X-ray Emission Spectroscopy of Proteinogenic Amino Acids at All Relevant Absorption Edges

Exact Two-Component Relativistic Polarizable Density Embedding

We have implemented the fragment-based polarizable density embedding (PDE) model within a relativistic framework building on the eXact 2-Component (X2C) relativistic Hamiltonian, thereby taking the PDE method to a relativistic framework. The PDE model provides a robust solution to the electron-leakage problem, and we show that this newly implemented model offers an accurate way to model solvated systems possessing significant relativistic effects. To demonstrate the model's performance, we perform comparative calculations of the K- and L2,3-edge spectra of water-solvated cysteine (both protonated and deprotonated) with the X2C Hamiltonian. Particularly, with counterions such as Na+ in the solvent, electron leakage clearly shows in the older polarizable embedding model through spurious peaks in the spectra. However, when the PDE model is employed, these spurious peaks disappear.

Valence-band hybridization in sulphides

The hybridization state in solids often defines the critical chemical and physical properties of a compound. However, it is difficult to spectroscopically detect and evaluate hybridization beyond just general fingerprint signatures. Here, the valence-band hybridization of metal d-derived bands (short: "metal d bands") in selected metal sulphides is studied with a combined spectroscopic and theoretical approach to derive deeper insights into the fundamental nature of such compounds. The valence bands of the studied sulphides are comprised of hybrid bands derived from the metal d, S 3s, and S 3p states. Employing S K and L2,3 X-ray emission spectroscopy and spectra calculations based on density functional theory, the degree of hybridization (i.e., the covalency) of these bands can be directly probed as a function of their relative energies. We find that the relative intensity of the "metal d band" features in the spectra scales with the inverse square of the energy separation to the respective sulfur-derived bands, which can be analytically derived from a simple two-orbital model. This study demonstrates that soft X-ray emission spectroscopy is a powerful tool to study valence state hybridization, in particular in combination with hard X-ray emission spectroscopy, promising a broad impact in many research fields.

Calibrating TDDFT Calculations of the X-ray Emission Spectrum of Liquid Water: The Effects of Hartree-Fock Exchange

The structure and dynamics of liquid water continue to be debated, with insight provided by, among others, X-ray emission spectroscopy (XES), which shows a split in the high-energy 1b1 feature. This split is yet to be reproduced by theory, and it remains unclear if these difficulties are related to inaccuracies in dynamics simulations, spectrum calculations, or both. We investigate the performance of different methods for calculating XES of liquid water, focusing on the ability of time-dependent density functional theory (TDDFT) to reproduce reference spectra obtained by high-level coupled cluster and algebraic-diagrammatic construction scheme calculations. A metric for evaluating the agreement between theoretical spectra termed the integrated absolute difference (IAD), which considers the integral of shifted difference spectra, is introduced and used to investigate the performance of different exchange-correlation functionals. We find that computed spectra of symmetric and asymmetric model water structures are strongly and differently influenced by the amount of Hartree-Fock exchange, with best agreement to reference spectra for ∼40-50%. Lower percentages tend to yield high density of contributing states, resulting in too broad features. The method introduced here is useful also for other spectrum calculations, in particular where the performance for ensembles of structures are evaluated.

Satellite-Dominated Sulfur L2,3 X-ray Emission of Alkaline Earth Metal Sulfides

The sulfur L_2,3 X-ray emission spectra of the alkaline earth metal sulfides BeS, MgS, CaS, SrS, and BaS are investigated and compared with spectra calculations based on density functional theory. Very distinct spectral shapes are found for the different compounds. With decreasing electronegativity of the cation, that is, increasing ionic bonding character, the upper valence band width and its relative spectral intensity decrease. These general trends are qualitatively reproduced by the spectra calculations, which give quite an accurate description of the spectral shapes in the upper valence band region. On the low energy side of the sulfur 3s → 2p transition dominating the spectra, we find strong satellites caused by "semi-Auger" decays involving configuration interaction. These satellites, previously believed to be energetically forbidden for sulfur L_2,3 emission and only observed for the L_2,3 emission of Cl to Cr, increase in intensity as the bonding character becomes more ionic and dominate the spectra for SrS and BaS. The intensities, energies, and widths of the satellites vary strongly between the investigated compounds, giving a very specific spectral fingerprint that can be used for speciation analysis.

Resonant Inelastic Soft X-ray Scattering and X-ray Emission Spectroscopy of Solid Proline and Proline Solutions

The amino group of proline is part of a pyrrolidine ring, which makes it unique among the proteinogenic amino acids. To unravel its full electronic structure, proline in solid state and aqueous solution is investigated using X-ray emission spectroscopy and resonant inelastic soft X-ray scattering. By controlling the pH value of the solution, proline is studied in its cationic, zwitterionic, and anionic configurations. The spectra are analyzed within a "building-block principle" by comparing with suitable reference molecules, i.e., acetic acid, cysteine, and pyrrolidine, as well as with spectral calculations based on density functional theory. We find that the electronic structure of the carboxyl group of proline is very similar to that of other amino acids as well as acetic acid. In contrast, the electronic structure of the amino group is significantly different and strongly influenced by the ring structure of proline.

Coupling Methylammonium and Formamidinium Cations with Halide Anions: Hybrid Orbitals, Hydrogen Bonding, and the Role of Dynamics

The electronic structures of four precursors for organic-inorganic hybrid perovskites, namely, methylammonium chloride and iodide, as well as formamidinium bromide and iodide, are investigated by X-ray emission (XE) spectroscopy at the carbon and nitrogen K-edges. The XE spectra are analyzed based on density functional theory calculations. We simulate the XE spectra at the Kohn-Sham level for ground-state geometries and carry out detailed analyses of the molecular orbitals and the electronic density of states to give a thorough understanding of the spectra. Major parts of the spectra can be described by the model of the corresponding isolated organic cation, whereas high-emission energy peaks in the nitrogen K-edge XE spectra arise from electronic transitions involving hybrids of the molecular and atomic orbitals of the cations and halides, respectively. We find that the interaction of the methylammonium cation is stronger with the chlorine than with the iodine anion. Furthermore, our detailed theoretical analysis highlights the strong influence of ultrafast proton dynamics in the core-excited states, which is an intrinsic effect of the XE process. The inclusion of this effect is necessary for an accurate description of the experimental nitrogen K-edge X-ray emission spectra and gives information on the hydrogen-bonding strengths in the different precursor materials.

Impact of n-Butylammonium Bromide on the Chemical and Electronic Structure of Double-Cation Perovskite Thin Films

2D/3D perovskite heterostructures have emerged as a promising material composition to reduce nonradiative recombination in perovskite-based LEDs and solar cells. Such heterostructures can be created by a surface treatment with large organic cations, for example, n-butylammonium bromide (BABr). To understand the impact of the BABr surface treatment on the double-cation (Cs0.17FA0.83Pb(I0.6Br0.4)3) (FA = formamidinium) perovskite thin film and further optimize the corresponding structures, an in-depth understanding of the chemical and electronic properties of the involved surfaces, interfaces, and bulk is required. Hence, we study the impact of the BABr treatment with a combination of surface-sensitive X-ray photoelectron spectroscopy and bulk-sensitive resonant inelastic soft X-ray scattering (RIXS). A quantitative analysis of the BABr-treated perovskite thin film shows a modified chemical perovskite surface environment of carbon, nitrogen, bromine, iodine, and lead, indicating that the treatment leads to a perovskite surface with a modified composition and bonding structure. With K-edge RIXS, the local environment at the nitrogen and carbon atoms is probed, allowing us to identify the presence of BABr in the perovskite bulk albeit with a modified bonding environment. This, in turn, identifies a "hidden parameter" for the optimization of the BABr treatment and overall performance of 2D/3D perovskite solar cell absorbers.

Assessing durum wheat ear and leaf metabolomes in the field through hyperspectral data

Hyperspectral techniques are currently used to retrieve information concerning plant biophysical traits, predominantly targeting pigments, water, and nitrogen-protein contents, structural elements, and the leaf area index. Even so, hyperspectral data could be more extensively exploited to overcome the breeding challenges being faced under global climate change by advancing high-throughput field phenotyping. In this study, we explore the potential of field spectroscopy to predict the metabolite profiles in flag leaves and ear bracts in durum wheat. The full-range reflectance spectra (visible (VIS)-near-infrared (NIR)-short wave infrared (SWIR)) of flag leaves, ears and canopies were recorded in a collection of contrasting genotypes grown in four environments under different water regimes. GC-MS metabolite profiles were analyzed in the flag leaves, ear bracts, glumes, and lemmas. The results from regression models exceeded 50% of the explained variation (adj-R² in the validation sets) for at least 15 metabolites in each plant organ, whereas their errors were considerably low. The best regressions were obtained for malate (82%), glycerate and serine (63%) in leaves; myo-inositol (81%) in lemmas; glycolate (80%) in glumes; sucrose in leaves and glumes (68%); γ-aminobutyric acid (GABA) in leaves and glumes (61% and 71%, respectively); proline and glucose in lemmas (74% and 71%, respectively) and glumes (72% and 69%, respectively). The selection of wavebands in the models and the performance of the models based on canopy and VIS organ spectra and yield prediction are discussed. We feel that this technique will likely to be of interest due to its broad applicability in ecophysiology research, plant breeding programmes, and the agri-food industry.

Local electronic structure of the peptide bond probed by resonant inelastic soft X-ray scattering

Soft X-ray emission spectroscopy and RIXS are used to determine the local electronic structure of the peptide bond.

Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs

We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid-base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen 1s core electron excitations to elucidate the roles of N-H σ* and N-C σ* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases Et _xNH_{3- x} ( x = 0...3; Et- = C₂H₅-) and the conjugate positively charged ethylammonium cation acids Et _yNH_{4- y}⁺ ( y = 0...4; Et- = C₂H₅-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post-edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H σ* to N-C σ* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.

Valence orbitals and local bond dynamics around N atoms of histidine under X-ray irradiation

The valence orbitals of aqueous histidine under basic, neutral and acidic conditions and their X-ray induced transformations have been monitored through N 1s resonant inelastic X-ray scattering. Using density functional ab initio molecular dynamics simulations in the core-hole state within the Z + 1 approximation, core-excitation-induced molecular transformations are quantified. Spectroscopic evidence for a highly directional X-ray-induced local N-H dissociation within the scattering duration is presented for acidic histidine. Our report demonstrates a protonation-state and chemical-environment dependent propensity for a molecular dissociation, which is induced by the absorption of high energy photons. This case study indicates that structural deformations in biomolecules under exposure to ionizing radiation, yielding possible alteration or loss of function, is highly dependent on the physiological state of the molecule upon irradiation.

Effect of amino group protonation on the carboxyl group in aqueous glycine observed by O 1s X-ray emission spectroscopy

The valence electronic structures of the amino acid glycine in aqueous solution were investigated in detail through X-ray emission spectroscopy at O 1s excitation under selective excitation conditions of the CO site in the carboxyl group.