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  • 1. Borowski, Thomasz
    et al.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Radon, Mariusz
    Zych, Konrad
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Mechanism of Selective Halogenation by SyrB2: A Computational Study2010In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 132, no 37, p. 12887-12898Article in journal (Refereed)
    Abstract [en]

    The mechanism of the chlorination reaction of SyrB2, a representative α-ketoglutarate dependent halogenase, was studied with computational methods. First, a macromolecular model of the Michaelis com- plex was constructed using molecular docking proce- dures. Based on this structure a smaller model com- prising the first- and some of the second shell residues of iron, and a model substrate was constructed and used in DFT investigations on the reaction mecha- nism. Computed relative energies and Mo ̈ssbauer iso- mer shifts and quadrupole splittings indicate that the two oxoferryl species observed experimentally are two stereoisomers resulting from an exchange of the coordi- nation sites occupied by the oxo and chloro ligands. In principle both FeIV =O species are reactive and decay to FeIIICl(OH)/carbon radical intermediates via C-H bond cleavage. In the final rebound step, which is very fast and thus precluding equilibration between the two forms of the radical intermediate, the ligand (oxo or chloro) placed closest to the carbon radical (trans to His235) is transfered to the carbon. For the native substrate (L-Thr) the lowest barrier for C-H cleavage was found for an isomer of the oxoferryl species favor- ing chlorination in the rebound step. CASPT2 cal- culations for the spin state splittings in the oxoferryl species support the conclusion that once the FeIV =O intermediate is formed, the reaction proceeds on the quintet potential energy surface.

  • 2.
    Georgiev, Valentin
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    A DFT Study on the Catalytic Reactivity of a Functional Model Complex for  Intradiol-Cleaving Dioxygenases2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 17, p. 5878-5885Article in journal (Refereed)
    Abstract [en]

    The enzymatic ring cleavage of catechol derivatives is catalyzed by two groups of dioxygenases: extradiol- and intradiol-cleaving dioxygenases. Although having different oxidation state of their nonheme iron sites and different ligand coordinations, both groups of enzymes involve a common peroxy intermediate in their catalytic cycles. The factors that lead to either extradiol cleavage resulting in 2-hydroxymuconaldehyde or intradiol cleavage resulting in muconic acid are not fully understood. Well-characterized model compounds that mimic the functionality of these enzymes offer a basis for direct comparison to theoretical results. In this study the mechanism of a biomimetic iron complex is investigated with density functional theory (DFT). This complex catalyzes the ring opening of catecholate with exclusive formation of the intradiol cleaved product. Several spin states are possible for the transition metal system, with the quartet state found to be of main importance during the reaction course. The mechanism investigated provides an explanation for the observed selectivity of the complex. First, a bridging peroxide is formed, which decomposes to an alkoxy radical by O−O homolysis. In contrast to the subsequent barrier-free intradiol C−C bond cleavage, the extradiol pathway proceeds via the formation of an epoxide, which requires an additional activation barrier.

  • 3.
    Johansson, Adam Johannes
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Xue, Gengianq
    Que Jr, Larry
    Observed enhancement of the reactivity of a biomimetic diiron complex by the addition of water - mechanistic insights from theoretical modeling2009In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 34, p. 6741-6750Article in journal (Refereed)
    Abstract [en]

    The biomimetic diiron complex [FeIIIFeIV(m-O)2(5-Me3-TPA)2](ClO4)3 (TPA = tris(2- pyridylmethyl)amine) has been found to be capable of oxidizing 9,10-dihydroanthracene in a solution of acetonitrile. Addition of water up to 1 M makes the reaction 200 times faster, suggesting that the water molecule in some way activates the catalyst for more efficient substrate oxidation. It is proposed that the enhanced reactivity results from the coordination of a water molecule to the iron(III) half of the complex, converting the bis-m-oxo structure of the diiron complex to a ring-opened form where one of the bridging oxo groups is transformed into a terminal oxo group on iron(IV). The suggested mechanism is supported by DFT (B3LYP) calculations and transition state theory. Two different computational models of the diiron complex are used to model the hydroxylation of cyclohexane to cyclohexanol. Model 1 has a bis-m-oxo diiron core (diamond core) while model 2 represents the “open core” analogue with one bridging m-oxo group, a terminal oxo ligand on iron(IV), and a water molecule coordinated to iron(III). The computational results clearly suggest that the terminal oxo group is more reactive than the bridging oxo group. The free energy of activation is 7.0 kcal mol-1 lower for the rate limiting step when the oxidant has a terminal oxo group than when both oxo groups are bridging the irons.

  • 4.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Biomimetic Iron Complexes involved in Oxygenation and Chlorination: A Theoretical Study2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomimetic chemistry is directed towards the simulation of enzymatic reactivity with synthetic analogues. In this thesis a quantum chemical method has been employed to study the mechanism of highly reactive iron-oxo complexes involved in oxygenation and chlorination of organic substrates. The aim of this research is to gain greater understanding for the reactivity paradigm of the iron-oxo group.

    One reaction deals with the conversion of cyclohexane into adipic acid, a key chemical in industrial chemistry, catalyzed by an iron(II)-porphyrin complex in the presence of dioxygen. This process constitutes a ’green’ alternative to conventional adipic acid production, and is thus of great interest to synthetic chemistry. Another reaction investigated herein regards the selective chlorination observed for a new group of non-heme iron enzymes. With help of theoretical modeling it was possible to propose a mechanism that explains the observed selectivity. It is furthermore demonstrated how a biomimetic iron complex simulates the enzymatic reactivity by a different mechanism.

    Other topics covered in this thesis regard the structure-reactivity relationship of a binuclear iron complex and the intradiol C-C bond cleavage of catechol catalyzed by an iron(III) complex.

  • 5.
    Noack, Holger
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Georgiev, Valentin
    Stockholm University, Faculty of Science, Department of Physics.
    Johannson, Johannes Adam
    Department fur Chemie, Universität in Aachen.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    The Conversion of Cyclohexane to Adipic Acid catalyzed by an Iron-Porphirin Complex. A theoretical studyManuscript (preprint) (Other academic)
  • 6.
    Noack, Holger
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical investigation on the oxidative chlorination performed by a biomimetic non-heme iron catalyst2007In: Journal of Biological Inorganic Chemistry, ISSN 0949-8257, E-ISSN 1432-1327, Vol. 12, p. 1151-1162Article in journal (Refereed)
    Abstract [en]

    The present study is a part of an effort to understand the mechanism of the oxidative chlorination, as performed by a biomimetic non-heme iron complex. This catalytically active complex is generated from a peroxide and [(TPA)FeIIICl2]+ [TPA is tris(2-pyridylmethyl)amine]. The reaction catalyzed by [(TPA)FeCl2]+/ROOH involves either [(TPA)ClFeV=O]2+ or [(TPA)ClFeIV=O]+ as an intermediate. On the basis of density functional theory the reaction of these two possible catalysts with cyclohexane is investigated. A question addressed is how the competing hydroxylation of the substrate is avoided. It is demon- strated that the high-valent iron complex [(TPA)Cl– FeV=O]2+ is capable of stereospecific alkane chlorination, based on an ionic rather than on a radical pathway. In contrast, the results found for [(TPA)ClFeIV=O]+ cannot explain the experimental findings. In this case the transition states for chlorination and hydroxylation are energetically too close. The exclusive chlorination of the substrate by Cl–FeIV=O may be explained by an indirect or a direct effect, altering the position of the competing rebound barriers.

  • 7.
    Noack, Holger
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Valentin, Georgiev
    Stockholm University, Faculty of Science, Department of Physics.
    Johansson, Adam Johannes
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E,M.
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical Insights into Heme Catalysed Oxidation of Cyclohexane to Adipic Acid Article in journal (Refereed)
    Abstract [en]

    Adipic acid is a key compound in the chemical industry, where it is mainly used in the production of polymers. The conventional process of its generation requires vast amounts of energy, and moreover, pro- duces environmentally deleterious substances. Thus, there is interest in alternative ways to gain adequate amounts of adipic acid. Experimental reports on a one-pot iron catalyzed conversion of cyclohexane to adipic acid motivated a theoretical investigation based on DFT calculations. The process investigated is interesting because it requires less energy than contemporary methods and does not produce environmentally harmful side products. The aim of the present contribution is to gain insight into the mechanism of the iron catalyzed cyclohexane conversion to provide a basis for further development of this process. The rate limiting step along the reaction path is discussed. Furthermore, it is shown that the C-C bond breaks spontaneously after an initial hydrogen atom abstraction from one of the cylohexane-1,2-diol hydroxides.

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