Accurate experimental XAFS (X‐ray absorption fine‐structure) data including uncertainties are required during analysis for valid comparison of results and conclusions of hypothesis testing on ...structural determinations. Here an approach is developed to investigate data without standard interpolation of experimental data and with minimal loss of information content in the raw data. Nickel coordination complexes bis(i‐n‐propylsalicylaldiminato)nickel(II) (i‐pr) and bis(N‐n‐propylsalicylaldiminato)nickel(II) (n‐pr) are investigated. The additional physical insight afforded by the correct propagation of experimental uncertainty is used to determine newly refined structures for the innermost co‐ordination shell. Two sets of data are investigated for each complex; one optimized for high point accuracy and one optimized for high point density. Clearly both are important and in this investigation the quality of the physical insight from each is directly provided by measured and propagated uncertainties to fairly represent the relevant accuracies. The results provide evidence for an approximate tetrahedral geometry for the i‐pr Ni complex that is more symmetric than previously concluded, with our high point accuracy data yielding ligand lengths of 2.017 ± 0.006 Å and 2.022 ∓ 0.006 Å for Ni—N and Ni—O bonds, respectively, and an even more skewed square‐planar (i.e. rhombohedral) arrangement for the n‐pr complex with corresponding bond lengths of 2.133 ± 0.004 Å and 1.960 ∓ 0.003 Å. The ability to distinguish using hypothesis testing between the subtle differences in XAFS spectra arising from the approximate local tetrahedral and square‐planar geometries of the complexes is also highlighted. The effect of standard interpolation on experimental XAFS spectra prior to fitting with theoretical model structures is investigated. While often performed as a necessary step for Fourier transformation into position space, this will nonetheless skew the fit away from actual data taken, and fails to preserve the information content within the data uncertainty. The artificial effects that interpolation imposes on χr2 are demonstrated. Finally, a method for interpolation is introduced which locally preserves the χr2 and thus information content, when a regular grid is required, e.g for further analysis in r‐space.
An approach to investigate XAS data without standard interpolation of experimental data and with minimal loss of information content has been developed. The additional physical insight accorded by the correct propagation of experimental uncertainty has been used to determine newly refined structures for the innermost co‐ordination shell of Ni(II) coordination complexes.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
The most accurate measurements of the mass attenuation coefficient for metals at low temperature for the zinc K‐edge from 9.5 keV to 11.5 keV at temperatures of 10 K, 50 K, 100 K and 150 K using the ...hybrid technique are reported. This is the first time transition metal X‐ray absorption fine structure (XAFS) has been studied using the hybrid technique and at low temperatures. This is also the first hybrid‐like experiment at the Australian Synchrotron. The measured transmission and fluorescence XAFS spectra are compared and benchmarked against each other with detailed systematic analyses. A recent method for modelling self‐absorption in fluorescence has been adapted and applied to a solid sample. The XAFS spectra are analysed using eFEFFIT to provide a robust measurement of the evolution of nanostructure, including such properties as net thermal expansion and mean‐square relative displacement. This work investigates crystal dynamics, nanostructural evolution and the results of using the Debye and Einstein models to determine atomic positions. Accuracies achieved, when compared with the literature, exceed those achieved by both relative and differential XAFS, and represent a state‐of‐the‐art for future structural investigations. Bond length uncertainties are of the order of 20–40 fm.
High‐accuracy measurement of the X‐ray absorption fine structure (XAFS) of zinc metal in a temperature series from 10 K to 150 K, including 298 K, simultaneously in transmission and fluorescence using the hybrid technique is presented: the first transition metal XAFS using the hybrid technique and at low temperatures; and the first (hybrid‐like) experiment at the Australian Synchrotron. A methodology for relative measurements and a methodology for cryostat measurements, and an approach to normalization, calibration of transmission measurements for scattering and other systematics to reference room‐temperature data and yield a defined uncertainty are presented.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
3.
Solving self-absorption in fluorescence Trevorah, Ryan M; Chantler, Christopher T; Schalken, Martin J
IUCrJ,
07/2019, Volume:
6, Issue:
Pt 4
Journal Article
Open access
One of the most common types of experiment in X-ray absorption spectroscopy (XAS) measures the secondary inelastically scattered fluorescence photon. This widespread approach has a dominant ...systematic of self-absorption of the fluorescence photon. The large impact of self-absorption compromises accuracy, analysis and insight. Presented here is a detailed self-consistent method to correct for self-absorption and attenuation in fluorescence X-ray measurements. This method and the resulting software package can be applied to any fluorescence data, for XAS or any other experimental approach detecting fluorescence or inelastically scattered radiation, leading to a general solution applicable to a wide range of experimental investigations. The high intrinsic accuracy of the processed data allows these features to be well modelled and yields deeper potential insight.
We present a new technology for analyzing the molecular structure and in particular subtle conformational differences in Ni complexes using X-ray absorption spectroscopy (XAS), enabling tighter and ...more robust constraints of structure and dynamic bond lengths. Self-absorption and attenuating effects have a large impact in fluorescence X-ray absorption spectroscopy (XAS), compromising accuracy and insight in structural and advanced analyses. We correct for these dominant systematic effects. We investigate nickel(II) complexes, that is, bis(N-n-propyl-salicylaldiminato) nickel(II), “n-pr”, and bis(N-i-propyl-salicylaldiminato) nickel(II), “i-pr”, in 15 mM solutions with 0.1% w/w Ni. One is “square-planar” and one is “tetrahedral”, with identical coordination numbers. We identify two key sources of uncertainty and provide robust estimates for them, reflecting the quality of the data, and provide meaningful estimates of χ r 2 suitable for hypothesis testing. We apply significance and model testing for fluorescence data, with direct uncertainty estimates. Two new peaks are revealed in the X-ray absorption fine structure (XAFS) at k ≈ 4.4 and 5.4 Å–1. The high intrinsic accuracy of our processed data allows these features to be well modeled and yields deeper potential insight. Three important notions in the field are addressed: resolvability of shell radii, estimation of the number of independent data points in least-squares or Bayesian analysis, and the effect of uncertainties on the determined structure and the determinability of key structural parameters. Conventional XAFS fitting requires a k min and a k max. The origin of these limits is explained from the data, in a quantitative manner. Being able to distinguish the isomers spectroscopically and structurally places strong demands on the data, the uncertainties, and the model interpretation, and this article reports success in this subtle structural identification. Two nearby shellsthe innermost two shellsare identified quantitatively, well below the conventional aliasing limit. This illustrates the application of new technology to gain new insight.
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IJS, KILJ, NUK, PNG, UL, UM
The first X‐ray Extended Range Technique (XERT)‐like experiment at the Australian Synchrotron, Australia, is presented. In this experiment X‐ray mass attenuation coefficients are measured across an ...energy range including the zinc K‐absorption edge and X‐ray absorption fine structure (XAFS). These high‐accuracy measurements are recorded at 496 energies from 8.51 keV to 11.59 keV. The XERT protocol dictates that systematic errors due to dark current nonlinearities, correction for blank measurements, full‐foil mapping to characterize the absolute value of attenuation, scattering, harmonics and roughness are measured over an extended range of experimental parameter space. This results in data for better analysis, culminating in measurement of mass attenuation coefficients across the zinc K‐edge to 0.023–0.036% accuracy. Dark current corrections are energy‐ and structure‐dependent and the magnitude of correction reached 57% for thicker samples but was still large and significant for thin samples. Blank measurements scaled thin foil attenuation coefficients by 60–500%; and up to 90% even for thicker foils. Full‐foil mapping and characterization corrected discrepancies between foils of up to 20%, rendering the possibility of absolute measurements of attenuation. Fluorescence scattering was also a major correction. Harmonics, roughness and bandwidth were explored. The energy was calibrated using standard reference foils. These results represent the most extensive and accurate measurements of zinc which enable investigations of discrepancies between current theory and experiments. This work was almost fully automated from this first experiment at the Australian Synchrotron, greatly increasing the possibility for large‐scale studies using XERT.
The first X‐ray Extended Range Technique (XERT)‐like experiment at the Australian Synchrotron measured 496 energies from 8.51 keV to 11.59 keV for zinc metal to 0.023–0.036% accuracy. Systematics are quantified.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
High‐accuracy X‐ray mass attenuation coefficients were measured from the first X‐ray Extended Range Technique (XERT)‐like experiment at the Australian Synchrotron. Experimentally measured mass ...attenuation coefficients deviate by ∼50% from the theoretical values near the zinc absorption edge, suggesting that improvements in theoretical tabulations of mass attenuation coefficients are required to bring them into better agreement with experiment. Using these values the imaginary component of the atomic form factor of zinc was determined for all the measured photon energies. The zinc K‐edge jump ratio and jump factor are determined and results raise significant questions regarding the definitions of quantities used and best practice for background subtraction prior to X‐ray absorption fine‐structure (XAFS) analysis. The XAFS analysis shows excellent agreement between the measured and tabulated values and yields bond lengths and nanostructure of zinc with uncertainties of from 0.1% to 0.3% or 0.003 Å to 0.008 Å. Significant variation from the reported crystal structure was observed, suggesting local dynamic motion of the standard crystal lattice. XAFS is sensitive to dynamic correlated motion and in principle is capable of observing local dynamic motion beyond the reach of conventional crystallography. These results for the zinc absorption coefficient, XAFS and structure are the most accurate structural refinements of zinc at room temperature.
Zinc metal XAFS to high accuracy determined K‐edge jump ratio and jump factors, revealing significant issues in theory and experiment. Nanostructure of zinc is determined to high accuracy with bond lengths with uncertainties from 0.1% to 0.3% or 0.003 to 0.008 ÅA, suggesting local dynamic motion of the crystal lattice.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
E-cadherin plays a role in carcinogenesis. For two genetic polymorphisms in the gene (
CDH1) promoter, a reduced transcription has been reported: a C/A single nucleotide polymorphism (SNP) and a G/GA ...SNP at −160 bp and −347 bp, respectively, upstream of the transcriptional start site. We studied the association between both polymorphisms and the risk of bladder cancer.
One hundred and ninety-seven patients with bladder cancer and 344 population controls were genotyped and haplotyped for both SNPs.
A borderline significantly increased risk for bladder cancer was found for A allele carriers (OR 1.36; 95% CI: 0.96–1.94). We did not find any association between the –347 G/GA SNP and bladder cancer. Haplotype analyses did not yield much stronger associations with bladder cancer than the –160 C/A genotype analyses.
This study supports earlier suggestions that the –160 C/A SNP in the
CDH1 promoter is a risk factor for bladder cancer.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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