Crystal structure of 2'-deoxycytidine hemidihydrogenphosphate reveals C+.C base pairs and tight, hydrogen-bonded (H2PO4-)infinity columns (1).
2'-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6(2) with a = 25.839(3), c = 12.529(1) A. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2'-deoxycytidine dimers and two H2PO4- anions. The C+.C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3) ... N(3) bonds being 2.850(7) and 2.884(5) A. The conformations of the four nucleosides fall in the same category (sugar puckers 2'-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H2PO4- anions are located on twofold axes and form two types of tight columns with P ... P separations about 4.18 A. The neighboring units along a column are linked via two very short O ... H ... O hydrogen bonds (O ... O about 2.49 A) leading to effective equalization of the P-O bonds. The base pairs of the two dC+.dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through O(5') ... O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H ... O-P and O(3')-H ... O-P] to the phosphate groups.
Jaskólski
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Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland.
Gdaniec
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M
Gilski
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Alejska
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Bratek-Wiewiórowska
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MD
D001482:Base Composition; D002412:Cations; D003460:Crystallization; D018360:Crystallography, X-Ray; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry*; D017550:Spectroscopy, Fourier Transform Infrared
D002412:Cations; D010710:Phosphates; D003841:Deoxycytidine