Gold Mining by Alkanethiol Radicals: Vacancies and Pits in the Self-Assembled Monolayers of 1-Propanethiol and 1-Butanethiol on Au(111)

Scanning-tunneling microscopy (STM) under electrochemical control (in situ STM) in aqueous solution, combined with a priori density functional theory (DFT) image simulations at room temperature, reveals the atomic nature of the interface between Au(111) and self-assembled monolayers (SAMs) of 1-propanethiol and 1-butanethiol. Use of single-crystal gold substrates allows for both high-resolution images of the surface cell internal structure and the evaluation of pit densities on large surface terraces, while room-temperature STM image simulations facilitate discrimination between possible atomic interface structures. For both adsorbates, the high. coverage c(4 x 2) phase is identified as (3 x 2 root 3)-4, while the medium-coverage striped phase of 1-propanethiol SAMs is identified as (7 x root 3)-4. All of these structures contain two adatom-bound adsorbates of the form RS-Au-SR (R=CnH2n+1S center dot) per surface unit cell. The observed pit coverages of 2.8-4.0% are much less than those typically found for methanethiol SAMs (ca. 12-20%), indicating that one of the two gold adatoms per cell in 1-propanethiol and 1-butanethiol SAMs is extracted to form a local surface vacancy rather than a coalesced surface pit. The surface vacancy appears free to diffuse within each cell on the STM time scale, with only small STM image changes associated with vacancy localization. Significantly, the c(4 x 2) phases of 1-propanethiol and 1-butanethiol SAMs give quite different STM images. 1-Butanethiol SAMs show characteristics similar to those of longer linear alkanethiols with four bright spots per cell, while the 1-propanethiol SAM displays five bright spots organized in a different pattern. These differences are rationalized by a more uniform vacancy distribution and rigid structure for 1-butanethiol SAMs, compared to the different diffusionally labile vacancy configurations and higher lateral S-C-C-C conformational flexibility found for 1-propanethiol. Also, the differences in interface structure from that of methanethiol SAMs are rationalized in terms of varying pit coalescence energies. These subtle differences underline the striking diversity in the electronic and molecular structural packing even within a single class of closely related molecular adsorbates.