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  • 1.
    Borowski, Tomasz
    et al.
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences.
    Georgiev, Valentin
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Catalytic Reaction Mechanism of Homogentisate Dioxygenase: A Hybrid DFT Study2005In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 127, no 49, p. 17303-17314Article in journal (Refereed)
  • 2.
    Georgiev, Valentin
    Stockholm University, Faculty of Science, Department of Physics.
    Reaction Mechanisms of Metalloenzymes and Synthetic Model Complexes Activating Dioxygen: A Computational study2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum chemistry has nowadays become a powerful and efficient tool that can be successfully used for studies of biosystems. It is therefore possibleto model the enzyme active-site and the reactions undergoing into it, as well as obtaining quite accurate energetic profiles. Important conclusions can be drawn from such profiles about the  plausibility of different putative mechanisms.

    Density Functional Theory is used in the present thesis for investigation of the catalytic mechanism of dioxygenase metallo-enzymes and synthetic model complexes. Three enzymes were studied – Homoprotocatechuate 2,3-dioxygenase isolated from Brevibacterium fuscum (Bf 2,3-HPCD), Manganese-Dependent Homoprotocatechuate 2,3-Dioxygenase (MndD) and Homogentisate Dioxygenase (HGD). Models consisting of 55 to 208 atoms have been built from X-ray crystal structures and used in the calculations. The computed energies were put in energy curves and were used for estimation of the feasibility of the suggested reaction mechanisms. A non-heme [(L4Me4)Fe(III)]+3 complex that mimics the reactivity of intradiol dioxygenases, and a heme [T(o-Cl)PPFe] complex catalyzing the stepwise oxidation of cyclohexane to adipic acid, were also studied.

    For the enzymes and the non-heme biomimetic complex the reaction was found to follow a mechanism that was previously suggested for extradiol and intradiol dioxygenases – ordered substrates binding and formation of peroxo species, which further undergoes homolytic O-O bond cleavage. Different reaction steps appear to be rate limiting in the particular cases: proton transfer from the substrate to the peroxide in Bf 2,3-HPCD, the formation of the peroxo bridge in HGD and the biomimetic complex, and notably, spin transition in MndD.

    The catalytic oxidation of cyclohexane to adipic acid in the presence of molecular oxygen as oxidant was studied, a reaction of great importance for the chemical industry. Reaction mechanism is suggested, involving several consecutive oxidative steps. The highest calculated enthalpy of activation is 17.8 kcal/mol for the second oxidative step.

  • 3.
    Georgiev, Valentin
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Borowski, Tomasz
    Polish Academy of Sciences.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese2008In: Journal of Biological Inorganic Chemistry, ISSN 0949-8257, E-ISSN 1432-1327, Vol. 13, no 6, p. 929-40Article in journal (Refereed)
    Abstract [en]

    Homoprotocatechuate (HPCA) dioxygenases are enzymes that take part in the catabolism of aromatic compounds in the environment. They use molecular oxygen to perform the ring cleavage of ortho-dihydroxylated aromatic compounds. A theoretical investigation of the catalytic cycle for HPCA 2,3-dioxygenase isolated from Brevibacterium fuscum (Bf 2,3-HPCD) was performed using hybrid DFT with the B3LYP functional, and a reaction mechanism is suggested. Models of different sizes were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the enzyme follows a reaction pathway similar to that for other non-heme iron dioxygenases, and for the manganese-dependent analog MndD, although with different energetics. The computational results suggest that the rate-limiting step for the whole reaction of Bf 2,3-HPCD is the protonation of the activated oxygen, with an energy barrier of 17.4 kcal/mol, in good agreement with the experimental value of 16 kcal/mol obtained from the overall rate of the reaction. Surprisingly, a very low barrier was found for the O-O bond cleavage step, 11.3 kcal/mol, as compared to 21.8 kcal/mol for MndD (sextet spin state). This result motivated additional studies of the manganese-dependent enzyme. Different spin coupling between the unpaired electrons on the metal and on the evolving substrate radical was observed for the two enzymes, and therefore the quartet spin state potential energy surface of the MndD reaction was studied. The calculations show a crossing between the sextet and the quartet surfaces, and it was concluded that a spin transition occurs and determines a barrier of 14.4 kcal/mol for the O-O bond cleavage, which is found to be the rate-limiting step in MndD. Thus the two 83% identical enzymes, using different metal ions as co-factors, were found to have similar activation energies (in agreement with experiment), but different rate-limiting steps.

  • 4.
    Georgiev, Valentin
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Borowski, Tomasz
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical study of the catalytic reaction mechanism of MndD2006In: Journal of Biological Inorganic Chemistry, ISSN 0949-8257, E-ISSN 1432-1327, Vol. 11, no 5, p. 571-85Article in journal (Refereed)
    Abstract [en]

    Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O-O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last reaction steps. Alternative reaction paths were considered, and their calculated barriers were found to be higher than for the suggested mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.

  • 5.
    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.

  • 6.
    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)
  • 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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