A Structural Analysis of Three Arabinosylpyrimidines

Citation

Sherfinski, James Stanley (1974) A Structural Analysis of Three Arabinosylpyrimidines. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/vc0r-8820. https://resolver.caltech.edu/CaltechTHESIS:06042021-210930114

Abstract

The crystal structures of three arabinosylpyrimidines are presented. Crystals of 1-β-D-arabinofuranosylcytosine hydrochloride are monoclinic, space group P2₁, with cell dimensions a = 6.540(2) Å, b = 15.260(2) Å, c = 6.758(3) Å, and β = 117.68(3)^o; Z = 2. The original structure solution was by Patterson-Fourier techniques; a second method of solution is presented which takes advantage of the chloride ion being an anomalous scatterer in a centrosymmetric array. Full-matrix least-squares refinement yielded a final R index of 0.022 for 2490 data; the estimated positional standard deviation of a carbon atom is 0.002 Å. The cation is in the gauche-trans and C(2')-endo conformations; the glycosidic torsion angle Ø_cn is 26.7°, Using the anomalous scattering of Cl-, O, and N in CuK∝ radiation, the absolute configuration of the sugar ring was determined,

The compound 1-β-D-arabinofuranosyluracil crystallizes in the orthorhombic space group P2₁2₁2₁ with cell dimensions a = 6.888(2) Å, b = 20.973(5) Å, c = 6.826(3) Å, and Z = 4. Solution was again by Patterson methods, and the structure was refined by full-matrix least squares to a final R index of 0.030 for 2034 counter-collected data (λ(CuK∝) = 1.5418Å). The estimated positional standard deviation of a carbon atom is 0,002 Å, The absolute configuration of this molecule was also established, this time using only O and N as anomalous scatterers. The sugar is in the C(2')-endo, gauche-gauche conformation which is stabilized by an intramolecular 0(2')...0(5') hydrogen bond. The glycosidic torsion angle is 35.0°.

The nucleotide 1-β-D-arabinofuranosylcytosine-5'monophosphate crystallizes from water in space group P2₁2₁2₁ as the trihydrate; there are four formula units per unit cell of dimensions a = 17.531(3) Å, b = 18.252(4) Å, c = 4.816(1)Å. Initial solution attempts centered on interpreting a projection Patterson map calculated with Beevers-Lipson strips and film data. Ultimately the structure solution was accomplished utilizing information from both a three-dimensional Patterson map and a direct methods solution in which no enantiomorph discrimination had been done. Least squares refinement was halted at R = 0.046 for 1859 diffractometer data; the estimated standard deviation in 0 the position of a carbon atom is 0.004 Å. The absolute configuration of the arabinose was determined utilyzing the anomalous scattering properties of P, O, and N in CuK∝. radiation. The sugar is in the C(3')-endo, gauche-gauche conformation; the glycosidic torsion angle is 30.7°.

For the three nucleotides and nucleosides studied, the glycosidic torsion angle is restricted to a very narrow range of values, whereas three quite different sugar conformations are exhibited. The results indicate that arabinofuranosylpyrimidines can with little effort conform to the same geometrical descriptions calculated for ribo- and deoxyribofuranosylpyrimidines in double-helical nucleic acid structures.

Thesis Files