In this paper, we employ molecular dynamics (MD) simulations to obtain microscopic structures and the energy picture of FcC11S-/X-C11S-Au as a function of the terminal groups (e.g., X = CH3, COOH, COO−, CH2NH2, CH2OH). A perturbation formalism has been performed to calculate the macroscopic redox properties of FcC11S-/X-C11S-Au as a function of the terminal groups. Since the shift as a function of the endgroups is fairly modest, it appears that the magnitude of the change in the simulated redox properties seems to vary with the polarity of the terminal groups of the alkanethiol coadsorbate. To deeply investigate the molecular scale architecture and its effect on the redox properties, the tilt angle, the film thickness and also the distribution of dihedral angles in the trans and gauche configurations have been determined as a function of the terminal groups. From this microscopic description, we have underlined the tendency of the carboxylate-functionalized alkanethiols to deviate from well-arranged structures. The results reported herein underscore the role of H-bonding in the structural properties. A link between the number of intra-layer hydrogen bonds and the disorder of monolayers is clearly established. This work is also completed with an energetic characterization of the SAMs.