Per E. M. Siegbahn's research while affiliated with Stockholm University and other places

Publications (515)

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The level of carbon dioxide in the atmosphere has increased in a dangerous way during the past century. Methods to decrease this level are therefore of high interest at present. Inspiration to do so in an efficient way could come from biological systems. Molybdenum-containing formate dehydrogenase (Mo-FDH) is one of the most interesting enzymes in...
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Nitrogenase is the only enzyme in nature that can fix N 2 from the air. The active cofactor of the leading form of this enzyme contains seven irons and one molybdenum, connected by sulfide bridges. In several recent experimental studies it has been suggested that the cofactor is very flexible, and may lose one of its sulfides during catalysis. In t...
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QM/MM calculations have been used to elucidate the reaction mechanism of the reduction of acetylene to ethylene catalyzed by a nitrogenase-like enzyme DCCPCh with an unusual [Fe8S9] double-cubane cluster. Various plausible reaction pathways, involving different oxidation states and protonation states of the iron-sulfur cluster, have been analyzed t...
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The present study concerns the technical aspects of obtaining the energetics for the E4 state of nitrogenase, the enzyme that fixes N2 in nature. EPR experiments have shown that the critical E4 structure that activates N2 should contain two bridging hydrides in the FeMo‐cofactor. It is furthermore in equilibrium with a structure where the two hydri...
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During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading elec...
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The energetics for proton reduction in FeFe-hydrogenase has been reinvestigated by theoretical modeling, in light of recent experiments. Two different mechanisms have been considered. In the first one, the bridging hydride position was blocked by the enzyme, which is the mechanism that has been supported by a recent spectroscopic study by Cramer et...
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The biological synthesis of acetyl-coenzyme A (acetyl-CoA), catalyzed by acetyl-CoA synthase (ACS), is of biological significance and chemical interest acting as a source of energy and carbon. The catalyst contains an unusual hexa-metal cluster with two nickel ions and a [Fe4S4] cluster. DFT calculations have been performed to investigate the ACS r...
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The mechanism for water oxidation in photosystem II (PSII) has been a major topic for several decades. The active catalyst has four manganese atoms connected by bridging oxo bonds, in a complex termed the oxygen-evolving complex (OEC), which also includes a calcium atom. The O-O bond of oxygen is formed after absorption of four photons in a state o...
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Recent electrochemical experiments have shown that the reduction of O2 can be driven backwards to water oxidation, which is the first case where that has been successfully demonstrated for an enzyme. In order to understand that ability of the enzyme, both the forward reduction and backward oxidation have been studied here. For the forward reaction,...
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The iron-porphyrin complex with four positively-charged N,N,N-trimethyl-4-ammoniumphenyl substituents (called WSCAT) is an efficient catalyst for the reduction of CO2 to CO in aqueous solution with excellent selectivity. Density functional calculations have been carried out to explore the reaction mechanism and the origin of selectivity. The porphy...
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The mechanism for oxidation of the hydrogen molecule by NiFe-hydrogenase is reinvestigated. In contrast to most earlier studies, the emphasis is on the entire mechanism including the oxidation steps. An estimate of the driving force is made, and the main effects of entropy are included. Two different mechanisms are investigated, not only the standa...
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The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-depende...
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The catalytic cofactor of the most common form of nitrogenase contains seven irons and one molybdenum bound together by sulfide bonds. Surprisingly, a central carbide has been demonstrated by experiments. Another noteworthy structural component is a large homocitrate ligand. In recent theoretical studies it has been shown that the central carbide is...
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Nickel-containing carbon monoxide (CO) dehydrogenase is an enzyme that catalyzes the important reversible carbon dioxide reduction. Several high-resolution structures have been determined at various stages of the reduction, which can be used as good starting points for the present computational study. The cluster model is used in combination with a...
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The heterotrinuclear complex A {[RuII(H2O)(trpy)]2(μ‐[MnII(H2O)2(bpp)2])}4+ was disclosed to catalyze water oxidation both electrochemically and photochemically with [Ru(bpy)3]3+ as the photosensitizer and Na2S2O8 as the electron acceptor in neutral phosphate buffer. The mechanism of water oxidation catalyzed by this unprecedented trinuclear comple...
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When DFT has been applied to study mechanisms of redox processes a common procedure has been to study the results for many different functionals. For redox reactions involving the first row transition metals, this approach has given very different results for different functionals. The conclusion has been that DFT cannot be used for these reactions...
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The mechanism of the H2O2 disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger...
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AurF is a diiron enzyme that utilizes two dioxygen molecules as the oxidant to catalyze the oxidation of p‐aminobenzoate to p‐nitrobenzoate. Density functional calculations were performed to elucidate the reaction mechanism of this enzyme. Two different models were considered, with the oxygenated intermediate being a diferric peroxo species or a di...
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Understanding the water oxidation mechanism, especially how the O-O bond formation takes place, provides crucial implication for the design of more efficient molecular catalysts for water oxidation in artificial photosynthesis. Density functional calculations have here been used to revisit the mechanism of O-O bond formation catalyzed by a pentanuc...
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Catalysts for oxidation of water to molecular oxygen are essential in solar-driven water splitting. In order to develop more efficient catalysts for this oxidatively demanding reaction, it is vital to have mechanistic insight in order to understand how the catalysts operate. Herein, we report the mechanistic details associated with the two Ru catal...
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The formation of O$_2$ from water requires four transitions, each one after the absorption of one light flash. The mechanism for one of these transitions, the one from S$_2$ to S$_3$, has been under considerable debate the past five years. There has since long been a concensus that one water molecule becomes inserted into the OEC in this transition...
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Mo-containing nitrogenase is the main enzyme that is able to take N2 from the air and form ammonia. The active-site cofactor of the enzyme, termed FeMoco, is unique in nature. It has seven Fe and one Mo atoms connected by S bridges, with a C atom in the center of the cofactor. Another unusual feature is that it has a large homocitrate ligand known...
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In the key enzyme for nitrogen fixation in nature, nitrogenase, the active site has a metal cluster with seven irons and one molybdenum bound by bridging sulfurs. Surprisingly, there is also a carbon in the center of the cluster, with a role that is not known. A mechanism has been suggested experimentally, where two hydrides leave as a hydrogen mol...
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The Cover Feature shows transition-metal-catalyzed oxygen evolution by water oxidation with the liberation of protons and electrons. Density functional calculations can be used to elucidate the catalytic mechanism, calculate pKas and redox potentials, and construct full energy diagram for the whole catalytic cycle. More information can be found in...
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The laboratory synthesis of complexes to mimic the structure of the Mn4Ca cluster in the oxygen-evolving complex (OEC) of photosystem II is a very challenging task to accomplish. The most encouraging breakthrough in this field was recently achieved with the synthesis of a Mn4Ca complex (Zhang et al., 2015) that shows a very similar core structure t...
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The design of efficient and robust water oxidation catalysts has proven challenging in the development of artificial photosynthetic systems for solar energy harnessing and storage. Tremendous progress has been made in the development of homogeneous transition metal complexes capable of mediating water oxidation. To improve the efficiency of the cat...
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Recent free-electron laser (X-FEL) studies have suggested S3 states with many features as expected based on previous model calculations and spectroscopy. However, in one of them there is one dramatic surprise. An hydroxide (at the O6 position) on Mn1 was expected, but this group is missing in that X-FEL structure. It has previously been concluded t...
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Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculati...
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Two different types of mechanisms are at present suggested for the O-O bond-formation step in photosystem II. The first one is a coupling between an oxyl radical and a bridging oxo. The second one is a nucleophilic water attack on a terminal oxo (or oxyl) group. In the present short paper, the six most reasonable versions of the latter mechanism ha...
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EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sul...
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Water oxidation is a fundamental step in artificial photosynthesis for solar fuels production. In this study, we report a single-site Ru-based water oxidation catalyst, housing a dicarboxylate-benzimidazole ligand, that mediates both chemical and light-driven oxidation of water efficiently under neutral conditions. The importance of the incorporati...
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The design and synthesis of biomimetic Mn complexes to catalyze oxygen evolution is a very appealing goal since water oxidation in nature employs manganese. A mononuclear Mn complex 1 [LMnII(H2O)2]2+ (L=Py2N(tBu)2) was recently reported to catalyze water oxidation electrochemically with an applied potential of 1.23 V at pH=12.2 in aqueous solution....
Article
Nitrogen activation by nitrogenase is one of the most important enzymatic processes on earth. In spite of the determination of X-ray structures of increasingly higher resolution, the nitrogenase mechanism is still not understood. In the most recent X-ray structures it has been shown that a carbon resides in the center of the MoFe-cofactor. Its role...
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PceA is a cobalamin-dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis-dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perc...
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The synthesis of two molecular iron complexes, a dinuclear iron(III,III) complex and a nonanuclear iron complex, based on the dinucleating ligand 2,2'-(2-hydroxy-5-methyl-1,3-phenylene)bis(1H-benzo[d]imidazole-4-carboxylic acid) is described. The two iron complexes were found to drive the oxidation of water by the oneelectron oxidant [Ru(bpy)3]³⁺.
Article
Quantum chemical calculations play an essential role in the elucidation of reaction mechanisms for redox-active metalloenzymes. For example, the cleavage and the formation of covalent bonds can usually not be described only on the basis of experimental information, but can be followed by the calculations. Conversely, there are properties, like redu...
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Development of efficient and robust catalysts for H2O oxidation is an essential element in solar water splitting. The reaction mechanism for a previously reported dinuclear Ru water oxidation catalyst (1) has been investigated in detail through quantum chemical calculations. The predicted mechanism starts from a Ru2III,III complex with two aqua lig...
Article
Water oxidation is a fundamental step in artificial photosynthesis for solar fuels production. In this study, we report a singlesite Ru-based water oxidation catalyst, housing a dicarboxylate-benzimidazole ligand, that mediates both chemical and light-driven oxidation of water efficiently under neutral conditions. The importance of the incorporatio...
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PhoX is a pentanuclear metalloenzyme that employs two ferric ions and three calcium ions to catalyze the hydrolysis of phosphomonoesters. On the basis of the X-ray structure of PhoX ( Science 2014 , 345 , 1170 - 1173 ), a model of the active site is designed, and quantum chemical calculations are used to investigate the reaction mechanism of this e...
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For the main parts of the mechanism for water oxidation in photosystem II there has recently been very strong experimental support for the mechanism suggested by theoretical model studies. The question addressed in the present study is to what extent this knowledge can be used for the design of artificial catalysts. A major requirement for a useful...
Article
The quantum chemical cluster approach was used to elucidate the reaction mechanism of debromination catalyzed by the B12-dependent reductive dehalogenase NpRdhA. Various pathways, involving different oxidation states of the cobalt ion and different protonation states of the model, have been analyzed in order to find the most favorable one. We find...
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Robust catalysts that mediate H2O oxidation are of fundamental importance for the development of novel carbon-neutral energy technologies. Herein we report the synthesis of a group of single-site Ru complexes. Structure–activity studies revealed that the individual steps in the oxidation of H2O depended differently on the electronic properties of t...
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One of the remaining mysteries regarding the respiratory enzyme cytochrome c oxidase is how proton pumping can occur in all reduction steps in spite of the low reduction potentials observed in equilibrium titration experiments for two of the active site cofactors, CuB(II) and Fea3(III). It has been speculated that, at least the copper cofactor can...
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The increasing energy demand calls for the development of sustainable energy conversion processes. Here, the splitting of H2O to O2 and H2, or related fuels, constitutes an excellent example of solar-to-fuel conversion schemes. The critical component in such schemes has proven to be the catalyst responsible for mediating the four-electron oxidation...
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Insight into how H2O is oxidized to O2 is envisioned to facilitate the rational design of artificial water oxidation catalysts, which is a vital component in solar-to-fuel conversion schemes. Herein, we report on the mechanistic features associated with a dinuclear Ru-based water oxidation catalyst. The catalytic action of the designed Ru complex w...
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The mechanism of water reduction catalysed by a mononuclear copper complex Cu(bztpen) (bztpen= N-benzyl-N,N’,N’-tris(pyridine-2-ylmethyl)ethylenediamine) has been elucidated by DFT calculations, revealing that hydrogen evolution proceeds via coupling of a Cu(II)-hydride and a pendant pyridinium, and providing important implications for the future d...
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In a previous detailed study of all the steps of water oxidation in photosystem II, it was surprisingly found that O2 release is as critical for the rate as O-O bond formation. A new mechanism for O2 release has now been found, which can be described as an opening followed by a closing of the interior of the oxygen evolving complex. A transition st...
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Most of the main features of water oxidation in photosystem II are now well understood, including the mechanism for O-O bond formation. For the intermediate S2 and S3 structures there is also nearly complete agreement between quantum chemical modeling and experiments. Given the present high degree of consensus for these structures, it is of high in...
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Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron emzymes. We report a density fun...
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Electrocatalytic water oxidation using the oxidatively robust 2,7-[bis(2-pyridylmethyl)aminomethyl]-1,8-naphthyridine ligand (BPMAN)-based dinuclear copper(II) complex, [Cu2(BPMAN)(μ-OH)]3+, has been investigated. This catalyst exhibits high reactivity and stability towards water oxidation in neutral aqueous solutions. DFT calculations suggest that...
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Electrocatalytic water oxidation using the oxidatively robust 2,7-[bis(2-pyridylmethyl)aminomethyl]-1,8-naphthyridine ligand (BPMAN)-based dinuclear copper(II) complex, [Cu2 (BPMAN)(μ-OH)](3+) , has been investigated. This catalyst exhibits high reactivity and stability towards water oxidation in neutral aqueous solutions. DFT calculations suggest...
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Herein is described the preparation of a dinuclear molecular Ru catalyst for H2O oxidation. The prepared catalyst mediates the photochemical oxidation of H2O with an efficiency comparable to state-of-the-art catalysts.
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Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present q...
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The synthesis of Mn-based catalysts to mimic the structural and catalytic properties of the oxygen-evolving complex in photosystem II is a long-standing goal for researchers. An interesting result in this field came with the synthesis of a Mn complex that enables water oxidation driven by the mild single-electron oxidant [Ru(bpy)3](3+). On the basi...
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Density functional calculations are used to revisit the reaction mechanism of water oxidation catalyzed by the Cp*Ir(bpy)Cl (Cp* = pentamethylcyclopentadienyl, bpy = 2,2′-bipyridine) complex. One of the experimentally suggested active species [(bpy)Ir(H2O)2(HCOO)Cl]+ can undergo very facile intramolecular formate oxidation at higher oxidation state...
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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 oxy...
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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 multifre...
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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 strongl...
Article
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 int...
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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...
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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 cat...
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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...
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The study focused on the mechanisms of redox-active metalloenzymes, while computational results on structural and spectroscopic issues which were directly related to the mechanisms were rarely treated. There were also some results for metalloenzymes that were not redox-active, such as the section on zinc-containing enzymes, since the modeling aspec...
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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 enti...
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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 p...
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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...
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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 p...
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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 be...
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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 t...
Article
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 th...
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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 generat...
Article
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. The...
Article
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) i...
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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 experi...
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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(4)Ca 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...
Article
Ni-containing methyl-coenzyme M reductase (MCR) is capable of catalyzing methane formation and has recently been observed to also be able to catalyze the reverse reaction, the anaerobic oxidation of methane. The forward reaction has been extensively studied theoretically before and was found to consist of two steps. The first step is rate-limiting...
Article
The catalytic mechanism of reduction of NO to N(2)O in the bacterial enzyme nitric oxide reductase has been investigated using hybrid density functional theory and a model of the binuclear center (BNC) based on the newly determined crystal structure. The calculations strongly suggest a so-called cis:b(3) mechanism, while the commonly suggested tran...
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6-Hydroxymethyl-6-methylcyclohexa-2,4-dienone is a mechanistic probe which when incubated with an extradiol dioxygenase yields a 2-tropolone product. This observation was originally interpreted as evidence supporting a direct heterolytic 1,2-alkenyl migration mechanism for a ring expansion reaction catalyzed by this class of Fe(II)-dependent nonhem...
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The mechanism for proton pumping in cytochrome c oxidase in the respiratory chain, has for decades been one of the main unsolved problems in biochemistry. However, even though several different suggested mechanisms exist, many of the steps in these mechanisms are quite similar and constitute a general consensus framework for discussing proton pumpi...