Practical aspects of electron energy-loss spectroscopy (EELS) calculations using FEFF8

Machine learning in electron microscopy for advanced nanocharacterization: current developments, available tools and future outlook

In the last few years, electron microscopy has experienced a new methodological paradigm aimed to fix the bottlenecks and overcome the challenges of its analytical workflow. Machine learning and artificial intelligence are answering this call providing powerful resources towards automation, exploration, and development. In this review, we evaluate the state-of-the-art of machine learning applied to electron microscopy (and obliquely, to materials and nano-sciences). We start from the traditional imaging techniques to reach the newest higher-dimensionality ones, also covering the recent advances in spectroscopy and tomography. Additionally, the present review provides a practical guide for microscopists, and in general for material scientists, but not necessarily advanced machine learning practitioners, to straightforwardly apply the offered set of tools to their own research. To conclude, we explore the state-of-the-art of other disciplines with a broader experience in applying artificial intelligence methods to their research (e.g., high-energy physics, astronomy, Earth sciences, and even robotics, videogames, or marketing and finances), in order to narrow down the incoming future of electron microscopy, its challenges and outlook.

Unveiling the atomic defects and electronic structure of Cu2.2Zn0.8SnSe4-xTex (x = 0 to 0.04) by X-ray absorption fine structure spectroscopy

The quaternary chalcogenides consisting of earth-abundant elements such as Cu2ZnSnSe4 (CZTSe) have promising electrical and optical properties prompting enormous technological interest. Understanding different types of defects including Cu/Zn ordering is believed to be the key point to tackle technological challenges such as a large open circuit voltage deficit in CZTSe. The Te doped Cu2.2Zn0.8SnSe4-xTex (x = 0.01-0.04) were investigated using X-ray absorption fine structure spectroscopy at the Cu, Zn, and Se K-edges as well as at the Te L3-edge. Cu at the zinc site with anti-site defects and oxygen interstitials are identified. The detailed electronic structure upon Te doping is studied, providing insights into the rich defect chemistry present in this compound.

Elastic distortion determining conduction in BiFeO3 phase boundaries

It is now well-established that boundaries separating tetragonal-like (T) and rhombohedral-like (R) phases in BiFeO₃ thin films can show enhanced electrical conductivity. However, the origin of this conductivity remains elusive. Here, we study mixed-phase BiFeO₃ thin films, where local populations of T and R can be readily altered using stress and electric fields. We observe that phase boundary electrical conductivity in regions which have undergone stress-writing is significantly greater than in the virgin microstructure. We use high-end electron microscopy techniques to identify key differences between the R–T boundaries present in stress-written and as-grown microstructures, to gain a better understanding of the mechanism responsible for electrical conduction. We find that point defects (and associated mixed valence states) are present in both electrically conducting and non-conducting regions; crucially, in both cases, the spatial distribution of defects is relatively homogeneous: there is no evidence of phase boundary defect aggregation. Atomic resolution imaging reveals that the only significant difference between non-conducting and conducting boundaries is the elastic distortion evident – detailed analysis of localised crystallography shows that the strain accommodation across the R–T boundaries is much more extensive in stress-written than in as-grown microstructures; this has a substantial effect on the straightening of local bonds within regions seen to electrically conduct. This work therefore offers distinct evidence that the elastic distortion is more important than point defect accumulation in determining the phase boundary conduction properties in mixed-phase BiFeO₃.

The localized crystallography of conducting and non-conducting phase boundaries in mixed-phase BiFeO₃ is directly compared using scanning transmission electron microscopy techniques.

Nanoscale Tungsten-Microbial Interface of the Metal Immobilizing Thermoacidophilic Archaeon Metallosphaera sedula Cultivated With Tungsten Polyoxometalate

Inorganic systems based upon polyoxometalate (POM) clusters provide an experimental approach to develop artificial life. These artificial symmetric anionic macromolecules with oxidometalate polyhedra as building blocks were shown to be well suited as inorganic frameworks for complex self-assembling and organizing systems with emergent properties. Analogously to mineral cells based on iron sulfides, POMs are considered as inorganic cells in facilitating prelife chemical processes and displaying "life-like" characteristics. However, the relevance of POMs to life-sustaining processes (e.g., microbial respiration) has not yet been addressed, while iron sulfides are very well known as ubiquitous mineral precursors and energy sources for chemolithotrophic metabolism. Metallosphaera sedula is an extreme metallophilic and thermoacidophilic archaeon, which flourishes in hot acid and respires by metal oxidation. In the present study we provide our observations on M. sedula cultivated on tungsten polyoxometalate (W-POM). The decomposition of W-POM macromolecular clusters and the appearance of low molecular weight W species (e.g., WO) in the presence of M. sedula have been detected by electrospray ionization mass spectrometry (ESI-MS) analysis. Here, we document the presence of metalloorganic assemblages at the interface between M. sedula and W-POM resolved down to the nanometer scale using scanning and transmission electron microscopy (SEM and TEM) coupled to electron energy loss spectroscopy (EELS). High-resolution TEM (HR-TEM) and selected-area electron diffraction (SAED) patterns indicated the deposition of redox heterogeneous tungsten species on the S-layer of M. sedula along with the accumulation of intracellular tungsten-bearing nanoparticles, i.e., clusters of tungsten atoms. These results reveal the effectiveness of the analytical spectroscopy coupled to the wet chemistry approach as a tool in the analysis of metal-microbial interactions and microbial cultivation on supramolecular self-assemblages based on inorganic metal clusters. We discuss the possible mechanism of W-POM decomposition by M. sedula in light of unique electrochemical properties of POMs. The findings presented herein highlight unique metallophilicity in hostile environments, extending our knowledge of the relevance of POMs to life-sustaining processes, understanding of the transition of POMs as inorganic prebiotic model to life-sustainable material precursors and revealing biogenic signatures obtained after the decomposition of an artificial inorganic compound, which previously was not associated with any living matter.

High-throughput computational X-ray absorption spectroscopy

X-ray absorption spectroscopy (XAS) is a widely-used materials characterization technique. In this work we present a database of computed XAS spectra, using the Green's formulation of the multiple scattering theory implemented in the FEFF code. With more than 500,000 K-edge X-ray absorption near edge (XANES) spectra for more than 40,000 unique materials, this database constitutes the largest existing collection of computed XAS spectra to date. The data is openly distributed via the Materials Project, enabling researchers across the world to access it for free and use it for comparisons with experiments and further analysis.

Basics and applications of ELNES calculations

The electron energy loss near edge structures (ELNES) appearing in an electron energy loss spectrum obtained through transmission electron microscopy (TEM) have the potential to unravel atomic and electronic structures with sub-nano meter resolution. For this reason, TEM-ELNES has become one of the most powerful analytical methods in materials research. On the other hand, theoretical calculations are indispensable in interpreting the ELNES spectrum. Here, the basics and applications of one-particle, two-particle and multi-particle ELNES calculations are reviewed. A key point for the ELNES calculation is the proper introduction of the core-hole effect. Some applications of one-particle ELNES calculations to huge systems of more than 1000 atoms, and complex systems, such as liquids, are reported. In the two-particle calculations, the importance of the correct treatment of the excitonic interaction is demonstrated in calculating the low-energy ELNES, for example at the Li-K edge. In addition, an unusually strong excitonic interactions in the O-K edge of perovskite oxides is identified. The multi-particle calculations are necessary to reproduce the multiplet structures appearing at the transition metal L2,3-edges and rare-earth M4,5-edges. Applications to dilute magnetic semiconductors and Li-ion battery materials are presented. Furthermore, beyond the 'conventional' ELNES calculations, theoretical calculations of electron/X-ray magnetic circular dichroism (MCD) and the vibrational information in ELNES, are reported.

Effect of the van der Waals interaction on the electron energy-loss near edge structure theoretical calculation

The effect of the van der Waals (vdW) interaction on the simulation of the electron energy-loss near edge structure (ELNES) by a first-principles band-structure calculation is reported. The effect of the vdW interaction is considered by the Tkatchenko-Scheffler scheme, and the change of the spectrum profile and the energy shift are discussed. We perform calculations on systems in the solid, liquid and gaseous states. The transition energy shifts to lower energy by approximately 0.1eV in the condensed (solid and liquid) systems by introducing the vdW effect into the calculation, whereas the energy shift in the gaseous models is negligible owing to the long intermolecular distance. We reveal that the vdW interaction exhibits a larger effect on the excited state than the ground state owing to the presence of an excited electron in the unoccupied band. Moreover, the vdW effect is found to depend on the local electron density and the molecular coordination. In addition, this study suggests that the detection of the vdW interactions exhibited within materials is possible by a very stable and high resolution observation.

In Situ STEM-EELS Observation of Nanoscale Interfacial Phenomena in All-Solid-State Batteries

Behaviors of functional interfaces are crucial factors in the performance and safety of energy storage and conversion devices. Indeed, solid electrode-solid electrolyte interfacial impedance is now considered the main limiting factor in all-solid-state batteries rather than low ionic conductivity of the solid electrolyte. Here, we present a new approach to conducting in situ scanning transmission electron microscopy (STEM) coupled with electron energy loss spectroscopy (EELS) in order to uncover the unique interfacial phenomena related to lithium ion transport and its corresponding charge transfer. Our approach allowed quantitative spectroscopic characterization of a galvanostatically biased electrochemical system under in situ conditions. Using a LiCoO2/LiPON/Si thin film battery, an unexpected structurally disordered interfacial layer between LiCoO2 cathode and LiPON electrolyte was discovered to be inherent to this interface without cycling. During in situ charging, spectroscopic characterization revealed that this interfacial layer evolved to form highly oxidized Co ions species along with lithium oxide and lithium peroxide species. These findings suggest that the mechanism of interfacial impedance at the LiCoO2/LiPON interface is caused by chemical changes rather than space charge effects. Insights gained from this technique will shed light on important challenges of interfaces in all-solid-state energy storage and conversion systems and facilitate improved engineering of devices operated far from equilibrium.

Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations

A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

Electronic structure of MgS and MgYb2S4: Electron Energy-Loss Spectroscopy and self-consistent multiple scattering calculations

The electronic structure of MgS and MgYb2S4 have been studied using the fine structure of the Mg-K, S-K, Mg-L2,3, S-L2,3 and Yb-N5 edges measured by electron energy-loss spectroscopy (EELS). Our experimental results are compared with real-space full multiple scattering calculations as incorporated in the FEFF9.6 code. All edges are very well reproduced. Total and partial densities of states have been calculated. The calculated densities of states of Mg and S are similar in both compounds. The energy distribution of these states suggests a covalent nature for both materials. For MgYb2S4 a band gap smaller than for MgS is predicted. In this compound the top of the valence band and the bottom of the conduction band are dominated by Yb states.

Electronic structure and hybridization of CaS by means of X-ray absorption spectroscopy at Ca and S K-edges

The cubic calcium sulfide (CaS) is a well known system and an attractive building block material for many luminescence technological applications. However, it is essential to achieve an accurate understanding of its electronic structure in order to engineer its band structure for optimized applications. Here a study of the electronic structure of CaS by means of X-ray absorption spectroscopy performed at both Ca and S K-edges, and calculations performed in the framework of the multiple-scattering theory and of the finite difference method are presented. At the Ca K-edge the presence of an anomalous d states feature is discussed while in the S K-edge spectrum the presence of a pre-edge shoulder owing to the hybridization among Ca d states and S p states is pointed out. Although the l-projected density of states of CaS is in good agreement with previous first-principles calculations, the standard muffin-tin potential is inadequate to reproduce near-edge structures at both Ca and S K-edges in this system. Indeed, with its highly symmetric and less compact structure, CaS is characterized by a large set of collinear atomic configurations that pose severe constraints on the construction of the atomic potential. On the contrary, the finite-difference method with no muffin-tin approximation is more suitable for X-ray absorption calculations in this system.

Strain-induce shift of the crystal-field splitting of SrTiO₃ embedded in scandate multilayers

Strained SrTiO₃ layers have become of interest, since the paraelectric-to-ferroelectric transition temperature can be increased to room temperature. A linear relationship between strain and energy splitting of the fundamental transitions in the fine structure of Ti L(₂,₃) and O K edges is observed, that can be exploited to measure strain from electronic transitions, complementary to measuring local strain directly via high-resolution transmission electron microscopy (HRTEM) images. In particular, for both methods, the geometrical phase analysis performed on high-resolution images and the measurement of the energy splitting by energy loss spectroscopy, tensile strain of SrTiO₃ layers was measured when grown on DyScO₃ and GdScO₃ substrates. The effect of strain on the electron loss near edge structure (ELNES) of the Ti L(₂,₃) edge in comparison to unstrained samples is analyzed. Ab initio calculations of the Ti L(₂,₃) and O K edge show a linear variation of the crystal field splitting with strain. Calculated and experimental values of the crystal field splitting show a very good agreement.

Local structural disorder in REFeAsO oxypnictides by RE L(3) edge XANES

The REFeAsO (RE = La, Pr, Nd and Sm) system has been studied by RE L(3) x-ray absorption near edge structure (XANES) spectroscopy to explore the contribution of the REO spacers between the electronically active FeAs slabs in these materials. The XANES spectra have been simulated by full multiple scattering calculations to describe the different experimental features and their evolution with the RE size. The near edge feature just above the L(3) white line is found to be sensitive to the ordering/disordering of oxygen atoms in the REO layers. In addition, shape resonance peaks due to As and O scattering change systematically, indicating local structural changes in the FeAs slabs and the REO spacers due to RE size. The results suggest that interlayer coupling and oxygen order/disorder in the REO spacers may have an important role in the superconductivity and itinerant magnetism of the oxypnictides.

First-principles calculations of x-ray absorption near edge structure and energy loss near edge structure: present and future

Computational methods for theoretical x-ray absorption near edge structure (XANES) and energy loss near edge structure (ELNES) are classified into a few groups. Depending on the absorption (or excitation) edge, required accuracy and desired information, one needs to select the most suitable method. In this paper, after providing a map of available computational methods, some examples of first-principles calculations of XANES/ELNES for selected wide gap materials are given together with references. For ZnO, for example, experimental spectra at three edges, Zn K, L(3), and O K, including their orientation dependence, are well reproduced by the supercell calculations with a core hole. Good agreement between theoretical and experimental spectra of ZnO alloys can also be seen. Theoretical fingerprints are satisfactorily obtained in this way. However, there are remaining issues beyond 'good agreements' which need to be solved in the future.

Core-level spectroscopy calculation and the plane wave pseudopotential method

A plane wave based method for the calculation of core-level spectra is presented. We provide details of the implementation of the method in the pseudopotential density functional code CASTEP, including technical issues concerning the calculations, and discuss the applicability and accuracy of the method. A number of examples are provided for comparing the results to both experiment and other density functional theory techniques.

Overlap population diagram for ELNES and XANES: peak assignment and interpretation

This article reviews overlap population (OP) diagrams for electron energy loss near-edge structure (ELNES) and x-ray absorption near-edge structure (XANES). By using the OP diagrams, peaks in ELNES and XANES of MgO, ZnO, AlN, GaN, InN, and YBa(2)Cu(3)O(7-x) are interpreted in terms of cation-anion and cation-cation interactions. Common features are found in the OP diagrams for different edges. A reconstruction of the unoccupied electronic structure is demonstrated by aligning the different edges with the common features in the OP diagrams. The OP diagram is also applied to the Cu/Al(2)O(3) hetero-interface to find the relationships among ELNES, atomic and electronic structures, and properties.

Auranofin disrupts selenium metabolism in Clostridium difficile by forming a stable Au-Se adduct

Clostridium difficile is a nosocomial pathogen whose incidence and importance are on the rise. Previous work in our laboratory characterized the central role of selenoenzyme-dependent Stickland reactions in C. difficile metabolism. In this work we have identified, using mass spectrometry, a stable complex formed upon reaction of auranofin (a gold-containing drug) with selenide in vitro. X-ray absorption spectroscopy supports the structure that we proposed on the basis of mass-spectrometric data. Auranofin potently inhibits the growth of C. difficile but does not similarly affect other clostridia that do not utilize selenoproteins to obtain energy. Moreover, auranofin inhibits the incorporation of radioisotope selenium ((75)Se) in selenoproteins in both Escherichia coli, the prokaryotic model for selenoprotein synthesis, and C. difficile without impacting total protein synthesis. Auranofin blocks the uptake of selenium and results in the accumulation of the auranofin-selenide adduct in the culture medium. Addition of selenium in the form of selenite or L-selenocysteine to the growth medium significantly reduces the inhibitory action of auranofin on the growth of C. difficile. On the basis of these results, we propose that formation of this complex and the subsequent deficiency in available selenium for selenoprotein synthesis is the mechanism by which auranofin inhibits C. difficile growth. This study demonstrates that targeting selenium metabolism provides a new avenue for antimicrobial development against C. difficile and other selenium-dependent pathogens.