In a search for a fundamental understanding of supported catalysts, supported metal catalysts with essentially molecular structures were synthesized by anchoring organometallic precursors with well-defined structures to uniform and highly crystalline supports. The supports include zeolite NaY, zeolite HSSZ-53 and MgO. The metals include osmium, iridium, and gold, and the corresponding precursors were Os3(CO)12, Ir(C2H4)2(acac), Ir(CO)2(acac), and Au(CH3)2(acac). Characterization of the supported species at the atomic scale was carried out by X-ray absorption (XAS) and infrared (IR) spectroscopies used in tandem with aberration-corrected scanning transmission electron microscopy (STEM). The transformations of these species were tracked, with the data taken under (a) working conditions of a catalyst (during a reaction), (b) in the presence of a reactive atmosphere, or (c) under the influence of the electron beam in the STEM. Time-resolved spectra and images demonstrate the structural changes in the catalysts involving the nuclearity of the metal species, the metal-ligand and metal-support interactions. Fully resolved structures were correlated with catalytic activity for ethylene hydrogenation and CO oxidation reactions. Influence of channel confinement and cage dimensions of a zeolite on cluster formation were investigated starting with Ir1 species. First steps of cluster formation giving Ir2 and Ir3 were tracked in 1D channels of zeolite HSSZ-53 and formation of Ir6 species in 3D supercages of zeolite NaY was examined. Moreover, last steps of cluster growth were revealed by the discovery a sinter-resistant catalyst with a critical diameter of ~1 nm (Ir~40). Characterization with single atom sensitivity help pinpoint atomically dispersed gold catalytic sites on zeolite NaY during CO oxidation and site-isolated Os(CO)2 species formed by fragmentation of Os3 carbonyls on MgO surface. The results show how fundamental understanding can guide the design of catalysts incorporating metal atoms in nanoscale spaces or on surfaces and help unravel the transport of metal atoms and characterize the bonding sites for catalytic species.