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Influence of fluorine substitution on the molecular conformation of 3′‐deoxy‐3′‐fluoro‐5‐methyluridine
Author(s) -
Aher Manisha N.,
Erande Namrata D.,
Kumar Vaijayanti A.,
Fernandes Moneesha,
Gonnade Rajesh G.
Publication year - 2020
Publication title -
acta crystallographica section c
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.304
H-Index - 17
ISSN - 2053-2296
DOI - 10.1107/s2053229620003083
Subject(s) - pseudorotation , furanose , chemistry , crystallography , orthorhombic crystal system , molecule , stereochemistry , ring (chemistry) , fluorine , hydrogen bond , crystal structure , alkane stereochemistry , cyclohexane conformation , organic chemistry
Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3′‐deoxy‐3′‐fluoro‐5‐methyluridine ( R T F ), C 10 H 13 FN 2 O 5 , we studied its stereochemistry in the crystalline state using X‐ray crystallography. The compound crystallizes in the chiral orthorhombic space group P 2 1 2 1 2 1 and contains two symmetry‐independent molecules ( A and B ) in the asymmetric unit. The furanose ring in molecules A and B adopts conformations between envelope ( 2 E, 2′‐ endo , P = 162°) and twisted ( 2 T 3 , 2′‐ endo and 3′ exo , P = 180°), with pseudorotation phase angles ( P ) of 164.3 and 170.2°, respectively. The maximum puckering amplitudes, ν max , for molecules A and B are 38.8 and 36.1°, respectively. In contrast, for 5‐methyluridine ( R T OH ), the value of P is 21.2°, which is between the 3 E (3′‐ endo , P = 18.0°) and 3 T 4 (3′‐ endo and 4′‐ exo , P = 36°) conformations. The value of ν max for R T OH is 41.29°. Molecules A and B of R T F generate respective helical assemblies across the crystallographic 2 1 ‐screw axis through classical N—H…O aand O—H…O hydrogen bonds supplemented by C—H…O contacts. Adjacent parallel helices of both molecules are linked to each other via O—H…O and O…π interactions.