The main objective of this PhD thesis is to link the atomic scale structure to the catalytic properties of self-assembled nanostructures. The growth and characterization of these nanostructures was carried out in an ultra-high vacuum (UHV) chamber initially designed for the study of the kinetics of epitaxial growth of thin films and nanostructures by variable temperature scanning tunneling microscopy. During this PhD thesis, we built a very sensitive and selective gas detector based on a quadrupole mass spectrometer and adapted to the geometry of this UHV system. The proper functioning of the gas detector is confirmed by temperature programmed desorptions of Xe on Ag(100) which demonstrate the very high sensitivity of the device of about $10^{-6}$~monolayer (ML). The zero-order desorption parameters obtained for the first monolayer of Xe adsorbed on Ag(100) are $E_d=0.22-0.23$~eV with a prefactor $\nu_0$ between $4\times10^{12}$~s$^{-1}$ and $1 \times10^{13}$~s$^{-1}$. An exchange process between Fe adatoms and Ag atoms from the Ag(100) surface is identified by means of temperature programmed desorption of N$_2$. Desorption spectra suggest that the exchange is complete from an annealing temperature of 140~K. Our study of the catalytic activity of metal nanostructures focuses on the ability of passivated Fe clusters to adsorb N$_2$ molecules without dissociating them, which is a fundamental step in the bio-inspired heterogeneous catalysis of ammonia. The first system investigated for the growth of Fe clusters is MgO/Ag(100). Diffusion of Fe adatoms deposited on a MgO monolayer is observed from an annealing temperature of 280~K onwards. Fe clusters with an average size of $12.1\pm 0.5$~atoms are obtained on a MgO monolayer by thermal ripening of 0.072~ML of Fe deposited at 40~K. No sign of N$_2$ adsorption was observed on these clusters by thermal programmed desorption investigation. The second system chosen for the growth of Fe clusters is graphene/Ir(111) obtained by chemical vapor deposition. The deposition of 0.3 and 0.4 ML of Fe on a graphene/Ir(111) sample at 50~K, followed by annealing at 300~K, generates a superlattice of Fe clusters which matches the periodicity of the moiré formed by graphene/Ir(111). The theoretically expected mean cluster size is 26 atoms for 0.3~ML of Fe, and 35 atoms for 0.4~ML of Fe. The temperature stability of the clusters obtained with 0.4~ML Fe is investigated from 300~K to 600~K. It is established that Smoluchowski ripening takes place as the annealing temperature increases and the superlattice structure has completely disappeared after annealing at 600~K. Temperature programmed desorption of molecularly adsorbed N$_2$ at 50~K on a sample with 0.4~ML of Fe deposited on graphene/Ir(111) reveals 3 desorption peaks at 120~K, 92~K, and 60~K. In addition, slow dissociation of nitrogen molecules at 50~K adsorbed on the higher energy adsorption sites is demonstrated.