Per E. M. Siegbahn

Stockholm University, Tukholma, Stockholm, Sweden

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Publications (451)2165.92 Total impact

  • Rong-Zhen Liao · Per E. M. Siegbahn
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    ABSTRACT: 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 enzyme. The calculations support the experimental suggestion, in which the two high spin ferric ions interact in an antiferromagnetic fashion. The two step mechanism proposed by experimentalists has been investigated. The nucleophilic attack of a trinuclear bridging oxo group on the phosphorus center was calculated to be the first step, which is concomitant with the departure of the phenolate, which is stabilized by a calcium ion. The second step is a reverse attack by a water molecule activated by a calcium-bound hydroxide, leading to the regeneration of the bridging oxo group. The second step was calculated to have a barrier of 27.6 kcal/mol. The high barrier suggests that the alternative mechanism involving phosphate release directly from the active site seems to be more likely. All five metal ions are involved in the catalysis by stabilizing the pentacoordinated trigonal bipyramidal transition states.
    No preview · Article · Dec 2015 · Inorganic Chemistry
  • Xichen Li · Per E M Siegbahn
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    ABSTRACT: 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 artificial catalyst is that it is small enough to be synthesized. Small catalysts also have the big advantage that they could improve the catalysis per surface area. To make the mechanism found for PSII useful in this context, it needs to be analyzed in detail. A small model system was therefore used and the ligands were replaced one by one by water-derived ligands. Only the main chemical step of OO bond formation was investigated in this initial study. The energetics for this small model and the larger one previously used for PSII are remarkably similar, which is the most important result of the present study. This shows that small model complexes have a potential for being very good water oxidation catalysts. It was furthermore found that there is a clear correlation between the barrier height for OO bond formation and the type of optimal structure for the S3 state. The analysis shows that a flexible central part of the complex is the key for efficient water oxidation.
    No preview · Article · Nov 2015 · Chemistry - A European Journal
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    ABSTRACT: 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 the introduced ligand substituents. The mechanistic details associated with these complexes were investigated experimentally along with quantum chemical calculations. It was found that O–O bond formation for the developed Ru complexes proceeds via high-valent RuVI species, where the capability of accessing this species is derived from the non-innocent ligand architecture. This cooperative catalytic involvement and the ability of accessing RuVI are intriguing and distinguish these Ru catalysts from a majority of previously reported complexes, and might generate unexplored reaction pathways for activation of small molecules such as H2O.
    No preview · Article · Nov 2015 · Catalysis Science & Technology
  • Rong-Zhen Liao · Shi-Lu Chen · Per E.M. Siegbahn
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    ABSTRACT: 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 that the reductive C-Br cleavage takes place exclusively at the CoI state via a heterolytic pathway in the singlet state. Importantly, the C-H bond formation and the C-Br bond cleavage proceeds via a concerted transition state, as opposed to the stepwise pathway suggested before. C-Br cleavage at the CoII state has a very high barrier, and the reduction of CoI to Co0 is associated with a very negative potential; thus, reductive dehalogenation at CoII and Co0 can be safely ruled out. Examination of substrates with different halogen substitutions (F, Cl, Br, I) shows that the dehalogenation reactivity follows the order C-I > C-Br > C-Cl > C-F, and the barrier for defluorination is so high that NpRdhA cannot catalyze that reaction.
    No preview · Article · Nov 2015 · ACS Catalysis
  • Margareta R.A. Blomberg · Per E M Siegbahn
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    ABSTRACT: 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 acquire two different states, one metastable activated state occurring during enzyme turnover, and one relaxed state with lower energy, reached only when the supply of electrons stops. The activated state should have a transiently increased CuB(II) reduction potential, allowing proton pumping. The relaxed state should have a lower reduction potential, as measured in the titration experiments. However, the structures of these two states are not known. Quantum mechanical calculations show that the proton coupled reduction potential for CuB is inherently high in the active site as it appears after reaction with oxygen, which explains the observed proton pumping. It is suggested here that, when the flow of electrons ceases, a relaxed resting state is formed by the uptake of one extra proton, on top of the charge compensating protons delivered in each reduction step. The extra proton in the active site decreases the proton coupled reduction potential for CuB by almost half a volt, leading to agreement with titration experiments. Furthermore, the structure for the resting state with an extra proton is found to have a hydroxo-bridge between CuB(II) and Fea3(III), yielding a magnetic coupling that can explain the experimentally observed EPR silence. Copyright © 2015. Published by Elsevier B.V.
    No preview · Article · Jun 2015 · Biochimica et Biophysica Acta
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    ABSTRACT: 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 of H2O to O2. Herein, we report on the unexpected formation of a single-site Ru complex from a ligand envisioned to accommodate two metal centers. Surprising N–N bond cleavage of the designed dinuclear ligand during metal complexation resulted in a single-site Ru complex carrying a carboxylate–amide motif. This ligand lowered the redox potential of the Ru complex sufficiently to permit H2O oxidation to be carried out by the mild one-electron oxidant [Ru(bpy)3]3+ (bpy = 2,2′-bipyridine). The work thus highlights that strongly electron-donating ligands are important elements in the design of novel, efficient H2O oxidation catalysts.
    No preview · Article · May 2015 · Inorganic Chemistry
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    ABSTRACT: 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 was studied by the combined use of high-resolution mass spectrometry, electrochemistry, and quantum chemical calculations. Based on the obtained results, it is suggested that the designed ligand scaffold in Ru complex 1 has a non-innocent behavior, in which metal-ligand cooperation is an important part during the four-electron oxidation of H2O. This feature is vital for the observed catalytic efficiency and highlights that the preparation of catalysts housing non-innocent molecular frameworks could be a general strategy for accessing efficient catalysts for activation of H2O.
    Full-text · Article · Apr 2015 · Chemistry
  • Rong-Zhen Liao · Mei Wang · Licheng Sun · Per E M Siegbahn
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    ABSTRACT: 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 design of new catalytic systems for water reduction.
    No preview · Article · Apr 2015 · Dalton Transactions
  • Xichen Li · Per E M Siegbahn
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    ABSTRACT: 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 state for peroxide rotation forming a superoxide radical, missed in the previous study, and a structural change around the outside manganese are two key steps in the new mechanism. However, O2 release may still remain rate-limiting. Additionally, for the step forming the O-O bond, an alternative, experimentally suggested, mechanism was investigated. The new model calculations can rule out the precise use of that mechanism. However, a variant with a rotation of the ligands around the outer manganese by about 30° will give a low barrier, competitive with the old DFT mechanism. Both these mechanisms use an oxyl-oxo mechanism for O-O bond formation involving the same two manganese atoms and the central oxo group (O5).
    No preview · Article · Apr 2015 · Physical Chemistry Chemical Physics
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    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.
    Full-text · Article · Mar 2015 · Proceedings of the National Academy of Sciences
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    Rong-Zhen Liao · Per E. M. 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.
    Full-text · Article · Mar 2015 · Chemical Science
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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.
    Full-text · Article · Feb 2015 · Angewandte Chemie International Edition in English
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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.
    Full-text · Article · Feb 2015 · Angewandte Chemie
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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.
    Full-text · Article · Dec 2014 · Chemical Communications
  • 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.
    No preview · Article · Dec 2014 · Biochimica et Biophysica Acta (BBA) - Bioenergetics
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    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.
    Full-text · Article · Dec 2014 · Journal of Photochemistry and Photobiology B Biology
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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.
    Full-text · Article · Dec 2014 · Inorganic Chemistry
  • Rong-Zhen Liao · Per E. M. Siegbahn
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    ABSTRACT: 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 even though it can also promote O–O bond formation. Therefore, [(bpy)Ir(H2O)2(CH3COO)Cl]+ is here proposed to be the most likely precatalyst as acetate was also experimentally observed after Cp* oxidation. O–O bond formation takes place at the high formal oxidation states of IrVI and IrVII, rather than that of IrV, as suggested before. Three sequential proton-coupled electron transfer oxidations result in the formation of a highly oxidized intermediate, [(bpy)IrVIO(OH)(CH3COO)Cl]+. From this formal IrVI intermediate, O–O bond formation takes place by a water attack on the IrVI=O moiety assisted by the acetate ligand, which abstracts a proton during the attack. The barrier was calculated to be very facile, being 14.7 kcal/mol, in good agreement with experimental kinetic results, which gave a barrier of around 18 kcal/mol. The attack leads to the formation of an IrIV-peroxide intermediate, which undergoes proton-coupled electron transfer to form an IrIII–O2 intermediate. Finally, O2 can be released, coupled with the binding of another water molecule, to regenerate the catalytic IrIII species. Water oxidation at IrVII has a slightly higher barrier, but it may also contribute to the activity. However, water oxidation at IrV has a significantly higher barrier. Acetate oxidation by C–H activation was found to have a much higher barrier, suggesting that [(bpy)Ir(H2O)2(CH3COO)Cl]+ is a remarkably stable catalyst. The possible catalytic species [(bpy-dc)IrIII(H2O)3Cl]2+ without acetate coordination has also been considered and also gave a reasonably feasible barrier for the water oxidation. O–O bond formation at IrVII is slightly preferred compared with at IrVI, which is different from the case with acetate.Keywords: water oxidation; reaction mechanism; density functional calculations; iridium; proton-coupled electron transfer
    No preview · Article · Nov 2014 · ACS Catalysis
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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.
    Full-text · Article · Aug 2014 · Journal of the American Chemical Society
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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.
    No preview · Article · Aug 2014 · Journal of the American Chemical Society

Publication Stats

21k Citations
2,165.92 Total Impact Points

Institutions

  • 1971-2015
    • Stockholm University
      • • Department of Organic Chemistry
      • • Department of Physics
      • • Department of Biochemistry and Biophysics
      • • Division of Chemical Physics
      Tukholma, Stockholm, Sweden
  • 2010
    • Yale-New Haven Hospital
      New Haven, Connecticut, United States
  • 2004-2009
    • AlbaNova University Center
      Tukholma, Stockholm, Sweden
  • 1995
    • University of Wisconsin–Madison
      Madison, Wisconsin, United States
  • 1989
    • University of Minnesota Duluth
      • Department of Chemistry and Biochemistry
      Duluth, Minnesota, United States
  • 1982-1989
    • Nordic Institute for Theoretical Physics
      Tukholma, Stockholm, Sweden