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[en] Following the seminal work of Von Dreele, powder X-ray diffraction studies on proteins are being established as a valuable complementary technique to single-crystal measurements. A wide range of small proteins have been found to give synchrotron powder diffraction profiles where the peak widths are essentially limited only by the instrumental resolution. The rich information contained in these profiles, combined with developments in data analysis, has stimulated research and development to apply the powder technique to microcrystalline protein samples. In the present work, progress in using powder diffraction for macromolecular crystallography is reported.
[en] A preliminary neutron crystallographic study of the proteolytic enzyme proteinase K is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the vapor-diffusion method. Data were collected to a resolution of 2.3 on the LADI-III diffractometer at the Institut Laue Langevin (ILL) in 2.5 days. The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure aimed at providing relevant information on the location of H atoms, particularly at the active site. This information will contribute to further understanding of the molecular mechanisms underlying proteinase K's catalytic activity and to an enriched understanding of the subtilisin clan of serine proteases
[en] 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-Al2O3) 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.
[en] Transient molecular structures along chemical reaction pathways are important for predicting molecular reactivity, understanding reaction mechanisms, as well as controlling reaction pathways. During the past decade, X-ray transient absorption spectroscopy (XTA, or LITR-XAS, laser-initiated X-ray absorption spectroscopy), analogous to the commonly used optical transient absorption spectroscopy, has been developed. XTA uses a laser pulse to trigger a fundamental chemical process, and an X-ray pulse(s) to probe transient structures as a function of the time delay between the pump and probe pulses. Using X-ray pulses with high photon flux from synchrotron sources, transient electronic and molecular structures of metal complexes have been studied in disordered media from homogeneous solutions to heterogeneous solution-solid interfaces. Several examples from the studies at the Advanced Photon Source in Argonne National Laboratory are summarized, including excited-state metalloporphyrins, metal-to-ligand charge transfer (MLCT) states of transition metal complexes, and charge transfer states of metal complexes at the interface with semiconductor nanoparticles. Recent developments of the method are briefly described followed by a future prospective of XTA. It is envisioned that concurrent developments in X-ray free-electron lasers and synchrotron X-ray facilities as well as other table-top laser-driven femtosecond X-ray sources will make many breakthroughs and realise dreams of visualizing molecular movies and snapshots, which ultimately enable chemical reaction pathways to be controlled.
[en] The element tellurium has a crystal structure made up of spiral chains of bonded atoms packed in a hexagonal array. Its symmetry leads to the existence of enantiomorphic forms containing spirals of opposite handedness, the right-handed one belonging to space group P3121 and the other to P3221, which have opposite optical rotatory powers. The normal methods of crystal structure determination cannot distinguish between the enantiomorphs, nor is this feasible using anomalous dispersion unless there is sufficient asphericity in the tellurium electron density due to bonding. Such asphericity also gives rise to small but measurable differences from unity in the flipping ratios for polarized neutron scattering due to the polarization dependence of the Schwinger scattering. This effect is easier to measure than is the intensity difference between Bijvoet pairs and it has been used to determine the absolute structural configuration that corresponds to a particular sense of optical rotation in a tellurium single crystal. The plane of polarization of the transmitted light rotates in the same sense as the bonded atoms in the spiral chains. This observation disagrees with a previous theoretical calculation based on the single polarizable ion model. (orig.)
[en] Bragg intensities from neutron and X-ray diffraction data of C60 single crystals were used to determine the nuclear- and electron-density distributions of C60 at room temperature. The anisotropic density distribution is reconstructed by the maximum-entropy method and evaluated in terms of symmetry-adapted spherical harmonics. From this analysis, the orientational probability density function f(ω) has been calculated and the rotational potential V(ω) that is experienced by a C60 molecule in the cubic surrounding at 295 K has been obtained. f(ω) shows strong deviations from the uniform orientational probability density function that would result from isotropic rotation. Accordingly, V(ω) exhibits well developed minima. The absolute potential minimum is found at an Euler-angle set ω1 and a second set of minima at slightly higher energy at ω2. The potential difference between V(ω1) and V(ω2) is 313 K, whereas the overall rotational potential barrier height amounts to 522 K. ω1 and ω2 are comparable with the major and minor orientations that are adopted by the molecules in their low-temperature arrangement. The angles ω1 and ω2 are fixed by the intrinsic geometry of the Euler-angle space (α, β, γ) under the combined action of the cubic site and the icosahedral molecular point group. (orig.)
[en] The viability of using the reverse Monte Carlo (RMC) method for quantitative analysis of the diffuse X-ray or neutron scattering from single crystals of disordered materials is investigated. The method has been applied to a number of two- and three-dimensional model examples in which both occupational and displacement disorder are present separately and in combination. While occupational or displacement disorder are each separately handled well, with the RMC simulation reproducing the input correlation structure of the models quite effectively, more difficulty was encountered when the different types of disorder were present in combination. In this case, it was necessary to employ a strategy where the occupation shifts and displacement shifts were carried out alternately with no more than 10% of the crystal being visited before switching between the two modes. It was also found to be advantageous to exclude all high-angle diffraction data when assessing occupation shifts. Furthermore, a new method of modelling distortions by swapping the displacements of two atom sites rather than shifting each atom individually was found to produce chemically more realistic bond-length distributions. (orig.)