QM/MM Calculations Suggest Concerted O−O Bond Cleavage and Substrate Oxidation by Nonheme Diiron Toluene/o‐Xylene Monooxygenase

Abstract

The nonheme diiron toluene/o-xylene monooxygenase (ToMO) is the most studied toluene monooxygenase that mediates an aromatic hydroxylation reaction. In this work, QM/MM calculations were performed to understand the reaction mechanism. It is revealed that the μ-η 2 :η 2 peroxodiferric species is the reactive intermediate after the binding of the O 2 molecule to the reduced diferrous center. Subsequently, both a stepwise and a concerted mechanism involving the critical OÀ O bond cleavage and CÀ O bond formation were considered. The latter was calculated to be more favorable, suggesting that the formation of a highvalent diferryl Q intermediate is not needed. The isomeric formation of the phenol product was found very facile. The first step was calculated to be rate-limiting, with a barrier of 17.6 kcal/mol for the ortho-hydroxylation.

Peroxo-Diiron(III/III) as the Reactive Intermediate for N-Hydroxylation Reactions in the Multidomain Metalloenzyme SznF: Evidence from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations

“…First, QM model calculations have been performed to identify the most likely structures of P. Figure 2 shows three candidate structures of P. It is seen that P1 with the side-on peroxo binding to both irons has the lowest energy. Such butterfly-like structure of P1 is analogous to those proposed in sMMO, 5,94 epoxidase BoxB, 25,50 ToMo, 51,95 CmlA, 52 and AurF. 49 For the end-on binding Z-like P2, its energy is 1.8 kcal/mol higher than that of P1.…”

“…In addition to the above two mechanistic pathways, one plausible mechanism involves the electrophilic attack of peroxo species onto the N site of guanidium, which may trigger the heterolytic cleavage of the O–O bond, leading to l -HMA (Scheme c). Such a mechanism in Scheme c is reminiscent of O 2 activation mechanisms by the diiron enzymes AurF, BoxB, ToMo, and CmlA …”

“…32 In addition to the above two mechanistic pathways, one plausible mechanism involves the electrophilic attack of peroxo species onto the N site of guanidium, which may trigger the heterolytic cleavage of the O−O bond, leading to L-HMA (Scheme 1c). Such a mechanism in Scheme 1c is reminiscent of O 2 activation mechanisms by the diiron enzymes AurF, 49 BoxB, 50 ToMo, 51 and CmlA. 52 To address the catalytic mechanism of the HDO domain in SznF, we have performed combined classical molecular dynamics (MD) simulations and hybrid QM/MM calculations.…”

Computational Exploration of Enzyme Promiscuity: Mechanisms of O2 and NO Reduction Activities of the Desulfovibrio gigas Flavodiiron Protein

“…The presence of these hydrogen bonds in React OR , along with the hydroxo-bridge between two iron ions, inclines the O 2 moiety to bind with the two irons in a side-on symmetric manner: oxyl fragment coordinates as a bridge between two iron ions in the μ-η 1 :η 1 mode (see Figure S4). 2,83 This binding mode is similar to the peroxo-diiron(III) species found in other nonheme diiron enzymes, like cyanobacterial aldehyde-deformylating oxygenase 90 and acyl carrier protein Δ 9 -desaturase. 91 Other possible candidates for React OR were also explored.…”

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…Several recent studies have investigated reactivity of non-haem diiron enzymes. [88][89][90][91] Song et al used ChemShell to model PhnZ, a mixed-valence diiron oxygenase, which catalyses the conversion of organophosphonic acids to inorganic phosphate via a mechanism involving the substrate bonding to one Fe(III) site and oxygen to the other. 92 [NiFe]-hydrogenases have also been explored, 93,94 which are of great interest in the development of the hydrogen economy due to their ability to catalyse H 2 oxidation at ambient conditions.…”