A density functional theory study of vibrational coupling between ribose and base rings of nucleic acids with ribosyl guanosine as a model system

Abstract

The vibrational coupling between the ribose and base rings of nucleic acids is modeled by the ribose–guanine vibrational interaction in ribosyl guanosine at the density functional theory (DFT) level. Two coupling patterns are revealed for the in-plane guanine vibrations depending on the strength of the kinematic interaction between ribose and guanine through the glicosidic bond. For relatively weak interactions the coupling can be described in terms of a resonance between two vibrations which are originally close in frequency (the difference in frequency between the vibrations is within ∼20 cm−1). This coupling produces two modes corresponding to the in-phase and out-of-phase combinations of the original ribose and guanine vibrations, analogous to the symmetric and antisymmetric coupled modes of the carbonyl groups in anhydrides, imides, and 1,3-diketo compounds. For strong interactions involving a significant glicosidic bond stretch, the ribose and guanine moieties can no longer be considered as quasi-independent subsystems preserving the forms of their inherent vibrations. An unambiguous identification of the original ribose and guanine vibrations contributing to these combined modes is hardly possible. Taking into account (i) the large number of intrinsic ribose and base vibrations which can potentially participate in the coupling and (ii) the resonant character of many of these interactions, these results suggest that small changes in the ribose ring conformation and glicosidic bond orientation should result in noticeable changes of the related combined modes. This explains the phenomenon of high conformational sensitivity of the corresponding conformational marker bands of nucleic acids in vibrational spectroscopy.