N-[3-(tert-Butyldimethylsiloxymethyl)-5-nitrophenyl]acetamide

The title compound, C15H24N2O4Si, was prepared by the reaction of (3-acetamido-5-nitrobenzyl)methanol with tert-butyldimethylsilyl chloride and is a key intermediate in the synthesis of novel nonsymmetrical DNA minor groove-binding agents. There are two independent molecules in the structure, which differ primarily in the rotation about the C—O bond next to the Si atom. Two strong N—H⋯O hydrogen bonds align the molecules into a wide ribbon extending approximately parallel to the b axis.

The title compound, C 15 H 24 N 2 O 4 Si, was prepared by the reaction of (3-acetamido-5-nitrobenzyl)methanol with tertbutyldimethylsilyl chloride and is a key intermediate in the synthesis of novel nonsymmetrical DNA minor groovebinding agents. There are two independent molecules in the structure, which differ primarily in the rotation about the C-O bond next to the Si atom. Two strong N-HÁ Á ÁO hydrogen bonds align the molecules into a wide ribbon extending approximately parallel to the b axis.

Comment
Due to the nucleophilic nature of benzylic hydroxyl groups these are usually protected during multi-step organic synthesis (Barker et al., 2008). Large numbers of protecting groups are reported including a variety of silyl ethers. Among the silyl ethers, the tert-butyldimethylsilyl ether is widely used due to it stability towards oxidative, reductive, and mild acidic and basic conditions (Jarowicki & Kocienski, 1998;Kocienski, 2004;Schelhaas & Waldmann, 1996;Wetter & Oertle, 1985;Wuts & Green, 2006). It can however be easily deprotected to give the parent hydroxyl group efficiently using different fluoride reagents without affecting other functionalities (Crouch, 2004;Nelson & Crouch, 1996). The asymmetric unit contains two independent molecules which differ primarily in the rotation about the C7 -O4 bond.

Refinement
All the hydrogens were clearly discernible in the difference electron density map. Nevertheless, the hydrogens were placed in calculated positions and refined using the riding model under the conditions:. C aryl -H aryl =0.93, C methyl -H methyl =0.96, C methylene -H methylene = 0.97, N-H = 0.86 Å, U iso (H) = 1.2U eq (C) except for the methyl hydrogens where U iso (H) = 1.5U eq (C).

Special details
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating Rfactors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.