The Pacific Northwest Consortium Collaborative Access Team (PNC-CAT) is constructing bending magnet and insertion device (ID) beamlines at the Advanced Photon Source. Both beamlines will be heavily used for XAFS and micro-XAFS experiments. This paper summarises their capabilities, and initial operational experience with the ID line. The ID beamline is based on APS undulator A, and has been running in an initial commissioning configuration since May 1997. Currently the undulator and monochromator energies can be scanned in synchrony for EXAFS measurements, and we have obtained focused beams as small as 0.7 micron using tapered capillaries. Initial testing has also begun on a MBE/UHV system for in-situ surface XAFS.

Obtaining accurate structural information on epitaxial films and interfaces is nowhere more critical than in semiconductor passivation layers, where details of the atomic structure and bonding determine the nature of the interface electronic states. Various non-destructive methods have been used to investigate the structure of films and interfaces, but their interpretation is model-dependent, leading occasionally to wrong conclusions. We have developed a new X-ray method for the direct determination of epitaxial structures, coherent Bragg rod analysis (COBRA). The usefulness of our technique is demonstrated by mapping, with atomic precision, the structure of the interfacial region of a Gd2O3 film grown epitaxially on a (100) GaAs substrate. Our findings reveal interesting behaviour not previously suggested by existing structural methods, in particular a lock-in of the in-plane Gd atomic positions to those of the Ga/As atoms of the substrate. Moreover, we find that the bulk stacking of the Gd2O3 atomic layers is abandoned in favour of a new structure that is directly correlated with the stacking sequence of the substrate. These results have important implications for Gd2O3 as an effective passivation layer for GaAs (ref. 7). Our work shows that the COBRA technique, taking advantage of the brilliance of insertion device synchrotron X-ray sources, is widely applicable to epitaxial films and interfaces.

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The paradigm of “detection-before-destruction” was tested for a metalloprotein complex exposed at room temperature to the high x-ray flux typical of third generation synchrotron sources. Following the progression of the x-ray induced damage by Mn Kβ x-ray emission spectroscopy, we demonstrated the feasibility of collecting room temperature data on the electronic structure of native Photosystem II, a trans-membrane metalloprotein complex containing a Mn4Ca cluster. The determined non-damaging observation timeframe (about 100 milliseconds using continuous monochromatic beam, deposited dose 1*107 photons/µm2 or 1.3*104 Gy, and 66 microseconds in pulsed mode using pink beam, deposited dose 4*107 photons/µm2 or 4.2*104 Gy) is sufficient for the analysis of this protein’s electron dynamics and catalytic mechanism at room temperature. Reported time frames are expected to be representative for other metalloproteins. The described instrumentation, based on the short working distance dispersive spectrometer, and experimental methodology is broadly applicable to time-resolved x-ray emission analysis at synchrotron and x-ray free-electron laser light sources.

Dissimilatory metal reducing bacteria (DMRB) can influence geochemical processes that affect the speciation and mobility of metallic contaminants within natural environments. Most investigations into the effect of DMRB on sediment geochemistry utilize various synthetic oxides as the Fe III source (e.g., ferrihydrite, goethite, hematite). These synthetic materials do not represent the mineralogical composition of natural systems, and do not account for the effect of sediment mineral composition on microbially mediated processes. Our experiments with a DMRB (Shewanella putrefaciens 200) and a divalent metal (Zn II ) indicate that, while complexity in sediment mineral composition may not strongly impact the degree of "microbial iron reducibility," it does alter the geochemical consequences of such microbial activity. The ferrihydrite and clay mineral content are key factors. Microbial reduction of a synthetic blend of goethite and ferrihydrite (VHSA-G) carrying previously adsorbed Zn II increased both [Zn II -aq] and the proportion of adsorbed Zn II that is insoluble in 0.5 M HCl. Microbial reduction of Fe III in similarly treated iron-bearing clayey sediment (Fe-K-Q) and hematite sand, which contained minimal amounts of ferrihydrite, had no similar effect. Addition of ferrihydrite increased the effect of microbial Fe III reduction on Zn II association with a 0.5 M HCl insoluble phase in all sediment treatments, but the effect was inconsequential in the Fe-K-Q. Zinc k-edge X-ray absorption spectroscopy (XAS) data indicate that microbial Fe III reduction altered Zn II bonding in fundamentally different ways for VHSA-G and Fe-K-Q. In VHSA-G, ZnO 6 octahedra were present in both sterile and reduced samples; with a slightly increased average Zn-O coordination number and a slightly higher degree of long-range order in the reduced sample. This result may be consistent with enhanced Zn II substitution within goethite in the microbially reduced sample, though these data do not show the large increase in the degree of Zn-O-metal interactions expected to accompany this change. In Fe-K-Q, microbial Fe III reduction transforms Zn-O polyhedra from octahedral to tetrahedral coordination and leads to the formation of a ZnCl 2 moiety and an increased degree of multiple scattering. This study indicates that, while many sedimentary iron minerals are easily reduced by DMRB, the effects of microbial Fe III reduction on trace metal geochemistry are dependent on sediment mineral composition.