[Show abstract][Hide abstract] ABSTRACT: Ring hydroxylation and coupled rearrangement reactions catalyzed by 4-hydroxyphenylpyruvate dioxygenase were studied with the QM/MM method ONIOM(B3LYP:AMBER). For electrophilic attack of the ferryl species on the aromatic ring, five channels were considered: attacks on the three ring atoms closest to the oxo ligand (C1, C2, C6) and insertion of oxygen across two bonds formed by them (C1-C2, C1-C6). For the subsequent migration of the carboxymethyl substituent, two possible directions were tested (C1->C2, C1->C6) and two different mechanisms were sought (step-wise radical, single-step heterolytic). In addition, formation of an epoxide (side)product and benzylic hydroxylation, as catalyzed by the closely related hydroxymandelate synthase, were investigated. From the computed reaction free energy profiles it follows that the most likely mechanism of 4-hydroxyphenylpyruvate dioxygenase involves electrophilic attack on the C1 carbon of the ring and subsequent single-step heterolytic migration of the substituent. Computed values of the kinetic isotope effect for this step are inverse, consistent with available experimental data. Electronic structure arguments for the preferred mechanism of attack on the ring are also presented.
Journal of the American Chemical Society 08/2014; · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The electronic structure of the Mn/Fe cofactor identified in a new class of oxidases (R2lox) described by Andersson and Högbom [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 μ-hydroxo/bis-μ-carboxylato bridging network. The Mn(III) ion is coordinated by a single water ligand. The R2lox cofactor is photoactive, converting into a second form (R2loxPhoto) 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 (55)Mn hyperfine axis. Analysis of the metal hyperfine tensors in combination with density functional theory (DFT) calculations suggest that this change is triggered by deprotonation of the μ-hydroxo bridge. These results have important consequences for mixed-metal R2c cofactor and the divergent chemistry these two systems perform.
Journal of the American Chemical Society 08/2014; · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Ni-containing methyl-coenzyme M reductase (MCR) is capable of catalyzing methane formation from methyl-coenzyme M (CH3-SCoM) and coenzyme B (CoB-SH), and also its reverse reaction (methane oxidation). Based on extensive experimental and theoretical investigations, it has turned out that a mechanism including an organometallic methyl-Ni(iii)F430 intermediate is inaccessible, while another mechanism involving a methyl radical and a Ni(ii)-SCoM species currently appears to be the most acceptable one for MCR. In the present paper, using hybrid density functional theory and an active-site model based on the X-ray crystal structure, two other mechanisms were studied and finally also ruled out. One of them, involving proton binding on the CH3-SCoM substrate, which should facilitate methyl-Ni(iii)F430 formation, is demonstrated to be quite unfavorable since the substrate has a much smaller proton affinity than the F430 cofactor. Another one (oxidative addition mechanism) is also shown to be unfavorable for the MCR reaction, due to the large endothermicity for the formation of the ternary intermediate with side-on C-S (for CH3-SCoM) or C-H (for methane) coordination to Ni.
Physical Chemistry Chemical Physics 06/2014; · 3.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The main parts of the water oxidation mechanism in photosystem II have now been established both from theory and experiments. Still, there are minor questions remaining. One of them concerns the charge and the protonation state of the oxygen evolving complex (OEC). Previously, theory and experiments have agreed that the two water derived ligands on the outer manganese should be one hydroxide and one water. In the present study it is investigated whether both of them could be water. This question is addressed by a detailed study of energy diagrams, but in this context it is more conclusive to compare the redox potential of the OEC to the one of TyrZ. Both procedures lead to the conclusion that one of the ligands is a hydroxide. Another question concerns the protonation of the second shell His337, where the results are more ambiguous. The final part of the present study describes results when calcium is removed from the OEC. Even though protons enter to compensate the charge of the missing Ca(2+), the redox potential and the pKa value of the OEC change dramatically and prevent the progress after S2.
Physical Chemistry Chemical Physics 03/2014; · 3.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O2 and solar fuels, such as H2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn2(II,III) catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O-O bond formation.
Physical Chemistry Chemical Physics 02/2014; · 3.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cytochrome c oxidase is a superfamily of membrane bound enzymes catalysing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested.This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
Biochimica et Biophysica Acta 01/2014; · 4.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Density functional calculations are used to elucidate the reaction mechanism of water oxidation catalyzed by iron tetraamido macrocyclic ligand (TAML) complexes. The oxidation of the starting TAML–Fe3+–OH2 complex by removing three electrons and two protons leads to the formation of a key intermediate, TAML· –Fe5+=O, which can undergo nucleophilic attack by either a water molecule or a nitrate ion. Both pathways involve attack on the oxo group and lead to the production of O2. The water attack is more favoured and has a total barrier of 15.4 kcal/mol. The alternative nitrate attack pathway has a barrier of 19.5 kcal/mol. Nitrate functions as a cocatalyst by first donating an oxygen atom to the oxo group to form O2 and a nitrite ion, which can then be re‐oxidized to regenerate a nitrate ion. Three possible competing pathways result in ligand modification, namely, water and nitrate attack on the ligand, as well as ligand amide oxidation. The water attack on the ligand has a low barrier of only 10.9 kcal/mol and leads to the opening of the benzene ring, which explains the observation of fast catalyst degradation. The lack of activity or lower activity of other catalysts with different substituents is also rationalized. The mechanism of water oxidation catalyzed by iron tetraamido macrocyclic ligand (TAML) complexes and catalyst deactivation are investigated by DFT calculations.
European Journal of Inorganic Chemistry 01/2014; 2014(4). · 3.12 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It has experimentally been found that certain mutations close to the entry point of the proton transfer channel in cytochrome c oxidase stop proton translocation but not the oxygen reduction chemistry. This effect is termed uncoupling. Since the mutations are 20 Å away from the catalytic center, this is very surprising. A new explanation for this phenomenon is suggested here, involving a local effect at the entry point of the proton channel, rather than the long range effects suggested earlier.
[Show abstract][Hide abstract] ABSTRACT: The full sequence of intermediates in the water oxidation process in photosystem II has recently been characterized by model calculations, in good agreement with experiments. In the present paper, the energy diagram obtained is used as a benchmark test for several density functionals. Only the results using B3LYP with 15% or 20% show good agreement with experiments. The other functionals tried show errors for some energy levels as large as 20–30 kcal/mol. The reason for these large errors is that the error for three consecutive oxidations of Mn(III) to Mn(IV) accumulates as the cluster is oxidized.
Journal of Chemical Theory and Computation 12/2013; 10(1):268–272. · 5.39 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Although metallocofactors are ubiquitous in enzyme catalysis, how metal binding specificity arises remains poorly understood, especially in the case of metals with similar primary ligand preferences such as manganese and iron. The biochemical selection of manganese over iron presents a particularly intricate problem because manganese is generally present in cells at a lower concentration than iron, while also having a lower predicted complex stability according to the Irving-Williams series (Mn(II) < Fe(II) < Ni(II) < Co(II) < Cu(II) > Zn(II)). Here we show that a heterodinuclear Mn/Fe cofactor with the same primary protein ligands in both metal sites self-assembles from Mn(II) and Fe(II) in vitro, thus diverging from the Irving-Williams series without requiring auxiliary factors such as metallochaperones. Crystallographic, spectroscopic, and computational data demonstrate that one of the two metal sites preferentially binds Fe(II) over Mn(II) as expected, whereas the other site is nonspecific, binding equal amounts of both metals in the absence of oxygen. Oxygen exposure results in further accumulation of the Mn/Fe cofactor, indicating that cofactor assembly is at least a two-step process governed by both the intrinsic metal specificity of the protein scaffold and additional effects exerted during oxygen binding or activation. We further show that the mixed-metal cofactor catalyzes a two-electron oxidation of the protein scaffold, yielding a tyrosine-valine ether cross-link. Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate.
Proceedings of the National Academy of Sciences 10/2013; · 9.81 Impact Factor
[Show abstract][Hide abstract] 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 CaMn$_4$O$_4$ 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$\cdot$ 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 Co$_4$O$_4$ complex with a defined structure, described by Dismukes et al, the calculated results are in excellent 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.
Journal of the American Chemical Society 08/2013; · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Detailed mechanisms for substrate water exchange in the oxygen evolving complex in photosystem II have been determined with DFT methods for large models. The experimental water exchange results have been the main argument against the water oxidation mechanism suggested by DFT, which otherwise is in line with most experiments. The problem has been that the mechanism requires a rather fast exchange of a bridging oxo ligand, which is not a common finding for smaller Mn-containing model systems. Three S-states have been studied and the rates have been well reproduced by the calculations. The surprising experimental finding that water exchange in S1 is slower than the one in S2 is reproduced and explained. The similar rate of the slow exchange in S2 and S3 has been rationalized based on earlier experiments combined with the present calculations. The results strongly support the previous DFT-suggested water oxidation mechanism, where the O-O bond should be formed between a bridging oxo ligand and a terminal oxyl radical in the center of the OEC.
Journal of the American Chemical Society 06/2013; · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The membrane-bound enzyme cNOR (cytochrome c dependent nitric oxide reductase) catalyses the reduction of NO in a non-electrogenic process. This is in contrast to the reduction of O2 in cytochrome c oxidase (CcO), the other member of the heme-copper oxidase family, which stores energy by generation of a membrane gradient. This difference between the two enzymes has not been understood, but it has been speculated to be of kinetic origin, since per electron the NO reduction is more exergonic than the O2 reduction, and the energy should thus be enough for an electrogenic process. However, it has not been clear how and why electrogenicity, which mainly affects the thermodynamics, would slow down the very exergonic NO reduction. Quantum chemical calculations are used to construct a free energy profile for the catalytic reduction of NO in the active site of cNOR. The energy profile shows that the reduction of the NO molecules by the enzyme and the formation of N2O are very exergonic steps, making the rereduction of the enzyme endergonic and rate-limiting for the entire catalytic cycle. Therefore the NO reduction cannot be electrogenic, i.e. cannot take electrons and protons from opposite sides of the membrane, since it would increase the endergonicity of the rereduction when the gradient is present, thereby increasing the rate-limiting barrier, and the reaction would become too slow. It also means that proton pumping coupled to electron transfer is not possible in cNOR. In CcO the corresponding rereduction of the enzyme is very exergonic.
Biochimica et Biophysica Acta 04/2013; · 4.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Activation of manganese-dependent class Ib ribonucleotide reductase by hydrogen peroxide was modeled using B3LYP* hybrid density functional theory. Class Ib ribonucleotide reductase R2 subunit (R2F) does not react with molecular oxygen. Instead R2F is proposed to react with H2O2 or HO2(-), provided by the unusual flavodoxin protein NrdI, to generate the observed manganese(III) manganese(III) tyrosyl-radical state. On the basis of the calculations, an energetically feasible reaction mechanism is suggested for activation by H2O2, which proceeds through two reductive half-reactions. In the first reductive half-reaction, H2O2 is cleaved with a barrier of 13.1 kcal mol(-1) [Mn(II)Mn(II) → Mn(III)Mn(III)], and in the second reductive half-reaction, H2O2 is cleaved with a barrier of 17.0 kcal mol(-1) [Mn(III)Mn(III) → Mn(IV)Mn(IV)]. Tyrosyl-radical formation from both the Mn(IV)Mn(IV) state and a Mn(III)Mn(IV) state, where an electron and proton have been taken up, is both kinetically and thermodynamically accessible. Hence, chemically, H2O2 is a possible oxidant for the manganese-dependent R2F. The selectivity between the second reductive half-reaction and a competing oxidative reaction, as in manganese catalase, may be the time scale for the availability of H2O2. The role of NrdI may be to provide H2O2 on the correct time scale.
[Show abstract][Hide abstract] ABSTRACT: Experiments have shown that the μ-η(2) :η(2) -peroxodicopper(II) complex [Cu(2) O(2) (N,N'-di-tert-butylethylenediamine)(2) ](2+) rapidly oxidizes 2,4-di-tert-butylphenolate into a mixture of catechol and quinone and that, at the extreme temperature of -120 °C, a bis-μ-oxodicopper(III)phenolate intermediate, labeled complex A, can be observed. These experimental results suggest a new mechanism of action for the dinuclear copper-containing enzyme tyrosinase, involving an early OO bond-cleavage step. However, whether phenolate binding occurs before or after the cleavage of the OO bond has not been possible to answer. In this study, hybrid density functional theory is used to study the synthetic reaction and, based on the calculated free-energy profile, a mechanism is suggested for the entire phenolate-oxidation reaction that agrees with the experimental observations. Most importantly, the calculations show that the very first step in the reaction is the cleavage of the OO bond in the peroxo complex and that, subsequently, the phenolate substrate coordinates to one of the copper ions in the bis-μ-oxodicopper(III) complex to yield the experimentally characterized phenolate intermediate (A). The oxidation of the phenolate substrate into a quinone then occurs in three steps: 1) CO bond formation, 2) coupled internal proton and electron transfer, and 3) electron transfer coupled to proton transfer from an external donor (acidic workup, experimentally). The first of these steps is rate limiting for the decay of complex A, with a calculated free-energy barrier of 10.7 kcal mol(-1) and a deuterium kinetic isotope effect of 0.90, which are in good agreement with the experimental values of 11.2 kcal mol(-1) and 0.83(±0.09). The tert-butyl substituents on both the phenol substrate and the copper ligands need to be included in the calculations to give a correct description of the reaction mechanism.
[Show abstract][Hide abstract] ABSTRACT: A series of [Ru(bpy)3]2+-type (bpy=2,2′-bipyridine) photosensitisers have been coupled to a ligand for Mn, which is expected to give a dinuclear complex that is active as a water oxidation catalyst. Unexpectedly, photophysical studies showed that the assemblies had very short lived excited states and that the decay patterns were complex and strongly dependent on pH. One dyad was prepared that was capable of catalysing chemical water oxidation by using [Ru(bpy)3]3+ as an oxidant. However, photochemical water oxidation in the presence of an external electron acceptor failed, presumably because the short excited-state lifetime precluded initial electron transfer to the added acceptor. The photophysical behaviour could be explained by the presence of an intricate excited-state manifold, as also suggested by time-dependent DFT calculations.
[Show abstract][Hide abstract] ABSTRACT: Hydroxymandelate synthase (HMS) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) are highly related enzymes using the same substrates, but catalyzing hydroxylation reactions yielding different products. The first steps of the HMS and HPPD catalytic reactions are believed to proceed in the same way and lead to a Fe(IV)=O / hydroxyphenylacetate (HPA) intermediate. Further down the catalytic cycles, HMS uses Fe(IV)=O to perform hydroxylation of the benzylic carbon, whereas in HPPD the reactive oxoferryl intermediate attacks the aromatic ring of HPA. The present study is focused on this part of the HMS catalytic cycle which starts from the oxoferryl intermediate, and is aimed at identifying interactions within the active site which are responsible for the enzyme specicity. To this end, a HMS-Fe(IV)=O-HPA complex was modelled with molecular dynamics simulations. Based on the MD-equilibrated structure an active site model suitable for quantum chemical investigations was constructed and used for DFT (B3LYP) calculations on the mechanism of the native reaction of HMS, i.e. benzylic hydroxylation, and the alternative electrophilic attack on the ring, which is a step of the HPPD catalytic cycle. The most important result of the present study is the finding that the conformation of the Ser201 side chain in the second coordination shell has a key role for directing the reaction of the Fe(IV)=O either into the HMS or the HPPD channel.
[Show abstract][Hide abstract] ABSTRACT: The present status of DFT studies on water oxidation in photosystem II is described. It is argued that a full understanding of all steps is close. In each S-transition, the manganese that is oxidized and the proton released are strongly implicated, and structures of all intermediates have been determined. For the S(2)-state, recent important experimental findings support key elements of the structure and the mechanism. In this mechanism, the O-O bond is formed between an oxyl radical in the center of the cluster and an Mn-bridging μ-oxo ligand, which was suggested already in 2006. The DFT structure of the oxygen evolving complex, suggested in 2008, is very similar to the recent high-resolution X-ray structure. Some new aspects of the interaction between P(680) and the OEC are suggested.
Biochimica et Biophysica Acta 10/2012; · 4.66 Impact Factor