Report of the Working Group on Synchrotron Radiation Nomenclature - brightness, spectral brightness or brilliance?
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Synchrotrons↗
Biomedical subjects
A Kvick
Publications and source records attributed to A Kvick.
A synchrotron-radiation study of the lactone form of rhodamine B at 120 K
The structure of the lactone form of rhodamine B, 3, 6-bis(diethylamino)-1',3'-dihydrospiro[xanthene-9, 3'-isobenzofuran]-1'-one, C(28)H(30)N(2)O(3), has been determined at 120 K using synchrotron radiation at a wavelength of 0.496 A. The structure contains two independent rhodamine B molecules with virtually identical geometry. The xanthene main planes of the molecules are inclined at an angle of 41.6 (2) degrees to one another. Molecule 2 has a statistically disordered ethyl group, with 71% in one orientation and 29% in a second orientation. The lactone C-O bonds are 1.497 (1) and 1.495 (1) A. There are no classical hydrogen bonds, but the structure is stabilized by two short C.O interactions. The crystals of the lactone form were produced by a novel hydrothermal reaction.
Journal Article↗
Physical estimation of triplet phases--effects of different radiation sources and modes for profile scans.
A comparative study has been made of the intensity profiles from three-beam experiments to estimate triplet phases using radiation from a conventional sealed-tube X-ray source and two different synchrotron sources. Synchrotron radiation, with its much smaller angular divergence, narrower spectral bandwidth and higher flux, distinctly improves the experimental conditions for physical phase estimation. Pure psi scans about the primary diffraction vector, such as can be made with a six-circle diffractometer, further improve the conditions compared with combined omega/psi scans with a four-circle instrument, where the rotation in psi is accomplished by combining rotations about the three axes omega, chi and varphi. Interference profiles collected by pure psi scans and unfocused synchrotron radiation have FWHM values reduced by factors in the range 20-35 relative to those obtained with combined omega-2theta/psi scans and radiation from a conventional source. As a consequence of these changes, which also involve greatly increased peak amplitudes, the 0/pi-type asymmetry of the profiles is exposed much more pronounced closer to the three-beam point, enabling unambiguous phase assignment for all triplets that were studied. The superiority of the pure psi scan will be even more important in studies of general phases for which the phase information lies also in the relative heights of the (sharp) interference maxima for a triplet and the Friedel-related triplet.
Journal Article↗
Protein Crystallography at Ultra-Short Wavelengths: Feasibility Study of Anomalous-Dispersion Experiments at the Xenon K-edge.
A protein crystallography experiment at the xenon K-edge (lambda = 0.358 A) has been successfully carried out at the materials science beamline (BL2/ID11) of the ESRF. The samples used in this methodological study were crystals of porcine pancreatic elastase, a 26 kDa protein of known structure. The diffraction data are of excellent quality. The combination of isomorphous replacement and anomalous dispersion of a single xenon heavy-atom derivative allowed accurate phase determination and the computation of a high-quality electron density map of the protein molecule. This is the first fully documented report on a complete protein crystallography experiment, from data collection up to phase determination and calculation of an electron density map, carried out with data obtained at ultra-short wavelengths. Experimental considerations as well as possible advantages and drawbacks of protein crystallography at very short and ultra-short wavelengths are discussed.
Journal Article↗
Time-resolved X-ray powder diffraction using a large-area CCD-based detector and Rietveld refinement: solid-state polymerization of S2N2 to (SN)x.
A kinetic study of the solid-state polymerization of disulfur dinitride (S2N2) to polysulfur nitride [(SN)x] has been performed, combining monochromatic high-energy (lambda = 0.3263 A) synchrotron radiation X-ray powder diffraction, a large-area (ø = 220 mm) CCD-based X-ray image-intensifier detector and Rietveld refinement. Recently developed techniques for detector calibration and reduction of two-dimensional images to one-dimensional diffraction patterns have been employed for data processing/analysis. Good fits were obtained after Rietveld refinement [Rp = 8.4%, wRp = 9.4%, sin(theta(max))/lambda = 0.585 A(-1)] of diffraction patterns of S2N2 from images with 2 s exposure time. The solid-state polymerization of S2N2 to (SN)x, was followed at a maximum rate of two diffraction images per minute. Scale factors and cell parameters for S2N2 and beta-(SN), as functions of time were readily obtained after Rietveld refinement of the diffraction patterns obtained from each individual image throughout the polymerization. The polymerization was preceded by a lattice distortion of S2N2, and at 50% conversion the a axis had decreased by about 1% and the c axis had increased about 1%. The polymerization yielded not only the expected polymer beta-(SN)x, but also a small amount of a compound that could be another phase of (SN)x.
Journal Article↗
Crystal structure study of (E)-3-(4-Nitrobenzyloxyimino)hexahydroazepin-2-one using synchrotron radiation.
NOHA, 3-(4-nitrobenzyloxyimino)hexahydroazepin-2-one, is a potent anticonvulsive agent. It occurs in two stereoisomers, the Z and E forms. (E)-NOHA is about 1.5 times more active than (Z)-NOHA. While accurate structural data are available for (Z)-NOHA, those for the E form have remained, until recently, highly speculative due to the lack of single crystals of suitable size for X-ray analysis and to the instability of the E isomer under radiation exposure. For structure-activity correlation purposes, efforts have been made to solve the crystal structure of the E isomer. Data collection from tiny needle crystals has been performed using synchrotron radiation. An initial molecular-packing model of this compound was obtained by energy-based and X-ray data modelling and successfully refined by molecular-dynamics methods: space group P2(1)/c, a = 6.225 (5), b = 17.885 (5), c = 12.157 (5) A, beta = 92.35 (5) degrees , R-factor = 3.5% for 343 reflections. In this contribution the crystal and molecular structure of (E)-NOHA is reported and the role of the hydrogen bond acting as the driving force in the intermolecular assembly in the (E)-NOHA crystal is highlighted.
Journal Article↗
The crystal structure of methyl beta-cellotrioside monohydrate 0.25 ethanolate and its relationship to cellulose II.
The crystal structure of methyl beta-cellotrioside (methyl O-beta-D-glucopyranosyl-(1-->4)-O-beta-d_guycopyranosyl-(1-->4)-be ta-D- glucopyranoside) complexed with water and ethanol, C19H34O16. H2O.0.25[C2H6O] was determined by combining Cu K alpha X-ray and synchrotron data collected at room temperature. The crystals have the monoclinic space group P21 with Z = 8 and unit cell parameters a = 7.9978(11), b = 76.38(4), c = 8.9908(6) A and beta = 116.40(1) degree. The structure, which was solved by direct methods and refined to a final R-factor of 0.067, contains four independent molecules of methyl beta-cellotrioside with an extended conformation. They are arranged parallel to the long b axis of the unit cell, and organized in two pairs of antiparallel molecules. Each beta-D-glucopyranosyl residue of the four independent molecules is in the 4C1 pyranose conformation, and each (O-6) primary hydroxyl group has the gt conformation. The crystal structure of methyl beta-cellotrioside has many points in common with that of cellotetraose hemihydrate as well as with the structure of cellulose II. Thus, it is likely that the precise atomic coordinates obtained in this study can be directly transposed to give an improved structure for cellulose II where, in particular, only the gt conformation would be present at the primary hydroxyl groups of both polysaccharide chains.
Carbohydrate Conformation↗
A model for vitamin B6--amino-acid-related metal complexes. Neutron diffraction study of aqua(N-salicylideneglycinato)copper(II) hemihydrate at 130 K.
A neutron diffraction study of aqua(N-salicylideneglycinato)copper(II) hemihydrate, [Cu(C9H7NO3)-(H2O)].0.5H2O, Mr = 267.7, a model for vitamin B6-amino-acid-related metal complexes, has been carried out at 130 K. Least-squares refinement based on 3800 reflections [(sin theta/lambda)max = 0.786 A-1] converged at R(F2) = 4.5%. The crystal is monoclinic, space group C2/c, Z = 8 with cell parameters at 130 K: a = 17.030 (3), b = 6.665 (1), c = 17.469 (5) A, beta = 111.13 (1) degree, V = 1849.50 A3. The bond distances between non-H atoms have been determined with estimated standard deviations in the range 0.0008-0.0012 A; the corresponding values for distances involving H atoms are 0.0017-0.0020 A. The presence of a Cu11 ion does not significantly change the bond distances around the alpha-C atom from those observed in glycine or glycylglycine. There are, however, indications of differences in distance and direction relative to the pi system for the two alpha-C-H bonds. These bond vectors are inclined at angles of 30 and 71 degrees to the plane of the conjugated pi system. A planar conjugated pi-system is stabilized by chelation to the Cu ion.
Amino Acids↗