I will present details of the TES Beamline at the National Synchrotron Light Source II, covering its design, commissioning, and early results. Its scientific mission includes static and in-situ/operando XRF imaging and spatially resolved (microbeam) XAS — in the tender energy range — for characterization of complex heterogeneous, structured and dynamic natural or engineered materials and systems. My approach for design of TES centered on two primary goals:
1) optimize for the tender energy range, which offers access to elements and edges not accessible (or not accessible with optimal performance) at either hard or soft X-ray beamlines.
2) bring the essential capabilities of an XAS beamline down to the microscale, so as to measure full EXAFS of a single particle or structure the same size as the probe beam.
TES offers routine operations from 2.0 to 5.5 keV, with capabilities to reach down to 1.2 keV with configuration change. It is also designed as an “EXAFS Microprobe” for applications of um-scale extended X-ray absorption spectroscopy fine structure to heterogeneous and small-particle samples. Beam size is user-tunable from ~2 um to 25 um. Energy may be scanned on-the-fly or in step scanning mode. Importantly, the position of the microbeam at the sample location does not move significantly during energy scanning, or when changing energy across the entire routine energy range. This enables full EXAFS of a particle or domain the same size as the probe beam, and measurement of the same spot at different energies. In addition, there is no measurable drift in energy calibration (repeatability) scan-to-scan and over >24 hours. This is critical in an energy range where simultaneous calibration measurements in transmission are generally not feasible, and for speciation mapping where precise and stable control of incident energy is essential. The sample environment is helium atmosphere at room pressure, with infrastructure for in-situ electrochemistry and catalysis in small sample cells or microreactors.
Great strides have been made over the past decade in the theory and calculation of X-ray and related spectra. Some advances involve predictions of material properties such as structure or dynamics in order to make a prediction more complete, thus requiring less input, or otherwise reducing the number of free parameters required to fit to experimental data. Other advances, e.g., GW/BSE approaches, improve common approximations for electron correlation or electron-phonon interactions. However, many of these advanced methods require a combination of approaches to obtain complete calculations. Thus users must be proficient in a variety of codes, with multiple input and output formats. Moreover, users must usually manually link codes by translating the output of one to a format consistent with the input of the next. These aspects of state-of-the-art approaches create barriers to their widespread use and hence reduce the overall quality of theory and analysis methods for X-ray spectra. To address this situation we present Corvus [1,2], a property driven workflow tool designed to combine and execute multiple codes. Corvus interfaces electronic structure, molecular or crystal structure, and molecular dynamics or phonon effects, with end-product codes for calculating spectroscopic quantities such as XAS. Thus Corvus serves to: (1) simplify and unify input and output formats; and (2) automatically create workflows based on target properties and input supplied by a user. The simplification of input/output works through a set of code-specific translation routines to eliminate the need for users to learn a multitude of formats, while automating the translation of output to be used in the next step in the workflow chain. The automatic generation of workflows sets up a dependency tree for target properties, which can be filled by user input, online database search, or calculations. This allows users to focus on physical properties of interest, rather than on details of any one calculation step. At present, translation tools exist for several DFT and MD codes as well as spectroscopy codes. More capabilities will be added as implementation of new code interfaces is relatively easy. We have applied Corvus to a variety of workflows, for example: structural optimization with ORCA [4], followed by calculations of XES and RXES using FEFF [3]; DFT/MD averaged XANES using NWCHEM [5] and FEFF; and FEFF calculations of XAS using ab initio Debye-Waller factors obtained from dynamical matrices provided by ABINIT [6]. Examples of Corvus simplified input, and automatically generated workflows are presented, together with results that yield improved agreement in comparison to experiment.
Story, S. M., Vila, F. D., Kas, J. J., Raniga, K. B., Pemmaraju, C. D. & Rehr, J. J. (2019). J. Synchrotron Rad. 26, 1694-1704. https://doi.org/10.1107/S1600577519007495
The oxidation state of the solid Earth influences, to a first order, the structure of the planet and the chemistry of rocks, ores and volcanic gases; mass transfer of oxygen between terrestrial reservoirs enables a habitable world. Fe K-edge XANES spectroscopy shows magmas erupted from continental crust, formed at subduction zones, are more oxidized than magmas erupted from oceanic crust, formed at mid-ocean ridges (e.g., Kelley and Cottrell 2009; Science). However, there is long-standing debate over the timing and mechanism of the processes that produce oxidized continental crust. The high-pressure mineral phase garnet is a key reservoir of iron in the crust and garnet Fe3+/ƩFe ratios record the transfer of oxygen throughout the subduction process. Here, I’ll use garnet Fe-XANES to quantify the oxidation state of two suites of subduction-related rocks to examine changes in the deep Earth oxygen cycle over space (scale of ~100 km) and time (scale of ~2.5 billion years).
M. D. Dyar, et al, Accurate determination of ferric iron in garnets by bulk Mössbauer spectroscopy and synchrotron micro-XAS American Mineralogist 97 pp 1726–1740 (2012) https://doi.org/10.2138/am.2012.4107
Presented will be a discussion of efforts to employ a wavelet transform (WT) analysis towards the quantitative structural determination of discrete molecular systems using an EXAFS analysis. Unlike a transition Fourier transform (FT) analysis, a WT analysis yields a 2D plot in both k- and R-space. Thus, information contained in k-space that can be lost in a FT analysis is retained. In theory, this can allow for the unambiguous assignment of different scattering pathways at similar distances, distinguishing multiple scatterer pathways from single scattering pathways and noise, and an increase in the resolution between shells. A WT EXAFS analysis has shown utility in the analysis of solid-state periodic samples, but there has been a paucity of examples of a WT analysis applied to small molecular species in solution. In this talk I will present our initial efforts towards determining the utility of a WT analysis applied towards such systems. Different data analysis strategies will be presented with examples of where we have found both success and “failure” in obtaining structural information using a WT analysis.
Modern electronic structure theory and computational methods now permit efficient calculations of ground state properties, as exemplified by the tabulation of many-thousands of structures in the Materials Project [1]. Complementary advances in the theory of excited states have led to efficient methods for calculations of x-ray and electron spectroscopies, e.g., using the real-space Green’s multiple scattering theory in the FEFF9 code [2]. Here we discuss these developments and how they have been applied to high throughput calculations of x-ray absorption spectra in the Materials Project [3]. In particular, the world’s largest x-ray database has been constructed, which currently contains nearly 200,000 computed K-edge spectra for over 40,000 materials [4]. Recently this data base has been exploited using Machine-Learning techniques to accurately predict local coordination environments [5]. The database including the FEFF input and output files, is freely available from the Materials Project [1]. Extensions to L-edge and XAFS spectra are in progress.
References:
[1] A. Jain et al., The Materials Project: A materials genome approach to accelerating materials innovation, APL Materials 1, 011002 (2013); https://www.materialsproject.org.
[2] John J. Rehr et al., Parameter-free calculations of X-ray spectra with FEFF9, Physical Chemistry Chemical Physics 12, 5503 (2010).
[3] K. Matthew, et al., High-throughput computational X-ray absorption spectroscopy, Scientific Data 5, 180151 (2018).
[4] Chen Zheng et al., Automated generation and ensemble-learned matching of X-ray absorption spectra, npj Computational Materials 4, 12 (2018).
[5] Chen Zheng et al., Random Forest Models for Accurate Identification of Coordination Environments from X-Ray Absorption Near-Edge Structure, Patterns 1, 100013 (2020).
The new painting materials used by the Impressionists, Fauvists, and Expressionists were critical components of their break with traditional modes of representation. These artists heavily exploited the synthetic organic and inorganic pigments that were newly available as a result of the industrial revolution. However, the bright and novel hues that made their way onto these artists’ palettes (and in many cases defined the movements listed above) were not always synthesized properly. Pigments in some of the greatest masterpieces of these movements have been found to be highly fugitive or rapidly discolored. These unstable materials can react with adjacent or admixed pigments, agents of degradation in the environment, and even the paint binding media surrounding them. The urgent need for preservation of these works calls for intensive materials engineering approaches to identify their mechanisms of degradation and ensure their longevity for future generations. As complex multilayered mesoscale inorganic-organic composites, these paintings present a wealth of analytical challenges.
Artists working in this period of the 1880s to the 1920s were aware of the limitations of the materials available to them, and they attempted to make choices based upon the most stable options at hand. Paint manufacturers were also aware that not all of their offerings were equally stable, and they would note the stability of the pigments offered for sale. Within this context, however, we still have monumental works from this period changing so substantially that they no longer represent the artists’ original vision. Pigments from this period that have been found to alter over time include chrome yellow (PbCrO4.PbSO4), zinc yellow (4ZnO.4CrO3,K2O.3H2O), cadmium yellow (CdS), emerald green (Cu(C2H3O2)2.3Cu(AsO2)2, eosin red (C20H8O5Br4, germanium lake), and purpurin (1,2,4-trihydroxyantrhaquinone).
Noninvasive methods for identifying these pigments (both before and after their alteration) including x-ray fluorescence, hyperspectral imaging, and ultraviolet-induced infrared fluorescence. To understand their mechanisms of degradation, however, requires microscale x-ray diffraction methods (XRD), x-ray absorption near edge spectroscopy (XANES) and mapping, and scanning transmission electron microscopy (STEM) based methodologies such as electron energy loss spectroscopy (EELS). Henri Matisse’s Le Bonheur de vivre (1905-1906) will be used as a case studies to identify highly degraded pigments, their technologies of manufacture, and their mechanisms of degradation. Adriaen de Coorte’s Still Life with Five Apricots (1704) will be discussed to probe degradation mechanisms in more traditional artists’ materials.
References:
Mass, J.L., Opila, R., Buckley, B. et al. The photodegradation of cadmium yellow paints in Henri Matisse’s Le Bonheur de vivre (1905–1906). Appl. Phys. A111, 59–68 (2013). https://doi.org/10.1007/s00339-012-7418-0
Cotte, M., Susini, J., Dik, J., and Janssens, K. Synchrotron-Based X-ray Absorption Spectroscopy for Art Conservation: Looking Back and Looking Forward, Accounts of Chemical Research43 705-714 (2010). https://doi.org/10.1021/ar900199m
Keune, K. et. al Tracking the transformation and transport of arsenic sulfide pigments in paints: synchrotron-based X-ray micro-analyses J. Anal. At. Spectrom., 30, 813-827 (2015) https://doi.org/10.1039/c4ja00424h
The presentation will be a collection of thoughts that I find interesting for the experimentalist employing hard X-ray photon-in/photon-out spectroscopy with a wavelength dispersive instrument. I would like to draw the attention to some experimental aspects and will give hopefully useful advice that may be considered for the experimental protocol. Furthermore, I will present the two instruments for X-ray emission spectroscopy at ESRF ID26 and discuss the challenges of a multi-crystal spectrometer.
References:
[1] Glatzel, P, et al. . “Reflections on Hard X-Ray Photon-in/Photon-out Spectroscopy for Electronic Structure Studies” J. Electron Spectros. Relat. Phenomena 2013, 188, 17–25; https://doi.org/10.1016/j.elspec.2012.09.004
[2] Rovezzi, M, et al.,. “High Energy-Resolution x-Ray Spectroscopy at Ultra-High Dilution with Spherically Bent Crystal Analyzers of 0.5 m Radius” Rev. Sci. Instrum. 2017, 88 (1) 013108 https://doi.org/10.1063/1.4974100;
[3] M. Rovezzi, et al., “TEXS: in-vacuum tender x-ray emission spectrometer with eleven Johansson crystal analysers.” Journal of Synchrotron Radiation 2020, 27, 813. https://doi.org/10.1107/S160057752000243X