| 1. |
- Ames, William, et al.
(author)
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Theoretical Evaluation of Structural Models of the S(2) State in the Oxygen Evolving Complex of Photosystem II : Protonation States and Magnetic Interactions
- 2011
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 133:49, s. 19743-19757
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Journal article (peer-reviewed)abstract
- Protonation states of water ligands and oxo bridges are intimately involved in tuning the electronic structures and oxidation potentials of the oxygen evolving complex (OEC) in Photosystem II, steering the mechanistic pathway, which involves at least five redox state intermediates S(n) (n = 0-4) resulting in the oxidation of water to molecular oxygen. Although protons are practically invisible in protein crystallography, their effects on the electronic structure and magnetic properties of metal active sites can be probed using spectroscopy. With the twin purpose of aiding the interpretation of the complex electron paramagnetic resonance (EPR) spectroscopic data of the OEC and of improving the view of the cluster at the atomic level, a complete set of protonation configurations for the S(2) state of the OEC were investigated, and their distinctive effects on magnetic properties of the cluster were evaluated. The most recent X-ray structure of Photosystem II at 1.9 Å resolution was used and refined to obtain the optimum structure for the Mn(4)O(5)Ca core within the protein pocket. Employing this model, a set of 26 structures was constructed that tested various protonation scenarios of the water ligands and oxo bridges. Our results suggest that one of the two water molecules that are proposed to coordinate the outer Mn ion (Mn(A)) of the cluster is deprotonated in the S(2) state, as this leads to optimal experimental agreement, reproducing the correct ground state spin multiplicity (S = 1/2), spin expectation values, and EXAFS-derived metal-metal distances. Deprotonation of Ca(2+)-bound water molecules is strongly disfavored in the S(2) state, but dissociation of one of the two water ligands appears to be facile. The computed isotropic hyperfine couplings presented here allow distinctions between models to be made and call into question the assumption that the largest coupling is always attributable to Mn(III). The present results impose limits for the total charge and the proton configuration of the OEC in the S(2) state, with implications for the cascade of events in the Kok cycle and for the water splitting mechanism.
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| 2. |
- Caldararu, Octav, et al.
(author)
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Binding free energies in the SAMPL5 octa-acid host–guest challenge calculated with DFT-D3 and CCSD(T)
- 2017
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In: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 31:1, s. 87-106
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Journal article (peer-reviewed)abstract
- We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO–CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by ~50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11–16 kJ/mol. DLPNO–CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates the entropy term. In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum–mechanical methods.
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| 3. |
- Chalupsky, Jakub, et al.
(author)
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Multireference ab initio calculations on reaction intermediates of the multicopper oxidases
- 2006
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 45:26, s. 11051-11059
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Journal article (peer-reviewed)abstract
- The multicopper oxidases (MCOs) couple the four-electron reduction of dioxygen to water with four one-electron oxidations of various substrates. Extensive spectroscopic studies have identified several intermediates in the MCO catalytic cycle, but they have not been able to settle the structures of three of the intermediates, viz. the native intermediate (NI), the peroxy intermediate (PI), and the peroxy adduct (PA). The suggested structures have been further refined and characterized by quantum mechanical/molecular mechanical (QM/MM) calculations. In this paper, we try to establish a direct link between theory and experiment, by calculating spectroscopic parameters for these intermediates using multireference wave functions from the multistate CASPT2 and MRDDCI2 methods. Thereby, we have been able to reproduce low-spin ground states (S = 0 or S = 1/2) for all the MCO intermediates, as well as a low-lying (similar to 150 cm(-1)) doublet state and a doublet-quartet energy gap of similar to 780 cm(-1) for the NI. Moreover, we reproduce the zero-field splitting (similar to 70 cm(-1)) of the ground E-2 state in a D-3 symmetric hydroxy-bridged trinuclear Cu(II) model of the NI and obtain a quantitatively correct quartet-doublet splitting (164 cm(-1)) for a mu 3-oxo-bridged trinuclear Cu( II) cluster. All results support the suggestion that the NI has an O-2-atom in the center of the trinuclear cluster, whereas both the PI and PA have an O-2(2-) ion in the center of the cluster, in agreement with the QM/MM results and spectroscopic measurements.
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| 4. |
- Chrysina, Maria, et al.
(author)
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Five-coordinate Mn-IV intermediate in the activation of nature's water splitting cofactor
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:34, s. 16841-16846
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Journal article (peer-reviewed)abstract
- Nature's water splitting cofactor passes through a series of catalytic intermediates (S-0-S-4) before O-O bond formation and O-2 release. In the second last transition (S-2 to S-3) cofactor oxidation is coupled to water molecule binding to Mn1. It is this activated, water-enriched all Mn-IV form of the cofactor that goes on to form the O-O bond, after the next light-induced oxidation to S-4. How cofactor activation proceeds remains an open question. Here, we report a so far not described intermediate (S-3') in which cofactor oxidation has occurred without water insertion. This intermediate can be trapped in a significant fraction of centers (> 50%) in (i) chemical-modified cofactors in which Ca2+ is exchanged with Sr2+; the Mn4O5Sr cofactor remains active, but the S-2-S-3 and S-3-S-0 transitions are slower than for the Mn4O5Ca cofactor; and (ii) upon addition of 3% vol/vol methanol; methanol is thought to act as a substrate water analog. The S-3' electron paramagnetic resonance (EPR) signal is significantly broader than the untreated S-3 signal (2.5 T vs. 1.5 T), indicating the cofactor still contains a 5-coordinate Mn ion, as seen in the preceding S-2 state. Magnetic double resonance data extend these findings revealing the electronic connectivity of the S-3' cofactor is similar to the high spin form of the preceding S-2 state, which contains a cuboidal Mn3O4Ca unit tethered to an external, 5-coordinate Mn ion (Mn-4). These results demonstrate that cofactor oxidation regulates water molecule insertion via binding to Mn-4. The interaction of ammonia with the cofactor is also discussed.
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| 5. |
- Cox, Nicholas, et al.
(author)
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Effect of Ca(2+)/Sr(2+) substitution on the electronic structure of the oxygen-evolving complex of photosystem II : a combined multifrequency EPR, (55)Mn-ENDOR, and DFT study of the S(2) State
- 2011
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 133:10, s. 3635-3648
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Journal article (peer-reviewed)abstract
- The electronic structures of the native Mn(4)O(x)Ca cluster and the biosynthetically substituted Mn(4)O(x)Sr cluster of the oxygen evolving complex (OEC) of photosystem II (PSII) core complexes isolated from Thermosynechococcus elongatus, poised in the S(2) state, were studied by X- and Q-band CW-EPR and by pulsed Q-band (55)Mn-ENDOR spectroscopy. Both wild type and tyrosine D less mutants grown photoautotrophically in either CaCl(2) or SrCl(2) containing media were measured. The obtained CW-EPR spectra of the S(2) state displayed the characteristic, clearly noticeable differences in the hyperfine pattern of the multiline EPR signal [Boussac et al. J. Biol. Chem.2004, 279, 22809-22819]. In sharp contrast, the manganese ((55)Mn) ENDOR spectra of the Ca and Sr forms of the OEC were remarkably similar. Multifrequency simulations of the X- and Q-band CW-EPR and (55)Mn-pulsed ENDOR spectra using the Spin Hamiltonian formalism were performed to investigate this surprising result. It is shown that (i) all four manganese ions contribute to the (55)Mn-ENDOR spectra; (ii) only small changes are seen in the fitted isotropic hyperfine values for the Ca(2+) and Sr(2+) containing OEC, suggesting that there is no change in the overall spin distribution (electronic coupling scheme) upon Ca(2+)/Sr(2+) substitution; (iii) the changes in the CW-EPR hyperfine pattern can be explained by a small decrease in the anisotropy of at least two hyperfine tensors. It is proposed that modifications at the Ca(2+) site may modulate the fine structure tensor of the Mn(III) ion. DFT calculations support the above conclusions. Our data analysis also provides strong support for the notion that in the S(2) state the coordination of the Mn(III) ion is square-pyramidal (5-coordinate) or octahedral (6-coordinate) with tetragonal elongation. In addition, it is shown that only one of the currently published OEC models, the Siegbahn structure [Siegbahn, P. E. M. Acc. Chem. Res.2009, 42, 1871-1880, Pantazis, D. A. et al. Phys. Chem. Chem. Phys.2009, 11, 6788-6798], is consistent with all data presented here. These results provide important information for the structure of the OEC and the water-splitting mechanism. In particular, the 5-coordinate Mn(III) is a potential site for substrate 'water' (H(2)O, OH(-)) binding. Its location within the cuboidal structural unit, as opposed to the external 'dangler' position, may have important consequences for the mechanism of O-O bond formation.
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| 6. |
- Cox, Nicholas, et al.
(author)
-
Electronic Structure of a Weakly Antiferromagnetically Coupled Mn(II)Mn(III) Model Relevant to Manganese Proteins : A Combined EPR, (55)Mn-ENDOR, and DFT Study
- 2011
-
In: Inorganic Chemistry. - : American Chemical Society. - 0020-1669 .- 1520-510X. ; 50:17, s. 8238-8251
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Journal article (peer-reviewed)abstract
- An analysis of the electronic structure of the [Mn(II)Mn(III)(μ-OH)-(μ-piv)(2)(Me(3)tacn)(2)](ClO(4))(2) (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-μ-hydroxo bridge, bis-μ-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the Mn(III). All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the (55)Mn-ENDOR constrains the (55)Mn hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the Mn(II) and Mn(III) ions. The large effective hyperfine tensor anisotropy of the Mn(II), a d(5) ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the Mn(III) ion strongly perturbs the zero-field energy levels of the Mn(II)Mn(III) complex. An estimate of the fine structure parameter (d) for the Mn(III) of -4 cm(-1) was made, by assuming the intrinsic anisotropy of the Mn(II) ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the Mn(III) is consistent with the known coordination environment of the Mn(III) ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.
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| 7. |
- Cox, Nicholas, et al.
(author)
-
Electronic Structure of a Weakly Antiferromagnetically Coupled MnIIMnIII Model Relevant to Manganese Proteins : A Combined EPR, 55Mn-ENDOR, and DFT Study
- 2011
-
In: Inorganic Chemistry. - : AMER CHEMICAL SOC. - 0020-1669 .- 1520-510X. ; 50:17, s. 8238-8251
-
Journal article (peer-reviewed)abstract
- An analysis of the electronic structure of the [(MnMnIII)-Mn-II(mu-OH)-(mu-piv)(2)(Me(3)tacn)(2)] (ClO4)(2) (PivOH) complex is reported. It displays features that include: (i) a ground 1/2 spin state; (ii) a small exchange (J) coupling between the two Mn ions; (iii) a mono-mu-hydroxo bridge, bis-mu-carboxylato motif; and (iv) a strongly coupled, terminally bound N ligand to the Mn-III. All of these features are observed in structural models of the oxygen evolving complex (OEC). Multifrequency electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) measurements were performed on this complex, and the resultant spectra simulated using the Spin Hamiltonian formalism. The strong field dependence of the Mn-55-ENDOR constrains the Mn-55 hyperfine tensors such that a unique solution for the electronic structure can be deduced. Large hyperfine anisotropy is required to reproduce the EPR/ENDOR spectra for both the Mn-II and Mn-III ions. The large effective hyperfine tensor anisotropy of the Mn-II, a d(5) ion which usually exhibits small anisotropy, is interpreted within a formalism in which the fine structure tensor of the Mn-III ion strongly perturbs the zero-field energy levels of the (MnMnIII)-Mn-II complex. An estimate of the fine structure parameter (d) for the Mn-III of -4 cm(-1) was made, by assuming the intrinsic anisotropy of the Mn-II ion is small. The magnitude of the fine structure and intrinsic (onsite) hyperfine tensor of the Mn-III is consistent with the known coordination environment of the Mn-III ion as seen from its crystal structure. Broken symmetry density functional theory (DFT) calculations were performed on the crystal structure geometry. DFT values for both the isotropic and the anisotropic components of the onsite (intrinsic) hyperfine tensors match those inferred from the EPR/ENDOR simulations described above, to within 5%. This study demonstrates that DFT calculations provide reliable estimates for spectroscopic observables of mixed valence Mn complexes, even in the limit where the description of a well isolated S = 1/2 ground state begins to break down.
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| 8. |
- Krewald, Vera, et al.
(author)
-
Metal oxidation states in biological water splitting
- 2015
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In: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 6:3, s. 1676-1695
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Journal article (peer-reviewed)abstract
- A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five Si states (i = 0-4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called "high-valent scheme"-where, for example, the Mn oxidation states in the S-2 state are assigned as III, IV, IV, IV-the competing "low-valent scheme" that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S-2 state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi) stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K Mn-55 ENDOR data of the S-2 state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S-0 (III, III, III, IV) to S-3 (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.
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| 9. |
- Lin, Po-Chi, et al.
(author)
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A vertebrate-type ferredoxin domain in the Na+-translocating NADH dehydrogenase from Vibrio cholerae
- 2005
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In: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 280:24, s. 22560-22563
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Journal article (peer-reviewed)abstract
- The Na(+)-translocating NADH:quinone oxidoreductase from Vibrio cholerae contains a single Fe-S cluster localized in subunit NqrF. Here we study the electronic properties of the Fe-S center in a truncated version of the NqrF subunit comprising only its ferredoxin-like Fe-S domain. Mössbauer spectroscopy of the Fe-S domain in the oxidized state is consistent with a binuclear Fe-S cluster with tetrahedral sulfur coordination by the cysteine residues Cys(70), Cys(76), Cys(79), and Cys(111). Important sequence motifs surrounding these cysteines are conserved in the Fe-S domain and in vertebrate-type ferredoxins. The magnetic circular dichroism spectra of the photochemically reduced Fe-S domain exhibit a striking similarity to the magnetic circular dichroism spectra of vertebrate-type ferredoxins required for the in vivo assembly of iron-sulfur clusters. This study reveals a novel function for vertebrate-type [2Fe-2S] clusters as redox cofactors in respiratory dehydrogenases.
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| 10. |
- Maganas, Dimitrios, et al.
(author)
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Combined Experimental and ab initio Multi Reference Configuration Interaction study of the Resonant Inelastic X-RayScattering spectrum of CO2
- 2014
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:35, s. 20163-20175
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Journal article (peer-reviewed)abstract
- The fundamental problem of the symmetry breaking in the resonant inelastic X-ray scattering (RIXS) of the CO2 gas molecule is studied. The measurements were performed under catalytically relevant conditions within an in-house constructed reaction cell. The experimental RIXS plane is constructed from a sequence of resonances, covering the near-edge X-ray absorption fine structure (NEXAFS) spectrum up to 539 eV. The spectra show significant sensitivity with respect to the excitation frequency. The NEXAFS absorption spectrum, as well as the corresponding RIXS spectra, is interpreted with the aid of multireference configuration interaction (MRCI) theory. In this framework, the configuration interaction space spans the space of the intermediate and final states with single and single-double excitations. The dynamic character of the RIXS spectra is investigated by considering the electronic-nuclear vibrational coupling with the bending and antisymmetric stretching vibrations in the important intermediate excited states. In addition, the vibronic coupling mechanism involving the Renner-Teller effect and the core-hole localization pseudo-Jahn-Teller effect of the intermediate states is fully considered. The physical origin of the observed spectral features is discussed qualitatively and quantitatively in terms of individual core-to-valence excitations and valence-to-core decays, respectively. The computational protocol presented here, based on multireference wave function ab initio theory, serves as an important reference for future theoretical and experimental applications of RIXS spectroscopy.
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