Here, we establish standardized conditions for the synthesis of a range of carboxylate capped zirconium oxo clusters. We develop PDF modeling tools to structurally characterize the oxo clusters. We find that excellent refinements are only obtained when the structural models include the contribution of the organic ligands. PDF analysis can clearly distinguish a Zr6 from a Zr12 cluster and dismiss other possible cluster structures such as Zr4. The organic ligand shell is then comprehensively characterized by FTIR, NMR and TGA. The molecular formula is finally confirmed by ESI-HR-MS. Using our characterization tools, we evaluate carboxylate for carboxylate ligand exchange and we find that the ligand is structure directing, determining whether a Zr6 or a Zr12 cluster is formed. These results are further generalized to hafnium oxo clusters. Finally, we test the notion that the fatty acid capped metal oxo clusters are the smallest conceivable nanocrystal prototypes. We compare the catalytic activity of Zr12-oleate clusters with oleic acid capped zirconium oxide nanocrystals, and find superior activity for the oxo clusters.