3′-O-Acetyl-2′-deoxyuridine

In the two independent but very similar molecules of the title compound, C11H14N2O6, both nucleobase fragments are nearly planar (both within 0.01 Å) while the furanose rings exhibit 2 E-endo envelope conformations. In the crystal, the two 3′-O-acetyl-2′-deoxyuridine molecules form a pseudosymmetric dimer of two bases connected via two nearly identical resonance-assisted N—H⋯O hydrogen bonds. The resulting pair is further connected with neighboring pairs via two similar O—H⋯O bonds involving the only hydroxyl group of the 2′-deoxyfuranose fragment and the remaining carbonyl oxygen of the nucleobase. These interactions result in the formation of an infinite ‘double band’ along the b axis that can be considered as a self-assembled analogue of a polynucleotide molecule with non-canonical Watson–Crick base pairs. The infinite chains of 3′-O-acetyl-2′-deoxyuridine pairs are additionally held together by C—H⋯O interactions involving C atoms of the uracyl base and O atoms of carbonyl groups. Only weak C—H⋯O contacts exist between neighboring chains.

In the two independent but very similar molecules of the title compound, C 11 H 14 N 2 O 6 , both nucleobase fragments are nearly planar (both within 0.01 Å ) while the furanose rings exhibit 2 E-endo envelope conformations. In the crystal, the two 3 0 -O-acetyl-2 0 -deoxyuridine molecules form a pseudosymmetric dimer of two bases connected via two nearly identical resonance-assisted N-HÁ Á ÁO hydrogen bonds. The resulting pair is further connected with neighboring pairs via two similar O-HÁ Á ÁO bonds involving the only hydroxyl group of the 2 0deoxyfuranose fragment and the remaining carbonyl oxygen of the nucleobase. These interactions result in the formation of an infinite 'double band' along the b axis that can be considered as a self-assembled analogue of a polynucleotide molecule with non-canonical Watson-Crick base pairs. The infinite chains of 3 0 -O-acetyl-2 0 -deoxyuridine pairs are additionally held together by C-HÁ Á ÁO interactions involving C atoms of the uracyl base and O atoms of carbonyl groups. Only weak C-HÁ Á ÁO contacts exist between neighboring chains.
In the crystal structure of title compound ( Fig.1), all bond lengths and bond angles have standard dimensions.
In the crystal of the title compound, the two independent acetyldeoxyuridine molecules form a pseudosymmetric dimer of two bases connected via two nearly identical N-H···O hydrogen bonds (Table 1, Figure 3). Such pseudosymmetric arrangment corresponds to a UU4 2 mode of base pairing (Jeffrey, 1997). Relatively short N···O separations (Table 1) demonstrate strong resonance-assisted hydrogen bonds. All eight cycle-forming atoms are located close to the mean plane (Figure 3), supplementary materials sup-2 making possible π-delocalization of the resonance fragment. This observation is also supported by longer C=O bond lengths in the participating carbonyl groups (1.236 (5) and 1.230 (5) Å) when compared to the other carbonyl groups of the same nucleobase (1.223 (5) and 1.212 (5) Å).
The resulting dimer is further connected with neighboring dimers via two similar O-H···O bonds involving the only hydroxy group of deoxyfuranose fragment and the remaining carbonyl oxygen of the base. These interactions result in the formation of infinitive "double bands" along the b axis of the crystal cell (Figure 4). Such a structure can be considered as a primitive self-assembled analogue of an RNA polymer molecule with non-canonical Watson-Crick base pairs. Two examples of similar UU-4-carbonyl-immino pairs in RNA structures can be found in an NMR structure (Jiang & Patel, 1998) and in a low resolution solid state structure (Ban et al., 2000). More information about flipped pyrimidine-pyrimidine mismatches can be found in (Nagaswamy et al., 2000).
The infinitive chains of acetyldeoxyuridine pairs in the title compound are additionally kept together by CH···O interactions involving carbon atoms of the uracyl base and oxygen atoms of carbonyl groups (Table 1, Figure 4 and 5). Similar bonds were observed in various uracyl-containg structures (Desiraju & Steiner, 1999). A short intramolecular contact between carbonyl oxygen O1 and hydrogen atom H5A may additionaly stabilize the conformation of the molecule.
Only weak C-H···O contacts exist between neighboring chains.

Experimental
The synthesis of the title compound was accomplished via a transetherification procedure dubbed "protecting group transfer" (Cabral et al., 2008). 3'-Acetyl-2'-deoxyuridine obtained in this way showed the same properties as the one obtained before by an independent procedure (Smrt & Sorm, 1960). Crystallization from a hexane-acetone system yielded colourless crystals suitable for single-crystal diffractometry (m.p. 460-461 K).

Refinement
The chirality of the title compound was known from the synthetic route; it was also examined using anomalous scattering.
Analysis of the absolute structure using likelihood methods (Hooft et al., 2008) was performed using PLATON (Spek, 2009); 1867 Bijvoet pairs were employed. The results confirmed that the absolute structure had been correctly assigned: the probability that the structure is inverted is smaller than 10 -11 with probability of racemic twinning at 0.001. Because no atom heavier than O is present, the standard deviation of the Flack parameter is relatively high. All H atoms were positioned geometrically with U iso (H) = 1.2 or 1.5 U eq (C).