Influence of crystallographic orientation of biogenic calcite on in situ Mg XANES analyses

Micro X‐ray absorption near‐edge spectroscopy at the Mg K‐edge is a useful technique for acquiring information about the environment of Mg²⁺ in biogenic calcite. These analyses can be applied to shell powders or intact shell structures. The advantage of the latter is that the XANES analyses can be applied to specific areas, at high (e.g. micrometre) spatial resolution, to determine the environment of Mg²⁺ in a biomineral context. Such in situ synchrotron analysis has to take into account the potential effect of crystallographic orientation given the anisotropy of calcite crystals and the polarized nature of X‐rays. Brachiopod shells of species with different crystallographic orientations are used to assess this crystallographic effect on in situ synchrotron measurements at the Mg K‐edge. Results show that, owing to the anisotropy of calcite, in situ X‐ray absorption spectra (XAS) are influenced by the crystallographic orientation of calcite crystals with a subsequent potentially erroneous interpretation of Mg²⁺ data. Thus, this study demonstrates the importance of crystallography for XAS analyses and, therefore, the necessity to obtain crystallographic information at high spatial resolution prior to spectroscopic analysis.     

Do formalin fixation and freeze‐thaw affect near‐infrared Raman spectroscopy of cartilaginous tissue? A preliminary ex vivo analysis of native human articular cartilage

Near‐infrared (NIR) Raman microprobe spectroscopy has been applied to the non‐invasive characterization of the biochemical structure of extracellular matrix in articular cartilage, a step forward along the path of in vivo diagnostic application of chondropathy. In most studies handling ex vivo cartilage specimens, formalin fixation or freeze‐thaw treatments have been applied in order to stabilize tissue and cell constituents prior to spectroscopic measurements. However, these pre‐processing manipulations might significantly affect certain target bands of the cartilage spectra, thus introducing biases in the characterizations, and potentially leading to data misinterpretation. In this study, we evaluated how formalin fixing and freeze‐thaw processes affect Raman spectra from human femur cartilage. Healthy cartilage specimens were fixed/stored either in a 10% neutral buffered formalin solution or in a deep freezer set at −80 °C. The results of this study show that formalin fixation significantly affects the NIR Raman spectra of cartilage specimens due to concurrent formalin absorption and water dehydration within both collagen and glycosaminoglycan macromolecules. Water dehydration was also confirmed in the amide I structure in the frozen‐thawed specimen, but to a much lesser extent. Furthermore, soaking the tissues in phosphate‐buffered saline solution minimized the storage‐induced Raman artifacts, but its immersion had limited effectiveness in formalin‐fixed specimens, predominantly due to an overlap of signals from the formalin liquid (i.e. emitting at 1046 and 1492 cm⁻¹). Therefore, to provide a highly accurate biochemical evaluation of extracellular matrix using NIR Raman spectroscopy, freeze‐thaw processes are more suitable for ex vivo samples of human cartilage than formalin fixation. Copyright © 2015 John Wiley & Sons, Ltd.     

FT‐IR and FT‐Raman investigations of the chemosensing material para‐hexafluoroisopropanol aniline

As an important chemosensing material involving hexafluoroisopropanol (HFIP) for detecting nerve agents, para‐HFIP aniline (p‐HFIPA) has been firstly synthesized through a new reaction approach and then characterized by nuclear magnetic resonance and mass spectrometry experiments. Fourier transform infrared absorption spectroscopy (FT‐IR) and FT‐Raman spectra of p‐HFIPA have been obtained in the regions of 4000–500 and 4000–200 cm⁻¹, respectively. Detailed identifications of its fundamental vibrational bands have been given for the first time. Moreover, p‐HFIPA has been optimized and vibrational wavenumber analysis can be subsequently performed via density functional theory (DFT) approach in order to assist these identifications in the experimental FT‐IR and FT‐Raman spectra. The present experimental FT‐IR and FT‐Raman spectra of p‐HFIPA are in good agreement with theoretical FT‐IR and FT‐Raman spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Monitoring synchrotron X‐ray‐induced radiolysis effects on metal (Fe,W) ions in high‐temperature aqueous fluids

Radiolysis‐induced effects on aqueous tungsten ions are observed to form a precipitate within seconds upon exposure to a synchrotron X‐ray micro‐beam in a WO₃ + H₂O system at 873 K and 200 MPa. In situ Fe K‐edge energy‐dispersive X‐ray absorption spectroscopy (ED‐XAS) measurements were made on Fe(II)Cl₂ aqueous solutions to 773 K in order to study the kinetics of high‐temperature reactions of Fe²⁺ and Fe³⁺ ions with transient radiolysis species. The radiolytic reactions in a fluid sample within a hydrothermal diamond anvil cell result in oxidation of the Fe²⁺ ion at 573 K and reduction of Fe³⁺ at temperatures between 673 and 773 K and of the Fe²⁺ ion at 773 K. The edge‐energy drift evident in the ED‐XAS data directly reflects the kinetics of reactions resulting in oxidation and/or reduction of the Fe²⁺ and Fe³⁺ ions in the aqueous solutions at high temperatures. The oxidation and reduction trends are found to be highly consistent, making reliable determinations of reaction kinetics possible.     

The status of strontium in biological apatites: an XANES/EXAFS investigation

Osteoporosis represents a major public health problem through its association with fragility fractures. The public health burden of osteoporotic fractures will rise in future generations, due in part to an increase in life expectancy. Strontium‐based drugs have been shown to increase bone mass in postmenopausal osteoporosis patients and to reduce fracture risk but the molecular mechanisms of the action of these Sr‐based drugs are not totally elucidated. The local environment of Sr²⁺ cations in biological apatites present in pathological and physiological calcifications in patients without such Sr‐based drugs has been assessed. In this investigation, X‐ray absorption spectra have been collected for 17 pathological and physiological calcifications. These experimental data have been combined with a set of numerical simulations using the ab initioFEFF9 X‐ray spectroscopy program which takes into account possible distortion and Ca/Sr substitution in the environment of the Sr²⁺ cations. For selected samples, Fourier transforms of the EXAFS modulations have been performed. The complete set of experimental data collected on 17 samples indicates that there is no relationship between the nature of the calcification (physiological and pathological) and the adsorption mode of Sr²⁺ cations (simple adsorption or insertion). Such structural considerations have medical implications. Pathological and physiological calcifications correspond to two very different preparation procedures but are associated with the same localization of Sr²⁺versus apatite crystals. Based on this study, it seems that for supplementation of Sr at low concentration, Sr²⁺ cations will be localized into the apatite network.     

SUT‐NANOTEC‐SLRI beamline for X‐ray absorption spectroscopy

The SUT‐NANOTEC‐SLRI beamline was constructed in 2012 as the flagship of the SUT‐NANOTEC‐SLRI Joint Research Facility for Synchrotron Utilization, co‐established by Suranaree University of Technology (SUT), National Nanotechnology Center (NANOTEC) and Synchrotron Light Research Institute (SLRI). It is an intermediate‐energy X‐ray absorption spectroscopy (XAS) beamline at SLRI. The beamline delivers an unfocused monochromatic X‐ray beam of tunable photon energy (1.25–10 keV). The maximum normal incident beam size is 13 mm (width) × 1 mm (height) with a photon flux of 3 × 10⁸ to 2 × 10¹⁰ photons s^?1 (100 mA)^?1 varying across photon energies. Details of the beamline and XAS instrumentation are described. To demonstrate the beamline performance, K‐edge XANES spectra of MgO, Al₂O₃, S₈, FeS, FeSO₄, Cu, Cu₂O and CuO, and EXAFS spectra of Cu and CuO are presented.     

Identification of epidermal L‐tryptophan and its oxidation products by in vivo FT‐Raman Spectroscopy further supports oxidative stress in patients with vitiligo

In the past, non‐invasive in vivo FT‐Raman spectroscopy has been used to detect H₂O₂‐mediated oxidation of methionine to methionine sulfoxide and methionine sulfone, as well as cysteine to cysteic acid, in the sequence of proteins in the epidermis of patients with vitiligo. L ‐tryptophan (Trp) is another potential target for this oxidation. Owing to the presence of 10⁻³M epidermal albumin which contains one Trp residue, it was tempting to follow the oxidation of this amino acid. Using in vivo and in vitro FT‐Raman spectroscopy, we show for the first time that epidermal Trp is oxidised in patients with vitiligo, yielding 5‐OH‐Trp at 930 cm⁻¹ and other oxidation products (i.e. N‐formyl kynurenine and kynurenine) from indole ring oxidation peaking at 1050 cm⁻¹. On the basis of detailed in vitro results, we could conclude that 5‐OH‐Trp as well as formyl kynurenine and kynurenine are formed via H₂O₂‐mediated Fenton chemistry. These results once again bring out the strength of non‐invasive in vivo FT‐Raman Spectroscopy in dermatology to follow the effect of oxidative stress in the skin of patients with vitiligo. Copyright © 2008 John Wiley & Sons, Ltd.     

Beam‐induced redox transformation of arsenic during As K‐edge XAS measurements: availability of reducing or oxidizing agents and As speciation

During X‐ray absorption spectroscopy (XAS) measurements of arsenic (As), beam‐induced redox transformation is often observed. In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam‐induced redox reactions as a function of sample properties including the redox state of FeS and the solid‐phase As speciation. The beam‐induced oxidation of reduced As species was found to be mediated by the atmospheric O₂ and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface‐complexed As(III) readily underwent the photo‐oxidation upon exposure to the atmospheric O₂ during XAS measurements. With strict O₂ exclusion, however, both As(0) and arsenic sulfide were less prone to the photo‐oxidation by Fe(III) (oxyhydr)oxides than NaAsO₂ and/or surface‐complexed As(III). In case of unaerated As(V)‐reacted FeS samples, surface‐complexed As(V) was photocatalytically reduced during XAS measurements, but arsenic sulfide did not undergo the photo‐reduction.     

On‐line optical and X‐ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states

X‐ray‐induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on‐line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X‐ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X‐ray crystallographic data collection. Here the implementation and utilization of optical and X‐ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy‐dispersive X‐ray fluorescence detector, allowing X‐ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type‐1 and type‐2 Cu centres. It is found that the type‐1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type‐2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on‐line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during crystallographic data collection.     

Food additives characterization by infrared,Raman, and surface‐enhanced Raman spectroscopies

Fourier‐transform infrared (FT‐IR), Raman (RS), and surface‐enhanced Raman scattering (SERS) spectra of β‐hydroxy‐β‐methylobutanoic acid (HMB), L ‐carnitine, and N‐methylglycocyamine (creatine) have been measured. The SERS spectra have been taken from species adsorbed on a colloidal silver surface. The respective FT‐IR and RS band assignments (solid‐state samples) based on the literature data have been proposed. The strongest absorptions in the FT‐IR spectrum of creatine are observed at 1398, 1615, and 1699 cm⁻¹, which are due to ν_s(COOH) + ν(CN) + δ(CN), ρ_s(NH₂), and ν(C O) modes, respectively, whereas those of L ‐carnitine (at 1396/1586 cm⁻¹ and 1480 cm⁻¹) and HMB (at 1405/1555/1585 cm⁻¹ and 1437–1473 cm⁻¹) are associated with carboxyl and methyl/methylene group vibrations, respectively. On the other hand, the strongest bands in the RS spectrum of HMB observed at 748/1442/1462 cm⁻¹ and 1408 cm⁻¹ are due to methyl/methylene deformations and carboxyl group vibrations, respectively. The strongest Raman band of creatine at 831 cm⁻¹ (ρ_w(R NH₂)) is accompanied by two weaker bands at 1054 and 1397 cm⁻¹ due to ν(CN) + ν(R NH₂) and ν_s(COOH) + ν(CN) + δ(CN) modes, respectively. In the case of L ‐carnitine, its RS spectrum is dominated by bands at 772 and 1461 cm⁻¹ assigned to ρ_r(CH₂) and δ(CH₃), respectively. The analysis of the SERS spectra shows that HMB interacts with the silver surface mainly through the  COO⁻, hydroxyl, and  CH₂ groups, whereas L ‐carnitine binds to the surface via  COO⁻ and  N⁺(CH₃)₃ which is rarely enhanced at pH = 8.3. On the other hand, it seems that creatine binds weakly to the silver surface mainly by  NH₂, and C O from the  COO⁻ group. Copyright © 2006 John Wiley & Sons, Ltd.     

Use of Soller slits to remove reference foil fluorescence from transmission spectra

Measurement of X‐ray absorption spectroscopy (XAS) in transmission is the method of choice for strong or concentrated samples. In a typical XAS experiment above 5 keV the sample is placed between the first (I₀) and second (I₁) ion chambers and a standard foil is placed between the second (I₁) and third (I₂) ion chambers for simultaneous calibration of energy during sample analysis. However, some fluorescence from the foil may be registered in I₁, causing anomalies in the transmission signal of the sample, especially when the sample edge jump is relatively small. To remedy this, Soller slits were constructed and placed between the foil and I₁ to minimize back‐fluorescence from the foil. A comparison of blank and standard samples, measured with or without Soller slits or under a worst‐case scenario, demonstrates the advantages of Soller slits when analyzing weak signal samples via transmission XAS.     

FT‐Raman investigation of human dental enamel surfaces

FT‐Raman spectra of human enamel surfaces from sound, affected (with 1 cavity) and highly affected (with at least 3 cavities) tooth samples were analyzed by principal component analysis (PCA). Major differences between the unaffected and affected tooth samples seem to arise from the structural changes along the c‐axis of hydroxyapatite, the chief crystalline component of human dental enamel. Based on Fisher index calculations, the most discriminative value was obtained for the intensity of the only Raman active ν₂PO₄³⁻ (E₁) symmetric deformation mode at 428 cm⁻¹. Moreover, these changes can be observed through the whole tooth enamel surface, establishing a predisposition to caries correlated to chemical and structural composition of tooth enamel. No spectral changes regarding the CO₃²⁻ substitution were detected by both nondestructive FT‐Raman and FTIR (Fourier transform infrared) spectroscopy of the powdered teeth samples. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational characterization of L‐valine phosphonate dipeptides: FT‐IR,FT‐RS,and SERS spectroscopy studies and DFT calculations

Four L ‐valine (L ‐Val) phosphonate dipeptides that are potent inhibitors of zinc metalloproteases, namely, L ‐Val‐C(Me)₂‐PO₃H₂ (V1), L ‐Val‐CH(iP)‐PO₃H₂ (V2), L ‐Val‐CH(iB)‐PO₃H₂ (V3), and L ‐Val‐C(Me)(iP)‐PO₃H₂ (V4), are studied by Fourier‐transform infrared (FT‐IR) spectroscopy, Fourier‐transform Raman spectroscopy (FT‐RS), and surface‐enhanced Raman scattering (SERS). The band assignment (wavenumbers and intensities) is made based on (B3LYP/6‐311 + + G**) calculations. Comparison of theoretical FT‐IR and FT‐RS spectra with those of SERS allows to obtain information on the orientation of these dipeptides as well as specific‐competitive interactions of their functionalities with the silver substrate. More specifically, V1 and V4 appear to interact with the silver substrate mainly via a  C_sgCH₃ moiety localized at the  N_amideC_sg(CH₃)P molecular fragment. In addition, the  POH and isopropyl units of V4 assist in the adsorption process of this molecule. In contrast, the  C_αNH₂ and  PO₃H⁻ groups of V2 and V3 interact with the silver nanoparticles, whereas their isopropyl and isobutyl fragments seem to be repelled by the silver substrate (except for the  CH₂  of V3), similar to the  C_β(CH₃)₂ fragment of L ‐Val for all L ‐Val phosphonate dipeptides investigated in this work. The adsorption mechanism of these molecules onto the colloidal silver surface is also affected by amide bond behavior. Copyright © 2010 John Wiley & Sons, Ltd.     

Blueprint XAS: a Matlab‐based toolbox for the fitting and analysis of XAS spectra

Blueprint XAS is a new Matlab‐based program developed to fit and analyse X‐ray absorption spectroscopy (XAS) data, most specifically in the near‐edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado‐Jaime & Kennepohl (2010), J. Synchrotron Rad. 17 , 119–128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near‐edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand‐alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.     

FT‐Raman and FTIR spectroscopic characterization of biogenic carbonates from Philippine venus seashell and Porites sp. coral

Some seashells of the Philippine venus species and sea coral of Porites sp. were studied by means of FT‐Raman, Fourier transform infrared spectroscopy (FTIR) and Far‐FTIR spectroscopic methods. The Raman spectra show that both Porites sp. and P. venus are of aragonite‐structured CaCO₃. Detailed spectral analysis, however, reveals some small differences, due to differences in the crystallite size or habit and to different minor element contents. IR spectra show that Porites sp. contains also some small quantities of calcite‐structured carbonates. The ν₂ band (shoulder) of calcite at 875.7 cm⁻¹ is present in the IR spectrum. The separation of the two ν₂ bands (856.4 cm⁻¹ for aragonite and 875.7 cm⁻¹ for calcite) suggests the absence of solid solution of the two polymorphic phases of CaCO₃. Spectroscopic results were confirmed also by X‐ray powder diffraction measurements. Copyright © 2008 John Wiley & Sons, Ltd.     

Soft X‐ray absorption spectroscopy and resonant inelastic X‐ray scattering spectroscopy below 100 eV: probing first‐row transition‐metal M‐edges in chemical complexes

X‐ray absorption and scattering spectroscopies involving the 3d transition‐metal K‐ and L‐edges have a long history in studying inorganic and bioinorganic molecules. However, there have been very few studies using the M‐edges, which are below 100 eV. Synchrotron‐based X‐ray sources can have higher energy resolution at M‐edges. M‐edge X‐ray absorption spectroscopy (XAS) and resonant inelastic X‐ray scattering (RIXS) could therefore provide complementary information to K‐ and L‐edge spectroscopies. In this study, M_2,3‐edge XAS on several Co, Ni and Cu complexes are measured and their spectral information, such as chemical shifts and covalency effects, are analyzed and discussed. In addition, M_2,3‐edge RIXS on NiO, NiF₂ and two other covalent complexes have been performed and different d–d transition patterns have been observed. Although still preliminary, this work on 3d metal complexes demonstrates the potential to use M‐edge XAS and RIXS on more complicated 3d metal complexes in the future. The potential for using high‐sensitivity and high‐resolution superconducting tunnel junction X‐ray detectors below 100 eV is also illustrated and discussed.     

Versatile variable temperature insert at the DEIMOS beamline for in situ electrical transport measurements

The design and the first experiments are described of a versatile cryogenic insert used for its electrical transport capabilities. The insert is designed for the cryomagnet installed on the DEIMOS beamline at the SOLEIL synchrotron dedicated to magnetic characterizations through X‐ray absorption spectroscopy (XAS) measurements. This development was spurred by the multifunctional properties of novel materials such as multiferroics, in which, for example, the magnetic and electrical orders are intertwined and may be probed using XAS. The insert thus enables XAS to in situ probe this interplay. The implementation of redundant wiring and careful shielding also enables studies on operating electronic devices. Measurements on magnetic tunnel junctions illustrate the potential of the equipment toward XAS studies of in operando electronic devices.     

Development and exploration of a new methodology for the fitting and analysis of XAS data

A new data analysis methodology for X‐ray absorption near‐edge spectroscopy (XANES) is introduced and tested using several examples. The methodology has been implemented within the context of a new Matlab‐based program discussed in a companion related article [Delgado‐Jaime et al. (2010), J. Synchrotron Rad. 17 , 132–137]. The approach makes use of a Monte Carlo search method to seek appropriate starting points for a fit model, allowing for the generation of a large number of independent fits with minimal user‐induced bias. The applicability of this methodology is tested using various data sets on the Cl K‐edge XAS data for tetragonal CuCl₄^2?, a common reference compound used for calibration and covalency estimation in M—Cl bonds. A new background model function that effectively blends together background profiles with spectral features is an important component of the discussed methodology. The development of a robust evaluation function to fit multiple‐edge data is discussed and the implications regarding standard approaches to data analysis are discussed and explored within these examples.     

Augmentation of the step‐by‐step Energy‐Scanning EXAFS beamline BL‐09 to continuous‐scan EXAFS mode at INDUS‐2 SRS

An innovative scheme to carry out continuous‐scan X‐ray absorption spectroscopy (XAS) measurements similar to quick‐EXAFS mode at the Energy‐Scanning EXAFS beamline BL‐09 at INDUS‐2 synchrotron source (Indore, India), which is generally operated in step‐by‐step scanning mode, is presented. The continuous XAS mode has been implemented by adopting a continuous‐scan scheme of the double‐crystal monochromator and on‐the‐fly measurement of incident and transmitted intensities. This enabled a high signal‐to‐noise ratio to be maintained and the acquisition time was reduced to a few seconds from tens of minutes or hours. The quality of the spectra (signal‐to‐noise level, resolution and energy calibration) was checked by measuring and analysing XAS spectra of standard metal foils. To demonstrate the energy range covered in a single scan, a continuous‐mode XAS spectrum of copper nickel alloy covering both Cu and Ni K‐edges was recorded. The implementation of continuous‐scan XAS mode at BL‐09 would expand the use of this beamline in in situ time‐resolved XAS studies of various important systems of current technological importance. The feasibility of employing this mode of measurement for time‐resolved probing of reaction kinetics has been demonstrated by in situ XAS measurement on the growth of Ag nanoparticles from a solution phase.