The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a highperformance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, ®ber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.
X-ray absorption fine structure spectroscopy (XAFS) is a powerful and versatile technique for studying structures of materials in chemistry, physics, biology and other fields. This textbook is a comprehensive, practical guide to carrying out and interpreting XAFS experiments. Assuming only undergraduate-level physics and mathematics, the textbook is ideally suited for graduate students in physics and chemistry starting XAFS-based research. It contains concise executable example programs in Mathematica 7. Supplementary material available at www.cambridge.org/9780521767750 includes Mathematica code from the book, related Mathematica programs, and worked data analysis examples. The textbook addresses experiment, theory, and data analysis, but is not tied to specific data analysis programs or philosophies. This makes it accessible to a broad audience in the sciences, and a useful guide for researchers entering the subject.
An EXAFS study on the oxidized and reduced forms of cytochromes c' from Rhodospirillum rubrum and Rhodospirillum molischianum was performed at pH 7. The cytochromes c' have an apparent coordination number of 5 in both oxidation states. Average Fe-ligand bond lengths of 2.02 +/- 0.025 and 2.06 +/- 0.025 A are obtained in their oxidized and reduced forms, respectively. By use of suitable values for the Fe-NHis bond length and Fe out-of-plane displacement, as determined by small molecule crystallographic techniques, the Fe-Npyrrole bond lengths and the porphyrin center-to-Npyrrole distance have been estimated for cytochrome c' in both of its oxidation states. With this model, estimates of the Fe-Npyrrole bond lengths are 2.01 +/- 0.03 and 2.05 +/- 0.03 A, for the oxidized and reduced cytochromes c', respectively. The center-to-Npyrrole distance is estimated to be 1.99 +/- 0.03 A for oxidized cytochrome c' and 2.03 +/- 0.03 A for reduced cytochrome c'.
Extended X-ray absorption fine structure (EXAFS) analysis of zinc sorption on montmorillonite showed that different types of surface complexes or surface precipitates were formed depending on the reaction time. With an initial zinc concentration of 10(-3) M at neutral pH, zinc remained octahedrally coordinated with about six oxygen atoms at Zn-O bond distances of 2.02-2.07 A for up to six months. For samples aged up to 11 days, the Zn-Zn contribution in the second shell suggested formation of multinuclear surface complexes or surface precipitates. For samples aged 20 days and more, Zn-Zn and Zn-Si contributions in the second shell suggested formation of mixed metal coprecipitates such as a Zn phyllosilicate-like phase. Formation of these mixed metal solids probably accounts for the slow continuous sorption reaction at aging times exceeding 20 days. Sequestration of Zn in mixed metal precipitates and the stability of these phases can reduce the concentration, mobility, and toxicity of Zn in soils or sediments.
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.
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