The synthesis of nanometer diameter Au/SiO2, Ag/SiO2, and Cu2O/SiO2 clusters is described. These heteronuclear clusters are grown as metal/silicon clusters of controlled composition and controlled size using a gas aggregation source and, by means of gas phase annealing, are transformed into "structured" particles. The final metal/silica or metal oxide/silica clusters are formed by air exposure. The atomic structures of these nanometer-scale particles are determined by depositing them on thin carbon substrates and studying them using electron diffraction and transmission electron microscopy. The minimum energy structures are single crystals of Au-0, Ag-0, and Cu2O encapsulated in amorphous SiO2.