A new outlook on the nature of short intramolecular non-bonded contacts between 6CH⋯O5′ in the crystals of pyrimidine nucleosides and their salts

Abstract

Short intramolecular contacts between the 6CH group and the O5′ oxygen have been propounded for a long time in the description of structures of some native pyrimidine nucleosides and their derivatives. The character of these interactions was not, however, fully resolved. On the basis of X-ray investigation, it is assumed that these contacts have the character of hydrogen bonds. For some time, however, doubts have been growing as to the validity of this opinion. Consequently we have started detailed investigations to elucidate this problem. Studies carried out for cytidine (Cyd), ethenocytidine (ϵCyd) and their hydrochloride, nitrate, and dihydrogenphosphate salts, were based upon X-ray analysis, IR spectra, and calculations of electron density by the CNDO/2 method. A detailed comparative examination of IR spectra of the eight chosen nucleoside, four of which showed evidence for the presence of such a short contact, proved that the relevant contact could not have the character of an intramolecular hydrogen bond, but instead has a repulsive nature. This conclusion was supported by hypsochromic shifts of the absorption bands of 6CH stretching vibrations participating in short intramolecular contacts, as well as by the positive value of electron density on the carbon atom 6C. On the basis of computer diagrams of the same projectiobs for the crystal structures of all studied compounds, we also tried to find the factors responsible for the existence or absence of the short intramolecular repulsive contact, and to predict the effect of such a contact on the conformational and functional dynamics of nucleic acid fragments.