Grant Bunker

Application of the ratio method of EXAFS analysis to disordered systems

Abstract When moderate disorder is present, the cumulant expansion/ratio method approach to EXAFS data analysis offers an attractive alternative to nonlinear least-squares fitting of the data. Analysis by nonlinear fitting, moment expansion, and cumulant expansion are compared, and useful formulae are derived. k-dependent mean free path is also treated.

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source.

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

An x-ray absorption study of the iron site in bacterial photosynthetic reaction centers.

Measurements were made of the extended x-ray absorption fine structure (EXAFS) of the iron site in photosynthetic reaction centers from the bacterium Rhodopseudomonas sphaeroides. Forms with two quinones, two quinones with added o-phenanthroline, and one quinone were studied. Only the two forms containing two quinones maintained their integrity and were analyzed. The spectra show directly that the added o-phenanthroline does not chelate the iron atom. Further analysis indicates that the iron is octahedrally coordinated by nitrogen and/or oxygen atoms located at various distances, with the average value of about 2.14 A. The analysis suggests that most of the ligands are nitrogens and that three of the nitrogen ligands belong to histidine rings. This interpretation accounts for several unusual features of the EXAFS spectrum. We speculate that the quinones are bound to the histidine rings in some manner. Qualitative features of the absorption edge spectra also are discussed and are related to the Fe-ligand distance.

A bent Laue analyzer for fluorescence EXAFS detection.

An analyzer for detection of fluorescence radiation was developed for fluorescence XAFS of dilute samples at energies above 13 keV. The analyzer is a bent Laue crystal of logarithmic spiral shape. The K fluorescence lines can be collected with a large solid angle and moderate reflectivity using the asymmetric [ 111 ] reflection of silicon crystals of 200 micron thick. Tuning of the analyzer diffraction energies for different samples can be made with one adjustment. Experiment was performed at the APS BioCAT ID bealrdine using a silicon crystal bent to an average radius of 200 mm to diffract silver fuorescence x-rays. The crystal (35 mm by 120 mm active area) covers a solid angle of 0.I SR of the sample fluorescence. The measured reflectivity was 10%.

The electronic structure in 3d transition metal complexes: Can we measure oxidation states?

We discuss the information on the electronic structure that can be obtained by K-shell absorption and emission spectroscopy in systems that contain 3d transition metals. We remind the reader that the chemical sensitivity of the X-ray absorption near edge structure (XANES) is strongly influenced by the local geometry. The X-ray fluorescence is mostly sensitive to the electronic structure and thus complementary to XANES.

Bent silicon crystal in the Laue geometry to resolve x-ray fluorescence for x-ray absorption spectroscopy

A highly strained, curved silicon crystal in the Laue geometry has been used as a large-area x-ray fluorescence analyzer for x-ray absorption spectroscopy. The analyzer is able to resolve the Lα fluorescence lines for neighboring actinide elements. A large gain in the signal to background ratio has been demonstrated for small quantities of Np in the presence of U, with the U fluorescence peak approaching 1000 times the magnitude of the off-peak background.

Modeling of pair distribution functions for XAFS in disordered systems

Abstract A commonly used expression for modeling the XAFS of highly disordered systems is shown to generate substantial systematic errors in the coordination number in many cases of practical interest. This expression is corrected and generalized. Further, a simpler and more flexible model distribution is proposed, and the corresponding XAFS expression is derived. Comparison with experimental and simulated data show that the new expressions are useful in cases of high disorder for which the cumulant expansion loses its utility, and they explicitly account for the k -dependence of the mean free path.

Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

Numerical modeling of tapered undulators

Abstract Tapered-undulator radiation will be used in at least one of the third generation synchrotron sources. While the spectral and angular characteristics of the radiation have been calculated for some specific configurations, the effects of tapering on the spectrum are still not well characterized. In this paper we have used an FFT-based method to calculate the spectral and angular distributions of the radiation from a tapered undulator with vertically-polarized magnetic field. The effect of tapering on the horizontal symmetry of the angular distribution of the radiation is investigated. A simple expression for the presence or absence of horizontal reflection symmetry as a function of the undulator parameters is derived. We have shown that for APS-type undulators and energies as high as 25 keV the radiation may be expected to exhibit horizontal reflection symmetry for observation angles up to 200 μrad. Our calculations are in agreement with recent measurements of the on-axis brightness of the prototype APS-CHESS undulator operated in the tapered configuration, and with results from well-established non-FFT programs.

New methods for EXAFS analysis in structural genomics

Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics. Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins.