Per E. M. Siegbahn

Stockholm University, Tukholma, Stockholm, Sweden

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Publications (411)1972.32 Total impact

  • Xichen Li, Per E M Siegbahn, Ulf Ryde
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    ABSTRACT: 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 interest to go back to previous suggestions concerning what happens in the S2-S3 transition. Analyses of extended X-ray adsorption fine structure (EXAFS) experiments have indicated relatively large structural changes in this transition, with changes of distances sometimes larger than 0.3 Å and a change of topology. In contrast, our previous density functional theory (DFT)(B3LYP) calculations on a cluster model showed very small changes, less than 0.1 Å. It is here found that the DFT structures are also consistent with the EXAFS spectra for the S2 and S3 states within normal errors of DFT. The analysis suggests that there are severe problems in interpreting EXAFS spectra for these complicated systems.
  • Rong-Zhen Liao, Per Siegbahn
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    ABSTRACT: 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 functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O2 molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O-O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal/mol, respectively. The barrier difference is 2.8 kcal/mol, corresponding to a diastereomeric excess of about 99:1. Further isomerization from epoxide to phenol is found to have quite high barrier, which can not compete with the product release step. After product release into solution, fast epoxide-oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2-O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3-O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal/mol. Further experimental studies are encouraged to verify our results.
    Chemical Science 03/2015; DOI:10.1039/C5SC00313J · 8.60 Impact Factor
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    ABSTRACT: 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 the OO bond formation takes place by an intramolecular direct coupling mechanism rather than by a nucleophilic attack of water on the high-oxidation-state Cu(IV) O moiety. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Angewandte Chemie International Edition in English 02/2015; DOI:10.1002/anie.201411625 · 13.45 Impact Factor
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    ABSTRACT: 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 the OO bond formation takes place by an intramolecular direct coupling mechanism rather than by a nucleophilic attack of water on the high-oxidation-state CuIVO moiety.
    Angewandte Chemie 02/2015; DOI:10.1002/ange.201411625
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    ABSTRACT: 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.
    Chemical Communications 12/2014; DOI:10.1039/c4cc08606f · 6.72 Impact Factor
  • Margareta R.A. Blomberg, Per E.M. Siegbahn
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    ABSTRACT: 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 quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labelled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover.
    Biochimica et Biophysica Acta (BBA) - Bioenergetics 12/2014; DOI:10.1016/j.bbabio.2014.12.005 · 4.83 Impact Factor
  • Rong-Zhen Liao, Per E M Siegbahn
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    ABSTRACT: Density functional theory calculations have been used to study the reaction mechanism of water oxidation catalyzed by a tetranuclear Mn-oxo cluster Mn4O4L6 (L=(C6H4)2PO4(-)). It is proposed that the OO bond formation mechanism is different in the gas phase and in a water solution. In the gas phase, upon phosphate ligand dissociation triggered by light absorption, the OO bond formation starting with both the Mn4(III,III,IV,IV) and Mn4(III,IV,IV,IV) oxidation states has to take place via direct coupling of two bridging oxo groups. The calculated barriers are 42.3 and 37.1kcal/mol, respectively, and there is an endergonicity of more than 10kcal/mol. Additional photons are needed to overcome these large barriers. In water solution, water binding to the two vacant sites of the Mn ions, again after phosphate dissociation triggered by light absorption, is thermodynamically and kinetically very favorable. The catalytic cycle is suggested to start from the Mn4(III,III,III,IV) oxidation state. The removal of three electrons and three protons leads to the formation of a Mn4(III,IV,IV,IV)-oxyl radical complex. The OO bond formation then proceeds via a nucleophilic attack of water on the Mn(IV)-oxyl radical assisted by a Mn-bound hydroxide that abstracts a proton during the attack. This step was calculated to be rate-limiting with a total barrier of 29.2kcal/mol. This is followed by proton-coupled electron transfer, O2 release, and water binding to start the next catalytic cycle. Copyright © 2014 Elsevier B.V. All rights reserved.
    Journal of Photochemistry and Photobiology B Biology 12/2014; DOI:10.1016/j.jphotobiol.2014.12.005 · 2.80 Impact Factor
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    ABSTRACT: 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 basis of hybrid density functional calculations, we herein propose a water oxidation mechanism for this bioinspired Mn catalyst, where the crucial O-O bond formation proceeds from the formal Mn4(IV,IV,IV,V) state by direct coupling of a Mn(IV)-bound terminal oxyl radical and a di-Mn bridging oxo group, a mechanism quite similar to the presently leading suggestion for the natural system. Of importance here is that the designed ligand is shown to be redox-active and can therefore store redox equivalents during the catalytic transitions, thereby alleviating the redox processes at the Mn centers.
    Inorganic Chemistry 12/2014; DOI:10.1021/ic5024983 · 4.79 Impact Factor
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    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; 136(41). DOI:10.1021/ja506378u · 11.44 Impact Factor
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    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; 136(38). DOI:10.1021/ja507435t · 11.44 Impact Factor
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    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.
    ChemPlusChem 07/2014; 79:936-950. DOI:10.1002/cplu.201402006 · 3.24 Impact Factor
  • Shi-Lu Chen, Margareta R A Blomberg, Per E M Siegbahn
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    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; 16(27). DOI:10.1039/c4cp01483a · 4.20 Impact Factor
  • Per E M Siegbahn
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    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; 16(24). DOI:10.1039/c3cp55329a · 4.20 Impact Factor
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    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; 16(24). DOI:10.1039/c3cp54800g · 4.20 Impact Factor
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    Rong‐Zhen Liao, Xi‐Chen Li, Per E. M. Siegbahn
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    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 02/2014; 2014(4). DOI:10.1002/ejic.201300710 · 2.97 Impact Factor
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    Chemical Reviews 01/2014; 114(7). DOI:10.1021/cr400388t · 45.66 Impact Factor
  • Margareta R A Blomberg, Per E M Siegbahn
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    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; DOI:10.1016/j.bbabio.2014.01.002 · 4.66 Impact Factor
  • Per E M Siegbahn, Margareta R A Blomberg
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    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.
    FEBS letters 12/2013; DOI:10.1016/j.febslet.2013.12.020 · 3.54 Impact Factor
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    Per E. M. Siegbahn, Margareta R. A. Blomberg
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    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. DOI:10.1021/ct401039h · 5.31 Impact Factor
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Publication Stats

15k Citations
1,972.32 Total Impact Points

Institutions

  • 1972–2015
    • Stockholm University
      • • Department of Organic Chemistry
      • • Department of Biochemistry and Biophysics
      • • Department of Physics
      • • Division of Chemical Physics
      Tukholma, Stockholm, Sweden
  • 2004–2012
    • AlbaNova University Center
      Tukholma, Stockholm, Sweden
  • 2010
    • Yale-New Haven Hospital
      New Haven, Connecticut, United States
  • 2008
    • Instytut Katalizy i Fizykochemii Powierzchni im. Jerzego Habera, Polskiej Akademii Nauk
      Cracovia, Lesser Poland Voivodeship, Poland
  • 2002
    • Yale University
      • Department of Chemistry
      New Haven, Connecticut, United States
  • 1989
    • University of Minnesota Duluth
      Duluth, Minnesota, United States