We report free energy calculations of FcC(6)S-/C4S-Au and FcC(6)S-/C12S-Au binary self-assembled monolayers (SAMs) formed by one ferrocenylhexanethiolate chain and alkylthiolate chains. We demonstrate that the free energy perturbation methods are able to reproduce the positive shift of die redox potential when the coadsorbed butanethiolate C4S chains are replaced by dodecanethiolate C12S chains. The different contributions to the Ewald summation involved in the perturbation process are thoroughly described. We complete the study by a microscopic description of the binary SAMs before and after oxidation. The molecular dynamics (MD) simulations evidence that the formation of the ion-pair between the ferricinium and a single perchlorate anion of the supporting electrolyte is more favored in FcC(6)S-/C2S-Au SAM.