R.B. Von Dreele

GSAS-II: the genesis of a modern open-source all purpose crystallography software package

The newly developed GSAS-II software is a general purpose package for data reduction, structure solution and structure refinement that can be used with both single-crystal and powder diffraction data from both neutron and X-ray sources, including laboratory and synchrotron sources, collected on both two- and one-dimensional detectors. It is intended that GSAS-II will eventually replace both the GSAS and the EXPGUI packages, as well as many other utilities. GSAS-II is open source and is written largely in object-oriented Python but offers speeds comparable to compiled code because of its reliance on the Python NumPy and SciPy packages for computation. It runs on all common computer platforms and offers highly integrated graphics, both for a user interface and for interpretation of parameters. The package can be applied to all stages of crystallographic analysis for constant-wavelength X-ray and neutron data. Plans for considerable additional development are discussed.

Addressing the Amorphous Content Issue in Quantitative Phase Analysis: The Certification of NIST Standard Reference Material 676a

A non-diffracting surface layer exists at any boundary of a crystal and can comprise a mass fraction of several percent in a finely divided solid. This has led to the long-standing issue of amorphous content in standards for quantitative phase analysis (QPA). NIST standard reference material (SRM) 676a is a corundum (α-Al(2)O(3)) powder, certified with respect to phase purity for use as an internal standard in powder diffraction QPA. The amorphous content of SRM 676a is determined by comparing diffraction data from mixtures with samples of silicon powders that were engineered to vary their specific surface area. Under the (supported) assumption that the thickness of an amorphous surface layer on Si was invariant, this provided a method to control the crystalline/amorphous ratio of the silicon components of 50/50 weight mixtures of SRM 676a with silicon. Powder diffraction experiments utilizing neutron time-of-flight and 25 keV and 67 keV X-ray energies quantified the crystalline phase fractions from a series of specimens. Results from Rietveld analyses, which included a model for extinction effects in the silicon, of these data were extrapolated to the limit of zero amorphous content of the Si powder. The certified phase purity of SRM 676a is 99.02% ± 1.11% (95% confidence interval). This novel certification method permits quantification of amorphous content for any sample of interest, by spiking with SRM 676a.

Extinction in time-of-flight neutron powder diffractometry

Time-of-flight data have been collected from polycrystalline specimens of magnesium oxide in which the grain size distribution is known. These data were obtained at scattering angles of 150, 90 and 60°. A primary extinction factor given in an analytical form by Sabine [Acta Cryst. (1988), A44, 368-373] is included in a Rietveld program. The experimental data from the two high-angle histograms are refined to give an effective mosaic block size and overall temperature factors. The effective mosaic block size is used in the calculation of an extinction factor for each reflection. This factor is then compared with the ratio of measured integrated intensities. The theoretical form of the extinction factor is verified to a level of 0.30. The temperature factors measured from each specimen are identical and in agreement with the best literature value.

Multipattern Rietveld refinement of protein powder data : an approach to higher resolution.

By using combinations of multiple protein powder diffraction patterns obtained from an image plate to a d-spacing of 2 A, which differ by solvent-induced and radiation-damage-induced lattice strains, the powder overlap problem is partially resolved in a stereochemically restrained Rietveld refinement. The results for hen egg white lysozyme (HEWL) include, for the first time with powder data, placement of a substantial number of water molecules and structural results that approach the quality normally obtained by single-crystal methods. This study explores the lattice strains induced by changes in salt concentration, changes in solvent pH and the effect of low-dose radiation damage. For HEWL, lattice strains are not monotonic, so that with increasing NaCl concentration (0.25–1.25 M) the a axis increases by ∼0.5%, while the c axis decreases by ∼1.5%, and this variation is pH dependent. Low-dose radiation damage similarly induces non-monotonic lattice strains, similar but smaller than those arising from increased salt concentration. The effect of using these powder data in a combined Rietveld analysis is effectively to deconvolute the overlapping reflections by differing shifts in their relative positions.

High-resolution powder X-ray data reveal the T6 hexameric form of bovine insulin

A series of bovine insulin samples were obtained as 14 polycrystalline precipitates at room temperature in the pH range 5.0-7.6. High-resolution powder X-ray diffraction data were collected to reveal the T6 hexameric insulin form. Sample homogeneity and reproducibility were verified by additional synchrotron measurements using an area detector. Pawley analyses of the powder patterns displayed pH- and radiation-induced anisotropic lattice modifications. The pronounced anisotropic lattice variations observed for T6 insulin were exploited in a 14-data-set Rietveld refinement to obtain an average crystal structure over the pH range investigated. Only the protein atoms of the known structure with PDB code 2a3g were employed in our starting model. A novel approach for refining protein structures using powder diffraction data is presented. In this approach, each amino acid is represented by a flexible rigid body (FRB). The FRB model requires a significantly smaller number of refinable parameters and restraints than a fully free-atom refinement. A total of 1542 stereochemical restraints were imposed in order to refine the positions of 800 protein atoms, two Zn atoms and 44 water molecules in the asymmetric unit using experimental data in the resolution range 18.2-2.7 Å for all profiles.

On the numerical corrections of time-of-flight neutron powder diffraction data.

Time-of-flight neutron powder diffraction data for NIST Standard Reference Materials have been used to study the adequacy of the peak profile model obtained from a convolution of back-to-back exponentials with a pseudo-Voigt function that is widely used in Rietveld refinement. It is shown that, while the empirical models for d-spacing (wavelength) dependence of Gaussian and Lorentzian components of the pseudo-Voigt function and rise exponent are satisfactory, the behavior of the decay exponent and peak positions demonstrate significant deviations, which can be corrected by numerical methods. The practical side of this process as implemented in GSAS and FULLPROF and the effect of the corrections on the Rietveld analysis results are discussed.

A scanning CCD detector for powder diffraction measurements

Several different approaches have traditionally been used for detection of X-ray powder diffraction patterns, including area detectors, point detectors and position-sensitive detectors. Each has advantages. This paper discusses use of a low-cost CCD detector attached to a diffractometer arm, where line-by-line readout of the CCD is coupled to continuous motion of the arm. When this type of detector is used and where X-ray optics are employed to focus the source image onto the detector plane both high-resolution and rapid measurements can be performed, with data collection over a complete 2θ range. This is particularly advantageous for synchrotron applications but valuable also for Guinier diffractometer laboratory instruments. Peak resolutions are shown to be moderately better than what can be obtained with a position-sensitive detector and significantly better than with an area detector. Many samples have intrinsically broadened peak shapes for which little improvement in data quality could be obtained with an analyzer-crystal detector. With comparable numbers of modules, these CCD data collection speeds can be close to those with position-sensitive detectors, but without the low-angle asymmetry seen in the latter.

Mechanical Design of a High-Resolution X-ray Powder Diffractometer at the Advanced Photon Source

A novel high-resolution x-ray powder diffractometer has been designed and commissioned at the bending magnet beamline 11-BM at the Advanced Photon Source (APS), Argonne National Laboratory (ANL). This state-of-the-art instrument is designed to meet challenging mechanical and optical specifications for producing high-quality powder diffraction data with high throughput. The 2600 mm (H) X 2100 mm (L) X 1700 mm (W) diffractometer consists of five subassemblies: a customized two-circle goniometer with a 3-D adjustable supporting base; a twelve-channel high-resolution crystal analyzer system with an array of precision x-ray slits; a manipulator system for a twelve scintillator x-ray detectors; a 4-D sample manipulator with cryo-cooling capability; and a robot-based sample exchange automation system. The mechanical design of the diffractometer as well as the test results of its positioning performance are presented in this paper.