Stereochemistry of nucleic acids and their constituents. XVII. Crystal and molecular structure of deoxycytidine 5'-phosphate monohydrate. Possible puckering for the furanoside ring in B-deoxyribonucleic acid

Abstract

The crystal structure of deoxycytidine 5'-phosphate monohydrate (5'-dCMP), C9H14N3O7PH2O, has been determined by X-ray diffraction techniques. Two entirely independent investigations were carried out.In one case, 1149 intensity data were collected by multiple-film equiinclination Weissenberg technique using CuKa radiation. In the other case, 1248 three-dimensional intensity data were collected on a four-circle diffractometer, also using Cu Ka radiation. In both cases the structure was refined by full-matrix least-squares techniques. The final R values for the two investigations were 0.070 (from film data) and 0.035 (from diffractometer data); in the latter case, when secondary extinction corrections were applied the R value was reduced to 0.023. The unit cell is orthorhombic, space group P212121, with average a = 6.786, b = 11.345, and c = 16.769 Á. The nucleotide exists as a zwitterion with N(l) protonated by one of the phosphate protons. A comparison of the geometries of the N(l)-protonated and neutral cytosine derivatives shows that there are marked differences in the bond angles and bond distances involving N(l), C(2), and C(4). A novel glycosyl torsion angle, -6.0°, and sugar conformation C(3')ex"-C(2 ')ex0, where both C(3') and C(2') are on the opposite side of C(5 0, are observed in 5 '-dCMP. The conformation about the C(4')-C(5') bond is gauche-gauche, the only conformation observed so far for the known 5 '-nucleotides. A correlation between the furanoside ring conformations and the glycosyl torsion angles is presented. All available hydrogens participate in the hydrogen bonds. The molecules related by the screw axis parallel to the a axis are linked together by pairs of hydrogen bonds, resulting in an infinitely extended spiral around the screw axis. The crystal structure can be considered essentially a close packing of these infinite spirals linked by hydrogen bonds to each other and the water of crystallization.

Three‐dimensional Hartree–Fock crystal‐orbital calculation on crystalline diprotonated deoxycytidine‐5′‐monophosphate monohydrate: Toward rationalizing nucleic acid semiconductivity

“…the cytosine acts mainly as an electron acceptor (from the phosphate) and once as an electron donor (to the water molecule); 3. the deoxyribose acts once as an electron acceptor (from the water molecule) and once as its donor ( t o the phosphate); and 4. the water molecule acts twice as an electron acceptor (from the phosphate and cytosine) and once as its donor ( t o the deoxyribose) . 25 Thus, there ought to be a strong deficiency in the charge density on the phosphate, a charge density excess on the cytosine residue and water molecule, and the zero charge on the deoxyribose, which is in full qualitative agreement with the present calculations (cf. the preceding section).…”

Crystal structures and conformations of 1-α-D-xylofuranosylcytosine and its protonated form (HCl salt)

“…Values of bond lengths in this portion of the cytosine ring are closely similar to those found in other protonated 1-substituted cytosines (35,(37)(38)(39)(40). Thus, relative to the parent 1, bonds C(2)-0(2) and C(4)-N (4) are shorter, and C(2)-N (3) and N(3)-C(4) slightly longer.…”

Structure and conformation of 3′-azido-3′-deoxythymidine (AZT), an inhibitor of the HIV (AIDS) virus

“…The most recent Cambridge Crystallographic Database (14), containing almost 600 nucleosides and nucleotides, lists only two structures with a furanose ring in a similar conformation ( P = 215 * 9"). In deoxycytidine 5'-phosphate, 5'-dCMP (15), and in 5'-methylthioadenosine, TMA (16), the ring pucker is also $T, the phase angles of pseudorotation, 213" and 216", respectively, being almost identical to that in molecule B in AZT. Interestingly, a low value of xc-(-6.0") was found in the N1-C6 bond eclipses C1'-04'.…”