Substrate radical intermediates in soluble methane monooxygenase

Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations

The determination of the diiron core intermediate structures involved in the catalytic cycle of soluble methane monooxygenase (sMMO), the enzyme that selectively catalyzes the conversion of methane to methanol, has been a subject of intense interest within the bioinorganic scientific community. Particularly, the specific geometry and electronic structure of the intermediate that precedes methane binding, known as intermediate Q (or MMOHQ), has been debated for over 30 years. Some reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer Fe-Fe distance. The lack of consensus calls for a thorough re-examination and reinterpretation of the spectroscopic data available on the MMOHQ intermediate. Herein, we report extensive simulations based on a hybrid quantum mechanics/molecular mechanics approach (QM/MM) approach that takes into account the complete enzyme to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum chemical approaches are used to correlate specific structural motifs with geometric parameters for comparison with crystallographic and EXAFS data, as well as with spectroscopic data from Mössbauer spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy (HERFD XAS), and resonance Raman 16O-18O difference spectroscopy. The results provide strong support for an open-core-type configuration in MMOHQ, with the most likely topology involving mono-oxo-bridged Fe ions and alternate terminal Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen bonding. The implications of an open-core intermediate Q on the reaction mechanism of sMMO are discussed.

Biotransformation of the insensitive munition constituents 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN) by aerobic methane-oxidizing consortia and pure cultures

We present the first report of biotransformation of 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN), replacements for the explosives 1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT), respectively, by methane-oxidizing cultures under aerobic conditions. Two consortia, dominated by Methylosinus spp., degraded both compounds with transient production of reduced NTO products, and non-stoichiometric production of reduced DNAN products. No release of inorganic nitrogen was observed with either compound, indicating that NTO and DNAN may be utilized as nitrogen sources by these consortia. The pure culture Methylosinus trichosporium OB3b also degraded both compounds. Degradation was observed in the presence of acetylene (a known inhibitor of methane monooxygenase; MMO) when methanol was supplied, indicating that MMO was not involved. Furthermore, studies with purified soluble MMO (sMMO) from OB3b indicated that neither compound was a substrate for sMMO. Degradation was inhibited by 2-iodosobenzoic acid, but not by dicoumarol, suggesting involvement of an oxygen- and dicoumarol-insensitive (nitro)reductase. These results indicate methanotrophs can aerobically degrade NTO and DNAN via one or more (nitro)reductases, with sMMO serving a supporting role deriving reducing equivalents from methane. This finding is important because methanotrophic bacteria are widely dispersed, and may represent a previously unrecognized route of NTO and DNAN biotransformation in aerobic environments.

A tale of two methane monooxygenases

Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.

ortho-Hydroxylation of aromatic acids by a non-heme Fe(V)=O species: how important is the ligand design?

There is a growing interest in probing the mechanism of catalytic transformations effected by non-heme iron-oxo complexes as these reactions set a platform for understanding the relevant enzymatic reactions. The ortho-hydroxylation of aromatic compounds is one such reaction catalysed by iron-oxo complexes. Experimentally [Fe(II)(BPMEN)(CH3CN)2](2+) (1) and [Fe(II)(TPA)(CH3CN)2](2+) (2) (where TPA = tris(2-pyridylmethyl)amine and BPMEN = N,N′-dimethyl-N,N′-bis(2-pyridylmethyl)ethane-1,2-diamine) complexes containing amino pyridine ligands along with H2O2 are employed to carry out these transformations where complex 1 is found to be more reactive than complex 2. Herein, using density functional methods employing B3LYP and dispersion corrected B3LYP (B3LYP-D) functionals, we have explored the mechanism of this reaction to reason out the importance of ligand design in fine-tuning the reactivity of such catalytic transformations. Dispersion corrected B3LYP is found to be superior to B3LYP in predicting the correct ground state of these species and also yields lower barrier heights than the B3LYP functional. Starting the reaction from the Fe(III)–OOH species, both homolytic and heterolytic cleavage of the O···O bond is explored leading to the formation of the transient Fe(IV)=O and Fe(V)=O species. For both the ligand systems, heterolytic cleavage was energetically preferable and our calculations suggest that both the reactions are catalyzed by an elusive high-valent Fe(V)=O species. The Fe(V)=O species undergoes the reaction via an electrophilic attack of the benzene ring to effect the ortho-hydroxylation reaction. The reactivity pattern observed for 1 and 2 are reflected in the computed barrier heights for the ortho-hydroxylation reaction. Electronic structure analysis reveals that the difference in reactivity between the ligand architectures described in complex 1 and 2 arise due to orientation of the pyridine ring(s) parallel or perpendicular to the Fe(V)=O bond. The parallel orientation of the pyridine ring is found to mix with the (πFe(dyz)–O(py))* orbital of the Fe-oxo bond leading to a reduction in the electrophilicity of the ferryl oxygen atom. Our calculations highlight the importance of ligand design in this chemistry and suggest that this concept can be used to (i) stabilize high-valent intermediates which can be trapped and thoroughly characterized (ii) enhance the reactivity and efficiency of the oxidants by increasing the electrophilicity of the ferryl oxygen containing FeVO species. Our computed results are in general agreement with the experimental results.

The "innocent" role of Sc(3+) on a non-heme Fe catalyst in an O2 environment

Density functional theory calculations have been used to investigate the reaction mechanism proposed for the formation of an oxoiron(iv) complex [Fe(IV)(TMC)O](2+) (P) (TMC = 1,4,8,11-tetramethylcyclam) starting from a non-heme reactant complex [Fe(II)(TMC)](2+) (R) and O2 in the presence of acid H(+) and reductant BPh4(-). We also addressed the possible role of redox-inactive Sc(3+) as a replacement for H(+) acid in this reaction to trigger the formation of P. Our computational results substantially confirm the proposed mechanism and, more importantly, support that Sc(3+) could trigger the O2 activation, mainly dictated by the availability of two electrons from BPh4(-), by forming a thermodynamically stable Sc(3+)-peroxo-Fe(3+) core that facilitates O-O bond cleavage to generate P by reducing the energy barrier. These insights may pave the way to improve the catalytic reactivity of metal-oxo complexes in O2 activation at non-heme centers.

Iron-promoted ortho- and/or ipso-hydroxylation of benzoic acids with H(2)O(2)

Regioselective hydroxylation of aromatic acids with hydrogen peroxide proceeds readily in the presence of iron(II) complexes with tetradentate aminopyridine ligands [Fe(II)(BPMEN)(CH(3)CN)(2)](ClO(4))(2) (1) and [Fe(II)(TPA)(CH(3)CN)(2)](OTf)(2) (2), where BPMEN=N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)-1,2-ethylenediamine, TPA=tris-(2-pyridylmethyl)amine. Two cis-sites, which are occupied by labile acetonitrile molecules in 1 and 2, are available for coordination of H(2)O(2) and substituted benzoic acids. The hydroxylation of the aromatic ring occurs exclusively in the vicinity of the anchoring carboxylate functional group: ortho-hydroxylation affords salicylates, whereas ipso-hydroxylation with concomitant decarboxylation yields phenolates. The outcome of the substituent-directed hydroxylation depends on the electronic properties and the position of substituents in the molecules of substrates: 3-substituted benzoic acids are preferentially ortho-hydroxylated, whereas 2- and, to a lesser extent, 4-substituted substrates tend to undergo ipso-hydroxylation/decarboxylation. These two pathways are not mutually exclusive and likely proceed via a common intermediate. Electron-withdrawing substituents on the aromatic ring of the carboxylic acids disfavor hydroxylation, indicating an electrophilic nature for the active oxidant. Complexes 1 and 2 exhibit similar reactivity patterns, but 1 generates a more powerful oxidant than 2. Spectroscopic and labeling studies exclude acylperoxoiron(III) and Fe(IV)=O species as potential reaction intermediates, but strongly indicate the involvement of an Fe(III)--OOH intermediate that undergoes intramolecular acid-promoted heterolytic O-O bond cleavage, producing a transient iron(V) oxidant.

Desaturase reactions complicate the use of norcarane as a mechanistic probe. Unraveling the mixture of twenty-plus products formed in enzyme-catalyzed oxidations of norcarane

Norcarane, bicyclo[4.1.0]heptane, has been widely used as a mechanistic probe in studies of oxidations catalyzed by several iron-containing enzymes. We report here that, in addition to oxygenated products, norcarane is also oxidized by iron-containing enzymes in desaturase reactions that give 2-norcarene and 3-norcarene. Furthermore, secondary products from further oxidation reactions of the norcarenes are produced in yields that are comparable to those of the minor products from oxidation of the norcarane. We studied oxidations catalyzed by a representative spectrum of iron-containing enzymes including four cytochrome P450 enzymes, CYP2B1, CYPDelta2B4, CYPDelta2E1, and CYPDelta2E1 T303A, and three diiron enzymes, soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath), toluene monooxygenase (ToMO) from Pseudomonas stutzeri OX1, and phenol hydroxylase (PH) from Pseudomonas stutzeri OX1. 2-Norcarene and 3-norcarene and their oxidation products were found in all reaction mixtures, accounting for up to half of the oxidation products in some cases. In total, more than 20 oxidation products were identified from the enzyme-catalyzed reactions of norcarane. The putative radical-derived product from the oxidation of norcarane, 3-hydroxymethylcyclohexene (21), and the putative cation-derived product from the oxidation of norcarane, cyclohept-3-enol (22), coelute with other oxidation products on low-polarity GC columns. The yields of product 21 found in this study are smaller than those previously reported for the same or similar enzymes in studies where the products from norcarene oxidations were ignored, and therefore, the limiting values for lifetimes of radical intermediates produced in the enzyme-catalyzed oxidation reactions are shorter than those previously reported.