The structures and interconversion pathway between the [Cu-2(mu-eta(2):eta(2)-O-2)](2+) and [Cu-2(mu-O)(2)](2+) isomers of model systems with three ammonia ligands per copper center are investigated using both density functional theory with a B3LYP functional (B3LYP-DFT) and multiconfigurational perturbation theory (CASSCF/CASPT2). Both methods lead to thoroughly different results for the relative energy of both isomers. The CASPT2 results reveal an intrinsic stabilization of the [Cu-2(mu-O)(2)](2+) isomer, thus indicating that the presence of a [Cu-2(mu-eta(2):eta(2)-O-2)](2+) core in the respiratory proteins must be brought back to the presence of bulky capping ligands and/or to external effects caused by solvents and counterions. Both isomers are found to be diamagnetic. For the [Cu-2(mu-eta(2):eta(2)-O-2)](2+) isomer an antiferromagnetic coupling constant, -2J, of 4209 cm(-1) is calculated at the CASPT2 level. On the other hand, in the [Cu-2(mu-O)(2)](2+) isomer, the lowest B-3(u) state is calculated at 9316 cm(-1), but is found to correspond instead to an oxygen pi* --> sigma* excitation.