It is well established that the electronic properties of metal-organic interfaces strongly depend on the conformations of the molecules, which are influenced by aspects like coverage, temperature, and the chemical bonding between the organic molecules and the electrodes. While the electronic properties of perfectly ordered metal-organic interfaces have been investigated in detail in the framework of density functional theory (DFT), large uncertainties remain regarding the impact of disorder. Thus, we performed molecular dynamics (MD) simulations on various aromatic and ester functionalized alkyl thiols on the Au(111) surface at different coverages and differently relaxed Au-surface geometries. For the full coverage bi- and triphenylthiol based monolayers, we find stable, highly ordered herringbone configurations independent of the attached functional groups. Upon reducing the coverage, we observe pronounced island formation where the order (and thus, also the tilt angle) within the islands approaches that of the densely packed monolayers. However, in the low coverage regime the degree of order appears to be more influenced by the structure of the adsorbed molecules. Furthermore, many test simulations were performed to determine the impact of certain parameters on the results. In the future, the results of the MD simulations are to be combined with quantum-mechanical modeling for understanding the electronic properties of metal-organic interfaces.