Structural properties of the acylperoxo complexes [(Salen)(MnRCO3)-R-III] (2) and [(Salen)(MnRCO3)-R-IV] (3), the critical intermediates in the Kochi-Jacobsen-Katsuki reaction utilizing organic peracids or O-2/aldehydes as oxygen source, have been studied with the density functional theory. Four distinct isomers, cis(O,N), cis(N,O), cis(N,N), and trans, of these complexes have been located. The isomer 2-cis(ON) in its quintet ground state, and nearly degenerate isomers 3-cis(O,N) and 3-cis(N,O) in their quartet ground states are found to be the lowest in energy among the other isomers. The O-O bond cleavage in the cis(O,N), cis(NO), and trans isomers of 2 and 3 has been elucidated. In complex 3, the O-O bond is inert. On the contrary, in complex 2, the O-O bond cleaves via two distinct pathways. The first pathway occurs exclusively on the quintet potential energy surface (PES) and corresponds to heterolytic O-O bond scission coupled with insertion of an oxygen atom into an Mn-N(Salen) bond to form 2-N-oxo species; this pathway has the lowest barrier of 14.9 kcal/mol and is 15.6 kcal/mol exothermic. The second pathway is tentatively a spin crossover pathway. In particular, for 2-cis(O,N) and 2-cis(N,O) the second pathway proceeds through a crucial minimum on the seam of crossing (MSX) between the quintet and triplet PESs followed by heterolytic O-O cleavage on the triplet PIES, and produces unusual triplet 2-cis(O,N)- and 2-cis(N,O)-oxo ([(Salen)Mn-v(O)RCO2]) species; this pathway requires 12.8 kcal/mol and is 1.4 kcal/mol endothermic. In contrast, for the 2-trans isomer, spin crossing is less crucial and the O-O cleavage proceeds homolytically to generate 2-trans-oxo [(Salen)Mn-IV(O)] species with RCO2 radical; this pathway, however, cannot compete with that in 2-cis because it needs 21.9 kcal/mol for activation and is 15.3 kcal/mol endothermic. In summary, the O-O cleavage occurs predominantly in the 2-cis complexes, and may proceed either through pure high spin or spin crossover heterolytic pathway to produce 2-cis-oxo and 2-N-oxo species.