Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

61Ni synchrotron radiation-based Mossbauer spectroscopy of nickel-based nanoparticles with hexagonal structure.

ABSTRACT: We measured the synchrotron-radiation (SR)-based Mössbauer spectra of Ni-based nanoparticles with a hexagonal structure that were synthesised by chemical reduction. To obtain Mössbauer spectra of the nanoparticles without (61)Ni enrichment, we developed a measurement system for (61)Ni SR-based Mössbauer absorption spectroscopy without X-ray windows between the (61)Ni84V16 standard energy alloy and detector. The counting rate of the (61)Ni nuclear resonant scattering in the system was enhanced by the detection of internal conversion electrons and the close proximity between the energy standard and the detector. The spectrum measured at 4 K revealed the internal magnetic field of the nanoparticles was 3.4 ± 0.9 T, corresponding to a Ni atomic magnetic moment of 0.3 Bohr magneton. This differs from the value of Ni3C and the theoretically predicted value of hexagonal-close-packed (hcp)-Ni and suggested the nanoparticle possessed intermediate carbon content between hcp-Ni and Ni3C of approximately 10 atomic % of Ni. The improved (61)Ni Mössbauer absorption measurement system is also applicable to various Ni materials without (61)Ni enrichment, such as Ni hydride nanoparticles.

SUBMITTER: Masuda R

PROVIDER: S-EPMC4756403 | biostudies-other | 2016

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Synchrotron-based Nickel Mossbauer Spectroscopy.

Project description:We used a novel experimental setup to conduct the first synchrotron-based (61)Ni Mössbauer spectroscopy measurements in the energy domain on Ni coordination complexes and metalloproteins. A representative set of samples was chosen to demonstrate the potential of this approach. (61)NiCr2O4 was examined as a case with strong Zeeman splittings. Simulations of the spectra yielded an internal magnetic field of 44.6 T, consistent with previous work by the traditional (61)Ni Mössbauer approach with a radioactive source. A linear Ni amido complex, (61)Ni{N(SiMe3)Dipp}2, where Dipp = C6H3-2,6-(i)Pr2, was chosen as a sample with an "extreme" geometry and large quadrupole splitting. Finally, to demonstrate the feasibility of metalloprotein studies using synchrotron-based (61)Ni Mössbauer spectroscopy, we examined the spectra of (61)Ni-substituted rubredoxin in reduced and oxidized forms, along with [Et4N]2[(61)Ni(SPh)4] as a model compound. For each of the above samples, a reasonable spectrum could be obtained in ?1 d. Given that there is still room for considerable improvement in experimental sensitivity, synchrotron-based (61)Ni Mössbauer spectroscopy appears to be a promising alternative to measurements with radioactive sources.

| S-EPMC6813798 | biostudies-literature

Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy.

Project description:Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.

| S-EPMC5662050 | biostudies-literature

Characterization of Different Types of Epiretinal Proliferations by Synchrotron Radiation-Based Fourier Transform Infrared Micro-Spectroscopy.

Project description:Pathological tissue on the surface of the retina that can be of different etiology and pathogenesis can cause changes in the retina that have a direct consequence on vision. Tissues of different etiology and pathogenesis have different morphological structures and also different macromolecule compositions usually characteristic of specific diseases. In this study, we evaluated and compared biochemical differences among samples of three different types of epiretinal proliferations: idiopathic epiretinal membrane (ERMi), membranes in proliferative vitreoretinopathy (PVRm), and proliferative diabetic retinopathy (PDRm). The membranes were analyzed by using synchrotron radiation-based Fourier transform infrared micro-spectroscopy (SR-FTIR). We used the SR-FTIR micro-spectroscopy setup, where measurements were set to achieve a high resolution that was capable of showing clear biochemical spectra in biological tissue. We were able to identify differences between PVRm, PDRm, and ERMi in protein and lipid structure; collagen content and collagen maturity; differences in proteoglycan presence; protein phosphorylation; and DNA expression. Collagen showed the strongest expression in PDRm, lower expression in ERMi, and very low expression in PVRm. We also demonstrated the presence of silicone oil (SO) or polydimethylsiloxane in the structure of PVRm after SO endotamponade. This finding suggests that SO, in addition to its many benefits as an important tool in vitreoretinal surgery, could be involved in PVRm formation.

| S-EPMC10003457 | biostudies-literature

Investigating Membrane-Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far-Infrared Spectroscopy.

Project description:Synchrotron radiation-based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio-molecular phenomena including folding-mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near-THz 400-40 cm-1 range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature-dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane-induced and folding-mediated activity of AMPs. The far-FTIR study offers a direct and information-rich probe of membrane-related antimicrobial interactions.

| S-EPMC9303692 | biostudies-literature

Synchrotron radiation circular dichroism spectroscopy-defined structure of the C-terminal domain of NaChBac and its role in channel assembly.

Project description:Extramembranous domains play important roles in the structure and function of membrane proteins, contributing to protein stability, forming association domains, and binding ancillary subunits and ligands. However, these domains are generally flexible, making them difficult or unsuitable targets for obtaining high-resolution X-ray and NMR structural information. In this study we show that the highly sensitive method of synchrotron radiation circular dichroism (SRCD) spectroscopy can be used as a powerful tool to investigate the structure of the extramembranous C-terminal domain (CTD) of the prokaryotic voltage-gated sodium channel (Na(V)) from Bacillus halodurans, NaChBac. Sequence analyses predict its CTD will consist of an unordered region followed by an alpha-helix, which has a propensity to form a multimeric coiled-coil motif, and which could form an association domain in the homotetrameric NaChBac channel. By creating a number of shortened constructs we have shown experimentally that the CTD does indeed contain a stretch of approximately 20 alpha-helical residues preceded by a nonhelical region adjacent to the final transmembrane segment and that the efficiency of assembly of channels in the membrane progressively decreases as the CTD residues are removed. Analyses of the CTDs of 32 putative prokaryotic Na(V) sequences suggest that a CTD helical bundle is a structural feature conserved throughout the bacterial sodium channel family.

| S-EPMC2922593 | biostudies-literature

Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.

Project description:We have used the combination of single-molecule Förster resonance energy transfer and kinetic synchrotron radiation circular dichroism experiments to probe the conformational ensemble of the collapsed unfolded state of the small cold shock protein CspTm under near-native conditions. This regime is physiologically most relevant but difficult to access experimentally, because the equilibrium signal in ensemble experiments is dominated by folded molecules. Here, we avoid this problem in two ways. One is the use of single-molecule Förster resonance energy transfer, which allows the separation of folded and unfolded subpopulations at equilibrium and provides information on long-range intramolecular distance distributions. From experiments with donor and acceptor chromophores placed at different positions within the chain, we find that the distance distributions in unfolded CspTm agree surprisingly well with a Gaussian chain not only at high concentrations of denaturant, where the polypeptide chain is expanded, but also at low denaturant concentrations, where the chain is collapsed. The second, complementary approach is synchrotron radiation circular dichroism spectroscopy of collapsed unfolded molecules transiently populated with a microfluidic device that enables rapid mixing. The results indicate a beta-structure content of the collapsed unfolded state of approximately 20% compared with the folded protein. This suggests that collapse can induce secondary structure in an unfolded state without interfering with long-range distance distributions characteristic of a random coil, which were previously found only for highly expanded unfolded proteins.

| S-EPMC1765419 | biostudies-literature

Electronic Structure and Surface Chemistry of Hexagonal Boron Nitride on HOPG and Nickel Substrates.

Project description:The effect of point defects and interactions with the substrate are shown by density functional theory calculations to be of significant importance for the structure and functional properties of hexagonal boron nitride (h-BN) films on highly ordered pyrolytic graphite (HOPG) and Ni(111) substrates. The structure, surface chemistry, and electronic properties are calculated for h-BN systems with selected intrinsic, oxygen, and carbon defects and with graphene hybrid structures. The electronic structure of a pristine monolayer of h-BN is dependent on the type of substrate, as h-BN is decoupled electronically from the HOPG surface and acts as bulk-like h-BN, whereas on a Ni(111) substrate, metallic-like behavior is predicted. These different film/substrate systems therefore show different reactivities and defect chemistries. The formation energies for substitutional defects are significantly lower than for intrinsic defects regardless of the substrate, and vacancies formed during film deposition are expected to be filled by either ambient oxygen or carbon from impurities. Significantly lower formation energies for intrinsic and oxygen and carbon substitutional defects were predicted for h-BN on Ni(111). In-plane h-BCN hybrid structures were predicted to be terminated by N-C bonding. Substitutional carbon on the boron site imposes n-type semiconductivity in h-BN, and the n-type character increases significantly for h-BN on HOPG. The h-BN film surface becomes electronically decoupled from the substrate when exceeding monolayer thickness, showing that the surface electronic properties and point defect chemistry for multilayer h-BN films should be comparable to those of a freestanding h-BN layer.

| S-EPMC10357548 | biostudies-literature

Synchrotron radiation Ca K-edge 2D-XANES spectroscopy for studying the stratigraphic distribution of calcium-based consolidants applied in limestones.

Project description:In Heritage Science, the evaluation of stone consolidation treatments by investigating the nature of in situ newly formed products and their penetration depth within the consolidated matrix is a grand challenge. A number of analytical methods have been proposed, but, currently, most of them are not able to supply a full overview of the spatial, structural and compositional information of the newly formed crystalline and amorphous phases with a submicrometric lateral resolution. Here, we examined, the capabilities of synchrotron radiation (SR)-based two-dimensional X-ray absorption near-edge structure (2D-XANES) spectroscopy at Ca K-edge for determining the structural and compositional properties of the compounds formed after the application of a calcium acetoacetate-based consolidant on a porous carbonatic stone (limestone) and for investigating their stratigraphic distribution at the submicrometric scale length. We evaluated advantages and drawbacks of three Ca K-edge 2D-XANES-based approaches: (i) transmission mode full-field-XANES (FF-XANES) imaging; (ii) micro-X-ray fluorescence (μ-XRF) mapping above the Ca K-edge combined with the acquisition of XRF mode μ-XANES spectra at a limited number of spots; (iii) full-spectral µ-XANES (FS µ-XANES) mapping in XRF mode and its variant called selectively induced X-ray emission spectroscopy (SIXES) mapping. Overall, Ca K-edge 2D-XANES spectroscopy provided accurate qualitative and semi-quantitative information on the newly formed calcium carbonates (i.e., amorphous calcium carbonate, vaterite and calcite) and their stratigraphic distribution at the submicrometric scale, thus opening a new scenario to study the carbonatation process of calcium-based consolidants in limestones.

| S-EPMC7459109 | biostudies-literature

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience.

Project description:Synchrotron radiation is the most versatile way to explore biological materials in different states: monocrystalline, polycrystalline, solution, colloids and multiscale architectures. Steady improvements in instrumentation have made synchrotrons the most flexible intense X-ray source. The wide range of applications of synchrotron radiation is commensurate with the structural diversity and complexity of the molecules and macromolecules that form the collection of substrates investigated by glycoscience. The present review illustrates how synchrotron-based experiments have contributed to our understanding in the field of structural glycobiology. Structural characterization of protein-carbohydrate interactions of the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution.

| S-EPMC5480326 | biostudies-literature

On the Sr1-xBaxFeO₂F Oxyfluoride Perovskites: Structure and Magnetism from Neutron Diffraction and Mossbauer Spectroscopy.

Project description:Four oxyfluorides of the title series (x = 0.00, 0.25, 0.50, 0.75) have been stabilized by topotactic treatment of perovskite precursors Sr1-xBaxFeO3-δ prepared by soft-chemistry procedures, yielding reactive materials that can easily incorporate a substantial amount of F atoms at moderate temperatures, thus avoiding the stabilization of competitive SrF₂ and BaF₂ parasitic phases. XRD and Neutron Powder Diffraction (NPD) measurements assess the phase purity and yield distinct features concerning the unit cell parameters' variation, the Sr and Ba distribution, the stoichiometry of the anionic sublattice and the anisotropic displacement factors for O and F atoms. The four oxyfluorides are confirmed to be cubic in all of the compositional range, the unit cell parameters displaying Vergard's law. All of the samples are magnetically ordered above room temperature; the magnetic structure is always G-type antiferromagnetic, as shown from NPD data. The ordered magnetic moments are substantially high, around 3.5 μB, even at room temperature (RT). Temperature-dependent Mössbauer data allow identifying Fe3+ in all of the samples, thus confirming the Sr1-xBaxFeO₂F stoichiometry. The fit of the magnetic hyperfine field vs. temperature curve yields magnetic ordering TN temperatures between 740 K (x = 0.00) and 683 K (x = 0.75). These temperatures are substantially higher than those reported before for some of the samples, assessing for stronger Fe-Fe superexchange interactions for these specimens prepared by fluorination of citrate precursors in mild conditions.

| S-EPMC5456977 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data