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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.
Iron Oxide Nanocubes as a New Certified Reference Material for Nanoparticle Size Measurements
(2023)
The rational design and increasing industrial use of nanomaterials require a reliable characterization of their physicochemical key properties like size, size distribution, shape, and surface chemistry. This calls for nanoscale reference materials (nanoRMs) for the validation and standardization of commonly used characterization methods closely matching real-world nonspherical nano-objects. This encouraged us to develop a nonspherical nanoRM of very small size consisting of 8 nm iron oxide nanocubes (BAM-N012) to complement spherical gold, silica, and polymer nanoRMs. In the following, the development and production of this nanoRM are highlighted including the characterization by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) as complementary methods for size and shape parameters, homogeneity and stability studies, and calculation of a complete uncertainty budget of the size features. The determination of the nanocubes’ edge length by TEM and SAXS allows a method comparison. In addition, SAXS measurements can also provide the mean particle number density and the mass concentration. The certified size parameters, area equivalent circular diameter and square edge length, determined by TEM with a relative expanded uncertainty below 9%, are metrologically traceable to a natural constant for length, the very precisely known (111) lattice spacing of silicon. Cubic BAM-N012 qualifies as a certified nanoRM for estimating the precision and trueness, validation, and quality assurance of particle size and shape measurements with electron microscopy and SAXS as well as other sizing methods suitable for nanomaterials. The production of this new iron oxide nanocube RM presents an important achievement for the nanomaterial community, nanomaterial manufacturers, and regulators.
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)).
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.
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.
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 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.
Continuing progress in the field of X-ray scattering methods empowers scientists with new possibilities to capture the most important piece of information about the structure of the sample - its 3D electron density.
Although the first methods appeared almost a century ago, recovering the density structure of a sample is still very problematic. Most avail-able imaging techniques transform a 3D electron density of a realspace structure into the 2D Fourier Transform of the intensity of scattered waves in the reciprocal space. This process causes a loss of information.
Firstly, instead of a 3D sample, a 2D image is created, and secondly, the phase information of the scattered waves is lost. The latter is known as the ”phase problem” and poses a serious obstacle on a way to recover a 3D electron density. In this work, we draw attention to the problem of forward and inverse Small Angle X-Ray Scattering. In the first, forward, part, we rethink the existing pipelines to computationally simulate such scattering experiments. Although there are efficient implementations of fast Fourier transformation, they often have some drawbacks. For instance, to calculate a 3D fast Fourier transform it is required to place its density in the RAM. For high-resolution structures of size > 1024 3 , this becomes very problematic, as the whole density structure requires more than 16 GB of memory.
CUDA solution allows for a very fast and parallelizable implementation of high-resolution data on hundreds of last-generation machines.
Such computations are very pricy and inaccessible for most scientists.
To bypass this limitation, we propose a solution for a split-up 3D fast Fourier transform, which is implemented as a sequence of 2D and 1D operations. We compare our implementation on the simulated 3D shapes and show the result of a proof-of-concept on 4096 3 Metallorganic framework density structure. In the second, inverse problem, we train an invertible neural network, that given scattering data can predict the shape and its parameters. The architecture is built such, that the inverse problem is learned together with the forward process - the Fourier Transformation. We achieved very good results with this architecture, nonetheless, further testing is required, as the current training set only encompasses three simple shapes: sphere, hard sphere and cylinder.
All code to reproduce and analyze the results is available at https: //github.com/sofyalaski/SAXS-simulations.