204. Evidence for the existence of C–H⋯O hydrogen bonds in crystals

Abstract

Since an activated C-H group may take part in hydrogen bonding, the angles involved in the " short " interaction have been calculated for various compounds of known crystal structure containing activated C-H groups and " short " C -* * 0 distances. I n these compounds, the conditions for hydrogen bonding are satisfied by the methylidyne group and probably by the methylene and the methyl group. This type of hydrogen bond occurs rather widely and may be of importance in the structures of biological molecules.AN investigation of '' short '' intermolecular and intramolecular C --* 0 contacts has shown that many of these are due to C-H * --0 hydrogen bonds. Here the term '' short " implies that the distance between the carbon and the oxygen atom is less than the sum of their van der Waals radii plus some allowance for the hydrogen atom or atoms attached to the carbon. Thus C ---0 distances in the region of 3.1 A are considered.*The present work was prompted by the discovery of an intermolecular distance of 3 0 0 A between a methyl group and an oxygen atom in the crystal structure of 1,3,7,9tetramethyluric acid.l This value, obtained originalIy from a two-dimensional analysis of * This is necessary because of the range of values found for hydrogen bonds. The 0 --0 distance in an O -H . * * O hydrogen bond is usually less than the van der Waals distance. However the less electronegative nitrogen atom forms N-H * * -0 and N-H ---N bonds in which the N --0 and N -* -N distances are frequently greater than the van der Waals distance. Carbon which is less electronegative and has to be activated in order to participate in a hydrogen bond should behave similarly to nitrogen, forming even longer bonds.Sutor, Actn Cryst., in the press.

1,3-Dimethyluracil: a crystal structure without hydrogen bonds

“…3, 4), the dimers being related by centres of symmetry and held together by C(1)... 0(2) contacts of 3.29 A. This is significantly shorter than the expected van der Waals distance of 3.4 A between methyl groups and O atoms and could be due to C-H...O hydrogen bonding (Sutor, 1963). The differences in intermolecular forces in crystals of 1,3-dimethyluracil and other uracil derivatives are also evident from the respective melting points: 121 for 1,3-dimethyluracil, 174 for 1-methyluracil and 338°C for uracil.…”

Packing Modes in Nitrobenzene Derivatives. II. The `Pseudo-Herringbone' Mode

“…As the common fragment of all the structures is a nitrobenzene, the possibilities of weak CH...O hydrogen interactions involving the NO2 groups were analysed. CH...X hydrogen bonds have been the subject of extensive study (Sutor, 1963;Taylor & Kennard, 1982;Panunto, Urbanozyk-Lfipkowska, Johnson & Etter, 1987;Steiner & Saenger, 1992;Desiraju, 1995;Allen, Lommerse, Hoy, Howard & Desiraju, 1996) and the importance of weak CH...O interactions in the stabilization of some structures has been demonstrated (Sarma & Desiraju, 1986Desiraju, 1991;Sharma & Desiraju, 1994). Among all -.O of and LINNAX, the chain observed along the twofold 2.7 (2) and 3.5 (2) A, respectively, which are close to the sum of the corresponding van der Waals radii (Bondi, 1964).…”

Computational support for the suggested contribution of C—H...O=C interactions to the stability of nucleic acid base pairs

“…Furthermore, purines and pyrimidines are well known to carry acidic C--H groups which are potent donors of C--H...O hydrogen bonds (recognised earlier by Sutor, 1963;Sundaralingam, 1966). In nucleic acid base pairing, a C--H.-.O interaction of close to ideal geometry (H.-.O = 2.3,A,, angle at H = 156 °) was observed in a trans U-U pair in the crystal structure of the RNA fragment r(UUCGCG) by Wahl, Rao & Sundaralingam (1996).…”