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Challenges in Enzyme Catalysis - Photosystem II and Orotidine Decarboxylase: A Density Functional Theory Treatment
Stockholm University, Faculty of Science, Department of Physics.
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.

The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.

Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.

Place, publisher, year, edition, pages
Stockholm: Fysikum , 2005. , 77 p.
Keyword [en]
photosystem II, oxyl radical, manganese systems, orotidine decarboxylase, reaction mechanism, density functional theory
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-486ISBN: 91-7155-057-7 (print)OAI: oai:DiVA.org:su-486DiVA: diva2:194516
Public defence
2005-05-27, sal FA32, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00
Opponent
Supervisors
Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
List of papers
1. Agreement Between Experiment and Hybrid DFT Calculations for O-H Bond Dissociation Enthalpies in manganese complexes
Open this publication in new window or tab >>Agreement Between Experiment and Hybrid DFT Calculations for O-H Bond Dissociation Enthalpies in manganese complexes
2005 In: Journal of Computational Chemistry, ISSN 0192-8651, Vol. 26, no 7, 661-667 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23778 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
2. Quantifying the Effects of the Self-interaction Error in DFT: When do the delocalized states appear?
Open this publication in new window or tab >>Quantifying the Effects of the Self-interaction Error in DFT: When do the delocalized states appear?
2005 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 22, 221403- p.Article in journal (Refereed) Published
Abstract [en]

The self-interaction error in density-functional theory leads to artificial stabilization of delocalized states, most evident in systems with an odd number of electrons. Clear examples are dissociations of carbocation radicals that often give delocalized states at long distances and large errors in computed binding energies. On the other hand, many mixed-valence transition-metal dimers known to exhibit valence trapping are correctly predicted to be localized. To understand the effects of the self-interaction error on these different systems, energy differences between delocalized and localized states are calculated with B3LYP. In the dissociation of radicals into symmetric fragments at infinite distance, this energy difference equals the error of the density-functional treatment. The energy difference decreases with increasing size of the system, from 55 kcal/mol in H2+ to 15 kcal/mol for C12H26+. Solvent corrections stabilize the localized state and result in smaller errors. Most reactions are asymmetric and this decreases the effect of the self-interaction error. In many systems, delocalization will not occur if the cost to move the electron from one fragment to the other is 70–80 kcal/mol (3.0–3.5 eV). This estimate refers to a situation where the distance between the fragments is infinite. The limit decreases with decreasing fragment distance. B3LYP calculations on the ferromagnetic state of a Mn(III,IV) dimer predict that the correct localized state is 22 kcal/mol more stable than the incorrect delocalized state. At short metal–metal distances the effect of the self-interaction error is predicted to be small. However, as the distance between the two manganese centers is increased to 7 Å, the dimer starts to delocalize and the energy artificially decreases. In the dissociation limit, the error is 10 kcal/mol. This is interpreted as an artifact originating from the self-interaction error. Delocalization is not encountered in many systems due to relatively short metal–metal distances and asymmetric ligand environments. However, some charge-transfer complexes cannot be properly calculated and delocalized states may become a problem in large models of enzyme systems with multiple transition-metal complexes.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:su:diva-23779 (URN)10.1063/1.1926277 (DOI)
Available from: 2005-04-27 Created: 2005-04-27 Last updated: 2017-12-13Bibliographically approved
3. Theoretical Investigations of Structure and Mechanism of the Oxygen-evolving Complex in PSII
Open this publication in new window or tab >>Theoretical Investigations of Structure and Mechanism of the Oxygen-evolving Complex in PSII
2004 In: Physical Chemistry Chemical Physics, ISSN 1463-9084, Vol. 6, no 20, 4772-4780 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23780 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
4. The Mechanism for Dioxygen Formation in PSII Studied by Quantum Chemical Methods
Open this publication in new window or tab >>The Mechanism for Dioxygen Formation in PSII Studied by Quantum Chemical Methods
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-23781 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27 Last updated: 2010-01-13Bibliographically approved
5. Modeling Water Exchange on Monomeric and Dimeric Mn Centers
Open this publication in new window or tab >>Modeling Water Exchange on Monomeric and Dimeric Mn Centers
2003 In: Theoretical Chemistry Accounts, ISSN 1432-881X, Vol. 110, 130-143 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23782 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
6. Oxyl Radical Required for O--O Bond Formation in Synthetic Mn-Catalyst
Open this publication in new window or tab >>Oxyl Radical Required for O--O Bond Formation in Synthetic Mn-Catalyst
2004 In: Inorganic Chemistry, ISSN 0020-1669, Vol. 43, no 1, 264-274 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23783 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
7. Minimum Energy Spin Crossings for an O-O Bond Formation Reaction
Open this publication in new window or tab >>Minimum Energy Spin Crossings for an O-O Bond Formation Reaction
2005 In: Chemical Physics Letters, ISSN 0009-2614, Vol. 401, no 4-6, 347-351 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23784 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
8. Small Molecule Activation
Open this publication in new window or tab >>Small Molecule Activation
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-23785 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27 Last updated: 2010-01-13Bibliographically approved
9. Optimized Spin Crossings and Transition States for Short-range Electron Transfer in Transition Metal Dimers
Open this publication in new window or tab >>Optimized Spin Crossings and Transition States for Short-range Electron Transfer in Transition Metal Dimers
2005 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 20, 10513-10520 p.Article in journal (Refereed) Published
Abstract [en]

Electron-transfer reactions in eight mixed-valence manganese dimers are studied using B3LYP. One of the dimers is a model of the active site of manganese catalase, while another represents a basic building block of the oxygen-evolving complex in photosystem II. The adiabatic reactions are characterized by fully optimized transition states where the single imaginary frequency represents the electron-transfer coordinate. When there is antiferromagnetic coupling between different high-spin centers, electron transfer must be accompanied by a spin transition. Spin transitions are characterized by minimum-energy crossing points between spin surfaces. Three reaction mechanisms have been investigated. First, a single-step reaction where spin flip is concerted with electron transfer. Second, an initial transition to a center with intermediate spin that can be followed by electron transfer. Third, an initial transition to a ferromagnetic state from which the electron can be transferred adiabatically. The complexes prefer the third route with rate-determining barriers ranging from 5.7 kcal/mol to 17.2 kcal/mol for different complexes. The origins of these differences are discussed in terms of oxidation states and ligand environments. Many DFT functionals overestimate charge-transfer interactions, but for the present complexes, the error should be limited because of short Mn−Mn distances

National Category
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-23786 (URN)10.1021/jp051116q (DOI)
Note

Part of urn:nbn:se:su:diva-486

Available from: 2005-04-27 Created: 2005-04-27 Last updated: 2017-12-13Bibliographically approved
10. Density Functional Models of the Mechanism for Decarboxylation in Orotidine Decarboxylase
Open this publication in new window or tab >>Density Functional Models of the Mechanism for Decarboxylation in Orotidine Decarboxylase
2002 In: Journal of Molecular Modeling, ISSN 1610-2940, Vol. 8, no 4, 119-130 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23787 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved
11. Developing Active Site Models of ODCase - from Large Quantum Models to a QM/MM approach
Open this publication in new window or tab >>Developing Active Site Models of ODCase - from Large Quantum Models to a QM/MM approach
2004 In: Topics in Current Chemistry, ISSN 0340-1022, Vol. 238, 79-112 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23788 (URN)
Note
Part of urn:nbn:se:su:diva-486Available from: 2005-04-27 Created: 2005-04-27Bibliographically approved

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