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The intermediate structures appearing until compound I formation in the monooxygenation reaction cycle by cytochrome P450 were determined by using the density functional theory. Protons were attached to an O2 molecule binding to the heme iron in a reduced oxy-ferrous state. When two protons were attached to the distal O atom, O−O bond cleavage occurred, and the compound I structure was formed. The structure had an energetic advantage compared to the situation in which one proton each was connected to the proximal and distal O atoms, and the structure would catalyze oxidation of a substrate. The calculated interaction energies between substrate and oxygen ligand of heme were 3−10 kcal/mol and suggests that an interaction between the substrate and the oxygen ligand of heme was maintained through the reaction process from the O2 incorporation to the generation of the compound I and that it contributed the stability of the reaction system.

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