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Iron oxide of various structures is frequently used as food colorant (E 172). The spectrum of colors ranges from yellow over orange, red, and brown to black, depending on the chemical structure of the material. E 172 is mostly sold as solid powder. Recent studies have demonstrated the presence of nanoscaled particles in E 172 samples, often to a very high extent. This makes it necessary to investigate the fate of these particles after oral uptake. In this study, 7 differently structured commercially available E 172 food colorants (2 x Yellow FeO(OH), 2 x Red Fe2O3, 1 x Orange Fe2O3 + FeO(OH) and 2 x Black Fe3O4) were investigated for particle dissolution, ion release, cellular uptake, crossing of the intestinal barrier and toxicological impact on intestinal cells. Dissolution was analyzed in water, cell culture medium and artificial digestion fluids. Small-angle X-ray scattering (SAXS) was employed for determination of the specific surface area of the colorants in the digestion fluids. Cellular uptake, transport and toxicological effects were studied using human differentiated Caco-2 cells as an in vitro model of the intestinal barrier. For all materials, a strong interaction with the intestinal cells was observed, albeit there was only a limited dissolution, and no toxic in vitro effects on human cells were recorded.
AbstractWe report on gold clusters with around 62 gold atoms and a diameter of 1.15±0.10 nm. Dispersions of the clusters are long‐term stable for two years at ambient conditions. The synthesis was performed by mixing tetrachloroauric acid (HAuCl4 ⋅ 3 H2O) with the ionic liquid 1‐ethyl‐3‐methylimidazolium dicyanamide ([Emim][DCA]) at temperatures of 20 to 80 °C. Characterization was performed with small‐angle X‐ray scattering (SAXS), UV‐Vis spectroscopy, and MALDI‐TOF mass spectrometry. A three‐stage model is proposed for the formation of the clusters, in which cluster growth from gold nuclei takes place according to the Lifshitz‐Slyozov‐Wagner (LSW) model followed by oriented attachment to form colloidal stable clusters.
In this article, we present a novel one-pot mechanochemical reaction for the surface activation of lignin.
The process involves environmentally friendly oxidation with hydrogen peroxide, depolymerization of fractions with high molecular mass, and introduction of new carbonyl functions into the lignin backbone. Kraft lignin was ground with sodium percarbonate and sodium hydroxide in a ball mill at different time intervals. Analyses by infrared spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), size exclusion chromatography (SEC), dynamic vapor sorption (DVS), and small-angle X-ray scattering (SAXS) showed significant improvements. After only 5 min of reaction, there was a 47% reduction in mass-average molecular weight and an increase in carboxyl functionalities.
Chemical activation resulted in an approximately 2.8-fold increase in water adsorption. Principal component analysis (PCA) provided further insight into the correlations between IR spectra and SAXS parameters
SASfit 0.94.12
(2023)
Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields.
Comparative study of the co-assembly behaviour of 3-chloro-4-hydroxy-phenylazo dyes with DTAB
(2023)
The co-assembly of three one-fold negatively charged 3-chloro-4-hydroxy-phenylazo dyes (Yellow, Blue and Red) with the cationic surfactant dodecyltrimethylammoniumbromide (DTAB) was studied to probe dye–DTAB binding stoichiometry and assembly morphology. For each dye, phase separation was observed above a given dye : DTAB ratio with the ratio depending on the dye. While Yellow and DTAB showed liquid/liquid phase separation above Yellow : DTAB = 1 : 1.67, crystalline dye–DTAB complexes were observed for Blue–DTAB and Red–DTAB above Blue : DTAB = 1 : 2.56 and Red : DTAB = 1 : 2.94 respecively. In homogeneous solution, UV/vis spectroscopic investigations suggest stochiometries of Yellow : DTAB = 1 : 2, Blue : DTAB = 1 : 3 and Red : DTAB = 1 : 4. It was concluded, that Yellow exhibits the highest dye : DTAB binding stoichiometry in both, dye–surfactant complexes in the 2-phase region and in solution, whereas the lowest dye : DTAB binding stoichiometry was observed for Red–DTAB in both cases. The observed stoichiometries are inversely correlated to the impact dye addition has on the morphology of DTAB micelles. Generally, addition of dye to DTAB micelles leads to a reduction in spontaneous curvature of these micelles and to the formation of triaxial ellipsoidal or cylindrical micelles from oblate ellipsoidal DTAB micelles. At a DTAB concentration of 30 mM and a dye concentration of 5 mM, this effect was most pronounced for Red and least pronounced for Yellow, whilst Blue showed an intermediate effect.
The complex nature of liquid water saturation of polymer electrolyte fuel cell (PEFC) catalyst layers (CLs) greatly affects the device performance. To investigate this problem, we present a method to quantify the presence of liquid water in a PEFC CL using small-angle X-ray scattering (SAXS). This method leverages the differences in electron densities between the solid catalyst matrix and the liquid water filled pores of the CL under both dry and wet conditions. This approach is validated using ex situ wetting experiments, which aid the study of the transient saturation of a CL in a flow cell configuration in situ. The azimuthally integrated scattering data are fitted using 3D morphology models of the CL under dry conditions. Different wetting scenarios are realized in silico, and the corresponding SAXS data are numerically simulated by a direct 3D Fourier transformation. The simulated SAXS profiles of the different wetting scenarios are used to interpret the measured SAXS data which allows the derivation of the most probable wetting mechanism within a flow cell electrode.
Small-angle X-ray scattering (SAXS) can be used for structural de- termination of biological macromolecules and polymers in their na- tive states. To improve the reliability of such experiments, the re- duction of radiation damage occurring from exposure to X-rays is needed.One method, is the use of scavenger molecules that protect macromolecules against radicals produced by radiation exposure.In this study we investigate the feasibility to apply the compatible solute, osmolyte and radiation protector Ectoine (THP(B)) as a scavenger throughout SAXS measurements of single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). Therefore we monitor the radiation induced changes of G5P during bio-SAXS. The resulting microscopic energy-damage relation was determined by particle scattering simu- lations with TOPAS/Geant4. The results are interpreted in terms of radical scavenging as well as post-irradiation effects, related to preferential-exclusion from the protein surface. Thus, Ectoine provides an non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations
(2023)
Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.
Today there are hundreds of products available containing silver in form of nanoparticles, so-called nanosilver. This situation and the foreseeable future growing market of nanosilver will supposedly cause an increased release of silver into the environment. In this way, silver can be also incorporated into the human body and accumulated in different organs, which can be toxic or at least an unknown risk to human health. For these reasons, it is important to constantly study materials containing silver nanoparticles, their production, application in products and technical processes, dissemination of silver nanoparticles in the environment, and effects on humans and nature. The state-of-the-art nanoparticle size and concentration characterization are illustrated in an extensive interlaboratory comparison. To guarantee the traceability of measurements and to secure the comparison of results of different analytical methods, reference materials (RM) and certified reference materials (CRM) are essential. As a case study, the objective of the presented project was to provide an aqueous suspension of silver nanoparticles as a reference material with a nominal diameter below 10 nm for application in the determination of the size and concentration of nanoparticles in an aqueous surrounding. Measurands are the particles’ diameter D, size distribution width σ, number density N, and concentration c. Target uncertainties, defined as one sigma of the measurand values, are 5% for D, 10% for σ, 20% for N, and 20% for c. The certification was carried out based on ISO 17867 and the relevant ISO-Guides to produce reference material. The process of using SAXS as a reliable method for testing homogeneity and short-term and long-term stability of the material is reported. The particle preparation is described in detail so that the user can carry out the steps of synthesis and characterization in his own laboratory if required. Optionally, one can also contact the author for the provision of the silver nanoparticles. Detailed information can be found elsewhere (BAM Certification Reports, BAM-N008 (2022)).
Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
This talk highlights a proof-of-concept that demonstrates the ability to calculate high-resolution Fourier transforms. These can be combined with multi-scale modeling to simulate scattering over a wide range, from small-angle scattering to XRD and PDF.
The preprint documenting this is available on the ArXiv here:
https://doi.org/10.48550/arXiv.2303.13435
The Jupyter notebook, VASP calculation details and MOUSE measured scattering patterns are available from this Zenodo repository: https://dx.doi.org/10.5281/zenodo.7764045
## Summary:
This notebook and associated datasets (including VASP details) accompany a manuscript available on the ArXiv (https://doi.org/10.48550/arXiv.2303.13435) and hopefully soon in a journal as short communication as well. Most of the details needed to understand this notebook are explained in that paper with the same title as above. For convenience, the abstract is repeated here:
## Paper abstract:
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is presented coupled to the scattering intensity, may offer a novel pathway for determining the degree of crystallinity.
The ``Ultima Ratio'' strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from $Q<0.01$\,$\mathrm{nm}^{-1}$ up to $Q\approx150$\,$\mathrm{nm}^{-1}$, with a resolution of 0.16\,\AA. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to $8000^3$ voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-$Q$ behaviour.
The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder.
While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts.
The progress in the VAMAS Project #15" Measurement of particle size and shape distribution of bipyramidal titania including deposition from liquid suspension" within TWA 34 Nanoparticle Populations is presented with highlight of the following points:
- Determine and compare particle size and shape distribution by means of:
• electron microscopy (SEM, TEM, STEM-in-SEM)
• atomic force microscopy (AFM)
• small angle X-ray scattering (SAXS)
- Determine uncertainty induced by deposition protocol from liquid suspension with comparison to known values from a prior ILC with already deposited nanoparticles on TEM grids.
- Provide comparative validation of protocols for the techniques other than TEM.
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is on the same scale as the scattering intensity, may offer a novel pathway for determining the degree of crystallinity.
The "Ultima Ratio" strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from Q < 0.01 1/nm up to Q < 150 1/nm, with a resolution of 0.16 Angstrom. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to 8000^3 voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-Q behaviour. The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder. While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts.
A Round Robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions, and two from powders.
Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5 % and half of the population width entries within 40 %, respectively. Due to the added complexity of the structure factor, much fewer people submitted answers on the powder datasets.
For those that did, half of the entries for the means and widths were within 44 % and 86 % respectively. This Round Robin experiment highlights several causes for the discrepancies, for which solutions are proposed.
Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
Showcasing research from the Federal Institute for Material Research and Testing Berlin and Fraunhofer Institute for Celltherapy and Immunology Branch Bioanalytics and Bioprocesses Potsdam.
Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine.
We aimed to increase the possible undisturbed exposure time during bio-SAXS measurements of single-stranded DNA-binding proteins. Therefore small angle X-ray scattering was performed on Gene-V Protein (G5P/GVP), which is involved in DNA repair processes. To achieve this, irradiations were performed in presence and absence of the hydroxyl-radical scavenger and osmolyte Ectoine, which showed efficient radiation protection and prevented protein aggregation, thus allows for a non-disturbing way to improve structure-determination of biomolecules.
X-ray scattering datasets for samples described in the 2022 publication "Side chain length dependent dynamics and conductivity in self assembled ion channels". This dataset includes both raw and processed X-ray scattering data for samples ILC8, ILC10, ILC12, ILC14 and ILC16 alongside background measurement files (BKG).
X-ray scattering datasets for samples described in the 2022 publication "Molecular Mobility of Polynorbornenes with Trimethylsiloxysilyl side groups: Influence of the Polymerization Mechanism". This dataset includes both raw and processed X-ray scattering data for samples APTCN and MPTCN, alongside background measurements files (BKG).
X-ray scattering datasets for samples described in the 2020 publication "Molecular Dynamics of Janus Polynorbornenes: Glass Transitions and Nanophase Separation". This dataset includes both raw and processed X-ray scattering data for samples PTCHSiO-Pr, Bu, Hx, Oc and De, alongside background measurements files (BKG). This data was collected using the MOUSE project (instrument and methodology).
Large, ink-bottle-shaped pores in mesocellular foams (MCFs) are desired for various applications requiring enhanced mass transfer or the immobilization of larger compounds. Hence, the cylindrical pores of COK-12, an ordered mesoporous silica structurally comparable to SBA-15 but synthesized at room-temperature at quasi-neutral pH, are chemically swollen into ink-bottle pores. Therefore, p-xylene is used as a more sustainable swelling agent compared to popular alternatives. Its high boiling point allows for an additional thermal aging step to amplify the mesostructure enlargement without needing additional chemicals. For COK-12, the MCFs obtained at room temperature reach an unprecedented plateau for the modal mesopore cell and window diameter of 19.9 and 5.5 nm, respectively, with an underlying broad pore size distribution and distorted hexagonal lattice up to 14.5 nm, involving hexagonal and spherical structures. The combined chemical and thermal swelling resulted in the selective enlargement of the window diameter to more than 200% and a slightly increased cell diameter, pore size distribution, and hexagonal lattice distortion in comparison to the room temperature synthesis. Such materials are thought to be promising alternatives to SBA-15-based MCFs, often utilizing toxic catalysts during synthesis. The presented results pave the way for enhanced adsorptive, catalytic, and drug delivery performances for COK-12-based materials.
Despite their inherent instability, 4n π systems have recently received significant attention due to their unique optical and electronic properties. In dibenzopentalene (DBP), benzanellation stabilizes the highly antiaromatic pentalene core, without compromising its amphoteric redox behavior or small HOMO−LUMO energy gap. However, incorporating such molecules in organic devices as discrete small molecules or amorphous polymers can limit the performance (e.g., due to solubility in the battery electrolyte solution or low internal surface area). Covalent organic frameworks (COFs), on the contrary, are highly ordered, porous, and crystalline materials that can provide a platform to align molecules with specific properties in a well-defined, ordered environment. We synthesized the first antiaromatic framework materials and obtained a series of three highly crystalline and porous COFs based on DBP. Potential applications of such antiaromatic bulk materials were explored: COF films show a conductivity of 4 × 10−8 S cm−1 upon doping and exhibit photoconductivity upon irradiation with visible light. Application as positive electrode materials in Li-organic batteries demonstrates a significant enhancement of performance when the antiaromaticity of the DBP unit in the COF is exploited in its redox activity with a discharge capacity of 26 mA h g−1 at a potential of 3.9 V vs. Li/Li+ . This work showcases antiaromaticity as a new design principle for functional framework materials.
Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
X-ray scattering and sorption data associated with the publication "Antiaromatic Covalent Organic Frameworks Based on Dibenzopentalenes". X-ray scattering data is provided for COF and POP materials, including data from stability tests, as three-column ascii files with columns q (nm-1), I (m-1) and uncertainty on I, as well as being provided in 2θ.
This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (https://doi.org/10.1039/D2CP05053F).
Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included.
TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry which is further described in https://doi.org/10.26272/opus4-55751.
This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission.
These are four datasets that were made available to the participants of the Small-angle Scattering data analysis round robin. The intent was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset.
In this repository, there are:
1) a PDF document with more details for the study,
2) the datasets for people to try and fit
3) an Excel spreadsheet to document the results.
Datasets 1 and 2 were modified from: Deumer, Jerome, & Gollwitzer, Christian. (2022). npSize_SAXS_data_PTB (Version 5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5886834
Datasets 3 and 4 were collected in-house on the MOUSE instrument.
Technical drawings and documents for building a compact, heated, vacuum compatible flow-through sample holder. This holder is in use at the BAM MOUSE instrument as well as at the I22 beamline at the Diamond Light Source (see references for instrument details).
This holder has several features:
- The holder can be used in vacuum environments as well as in atmosphere
- It has two G 1/4" UNF fittings to attach HPLC tubing for (optionally) flowing a medium through the sample cell
- There are two additional (unflowed) sample positions for backgrounds and calibrants, held at the same temperature
- The low-mass design coupled with a 250W heating element can achieve heating rates of 1 degree C per second, when coupled (for example) with an Omron E5CC PID controller.
- The sample holder insert can be made from various materials depending on the application. Sealing the sample from the vacuum can be achieved using kapton, teflon or Magic tape, depending on the temperature requirements. The inlet and outlet holes will need to be punctured with a needle to enable flow.
- Large exit cones ensure a clear exit angle of at least 45 degrees two theta.
- It has been tested with temperatures up to 400 degrees C.
- Compression area has been raised and polished to ensure a good vacuum seal.
OpenSCAD, STL and technical drawings for the solid sample rack designed primarily for use with The MOUSE instruments.
This solid sample rack can be used in conjunction with:
- Laser-cut sample holder (10.5281/zenodo.7499437)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
PDF file for the laser-cut sample holder designed primarily for use with The MOUSE instruments.
This sample holder can be used in conjunction with:
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
OpenSCAD, STL and technical drawings for the capillary flow-through cell designed primarily for use with The MOUSE instruments.
This flow-through cell can be used in conjunction with:
- Modular sample holder (10.5281/zenodo.7499416)
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Laser-cut sample holder (10.5281/zenodo.7499437)
OpenSCAD, STL and technical drawings for the Modular sample holder designed primarily for use with The MOUSE instruments.
This modular sample holder can be used in conjunction with the following:
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Laser-cut sample holder (10.5281/zenodo.7499437)
This dataset is a complete set of raw, processed and analyzed data, associated with the manuscript mentioned in the title.
All associated metadata and processing history has been added. Particle size distribution analyses using McSAS are included as well.
The samples consisted of a 4.2 mass% dispersion of yttria-stabilized zirconia nanoparticles in a cross-linked matrix. The measurements show a good dispersion with minimal agglomeration. The wide-angle region shows diffraction information consistent with zirconia.
Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243–277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983–994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.
A tool for merging and/or rebinning single or multiple datasets to achieve a lower point density with best possible statistics. highly scriptable, CLI, no GUI
Version 0.1: works but could do with a cleanup. Weighting by uncertainty currently always on, but should be optional for use as an azimuthal or radial averager
Calcium sulfate minerals are abundant in natural and engineered environments and they exist in the form of three hydrates: gypsum (CaSO4·2H2O), bassanite (CaSO4·0.5H2O), and anhydrite (CaSO4). Due to their relevance in natural and industrial processes, the formation pathways of these calcium sulfate phases from aqueous solution have been the subject of intensive research1.
The state-of-the-art of the calcium sulfate formation mechanisms builds upon and goes beyond what we have come to appreciate in the astounding intricacy of other mineral formation processes from ions in aqueous solutions. The original, and rather naive, 'textbook' image of these phenomena, stemming from the adaptation of classical nucleation and growth theories, has increased in complexity due to the discovery of a variety of precursor and intermediate species2. These include solute clusters (e.g. prenucleation clusters, PNCs), liquid(-like) phases, as well as amorphous and nanocrystalline solids etc.. In this context, a number of studies have already revealed that nucleation in the CaSO4-H2O system is non-classical, where the formation of the different crystalline phases involves several steps including a common amorphous precursor1, 3, 4.
In this contribution we show that the formation of the amorphous phase involves the aggregation of small primary particles into larger disordered aggregates exhibiting a "brick-in-the-wall" structure5, 6. The actual crystallization occurs by the restructuring and coalescence of the particles ("bricks") into a given calcium sulfate phase depending on the physicochemical conditions of the solution. Importantly, the rearrangement process does not continue until a (nearly-)perfect homogeneous single crystal is obtained. Instead it comes to a stop, or at least significantly slows down. Such a process thus yields a final imperfect mesocrystal, composed of smaller domains rather than a continuous crystal structure, within which the domains are separated by an amorphous (i.e. less ordered) calcium sulfate phase.
Hence, the non-classical crystallization process of CaSO4 yields a final imperfect mesocrystal with an overall morphology resembling that of a single crystal, yet composed of smaller nano-domains. Importantly, these observations reveal that organic-free calcium sulfate mesocrystals grown by a particle mediated-pathway preserve in the final crystal structure a “memory” or “imprint” of their non-classical nucleation process, something that has been overlooked until now. Furthermore, the nano-scale misalignment of the structural sub-units within these crystals can propagate through the length-scales, and be expressed macroscopically as misaligned zones/domains in large single crystals. Indeed, by considering large anhydrite crystals from the famous Naica Mine (“Cueva de los cristales”) we observed a suite of correlated self-similar void defects spanning multiple length-scales7. These flaws, in the macroscopic crystal, stem from “seeds of imperfection” originating from a particle-mediated nucleation pathway. Hence, building a crystal could be viewed as Nature stacking blocks in a game of Tetris, whilst slowly forgetting the games core concept and failing to fill rows completely.
Models for TOPAS/Geant4 to estimate the microscopic dose received by biomolecules during bioSAXS experiments.
The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org).
Measuring an X-ray scattering pattern is relatively easy, but measuring a steady stream of high-quality, useful patterns requires significant effort and good laboratory organization.
Such laboratory organization can help address the reproducibility crisis in science, and easily multiply the scientific output of a laboratory, while greatly elevating the quality of the measurements. We have demonstrated this for small- and wide-angle X-ray scattering in the MOUSE project (Methodology Optimization for Ultrafine Structure Exploration).
With the MOUSE, we have combined a comprehensive and highly automated laboratory workflow with a heavily modified X-ray scattering instrument. This combination allows us to collect fully traceable scattering data, within a well-documented, FAIR-compliant data flow (akin to what is found at the more automated synchrotron beamlines). With two full-time researchers, our lab collects and interprets thousands of datasets, on hundreds of samples, for dozens of projects per year, supporting many users along the entire process from sample selection and preparation, to the analysis of the resulting data.
This talk will briefly introduce the foundations of X-ray scattering, present the MOUSE project, and will highlight the proven utility of the methodology for materials science. Upgrades to the methodology will also be discussed, as well as possible avenues for transferring this holistic methodology to other instruments
A versatile software package in the form of a Python extension, named CDEF (computing Debye’s scattering formula for extraordinary form factors), is proposed to calculate approximate scattering profiles of arbitrarily shaped nanoparticles for small-angle X-ray scattering (SAXS). CDEF generates a quasi-randomly distributed point cloud in the desired particle shape and then applies the open-source software DEBYER for efficient evaluation of Debye’s scattering formula to calculate the SAXS pattern (https://github.com/j-from-b/CDEF). If self-correlation of the scattering signal is not omitted, the quasi-random distribution provides faster convergence compared with a true-random distribution of the scatterers, especially at higher momentum transfer. The usage of the software is demonstrated for the evaluation of scattering data of Au nanocubes with rounded edges, which were measured at the four-crystal monochromator beamline of PTB at the synchrotron radiation facility BESSY II in Berlin. The implementation is fast enough to run on a single desktop computer and perform model fits within minutes. The accuracy of the method was analyzed by comparison with analytically known form factors and verified with another implementation, the SPONGE, based on a similar principle with fewer approximations. Additionally, the SPONGE coupled to McSAS3 allows one to retrieve information on the uncertainty of the size distribution using a Monte Carlo uncertainty estimation algorithm.
Post-assembly modifications are efficient tools to adjust colloidal features of block copolymer (BCP) particles. However, existing methods often address particle shape, morphology, and chemical functionality individually. For simultaneous control, we transferred the concept of seeded polymerization to phase separated BCP particles. Key to our approach is the regioselective polymerization of (functional) monomers inside specific BCP domains. This was demonstrated in striped PS-b-P2VP ellipsoids. Here, polymerization of styrene preferably occurs in PS domains and increases PS lamellar thickness up to 5-fold. The resulting asymmetric lamellar morphology also changes the particle shape, i.e., increases the aspect ratio. Using 4-vinylbenzyl azide as co-monomer, azides as chemical functionalities can be added selectively to the PS domains. Overall, our simple and versatile method gives access to various multifunctional BCP colloids from a single batch of pre-formed particles.
Designing the shape and size of catalyst particles, and their interfacial charge, at the nanometer scale can radically change their performance. We demonstrate this with ceria nanoparticles. In aqueous media, nanoceria is a functional mimic of haloperoxidases, a group of enzymes that oxidize organic substrates, or of peroxidases that can degrade reactive oxygen species (ROS) such as H2O2 by oxidizing an organic substrate. We show that the chemical activity of CeO2−x nanoparticles in haloperoxidase- and peroxidaselike reactions scales with their active surface area, their surface charge, given by the ζ-potential, and their surface defects (via the Ce3+/Ce4+ ratio). Haloperoxidase-like reactions are controlled through the ζ-potential as they involve the adsorption of charged halide anions to the CeO2 surface, whereas peroxidase-like reactions without charged substrates are controlled through the specific surface area SBET. Mesoporous CeO2−x particles, with large surface areas, were prepared via template-free hydrothermal reactions and characterized by small-angle X-ray scattering. Surface area, ζ-potential and the Ce3+/Ce4+ ratio are controlled in a simple and predictable manner by the synthesis time of the hydrothermal reaction as demonstrated by X-ray photoelectron spectroscopy, sorption and ζ-potential measurements. The surface area increased with synthesis time, whilst the Ce3+/Ce4+ ratio scales inversely with decreasing ζ-potential. In this way the catalytic activity of mesoporous CeO2−x particles could be tailored selectively for haloperoxidase- and peroxidase-like reactions. The ease of tuning the surface properties of mesoporous CeO2x particles by varying the synthesis time makes the synthesis a powerful general tool for the preparation of nanocatalysts according to individual needs.
One aim of the EMPIR nPSize project 17NRM04 was to develop and validate three classes of candidate reference (test) materials (RTMs), with i) well-defined non-spherical shape, ii) relatively high polydispersity index, and iii) accurate particle concentrations.
To fulfil the requirements of the project, 11 different types of materials were prepared. Following the initial assessment of the materials suitability, nPSize5_PT_UNITO, nPSize6_AC_UNITO and nPSize7_GN_CEA materials were found unsuitable for the project, due to various reasons. PT material was deemed unsuitable due to its predominantly agglomerated nature. AC material contained relatively high amount of impurities (other particle forms). GN material was found too heterogeneous in both the length and width for the purpose of the project. The remaining 8 candidate RTMs were assessed for their homogeneity and stability and used for successful delivery of the associated activities within the nPSize project.
BAM is currently building up a platform of novel nanoRMs relying on iron oxide nanoparticles of different shape, size and surface chemistry. Iron oxide was chosen as a core material because of its relevance to the material and life sciences.
As a first candidate of this series, we present cubic iron oxide nanoparticles with a nominal edge length of 8 nm. These particles were synthesized by thermal decomposition of iron oleate in high boiling organic solvents adapting well-known literature procedures. After dilution to a concentration suitable for electron microscopy (TEM and SEM) as well as for small-angle X-ray scattering (SAXS) measurements, the candidate nanoRM was bottled and assessed for homogeneity and stability by both methods following the guidelines of ISO 17034 and ISO Guide 35.
The particle sizes obtained by both STEM-in-SEM and TEM are in excellent agreement with a minimum Feret of 8.3 nm ± 0.7 nm. The aspect ratio (AR) of the iron oxide cubes were extracted from the images as the ratio of minimum Feret to Feret resulting in an AR of 1.18 for TEM to 1.25 for SEM. Alternatively, a rectangular bounding box was fitted originating from the minimum Feret and the longest distance through the particle in perpendicular direction. This led to AR values of 1.05 for TEM and 1.12 for SEM, respectively. The results confirm the almost ideal cubic shape.
Mechanically stable structures with interconnected hierarchical porosity combine the benefits of both small
and large pores, such as high surface area, pore volume, and good mass transport capabilities. Hence, lightweight micro-/meso-/macroporous monoliths are prepared from ordered mesoporous silica COK-12 by means of spark plasma sintering (SPS, S-sintering) and compared to conventionally (C-) sintered monoliths. A multi-scale model is developed to fit the small angle X-ray scattering data and obtain information on the hexagonal lattice parameters, pore sizes from the macro to the micro range, as well as the dimensions of the silica population. For both sintering techniques, the overall mesoporosity, hexagonal pore ordering, and amorphous character are preserved. The monoliths' porosity (77–49%), mesopore size (6.2–5.2 nm), pore volume (0.50–0.22 g cm-3
), and specific surface area (451–180 m2 g-1) decrease with increasing processing temperature and pressure. While the difference in porosity is enhanced, the
structural parameters between the C-and S-sintered monoliths are largely converging at 900 C, except for the mesopore size and lattice parameter, whose dimensions are more extensively preserved in the
S-sintered monoliths, however, coming along with larger deviations from the theoretical lattice. Their higher mechanical properties (biaxial strength up to 49 MPa, 724 MPa HV 9.807 N) at comparable porosities and ability to withstand ultrasonic treatment and dead-end filtration up to 7 bar allow S-sintered monoliths to reach a high permeance (2634 L m-2 h-1 bar-1), permeability (1.25 x 10^-14 m2), and ability to reduce the chemical oxygen demand by 90% during filtration of a surfactant-stabilized oil in water emulsion, while indicating reasonable resistance towards fouling.
Li-rich nanoparticles of Li1+xMn2–xO4 doped with Al, Co, or Ni are successfully synthesized using a facile, fast, and efficient microwave-assisted hydrothermal route. Synchrotron X-ray diffraction confirms the formation of the crystalline cubic spinel phase type. X-ray absorption spectroscopy analysis at the Co and Ni K- and L-edges verifies that the dopants are within the Li1+xMn2–xO4 spinel structure and are inactive during cycling in the bulk and at the surface. Moreover, we demonstrate that nanocrystallinity and cationic doping play an important role in improving the electrochemical performance with respect to LiMn2O4 microparticles. They significantly reduce the charge-transfer resistance, lower the first cycle irreversible capacity loss to 6%, and achieve a capacity retention between 85 and 90% after 380 cycles, with excellent Coulombic efficiency close to 99% without compromising the specific charge at a 5C cycling rate. Furthermore, the Mn K- and L-edges attest that after long cycling, the Mn oxidation state in the bulk differs from that at the surface caused by the Mn disproportion reaction; however, the cationic doping helps mitigate the Mn dissolution with respect to the undoped Li1+xMn2–xO4 nanoparticles, as indicated by inductively coupled plasma atomic emission spectrometry.
Advanced peptide-based nanomaterials composed of self-assembling peptides (SAPs) are of emerging interest in pharmaceutical and biomedical applications. The introduction of fluorine into peptides, in fact, offers unique opportunities to tune their biophysical properties and intermolecular interactions. In particular, the degree of fluorination plays a crucial role in peptide engineering as it can be used to control the characteristics of fluorine-specific interactions and, thus, peptide conformation and self-assembly. Here, we designed and explored a series of amphipathic peptides by incorporating the fluorinated amino acids (2S)-4-monofluoroethylglycine (MfeGly), (2S)-4,4-difluoroethylglycine (DfeGly) and (2S)-4,4,4-trifluoroethylglycine (TfeGly) as hydrophobic components. This approach enabled studying the impact of fluorination on secondary structure formation and peptide self-assembly on a systematic basis. We show that the interplay between polarity and hydrophobicity, both induced differentially by varying degrees of side chain fluorination, does affect peptide folding significantly. A greater degree of fluorination promotes peptide fibrillation and subsequent formation of physical hydrogels in physiological conditions. Molecular simulations revealed the key role played by electrostatically driven intra-chain and inter-chain contact pairs that are modulated by side chain fluorination and give insights into the different self-organization behaviour of selected peptides. Our study provides a systematic report about the distinct features of fluorinated oligomeric peptides with potential applications as peptide-based biomaterials.
Herein, a simple one-pot procedure is reported to obtain aqueous zinc oxide (ZnO) nanoparticle dispersions from ZnO nanoparticles dispersed in cyclohexane. In the process, polyoxyethylene (20) sorbitan monooleate (polysorbate 80, Tween 80) functions as a phase transfer agent and colloidal stabilizer. The particles grow in a defined manner during the transfer, presumably via coalescence. The final particle radii are tuneable in the range from 2.3 ± 0.1 nm to 5.7 ± 0.1 nm depending on the incubation time of the dispersion at 90 °C. Small-angle X-ray scattering is employed to determine the particle radius distributions before and after phase transfer. The larger ZnO particle radii are associated with a redshift of the optical bandgap and luminescence emission, as expected for semiconductor nanoparticles. The particles presented here exhibit a relative size distribution width of 20%, rendering them attractive for applications in, e.g., biology or catalysis. The latter application is demonstrated at the photocatalytic degradation of methylene blue dye.
The continuously increasing use of plastics is supposed to result in a rising exposure of MNPs to humans. Available data on human health risks of microplastics after oral uptake increased immensely in the past years and indicates very likely only low risks after oral consumption. Concerning nanoplastics, uptake, transport and potential adverse effects after oral uptake are less well understood. This study aims to investigate differences between microplastic particles and particles in the submicron- and nanoscaled size derived from food-relevant polymers with a particle size range consistent with higher potential for cellular uptake, fate, and effects when applied to human intestinal and liver cells. This work includes the development of cellular and subcellular detection methods for synthetic polymeric particles in the micro- and nanometer-range, using Scanning Electron Microscopy, Small-Angle X-ray and Dynamic Light Scattering methods, Asymmetric Flow Field Flow Fractionation, octanol-water fractionation, fluorescence microscopy and flow cytometry. Polylactic acid (250 nm and 2 μm (polydisperse)), melamine formaldehyde (366 nm) and polymethylmethacrylate (25 nm) were thoroughly characterized. The submicro- and nanoplastic test particles showed an increased uptake and transport quantity through intestinal cells. Both types of particles resulted in observed differences of uptake behavior, most likely influenced by different lipophilicity, which varied between the polymeric test materials. Toxic effects were detected after 24 h only in overload situations for the particles in the submicrometer range. This study provides further evidence for gastrointestinal uptake of submicro- and nanoplastics and points towards differences regarding bioavailability between microplastics and smaller plastic particles that may result following the ingestion of contaminated food and beverages. Furthermore, the results reinforce the importance for studying nanoplastics of different materials of varying size, surface properties, polymer composition and hydrophobicity.
Iron nitride (Fe3N) and iron carbide (Fe3C) nanoparticles can be prepared via sol−gel synthesis. While sol−gel methods are simple, it can be difficult to control the crystalline composition, i.e., to achieve a Rietveld-pure product. In a previous in situ synchrotron study of the sol−gel synthesis of Fe3N/Fe3C, we showed that the reaction proceeds as follows:
Fe3O4 → FeOx → Fe3N → Fe3C. There was considerable overlap between the different phases, but we were unable to ascertain whether this was due to the experimental setup (side-on heating of a quartz capillary which could lead to thermal gradients) or whether individual particle reactions proceed at different rates. In this paper, we use in situ wide- and small-angle X-ray scattering (wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS)) to demonstrate that the overlapping phases are indeed due to variable reaction rates. While the initial oxide nanoparticles have a small range of diameters, the size range expands considerably and very rapidly during the oxide−nitride transition. This has implications for the isolation of Rietveld-pure Fe3N, and in an extensive laboratory study, we were indeed unable to isolate phasepure Fe3N. However, we made the surprising discovery that Rietveld-pure Fe3C nanoparticles can be produced at 500 °C with a sufficient furnace dwell time. This is considerably lower than the previous reports of the sol−gel synthesis of Fe3C nanoparticles.
The main outcomes of the EMPIR project nPSize are presented and the suitability of the new capabilities, e.g. reference materials, sample preparation protocols, measurement procedures, and data analysis, to be standardized and implemented in accredited analytical laboratories is discussed. Complementation and/or filling gaps of published and ongoing standardisation projects on size, shape and number concentration measurements under ISO/TC 229/JWG 2 are offered.
The two VAMAS inter-laboratory comparisons resulted from the nSPize project and just started under TWA 34 Nanoparticle Populations (Projects #15 and #16) of bipyramidal TiO2 anatase and bimodal SiO2 nanoparticles are presented in detail.