X-ray and 1H nmr analyses of 5-(m-benzyloxybenzyl)-1-[(1,3-dihydroxy-2-propoxy)methyl]uracil, an acyclonucleoside inhibitor of uridine phosphorylase

The title compound crystallizes in the triclinic space group [Formula: see text] and the cell dimensions are a = 16.890(3), b = 9.586(2), c = 6.316(1) Å, α = 91.09(1), β = 93.50(1), γ = 93.04(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.056 for 3454 observed reflections. Adjacent six-membered rings are approximately perpendicular to one another. The glycosidic torsion angle [C(6)—N(1)—C(1′)—O(4′)] is 96.2(2)°. In the acyclic moiety, both C—OH bonds are gauche with respect to C(4′)—O(4′). The gauche conformation is also dominant in solution, as determined by high-resolution 1H nmr spectroscopy. Results of nuclear Overhauser experiments lead to conclusions about the flexibility of the molecule.

Solid state and solution conformations of 1 -(β-D-2′,3′-secoribofuranosyl)-5,6-dichlorobenzimidazole, an acyclonucleoside analogue

The title compound crystallizes in the monoclinic space group P21, with two independent molecules in the asymmetric unit (Z = 4). The unit cell dimensions are a = 11.861(2), b = 7.897(1), c = 14.527(3) Å, β = 91.28(1)°. X-ray intensity data were measured on a diffractometer, and the crystal structure was determined by direct methods. Least-squares refinement converged at R = 0.036 for 2980 reflections. The glycosidic torsion angle [C(2)—N(1)—C(1′)—O(1′)] is 53.9° in molecule A and 129.8° in molecule B. In both molecules, the orientation of C(1′)—O(1′) to C(2′)—O(2′) is trans. The conformations about C(3′)—C(4′) and C(4′)—C(5′) are different in each of the two molecules. These features are compared with those of acyclonucleoside analogues with antiviral activity. The conformation in aqueous medium was examined with the aid of high-resolution 1H nmr spectroscopy, and the results are compared with those obtained from the X-ray analysis.

The crystal and molecular structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil. A very short C≡C triple bond

The crystal structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil, an analog of the active antiherpes nucleoside 1-(β-D-arabinofuranosyl)thymine, was determined by X-ray diffraction. The compound crystallizes in the space group P212121 with a = 4.925(1), b = 14.326(2), c = 17.454 Å. Reflections were measured on a diffractometer and the structure was solved by direct methods. Least-squares refinement converged at R = 0.032 for 1159 observed reflections. The sugar ring exhibits an 3E or a C(3′)endo conformation with a pseudorotation angle P = 28.3° and puckering amplitude τm = 31.7°. The orientation of the —CH2OH side chain is g+. The base is in an anti conformation with respect to the sugar ring, with a glycosidic torsion angle χ = 33.7°. Changes in the C(5)—C(6) and C(6)—N(1) bond lengths suggest some interaction of the propynyl group with the pyrimidine ring. The C≡C bond length of 1.121 Å is very short. Its shortening could result from intermolecular interactions with the neighboring pyrimidine ring and nearby oxygen atoms.