[Crystallographic and molecular structure determination of beta-5-isopropyl-2'-deoxyuridine by x-ray diffraction and...

X-ray crystal structure determination of beta-5-isopropyl-2'-deoxyuridine was performed yielding a structure model at R = 0.061 for 992 data. C(8) terminal methyl carbon atom of the isopropyl moiety lies in the pyrimidine base plane while C(7) and C(9) is displaced from this plane by 0.2 and 1.59 A. The glycosidic torsion angle is 64.4 degrees corresponding to anti conformation. The O5' atom is placed in a gauche-gauche position with respect to O(1') and C(3'). Steric position of the isopropyl moiety suggests that is may considerably hinder development of base stacking in DNA synthesis due to the protruding C(9) atom. Conformation of the molecule was compared for similar structures in the Cambridge Structural Database in order to shed light on the occurrence of such peculiar alignment of bulky 5-substrates.