Our direct density function-based simulations of Ru-, Pt- and mixed Ru-Pt clusters on carbon-based supports reveal that substrates can mediate the PtRu5 particles . Oblate structure of PtRu5 on C has been found . Nevertheless, the cluster-substrate interface interactions are still unknown. In this work, we present the applications of combinations of quantitative z-contrast imaging and high resolution electron microscopy in investigating the effect of different substrates and ligand shells on metal particles. Specifically, we developed a relatively new and powerful method to determine numbers of atoms in a nanoparticle as well as three-dimensional structures of particles including size and shape of particles on the substrates by very high angle (∼96mrad) annular dark-field (HAADF) imaging [2-4] techniques. Recently, we successfully synthesize icosahedra Au13 clusters with mixed ligands and cuboctahedral Au13 cores with thiol ligands, which have been shown by TEM to be of sub-nanometer size (0.84nm) and highly monodisperse narrow distribution. X-ray absorption and UV-visible spectra indicate many differences between icosahedra and cuboctahedral Aun cores. Particles with different ligands show different emissions and higher quantum efficiency has been found in Au11 (PPH3) SC 12)2Cl2. We plan to deposit those ligands-protected gold clusters onto different substrates, such as, TiO 2 and graphite, etc. Aforementioned analysis procedure will be performed for those particles on the substrates and results will be correlated with that of our simulations and activity properties. This approach will lead to an understanding of the cluster-substrates relationship for consideration in real applications.