An ensemble of Ru12Cu4C2 bimetallic clusters derived from organometallic precursors and anchored within mesoporous silica is investigated with molecular mechanics (MM) and ab initio techniques. The computational study, guided by experiment, yields a representative cluster structure which is compared with EXAFS data. The comparison yields possible insights into the effects of cluster structure upon the thermal decomposition of the carbonyl ligands. Density functional theory (DFT) calculations suggest an unexpected structural modification of the silica-supported cluster upon removal of the attendent carbonyl ligands, in particular the displacement of the central carbido atoms.