Per E M Siegbahn

Summary

Affiliation: Stockholm University
Country: Sweden

Publications

  1. ncbi request reprint Nickel superoxide dismutase reaction mechanism studied by hybrid density functional methods
    Vladimir Pelmenschikov
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    J Am Chem Soc 128:7466-75. 2006
  2. doi request reprint A structure-consistent mechanism for dioxygen formation in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, 106 91 Stockholm, Sweden
    Chemistry 14:8290-302. 2008
  3. doi request reprint Mechanisms for proton release during water oxidation in the S2 to S3 and S3 to S4 transitions in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, SE 106 91, Stockholm, Sweden
    Phys Chem Chem Phys 14:4849-56. 2012
  4. doi request reprint Substrate water exchange for the oxygen evolving complex in PSII in the S1, S2, and S3 states
    Per E M Siegbahn
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE 106 91, Sweden
    J Am Chem Soc 135:9442-9. 2013
  5. doi request reprint Water oxidation mechanism in photosystem II, including oxidations, proton release pathways, O-O bond formation and O2 release
    Per E M Siegbahn
    Department of Physics, Stockholm University, Stockholm, Sweden
    Biochim Biophys Acta 1827:1003-19. 2013
  6. ncbi request reprint The mechanism of the Ni-Fe hydrogenases: a quantum chemical perspective
    P E Siegbahn
    Department of Physics, Stockholm University, Box 6730, 113 85 Stockholm, Sweden
    J Biol Inorg Chem 6:460-6. 2001
  7. ncbi request reprint Computational studies of [NiFe] and [FeFe] hydrogenases
    Per E M Siegbahn
    Department of Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    Chem Rev 107:4414-35. 2007
  8. ncbi request reprint Energy diagrams and mechanism for proton pumping in cytochrome c oxidase
    Per E M Siegbahn
    Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    Biochim Biophys Acta 1767:1143-56. 2007
  9. ncbi request reprint Modeling enzymatic reactions involving transition metals
    Per E M Siegbahn
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Acc Chem Res 39:729-38. 2006
  10. ncbi request reprint The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes
    Per E M Siegbahn
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 11:695-701. 2006

Collaborators

Detail Information

Publications86

  1. ncbi request reprint Nickel superoxide dismutase reaction mechanism studied by hybrid density functional methods
    Vladimir Pelmenschikov
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    J Am Chem Soc 128:7466-75. 2006
    ..Comparisons are made to the Cu- and Zn-dependent SOD, studied previously using similar models...
  2. doi request reprint A structure-consistent mechanism for dioxygen formation in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, 106 91 Stockholm, Sweden
    Chemistry 14:8290-302. 2008
    ..The optimal O-O bond formation occurs between an oxygen radical and an oxo ligand. The alternative mechanism, where the oxygen radical reacts with an external water, has a barrier about 20 kcal mol(-1) higher...
  3. doi request reprint Mechanisms for proton release during water oxidation in the S2 to S3 and S3 to S4 transitions in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, SE 106 91, Stockholm, Sweden
    Phys Chem Chem Phys 14:4849-56. 2012
    ..An interesting new result is that the barrier for proton transfer within the OEC actually competes with the O-O bond formation step of being rate-limiting...
  4. doi request reprint Substrate water exchange for the oxygen evolving complex in PSII in the S1, S2, and S3 states
    Per E M Siegbahn
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE 106 91, Sweden
    J Am Chem Soc 135:9442-9. 2013
    ..The similar rate of the slow exchange in S2 and S3 has been rationalized on the basis of earlier experiments combined with the present calculations. The results strongly support the previous DFT-suggested water oxidation mechanism. ..
  5. doi request reprint Water oxidation mechanism in photosystem II, including oxidations, proton release pathways, O-O bond formation and O2 release
    Per E M Siegbahn
    Department of Physics, Stockholm University, Stockholm, Sweden
    Biochim Biophys Acta 1827:1003-19. 2013
    ..Some new aspects of the interaction between P680 and the OEC are suggested. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. ..
  6. ncbi request reprint The mechanism of the Ni-Fe hydrogenases: a quantum chemical perspective
    P E Siegbahn
    Department of Physics, Stockholm University, Box 6730, 113 85 Stockholm, Sweden
    J Biol Inorg Chem 6:460-6. 2001
    ..The mechanisms proposed are described and compared. Although there are clear differences in these mechanisms and in the assignments of the different states observed experimentally, there are also important points of concensus...
  7. ncbi request reprint Computational studies of [NiFe] and [FeFe] hydrogenases
    Per E M Siegbahn
    Department of Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    Chem Rev 107:4414-35. 2007
  8. ncbi request reprint Energy diagrams and mechanism for proton pumping in cytochrome c oxidase
    Per E M Siegbahn
    Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    Biochim Biophys Acta 1767:1143-56. 2007
    ..Variations of key redox potentials and pK(a) values during the pumping process are derived for comparison to experiments...
  9. ncbi request reprint Modeling enzymatic reactions involving transition metals
    Per E M Siegbahn
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Acc Chem Res 39:729-38. 2006
    ..In this Account, methods and models will be described and examples of recent applications given. The examples are chosen to illustrate trends and to show cases where theory has predicted new mechanisms not suggested previously...
  10. ncbi request reprint The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes
    Per E M Siegbahn
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 11:695-701. 2006
    ..A minor general improvement of the accuracy can probably be obtained by slightly reducing the amount of exact exchange in the B3LYP functional...
  11. ncbi request reprint Hydroxide instead of bicarbonate in the structure of the oxygen evolving complex
    Per E M Siegbahn
    Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE 106 91, Stockholm, Sweden
    J Inorg Biochem 100:1035-40. 2006
    ..The computed results reproduce the results observed experimentally that magnesium and cadmium suppress water oxidation and that strontium slows it down. For both magnesium and cadmium the process stops already at S(2)...
  12. ncbi request reprint The catalytic cycle of catechol oxidase
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden
    J Biol Inorg Chem 9:577-90. 2004
    ..The calculated energetics is in reasonable agreement with experiments. Comparisons are made to other similar enzymes studied previously...
  13. ncbi request reprint Mechanism for catechol ring-cleavage by non-heme iron extradiol dioxygenases
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, S 106 91 Stockholm, Sweden
    J Am Chem Soc 126:8919-32. 2004
    ..The partly anionic character is found to determine the selectivity of the enzyme. The results are compared to available experimental information and to previous studies...
  14. ncbi request reprint Hybrid DFT study of the mechanism of quercetin 2,3-dioxygenase
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 43:5944-53. 2004
    ..The results are in good agreement with experimental findings. The mechanism is compared to the ones for other similar enzymes studied recently by similar methods...
  15. ncbi request reprint The mechanism for dioxygen formation in PSII studied by quantum chemical methods
    Per E M Siegbahn
    Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE 106 91, Stockholm, Sweden
    Photochem Photobiol Sci 4:1035-43. 2005
    ..The calculated energetics is reasonable but still not fully consistent with a correct mechanism. It is suggested that some part of the structure is not correct, probably the presence of the bicarbonate...
  16. ncbi request reprint Methods and models for studying mechanisms of redox-active enzymes
    Per E M Siegbahn
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    Philos Trans A Math Phys Eng Sci 363:847-60; discussion 1035-40. 2005
    ..The main advantage of using theoretical methods to study these systems is that short-lived intermediates and transition states can be investigated as easily as stable structures...
  17. pmc Mechanism and energy diagram for O-O bond formation in the oxygen-evolving complex in photosystem II
    Per E M Siegbahn
    Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
    Philos Trans R Soc Lond B Biol Sci 363:1221-8; discussion 1228. 2008
    ..Optimal orbital overlap puts further constraints on the structure of the OEC. An alternating spin alignment is necessary for a low barrier. The computed rate-limiting barrier of 14.7 kcal mol(-1) is in good agreement with experiments...
  18. doi request reprint Theoretical studies of O-O bond formation in photosystem II
    Per E M Siegbahn
    Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
    Inorg Chem 47:1779-86. 2008
    ..The loss of energy in the electron transfer from Tyrz to P680 has also been incorporated into the diagrams. A good agreement with experimental observations is demonstrated...
  19. ncbi request reprint Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SC FAB, Stockholm University, S 106 91 Stockholm, Sweden
    J Comput Chem 26:888-98. 2005
    ..These results agree well with experimental findings...
  20. ncbi request reprint The catalytic cycle of tyrosinase: peroxide attack on the phenolate ring followed by O[bond]O cleavage
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 8:567-76. 2003
    ..4 kcal/mol, in reasonable agreement with the experimental overall rate for the catalytic cycle. For the other steps of the mechanism, only a preliminary investigation was made, indicating a few problems which require future QM/MM studies...
  21. doi request reprint The effect of backbone constraints: the case of water oxidation by the oxygen-evolving complex in PSII
    Per E M Siegbahn
    Department of Physics, ALBA NOVA and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    Chemphyschem 12:3274-80. 2011
    ..It is concluded that the mechanism remains the same, with a similar barrier height. Finally, a connection between the OEC structure and Mn,Ca-containing minerals is also briefly discussed...
  22. doi request reprint Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
    Per E M Siegbahn
    Department of Physics, Alba Nova, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
    J Biol Inorg Chem 14:643-51. 2009
    ..Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II...
  23. ncbi request reprint Quantum chemical studies of manganese centers in biology
    Per E M Siegbahn
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, S 106 91, Stockholm, Sweden
    Curr Opin Chem Biol 6:227-35. 2002
    ..This radical is immediately quenched by a manganese center. Parallels between these enzymes are highlighted. Jahn-Teller and trans effects are emphasized...
  24. doi request reprint An energetic comparison of different models for the oxygen evolving complex of photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Arrhenius Laboratory, Stockholm University, SE 106 91, Stockholm, Sweden
    J Am Chem Soc 131:18238-9. 2009
    ..The comparison between different structures rules out several suggestions. Only one suggested structure remains...
  25. ncbi request reprint A comparison of the thermodynamics of O[bond]O cleavage for dicopper complexes in enzymes and synthetic systems
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 8:577-85. 2003
    ..The conclusion, drawn in an earlier study, that the Cu(2)(III,III) state is an unlikely intermediate in the enzyme mechanisms of tyrosinase and catechol oxidase, still remains...
  26. doi request reprint Recent theoretical studies of water oxidation in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, SE 106 91 Stockholm, Sweden
    J Photochem Photobiol B 104:94-9. 2011
    ....
  27. ncbi request reprint Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 10691 Stockholm, Sweden
    Chemistry 12:8835-46. 2006
    ..The reaction is assisted by bicarbonate located in the second coordination sphere of the metal...
  28. ncbi request reprint A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 43:3277-91. 2004
    ..The calculated activation barrier (enthalpy and entropy) and the overall reaction energy profile agree well with experimental data. A comparison to the enzymatic process, which is suggested to occur on the quintet surface, has been made...
  29. doi request reprint A comparison of the reaction mechanisms of iron- and manganese-containing 2,3-HPCD: an important spin transition for manganese
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 13:929-40. 2008
    ..Thus the two 83% identical enzymes, using different metal ions as co-factors, were found to have similar activation energies (in agreement with experiment), but different rate-limiting steps...
  30. pmc Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein
    Julia J Griese
    Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics and Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Proc Natl Acad Sci U S A 110:17189-94. 2013
    ..Theoretical modeling of the reaction by density functional theory suggests a multistep mechanism including a valyl radical intermediate. ..
  31. doi request reprint Theoretical insights into heme-catalyzed oxidation of cyclohexane to adipic acid
    Holger Noack
    Department of Physics, AlbaNova, Arrhenius Laboratories, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 50:1194-202. 2011
    ..Hydrogen-atom transfer from one of the OH groups of cyclohexane-1,2-diol makes the intradiol cleavage occur spontaneously...
  32. ncbi request reprint Copper-zinc superoxide dismutase: theoretical insights into the catalytic mechanism
    Vladimir Pelmenschikov
    Department of Physics, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 44:3311-20. 2005
    ..Modifications applied to the initial model allow the importance of Asp122 for catalysis to be estimated...
  33. doi request reprint Why is the reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR) not electrogenic?
    Margareta R A Blomberg
    Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
    Biochim Biophys Acta 1827:826-33. 2013
    ..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...
  34. ncbi request reprint A theoretical study on the binding of O(2), NO and CO to heme proteins
    L Mattias Blomberg
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    J Inorg Biochem 99:949-58. 2005
    ..It is found that the Cu(B) center in cytochrome oxidase has a similar effect on the binding of the diatomics as the distal histidine in myoglobin...
  35. ncbi request reprint Quantum chemical studies of redox-active enzymes
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    Faraday Discuss 124:289-96; discussion 343-52, 453-5. 2003
    ..The question whether this is due to the B3LYP method or to the chemical models used is addressed...
  36. ncbi request reprint Metal-bridging mechanism for O-O bond cleavage in cytochrome C oxidase
    Margareta R A Blomberg
    Department of Physics, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 42:5231-43. 2003
    ..Alternatively, the fourth electron might initially be supplied by a residue in the vicinity other than the tyrosine...
  37. ncbi request reprint A theoretical study of the cis-dihydroxylation mechanism in naphthalene 1,2-dioxygenase
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 9:439-52. 2004
    ..In contrast, a reasonably low barrier might lead to a high-valent iron-oxo species [i.e. iron(IV)-oxo] if a second external electron is supplied to the mononuclear iron center before dioxygenation...
  38. ncbi request reprint A theoretical study on nitric oxide reductase activity in a ba(3)-type heme-copper oxidase
    L Mattias Blomberg
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochim Biophys Acta 1757:31-46. 2006
    ..3 kcal/mol, close to the experimental value of 19.5 kcal/mol. The overall exergonicity is fitted to experimental data and is 45.6 kcal/mol...
  39. doi request reprint Density functional theory study of the manganese-containing ribonucleotide reductase from Chlamydia trachomatis: why manganese is needed in the active complex
    Katarina Roos
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochemistry 48:1878-87. 2009
    ..This may be a reason why conventional class I RNR has an Asp, while Ct R2, lacking the tyrosine, has a Glu...
  40. ncbi request reprint Theoretical studies of enzyme mechanisms involving high-valent iron intermediates
    Arianna Bassan
    Department of Physics, Stockholm University, AlbaNova University Center, Stockholm Center for Physics, Astronomy and Biotechnology, SE 106 91, Stockholm, Sweden
    J Inorg Biochem 100:727-43. 2006
    ..Similarities between the three classes of enzymes dominate, but significant differences also exist...
  41. ncbi request reprint Mechanisms of metalloenzymes studied by quantum chemical methods
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, S 106 91 Stockholm, Sweden
    Q Rev Biophys 36:91-145. 2003
    ..In the descriptions below high emphasis is put on the actual determination of the transition states, which are the key points determining the mechanisms...
  42. doi request reprint Proton pumping mechanism in cytochrome c oxidase
    Per E M Siegbahn
    Department of Physics, AlbaNova, SE 106 91, Stockholm, Sweden
    J Phys Chem A 112:12772-80. 2008
    ..Barriers and water binding energies were computed using hybrid density functional theory (DFT) to investigate this question...
  43. ncbi request reprint Class I ribonucleotide reductase revisited: the effect of removing a proton on Glu441
    Vladimir Pelmenschikov
    Department of Physics, Stockholm University, S 106 91 Stockholm, Sweden
    J Comput Chem 25:311-21. 2004
    ..The results are compared to experimental results and suggestions...
  44. doi request reprint A comparison of two-electron chemistry performed by the manganese and iron heterodimer and homodimers
    Katarina Roos
    Department of Physics, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 17:363-73. 2012
    ....
  45. ncbi request reprint A density functional study on a biomimetic non-heme iron catalyst: insights into alkane hydroxylation by a formally HO-FeV=O oxidant
    Arianna Bassan
    Department of Physics, SE 106 91, Stockholm, Sweden
    Chemistry 11:692-705. 2005
    ....
  46. ncbi request reprint O-O bond cleavage in dinuclear peroxo complexes of iron porphyrins: a quantum chemical study
    Margareta R A Blomberg
    Department of Physics, Stockholm University, S 106 91 Stockholm, Sweden mb physto se
    Inorg Chem 46:7992-7. 2007
    ....
  47. doi request reprint DFT study on the catalytic reactivity of a functional model complex for intradiol-cleaving dioxygenases
    Valentin Georgiev
    Department of Physics, Arrhenius Laboratories, Stockholm University, S 106 91, Stockholm, Sweden
    J Phys Chem B 114:5878-85. 2010
    ..In contrast to the subsequent barrier-free intradiol C-C bond cleavage, the extradiol pathway proceeds via the formation of an epoxide, which requires an additional activation barrier...
  48. ncbi request reprint Catalytic mechanism of matrix metalloproteinases: two-layered ONIOM study
    Vladimir Pelmenschikov
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, S 106 91 Stockholm, Sweden
    Inorg Chem 41:5659-66. 2002
    ..The direct inclusion of the auxiliary water molecule decreases the activation free energy by about 5 kcal/mol via donation of a strong hydrogen bond. The calculated activation barrier of 13.1 kcal/mol agrees well with experimental rates...
  49. ncbi request reprint 4-Hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy, and Biotechnology, Stockholm University, S 106 91, Stockholm, Sweden
    Biochemistry 43:12331-42. 2004
    ..In addition, the benzylic hydroxylation reaction, catalyzed by 4-hydroxymandelate synthase, was also studied. The results are in good agreement with the experimental findings...
  50. ncbi request reprint Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 10691 Stockholm, Sweden
    J Comput Chem 27:740-8. 2006
    ..The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases...
  51. ncbi request reprint A mechanism from quantum chemical studies for methane formation in methanogenesis
    Vladimir Pelmenschikov
    Department of Physics, Stockholm University, Box 6730, S 113 85 Stockholm, Sweden
    J Am Chem Soc 124:4039-49. 2002
    ..Heterodisulfide CoB-S-S-CoM formation is proposed in the final step in which nickel is reduced back to Ni(I). The suggested mechanism agrees well with experimental observations...
  52. doi request reprint Mechanism for N₂O generation in bacterial nitric oxide reductase: a quantum chemical study
    Margareta R A Blomberg
    Department of Physics, AlbaNova University Center, and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochemistry 51:5173-86. 2012
    ....
  53. doi request reprint The mechanism for proton pumping in cytochrome c oxidase from an electrostatic and quantum chemical perspective
    Margareta R A Blomberg
    Department of Physcis, Stockholm University, Stockholm, Sweden
    Biochim Biophys Acta 1817:495-505. 2012
    ..The mechanism has now been tested by large model DFT calculations, and these calculations give strong support for the suggested mechanism...
  54. ncbi request reprint Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91 Stockholm, Sweden
    Chemistry 10:1031-41. 2004
    ..The relative stability of different forms of the active iron-oxo species is assessed, and the quintet five-coordinate complex is found to be most stable...
  55. ncbi request reprint Theoretical study of the catalytic reaction mechanism of MndD
    Valentin Georgiev
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 11:571-85. 2006
    ..The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state...
  56. ncbi request reprint Theoretical study of the reduction of nitric oxide in an A-type flavoprotein
    L Mattias Blomberg
    Department of Physics, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 12:79-89. 2007
    ..It is also discussed how to experimentally discriminate between the two mechanisms...
  57. ncbi request reprint Mechanism of aromatic hydroxylation by an activated FeIV=O core in tetrahydrobiopterin-dependent hydroxylases
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics Astronomy and Biotechnology, Stockholm University 106 91, Stockholm, Sweden
    Chemistry 9:4055-67. 2003
    ..The computed energetics lead to the conclusion that Fe(IV)=O is capable not only of aromatic hydroxylation, but also of benzylic hydroxylation...
  58. doi request reprint Is there a Ni-methyl intermediate in the mechanism of methyl-coenzyme M reductase?
    Shi Lu Chen
    Department of Physics, Stockholm University, SE 10691 Stockholm, Sweden
    J Am Chem Soc 131:9912-3. 2009
    ..These results agree well with the current experiments...
  59. doi request reprint Structures and energetics for O2 formation in photosystem II
    Per E M Siegbahn
    Department of Physics, Alba Nova, Stockholm University, SE 106 91 Stockholm, Sweden
    Acc Chem Res 42:1871-80. 2009
    ..In these later transitions, the oxidation of the OEC is coupled to deprotonations of water...
  60. ncbi request reprint Different types of biological proton transfer reactions studied by quantum chemical methods
    Margareta R A Blomberg
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology SC FAB, Stockholm University, Stockholm, Sweden
    Biochim Biophys Acta 1757:969-80. 2006
    ..In CcO, the essential proton transfer for the OO bond cleavage, and the most recent modelings of proton translocation are described, indicating a few remaining major problems...
  61. ncbi request reprint Mechanism of dioxygen cleavage in tetrahydrobiopterin-dependent amino acid hydroxylases
    Arianna Bassan
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, 106 91, Stockholm, Sweden
    Chemistry 9:106-15. 2003
    ..In the proposed mechanism, the formation of the bridging C-O bond is rate-limiting in the formation of Fe(IV)=O...
  62. doi request reprint Oxygen cleavage with manganese and iron in ribonucleotide reductase from Chlamydia trachomatis
    Katarina Roos
    Department of Physics, Stockholm University, Stockholm, Sweden
    J Biol Inorg Chem 16:553-65. 2011
    ..A tentative energy profile of the thermodynamics of the radical transfer from R2 to subunit I is constructed to illustrate how the stability of the active states can be understood from a thermodynamical point of view...
  63. ncbi request reprint A theoretical study of myoglobin working as a nitric oxide scavenger
    L Mattias Blomberg
    Department of Physics, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 9:923-35. 2004
    ..Forming the product, nitrate bound to the heme iron has a barrier of less than approximately 7 kcal/mol. The overall reaction going from a free nitric oxide and oxy-Mb to the heme bound nitrate is exergonic by more than 30 kcal/mol...
  64. ncbi request reprint A density functional study of O-O bond cleavage for a biomimetic non-heme iron complex demonstrating an Fe(v)-intermediate
    Arianna Bassan
    Contribution from the Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91, Stockholm, Sweden
    J Am Chem Soc 124:11056-63. 2002
    ..The difference between hydroperoxide and alkylperoxide as oxidant derives from the higher O-O bond strength for hydrogen peroxide (by 8.0 kcal/mol)...
  65. ncbi request reprint Catalysis by methyl-coenzyme M reductase: a theoretical study for heterodisulfide product formation
    Vladimir Pelmenschikov
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, 106 91, Stockholm, Sweden
    J Biol Inorg Chem 8:653-62. 2003
    ..The mechanism suggested is discussed in the context of available experimental data. An analysis of the flexibility of the F(430) cofactor during the reaction cycle is also given...
  66. ncbi request reprint Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case
    Margareta R A Blomberg
    Department of Physics, AlbaNova University Center Stockholm University, S 10691 Stockholm, Sweden
    J Comput Chem 27:1373-84. 2006
    ..A conclusion from the present study is, therefore, that something is probably still missing in the modeling of the active site...
  67. ncbi request reprint Theoretical investigation on the oxidative chlorination performed by a biomimetic non-heme iron catalyst
    Holger Noack
    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
    J Biol Inorg Chem 12:1151-62. 2007
    ..The exclusive chlorination of the substrate by Cl-Fe(IV)=O may be explained by an indirect or a direct effect, altering the position of the competing rebound barriers...
  68. ncbi request reprint A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs)
    Rajeev Prabhakar
    Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    J Comput Chem 24:1599-609. 2003
    ..In other steps the role of lysine is taken over by an asparagine. All results are compared with experimental observations and good agreement is generally found...
  69. ncbi request reprint Reduction of nitric oxide in bacterial nitric oxide reductase--a theoretical model study
    L Mattias Blomberg
    Department of Physics, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochim Biophys Acta 1757:240-52. 2006
    ..The formation of a ferrylic non-heme Fe(B) in the proposed reaction mechanism could be one reason for having an iron as the non-heme metal ion in NOR instead of a Cu as in cytochrome oxidase...
  70. ncbi request reprint Density functional study of the O2 binding to [CuI(TPAR)]+ (TPA = tris(2-pyridylmethyl)amine) in THF and EtCN
    Adam Johannes Johansson
    Department of Physics, Stockholm University, Sweden
    Inorg Chem 45:1491-7. 2006
    ..However, an analysis of the partitioning of the free energy barriers in enthalpic and entropic contributions indicates that the computationally studied reaction pathway might differ from the one observed experimentally...
  71. ncbi request reprint Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study
    Tomasz Borowski
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    J Am Chem Soc 127:17303-14. 2005
    ..Interestingly, the results indicate that the type of ring scission, intra or extra with respect to the substituents coordinating to iron, is controlled by the barrier heights for the decay of the arene oxide radical intermediate...
  72. doi request reprint An autocatalytic mechanism for NiFe-hydrogenase: reduction to Ni(I) followed by oxidative addition
    Sten O Nilsson Lill
    Department of Physics, AlbaNova, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochemistry 48:1056-66. 2009
    ..This was mainly an effect of overestimation of polarization effects of the QM region by the MM region due to the particular treatment of the electrostatic interactions and the use of a standard (nonpolarizable) force field...
  73. ncbi request reprint Important roles of tyrosines in photosystem II and cytochrome oxidase
    Per E M Siegbahn
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, AlbaNova, SE 106 91 Stockholm, Sweden
    Biochim Biophys Acta 1655:45-50. 2004
    ..In cytochrome oxidase, mechanisms for O-O bond cleavage involving tyrosyl radical formation are investigated, together with possible roles for the tyrosine in the proton translocation...
  74. ncbi request reprint A theoretical study of the mechanism for peptide hydrolysis by thermolysin
    Vladimir Pelmenschikov
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology SCFAB, Stockholm University, 106 91 Stockholm, Sweden
    J Biol Inorg Chem 7:284-98. 2002
    ..The significance of the protein frame rigidity around the active site was estimated by fixing and subsequently releasing the edge atom positions. Finally, alternative mechanistic proposals are briefly summarized...
  75. doi request reprint How is a co-methyl intermediate formed in the reaction of cobalamin-dependent methionine synthase? Theoretical evidence for a two-step methyl cation transfer mechanism
    Shi Lu Chen
    Key Laboratory of Cluster Science of Ministry of Education, Department of Chemistry, School of Science, Beijing Institute of Technology, Beijing 100081, P R China
    J Phys Chem B 115:4066-77. 2011
    ....
  76. ncbi request reprint Optimized spin crossings and transition states for short-range electron transfer in transition metal dimers
    Marcus Lundberg
    Department of Physics, Stockholm University, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    J Phys Chem B 109:10513-20. 2005
    ..Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn-Mn distances...
  77. ncbi request reprint A theoretical study of the mechanism for the biogenesis of cofactor topaquinone in copper amine oxidases
    Rajeev Prabhakar
    Department of Physics, Stockholm Centre for Physics, Astronomy and Biotechnology, Stockholm University, S 106 91 Stockholm, Sweden
    J Am Chem Soc 126:3996-4006. 2004
    ..A complex, spin-forbidden formation of H(2)O(2) with and without the involvement of the copper metal center is discussed. The results are discussed in detail, and comparisons are made to experimental findings and suggestions...
  78. ncbi request reprint Density functional models of the mechanism for decarboxylation in orotidine decarboxylase
    Marcus Lundberg
    Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, Sweden
    J Mol Model 8:119-30. 2002
    ..Further modifications of this mechanism are discussed...
  79. pmc Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives
    Mats H M Olsson
    University of Southern California, 3620 McClintock Avenue, Department of Chemistry, SGM 418, Los Angeles, CA 90089 1062, USA
    Biochim Biophys Acta 1767:244-60. 2007
    ....
  80. ncbi request reprint Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase
    Mats H M Olsson
    Chemistry Department, University of Southern California, Los Angeles, California 90089 1062, USA
    J Am Chem Soc 126:2820-8. 2004
    ..We also reached similar conclusions in studies of other enzymes...
  81. ncbi request reprint Mechanism for catechol ring cleavage by non-heme iron intradiol dioxygenases: a hybrid DFT study
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul Niezapominajek 8, 30 239 Cracow, Poland
    J Am Chem Soc 128:12941-53. 2006
    ..Another interesting result is that under some conditions, a homolytic O-O bond cleavage might compete with the Criegee rearrangement. The role of the second-shell residues and the substituent effects are also discussed...
  82. ncbi request reprint Theoretical study of the catalytic mechanism of catechol oxidase
    Mireia Güell
    Institut de Quimica Computacional, Universitat de Girona, Campus de Montilivi, Girona, Spain
    J Biol Inorg Chem 12:1251-64. 2007
    ..Since no protons leave or enter the active site during the catalytic cycle, no external base is required. Unlike the previous density functional theory study, the dicopper complex has a charge of +2...
  83. ncbi request reprint Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes
    Mats H M Olsson
    Chemistry Department, SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    J Biol Inorg Chem 9:96-9. 2004
    ..The simulation reproduces quite well the experimental kinetic information and the corresponding difference between the classical and quantum mechanical activation free energies for the H and D transfer reactions...
  84. doi request reprint The mechanism for isopenicillin N synthase from density-functional modeling highlights the similarities with other enzymes in the 2-His-1-carboxylate family
    Marcus Lundberg
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34 4 Takano Nishihiraki cho, Sakyo, Kyoto 606 8103, Japan
    Biochemistry 47:1031-42. 2008
    ..The ring formation sequence is determined by the relative strengths of the two C-H bonds. Only the ferryl-oxo intermediate is capable of activating the stronger valine beta-C-H bond...
  85. doi request reprint Reaction mechanism of apocarotenoid oxygenase (ACO): a DFT study
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences ul Niezapominajek 8, 30 239 Cracow, Poland
    Chemistry 14:2264-76. 2008
    ..The calculated activation barriers favor the dioxetane mechanism, yet the mechanism involving the epoxide intermediate cannot be ruled out...
  86. ncbi request reprint Quantum chemical studies of radical-containing enzymes
    Fahmi Himo
    Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, SCFAB, SE 106 91 Stockholm, Sweden
    Chem Rev 103:2421-56. 2003