| 11. |
- Andrejic, Milica, et al.
(författare)
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Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems
- 2014
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Ingår i: ChemPhysChem. - : Wiley. - 1439-7641 .- 1439-4235. ; 15:15, s. 3270-3281
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a method to calculate interaction energies of large systems (such as host-guest or even protein-ligand systems) at the local coupled-cluster with singles, doubles, and perturbative triples level, and with extrapolation to the limit of a complete basis set. The method is based on the polarizable multipole interactions with supermolecular pairs molecular fractionation approach, which combines a pairwise quantum-mechanical evaluation of the short-range interactions with a polarizable multipole treatment of many-body effects. The method is tested for nine guest molecules binding to an octa-acid host (in total 198-207 atoms), as part of the SAMPL4 blind challenge. From the test calculations, the accuracy of the approach is found to be 10 kJ mol(-1) or better. Comparison with dispersion-corrected density functional theory reveals that the latter underestimates the dispersion contribution for this type of system, which leads to a difference in the ranking of the ligands.
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| 12. |
- Arnstein Lye, Kåre, et al.
(författare)
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Norske bjørnebær 6. Sørlandsbjørnebær Rubus ”firmus”
- 2021
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Ingår i: Blyttia: norsk botanisk forenings tidsskrift. - 0006-5269. ; 79:1, s. 39-45
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Tidskriftsartikel (refereegranskat)abstract
- Rubus "firmus" is a very rare plant in Norway; it is only known from a 500 m long coastal strip nearthe sea- shore in Grimstad, Aust-Agder fylke. The identity of the name R. firmus is obscure, and it is not known whether the original plant is a species or a hybrid; we do not accept this name as correct for the Norwegian plant. The Norwegian plants are not very homogeneous and have the chromosome number 2n = 42. We believe they are the primary hybrid between Rubus caeslus and probably R. norvegicus. This hybrid is abundantly fertile and produces the earliest mature fruits of any Norwegian blackberries.
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| 13. |
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| 14. |
- Ballmann, Joachim, et al.
(författare)
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Secondary bonding interactions in biomimetic [2Fe-2S] clusters
- 2008
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 47:5, s. 1586-1596
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Tidskriftsartikel (refereegranskat)abstract
- A series of synthetic [2Fe-2S] complexes with terminal thiophenolate ligands and tethered ether or thioether moieties has been prepared and investigated in order to provide models for the potential interaction of additional donor atoms with the Fe atoms in biological [2Fe-2S] clusters. X-ray crystal structures have been determined for six new complexes that feature appended Et (1(C)), OMe (1(O)), or SMe (1(S)) groups, or with a methylene group (2(C)), an ether-O (2(O)), or an thioether-S (2(S)) linking two aryl group. The latter two systems provide a constrained chelate arrangement that induces secondary bonding interactions with the ether-O and thioether-S, which is confirmed by density functional theory (DFT) calculations that also reveal significant spin density on those fifth donor atoms. Structural consequences of the secondary bonding interactions are analyzed in detail, and effects on the spectroscopic and electronic properties are probed by UV-vis, Mossbauer, and H-1 NMR spectroscopy, as well by SQUID measurements and cyclic voltammetry. The potential relevance of the findings for biological [2Fe-2S] sites is considered.
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| 15. |
- Bergmann, Justin, et al.
(författare)
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Can the results of quantum refinement be improved with a continuum-solvation model?
- 2021
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Ingår i: Acta Crystallographica. Section B: Structural Science. - 0108-7681. ; 77:6, s. 906-918
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Tidskriftsartikel (refereegranskat)abstract
- Quantum refinement has repeatedly been shown to be a powerful approach to interpret and improve macromolecular crystal structures, allowing for the discrimination between different interpretations of the structure, regarding the protonation states or the nature of bound ligands, for example. In this method, the empirical restraints, used to supplement the crystallographic raw data in standard crystallographic refinement, are replaced by more accurate quantum mechanical (QM) calculations for a small, but interesting, part of the structure. Previous studies have shown that the results of quantum refinement can be improved if the charge of the QM system is reduced by adding neutralizing groups. However, this significantly increases the computation time for the refinement. In this study, we show that a similar improvement can be obtained if the original highly charged QM system is instead immersed in a continuum solvent in the QM calculations. The best results are typically obtained with a high dielectric constant (ε). The continuum solvent improves real-space it Z values, electron-density difference maps and strain energies, and it normally does not affect the discriminatory power of the calculations between different chemical interpretations of the structure. However, for structures with a low charge in the QM system or with a low crystallographic resolution (>2Å), no improvement of the structures is seen.
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| 16. |
- Bergmann, Justin, et al.
(författare)
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Combining crystallography with quantum mechanics
- 2022
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Ingår i: Current Opinion in Structural Biology. - : Elsevier BV. - 0959-440X. ; 72, s. 18-26
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Forskningsöversikt (refereegranskat)abstract
- In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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| 17. |
- Bergmann, Justin, et al.
(författare)
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Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands
- 2021
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 26:2-3, s. 341-353
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Tidskriftsartikel (refereegranskat)abstract
- Recently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three μ2 bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381–1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N2 ligands, but not lower than for several of the μ3 bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N2 binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding. Graphic abstract: [Figure not available: see fulltext.].
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| 18. |
- Bergmann, Justin, et al.
(författare)
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Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase
- 2021
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Ingår i: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134. ; 219
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.
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| 19. |
- Brânzanic, Adrian M.V., et al.
(författare)
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Importance of the iron–sulfur component and of the siroheme modification in the resting state of sulfite reductase
- 2020
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Ingår i: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134. ; 203
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Tidskriftsartikel (refereegranskat)abstract
- The active site of sulfite reductase (SiR) consists of an unusual siroheme–Fe4S4 assembly coupled via a cysteinate sulfur, and serves for multi-electron reduction reactions. Clear explanations have not been demonstrated for the reasons behind the choice of siroheme (vs. other types of heme) or for the single-atom coupling to an Fe4S4 center (as opposed to simple adjacency or to coupling via chains consisting of more than one atom). Possible explanations for these choices have previously been invoked, relating to the control of the spin state of the substrate-binding (siro)heme iron, modulation of the trans effect of the (Fe4S4–bound) cysteinate, or modulation of the redox potential. Reported here is a density functional theory (DFT) investigation of the structural interplay (in terms of geometry, molecular orbitals and magnetic interactions) between the siroheme and the Fe4S4 center as well as the importance of the covalent modifications within siroheme compared to the more common heme b, aiming to verify the role of the siroheme modification and of the Fe4S4 cluster at the SiR active site, with focus on previously-formulated hypotheses (geometrical/sterics, spin state, redox and electron-transfer control). A calibration of various DFT methods/variants for the correct description of ground state spin multiplicity is performed using a set of problematic cases of bioinorganic Fe centers; out of 11 functionals tested, M06-L and B3LYP offer the best results – though none of them correctly predict the spin state for all test cases. Upon examination of the relative energies of spin states, reduction potentials, energy decomposition (electrostatic, exchange-repulsion, orbital relaxation, correlation and dispersion interactions) and Mayer bond indices in SiR models, the following main roles of the siroheme and cubane are identified: (1) the cubane cofactor decreases the reduction potential of the siroheme and stabilizes the siroheme–cysteine bond interaction, and (2) the siroheme removes the quasi-degeneracy between the intermediate and high-spin states found in ferrous systems by preserving the latter as ground state; the higher-spin preference and the increased accessibility of multiple spin states are likely to be important in selective binding of the substrate and of the subsequent reaction intermediates, and in efficient changes in redox states throughout the catalytic cycle.
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| 20. |
- Brânzanic, Adrian M.V., et al.
(författare)
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Why does sulfite reductase employ siroheme?
- 2019
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 55:93, s. 14047-14049
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Tidskriftsartikel (refereegranskat)abstract
- Sulfite reductase (SiR) contains in the active site a unique assembly of siroheme and a [4Fe4S] cluster, linked by a cysteine residue. Siroheme is a doubly reduced variant of heme that is not used for a catalytic function in any other enzyme. We have used non-equilibrium Green's function methods coupled with density functional theory computations to explain why SiR employs siroheme rather than heme. The results show that direct, through vacuum, charge-transfer routes are inhibited when heme is replaced by siroheme. This ensures more efficient channelling of the electrons to the catalytic iron during the six-electron reduction of sulfite to sulfide, limiting potential side-reactions that could occur if the incoming electrons were delocalized onto the macrocyclic ring.
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