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UBC Theses and Dissertations

Structure determination of some organic, inorganic and organometallic compounds by X-ray diffraction Gibbons, Cyril Stephen


The structures of four compounds representing each of the organic (natural product), inorganic and organometallic classes of compounds have been determined by single-crystal X-ray diffraction, and the methods employed in solution of the structures have been discussed briefly. For all four structures, the intensity data were collected on a single-crystal diffractometer with [formula omitted] radiation and a scintillation counter. The structure of the alkaloid, daphmacrine methiodide (acetone solvate), was determined from heavy-atom Patterson and Fourier syntheses, and refined by block-diagonal least-squares methods to a final R value of 0.089 for 1834 observed reflections. The absolute configuration was determined by the anomalous dispersion method. The molecule consists of two cage-structures which are linked by a chain of two carbon atoms, and the bond lengths and valency angles do not differ from normal values. 2 4-, For both exo-tricyclo [formula omitted] silver nitrate and silver nitrate itself, the silver ion was determined from Patterson syntheses to be lying in a pseudo-special position, so that the resulting electron-density maps exhibited pseudo-symmetry. A trial-and-error method based on detailed study of the shape of the Ag-Ag Patterson peaks was adopted to find the exact location of the silver ions, and from the resulting electron-density maps the true light atom peaks could be discerned from their images. The refinement was carried out by full-matrix least-squares, and the final R for the complex of silver nitrate was 0.105 and for silver nitrate was 0.067. The structure of the complex consists of thick layers perpendicular to the a crystallographic axis, and separated by ½ a. The silver ion is coordinated roughly tetrahedrally to the double bond of the hydrocarbon (in the exo-position, [formula omitted]), and to three nitrate groups [formula omitted]. The layers are held together by van der Waals forces. The silver nitrate structure consists of layers of silver ions parallel to the b crystallographic axis, and separated by ½ b, with the nitrate groups bridging the gap between layers. Previously observed inequalities in the N—O distances have been removed, all three bond lengths in the nitrate ion being 1.26 (l)Ǻ. The anisotropic thermal motion has been described. The N,N-dimethyl(ferrocenylmethyl)ammonium tetrachlorozincate hydrate structure contains seven heavy atoms, and it was not possible to resolve the Patterson peaks because of the overlap. A direct sign-determining procedure was employed to locate the heavy atoms, and the light atoms were located from resulting electron-density maps. The structure was refined to a final R value of 0.068 for 2012 observed reflections. The mean bond distances are Fe-C = 2. 04Ǻ and C-C (cyclopentadienyl rings) = 1.43Ǻ. Groups of four cations, two anions and two water molecules (two formula units), are linked around centres of symmetry by N-H...Cl (3.11Ǻ), N-H...0 (2.76Ǻ) and 0-H...Cl (3.05, 3.17Ǻ) hydrogen bonds.

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