The determination and refinement of the molecular structures of some organic compounds
Creators: name: Fawcett, John Keith
Publisher: name: University of British Columbia
Year: 2011

description: The molecular structures of two polynuclear aromatic hydrocarbons, biphenylene and coronene, have been refined from new three-dimensional data. The positional and thermal parameters of the carbon and hydrogen atoms were refined by least squares and the gross features of the structures, previously determined, were confirmed. The anisotropic thermal parameters of the carbon atoms were interpreted in terms of rigid-body vibrations, and the measured carbon-carbon bond lengths were then corrected for rotational oscillation effects. The bond lengths for biphenylene reinforce the conclusion that the molecule must be considered as a cyclobutane derivative. The bonds joining the six-membered rings measure 1.514 ± 0.003Å, and the bonds in the six-membered rings, starting with the bond in the four-membered ring, are 1.426 + 0.003Å, 1.372 ± 0.002Å, 1.423 ± 0.003Å, and 1.385 ± 0.004Å. The molecule situated at a centre of symmetry is planar, the other molecule is slightly non-planar as a result of crystal packing forces. All intermolecular contacts correspond to normal van der Waals interactions. For coronene, the bond lengths measure 1.425 ± 0.004Å in the centre ring, 1.433 ± 0.004Å for the "spokes", 1.346 ± 0.005Å and 1.415 ± 0.003Å for the two types of outer bond. Only the shortest bonds (1.346Å) are significantly less than the theoretical values predicted by valence-bond and molecular-orbital calculations and, since this discrepancy is observed also for all other polynuclear aromatic hydrocarbons for which accurate bond distances are available, an amended order/length correlation curve is suggested which improves the agreement between theory and experiment for these shorter bonds. Small, but significant, deviations from planarity, which reduce the molecular symmetry from 6/mmm to 3, may be a result of either intra- or inter-molecular forces. All intermolecular separations correspond to van der Waals interactions; the perpendicular distance between the molecular planes is 3.46Å. The crystal and molecular structure of the hydroiodide of 1,2-0-aminoisopropylidene-∝-D-glucopyranose has been determined. The iodine position was located by Patterson methods, and all carbon, nitrogen and oxygen atoms were found on successive three-dimensional electron-density distributions. The positional and isotropic thermal parameters of the seventeen I, C, N, O, atoms in the asymmetric unit were refined by least squares. The configuration of the asymmetric dioxolane 2-car-bon atom was determined and the absolute configuration is established since the compound is derived from V-glucose. The five-membered ring has an envelope conformation with C(7) displaced from the plane of the other four atoms, and the pyranose ring has a twisted chair conformation. The bond distances and valency angles are normal. The crystal is held together by a system of O-H...O, N-H...O, and O-H...I hydrogen bonds. To investigate the structure of an intermediate in an attempted removal of the 14∝-methyl group of 3-β-acetoxylanost-8-ene, the structure of the dibromo derivative of the intermediate has been determined by X-ray analysis. The bromine positions were determined by Patterson methods and all carbon and oxygen atoms were located on successive three-dimensional electron-density distributions. Positional and anisotropic temperature parameters were refined by least squares. The absolute configuration was determined by the anomalous dispersion method. The derivative is 3-β-acetoxy-7∝,11∝-dibromolanostane-8∝,9∝-epoxide. Steroid ring A is in the normal chair form and ring D has a half-chair conformation. The epoxide prevents rings B and C from adopting the chair form. The bond lengths and valency angles are normal, and the intermolecular separations correspond to van der Waals interactions.