity; see Ref. [24] for an evaluation. All reported trajectories were performed in a 2 2 supercell of the 3 p 3 p R30 structure, modeled as a 4 Au atom layer slab with a 10 Å vacuum layer, and the ÿ point for Brillouin zone sampling.…”

Molecular Dynamics Description of Grafted Monolayers: Effect of the Surface Coverage

“…Following the pioneering work of Klein’s group, − a number of simulations employed force field to explore the structure and dynamics of SAMs. However, the majority of the work was limited to the study of alkanethiols of different tail groups, self-assembled on the Au(III) surface in the presence of water. − Several molecular dynamics and Monte Carlo computer simulation studies of carboxylic acid-functionalized SAMs − and of oligo(ethylene oxide) or poly(ethylene oxide) SAMs have recently been reported. , However, few theoretical chemical studies of monolayers on others surfaces than gold have been reported, − and none of them has focused on negatively charged monolayers of chelating metal compounds immobilized onto the graphite surface via the tetradentate NTA acid (Figure ).…”