Small-angle X-ray Scattering Data Research Articles

Structural Characterization of Silver Nanoparticles Produced by Biogenic Synthesis Using SAXS

Nanotechnology applied to the agricultural sector has highlighted in recent decades, making important contributions, including systems for pest control as biogenic nanoparticles. These nanoparticles are used to control phytopathogens, demonstrating the need to understand its composition, mechanisms of action and toxicity. Their capping of biomolecules, derived from the organism used in the synthesis, contributes to their stability and biological activity. Ag nanoparticles were produced by the fungus Trichoderma harzianum in aqueous solutions containing silver nitrate as a precursor for the silver nanoparticles. Some of the samples were exposed to the phytopathogenic fungus Sclerotinia sclerotiorum responsible for the white mold. After preparation, a fraction of the samples was submitted to physico-chemical processes to remove organic cap layer on nanoparticles surface formed during the preparation process. In this study we determined the effect of the phytopathogenic fungus and cap removal process in the average radius, radius dispersion, number density of the nanoparticles using small angle X-ray scattering (SAXS), where we considered their almost spherical shape in aqueous solution obtained by the biogenic route. The SAXS data analyses suggest that the presence of the pathogenic fungus results in a diminution of number and total volume of Ag NPs without significant effects on average radius and radius dispersion. Our results also indicate that the physic-chemical process to remove the organic cap surrounding the Ag NPs leads to a decrease in the fraction of the smaller nanoparticles.

Grain boundary as an influential feature endues β-HMX powder with enhanced impact tolerance

The handling safety of high explosives, as routinely characterized by the drop-weight impact sensitivity (IS), has important repercussions on the development of explosives. Herein, the impressive low IS of β-HMX (1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane) spherulite and the corresponding desensitization mechanism are elaborated with the influential role of the grain boundary. The sensitivity was evaluated by a substantial number of IS tests using “X out of 25”, Bruceton “up and down” and high-speed photography technology. The collected data, comprising over 12 batches of samples for a total of about 400 impact tests, were analyzed as a function of the particle structure parameters. The IS was found to positively relate to the porosity calculated from Small-Angle X-ray Scattering data which semi-quantitatively reflected the grain boundary in spherulite. The investigation into the influence of shape suggests that while particle shape did contribute to desensitization, the primary factor affecting the reduction in HMX sensitivity was the presence of grain boundaries. The grain boundary strengthening and spherical envelope were found to be influential as they may be beneficial for energy de-localization, thereby mitigating localized heating. The polycrystalline spherulite with purity (>98.5%), sphericity (>80.0%) and porosity (>0.4%) carefully controlled exhibited the ignition probability of 0% and H50 of c.a. 99.0 cm, outperforming any other monocrystalline β-HMX particles. This work introduces the grain boundary as a new consideration for desensitization in energetic crystals, which has been previously underestimated but holds promise for the design of high explosives with improved handling safety.

Simple Scattering: Lipid nanoparticle structural data repository.

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

Randomly Layered Superstructure of In2O3 Truncated Nano-Octahedra and Its High-Pressure Behavior.

This study outlines the preparation and characterization of a unique superlattice composed of indium oxide (In2O3) vertex-truncated nano-octahedra, along with an exploration of its response to high-pressure conditions. Transmission electron microscopy and scanning transmission electron microscopy were employed to determine the average circumradius (15.2 nm) of these vertex-truncated building blocks and their planar superstructure. The resilience and response of the superlattice to pressure variations, peaking at 18.01 GPa, were examined using synchrotron-based wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS) techniques. The WAXS data revealed no phase transitions, reinforcing the stability of the 2D superlattice composed of random layers in alignment with a p31m planar symmetry as discerned by SAXS. Notably, the SAXS data also unveiled a pressure-induced, irreversible translation of octahedra and ligand interaction occurring within the random layer. Through our examination of these pressure-sensitive behaviors, we identified a distinctive translation model inherent to octahedra and observed modulation of the superlattice cell parameter induced by pressure. This research signifies a noteworthy advancement in deciphering the intricate behaviors of 2D superlattices under a high pressure.

Structural insights into the C-terminus of the histone-lysine N-methyltransferase NSD3 by small-angle X-ray scattering.

NSD3 is a member of six H3K36-specific histone lysine methyltransferases in metazoans. Its overexpression or mutation is implicated in developmental defects and oncogenesis. Aside from the well-characterized catalytic SET domain, NSD3 has multiple clinically relevant potential chromatin-binding motifs, such as the proline-tryptophan-tryptophan-proline (PWWP), the plant homeodomain (PHD), and the adjacent Cys-His-rich domain located at the C-terminus. The crystal structure of the individual domains is available, and this structural knowledge has allowed the designing of potential inhibitors, but the intrinsic flexibility of larger constructs has hindered the characterization of mutual domain conformations. Here, we report the first structural characterization of the NSD3 C-terminal region comprising the PWWP2, SET, and PHD4 domains, which has been achieved at a low resolution in solution by small-angle X-ray scattering (SAXS) data on two multiple-domain NSD3 constructs complemented with size-exclusion chromatography and advanced computational modeling. Structural models predicted by machine learning have been validated in direct space, by comparison with the SAXS-derived molecular envelope, and in reciprocal space, by reproducing the experimental SAXS profile. Selected models have been refined by SAXS-restrained molecular dynamics. This study shows how SAXS data can be used with advanced computational modeling techniques to achieve a detailed structural characterization and sheds light on how NSD3 domains are interconnected in the C-terminus.

Automated selection of nanoparticle models for small-angle X-ray scattering data analysis using machine learning.

Small-angle X-ray scattering (SAXS) is widely used to analyze the shape and size of nanoparticles in solution. A multitude of models, describing the SAXS intensity resulting from nanoparticles of various shapes, have been developed by the scientific community and are used for data analysis. Choosing the optimal model is a crucial step in data analysis, which can be difficult and time-consuming, especially for non-expert users. An algorithm is proposed, based on machine learning, representation learning and SAXS-specific preprocessing methods, which instantly selects the nanoparticle model best suited to describe SAXS data. The different algorithms compared are trained and evaluated on a simulated database. This database includes 75 000 scattering spectra from nine nanoparticle models, and realistically simulates two distinct device configurations. It will be made freely available to serve as a basis of comparison for future work. Deploying a universal solution for automatic nanoparticle model selection is a challenge made more difficult by the diversity of SAXS instruments and their flexible settings. The poor transferability of classification rules learned on one device configuration to another is highlighted. It is shown that training on several device configurations enables the algorithm to be generalized, without degrading performance compared with configuration-specific training. Finally, the classification algorithm is evaluated on a real data set obtained by performing SAXS experiments on nanoparticles for each of the instrumental configurations, which have been characterized by transmission electron microscopy. This data set, although very limited, allows estimation of the transferability of the classification rules learned on simulated data to real data.

Structural and compositional characterization of Ca- and β-casein enriched casein micelles

There is an increased interest in understanding the potential of modifying casein micelles composition, or even creating them de novo. In this study, soluble casein fractions were created by dissociation from native casein micelles, and their properties were studied in isolation, and after their addition to native casein micelles. The structure of these enriched casein micelles was investigated by small-angle X-ray scattering (SAXS) to evaluate if the enrichment caused changes in their internal structure. Acidification of native casein micelles from pH 6.8 to 5.6 caused colloidal calcium phosphate dissociation, and SAXS data showed a decrease in intensity at q = 0.08 Å−1, where q is the modulus of the scattering vector. Additionally, the acidification of native casein micelles (to pH 6.0) and incubation at 4 °C caused a decrease in scattering intensity at the intermediate q region (0.01–0.02 Å−1), signifying a loss of heterogeneity among the intermediate structure elements in the casein micelle. This change was caused by micellar dissolution of calcium phosphate and the release of β-casein at 4 °C. After the resuspension of casein micelles with a β-casein enriched serum, the absence of soluble β-casein suggested that most β-casein was re-associated in the colloidal fraction. These samples showed no changes in the structural features probed by SAXS. The work brings new evidence that, while a small extent of dissociation may affect the structure of the casein micelles, the enrichment with β-casein results in similar structures as those of the native micelle.

In Operando Analysis of Milk-Based Oral Formulations during Digestion Using Synchrotron Small-Angle X-ray Scattering Coupled to Low-Frequency Raman Spectroscopy.

A low-frequency Raman (LFR) probe was coupled to an in-line small-angle X-ray scattering (SAXS) beamline to test the capabilities of a combinatory approach for the determination of lipid and drug behavior during the enzymatic lipolysis of milk-based oral formulations. Cinnarizine was used as the model drug, and its solubilization dynamics as well as its potential impact on the supramolecular structures formed by the digestion products of bovine milk were evaluated from the perspective of both techniques. The SAXS data were superior in distinguishing various liquid crystalline assemblies formed during the digestion process, with LFR providing complementary information regarding the formation of calcium soaps. On the other hand, studying changes in the LFR domain allowed the differentiation of drug solubilization and precipitation; processes that were less clear from the X-ray scattering data. Given the relative simplicity of the combined experimental setup, these results highlight the advantages that the combination of the two techniques can provide for understanding and developing new lipid-based formulations and will help to translate the results obtained at synchrotron facilities to routine analysis procedures in laboratory/industry-based environments.

Small-Angle X-Ray Scattering for Macromolecular Complexes.

Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography. We include practical advice on experimental design and point out common pitfalls of the technique.

Controlled formation of multi-scale porosity in ionosilica templated by ionic liquid.

Mesoporous systems are ubiquitous in membrane science and applications due to their high internal surface area and tunable pore size. A new synthesis pathway of hydrolytic ionosilica films with mesopores formed by ionic liquid (IL) templating is proposed and compared with the traditional non-hydrolytic strategy. For both pathways, the multi-scale formation of pores has been studied as a function of IL content, combining the results of thermogravimetric analysis (TGA), nitrogen sorption, and small-angle X-ray scattering (SAXS). The combination of TGA and nitrogen sorption provides access to ionosilica and pore volume fractions, with contributions of meso- and macropores. We then elaborate an original and quantitative geometrical model to analyze the SAXS data based on small spheres (Rs = 1-2 nm) and cylinders (Lcyl = 10-20 nm) with radial polydispersity provided by the nitrogen sorption isotherms. As a result, we found that for a given incorporation of a templating IL, both synthesis pathways produce very similar pore geometries, but the better incorporation efficacy of the new hydrolytic films provides higher mesoporosity. Our combined study provides a coherent view of mesopore geometry, and thereby an optimization pathway of porous ionic membranes in terms of accessible mesoporosity contributing to the specific surface. Possible applications include electrolyte membranes with improved ionic properties, e.g., in fuel cells and batteries, as well as molecular storage.

Fractal character of coal nanopore and effect of deviation corrected, coal rank, and gas adsorption

Pore structure in coal is fundamental to determining the flowability properties and mechanical functions. Various insights into pore structure, including pore size distribution, specific area, and pore volume, have been obtained in experiments with many methods. Systematic research is lacking on how to characterize pore structure with more detailed information using fractal theory. Here, using the small-angle X-ray scattering (SAXS) method, we studied the fractal characters of four coal samples and showed how the deviation corrected, coal rank, and gas adsorption affected the fractal dimension of the pore structure. The average pore diameters of four samples obtained by the gyration radius using Guinier curves were 50.25–52.95 nm. The surface fractal of coal samples was the dominant feature, and the fractal features altered with the q value. Scattering information of simple bodies, such as pores and fractures, could superimpose the non-integer nature of the fractal dimension. The Porod and Debye laws guided the deviation correction process in the high q region. Pore fractals might be changed into surface fractals through the fractal dimension after the deviation correction, and the SAXS data obtained by Debye law correction maintained the originality and validity better than Porod law correction. The irregular shape of M was observed on the curve of fractal dimension as the maximum reflectance of vitrinite increases, resulting in three stages. More adsorption sites per unit projection area could be found in a larger fractal dimension of the pore surface, which results in an increase in Langmuir adsorption volume. The increase in the adsorption pressure reduced the fractal dimension. Our findings enhance the experimental support for comprehending the structure of coal nanopores.

Small-angle X-ray scattering simulations on a single Pt nanoparticle system: An analysis of structural characteristics

Small-angle X-ray scattering (SAXS) is an operando structure characterization tool that is unique in its ability to detect diverse nano-particulate materials. Guinier approximation and form factor can efficiently extract statistically meaningful structure information such as size and morphology from SAXS data. Herein, by employing a simulation of scattering intensities via a lattice-atoms-based code, we demonstrate quantitative correlation between SAXS data and the structural characteristics in real space for single Pt nanoparticle with different size and structure motifs. It is shown that, for particles with varied morphologies, the symmetry of 2D patterns strongly depend on the orientation of facets. However, the oscillation in frequencies and amplitudes of 1D profile, the azimuthally averaged and integrated 2D patterns, are not so sensitive to structure motifs. Regardless of particle shapes, the discrepancy between the actual particle sizes and evaluated values from 1D profile, obtained by utilizing the form factors or Guinier approximation, are pretty small. Such discrepancy is more apparent for smaller particles, attributed to strong size-dependence of surface constitution, especially for spheres. By conducting a detailed analysis of the correlation between real-space and reciprocal-space lattice information, this work highlights the continuous-to-discrete transition of nano-objects and paves the way to accurately determining structural features from SAXS data.

Determination of the Shape of a Helix Particle Based on Small-Angle X-ray Scattering Data: Modification of the “Simulated Annealing” Algorithm

Determination of the Shape of a Helix Particle Based on Small-Angle X-ray Scattering Data: Modification of the “Simulated Annealing” Algorithm

Structural characterization of human de novo protein NCYM and its complex with a newly identified DNA aptamer using atomic force microscopy and small-angle X-ray scattering

NCYM, a Homininae-specific oncoprotein, is the first de novo gene product experimentally shown to have oncogenic functions. NCYM stabilizes MYCN and β-catenin via direct binding and inhibition of GSK3β and promotes cancer progression in various tumors. Thus, the identification of compounds that binds to NCYM and structural characterization of the complex of such compounds with NCYM are required to deepen our understanding of the molecular mechanism of NCYM function and eventually to develop anticancer drugs against NCYM. In this study, the DNA aptamer that specifically binds to NCYM and enhances interaction between NCYM and GSK3β were identified for the first time using systematic evolution of ligands by exponential enrichment (SELEX). The structural properties of the complex of the aptamer and NCYM were investigated using atomic force microscopy (AFM) in combination with truncation and mutation of DNA sequence, pointing to the regions on the aptamer required for NCYM binding. Further analysis was carried out by small-angle X-ray scattering (SAXS). Structural modeling based on SAXS data revealed that when isolated, NCYM shows high flexibility, though not as a random coil, while the DNA aptamer exists as a dimer in solution. In the complex state, models in which NCYM was bound to a region close to an edge of the aptamer reproduced the SAXS data. Therefore, using a combination of SELEX, AFM, and SAXS, the present study revealed the structural properties of NCYM in its functionally active form, thus providing useful information for the possible future design of novel anti-cancer drugs targeting NCYM.

Ferritin-based fusion protein shows octameric deadlock state of self-assembly

Ferritin is a universal protein complex responsible for iron perception in almost all living organisms and has applications from fundamental biophysics to drug delivery and structure-based immunogen design. Different platforms based on ferritin share similar technological challenges limiting their development – control of self-assembling processes of ferritin itself as well as ferritin-based chimeric recombinant protein complexes. In our research, we studied self-assembly processes of ferritin-based protein complexes under different expression conditions. We fused a ferritin subunit with a SMT3 protein tag, a homolog of human Small Ubiquitin-like Modifier (SUMO-tag), which was taken to destabilize ferritin 3-fold channel contacts and increase ferritin-SUMO subunits solubility. We first obtained the octameric protein complex of ferritin-SUMO (8xFer-SUMO) and studied its structural organization by small-angle X-ray scattering (SAXS). Obtained SAXS data correspond well with the high-resolution models predicted by AlphaFold and CORAL software of an octameric assembly around the 4-fold channel of ferritin without formation of 3-fold channels. Interestingly, three copies of 8xFer-SUMO do not assemble into 24-meric globules. Thus, we first obtained and structurally characterized ferritin-based self-assembling oligomers in a deadlock state. Deadlock oligomeric states of ferritin extend the known scheme of its self-assembly process, being new potential tools for a number of applications. Finally, our results might open new directions for various biotechnological platforms utilizing ferritin-based tools.

Carboxylated cellulose nanocrystal cryogel monoliths: a multi-tool study of morphology and porosity of pure and magnetite nanoparticle-decorated CNC scaffolds

Tissue scaffolds are known to benefit from incorporation of nanoscale bio-additives like cellulose nanocrystals (CNC), which can affect porosity as an important tunable design parameter for bio-based scaffolds. In this paper, we probe how freeze-casting of carboxylated cellulose nanocrystals and CNC derivatized with magnetite nanoparticles yields macroscale cryogel scaffold monoliths. Cryogel topographical features and macropore morphologies depend on the conditions under which ice formation takes place, and on exposure to static magnetic fields. We examine porosity over several length scales with scanning electron microscopy (SEM) coupled with Local Thickness Euclidean distance image processing, small angle X-ray scattering (SAXS), and dynamic vapor sorption (DVS). SAXS data fitted with a mass fractal model and power law suggest that CNC particles aggregate to form well-defined compact walls in the range of 96.7–27.3 nm for all samples, while inclusion of Fe3O4 nanoparticles disrupts this compactness in the range of 27.3–4.8 nm. Analysis of DVS reveals that nanoparticles directly impact water uptake by the cryogel scaffolds and can reduce water sorption in mesopores with a radius of 5–6 nm.

Study of the Formation of Precursor Clusters in an Aqueous Solution of KH2PO4 by Small-Angle X-ray Scattering and Molecular Dynamics

The structure of an aqueous solution of potassium dihydrogen phosphate (KH2PO4, KDP) was studied by small-angle X-ray scattering (SAXS) and molecular dynamics (MD). According to SAXS data, the octameric species (KH2PO4)8 are formed in solution in addition to K+, (H2PO4)−, and KH2PO4, while the presence of other types of oligomers is not observed. When the temperature drops below the saturation temperature (~60 °C), the volume fraction of octamers increases sharply, reaching 50% at 4 °C. The results of MD calculations of the temporal stability relationships of dimers (KH2PO4)2, tetramers (KH2PO4)4, and octamers (KH2PO4)8 show that the dimers and tetramers disintegrate rapidly (50–100 ps), while the octamers remain stable. A comparative analysis of the bonds between the octamers and the KDP crystal lattice was carried out when the octamer was inserted during crystal growth in the directions [001] and [100]. The possible relationship of the obtained results with the changes in the anisotropy of growth rates (habitus) of KDP crystals at different degrees of supersaturation is discussed.

ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding

The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.

Microstructure of Virgin, aged and recycled asphalt based on small-angle X-ray scattering

The microstructure of asphalt plays a crucial role in determining its overall performance. However, the lack of comprehensive research on parameterizing the microstructure of asphalt has hindered the establishment of a clear relationship between microstructure and macroscopic performance. To address this gap, this paper conducted a study involving small-angle X-ray scattering (SAXS) experiments to investigate the changes in the microstructure of asphalt during aging and regeneration processes. The SAXS experimental results were then subjected to fitting using the Unified function, enabling us to derive key microstructural parameters. The SAXS data profiles obtained from virgin, aged, and recycled asphalt samples exhibit a remarkable degree of similarity, suggesting that their microstructural features are highly comparable. Additionally, the scattering characteristics observed in the SAXS data point to the presence of secondary structure scatterers within the asphalt samples. The presence of secondary structure scatterers suggests that the asphalt samples consist of microstructural entities, such as micelles or aggregates, which form the basis for the scattering patterns observed. During the aging of asphalt, the size of micelles and the heterogeneity of their sizes undergo a progressive increase. Simultaneously, the surface activity of these micelles gradually diminishes. However, a notable reduction in micelle size and size heterogeneity is achieved when regenerating aged asphalt using virgin asphalt. Furthermore, the surface activity of micelles is improved through the regeneration process. On the contrary, the rejuvenator used in this study did not exhibit a significant restorative effect on the microstructure of aged asphalt. Rheological analysis indicates that the observed viscoelastic changes in asphalt during aging and regeneration align with microstructural variations, but the effect of the rejuvenators on viscoelasticity do not correlate directly with their impact on microstructure. The differences between rejuvenators in improving the properties of aged asphalt cannot be solely inferred from their effect on microstructure. The findings in this paper contribute significantly to our understanding of asphalt microstructure and its evolution during aging and regeneration processes.

Structure and antiradical activity of N-monosubstituted amino acid derivatives of fullerene C60 in aqueous colloidal solutions

The dimensional characteristics of nanoparticles of N-mono- substituted amino acid derivatives of fullerene C60 (AAFDs) in aqueous colloidal solutions, determined by dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS), were compared. The DLS data on the dimensional characteristics of fullerene C60 and AAFD nanoparticles, obtained at scattering angles of 90° and 173°, are close in values with a correlation coefficient of 0.89, and the SAXS data indicate that AAFDs form ordered structures in solution. Based on the results of DLS and the ability of fullerene and AAFDs to inhibit peroxyl radicals, it can be concluded that varying the concentrations of the studied compounds in the range from 10-7 to 10-3 m does not affect the degree of aggregation of their nanoparticles.