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 s ensitivity infrared reflection spectroscopy (IRS) measurements have been co mbined to characterize the structures of mixed self-assembled monolayers (S AMs) of fully conjugated, linear thiolate-terminated molecules and short ch ain (8-12) fl-alkanethiolates on Au{111}. Immersion of preformed, ordered a lkanethiolate SAMs into dilute solutions of the conjugated molecules result s in two-dimensional matrix isolation of conjugated adsorbates in the host SAM. The post-immersion host SAM matrix shows retained alkanethiolate order ing with the guest molecules inserted both singly into boundaries between S AM structural domains and in bundles at substrate step edges. Inserted mole cules of lengths in the similar to 15 Angstrom range adopt surface orientat ions similar to those of alkanethiolate molecules at all compositions, incl uding the pure conjugated SAMs. In contrast, the configuration of an insert ed, 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 de creases and approaches alignment with the host SAM. Combined quantum chemic al calculations and IRS data for the short guest-host SAMs support a pictur e of a dense local environment of the host SAM around the guest molecules, despite their insertion at host defects. These results have important impli cations for designing electronic devices based on the addressing of individ ual, fully conjugated molecules self-assembled at gold electrodes.