| 1. |
- Sigfridsson Clauss, Kajsa, et al.
(författare)
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Rapid X-ray photoreduction of dimetal-oxygen cofactors in ribonucleotide reductase.
- 2013
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Ingår i: Journal of Biological Chemistry. - 1083-351X .- 0021-9258.
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Tidskriftsartikel (refereegranskat)abstract
- Prototypic dinuclear metal cofactors with varying metallation constitute a class of O2-activating catalysts in numerous enzymes such as ribonucleotide reductase (RNR1). Reliable structures are required to unravel the reaction mechanisms. However, protein crystallography data may be compromised by X-ray photoreduction (XPR). We studied XPR of Fe(III)Fe(III) and Mn(III)Fe(III) sites in the R2 subunit of Chlamydia trachomatis RNR using X-ray absorption spectroscopy. Rapid and biphasic XPR kinetics at 20 K and 80 K for both cofactor types suggested sequential formation of (III,II) and (II,II) species and similar redox potentials of Fe and Mn sites. Comparing with typical X-ray doses in crystallography implies that (II,II) states are reached in <1 s in such studies. First-sphere metal coordinations and metal-metal distances differed after chemical reduction at room temperature and after XPR at cryogenic temperatures, as corroborated by model structures from density functional theory calculations. The inter-metal distances in the (II,II) states, however, are similar to R2 crystal structures. Therefore, crystal data of initially oxidized R2-type proteins mostly contain photoreduced (II,II) cofactors, which deviate from the native structures functional in O2-activation, explaining observed variable metal ligation motifs. This situation may be remedied by novel femtosecond free-electron-laser protein crystallography techniques.
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| 2. |
- Bjelčić, Monika, et al.
(författare)
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Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes
- 2023
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Ingår i: Acta Crystallographica Section D: Structural Biology. - 2059-7983. ; 79:Pt 11, s. 1018-1025
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, the emergence of serial crystallography, initially pioneered at X-ray free-electron lasers (XFELs), has sparked a growing interest in collecting macromolecular crystallographic data at room temperature. Various fixed-target serial crystallography techniques have been developed, ranging from commercially available chips to in-house designs implemented at different synchrotron facilities. Nevertheless, there is currently no commercially available chip (known to the authors) specifically designed for the direct handling of oxygen-sensitive samples. This study presents a methodology employing silicon nitride chips arranged in a 'sandwich' configuration, enabling reliable room-temperature data collection from oxygen-sensitive samples. The method involves the utilization of a custom-made 3D-printed assembling tool and a MX sample holder. To validate the effectiveness of the proposed method, deoxyhemoglobin and methemoglobin samples were investigated using the BioMAX X-ray macromolecular crystallography beamline, the Balder X-ray absorption spectroscopy beamline and UV-Vis absorption spectroscopy.
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| 3. |
- Börjesson Axén, Jenny, 1986-, et al.
(författare)
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A Structural Investigation into the OCV Hysteresis of the Ni(OH)2 Electrode
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Powder X-ray diffraction (XRPD), X-ray absorption spectroscopy (EXAFS and XANES) and Raman spectroscopy were used to study chemical changes in the polycrystalline nickel hydroxide positive electrode material of a NiMH battery at four states of charge: 0%, 50% and 100% charged, and 50% discharged. The two 50% samples were at the same state of charge but in different hysteresis states, manifested by differences in the open circuit potential. The nickel hydroxide electrodes consist of particles in the µm size range, and all measurements were performed ex situ. The material studied was taken from commercial batteries and as such contained both metallic nickel particles, cobalt, and zinc dopants in the active Ni(OH)2 material as well as a cobalt oxide surface layer. Combining the results from all the characterization methods was necessary to better understand the chemistry behind the physio-chemical hysteresis behavior in this complex system. Our results show that there are structural differences between the two 50% samples. Comparison of the XRPD results and the EXAFS results on the nickel edge indicate a presence of the kinetically favored TP2-NiOOH phase in the transition between β-Ni(OH)2 and β-NiOOH and that the amount differs between the two hysteresis states. The measurements on the zinc edge using EXAFS and XANES suggest short range differences in the active material bulk that stems from disorder. Raman spectroscopy measurements show a difference in degree of lithium intercalation in the LiCoO2 surface layer between the hysteresis states. As electrochemistry takes place on the surface of the particles, it is likely that differences in the surface structure are responsible for the open circuit voltage hysteresis. However, due to the coherence of the structure differences detected, it is probable that they are all connected and have a part in the observed behavior.
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| 4. |
- Dalgaard, Kirstine Junker, et al.
(författare)
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Local structure of Nb in superconducting Nb-doped Bi2Se3
- 2021
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Ingår i: Physical Review B. - 2469-9950. ; 103:18
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Tidskriftsartikel (refereegranskat)abstract
- In the prospect of realizing bulk superconductivity in a topological insulator, metal-doped Bi2Se3 has been investigated with increased interest, where the Cu-, Sr-, and Nb-doped systems appear particularly promising. It is generally assumed that metal intercalation into the van der Waals (vdW) gap is responsible for the superconductivity. We have investigated the local structure of Nb in samples with nominal composition Nb0.25Bi2Se3 and Nb0.25Bi1.75Se3 using the X-ray absorption fine structure technique. It is found that that Nb is primarily located in a local environment consistent with that of the misfit layered structure (BiSe)1+δNbSe2, which has a δ-dependent superconducting transition in the same temperature range. We explore the possibility of Nb occupancy on various sites in the Bi2Se3 structure, but neither intercalation nor substitution lead to physically meaningful improvements of the models. Furthermore, we report single crystal X-ray diffraction analysis of Nb-doped Bi2Se3. Difference density maps are found to show negligible occupancy in the vdW gap. The misfit layer compound has recently been suggested as an alternative origin for superconductivity in the Nb-doped Bi2Se3 system, in good agreement with the present study. Our findings stress the necessity of thorough structural characterization of these samples. In more general terms, it raises the question of whether metal intercalation is responsible for the superconductivity in the Cu- A nd Sr-doped Bi2Se3 systems or phase segregation plays a role as well.
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| 5. |
- Fornell, Anna, et al.
(författare)
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AdaptoCell : Microfluidics at MAX IV Laboratory
- 2022
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Ingår i: 25th Swedish Conference on Macromolecular Structure and Function.
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Konferensbidrag (refereegranskat)abstract
- The AdaptoCell project at MAX IV has developed a microfluidic sample delivery platform for academic and industrial users to enable studies of protein samples in solution and in microcrystals underflow. The platform is compatible with various X-ray techniques and has so far been integrated onto two beamlines at MAX IV: the CoSAXS beamline for small angle X-ray scattering studies and the Balder beamline for X-ray absorption spectroscopy studies. Initial implementation of the platform for serial crystallography sample delivery is ongoing and will be integrated onto the BioMAX and MicroMAX beamlines once commissioned. With this platform, we aim to meet the demand from our user community for studying proteins at physiologically relevant temperatures and give the ability to follow dynamical processes in situ as well as decreasing sample volumes and radiation damage.To determine the optimized flow rates and components for mixing etc. using different microfluidic chips, a dedicated off(beam)line test station with a microscope has been established at the Biolab. The Biolab also provides a number of characterization techniques, such as Dynamic Light Scattering, UV-Vis spectrophotometry, for quality control of the samples; as well as an anaerobic chamber for preparation and characterization of metalloproteins. The microfluidic flows are controlled via syringe pumps or a pressure-driven system. Channel design varies, depending on the needs of the experiment, from straight channel, cross-junction to herringbone micromixers etc. On-chip mixing of buffers with different viscosity, pH, ion strength and protein concentrations has been demonstrated successful and will be presented.
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| 6. |
- Gericke, Sabrina Maria, et al.
(författare)
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In Situ H2 Reduction of Al2O3-Supported Ni- and Mo-Based Catalysts
- 2022
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Ingår i: Catalysts. - : MDPI. - 2073-4344. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Nickel (Ni)-promoted Molybdenum (Mo)-based catalysts are used for hydrotreatment processes in the chemical industry where the catalysts are exposed to high-pressure H2 at elevated temperature. In this environment, the catalyst transforms into the active phase, which involves the reduction of the oxide. Here, we report on the first in situ study on the reduction of alumina supported Ni- and Mo-based catalysts in 1 mbar H2 using ambient-pressure X-ray photoelectron spectroscopy (APXPS). The study confirms that mixing Ni and Mo lowers the reduction temperature of both Ni- and Mo-oxide as compared to the monometallic catalysts and shows that the MoO3 reduction starts at a lower temperature than the reduction of NiO in NiMo/Al2O3 catalysts. Additionally, the reduction of Ni and Mo foil was directly compared to the reduction of the Al2O3-supported catalysts and it was observed that the reduction of the supported catalysts is more gradual than the reduction of the foils, indicating a strong interaction between the Ni/Mo and the alumina support. © 2022 by the authors.
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| 7. |
- Łyczko, Krzysztof, et al.
(författare)
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Striking stability of a mixed-valence thallium(III)-thallium(I) complex in some solvents
- 2023
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Ingår i: Journal of Molecular Liquids. - 0167-7322. ; 385
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Tidskriftsartikel (refereegranskat)abstract
- At the dissolution of solid anhydrous thallium(III) trifluoromethanesulfonate, Tl(CF3SO3)3, or thallium(III) trifluoroacetate, Tl(CF3COO)3, in dimethylsulfoxide (dmso) or N,N,N’,N’-tetramethylurea (tmu), intensely red-colored complexes are formed. This red thallium complex is stable for years in dmso, while it is reduced fairly rapidly to thallium(I) in tmu with a half-life time of an hour. At the dissolution of Tl(CF3SO3)3 in N,N-dimethylpropyleneurea (dmpu) an immediate reduction to thallium(I) takes place. A stable colorless aqueous thallium(III) solution is obtained at the dissolution in acidic water. Stable dmso solutions and solid dmso solvates of thallium(III) perchlorate, nitrate and trifluormethanesulfonate can be prepared by adding dmso to concentrated acidic aqueous thallium(III) solutions. These experimental observations conclude that the pure solids Tl(CF3SO3)3 and Tl(CF3COO)3 play an essential role in the formation of the red-colored thallium complexes. 205Tl NMR data show that the red thallium complex contains equal amounts of thallium(III) and thallium(I). The structure of the red thallium complex in dmso, as determined by EXAFS, has Tl–O bond distances of 2.216(3) and 2.80(2) Å, which are in very close agreement with the bond distances obtained in the pure dmso solvates of the thallium(III) and thallium(I) ions, respectively, and a Tl···Tl distance of 3.49(1) Å bridged by oxygen atoms. From the EXAFS data it is impossible to distinguish if dmso molecules and/or trifluoromethanesulfonate ions act as bridges. DFT calculations could eliminate some structures due to the irrelevant structural parameters or the energetics of the proposed reactions.
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| 8. |
- Micheal Raj, Pushparani, et al.
(författare)
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Fabrication and characterisation of a silicon-borosilicate glass microfluidic device for synchrotron-based hard X-ray spectroscopy studies
- 2021
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Ingår i: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 11:47, s. 29859-29869
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Tidskriftsartikel (refereegranskat)abstract
- Some of the most fundamental chemical building blocks of life on Earth are the metal elements. X-ray absorption spectroscopy (XAS) is an element-specific technique that can analyse the local atomic and electronic structure of, for example, the active sites in catalysts and energy materials and allow the metal sites in biological samples to be identified and understood. A microfluidic device capable of withstanding the intense hard X-ray beams of a 4th generation synchrotron and harsh chemical sample conditions is presented in this work. The device is evaluated at the K-edges of iron and bromine and the L-3-edge of lead, in both transmission and fluorescence mode detection and in a wide range of sample concentrations, as low as 0.001 M. The device is fabricated in silicon and glass with plasma etched microchannels defined in the silicon wafer before anodic bonding of the glass wafer into a complete device. The device is supported with a well-designed printed chip holder that made the microfluidic device portable and easy to handle. The chip holder plays a pivotal role in mounting the delicate microfluidic device on the beamline stage. Testing validated that the device was sufficiently robust to contain and flow through harsh acids and toxic samples. There was also no significant radiation damage to the device observed, despite focusing with intense X-ray beams for multiple hours. The quality of X-ray spectra collected is comparable to that from standard methods; hence we present a robust microfluidic device to analyse liquid samples using synchrotron XAS.
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| 9. |
- Persson, Ingmar, et al.
(författare)
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EXAFS Study on the Coordination Chemistry of the Solvated Copper(II) Ion in a Series of Oxygen Donor Solvents
- 2020
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 59:14
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Tidskriftsartikel (refereegranskat)abstract
- The structures of the solvated copper(II) ion in water and nine organic oxygen donor solvents with similar electron-pair donor ability, but with different space-demanding properties at coordination, have been studied by EXAFS. N,N′-Dimethylpropyleneurea and N,N,N′,N′-tetramethylurea are sufficiently space demanding at coordination to make the axial positions not accessible, resulting in square-planar copper(II) solvate complexes with an intense green color. The mean Cu-O bond distances in these two solvate complexes are 1.939(3) and 1.935(3) Å, respectively. The best fits of the remaining solvates, which are light blue in different hues, are obtained with a Jahn-Teller distorted-octahedral model consisting of four strongly bound solvent molecules in the equatorial positions at 1.96(2) Å and two in the axial positions but with different Cu-Oax bond distances: ca. 2.15 and 2.32 Å. This is in agreement with observations in solid-state structures of compounds containing hexaaquacopper(II) complexes crystallizing in noncentrosymmetric space groups and all reported crystal structures containing a [Cu(H2O)5(O-ligand)] complex with Jahn-Teller distortion. Such a structure is in agreement with previous EPR and EXAFS studies proving the hydrated copper(II) ion to be a noncentrosymmetric complex in aqueous solution. The refinements of the EXAFS data of the solids [Cu(H2O)6](ClO4)2, [Cu(H2O)6](BrO3)2, [Cu(H2O)6]SiF6, Cu(NO3)2·2.5H2O, and CuSO4·5H2O gave Cu-O bond distances significantly different from those reported in the crystallographic studies but similar to the configuration and bond distances in the hydrated copper(II) ion in aqueous solution. This may depend on whether the orientation of the axial positions is random in one or three dimensions, giving a mean structure of the solid with symmetry higher than that of the individual complexes. This study presents the very first experimental data from the new X-ray absorption spectroscopy beamline Balder at the MAX IV synchrotron radiation facility in Lund, Sweden, as well as the utilized properties of the beamline.
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| 10. |
- Raj, Pushparani, et al.
(författare)
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Fabrication and characterisation of a silicon-borosilicate glass microfluidic device for synchrotron-based hard X-ray spectroscopy studies
- 2021
-
Ingår i: RSC Advances. - Cambridge : RSC Publishing. - 2046-2069. ; 11:47, s. 29859-29869
-
Tidskriftsartikel (refereegranskat)abstract
- Some of the most fundamental chemical building blocks of life on Earth are the metal elements. X-ray absorption spectroscopy (XAS) is an element-specific technique that can analyse the local atomic and electronic structure of, for example, the active sites in catalysts and energy materials and allow the metal sites in biological samples to be identified and understood. A microfluidic device capable of withstanding the intense hard X-ray beams of a 4th generation synchrotron and harsh chemical sample conditions is presented in this work. The device is evaluated at the K-edges of iron and bromine and the L3-edge of lead, in both transmission and fluorescence mode detection and in a wide range of sample concentrations, as low as 0.001 M. The device is fabricated in silicon and glass with plasma etched microchannels defined in the silicon wafer before anodic bonding of the glass wafer into a complete device. The device is supported with a well-designed printed chip holder that made the microfluidic device portable and easy to handle. The chip holder plays a pivotal role in mounting the delicate microfluidic device on the beamline stage. Testing validated that the device was sufficiently robust to contain and flow through harsh acids and toxic samples. There was also no significant radiation damage to the device observed, despite focusing with intense X-ray beams for multiple hours. The quality of X-ray spectra collected is comparable to that from standard methods; hence we present a robust microfluidic device to analyse liquid samples using synchrotron XAS.
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