X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction.

Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. To better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ∼13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe-Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO3) and K-citrate [K3(C6H5O7)·H2O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO3 has both the lowest and highest lying energy features, and K3(C6H5O7)·H2O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.

Ab initio calculation of X-ray and related core-level spectroscopies: Green's function approaches.

X-Ray and related spectroscopies are powerful probes of atomic, vibrational, and electronic structure. In order to unlock the full potential of such experimental techniques, accurate and efficient theoretical and computational approaches are essential. Here we review the status of a variety of first-principles and nearly first principles techniques for X-ray spectroscopies such as X-ray absorption, X-ray emission, and X-ray photoemission, with a focus on Green's function based methods. In particular, we describe the current state of multiple scattering Green's function techniques available in the FEFF10 code and cumulant Green's function techniques for including the effects of many-body electronic excitations. Illustrative examples are shown for a variety of materials and compared with other theoretical and experimental results.

Database of ab initio L-edge X-ray absorption near edge structure.

The L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.

Energy-Dependent Relative Cross Sections in Carbon 1s Photoionization: Separation of Direct Shake and Inelastic Scattering Effects in Single Molecules.

We demonstrate that the possibility of monitoring relative photoionization cross sections over a large photon energy range allows us to study and disentangle shake processes and intramolecular inelastic scattering effects. In this gas-phase study, relative intensities of the carbon 1s photoelectron lines from chemically inequivalent carbon atoms in the same molecule have been measured as a function of the incident photon energy in the range of 300-6000 eV. We present relative cross sections for the chemically shifted carbon 1s lines in the photoelectron spectra of ethyl trifluoroacetate (the "ESCA" molecule). The results are compared with those of methyl trifluoroacetate and S-ethyl trifluorothioacetate as well as a series of chloro-substituted ethanes and 2-butyne. In the soft X-ray energy range, the cross sections show an extended X-ray absorption fine structure type of wiggles, as was previously observed for a series of chloroethanes. The oscillations are damped in the hard X-ray energy range, but deviations of cross-section ratios from stoichiometry persist, even at high energies. The current findings are supported by theoretical calculations based on a multiple scattering model. The use of soft and tender X-rays provides a more complete picture of the dominant processes accompanying photoionization. Such processes reduce the main photoelectron line intensities by 20-60%. Using both energy ranges enabled us to discern the process of intramolecular inelastic scattering of the outgoing electron, whose significance is otherwise difficult to assess for isolated molecules. This effect relates to the notion of the inelastic mean free path commonly used in photoemission studies of clusters and condensed matter.

Extended X-Ray Absorption Fine Structure of ZrW2O8: Theory vs. Experiment.

Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8.

Polarization dependent high energy resolution X-ray absorption study of dicesium uranyl tetrachloride.

Dicesium uranyl tetrachloride (Cs2UO2Cl4) has been a model compound for experimental and theoretical studies of electronic structure of U(VI) in the form of UO2(2+) (uranyl ion) for decades. We have obtained angle-resolved electronic structure information for oriented Cs2UO2Cl4 crystal, specifically relative energies of 5f and 6d valence orbitals probed with extraordinary energy resolution by polarization dependent high energy resolution X-ray absorption near edge structure (PD-HR-XANES) and compare these with predictions from quantum chemical Amsterdam density functional theory (ADF) and ab initio real space multiple-scattering Green's function based FEFF codes. The obtained results have fundamental value but also demonstrate an experimental approach, which offers great potential to benchmark and drive improvement in theoretical calculations of electronic structures of actinide elements.

Effects of adsorbate coverage and bond-length disorder on the d-band center of carbon-supported Pt catalysts.

Determination of the factors that affect the d-band center of catalysts is required to explain their catalytic properties. Resonant inelastic X-ray scattering (RIXS) enables direct imaging of electronic transitions in the d-band of Pt catalysts in real time and in realistic environmental conditions. Through a combination of in situ, temperature-resolved RIXS measurements and theoretical simulations we isolated and quantified the effects of bond-length disorder and adsorbate coverage (CO and H2) on the d-band center of 1.25 nm size Pt catalysts supported on carbon. We found that the decrease in adsorbate coverage at elevated temperatures is responsible for the d band shifts towards higher energies relative to the Fermi level, whereas the effect of the increase in bond-length disorder on the d-band center is negligible. Although these results were obtained for a specific case of non-interacting support and weak temperature dependence of the metal-metal bond length in a model catalyst, this work can be extended to a broad range of real catalysts.

Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing.

Reported here are measurements of the penetration depth and spatial distribution of photoelectron (PE) damage excited by 18.6 keV X-ray photons in a lysozyme crystal with a vertical submicrometre line-focus beam of 0.7 µm full-width half-maximum (FWHM). The experimental results determined that the penetration depth of PEs is 5 ± 0.5 µm with a monotonically decreasing spatial distribution shape, resulting in mitigation of diffraction signal damage. This does not agree with previous theoretical predication that the mitigation of damage requires a peak of damage outside the focus. A new improved calculation provides some qualitative agreement with the experimental results, but significant errors still remain. The mitigation of radiation damage by line focusing was measured experimentally by comparing the damage in the X-ray-irradiated regions of the submicrometre focus with the large-beam case under conditions of equal exposure and equal volumes of the protein crystal, and a mitigation factor of 4.4 ± 0.4 was determined. The mitigation of radiation damage is caused by spatial separation of the dominant PE radiation-damage component from the crystal region of the line-focus beam that contributes the diffraction signal. The diffraction signal is generated by coherent scattering of incident X-rays (which introduces no damage), while the overwhelming proportion of damage is caused by PE emission as X-ray photons are absorbed.

Intensity oscillations in the carbon 1s ionization cross sections of 2-butyne.

Carbon 1s photoelectron spectra for 2-butyne (CH3C≡CCH3) measured in the photon energy range from threshold to 150 eV above threshold show oscillations in the intensity ratio C2,3/C1,4. Similar oscillations have been seen in chloroethanes, where the effect has been attributed to EXAFS-type scattering from the substituent chlorine atoms. In 2-butyne, however, there is no high-Z atom to provide a scattering center and, hence, oscillations of the magnitude observed are surprising. The results have been analyzed in terms of two different theoretical models: a density-functional model with B-spline atom-centered functions to represent the continuum electrons and a multiple-scattering model using muffin-tin potentials to represent the scattering centers. Both methods give a reasonable description of the energy dependence of the intensity ratios.

X-ray-Raman-scattering-based EXAFS beyond the dipole limit.

X-ray Raman scattering (XRS) provides a bulk-sensitive method of measuring the extended X-ray absorption fine structure (EXAFS) of soft X-ray absorption edges. Accurate measurements and data analysis procedures for the determination of XRS-EXAFS of polycrystalline diamond are described. The contributions of various angular-momentum components beyond the dipole limit to the atomic background and the EXAFS oscillations are incorporated using self-consistent real-space multiple-scattering calculations. The properly extracted XRS-EXAFS oscillations are in good agreement with calculations and earlier soft X-ray EXAFS results. It is shown, however, that under certain conditions multiple-scattering contributions to XRS-EXAFS deviate from those in standard EXAFS, leading to noticeable changes in the real-space signal at higher momentum transfers owing to non-dipole contributions. These results pave the way for the accurate application of XRS-EXAFS to previously inaccessible light-element systems.

Valence electron photoemission spectrum of semiconductors: ab initio description of multiple satellites.

The experimental valence band photoemission spectrum of semiconductors exhibits multiple satellites that cannot be described by the GW approximation for the self-energy in the framework of many-body perturbation theory. Taking silicon as a prototypical example, we compare experimental high energy photoemission spectra with GW calculations and analyze the origin of the GW failure. We then propose an approximation to the functional differential equation that determines the exact one-body Green's function, whose solution has an exponential form. This yields a calculated spectrum, including cross sections, secondary electrons, and an estimate for extrinsic and interference effects, in excellent agreement with experiment. Our result can be recast as a dynamical vertex correction beyond GW, giving hints for further developments.

Spatial dependence and mitigation of radiation damage by a line-focus mini-beam.

Recently, strategies to reduce primary radiation damage have been proposed which depend on focusing X-rays to dimensions smaller than the penetration depth of excited photoelectrons. For a line focus as used here the penetration depth is the maximum distance from the irradiated region along the X-ray polarization direction that the photoelectrons penetrate. Reported here are measurements of the penetration depth and distribution of photoelectron damage excited by 18.6 keV photons in a lysozyme crystal. The experimental results showed that the penetration depth of ~17.35 keV photoelectrons is 1.5 ± 0.2 µm, which is well below previous theoretical estimates of 2.8 µm. Such a small penetration depth raises challenging technical issues in mitigating damage by line-focus mini-beams. The optimum requirements to reduce damage in large crystals by a factor of 2.0-2.5 are Gaussian line-focus mini-beams with a root-mean-square width of 0.2 µm and a distance between lines of 2.0 µm. The use of higher energy X-rays (> 26 keV) would help to alleviate some of these requirements by more than doubling the penetration depth. It was found that the X-ray dose has a significant contribution from the crystal's solvent, which initially contained 9.0%(w/v) NaCl. The 15.8 keV photoelectrons of the Cl atoms and their accompanying 2.8 keV local dose from the decay of the resulting excited atoms more than doubles the dose deposited in the X-ray-irradiated region because of the much greater cross-section and higher energy of the excited atom, degrading the mitigation of radiation damage from 2.5 to 2.0. Eliminating heavier atoms from the solvent and data collection far from heavy-atom absorption edges will significantly improve the mitigation of damage by line-focus mini-beams.

L-edge XANES analysis of photoexcited metal complexes in solution.

Ultrafast X-ray absorption spectroscopy is a powerful tool to observe electronic and geometric structures of short-lived reaction intermediates. The ab initio FEFF9 code is applied to simulate the Pt L(3)-edge XANES spectrum of the photocatalytic diplatinum molecule [Pt(2)(P(2)O(5)H(2))(4)](4-) and the photo-induced changes that occur therein. The spectra are interpreted within a XAFS-like scattering theoretical framework (bound-continuum transitions) or in terms of a final-state local l-projected density of states (LDOS) (bound-bound transitions). By using a novel Bayesian fitting procedure, we show that the ground-state structures obtained independently from the XANES and EXAFS regions of the spectrum are in good agreement with each other. The semi-quantitative result obtained for the Pt-Pt contraction in the excited state is in line with recently published values. The improved theoretical treatment of inelastic losses has shown to result in more accurate peak positions in the above-continuum region of the spectrum which is an important prerequisite for obtaining quantitative structural information from (time-resolved) XANES spectra.

Parameter-free calculations of X-ray spectra with FEFF9.

We briefly review our implementation of the real-space Green's function (RSGF) approach for calculations of X-ray spectra, focusing on recently developed parameter free models for dominant many-body effects. Although the RSGF approach has been widely used both for near edge (XANES) and extended (EXAFS) ranges, previous implementations relied on semi-phenomenological methods, e.g., the plasmon-pole model for the self-energy, the final-state rule for screened core hole effects, and the correlated Debye model for vibrational damping. Here we describe how these approximations can be replaced by efficient ab initio models including a many-pole model of the self-energy, inelastic losses and multiple-electron excitations; a linear response approach for the core hole; and a Lanczos approach for Debye-Waller effects. We also discuss the implementation of these models and software improvements within the FEFF9 code, together with a number of examples.