The structure and growth of two classes of self-assembled monolayers (SAMs) on Au(111) derived from the adsorption of the functionalized thiol hexyl-azobenzenethiol (12-(4-(4-hexylphenylazo)phenoxy)dodecane-1-thiol) and the partially fluorinated alkanethiols (CF3(CF2)(9)(CH2)(11)SH and CF3(CF2)(7)(CH2)(6)SH were examined. The structural properties of the SAMs were strongly influenced by the interactions between the functional groups comprising the tails of the molecules. Molecular resolution atomic force microscopy (AFM) images of the hexyl-azobenzenethiol SAMs revealed an expanded lattice (nearest neighbor spacing, a = 0. 53 nm, b, = 0.56 nm, and angle between the two axes, theta = 85 degrees) relative to those of simple azobenzene-terminated SAMs. The expanded lattice probably results from the presence of the hexyl tail groups. The structure of the SAMs formed from the fluorinated alkanethiols was also probed by AFM, Fourier transform infrared spectroscopy (FTIR-RAS) and dynamic contact angle measurements. The degree of molecular tilt of the fluorocarbon helix appears to be influenced by the length of the methylene spacer moieties, which might result from the introduction of flexibility into the molecular chains.