Small gold nanoparticles capped with 4-trimethylsilylethynyl-1-acetylthiobenzene (SEB) were prepared with spherical shape and different mean sizes (5-8 nm). The functionalized gold nanoparticles (AuNPs-SEB) were deposited onto TiO2 substrates, and the interaction at the molecule-gold interface, the molecular layer thickness, and the ligand organization on the surface of Au nanospheres were investigated by means of synchrotron radiation induced X-ray photoelectron spectroscopy (SR-XPS) and angular dependent near edge X-ray absorption spectroscopy (NEXAFS) at the C K-edge. In order to obtain better insight into the molecular shell features, the same measurements were also carried out on a self-assembling monolayer (SAM) of SEB anchored on a "flat" gold surface (Au/Si(111) wafer). The comparison between angular dependent NEXAFS spectra collected on the self-assembling monolayer and AuNPs-SEB allowed for successfully probing the molecular arrangement of SEB molecules on the gold nanospheres surface. Furthermore, DFT calculations on the free SEB molecule as well as bonded to a small cluster of gold atoms were developed. The comparison with experimental results allowed better understanding of the spectroscopic signatures in the experimental absorption spectra and rationalization of the molecular organization in the SAM, NPs having a thin molecular shell, and NPs covered by a thick layer of ligands.