Normal coordinate analysis treatment on uracil in solid state

Abstract

A normal coordinate analysis has been performed on the unit cell of uracil. Transition dipole—dipole coupling interaction between CO groups within the four molecules in the unit cell was found necessary to explain the observed band splittings in the double-bond region. It has been proposed that this new interaction may be important in our future attempts to distinguish between various conformations in polynucleotides and nucleic acids. Bands due to NH in-plane and out-of-plane bending modes were assigned by means of the spectra of uracil, 1-methyluracil and 3-methyluracil. Spectra of uracil and C 5-deuterouracil were made use of in assigning bands due to CH deformation modes. Bands due to C 2O and C 4O deformation modes were assigned by studying the spectra of uracil, 2-thiouracil and 2,4-dithiouracil. NH in-plane bending mode bands have shown no indications of effects due to interactions through transition dipole—dipole coupling. NH out-of-plane bending mode bands were found to be unusually sensitive to the strengths of hydrogen bonding. Normal mode calculations have shown a mixing of in-plane and out-of-plane bending modes below 1000 cm −1. It is hoped that the calculations performed here will provide the basis for future studies of polynucleotide as well as nucleic acid conformations by making use of the conformational sensitivity of the CO stretching bands.