Mechanism of aromatic hydroxylation by an activated FeIV=O core in tetrahydrobiopterin-dependent hydroxylases

Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one?

Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...

Selective Oxidation of Simple Aromatics Catalyzed by Nano-Biomimetic Metal Oxide Catalysts: A Mini Review

The process of selective oxy-functionalization of hydrocarbons using peroxide, O3, H2O2, O2, and transition metals can be carried out by the reactive oxygen species such as hydroxyl/hydroperoxyl radical and/or metal oxygenated species generated in the catalytic reaction. Thus, a variety of mechanisms have been proposed for the selective catalytic oxidation of various hydrocarbons including light alkanes, olefins, and simple aromatics by the biological metalloproteins and their biomimetics either in their homogeneous or heterogeneous platforms. Most studies involving these metalloproteins are Fe or Cu monooxygenases. The pathways carried out by these metalloenzymes in the oxidation of C-H bonds invoke either radical reaction mechanisms including Fenton's chemistry and hydrogen atom transfer followed by radical rebound reaction mechanism or electrophilic oxygenation/O-atom transfer by metal-oxygen species. In this review, we discuss the metal oxide nano-catalysts obtained from metal salts/molecular precursors (M = Cu, Fe, and V) that can easily form in situ through the oxidation of substrates using H2O2(aq) in CH3CN, and be facilely separated from the reaction mixtures as well as recycled for several times with comparable catalytic efficiency for the highly selective conversion from hydrocarbons including aromatics to oxygenates. The mechanistic insights revealed from the oxy-functionalization of simple aromatics mediated by the novel biomimetic metal oxide materials can pave the way toward developing facile, cost-effective, and highly efficient nano-catalysts for the selective partial oxidation of simple aromatics.

Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis

ChaP is a non-heme iron-dependent dioxygenase belonging to the vicinal oxygen chelate (VOC) enzyme superfamily that catalyzes the final α-pyrone ring formation in the biosynthesis of chartreusin. In contrast to other common dioxygenases, for example, 2,3-catechol dioxygenase which uses the dioxygen molecule as the oxidant, ChaP requires the flavin-activated oxygen (O₂^2-) as the equivalent. Previous experiments showed that the ChaP-catalyzed ring rearrangement contains two successive C-C bond cleavages and one lactonization; however, the detailed reaction mechanism is unknown. In this work, on the basis of the recently obtained crystal structure of ChaP, the computational model was constructed and the catalytic mechanism of ChaP was explored by performing quantum mechanical/molecular mechanical (QM/MM) calculations. Our calculation results reveal that ChaP uses the proximal oxygen in iron-coordinated HOO^- to attack the carbonyl carbon of the substrate, whereas the previous proposal that Asp49 acts as a base to deprotonate the iron-coordinated HOO^- to generate O₂^2- is unlikely. In the first stage reaction, owing to the coordination of the substrate with iron, the substrate is activated by accepting an electron from iron and the resulting oxy-radical intermediate formed by O-O cleavage can easily trigger the ring rearrangement. In the final decarboxylation, the phenolic anion of the substrate cooperatively accepts the proton of iron-coordinated HOO^- to facilitate the attack of the distal oxygen, and the proton-coupled electron transfer (PCET) from the substrate to the Fe^IV═O plays a key role for the decarboxylation. These findings may provide useful information for understanding the ChaP-catalyzed oxidative rearrangement and other flavin-dependent non-heme dioxygenases.

Carbon-fluorine bond cleavage mediated by metalloenzymes

Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.

Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates.

A New Domain of Reactivity for High-Valent Dinuclear [M(μ-O)2 M'] Complexes in Oxidation Reactions

The strikingly different reactivity of a series of homo- and heterodinuclear [(MIII )(μ-O)2 (MIII )']2+ (M=Ni; M'=Fe, Co, Ni and M=M'=Co) complexes with β-diketiminate ligands in electrophilic and nucleophilic oxidation reactions is reported, and can be correlated to the spectroscopic features of the [(MIII )(μ-O)2 (MIII )']2+ core. In particular, the unprecedented nucleophilic reactivity of the symmetric [NiIII (μ-O)2 NiIII ]2+ complex and the decay of the asymmetric [NiIII (μ-O)2 CoIII ]2+ core through aromatic hydroxylation reactions represent a new domain for high-valent bis(μ-oxido)dimetal reactivity.

Catalytic oxidation of aromatic hydrocarbons by a molecular iron–NHC complex

An iron–NHC complex bearing a tetradentate bis(N-heterocyclic carbene) ligand is applied as catalyst for the oxidation of methyl substituted arene substrates.

Molecular iron complexes as catalysts for selective C–H bond oxygenation reactions

This feature article summarises recent developments in homogeneous C–H bond oxygenation catalysed by molecular iron complexes.

Estimating hydroxyl radical photochemical formation rates in natural waters during long-term laboratory irradiation experiments

In this study it was observed that, during long-term irradiations (>1 day) of natural waters, the methods for measuring hydroxyl radical (˙OH) formation rates based upon sequentially determined cumulative concentrations of photoproducts from probes significantly underestimate actual ˙OH formation rates. Performing a correction using the photodegradation rates of the probe products improves the ˙OH estimation for short term irradiations (<1 day), but not long term irradiations. Only the 'instantaneous' formation rates, which were obtained by adding probes to aliquots at each time point and irradiating these sub-samples for a short time (≤2 h), were found appropriate for accurately estimating ˙OH photochemical formation rates during long-term laboratory irradiation experiments. Our results also showed that in iron- and dissolved organic matter (DOM)-rich water samples, ˙OH appears to be mainly produced from the Fenton reaction initially, but subsequently from other sources possibly from DOM photoreactions. Pathways of ˙OH formation in long-term irradiations in relation to H2O2 and iron concentrations are discussed.

Chiral hydroxylation at the mononuclear nonheme Fe(II) center of 4-(S) hydroxymandelate synthase--a structure-activity relationship analysis

(S)-Hydroxymandelate synthase (Hms) is a nonheme Fe(II) dependent dioxygenase that catalyzes the oxidation of 4-hydroxyphenylpyruvate to (S)-4-hydroxymandelate by molecular oxygen. In this work, the substrate promiscuity of Hms is characterized in order to assess its potential for the biosynthesis of chiral α-hydroxy acids. Enzyme kinetic analyses, the characterization of product spectra, quantitative structure activity relationship (QSAR) analyses and in silico docking studies are used to characterize the impact of substrate properties on particular steps of catalysis. Hms is found to accept a range of α-oxo acids, whereby the presence of an aromatic substituent is crucial for efficient substrate turnover. A hydrophobic substrate binding pocket is identified as the likely determinant of substrate specificity. Upon introduction of a steric barrier, which is suspected to obstruct the accommodation of the aromatic ring in the hydrophobic pocket during the final hydroxylation step, the racemization of product is obtained. A steady state kinetic analysis reveals that the turnover number of Hms strongly correlates with substrate hydrophobicity. The analysis of product spectra demonstrates high regioselectivity of oxygenation and a strong coupling efficiency of C-C bond cleavage and subsequent hydroxylation for the tested substrates. Based on these findings the structural basis of enantioselectivity and enzymatic activity is discussed.

Formation of the iron-oxo hydroxylating species in the catalytic cycle of aromatic amino acid hydroxylases

The first part of the catalytic cycle of the pterin-dependent, dioxygen-using nonheme-iron aromatic amino acid hydroxylases, leading to the Fe(IV)=O hydroxylating intermediate, has been investigated by means of density functional theory. The starting structure in the present investigation is the water-free Fe-O(2) complex cluster model that represents the catalytically competent form of the enzymes. A model for this structure was obtained in a previous study of water-ligand dissociation from the hexacoordinate model complex of the X-ray crystal structure of the catalytic domain of phenylalanine hydroxylase in complex with the cofactor (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) (PAH-Fe(II)-BH(4)). The O-O bond rupture and two-electron oxidation of the cofactor are found to take place via a Fe-O-O-BH(4) bridge structure that is formed in consecutive radical reactions involving a superoxide ion, O(2)(-). The overall effective free-energy barrier to formation of the Fe(IV)=O species is calculated to be 13.9 kcal  mol(-1), less than 2 kcal  mol(-1) lower than that derived from experiment. The rate-limiting step is associated with a one-electron transfer from the cofactor to dioxygen, whereas the spin inversion needed to arrive at the quintet state in which the O-O bond cleavage is finalized, essentially proceeds without activation.

Experimentally calibrated computational chemistry of tryptophan hydroxylase: trans influence, hydrogen-bonding, and 18-electron rule govern O2-activation

Insight into the nature of oxygen activation in tryptophan hydroxylase has been obtained from density functional computations. Conformations of O(2)-bound intermediates have been studied with oxygen trans to glutamate and histidine, respectively. An O(2)-adduct with O(2)trans to histidine (O(his)) and a peroxo intermediate with peroxide trans to glutamate (P(glu)) were found to be consistent (0.57-0.59mm/s) with experimental Mössbauer isomer shifts (0.55mm/s) and had low computed free energies. The weaker trans influence of histidine is shown to give rise to a bent O(2) coordination mode with O(2) pointing towards the cofactor and a more activated O-O bond (1.33A) than in O(glu) (1.30A). It is shown that the cofactor can hydrogen bond to O(2) and activate the O-O bond further (from 1.33 to 1.38A). The O(his) intermediate leads to a ferryl intermediate (F(his)) with an isomer shift of 0.34mm/s, also consistent with the experimental value (0.25mm/s) which we propose as the structure of the hydroxylating intermediate, with the tryptophan substrate well located for further reaction 3.5A from the ferryl group. Based on the optimized transition states, the activation barriers for the two paths (glu and his) are similar, so a two-state scenario involving O(his) and P(glu) is possible. A structure of the activated deoxy state which is high-spin implies that the valence electron count has been lowered from 18 to 16 (glutamate becomes bidentate), giving a "green light" that invites O(2)-binding. Our mechanism of oxygen activation in tryptophan hydroxylase does not require inversion of spin, which may be an important observation.

Theoretical study of cyclohexane hydroxylation by three possible isomers of [FeIV(O)(R-TPEN)] 2+: does the pentadentate ligand wrapping around the metal center differently lead to the different stability and reactivity?

Density functional theory calculations have been carried out to elucidate the mechanism of cyclohexane hydroxylation by three possible isomers of [Fe(IV)(O)(N-R-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine)](2+) (R is methyl or benzyl) (Klinker et al. in Angew Chem Int Ed 44:3690-3694, 2005). The calculations offer a mechanistic view and reveal the following features: (a) all the three isomers possess triplet ground states and low-lying quintet excited states, (b) the relative stability follows the order isomer A > isomer B > isomer C, in agreement with the conclusions of Klinker et al., (c) the theoretical investigations provide a rationale to explain the interconversion of the three isomers, (d) the reaction pathways of the C-H hydroxylation are initiated by a hydrogen-abstraction step, and (e) the three isomers react with cyclohexane via two-state-reactivity patterns on competing triplet and quintet spin-state surfaces. As such, in the gas phase, the relative reactivity exhibits the trend isomer B > isomer A, while at the highest level, B2//B1 with zero point energy and solvation corrections, the relative reactivity follows the order isomer B > isomer A > isomer C. Thus, the calculated reaction pathway shows that pyridine rings perpendicular to the Fe-O axis result in more reactive species, and a pyridine ring coordinated trans to the oxygen atom leads to the least reactive isomer.

Kinetic isotope effects on aromatic and benzylic hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase as probes of chemical mechanism and reactivity

Phenylalanine hydroxylase from Chromobacterium violaceum (CvPheH) is a non-heme iron monooxygenase that catalyzes the hydroxylation of phenylalanine to tyrosine. In this study, we used deuterium kinetic isotope effects to probe the chemical mechanisms of aromatic and benzylic hydroxylation to compare the reactivities of bacterial and eukaryotic aromatic amino acid hydroxylases. The (D) k cat value for the reaction of CvPheH with [(2)H 5]phenylalanine is 1.2 with 6-methyltetrahydropterin and 1.4 with 6,7-dimethyltetrahydropterin. With the mutant enzyme I234D, the (D) k cat value decreases to 0.9 with the latter pterin; this is likely to be the intrinsic effect for addition of oxygen to the amino acid. The isotope effect on the subsequent tautomerization of a dienone intermediate was determined to be 5.1 by measuring the retention of deuterium in tyrosine produced from partially deuterated phenylalanine; this large isotope effect is responsible for the normal effect on k cat. The isotope effect for hydroxylation of the methyl group of 4-CH 3-phenylalanine, obtained from the partitioning of benzylic and aromatic hydroxylation products, is 10. The temperature dependence of this isotope effect establishes the contribution of hydrogen tunneling to benzylic hydroxylation by this enzyme. The results presented here provide evidence that the reactivities of the prokaryotic and eukaryotic hydroxylases are similar and further define the reactivity of the iron center for the family of aromatic amino acid hydroxylases.

The violacein biosynthetic enzyme VioE shares a fold with lipoprotein transporter proteins

VioE, an unusual enzyme with no characterized homologues, plays a key role in the biosynthesis of violacein, a purple pigment with antibacterial and cytotoxic properties. Without bound cofactors or metals, VioE, from the bacterium Chromobacterium violaceum, mediates a 1,2 shift of an indole ring and oxidative chemistry to generate prodeoxyviolacein, a precursor to violacein. Our 1.21 A resolution structure of VioE shows that the enzyme shares a core fold previously described for lipoprotein transporter proteins LolA and LolB. For both LolB and VioE, a bound polyethylene glycol molecule suggests the location of the binding and/or active site of the protein. Mutations of residues near the bound polyethylene glycol molecule in VioE have identified the active site and five residues important for binding or catalysis. This structural and mutagenesis study suggests that VioE acts as a catalytic chaperone, using a fold previously associated with lipoprotein transporters to catalyze the production of its prodeoxyviolacein product.

Versatility of biological non-heme Fe(II) centers in oxygen activation reactions

Oxidase and oxygenase enzymes allow the use of relatively unreactive O2 in biochemical reactions. Many of the mechanistic strategies used in nature for this key reaction are represented within the 2-histidine-1-carboxylate facial triad family of non-heme Fe(II)-containing enzymes. The open face of the metal coordination sphere opposite the three endogenous ligands participates directly in the reaction chemistry. Here, data from several studies are presented showing that reductive O2 activation within this family is initiated by substrate (and in some cases cosubstrate or cofactor) binding, which then allows coordination of O2 to the metal. From this starting point, the O2 activation process and the reactions with substrates diverge broadly. The reactive species formed in these reactions have been proposed to encompass four oxidation states of iron and all forms of reduced O2 as well as several of the reactive oxygen species that derive from O-O bond cleavage.

OH radical reactions with phenylalanine in free and peptide forms

Density functional theory has been used to model the reaction of OH with l-phenylalanine, as a free molecule and in the Gly-Phe-Gly peptide. The influence of the environment has been investigated using water and benzene as models for polar and non-polar surroundings, in addition to gas phase calculations. Different paths of reaction have been considered, involving H abstractions and addition reactions, with global contributions to the overall reaction around 10% and 90% respectively when Phe is in its free form. The ortho-adducts (o-tyrosine) were found to be the major products of the Phe+OH reaction, for all the modeled environments and especially in water solutions. The reactivity of phenylalanine towards OH radical attacks is predicted to be higher in its peptidic form, compared to the free molecule. The peptidic environment also changes the sites' reactivity, and for the Gly-Phe-Gly+OH reaction H abstraction becomes the major path of reaction. The good agreement found between the calculated and the available experimental data supports the methodology used in this work, as well as the data reported here for the first time.

Copper(II)-Mediated Aromaticortho-Hydroxylation: A Hybrid DFT and Ab Initio Exploration

Mechanistic pathways for the aromatic hydroxylation by [CuII(L1)(TMAO)(O)](-) (L1=hippuric acid, TMAO=trimethylamine N-oxide), derived from the O--N bond homolysis of its [CuII(L1)(TMAO)2] precursor, were explored by using hybrid density functional theory (B3LYP) and highly correlated ab initio methods (QCISD and CCSD). Published experimental studies suggest that the catalytic reaction is triggered by a terminal copper-oxo species, and a detailed study of electronic structures, bonding, and energetics of the corresponding electromers is presented. Two pathways, a stepwise and a concerted reaction, were considered for the hydroxylation process. The results reveal a clear preference for the concerted pathway, in which the terminal oxygen atom directly attacks the carbon atom of the benzene ring, leading to the ortho-selectively hydroxylated product. Solvent effects were probed by using the PCM and CPCM solvation models, and the PCM model was found to perform better in the present case. Excellent agreement between the experimental and computational results was found, in particular also for changes in reactivity with derivatives of L1.

Kinetic analysis of the conversion of nonheme (alkylperoxo)iron(III) species to iron(IV) complexes

Low-spin mononuclear (alkylperoxo)iron(III) complexes decompose by peroxide O-O bond homolysis to form iron(IV) species. We examined the kinetics of previously reported homolysis reactions for (alkylperoxo)iron(III) intermediates supported by TPA (tris(2-pyridylmethyl)amine) in CH3CN solution and promoted by pyridine N-oxide, and by BPMCN (N,N-bis(2-pyridylmethyl)-N,N-dimethyl-trans-1,2-diaminocyclohexane) in its cis-beta configuration in CH3CN and CH2Cl2, as well as for the previously unreported chemistry of TPA and 5-Me3TPA intermediates in acetone. Each of these reactions forms an oxoiron(IV) complex, except for the beta-BPMCN reaction in CH2Cl2 that yields a novel (hydroxo)(alkylperoxo)iron(IV) product. Temperature-dependent rate measurements suggest a common reaction trajectory for each of these reactions and verify previous theoretical estimates of a ca. 60 kJ/mol enthalpic barrier to homolysis. However, both the tetradentate supporting ligand and exogenous ligands in the sixth octahedral coordination site significantly perturb the homolyses, such that observed rates can vary over 2 orders of magnitude at a given temperature. This is manifested as a compensation effect in which increasing activation enthalpy is offset by increasingly favorable activation entropy. Moreover, the applied kinetic model is consistent with geometric isomerism in the low-spin (alkylperoxo)iron(III) intermediates, wherein the alkylperoxo ligand is coordinated in either of the inequivalent cis sites afforded by the nonheme ligands.

Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT Study

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.

Insights into the catalytic mechanisms of phenylalanine and tryptophan hydroxylase from kinetic isotope effects on aromatic hydroxylation

Phenylalanine hydroxylase (PheH) and tryptophan hydroxylase (TrpH) catalyze the aromatic hydroxylation of phenylalanine and tryptophan, forming tyrosine and 5-hydroxytryptophan, respectively. The reactions of PheH and TrpH have been investigated with [4-(2)H]-, [3,5-(2)H(2)]-, and (2)H(5)-phenylalanine as substrates. All (D)k(cat) values are normal with Delta117PheH, the catalytic core of rat phenylalanine hydroxylase, ranging from 1.12-1.41. In contrast, for Delta117PheH V379D, a mutant protein in which the stoichiometry between tetrahydropterin oxidation and amino acid hydroxylation is altered, the (D)k(cat) value with [4-(2)H]-phenylalanine is 0.92 but is normal with [3,5-(2)H(2)]-phenylalanine. The ratio of tetrahydropterin oxidation to amino acid hydroxylation for Delta117PheH V379D shows a similar inverse isotope effect with [4-(2)H]-phenylalanine. Intramolecular isotope effects, determined from the deuterium contents of the tyrosine formed from [4-(2)H]-and [3,5(2)H(2)]-phenylalanine, are identical for Delta117PheH and Delta117PheH V379D, suggesting that steps subsequent to oxygen addition are unaffected in the mutant protein. The inverse effects are consistent with the reaction of an activated ferryl-oxo species at the para position of the side chain of the amino acid to form a cationic intermediate. The normal effects on the (D)k(cat) value for the wild-type enzyme are attributed to an isotope effect of 5.1 on the tautomerization of a dienone intermediate to tyrosine with a rate constant 6- to7-fold that for hydroxylation. In addition, there is a slight ( approximately 34%) preference for the loss of the hydrogen originally at C4 of phenylalanine. With (2)H(5)-indole-tryptophan as a substrate for Delta117PheH, the (D)k(cat) value is 0.89, consistent with hydroxylation being rate-limiting in this case. When deuterated phenylalanines are used as substrates for TrpH, the (D)k(cat) values are within error of those for Delta117PheH V379D. Overall, these results are consistent with the aromatic amino acid hydroxylases all sharing the same chemical mechanism, but with the isotope effect for hydroxylation by PheH being masked by tautomerization of an enedione intermediate to tyrosine.

Theoretical study of the reduction of nitric oxide in an A-type flavoprotein

The mechanism for the reduction of nitric oxide to nitrous oxide and water in an A-type flavoprotein (FprA) in Moorella thermoacetica, which has been proposed to be a scavenging type of nitric oxide reductase, has been investigated using density functional theory (B3LYP). A dinitrosyl complex, [{FeNO}(7)](2), has previously been proposed to be a key intermediate in the NO reduction catalyzed by FprA. The electrons and protons involved in the reduction were suggested to "super-reduce" the dinitrosyl intermediate to [{FeNO}(8)](2) or the corresponding diprotonated form, [{FeNO(H)}(8)](2). In this type of mechanism the electron and/or proton transfers will be a part of the rate-determining step. In the present study, on the other hand, a reaction mechanism is suggested in which N(2)O can be formed before the protons and electrons enter the catalytic cycle. One of the irons in the diiron center is used to stabilize the formation of a hyponitrite dianion, instead of binding a second NO. Cleaving the N-O bond in the hyponitrite dianion intermediate is the rate-determining step in the proposed reaction mechanism. The barrier of 16.5 kcal mol(-1) is in good agreement with the barrier height of the experimental rate-determining step of 14.8 kcal mol(-1). The energetics of some intermediates in the "super-reduction" mechanism and the mechanism proceeding via a hyponitrite dianion are compared, favoring the latter. It is also discussed how to experimentally discriminate between the two mechanisms.

Two-State Reactivity in Alkane Hydroxylation by Non-Heme Iron−Oxo Complexes

Density functional theory is used to explore the mechanisms of alkane hydroxylation for four synthetic non-heme iron(IV)-oxo complexes with three target substrates (Kaizer, J.; Klinker, E. J.; Oh, N. Y.; Rohde; J.-U.; Song, W. J.; Stubna, A.; Kim, J.; Münck, E.; Nam, W.; Que, L., Jr. J. Am. Chem. Soc. 2004, 126, 472-473; Rohde, J.-U.; Que, L., Jr. Angew. Chem. Int. Ed. 2005, 44, 2255-2258.). The iron-oxo reagents possess triplet ground states and low-lying quintet excited states. The set of experimental and theoretical reactivity trends can be understood if the reactions proceed on the two spin states, namely two-state reactivity (TSR); an appropriate new model is presented. The TSR model makes testable predictions: (a) If crossing to the quintet state occurs, the hydroxylation will be effectively concerted; however, if the process transpires only on the triplet surface, stepwise hydroxylation will occur, and side products derived from radical intermediates would be observed (e.g., loss of stereochemistry). (b) In cases of crossing en route to the quintet transition state, one expects kinetic isotope effects (KIEs) typical of tunneling. (c) In situations where the two surfaces contribute to the rate, one expects intermediate KIEs and radical scrambling patterns that reflect the two processes. (d) Solvent effects on these reactions are expected to be very large.

Reduction of nitric oxide in bacterial nitric oxide reductase--a theoretical model study

The mechanism of the nitric oxide reduction in a bacterial nitric oxide reductase (NOR) has been investigated in two model systems of the heme-b(3)-Fe(B) active site using density functional theory (B3LYP). A model with an octahedral coordination of the non-heme Fe(B) consisting of three histidines, one glutamate and one water molecule gave an energetically feasible reaction mechanism. A tetrahedral coordination of the non-heme iron, corresponding to the one of Cu(B) in cytochrome oxidase, gave several very high barriers which makes this type of coordination unlikely. The first nitric oxide coordinates to heme b(3) and is partly reduced to a more nitroxyl anion character, which activates it toward an attack from the second NO. The product in this reaction step is a hyponitrite dianion coordinating in between the two irons. Cleaving an NO bond in this intermediate forms an Fe(B) (IV)O and nitrous oxide, and this is the rate determining step in the reaction mechanism. In the model with an octahedral coordination of Fe(B) the intrinsic barrier of this step is 16.3 kcal/mol, which is in good agreement with the experimental value of 15.9 kcal/mol. However, the total barrier is 21.3 kcal/mol, mainly due to the endergonic reduction of heme b(3) taken from experimental reduction potentials. After nitrous oxide has left the active site the ferrylic Fe(B) will form a mu-oxo bridge to heme b(3) in a reaction step exergonic by 45.3 kcal/mol. The formation of a quite stable mu-oxo bridge between heme b(3) and Fe(B) is in agreement with this intermediate being the experimentally observed resting state in oxidized NOR. The formation of a ferrylic non-heme Fe(B) in the proposed reaction mechanism could be one reason for having an iron as the non-heme metal ion in NOR instead of a Cu as in cytochrome oxidase.

Theoretical studies of enzyme mechanisms involving high-valent iron intermediates

Recent theoretical contributions to the elucidation of mechanisms for iron containing enzymes are reviewed. The method used in most of these studies is hybrid density functional theory with the B3LYP functional. Three classes of enzymes are considered, the mononuclear non-heme enzymes, enzymes containing iron dimers, and heme-containing enzymes. Mechanisms for both dioxygen and substrate activations are discussed. The reactions usually go through two half-cycles, where a high-valent intermediate Fe(IV)O species is created in the first half-cycle, and the substrate reactions involving this intermediate occur in the second half-cycle. Similarities between the three classes of enzymes dominate, but significant differences also exist.

Intrinsic isotope effects on benzylic hydroxylation by the aromatic amino acid hydroxylases: evidence for hydrogen tunneling, coupled motion, and similar reactivities

Deuterium kinetic isotope effects for hydroxylation of the methyl group of 4-methylphenylalanine have been used as a probe of the relative reactivities of the hydroxylating intermediates in the aromatic amino acid hydroxylases phenylalanine, tyrosine, and tryptophan hydroxylase. When there are three deuterium atoms in the methyl group, all three enzymes exhibit an intrinsic isotope effect of about 13. The temperature dependence of the isotope effect is consistent with moderate tunneling, with the extent of tunneling identical for all three enzymes. In the case of phenylalanine hydroxylase, the presence of the regulatory domain has no effect on the values. The intrinsic primary and secondary isotope effects were determined using 4-methylphenylalanine containing one or two deuterium atoms in the methyl group. With one deuterium atom, the intrinsic primary and secondary effects have average values of 10 and 1.1, respectively. With two deuterium atoms, the primary effects decrease to 7.4 and the secondary effect increases to 1.3, consistent with coupled motion of the primary and secondary hydrogens. The results with all three enzymes are consistent with a hydrogen abstraction mechanism. The similarities of the isotope effects and extent of tunneling establish that the reactivities of the hydroxylating intermediates in the three enzymes are essentially identical.