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A DFT Study on the Catalytic Reactivity of a Functional Model Complex for  Intradiol-Cleaving Dioxygenases
Stockholm University, Faculty of Science, Department of Physics. (Theoretical Biochemistry)
Stockholm University, Faculty of Science, Department of Physics. (Theoretical Biochemistry)
Stockholm University, Faculty of Science, Department of Physics. (Theoretical Biochemistry)
Stockholm University, Faculty of Science, Department of Physics. (Theoretical Biochemistry)
2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 17, 5878-5885 p.Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
2010. Vol. 114, no 17, 5878-5885 p.
Keyword [en]
homogeneous catalysis, density functional theory, intradiol, extradiol, dioxy- genase, non-heme iron, biomimetic, oxo-radical
National Category
Natural Sciences
Research subject
Chemical Physics
Identifiers
URN: urn:nbn:se:su:diva-30776DOI: 10.1021/jp911217jISI: 000277053900033OAI: oai:DiVA.org:su-30776DiVA: diva2:273971
Available from: 2009-10-26 Created: 2009-10-26 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Reaction Mechanisms of Metalloenzymes and Synthetic Model Complexes Activating Dioxygen: A Computational study
Open this publication in new window or tab >>Reaction Mechanisms of Metalloenzymes and Synthetic Model Complexes Activating Dioxygen: A Computational study
2009 (English)Doctoral 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.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2009. 104 p.
Keyword
catalysis, density functional theory, extradiol, intradiol, dioxygenases, oxygen, biomimetic complexes, heme, spin transition, adipic acid
National Category
Atom and Molecular Physics and Optics
Research subject
Quantum Chemistry
Identifiers
urn:nbn:se:su:diva-30706 (URN)978-91-7155-965-4 (ISBN)
Public defence
2009-11-20, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, Sweden, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In progress, Paper 5: In progressAvailable from: 2009-10-28 Created: 2009-10-23 Last updated: 2010-04-09Bibliographically approved
2. Biomimetic Iron Complexes involved in Oxygenation and Chlorination: A Theoretical Study
Open this publication in new window or tab >>Biomimetic Iron Complexes involved in Oxygenation and Chlorination: A Theoretical Study
2010 (English)Doctoral 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.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2010. a-d, viii, 75 p.
Keyword
biomimetic, iron, density functional theory, intradiol, chlorination, adpic acid, diamond core, reactivity
National Category
Inorganic Chemistry Theoretical Chemistry
Research subject
Chemical Physics
Identifiers
urn:nbn:se:su:diva-38197 (URN)978–91–7447–013–0 (ISBN)
Public defence
2010-04-30, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Submitted. Paper 2: Accepted. Paper 3: Submitted.Available from: 2010-04-08 Created: 2010-03-31 Last updated: 2010-04-07Bibliographically approved

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