High covalence in CuSO4 and the radicalization of sulfate: an X-ray absorption and density functional study

Sulfur K-edge X-ray absorption spectroscopy (XAS) of anhydrous CuSO(4) reveals a well-resolved preedge transition feature at 2478.8 eV that has no counterpart in the XAS spectra of anhydrous ZnSO(4) or copper sulfate pentahydrate. Similar but weaker preedge features occur in the sulfur K-edge XAS spectra of [Cu(itao)SO(4)] (2478.4 eV) and [Cu[(CH(3))(6)tren]SO(4)] (2477.7 eV). Preedge features in the XAS spectra of transition metal ligands are generally attributed to covalent delocalization of a metal d-orbital hole into a ligand-based orbital. Copper L-edge XAS of CuSO(4) revealed that 56% of the Cu(II) 3d hole is delocalized onto the sulfate ligand. Hybrid density functional calculations on the two most realistic models of the covalent delocalization pathways in CuSO(4) indicate about 50% electron delocalization onto the sulfate oxygen-based 2p orbitals; however, at most 14% of that can be found on sulfate sulfur. Both experimental and computational results indicated that the high covalence of anhydrous CuSO(4) has made sulfate more like the radical monoanion, inducing an extensive mixing and redistribution of sulfur 3p-based unoccupied orbitals to lower energy in comparison to sulfate in ZnSO(4). It is this redistribution, rather than a direct covalent interaction between Cu(II) and sulfur, that is the origin of the observed sulfur XAS preedge feature. From pseudo-Voigt fits to the CuSO(4) sulfur K-edge XAS spectrum, a ground-state 3p character of 6% was quantified for the orbital contributing to the preedge transition, in reasonable agreement with the DFT calculation. Similar XAS fits indicated 2% sulfur 3p character for the preedge transition orbitals in [Cu(itao)SO(4)] and [Cu[(CH(3))(6)tren]SO(4)]. The covalent radicalization of ligands similar to sulfate, with consequent energy redistribution of the virtual orbitals, represents a new mechanism for the induction of ligand preedge XAS features. The high covalence of the Cu sites in CuSO(4) was found to be similar to that of Cu sites in oxidized cupredoxins, including its anistropic nature, and can serve as the simplest inorganic examples of intramolecular electron-transfer processes.     

X-ray absorption spectroscopy measurements of liquid water

Recent studies, based on X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS), have shown that the hydrogen bond network in liquid water consists mainly of water molecules with only two strong hydrogen bonds. Since this result is controversial, it is important to demonstrate the reliability of the experimental data, which is the purpose of this paper. Here we compare X-ray absorption spectra of liquid water recorded with five very different techniques sensitive to the local environment of the absorbing molecule. Overall, the spectra obtained with photon detection show a very close similarity and even the observable minor differences can be understood. The comparison demonstrates that XAS and XRS can indeed be applied reliably to study the local bonding of the water molecule and thus to reveal the hydrogen bond situation in bulk water.     

Combined X-ray absorption spectroscopy and density functional theory examination of ferrocene-labeled peptides

A combination of soft X-ray absorption spectroscopy (XAS) measurements and StoBe density functional theory (DFT) calculations has been used to study the electronic structures of the ferrocene-labeled peptides Fc-Pro(n)-OBz (n = 1-4). Excellent agreement between the measured and the simulated data is observed in all cases, and the origin of all major spectral features was assigned. The breaking of the degeneracy of the ferrocene 3e(2u)-like unoccupied molecular orbital under the influence of a substituent attached to a Cp ring was observed experimentally. The influence of the bonding environment on the O 1s and N 1s XAS spectra was examined. A corrected assignment of one of the major features in the Fe 2p XAS spectra of ferrocene is proposed and supported by the DFT simulations, as well as the measured spectra.     

The effect of cryogenic sample cooling on X-ray absorption spectra

It is common for samples to be cooled to near liquid He temperature (4 K) during measurement of their X-ray absorption spectra (XAS). This procedure is believed to improve spectrum quality either by minimizing radiation damage, or by decreasing thermal motions of atoms. The actual benefits realized by cooling are rarely assessed, since that would require duplicate measurements at multiple temperatures, followed by duplicate data analyses. With a cryostat installed, it is difficult to measure room temperature or hotter spectra, which often requires removing the cryostat from the beam path.Here we investigate the effect of cooling and show that it is not globally useful in X-ray absorption spectroscopy. Photolysis does not occur, or its consequences are not controlled by cooling. Secondary photochemical damage is delayed and is remote from the absorption site. Thermal motions do not usually contribute significantly to disorder and consequent damping of EXAFS, either because vibrational amplitudes are small, or because static disorder and structural complexity affect EXAFS in the same way but more profoundly.The low probability of photochemical effects on XAS is in contrast to the situation with crystallography of biological specimens, where photochemical damage anywhere in the sample degrades the data set regardless of proximity to atoms of one specific element. Thermal disorder becomes important in certain types of samples and when the Debye-Waller factor is itself used as a tool. In most cases, it is more efficient to first measure room temperature spectra, and then repeat measurement using a cryostat of only those spectra where the objectives of the analysis justify an attempt to gain more information.     

Near edge X-ray absorption fine structure spectroscopy of bacterial hydroxamate siderophores in aqueous solutions

X-ray absorption spectroscopy (XAS) is widely used to explore the coordination environments and structures of metal complexes in aqueous solutions and disordered phases. Although soft-XAS studies on gaseous phases, solid phases and their interfaces have shown that XAS is a versatile tool in studying the functional group composition of organic molecules, the application of XAS to studying aqueous solutions is seriously limited because of experimental difficulties. In this report, using a modified synchrotron endstation geometry, we show how soft-XAS was used to study the changes in electronic states of reactive functional groups in a bacterial macromolecule, desferrioxamine B (desB, a hydroxamate siderophore) and its structural analogue (acetohydroxamic acid (aHa)). We collected C, N, and O near edge X-ray absorption fine structure (NEXAFS) spectra of these molecules in aqueous solutions and complemented their spectral interpretation with calculated X-ray spectra of "hydrated" aHa. The experimental spectra of desB are similar to those for aHa at the C, N, and O K-edges. In addition, the electronic transitions of amide and hydroxamate functional groups in the macromolecule can be distinguished from the N spectra. Small energy differences in the pi*(C=O)NO and the transitions at the C- and N-edges of aHa and desB indicate that the substituent attached to N in desB ((CH2)n) determines the electron density in the (C=O)NO core. As the solution pH increased, the pi*(C=O)NO transition of the hydroxamate group of these two molecules exhibit energy shifts at the C-, N-, and O-edges, which are consistent with increased electron delocalization in the (C=O)NO core of aHa (and desB), predicted from the calculations. The spectra of the aHa(H2O)3- anion also provide evidence for partial N-deprotonation at pH values usually attributed to an O-acid. These results indicate that soft-XAS is well suited for studying the electronic states of different functional groups in aqueous organic macromolecules.     

Probing the local structure of liquid water by X-ray absorption spectroscopy

It was recently suggested that liquid water primarily comprises hydrogen-bonded rings and chains, as opposed to the traditionally accepted locally tetrahedral structure (Wernet et al. Science 2004, 304, 995). This controversial conclusion was primarily based on comparison between experimental and calculated X-ray absorption spectra (XAS) using computer-generated ice-like 11-molecule clusters. Here we present calculations which conclusively show that when hydrogen-bonding configurations are chosen randomly, the calculated XAS does not reproduce the experimental XAS regardless of the bonding model employed (i.e., rings and chains vs tetrahedral). Furthermore, we also present an analysis of a recently introduced asymmetric water potential (Soper, A. K. J. Phys.: Condens. Matter 2005, 17, S3273), which is representative of the rings and chains structure, and make comparisons with the standard SPC/E potential, which represents the locally tetrahedral structure. We find that the calculated XAS from both potentials is inconsistent with the experimental XAS. However, we also show the calculated electric field distribution from the rings and chains structure is strongly bimodal and highly inconsistent with the experimental Raman spectrum, thus casting serious doubt on the validity of the rings and chains model for liquid water.     

Electron spectroscopy and microscopy on chromium oxide nanowires on templated block copolymers

Electronic and geometric properties of chromium oxide nanowires deposited on self-assembled block copolymer templates are evaluated by means of synchrotron radiation based spectroscopic methods like X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS). The geometric distribution of the nanowires is monitored with X-ray photoelectron emission microscopy (XPEEM) and atomic force microscopy (AFM). XAS and XPS of Cr 2p emissions for chromium oxide nanostructures determine an oxidation state different from the most common chromium oxides and additional satellite peaks are derived from localization effects induced by the nanostructuring.     

Electronic structure of A- and B-site doped lanthanum manganites: a combined X-ray spectroscopic study

The electronic properties of a series of colossal magnetoresistance (CMR) compounds, namely LaMnO3, La(1-x)Ba(x)(MnO3 (0.2 < or = x < or = 0.55), La(0.76)Ba(0.24)Mn(0.84)Co(0.16)O3, and La(0.76)Ba(0.24)Mn(0.78)Ni(0.22)O3, have been investigated in a detailed spectroscopic study. A combination of X-ray photoelectron spectroscopy (XPS), X-ray emission spectroscopy (XES), X-ray absorption spectroscopy (XAS), and resonant inelastic X-ray scattering (RIXS) was used to reveal a detailed picture of the electronic structure in the presence of Ba, Co, and Ni doping in different concentrations. The results are compared with available theory. The valence band of La(1-x)()Ba(x)MnO3 (0 < or = x < or = 0.55) is dominated by La 5p, Mn 3d, and O 2p states, and strong hybridization between Mn 3d and O 2p states is present over the whole range of Ba concentrations. Co-doping at the Mn site leads to an increased occupancy of the e(g) states near the Fermi energy and an increase in the XPS valence band intensity between 0.5 and 5 eV, whereas the Ni-doped sample shows a lower density of occupied states near the Fermi energy. The Ni d states are located in a band spanning the energy range of 1.5-5 eV. XAS spectra indicate that the hole doping leads to mixed Mn 3d-O 2p states. Furthermore, RIXS at the Mn L edge has been used to probe d-d transitions and charge-transfer excitations in La(1-x)Ba(x)MnO3.     

Automatic spike correction using UNIFIT 2020

The improvement of the software UNIFIT 2020 from an analysis processing software for photoelectron spectroscopy (XPS) only to a powerful tool for XPS, Auger electron spectroscopy (AES), X-ray absorption spectroscopy (XAS), and Raman spectroscopy requires new additional programme routines. Particularly, the implementation of the analysis of Raman spectra needs a well-working automatic spike correction. The application of the modified discrete Laplace operator method allows for a perfect localization and correction of the spikes and finally a successful peak fit of the spectra. The theoretical basis is described. Test spectra allow for the evaluation of the presented method. A comparison of the original and spike-corrected real measurements demonstrates the high quality of the method used.     

X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy

In this work, the chemical changes in calf thymus DNA samples were analyzed by X-ray photoelectron spectroscopy (XPS). The DNA samples were irradiated for over 5 h and spectra were taken repeatedly every 30 min. In this approach the X-ray beam both damages and probes the samples. In most cases, XPS spectra have complex shapes due to contributions of C, N, and O atoms bonded at several different sites. We show that from a comparative analysis of the modification in XPS line shapes of the C 1s, O 1s, N 1s, and P 2p peaks, one can gain insight into a number of reaction pathways leading to radiation damage to DNA.     

Trivalent atom contribution on solid-solid transformation of Ga13 polycation intercalated clay into sodalite investigated by X-ray absorption spectroscopy

Solid-solid transformation mechanism of Ga Keggin-type ion intercalated clay into sodalite has been clarified by X-ray diffraction (XRD), FT-IR spectroscopy, and X-rayabsorption spectroscopy (XAS). To follow the structural evolution precisely by XANES and EXAFS, the XAS active element containing polycation [Ga13O4(OH)24(H2O)12]7+ was intercalated into montmorillonite (MMT). FT-IR and XAS spectra confirm that the formation of sodalite framework is initiated by the delocalized rearrangement between silicate networks and collapsed interlayered Ga species, and is followed by the incorporation of Al in the octahedral sheet of clay (MMT). According to the XAS studies, it is found that the formation of Ga(Al)-O-Si species is strongly influenced by the trivalent cations, which are rapidly changed in the environment, followed by reaction with the silicate network of clay during the solid-solid transformation.     

Exploiting soft and hard X-ray absorption spectroscopy to characterize metallodrug/protein interactions: the binding of [trans-RuCl4(Im)(dimethylsulfoxide)][ImH] (Im = imidazole) to bovine serum albumin

The reaction of bovine serum albumin (BSA) with [ trans-RuCl 4(Im)(dimethylsulfoxide)][ImH] (Im = imidazole) (NAMI-A), an experimental ruthenium(III) anticancer drug, and the formation of the respective NAMI-A/BSA adduct were investigated by X-ray absorption spectroscopy (XAS) at the sulfur and chlorine K-edges and at the ruthenium K- and L 3-edges. Ruthenium K and L 3-edge spectra proved unambiguously that the ruthenium center remains in the oxidation state +3 after protein binding. Comparative analysis of the chlorine K-edge XAS spectra of NAMI-A and NAMI-A/BSA, revealed that the chlorine environment is greatly perturbed upon protein binding. Only modest changes were observed in the sulfur K-edge spectra that are dominated by several protein sulfur groups. Overall, valuable information on the nature of this metallodrug/protein adduct and on the mechanism of its formation was gained; XAS spectroscopy turns out to be a very suitable method for the characterization of this kind of systems.     

X-ray absorption spectroscopy study of the hydrogen bond network in the bulk water of aqueous solutions

We utilized X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS) in order to study the ion solvation effect on the bulk hydrogen bonding structure of water. The fine structures in the X-ray absorption spectra are sensitive to the local environment of the probed water molecule related to the hydrogen bond length and angles. By varying the concentration of ions, we can distinguish between contributions from water in the bulk and in the first solvation sphere. We show that the hydrogen bond network in bulk water, in terms of forming and breaking hydrogen bonds as detected by XAS/XRS, remains unchanged, and only the water molecules in the close vicinity to the ions are affected.     

X-ray absorption spectral analysis with a 9 V battery X-ray generator.

X-ray absorption spectral (XAS) analysis is performed with a combination of a 9 V dry electric battery X-ray generator and a portable Si PIN X-ray detector. The calcium K edge (4.0 keV) in paper is measured with a grazing incidence geometry, which suppressed the artifact due to the Kalpha X-ray fluorescence peak at 3.5 keV. The 9 V dry battery X-ray emitter is useful for portable XAS measurements.     

Excitation energy dependence for the Li 1s X-ray photoelectron spectra of LiMn2O4.

The Li 1s XPS (X-ray Photoelectron Spectroscopy) spectra of LiMn2O4, which is one of the major positive-electrode materials in lithium-ion rechargeable batteries, and MnO2 as a reference material, were measured by a laboratory-type XPS spectrometer. The Li 1s peak was not observed in the spectra excited by the Mg Kalpha line (1253.6 eV), because the Li 1s peak overlapped the background of the Mn 3p peak of LiMn2O4. The photoionization cross section of Mn 3p was larger than that of Li 1s for Mg Kalpha excitation. Therefore, the XPS measurement of LiMn2O4 by soft X-ray synchrotron excitation was carried out at beamline BL-7B on NewSUBARU synchrotron facility. Excitation energies of 110, 120, 130, 140, 150 and 151.4 eV were selected. The Li 1s peak was clearly observed in these XPS spectra. In order to investigate the excitation energy dependence, the area ratio of the Li 1s and Mn 3p peaks in the XPS spectra was plotted against the excitation energy. As a result, when the excitation energy was 110 eV, the area ratio had the maximum value.     

Speciation of metal(loid)s in environmental samples by X-ray absorption spectroscopy: A critical review

Element specificity is one of the key factors underlying the widespread use and acceptance of X-ray absorption spectroscopy (XAS) as a research tool in the environmental and geo-sciences. Independent of physical state (solid, liquid, gas), XAS analyses of metal(loid)s in complex environmental matrices over the past two decades have provided important information about speciation at environmentally relevant interfaces (e.g. solid–liquid) as well as in different media: plant tissues, rhizosphere, soils, sediments, ores, mineral process tailings, etc. Limited sample preparation requirements, the concomitant ability to preserve original physical and chemical states, and independence from crystallinity add to the advantages of using XAS in environmental investigations. Interpretations of XAS data are founded on sound physical and statistical models that can be applied to spectra of reference materials and mixed phases, respectively. For spectra collected directly from environmental matrices, abstract factor analysis and linear combination fitting provide the means to ascertain chemical, bonding, and crystalline states, and to extract quantitative information about their distribution within the data set. Through advances in optics, detectors, and data processing, X-ray fluorescence microprobes capable of focusing X-rays to micro- and nano-meter size have become competitive research venues for resolving the complexity of environmental samples at their inherent scale. The application of μ-XANES imaging, a new combinatorial approach of X-ray fluorescence spectrometry and XANES spectroscopy at the micron scale, is one of the latest technological advances allowing for lateral resolution of chemical states over wide areas due to vastly improved data processing and detector technology.     

Electronic structure of transition metal-cysteine complexes from X-ray absorption spectroscopy

The electronic structures of HgII, NiII, CrIII, and MoV complexes with cysteine were investigated by sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. The covalency in the metal-sulfur bond was determined by analyzing the intensities of the electric-dipole allowed pre-edge features appearing in the XANES spectra below the ionization threshold. Because of the well-defined structures of the selected cysteine complexes, the current work provides a reference set for further sulfur K-edge XAS studies of bioinorganic active sites with transition metal-sulfur bonds from cysteine residues as well as more complex coordination compounds with thiolate ligands.     

Pitfalls in X-ray absorption spectroscopy analysis and interpretation: A practical guide for general users

Despite the growing popularity of X-ray absorption spectroscopy (XAS) in scientific research, many researchers do not receive formalized training on this technique. Some of them learned from online resources, which only briefly introduce XAS and its applications. Here, this article aims to provide the overview of tips about the XAS analysis, general rules, as well as required information for presenting XAS data in publications, and some common mistakes in XAS data interpretations. Armed with these basics, the motivated aspiring XAS researchers will find existing resources more accessible and can progress much faster in understanding and using XAS.     

Electronic structure of a vapor-deposited metal-free phthalocyanine thin film

The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine (H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1s XAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.