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- Blomberg, L. Mattias, et al.
(author)
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Reduction of Nitric Oxide in Bacterial Nitric Oxide Reductase : A Theoretical Model Study
- 2006
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In: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1757:4, s. 240-252
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Journal article (peer-reviewed)abstract
- The mechanism of the nitric oxide reduction in a bacterial nitric oxide reductase (NOR) has been investigated in two model systems of the heme-b3-FeB active site using density functional theory (B3LYP). A model with an octahedral coordination of the non-heme FeB 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 CuB in cytochrome oxidase, gave several very high barriers which makes this type of coordination unlikely. The first nitric oxide coordinates to heme b3 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 FeB (IV)O and nitrous oxide, and this is the rate determining step in the reaction mechanism. In the model with an octahedral coordination of FeB 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 b3 taken from experimental reduction potentials. After nitrous oxide has left the active site the ferrylic FeB will form a μ-oxo bridge to heme b3 in a reaction step exergonic by 45.3 kcal/mol. The formation of a quite stable μ-oxo bridge between heme b3 and FeB is in agreement with this intermediate being the experimentally observed resting state in oxidized NOR. The formation of a ferrylic non-heme FeB 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.
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- Bassan, Arianna, et al.
(author)
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A Density Functional Study of a Biomimetic Non-Heme Iron Catalyst : Insights into Alkane Hydroxylation and Olefin Oxidation by a Formally HO-Fe(V)=O Oxidant
- 2004
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In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 11:2, s. 692-705
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Journal article (peer-reviewed)abstract
- The reactivity of [HO(tpa)FeVO] (TPA=tris(2-pyridylmethyl)amine), derived from OO bond heterolysis of its [H2O(tpa)FeIIIOOH] precursor, was explored by means of hybrid density functional theory. The mechanism for alkane hydroxylation by the high-valent iron–oxo species invoked as an intermediate in Fe(tpa)/H2O2 catalysis was investigated. Hydroxylation of methane and propane by HOFeVO was studied by following the rebound mechanism associated with the heme center of cytochrome P450, and it is demonstrated that this species is capable of stereospecific alkane hydroxylation. The mechanism proposed for alkane hydroxylation by HOFeVO accounts for the experimentally observed incorporation of solvent water into the products. An investigation of the possible hydroxylation of acetonitrile (i.e., the solvent used in the experiments) shows that the activation energy for hydrogen-atom abstraction by HOFeVO is rather high and, in fact, rather similar to that of methane, despite the similarity of the HCH2CN bond strength to that of the secondary CH bond in propane. This result indicates that the kinetics of hydrogen-atom abstraction are strongly affected by the cyano group and rationalizes the lack of experimental evidence for solvent hydroxylation in competition with that of substrates such as cyclohexane.
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- Bassan, Arianna, et al.
(author)
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A Theoretical Study of the Cis-Dihydroxylation Mechanism in Naphthalene 1,2-dioxygenase
- 2004
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In: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 9:4, s. 439-452
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Journal article (peer-reviewed)abstract
- The catalytic mechanism of naphthalene 1,2-dioxygenase has been investigated by means of hybrid density functional theory. This Rieske-type enzyme, which contains an active site hosting a mononuclear non-heme iron(II) complex, uses dioxygen and two electrons provided by NADH to carry out the cis-dihydroxylation of naphthalene. Since a (hydro)peroxo-iron(III) moiety has been proposed to be involved in the catalytic cycle, it was probed whether and how this species is capable of cis-dihydroxylation of the aromatic substrate. Different oxidation and protonation states of the Fe–O2 complex were studied on the basis of the crystal structure of the enzyme with oxygen bound side-on to iron. It was found that feasible reaction pathways require a protonated peroxo ligand, FeIII–OOH; the deprotonated species, the peroxo-iron(III) complex, was found to be inert toward naphthalene. Among the different chemical patterns which have been explored, the most accessible one involves an epoxide intermediate, which may subsequently evolve toward an arene cation, and finally to the cis-diol. The possibility that an iron(V)-oxo species is formed prior to substrate hydroxylation was also examined, but found to implicate a rather high energy barrier. In contrast, a reasonably low barrier might lead to a high-valent iron-oxo species [i.e. iron(IV)-oxo] if a second external electron is supplied to the mononuclear iron center before dioxygenation.
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