A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective

Abstract

In this article, we investigated the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme, through a radical rebound mechanism. All intermediates and transition states along the reaction coordinate were located and the energies involved in the mechanism calculated using the B3LYP functional including dispersion effects. Our B3LYP-D2 results show that the singlet state of the (μ-1,2-peroxo)Cu(II)2 complex plays an important role as the lowest energy species prior to C-H bond activation. A crossing between the singlet and triplet PES is suggested to occur before the cleavage of the C-H bond of methane, where the triplet (bis-μ-oxo)Cu(III)2 is very reactive towards activation of the strong C-H bond of methane. The C-H bond activation is the rate-determining step of the reaction, with an activation energy of 18.6 kcal mol(-1) relative to the singlet (μ-1,2-peroxo)Cu(II)2 species. Comparison with previous theoretical results for a non-synchronous concerted mechanism suggests the radical rebound mechanism as a possible alternative pathway.

Understanding trends in C–H bond activation in heterogeneous catalysis

“…For some catalysts, such as non-noble metals and certain oxides, unsaturated surface atoms are available to stabilize the methyl group in the TS [3][4][5][6] . However, if the CH 3 -surface interaction is energetically unfavorable 7 or geometrically inaccessible 8 , a radical-like TS is observed 2,[9][10][11][12][13] . Many of the most promising catalysts for alkane activation fall into this second category: cation-exchanged zeolites 11,[14][15][16][17] , Metal Organic Frameworks (MOFs) 18,19 and decorated graphene nanosheets (GN) 20 for the partial oxidation of alkanes, and certain oxides 2,21 and zeolites 22 for oxidative coupling of methane (OCM).…”

Propene Hydroformylation Reaction Catalyzed by HRh(CO)(BISBI): A Thermodynamic and Kinetic Analysis of the Full Catalytic Cycle

“…Our experience involving theoretical studies of homogeneous catalytic process promoted by transition metal catalysts has shown that DFT methods provide energetic results deviating 4–6 kcal mol –1 from ab initio methods. [ 39,40,55,75 ] In the absence of accurate experimental data, the way to evaluate the accuracy of DFT methods is usually to make a comparison with ab initio correlated methods. In this context, the emergence of new correlated methods, for instance, the newly developed version of the coupled‐cluster method with explicit correlation [CCSD(T)‐F12] [ 76 ] and local‐pair natural orbital coupled‐cluster [LPNO‐CCSD(T)], [ 77 ] together with the increased processing capacity of the computers and more efficient implementation schemes have allowed the accurate determination of kinetic and thermodynamic properties present in homogeneous catalytic processes.…”

“…In this context, the emergence of new correlated methods, for instance, the newly developed version of the coupled‐cluster method with explicit correlation [CCSD(T)‐F12] [ 76 ] and local‐pair natural orbital coupled‐cluster [LPNO‐CCSD(T)], [ 77 ] together with the increased processing capacity of the computers and more efficient implementation schemes have allowed the accurate determination of kinetic and thermodynamic properties present in homogeneous catalytic processes. [ 64,74,75,78 ] However, due to the high computational demanding of these methods, their applications remain limited to model systems. In any case, the elaboration of computational kinetic models, even constructed from electronic structure method of limited accuracy, can be useful in order to get a detailed understanding about the complicated catalytic processes, making possible to simulate some experimental conditions and so allowing a better comparison between computational data and experimental measurements.…”

Pemanfaatan Bakteri Sebagai Pereduksi Emisi Gas Metana Pada Limbah Cair Kelapa Sawit (Elaeis guineesis Jacq.)

“…Interaksi antara molekul oksigen dengan Cu (I) menghasilkan kompleks (µ-η2 :η2 -peroxo)Cu(II)2 yang dapat diisomerasi menjadi bis(µ-oxo)Cu(III)2. Hasil isomerasi tersebut merupakan senyawa yang mampu memecah ikatan C-H alkana (Silva et al 2016). Proses selanjutnya adalah konversi metanol menjadi formaldehid, yang merupakan senyawa antara utama sebelum memasuki jalur metabolisme berikutnya.…”