Self-assembled monolayers (SAMs) provide well-defined and ordered films of molecules spontaneously chemisorbed on a surface. By designing molecules with desired functionalities, such molecular film can be interesting for a range of applications from molecular electronics to catalysis. Important parameters for SAM applications are the film structure and quality, which are dependent on the structure of molecular constituents, the substrate, and the self-assembly process. In this work, SAMs on Au(111) of a variety of functionalized molecules, with thiol and silane headgroups, have been studied using high-resolution X-ray photoemission spectroscopy (HRXPS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, Infrared reflection absorption spectroscopy (IRRAS), contact angle measurements and Kelvin probe measurements. In particular, the effects of varying the size of the backbone, varying the headgroup, inclusion of a porphyrin tailgroup, different ways of deprotection of the headgroups, and mixed molecular layers have been investigated. The first part of thesis work is focused on SAMs of oligo(phenyleneethynylene) (OPE) derivatives. First the effect of the extent of the conjugated system on the structure of SAM was investigated. As the lateral π-system in the OPE backbone increases, molecular surface densities become lower and molecular inclinations larger. Subsequently, a bulky porphyrin tailgroup was added onto the OPE molecule. Porphyrin-functionalized OPE with several headgroups were compared and the thioacetyl anchor group was found to form a high quality SAM. In the second part of the work, the molecular orientation of thiol-derivatized tetraphenylporphyrin layers was studied. The geometry of the molecular layer and the number of linkers that bind to the gold surface depend strongly on preparation schemes, i.e. whether or not the acetyl protection groups on the thiol were removed before adsorption. Finally, mixed SAMs of a ferrocene-terminated alkanethiol and alkanethiols were studied. By diluting the ferrocene-functionalized molecules in unfunctionalized alkanethiols, the orientational order and the packing density improved. The geometrical structure and the fraction of the ferrocene-terminated molecules can be tuned by controlling the parameters in the preparation scheme.