The mechanisms of oxidations of amines, sulfides, and alkenes by peroxynitrous acid, as well as the mechanism for the conversion of peroxynitrous acid to nitric acid, have been investigated with density functional theory methods using the Becke3LYP functional and the 6-31G* basis set. Theoretical evidence is obtained for the mechanisms and transition states of oxidations by peroxynitrous acid both by one-and two-electron processes. Transition structures for two-electron oxidations of amines, sulfides, and alkenes are reported. An activated form of peroxynitrous acid, HOONO*, is often invoked to account for the potent oxidative chemistry of peroxynitrous acid and derivatives; a structure with the appropriate characteristics has been located. The structure of the CO2 adduct of peroxynitrite is also explored, and a mechanistic scheme is proposed for the acceleration of peroxynitrite oxidations in the presence of CO2. Energetics are described in detail for each of these species and oxidation transition structures.