James C. Phillips

EXAFS study of alkali galliosilicate glasses

Abstract The extended X-ray absorption fine structure (EXAFS) of Na2OGa3SiO2 glasses of 3 compositional series containing either a constant Na2O or SiO2 content, or a constant Ga/Na ratio of 1.0, analogous crystalline compounds and 4 potassium-containing glasses were measured on the SUNY X21 beamline of the National Synchrotron Light Source at Brookhaven National Laboratory. The data were analyzed to extract Ga K-edge position, coordination numbers and GaO bond lengths for each glass composition. This study indicates that the GaO bond length is 1.83 A, and that the coordination number of oxygen about gallium is constant at 4, regardless of glass composition.

The SUNY X21 beamline at NSLS: A multi-use port on a dedicated high brightness synchrotron radiation source☆

Abstract The State University of New York is developing a beamline on the X-ray ring at NSLS, Brookhaven. The beamline has one part operating, at present. It has monochromator/mirror optics. There are two tandem experimental hutches. The upstream hutch contains diffractometry and X-ray spectroscopy apparatus. The downstream hutch houses a small angle scattering bench. Crystallography, spectroscopy, diffraction and scattering techniques can thus be used with the synchrotron source. Optical design is discussed with reference to the possibilities and constraints of bending magnet ports at NSLS and the requirements of the varied experimental program. Measurements made so far indicate that NSLS is indeed a high brightness X-ray source. High resolution edge spectra have been obtained of the “white line” at the L III edge of Ho and of Cu metal without slits in the beamline and with the expected structure resolved. This infers that the vertical opening angle of the X-ray beam appears dominated by the intrinsic opening angle of radiation from each electron with no further spreading from crossfire in the electron beam. For this particular measure of brightness the ring is thus as bright as it can be . The beam has been focused with a 1:1 bent toroidal mirror to a 1.5×1.5 mm (fwhm) focal spot. The horizontal focus correlates well with NSLS design parameters. The vertical height is not minimised but provides a symmetric beam for crystallography experiments. Measurements indicate little loss of energy resolution on focusing. These results are believed to be the first direct evidence of the achievement of high brightness in a synchrotron radiation X-ray source. Later measurements on other beamlines confirmed some of our conclusions about the source brightness. To demonstrate beamline performance, examples of results in crystallography, diffraction and spectroscopy are given.

A proposal for the metal geometry in yeast superoxide dismutase based on results from EXAFS spectroscopy.

Extended x-ray absorption fine structure (EXAFS) spectra have been recorded at the Cu edge and Zn edge in native yeast superoxide dismutase and at the Cu edge and Cd edge in the yeast superoxide dismutase derivative, where Zn has been substituted with Cd. Two different metal ligand distances in the range 1.9-2.0 A and 2.3-2.4 are determined for the Cu and Zn metals. For Cd in the Zn site two different metal ligand distances about 2.2 A and 2.6 A, respectively, were found. The striking feature is the similarity between the amplitude and radii determined for both the Cu and Zn sites. The increased distances for Cd can be explained by the increased ionic radius of Cd relative to Cu and Zn. Based on these EXAFS results and other relevant knowledge about the metal geometries, we propose that histidine 61 (63) positioned between the Cu and Zn metals are in one subunit bound to Zn and in the other to Cu. This model explains the recently observed difference between the two metal sites in each subunit.

A time-resolved scattering data acquisition system at the SUNY X21A beamline at NSLS

Abstract Details of a versatile data acquisition system for time-resolved X-ray scattering and diffraction experiments are presented. Specific examples from SAXS biophysics experiments are used to illustrate the capabilities of the system when coupled with focused X-rays from the SUNY X21A beamline at NSLS. Difficulties encountered with the time variation of the X-ray beam are discussed.

SUNY X3 beamline at NSLS

The State University of New York (SUNY) beamline at National Synchrotron Light Source [NSLS] has been moved to the X3 port during the NSLS Phase II shutdown. Additional floorspace and new equipment have enabled several changes and additions to the line to be made. There will be four sets of optics with independent operation. These will feed a short wavelength crystallography station, an x‐ray spectroscopy station, a time‐sharing crystallography/SAXS station, and a surface science chamber. The new design of the line is presented.

Application of X-ray absorption spectroscopy and anomalous small angle scattering to RNA polymerase

Abstract X-ray absorption spectroscopy is ideally suited for the investigation of the electronic structure and the local environment (≤ ∼ 5 A) of specific atoms in biomolecules. While the edge region provides information about the valence state of the absorbing atom, the chemical identity of neighboring atoms, and the coordination geometry, the EXAFS region contains information about the number and average distance of neighboring atoms and their relative disorder. The development of sensitive detection methods has allowed studies using near-physiological concentrations (as low as ∼ 100 μM). With careful choice of model compounds, judicious use of fitting procedures, and consideration of the results of biochemical and other spectroscopic results, this data has provided pivotal information about the structures of these active sites which store energy in their conformation changes or ligand exchanges. Although the application of anomalous small angle scattering to biomolecules has occurred more recently, it clearly provides a method of determining distances between active sites that are outside the range of X-ray absorption spectroscopy. The wavelength dependence of the X-ray scattering power varies rapidly near the edge of the absorbing atom in both amplitude and phase. This behavior selectively alters the contribution of the absorbing atom to the scattering pattern. The structure-function relationship of the intermediate states provide the key to understanding the mechanisms of these complex molecules. It is this precise structural information about the active sites that is not obtainable by other spectroscopic techniques. Combination of these techniques offers a unique approach to the determination of the organization of active sites in biomolecules, especially metalloenzymes. Application of these methods to the substrate and template binding sites of RNA polymerase which contain zinc atoms demonstrates the versatility of this approach.