Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

Abstract

Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.2

Proton–Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

“…Nevertheless, a somewhat smaller energy barrier of ∼10 and 12–19 kcal·mol –1 was obtained from the CASPT2- and MC-PDFT-based QM/MM calculations, respectively (for MC-PDFT, the range of energies reflects usage of six different functionals on top of the (20e,16o) CASSCF reference wave function). We note in passing that understabilization of the Q -like intermediate at the B3LYP level was already recognized in the computational studies of the sMMO as well as the BoxB enzymes.…”

“…A range of HAA reactive intermediates has been previously suggested for Δ 9 D or other NHFe 2 enzymes (examples are given in Figure ). ,− However, none of these has been experimentally captured and characterized for Δ 9 D. This contrasts, for example, soluble methane monooxygenase (sMMO), where the Fe III Fe III P intermediate converts to the high-valent (Fe IV Fe IV ) intermediate Q , − or to the R2 subunit of class I ribonucleotide reductase (RNR), where the peroxo moiety P is proposed to be first protonated to yield a 1,2-μ-hydroperoxo Fe III Fe III , P′ , that accepts an exogenous electron, leading to a mixed-valence Fe IV Fe III intermediate, X . − …”

Mechanism of the Dinuclear Iron Enzyme p‐Aminobenzoate N‐oxygenase from Density Functional Calculations

“…An alternative pathway B has also been considered, namely substrate oxidation by the superoxide/peroxide directly, before the O−O bond cleavage. This kind of mechanism has also been taken into account for the related di‐iron enzymes, namely, BoxB, phnZ,ADO and MIOX ,,,,. From React, the peroxide can attack the nitrogen atom (N1) of p ABA directly via B‐TS1 (see Figure ).…”

Computational Understanding of the Selectivities in Metalloenzymes

“…Later, Rokob used the ONIOM (B3LYP/BP86/Amber) method to re-investigate this enzyme (Rokob, 2016). Four different pathways were considered for the aromatic ring oxidation, namely an electrophilic attached by a bis(μ-oxo)-diiron(IV) species, electrophilic attack via the σ * orbital of a μ-η 2 :η 2 -peroxo-diiron(III) intermediate, radical attach via the π * -orbital of a superoxo-diiron(II,III) species, and radical attach of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Rokob, 2016). Importantly, the most favorable pathway (barrier of 20.9 kcal/mol) was found to be very similar as those obtained by Liao and Siegbahn (Liao and Siegbahn, 2015).…”