Background subtraction for fluorescence EXAFS data of a very dilute dopant Z in Z + 1 host

When conducting EXAFS at the Cu K‐edge for ZnS:Cu with very low Cu concentration (<0.04% Cu), a large background was present that increased with energy. This background arises from a Zn X‐ray Raman peak, which moves through the Cu fluorescence window, plus the tail of the Zn fluorescence peak. This large background distorts the EXAFS and must be removed separately before reducing the data. A simple means to remove this background is described.     

EDNA: a framework for plugin‐based applications applied to X‐ray experiment online data analysis

EDNA is a framework for developing plugin‐based applications especially for online data analysis in the X‐ray experiments field. This article describes the features provided by the EDNA framework to ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.     

Position and flux stabilization of X‐ray beams produced by double‐crystal monochromators for EXAFS scans at the titanium K‐edge

The simultaneous and active feedback stabilization of X‐ray beam position and monochromatic beam flux during EXAFS scans at the titanium K‐edge as produced by a double‐crystal monochromator beamline is reported. The feedback is generated using two independent feedback loops using separate beam flux and position measurements. The flux is stabilized using a fast extremum‐searching algorithm that is insensitive to changes in the synchrotron ring current and energy‐dependent monochromator output. Corrections of beam height are made using an innovative transmissive beam position monitor instrument. The efficacy of the feedback stabilization method is demonstrated by comparing the measurements of EXAFS spectra on inhomogeneous diluted Ti‐containing samples with and without feedback applied.     

Beam‐size‐related phenomena and effective normalization in energy‐dispersive EXAFS for the study of heterogeneous catalysts,powder materials and the processes they mediate: observations and (some) solutions

The effects of focal spot size and the nature of powder samples (such as heterogeneous catalysts) on the quality of data obtainable from a dispersive EXAFS experiment are characterized at ID24 of the ESRF. Using examples of supported Pd catalysts, it is shown that, for a given photon flux, massive improvements in data quality can be achieved by increasing the size of the dispersive beam in the vertical, whilst concurrently applying a methodology to account for scattering effects emanating from the samples under study. These improvements are demonstrated using progressively practical and demanding examples. Questions regarding optimal beam dimensions for the study of such materials, how to counter undesirable effects that arise from the coherence of the source, how to obtain similar results consistently across the 5–30 keV bandwidth of ID24, and whether a methodology for simultaneous normalization in dispersive EXAFS is of significant utility in such circumstances are discussed.     

miXAFS: a program for X‐ray absorption fine‐structure data analysis

A new program called miXAFS for the analysis of X‐ray absorption fine‐structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X‐ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R‐factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.     

The key Cl− ligand for metal‐to‐ligand charge transfer in mononuclear terpyridine ruthenium(II) and binuclear ruthenium(II) tetrapyridylpyrazine complexes

Electronic structures of binuclear ruthenium complexes [Ru₂(terpy)₂(tppz)]⁴⁺ ( 1A ) and [Ru₂Cl₂(L)₂(tppz)]²⁺ {L = bpy ( 2A ), phen ( 3A ), and dpphen ( 4A )} were studied by density functional theory calculations. Abbreviations of the ligands (Ls) are bpy = 2,2′‐bipyridine, phen = 1,10‐phenanthroline, dpphen = 4,7‐diphenyl‐1,10‐phenanthroline, terpy = 2,2′:6′,2″‐terpyridine, and tppz = tetrakis(2‐pyridyl)pyrazine. Their mononuclear reference complexes [Ru(terpy)₂]²⁺ ( 1B ) and [RuClL(terpy)]⁺ {L = bpy ( 2B ), phen ( 3B ), and dpphen ( 4B )} were also examined. Geometries of these mononuclear and binuclear Ru(II) complexes were fully optimized. Their geometric parameters are in good agreement with the experimental data. The binuclear complexes were characterized by electrospray ionization mass spectrometry, UV–Vis spectroscopy, and cyclic voltammograms. Hexafluorophosphate salts of binuclear ruthenium complexes of 3A and 4A were newly prepared. The crystal structure of binuclear complex 1A (PF₆)₄ was also determined. Orbital interactions were analyzed to characterize the metal‐to‐ligand charge‐transfer (MLCT) states in these complexes. The Cl^? ligand works to raise the orbital energy of the metal lone pair, which leads to the low MLCT state. Copyright © 2011 John Wiley & Sons, Ltd.     

Isomerization and rearrangement of (E)‐ and (Z)‐phenylhydrazones of 3‐benzoyl‐5‐phenyl‐1,2,4‐oxadiazole: evidence for a ‘new’ type of acid‐catalysis by copper(II) salts in mononuclear rearrangement of heterocycles

A kinetic investigation in methanol of the title reaction has evidenced the occurrence of two processes: the 1‐ E 1‐ Z isomerization and the rearrangement of the (Z)‐isomer into the relevant 4‐benzoylamino‐2,5‐diphenyl‐1,2,3‐triazole ( 1‐ Z → T ). The latter reaction is in line with the ability of the (Z)‐phenylhydrazones of 3‐benzoyl‐1,2,4‐oxadiazoles to undergo the so called mononuclear rearrangement of heterocycles (MRH). The occurrence of both the examined reactions is dependent on a Lewis‐acid‐catalysis. The obtained results have shown the possibility of a ‘new’ type of acid‐catalysis (bifunctional catalysis by Lewis salts) in the MRH. This catalysis operates through a completely different mechanism with respect to the one recently observed, and deeply investigated, in the presence of protic acids for the (Z)‐phenylhydrazone of 5‐amino‐3‐benzoyl‐1,2,4‐oxadiazole, in both dioxane/water and toluene, for which the catalytic process was dependent on the protonation of N(4) ring‐nitrogen of the 1,2,4‐oxadiazole. As a matter of fact, the copper salts seem able to interact with the >C?N? NH? C₆H₅ moiety, yielding adducts which, in some cases, are prone to both isomerize and rearrange. Therefore, a similar behaviour in some manner parallel to that already observed in benzene in the presence of aliphatic amines (base‐catalysis) has been evidenced. Copyright © 2008 John Wiley & Sons, Ltd.     

Linear free‐energy relationships in semiquinone species and their Mn(II) and Cu(II) complexes

Linear free‐energy relationships for a series of functionalized semiquinone ligands and their Mn^II‐ and Cu^IIhydro‐tris(3‐cumenyl‐5‐methylpyrazolyl) borate complexes were examined. Quinone–semiquinone cycle half‐wave reduction potentials and semiquinone hydrogen hyperfine coupling constants (a_H) were determined and their correlation with Hammett σ parameters reported. A new σ parameter, σ_aH, has been proposed. Mn^II and Cu^II metal complex metal–ligand charge transfer and n → π* UV transitions were found to be modulated by substituents. Satisfactory Hammett correlations between UV transitions and various σ values have been determined and compared in a number of instances. Copyright © 2011 John Wiley & Sons, Ltd.     

Spectroscopic set‐up for simultaneous UV‐Vis/(Q)EXAFS in situ and in operando studies of homogeneous reactions under laboratory conditions

A novel experimental set‐up for in operando studies of homogeneous catalyzed reactions under laboratory conditions has been developed and tested. It combines time‐resolved X‐ray absorption spectroscopy with UV/Vis spectroscopy. The reaction solution is stirred in a vessel and pumped in a circle by a peristaltic free gear‐wheel through a measurement cell. The X‐ray and UV/Vis beams probe the same sample volume of the cell orthogonally. Reactants can be added to the reaction mixture in the course of the measurements and a defined gas atmosphere can be adjusted up to a pressure of 10 bar. The in situ reduction of cerium(IV) ammonium nitrate to cerium(III) by isopropanol is studied as a test reaction with quick‐XANES and UV/Vis measurements with a time resolution of 60 s and 1 s, respectively.     

A stainless steel multi‐well plate (SS‐MWP) for high‐throughput Raman analysis of dilute solutions

The use of Raman spectroscopy for the qualitative and quantitative analysis of dilute aqueous solutions is of interest to the biopharmaceutical manufacturing sector. However, the inherent weakness of the Raman effect, coupled with spectral variability due to spurious signals from sample holders, can produce significant problems for chemometric‐based high‐throughput assays. Therefore, there is a need for a multi‐well sample holder that ensures robust and repeatable measurements, in particular from dilute aqueous solutions such as cell culture media. Here we demonstrate the efficacy of a novel, electropolished, stainless steel multi‐well plate (SS‐MWP) sample holder with 96 wells for dilute aqueous solution analysis. A comprehensive study of the spectroscopic behaviour was carried out and comparisons made with multi‐well plates fabricated from polystyrene, polypropylene, and aluminium. A key factor in the validation studies is the use of intrinsically weak Raman scattering systems, e.g. water and dilute glucose solutions. The data collected show that the SS‐MWPs are much superior in terms of robustness, resistance to chemical attack, and measurement reproducibility and as such are the ideal sample holders for Raman analysis of dilute solutions. Copyright © 2010 John Wiley & Sons, Ltd.     

Experimental (FT‐IR) and theoretical (DFT) studies on prototropy and H‐bond formation for pyrazine‐2‐amidoxime

The results of the first structural studies (with the use of both experimental and theoretical methods) on pyrazine‐2‐amidoxime (PAOX) were shown and discussed. FT‐IR spectra were recorded in different concentrations of the PAOX in apolar solvent to check the possibility of the inter‐ or intramolecular hydrogen‐bond formation. All possible tautomers–rotamers of PAOX were then theoretically considered at the DFT(B3LYP)/6‐311+G** level in vacuo. For selected isomers, calculations were also performed at higher levels of theory {B3LYP/6‐311+G(3df,2p) and G3B3}. Based on the results of DFT calculations, the most stable isomers were found, and their total free energies and infrared spectra were calculated. The energy variation plots for the N8?C7?N9?O10 and N1?C2?C7?N9 dihedral angles were also computed to find two energy barriers, one for E/Z isomerization around the C7?N9 double bond and the other one for rotation of the pyrazinyl ring around the C2?C7 single bond. The results show that the stability of the PAOX isomers strongly depend on their configuration and orientation of the substituents. The possibilities of inter‐ and intramolecular hydrogen bonds were also experimentally and theoretically checked. Finally, a potential of mean force was determined in CHCl₃ for a dimer of PAOX with hexamethylphosphoramide. Both, experimental and theoretical results are in agreement. Copyright © 2016 John Wiley & Sons, Ltd.     

Spectroscopic and computational studies on self‐assembly complexes of bis(pyrrol‐2‐ ylmethyleneamine) ligands linked by alkyl spacers with Cu(II)

Bis(pyrrol‐2‐ylmethyleneamine) ligands and their mononuclear monomeric and dinuclear dimeric self‐assembly complexes with Cu(II) were investigated by means of IR and Raman spectroscopies and density functional theory. The ground‐state geometries were calculated by using the Becke Lee Yang Parr composite exchange‐correlation functional (B3LYP) and a combined basis set (LanL2DZ for Cu; 6–31G(d) for C, H, N), and they were compared with the single‐crystal X‐ray diffraction (XRD) structures. The DFT‐calculated Cu N bond lengths are generally higher by 0.001–0.040 Å than those determined through XRD. The vibrational spectra were also calculated at the same level of theory for the optimized geometries. The calculated wavenumbers were scaled by a uniform scaling factor and compared with the experimental fundamentals. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm⁻¹. In comparison with the spectra of the ligands, the coordination effect shifts the υ(CN) wavenumber by about 50 cm⁻¹ toward a lower value. Because of the weak intermolecular C H···Cu hydrogen bond, the Cu N stretching mode is shifted toward a lower wavenumber. Copyright © 2006 John Wiley & Sons, Ltd.     

Loose‐powder technique for X‐ray fluorescence analysis of ancient pottery using a small (100 mg) powdered sample

A molded‐loose‐powder technique using a small powdered sample (100 mg) was developed for the X‐ray fluorescence analysis of 22 components (Na₂O, MgO, Al₂O₃, SiO₂, P₂O₅, K₂O, CaO, TiO₂, MnO, Fe₂O₃, V, Cr, Ni, Cu, Zn, Rb, Sr, Y, Zr, Nb, Ba, and Pb) in ancient pottery. This loose powder specimen was prepared by pressing the small powdered sample into a sample holder, formed from a stainless steel disk (48‐mm diameter × 0.8‐mm height) with a hole (11‐mm diameter), by hand. Calibration standards were prepared by homogenizing chemical reagents containing these 22 analytes using the concentration ranges of 166 ancient potteries and three clay materials from Japan. The calibration curves of these benchmark mixtures exhibited a good linearity (correlation coefficient, r = 0.990–1.000), accuracy, and reproducibility compared with those of other synthesized specimens and three reference standards. The lower limits of detection were less than tens of mg kg^?1 (e.g., 94 mg kg^?1 for Na₂O, 11 mg kg^?1 for P₂O₅, 1.1 mg kg^?1 for Rb, and 0.9 mg kg^?1 for Y). Using the present method, we determined 22 components in two prehistoric potteries from Japan. The advantage of this method is that only a small amount of sample is required, which can be prepared easily and rapidly and reused for other analyses. Copyright © 2012 John Wiley & Sons, Ltd.     

Ru(III), Os(VIII), Pd(II) and Pt(IV) catalysed oxidation of glycyl–glycine by sodium N‐chloro‐p‐toluenesulfonamide: comparative mechanistic aspects and kinetic modelling

The Ru(III)/Os(VIII)/Pd(II)/Pt(IV)‐catalysed kinetics of oxidation of glycyl–glycine (Gly‐Gly) by sodium N‐chloro‐p‐ toluenesulfonamide (chloramine‐T; CAT) in NaOH medium has been investigated at 308 K. The stoichiometry and oxidation products in each case were found to be the same but their kinetic patterns observed are different. Under comparable experimental conditions, the oxidation‐kinetics and mechanistic behaviour of Gly‐Gly with CAT in NaOH medium is different for each catalyst and obeys the underlying rate laws:

• Rate = k [CAT]_t [Gly‐Gly]⁰ [Ru(III)][OH^?]^x
• Rate = k [CAT]_t[Gly‐Gly]^x [Os(VIII)]^y[OH^?]^z
• Rate = k [CAT]_t[Gly‐Gly]^x [Pd(II)][OH^?]^y
• Rate = k [CAT]_t[Gly‐Gly]⁰ [Pt(IV)]^x[OH^?]^y

Here, and x, y, z < 1 in all the cases. The anion of CAT, CH₃C₆H₄SO₂NCl^?, has been postulated as the common reactive oxidising species in all the cases. Under comparable experimental conditions, the relative ability of these catalysts towards oxidation of Gly‐Gly by CAT are in the order: Os(VIII) > Ru(III) > Pt(IV) > Pd(II). This trend may be attributed to the different d‐electronic configuration of the catalysts. Further, the rates of oxidation of all the four catalysed reactions have been compared with uncatalysed reactions, under identical experimental conditions. It was found that the catalysed reaction rates are 7‐ to 24‐fold faster. Based on the observed experimental results, detailed mechanistic interpretation and the related kinetic modelling have been worked out for each catalyst. Copyright © 2008 John Wiley & Sons, Ltd.     

Structural,vibrational spectra and normal coordinate analysis for two tautomers of 4(5)‐(2′‐furyl)‐imidazole

We have synthesized both the 4 and 5 tautomeric forms of 4(5)‐(2′‐furyl)‐imidazole (1) and investigated their molecular vibrations by infrared and Raman spectroscopies as well as by calculation based on the density functional theory (DFT) approach. Examination of the temperature dependence of IR intensity revealed the band characteristics of the 4 and 5 tautomers of (1). Comparison of experimental and calculated chemical shifts in nuclear magnetic resonance (NMR) spectroscopy was made in order to identify the two tautomeric forms. The assignment of vibrational normal modes was performed, and the force field obtained reproduced the experimental vibrational wavenumbers with a root mean‐square deviation (RMSD) value of ca. 13 cm⁻¹ for both tautomers. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two tautomeric structures. Copyright © 2009 John Wiley & Sons, Ltd.     

Direct visual evidence for the chemical mechanism of surface‐enhanced resonance Raman scattering via charge transfer: (II) Binding‐site and quantum‐size effects

We describe quantum‐size and binding‐site effects on the chemical and local field enhancement mechanisms of surface‐enhanced resonance Raman scattering (SERRS), in which the pyridine molecule is adsorbed on one of the vertices of the Ag₂₀ tetrahedron. We first investigated the influence of the binding site on normal Raman scattering (NRS) and excited state properties of optical absorption spectroscopy. Second, we investigated the quantum‐size effect on the electromagnetic (EM) and chemical mechanism from 300 to 1000 nm with charge difference density. It is found that the strong absorption at around 350 nm is mainly the charge transfer (CT) excitation (CT between the molecule and the silver cluster) for large clusters, which is the direct evidence for the chemical enhancement mechanism for SERRS; for a small cluster the strong absorption around 350 nm is mainly intracluster excitation, which is the direct evidence for the EM enhancement mechanism. This conclusion is further confirmed with the general Mie theory. The plasmon peak in EM enhancement will be red‐shifted with the increase of cluster size. The influence of the binding site and quantum‐size effects on NRS, as well as chemical and EM enhancement mechanisms on SERRS, is significant. Copyright © 2009 John Wiley & Sons, Ltd.