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| 2. |
- Blomberg, Margareta R A, et al.
(författare)
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A Quantum Chemical Study of Hydrogen Abstraction from Manganese-Coordinated Water by a Tyrosyl Radical: A Model for Water Oxidation in Photosystem II
- 1997
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:35, s. 8285-8292
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Tidskriftsartikel (refereegranskat)abstract
- Recently, water oxidation in photosystem II was proposed to involve direct abstraction of hydrogen atoms from water molecules terminally ligated to manganese ions in the oxygen-evolving complex by the oxidized tyrosine radical, TyrZ. This model is tested here by performing quantum chemical calculations. An empirically parametrized hybrid density functional method is used, and both monomeric and dimeric manganese model systems are studied. It is found that, by coordination to a manganese center, the first O-H bond strength of water is lowered from 113.4 to 84.3 kcal/mol. This O-H bond strength is only 2.8 kcal/mol stronger than that in tyrosine. Using an extended basis set, we find that this difference decreases still further. The second hydrogen abstraction energy is quite similar. Since thermoneutrality in the reaction (or a weak exothermicity) is a requirement for the hydrogen abstraction model, the present calculations support this model. Possible functions of a coordinated chloride and a nearby calcium complex are suggested. Five- or six-coordination and ferro- or antiferromagnetic spin couplings of the manganese centers are discussed.
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| 3. |
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| 4. |
- Borowski, Thomasz, et al.
(författare)
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Mechanism of Selective Halogenation by SyrB2 : A Computational Study
- 2010
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 132:37, s. 12887-12898
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Brena, Barbara, et al.
(författare)
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Modeling near-edge fine structure x-ray spectra of the manganese catalytic site for water oxidation in photosystem II
- 2012
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 134:41, s. 17157-17167
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Tidskriftsartikel (refereegranskat)abstract
- The Mn 1s near-edge absorption fine structure (NEXAFS) has been computed by means of transition-state gradient-corrected density functional theory (DFT) on four Mn 4Ca clusters modeling the successive S 0 to S 3 steps of the oxygen-evolving complex (OEC) in photosystem II (PSII). The model clusters were obtained from a previous theoretical study where they were determined by energy minimization. They are composed of Mn(III) and Mn(IV) atoms, progressing from Mn(III) 3Mn(IV) for S 0 to Mn(III) 2Mn(IV) 2 for S 1 to Mn(III)Mn(IV) 3 for S 2 to Mn(IV) 4 for S 3, implying an Mn-centered oxidation during each step of the photosynthetic oxygen evolution. The DFT simulations of the Mn 1s absorption edge reproduce the experimentally measured curves quite well. By the half-height method, the theoretical IPEs are shifted by 0.93 eV for the S 0 → S 1 transition, by 1.43 eV for the S 1 → S 2 transition, and by 0.63 eV for the S 2 → S 3 transition. The inflection point energy (IPE) shifts depend strongly on the method used to determine them, and the most interesting result is that the present clusters reproduce the shift in the S 2 → S 3 transition obtained by both the half-height and second-derivative methods, thus giving strong support to the previously suggested structures and assignments.
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| 6. |
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| 7. |
- Li, Xichen, et al.
(författare)
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Water Oxidation Mechanism for Synthetic Co-Oxides with Small Nuclearity
- 2013
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 135:37, s. 13804-13813
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Tidskriftsartikel (refereegranskat)abstract
- Hybrid DFT model calculations have been performed for some cobalt complexes capable of oxidizing water. Since a very plausible mechanism for the oxygen-evolving complex involving the cuboidal Mn4Ca structure in photosystem II (PSII) has recently been established, the most important part of the present study concerns a detailed comparison between cobalt and manganese as water oxidation catalysts. One similarity found is that a M(IV)-O-center dot state is the key precursor for O-O bond formation in both cases. This means that simply getting a M(IV) state is not enough; a formal M(V)=O state is required, with two oxidations on one center from M(III). For cobalt, not even that is enough. A singlet coupled state is required at this oxidation level, which is not the ground state. It is shown that there are also more fundamental differences between catalysts based on these metals. The favorable low-barrier direct coupling mechanism found for PSII is not possible for the corresponding cobalt complexes. The origin of this difference is explained. For the only oxygen-evolving cubic Co4O4 complex with a defined structure, described by Dismukes et al., the calculated results are in good agreement with experiments. For the Co-4 models of the amorphous cobalt-oxo catalyst found by Nocera et al., higher barriers are found than the one obtained experimentally. The reasons for this are discussed.
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| 8. |
- Pelmenschikov, Vladimir, et al.
(författare)
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A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis
- 2002
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 124:15, s. 4039-4049
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism for methane formation in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and chemical models consisting of 107 atoms. The experimental X-ray crystal structure of the enzyme in the inactive MCRox1-silent state was used to set up the initial model structure. The calculations suggest a mechanism not previously proposed, in which the most remarkable feature is the formation of an essentially free methyl radical at the transition state. The reaction cycle suggested starts from a Michaelis complex with CoB and methyl-CoM coenzymes bound and with a squareplanar coordination of the Ni(I) center in the tetrapyrrole F430 prosthetic group. In the rate-limiting step the methyl radical is released from methyl-CoM, induced by the attack of Ni(I) on the methyl-CoM thioether sulfur. In this step, the metal center is oxidized from Ni(I) to Ni(II). The resulting methyl radical is rapidly quenched by hydrogen-atom transfer from the CoB thiol group, yielding the methane molecule and the CoB radical. The estimated activation energy is around 20 kcal/mol, which includes a significant contribution from entropy due to the formation of the free methyl. The mechanism implies an inversion of configuration at the reactive carbon. The size of the inversion barrier is used to explain the fact that CF3−S−CoM is an inactive substrate. Heterodisulfide CoB−S−S−CoM formation is proposed in the final step in which nickel is reduced back to Ni(I). The suggested mechanism agrees well with experimental observations.
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| 9. |
- Pelmenschikov, Vladimir, et al.
(författare)
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Nickel superoxide dismutase reaction mechanism studied by hybrid density functional methods
- 2006
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 128:23, s. 7466-7475
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Tidskriftsartikel (refereegranskat)abstract
- The reaction mechanism for the disproportionation of the toxic superoxide radical to molecular oxygen and hydrogen peroxide by the nickel-dependent superoxide dismutase (NiSOD) has been studied using the B3LYP hybrid DFT method. Based on the recent X-ray structures of the enzyme in the resting oxidized Ni(III) and X-ray-reduced Ni(II) states, the model investigated includes the backbone spacer of six residues (sequence numbers 1−6) as a structural framework. The side chains of residues His1, Cys2, and Cys6, which are essential for nickel binding and catalysis, were modeled explicitly. The catalytic cycle consists of two half-reactions, each initiated by the successive substrate approach to the metal center. The two protons necessary for the dismutation are postulated to be delivered concertedly with the superoxide radical anions. The first (reductive) phase involves Ni(III) reduction to Ni(II), and the second (oxidative) phase involves the metal reoxidation back to its resting state. The Cys2 thiolate sulfur serves as a transient protonation site in the interim between the two half-reactions, allowing for the dioxygen and hydrogen peroxide molecules to be released in the reductive and oxidative phases, respectively. The His1 side chain nitrogen and backbone amides of the active site channel are shown to be less favorable transient proton locations, as compared to the Cys2 sulfur. Comparisons are made to the Cu- and Zn-dependent SOD, studied previously using similar models.
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| 10. |
- Shafaat, Hannah S., et al.
(författare)
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Electronic Structural Flexibility of Heterobimetallic Mn/Fe Cofactors : R2lox and R2c Proteins
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:38, s. 13399-13409
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of the Mn/Fe cofactor identified in a new class of oxidases (R2lox) described by Andersson and Hogbom [Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5633] is reported. The R2lox protein is homologous to the small subunit of class Ic ribonucleotide reductase (R2c) but has a completely different in vivo function. Using multifrequency EPR and related pulse techniques, it is shown that the cofactor of R2lox represents an antiferromagnetically coupled Mn-III/Fe-III dimer linked by a mu-hydroxo/bis-mu-carboxylato bridging network. The Mn-III ion is coordinated by a single water ligand. The R2lox cofactor is photoactive, converting into a second form (R2lox(photo)) upon visible illumination at cryogenic temperatures (77 K) that completely decays upon warming. This second, unstable form of the cofactor more closely resembles the Mn-III/Fe-III cofactor seen in R2c. It is shown that the two forms of the R2lox cofactor differ primarily in terms of the local site geometry and electronic state of the Mn-III ion, as best evidenced by a reorientation of its unique Mn-55 hyperfine axis. Analysis of the metal hyperfine tensors in combination with density functional theory (DFT) calculations suggests that this change is triggered by deprotonation of the mu-hydroxo bridge. These results have important consequences for the mixed-metal R2c cofactor and the divergent chemistry R2lox and R2c perform.
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