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UBC Theses and Dissertations

Determination of the crystal structure of three organic compounds by X-ray diffraction Schaffrin, Roger Michael


The crystal structure of dibenzothiophene has been determined by X-ray diffraction. Mo-Kα [subscript omitted] scintillation counter data were used for this analysis; the sulfur atom position was determined by means of a Patterson function; the carbon atoms were located from a Fourier synthesis, and the hydrogen atoms, from a difference synthesis. Refinement of positional and thermal parameters was by least-squares methods. The molecule is slightly folded, the dihedral angles between the five-membered ring and the six-membered rings being 0.4° and 1.2°. The bond distances and valency angles are similar to those in related molecules. The C-S bond length is 1.740 A, and the C-S-C angle is 91.5°. The crystal structure of DL-ornithine hydrobromide has been determined by means of visual Cu-Kα [subscript omitted] data. The bromine ion position was found by Patterson methods; carbon, nitrogen, and oxygen atoms were located on Fourier summations and the hydrogen atoms, on a difference synthesis. The positional and thermal parameters were refined by least-squares. The ornithine molecule is a zwitterion, with both nitrogens accepting protons. The mean bond distances are C-0, 1.249 A; C-N, 1.469 A; C-C, 1.532 A. The structure is held together by a system of N—H …… 0 (2.84, 2.84, 2.89 A) and N—H…..Br (3.29, 3.36,.3.46 A) hydrogen bonds. The crystal and molecular structure of histamine diphosphate monohydrate has been determined with scintillation counter Mo-Kα [subscript omitted] data. The positions of the phosphorus atoms were determined by Patterson methods; the carbon, nitrogen and oxygen atoms were located by means Fourier syntheses; the hydrogen atoms were found on a difference synthesis. The thermal and positional parameters were refined by least-squares. The atoms of this histamine cation lie in two almost perpendicular planes, the plane of the imidazole ring and that of the side chain. The bond lengths and angles are similar to the corresponding values in histidine hydrochloride monohydrate. The dimensions of the two P0₂(OH) ₂⁻ ions are P-0 1.51 A, P-OH 1.57 A, O-P-0 115.5°, and HO-P-OH 107.0°. The most important feature of the packing is a complex system of 0-H.....0 and N-H...0 hydrogen bonds.

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