Structure of nucleoside analogs 3'-fluoro-2',3'-dideoxyuridine, 3'-fluoro-2',3'-dideoxy-5-bromouridine and 3'-azido-2',3'-dideoxy-5-bromouridine

摘要

(I) 1-(3-Fluoro-2,3-dideoxy-beta-D-erythropentofuranosyl)uracil, C9H11FN2O4, M(r) = 230.20, monoclinic, P2(1), a = 9.046 (5), b = 6.994 (4), c = 15.826 (8) angstrom, beta = 101.19 (4)-degrees, V = 982.3 (9) angstrom 3, Z = 4, D(m) = 1.56, D(x) = 1.557 Mg m-3, lambda(Mo K-alpha radiation) = 0.71073 angstrom, mu = 0.127 mm-1, F(000) = 480, T = 290 K, final R = 0.029 for 1495 unique observed reflections. The asymmetric unit contains two molecules (A and B). For molecule A: the N-glycosidic torsion angle chi has a value of -121.1 (2)degrees in the anti range; the sugar pucker is 2E with P = 165 (1)degrees and psi-m = 35 (1)degrees and the C4'-C5' conformation is + sc (synclinal) with gamma = 51.3 (3)degrees. For molecule B: the N-glycosidic torsion angle chi has a value of -150.5 (2)degrees in the anti range; the sugar pucker is 2(3)T with P = 176 (1)degrees and psi-m = 26 (1)degrees and the C4'-C5' conformation is + sc with gamma = 47.4 (3)degrees. (II) 1-(3-Fluoro-2,3-dideoxy-beta-D-erythropentofuranosyl)-5-bromouracil, C9H10BrFN2O4, M(r) = 309.09, monoclinic, P2(1), a = 5.701 (4), b = 18.192 (9), c = 10.538 (5) angstrom, beta = 95.67 (5)degrees, V = 1088 (1) angstrom 3, Z = 4, D(m) = 1.89, D(x) = 1.888 Mg m-3, lambda(Mo K-alpha) = 0.71073 angstrom, mu = 3.759 mm-1, F(000) = 616, T = 290 K, final R = 0.034 for 1597 unique observed reflections. The asymmetric unit contains two molecules (A and B). For molecule A: the N-glycosidic torsion angle chi has a value of -168.8 (6)degrees in the anti range; the sugar pucker is 3(2)T with P = 179 (1)degrees and psi-m = 31 (1)degrees and the C4'-C5' conformation is + sc with gamma = 53.9 (9)degrees. For molecule B: the N-glycosidic torsion angle chi has a value of -131.8 (7)degrees in the anti range; the sugar pucker is 2E with P = 161 (1)degrees and psi-m = 35 (1)degrees and the C4'-C5' conformation is + sc with gamma = 51.2 (9)degrees. (III) 1-(3-Azido-2,3-dideoxy-beta-D-erythro-pentofuranosyl)-5-bromouracil, C9H10BrN5O4, M(r) = 332.11, monoclinic, P2(1), a = 5.858 (3), b = 11.813 (6), c = 17.757 (9) angstrom, beta = 92.70 (4)degrees, V = 1227 (1) angstrom 3, Z = 4, D(m) = 1.80, D(x) = 1.797 Mg m-3, lambda(Mo K-alpha) = 0.71073 angstrom, mu = 3.332 mm-1, F(000) = 664, T = 290 K, final R = 0.027 for 1713 unique observed reflections. The asymmetric unit contains two molecules (A and B). For molecule A: the N-glycosidic torsion angle chi has a value of -168.4 (4)degrees in the anti range; the sugar pucker is 3T4 with P = 203 (1)degrees and psi-m = 33 (1)degrees and the C4'-C5' conformation is ap (antiperiplanar) with gamma = 50.5 (7)degrees. All the conformational parameters are in accordance with the IUPAC-IUB Joint Commission on Biochemical Nomenclature [Pure Appl. Chem. (1983), 55, 1273-1280] guidelines. Base-pair formation occurs in each of the three crystal structures.