A novel type of nanoparticles have been designed based on self-organization of the metal centers with organic functional groups. Size- and shape-controlled synthetic procedures were developed to prepare nanostructured Pd and Ni particles in high yields from easily available precursors. The presence of the non-metallic functional groups in the particle’s core forced the metal centers to adopt a divalent oxidation state bearing polar chemical bonds (“nanosalt”). The Pd and Ni particles were excellent catalysts to accomplish a highly selective synthetic route to vinyl chalcogenides. The mechanisms of the catalytic reactions via the heterogeneous and homogeneous pathways were revealed and studied in detail.