[This corrects the article DOI: 10.1371/journal.pone.0323678.].

With the growing volume of measured X-ray Absorption Spectroscopy (XAS) data and their need for machine-learning and reference purposes across different facilities, both spectral quality and documentation of the XAS measurements need to be standardized. The documentation is also important to avoid unnecessarily repeating reference measurements and therefore wasting precious beamtime. In this article, we have discussed the classification of quality control with respect to meta data and scientific quality, important for standard documentation and curation of the XAS data. As an example, we take the use case of the RefXAS database developed under the DAPHNE4NFDI project. Considering that the database is under development, the initial requirement for an XAS database is a comprehensive set of metadata fields, that enhances the interpretation of XAS spectra; thereby improving its reusability and the reproducibility. The metadata schema should be able to provide details about the sample, optimized equipment and measurement conditions thereby making the process of acquiring the data clear. The next important component is the evaluation of the quality of the spectra as raw data and the metadata set to ensure the accuracy and reliability of the data stored in the database. Quality criteria need to be formulated for automated initial screening of any uploaded data set followed by manual curation involving utilization of details of metadata provided during upload and scientific quality of the XAS data. In this way, metadata and scientific quality control for XAS data uploaded at a database will provide a well-defined protocol for curation of the data and strengthen its distribution under FAIR data principles.

Under the DAPHNE4NFDI consortium, RefXAS has evolved as a comprehensive open-access database for X-ray absorption spectroscopy (XAS). We have implemented a platform that allows users to submit raw datasets and associated metadata via a web interface. The database supports automated metadata handling and quality control, ensuring that uploaded data adheres to predefined standards. Recent developments include the integration of a standardised download package, improved filtering systems, and the transition to institutional data storage at DESY, alongside future plans to incorporate the NeXus format, enhancing machine learning applications. This paper provides an overview of these advancements and their implications for the XAS community.

While X-ray diffraction (XRD) is a commonly used method for quantification analysis using Rietveld refinement and quantitative Mössbauer spectroscopy is sporadically used primarily for iron speciation, laboratory X-ray Absorption Fine Structure Spectroscopy (lab-XAFS) is rarely applied for the quantitative determination of sample compositions. With the recent developments of laboratory-based XAFS spectrometers, this method becomes more interesting for many applications as well as for quantification. The goal of this study is to compare quantitative lab-XAFS via Linear Combination Fitting (LCF) of reference spectra with XRD and Mössbauer spectroscopy. Iron species analysis with the focus on the determination of the mass ratio alpha-iron(III) oxide (α-Fe2O3)/iron(II, III) oxide (Fe3O4) was used as an example. The examinations were performed on synthetic α-Fe2O3/Fe3O4 model mixtures and, predominantly, on a natural iron ore sample mainly consisting of the minerals hematite and magnetite, thus, these two iron oxides. For the iron K-edge lab-XAFS measurements an X-ray tube-based spectrometer using the von Hamos geometry with Highly Annealed Pyrolytic Graphite (HAPG) mosaic crystal optic was used. The capabilities and challenges of each method are discussed. The quantitative model mixtures examinations by lab-XAFS show results and accuracies similar to those obtained by XRD and Mössbauer spectroscopy. However, while the quantitative results for the iron ore investigations by lab-XAFS are in good agreement (deviation of 2 percent points) with the XRD results, the composition determined by Mössbauer spectroscopy differs clearly from the lab-XAFS and XRD results. Furthermore, the Mössbauer spectroscopic examinations hint the presence of an additional iron oxide species affecting the quantification. Besides the still common challenges in identification, differentiation and quantification of different iron oxides, the results show that quantitative lab-XAFS can particularly compete with quantitative XRD when determining the species composition of one element. This makes lab-XAFS particularly well-suited for routine analytics.

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

A gas cell for in-situ measurements of Volatile Organic Compounds (VOCs) and their adsorption behaviour on different surfaces by means of X-ray Fluorescence (XRF) and X-ray Absorption Fine-Structure (XAFS) spectroscopy has been developed. The cell is especially designed to allow for the efficient excitation and detection of low-Z elements such as carbon, oxygen or nitrogen as main components of VOCs. Two measurement modes are available. In the surface mode, adsorption on a surface can be studied using XAFS by fluorescence detection under shallow angles of incidence. The transmission mode enables the simultaneous investigation of gaseous samples via XAFS in transmittance and fluorescence detection modes. Proof-of-principle experiments were performed at the PTB plane grating monochromator beamline for soft X-ray radiation at the synchrotron radiation facility BESSY II. The flexible design and high versatility of the cell are demonstrated with the investigation of ethanol (EtOH) as one of the most abundant VOCs. The comparison of Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectra under transmission and fluorescence detection in the gas phase with measurements of adsorbed molecules on a Si-wafer surface both at the C and O-K absorption edges proves the applicability of the cell for the monitoring of adsorption processes.

X-ray absorption spectroscopy is important to analyse solid materials, in particular amorphous materials, disordered or multicomponent materials. Due to its vast application in diverse fields XAS has become an essential tool for studying, e.g., catalytic reactions or battery materials to mention just a few. In the field of XAS, data are often evaluated by comparing them to previously measured or calculated reference spectra [1]. This sets the high requirements concerning both spectral quality and documentation of the measurements. Under DAPHNE4NFDI, we have been working on to set up a XAS reference database including raw and processed data with an interface developed for uploading and evaluating the data. In this context, defining metadata fields about an XAS experiments and documenting this information along with data is essential to make the measured data reusable by any researcher in a similar field and beyond. Another important aspect of a curated database is that users should be able to easily judge the quality and the usability of each data set by looking at the mentioned quality criteria. In the present work, we have discussed and highlighted the importance of metadata fields and quality criteria for the data to be uploaded at the XAS database.

This paper presents the application of laboratory X-ray Absorption Fine Structure Spectroscopy (XAFS) in the field of iron coordination chemistry, especially for compounds with larger organic ligands and usually low contents of the metal.

Trace elements, functionalized nanoparticles and labeled entities can be localized with sub-mm spatial resolution by X-ray fluorescence imaging (XFI). Here, small animals are raster scanned with a pencil-like synchrotron beam of high energy and low divergence and the X-ray fluorescence is recorded with an energy-dispersive detector. The ability to first perform coarse scans to identify regions of interest, followed by a close-up with a sub-mm X-ray beam is desirable, because overall measurement time and X-ray dose absorbed by the (biological) specimen can thus be minimized. However, the size of X-ray beams at synchrotron beamlines is usually strongly dependent on the actual beamline setup and can only be adapted within specific pre-defined limits. Especially, large synchrotron beams are non-trivial to generate. Here, we present the concept of graphite-based, convex reflection optics for the one-dimensional enlargement of a 1 mm wide synchrotron beam by a factor of 5 to 10 within a 1 m distance. Four different optics are tested and characterized and their reflection properties compared to ray tracing simulations. The general shape and size of the measured reflection profiles agree with expectations. Enhancements with respect to homogeneity and efficiency can be expected with improved optics manufacturing. A mouse phantom is used for a proof-of-principle XFI experiment demonstrating the applicability of coarse and fine scans with the suggested optics design.

In recent years, novel instrumentation for laboratory X-ray Absorption Spectroscopy (XAS) raised some interest and debate about its usefulness. Within the last two years then, a growing number of experiments and analytical applications using these new spectrometers were published. This review presents these applications and gives an overview of the fields of applications and the ways, the laboratory XAS instruments were utilized so far. The principles of the laboratory XAS spectrometer are described. The use of X-ray tube driven spectrometers for XAS, however, is not a novelty. First X-ray absorption spectra were taken long before synchrotron radiation facilities existed. And, more important for the scope of this review, beginning with the 80s, the XAS community undertook a considerable effort to create laboratory XAS spectrometers which were powerful enough for research in chemistry or materials science. The motivation of this effort as well as the application of laboratory XAS spectrometers have a lot in common with the current activities. We included a review of literature from this period and a discussion of commonalities and differences with contemporary

New developments in the description and modeling of Highly Annealed Pyrolytic Graphite (HAPG) mosaic crystals have led to the possibility of designing optimized optical solutions for X-ray absorption fine structure (XAFS) spectroscopy.

We have built a laboratory spectrometer for X-ray emission spectroscopy. The instrument is employed in catalysis research. The key component is a von Hamos full cylinder optic with Highly Annealed Pyrolytic Graphite (HAPG) as a dispersive element. With this very efficient optic, the spectrometer subtends an effective solid angle of detection of around 1 msr, allowing for the analysis of dilute samples. The resolving power of the spectrometer is approximately E/ΔE = 4000, with an energy range of ∼2.3 keV-10 keV. The instrument and its characteristics are described herein. Further, a comparison with a prototype spectrometer, based on the same principle, shows the substantial improvement in the spectral resolution and energy range for the present setup. The paper concludes with a discussion of sample handling. A compilation of HAPG fundamentals and related publications are given in a brief Appendix.

To further widen the applicability of confocal micro-X-ray fluorescence spectroscopy (CMXRF) a novel setup using a liquid metal jet source as excitation was build up and characterized. We present a comparison concerning lateral, depth resolution and performance with state-of-the-art spectrometers using microfocus X-ray tubes. The efficiency of this setup scales with the used power, resulting in a >8-fold intensity increase in the excitation radiation, or measurement time decrease compared to low power X-ray tubes. The adaptation of the excitation lens' transmission to the energy of the characteristic lines additionally increases the sensitivity of the setup, yielding for selected elements an intensity gain of up to a factor of 60. As an application example, a 3D map of a millet seed is evaluated with an uncertainty estimation for incomplete pathway information. With the presented superior performance, full 3D elemental mapping in the laboratory is rendered feasible for classes of samples with low fluorescence intensities such as biological specimen.

This paper presents the development of a new reflection model for describing X-ray diffraction from mosaic crystals. In contrast to the well established diffraction model of Zachariasen [Zachariasen (1994), Theory of X-ray Diffraction in Crystals. Mineola: Dover Publications], it gives additional information on the spatial reflection behaviour and not just on the depth-integrated reflectivity of the crystal material. The new reflection model enables a concrete description of mosaic crystal performance in an arbitrary X-ray spectrometer configuration. Multiple reflections inside the crystal are described by splitting the calculation into a discrete number of reflections. Hence, the influence of each number of reflections is investigated, leading to a laterally resolved solution for the reflectivity. In addition, the model can use a mosaicity of arbitrary shape. This is important because the present work uses a Lorentzian-shaped mosaicity instead of a Gaussian one, which is usually the case in the most widely used simulation programs. A comparison between the new model and that of Zachariasen is performed, and it predicts a similar integrated reflectivity with a deviation lower than 0.7%. Further, a ray-tracing simulation with multiple reflections based on the new model is compared with a measurement, showing a deviation of lower than 5%.

The selective oxidation of methane to methanol is a highly challenging target, which is of considerable interest to gain value-added chemicals directly from fuel gas. Copper containing zeolites, such as Cu/mordenite, have been currently reported to be the most efficient catalysts for this reaction. In this work, it is shown that solid-state ion-exchanged Cu/mordenites exhibit a significantly higher activity for the partial oxidation of methane to methanol than comparable reference catalysts, i.e., Cu/mordenites prepared by the conventional liquid-phase ion exchange procedure. The efficiency of these Cu/mordenites remained unchanged over several successive cycles. From temperature-programmed reduction (TPR) measurements, it can be concluded that the solid-state protocol accelerates Cu exchange at the small pores of mordenite: those are positions where the most active Cu species are presumably located. In situ ultraviolet-visible (UV-vis) spectroscopy furthermore indicates that different active clusters including dicopper- and tricopper-oxo complexes are formed in the catalyst upon oxygen treatment. Notably after activation of methane, different methoxy intermediates seem to be generated at the Cu sites from which one is preferably transformed to methanol by reaction with water. It is furthermore described that the applied reaction conditions have considerable influence on the finally observed methanol production from methane.

The mutual interaction between Rh nanoparticles and manganese/iron oxide promoters in silica-supported Rh catalysts for the hydrogenation of CO to higher alcohols was analyzed by applying a combination of integral techniques including temperature-programmed reduction (TPR), X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS) and Fourier transform infrared (FTIR) spectroscopy with local analysis by using high angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) in combination with energy dispersive X-ray spectroscopy (EDX). The promoted catalysts show reduced CO adsorption capacity as evidenced through FTIR spectroscopy, which is attributed to a perforated core-shell structure of the Rh nano-particles in accordance with the microstructural analysis from electron microscopy. Iron and manganese occur in low formal oxidation states between 2+ and zero in the reduced catalysts as shown by using TPR and XAS. Infrared spectroscopy measured in diffuse reflectance at reaction temperature and pressure indicates that partial coverage of the Rh particles is maintained at reaction temperature under operation and that the remaining accessible metal adsorption sites might be catalytically less relevant because the hydrogenation of adsorbed carbonyl species at 523 K and 30 bar hydrogen essentially failed. It is concluded that Rh0 is poisoned due to the adsorption of CO under the reaction conditions of CO hydrogenation. The active sites are associated either with a (Mn,Fe)Ox (x < 0.25) phase or species at the interface between Rh and its co-catalyst (Mn,Fe)Ox.

The rapid development of new classes of nanomaterials calls for easy access methods in order to quantify properties essential for their functionality, e.g., interdiffusion of elements at interfaces, or elemental dopant, or depth profiles. Non-destructive methods, like X-ray fluorescence (XRF), are of special interest, for preserving materials and offering the possibility to incorporate the analysis in a production process. In-depth XRF methods for the characterization of nanomaterials are up until now limited to synchrotron radiation facilities. A novel scan-free grazing emission XRF (GEXRF) setup is presented utilizing conventional and low-cost hardware, acting as a transfer of a synchrotron method into the laboratory. A chromium target X-ray tube with a polycapillary lens is used as X-ray source and a conventional CCD as the 2D energy-dispersive detector. To confirm the feasibility of the described setup a nanometer-layered titanium-aluminium sample is measured. An energy-dispersive spectrum is obtained in single-photon-counting-mode from the CCD measurements and first GEXRF profiles generated. A semi-quantitative evaluation of this setup is implemented by comparing the measured results with simulations, allowing conclusions about the investigated samples' elemental, compositional, and structural layer-by-layer characteristics.

Highly annealed pyrolytic graphite (HAPG) is an advanced type of pyrolytic graphite that, as a mosaic crystal, combines high integral reflectivity with a very low mosaicity of typically less than 0.1°. When used as dispersive X-ray optics, a high resolving power has been observed, rendering HAPG very suitable for applications in high-resolution X-ray spectroscopy, which conventionally relies on ideal crystals. For the design and modelling of HAPG crystals in applications requiring high spectral resolution, the diffraction properties must be known very accurately. To close this gap, a comprehensive characterization of HAPG crystals was performed that allows for modelling of the diffraction properties in different diffraction orders over a broad spectral range. The crystal properties under investigation are the mosaic spread, the peak reflectivity and the intrinsic reflection width. The investigations were carried out for different thickness crystal films, which were mounted adhesively on a substrate. It is shown that the diffraction properties are strongly correlated to the grade of adhesion, which depends crucially on the substrate material and its surface properties. The investigations were performed using monochromated tunable synchrotron radiation of high spectral purity with a high-precision experimental setup and calibrated detection devices at the electron storage ring BESSY II.