Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin

Abstract

Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pK_a values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.

Keywords: compound I; compound II; density functional calculations; ferryl oxygen; peroxidase; reduction potential.

Scheme 1

Peroxidase and chlorination cycles showing the interconversion between different species: Fe(III)-PO, ferric state; Fe(II)-PO, ferrous state; PO-I, compound I; PO-II, compound II. Note that the ferrous state does not participate in the reactions catalysed by heme peroxidases.

Figure 1

Molecular model of the active site of peroxidases.

Figure 2

Iron out-of-plane distance (Fe–pp), defined as the distance between the plane determined by the four pyrrole nitrogen atoms and the iron.

Figure 3

Structures optimised at the B3LYP/cc-pVDZ computational level for Fe(III) native peroxidase, ferrous species, compound I, and compound II at the most stable feasible spin state, either non-protonated, with a H₂O discrete molecule, or protonated at a distal axial position.

Figure 4

UV-vis spectra at the Soret region calculated by the TD-DFT functional with the B3LYP/cc-pVDZ computational level at the most stable spin state for (A) non-protonated Fe(III)-PO (─), Fe(II)-PO (─), PO-I (─), and PO-II (─); (B) corresponding aquo complexes; and (C) protonated species.