  Two new thiol compounds with {\sigma}-{\pi}-{\sigma} 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 3TSH and 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.
