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UBC Theses and Dissertations

The crystal and molecular structures of some inorganic, organic, and biological compounds Camerman, Norman


The crystal and molecular structures of cyanodi-methylarsine (cacodyl cyanide), diiodomethylarsine, and "cacodyl disulphide" (dimethylarsi.no dimethylditbioarsinate) have been determined by x-ray diffraction of single crystals, in order to investigate the stereochemistry of arsenic. The structure of cyanodimethylarsine was determined from projections along the three crystallographic axes. The central arsenic bond angle of 105° agrees well with that found in the halogendiphenylarsines, and is considerably larger than the value assumed in an electron-diffraction investigation of the corresponding dimethyl derivatives. There is an unusually short As….N inter-molecular separation, which is indicative of charge-transfer bonding involving donation of nitrogen lone pair electrons to vacant arsenic 4d-orbitals, which probably accounts for the solidity of the compound whereas the halogendimethylarsines are all liquid at room temperature. Diiodomethylarsine, one of the few simple arsenic derivatives which are solid at room temperature, was structurally determined from partial three-dimensional data in normal and generalized projections. Though severe absorption corrections had to be applied, values of the bond distances, valency angles, and intermolecular separations were obtained. The molecular structure of "cacodyl disulphide" was determined precisely, utilizing the full three-dimensional data, and the analysis revealed the compound to be dimethylarsino dimethyldithioarsinate, an unusual structure, having one trivalent and one pentavalent arsenic atom in the molecule. The former atom has a trigonal-pyramidal configuration, while the latter is roughly tetrahedral. There is an unusually short intermolecular As[superscript III].. .As[superscript III] separation which suggests charge-transfer bonding involving donation of lone pair electrons on each As[superscript III] to vacant 4d-orbitals on the other As[superscript III]. The structure of the alkaloid cleavamine, a product of the acidification of the Vinca rosea Linn alkaloid catharanthine, was determined from a three-dimensional x-ray analysis of cleavamine methiodide. The indole system is retained in cleavamine but the rest of the molecule undergoes rearrangement via bond fission, the result: being a tetracyclic alkaloid structurally resembling the known alkaloid quebrachamine. The presence of the iodide ion prevented accurate measurements of the bond distances and angles, but, the measurements were sufficiently precise to differentiate between the different types of bonds and angles. The absolute configuration of cleavamine was also established. The crystal and molecular structure of 5-iodo-2'-deoxy-uridine, the first anti-viral agent to have proven clinical chemotherapeutic value, was elucidated by a three-dimensional x-ray investigation. The bond lengths and angles in the nucleoside were determined accurately, and indicated that, the pyrimidine base is in the di-keto form. The deoxyribose ring is puckered with C2' displaced 0.59 Å from the plane of the other four atoms; the distances and angles in the sugar ring are all normal. The most significant intermolecular distance is an I....0 (carbonyl) separation of 2.96 Å; this is considerably shorter than the usual van der Waals contact (3.55 Å) and suggests charge-transfer bonding involving donation of oxygen lone pair electrons to vacant 5d-orbitals of the iodine atom. A strong intermolecular attraction of this type may be the cause of the increase in "melting temperature" observed when 5-iodo-2'-deoxyuridine is substituted for thymidine in DNA, and hence may be the molecular basis for the compound's anti-viral activity. A preliminary x-ray investigation was carried out: on crystals of sodium thymidylyl-(53')-thymidylate-(51). The cell constants and space group of the dinucleotide were determined, and the intensities of the three-dimensional diffraction maxima were recorded, but the absence of a relatively heavy atom made attempts at: a complete structural elucidation unsuccessful. A number of crystallographic computer programmes have been written for the IBM 1620 and 7040 computers; a list of these is given in an appendix.

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