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UBC Theses and Dissertations

The determination and refinement of the molecular structures of some organic compounds by single crystal x-ray diffraction Camerman, Arthur


The crystal and molecular structure of perylene has been refined from new three-dimensional data, confirming the gross features of the structure previously determined from two projections. The positional and thermal parameters of the carbon atoms have been refined by least-squares and differential syntheses and the hydrogen atoms have been approximately located. There are small but significant deviations from a completely planar arrangement; seemingly a result of slight intermolecular steric effects. A comparison of the measured bond lengths with those predicted by the valence-bond and molecular-orbital theory shows fairly close agreement with both sets of figures; the peri-bond lengths are 1.471-0.005 Å. In a similar vein the molecular structure of pyrene was refined by least-squares and differential synthesis treatment of new three-dimensional data. The thermal motion of the atoms was found to be anisotropic and was interpreted in terms of rigid body vibrations. Small corrections were made to the bond lengths to correct errors due to rotational oscillations. The general variation of the mean bond distances is in agreement with trends predicted by valence-bond and molecular-orbital calculations, but the individual agreements are not very good. The molecule is slightly non-planar, probably as a result of crystal packing forces. Hydroformylation of tri-O-acetyl-D-glucal yields two isomeric products and, to establish the configurations, X-ray analysis of the p-bromobenzenesulphonyl derivative of one of these has been carried out. The bromine and sulphur positions were determined from the three-dimensional Patterson function and the other atoms were located from successive three-dimensional Fourier summations. Refinement was carried out by least-squares methods. The derivative studied is 1-0-(p-bromobenzenesulphonyl)-4,5,7-tri-0-acetyl-2, 6-anhydro-3-deoxy-b-glucoheptitol, and this establishes the configurations of the triacetyl derivatives and parent polyols. The sugar ring is in the chair position with all substituents equatorial. 10-Chloro-5,10-dihydrophenarsazine crystallizes from xylene with half a molecule of xylene of crystallization in a monoclinic space group. This material rapidly loses the solvent of crystallization, the solvent-free crystals being orthorhombic. The complete structure of the orthorhombic crystals has been determined using Patterson methods to determine the arsenic and chlorine positions and a three-dimensional electron-density distribution map to locate the other atoms. All the positional and anisotropic thermal parameters were refined by least-squares. The molecule is slightly folded about the As-N axis, the angle between the two o-phenylene groups being 169°, and the chlorine atom being outside this angle. The deviation from planarity is thus not very large and it is unlikely that geometrical isomers could be isolated.

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