Combined scanning tunneling microscopy and infrared spectroscopic characterization of mixed surface assemblies of linear conjugated guest molecules in host alkanethiolate monolayers on gold

Molecular resolution scanning tunneling microscopy (STM) imaging and high sensitivity infrared reflection spectroscopy (IRS) measurements have been combined to characterize the structures of mixed self-assembled monolayers (SAMs) of fully conjugated, linear thiolate-terminated molecules and short chain (8-12) fl-alkanethiolates on Au{111}. Immersion of preformed, ordered alkanethiolate SAMs into dilute solutions of the conjugated molecules results in two-dimensional matrix isolation of conjugated adsorbates in the host SAM. The post-immersion host SAM matrix shows retained alkanethiolate ordering with the guest molecules inserted both singly into boundaries between SAM structural domains and in bundles at substrate step edges. Inserted molecules of lengths in the similar to 15 Angstrom range adopt surface orientations similar to those of alkanethiolate molecules at all compositions, including the pure conjugated SAMs. In contrast, the configuration of an inserted, long conjugated molecule (similar to 40 Angstrom), varies monotonically with the final SAM composition. When inserted at decreasing fractions into an n-octanethiolate matrix, the average tilt of the long molecular axis decreases and approaches alignment with the host SAM. Combined quantum chemical calculations and IRS data for the short guest-host SAMs support a picture of a dense local environment of the host SAM around the guest molecules, despite their insertion at host defects. These results have important implications for designing electronic devices based on the addressing of individual, fully conjugated molecules self-assembled at gold electrodes.