Two new thiol compounds with σ-π-σ structure were synthesized and self-assembled on gold substrates. The morphology and the structural characterization of SAMs assessed by infrared spectroscopy, contact angle, XPS, electrochemistry and scanning tunneling microscopy (STM) show the formation of monolayers. SAMs with a terthiophene (3TSH) core as conjugated system are much better organized compared to those with a naphthalene carbodiimide (NaphSH) core as demonstrated by the cyclic voltammetry and STM studies. The surface concentration of 3TSHand NaphSH is respectively three and six times lower than ordered SAMs of pure alkyl chains.A large number of I/V characteristics have been studied either by STS measurements on gold substrates or by C-AFM on gold nanodots. Transition Voltage Spectroscopy (TVS) was used to clearly identify the transport in these partially organized monolayers. The chemical nature of the conjugated system, donor for 3TSH and acceptor for NaphSH, involves an opposite rectification associated to the asymmetrical coupling of the molecular orbitals and the electrodes. The conductance histograms show that the 3TSH junctions are less dispersed than those of NaphSH junctions. This is explained by a better control of the molecular organization in the molecular junctions.

P-aminothiophenol (PATP) is a well-known molecule for the preparation of self-assembled monolayers on gold via its thiol functional group. After adsorption, it has been demonstrated that this molecule is anchored to gold through its thiol group, and standing nearly upright at the surface with the amino functional group on top. This molecule has been extensively studied by surface enhanced Raman spectroscopy but its exact SERS spectrum remains unclear. Here, we demonstrate that it can be strongly affected by at least two experimental parameters: laser power and layer density. Those features are discussed in terms of a dimerization of the PATP molecules. The free amino group affords the adsorption of other molecules such as C(60). In this case, a complex multilayer system is formed and the question of its precise characterisation remains a key point. In this article, we demonstrate that surface enhanced Raman spectroscopy combined with x ray photoelectron spectroscopy can bring very important information about the organization of such a self-assembled multilayer on gold. In our study, the strong evolution of Raman modes after C(60) adsorption suggests a change in the organization of aminothiophenol molecules during C(60) adsorption. These changes, also observed when the aminothiophenol layer is annealed in toluene, do not prevent the adsorption of C(60) molecules.