Analysis of the structural and vibrational properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations Original Research Article

Vibrational spectra of the major building blocks of RNA (bases and ribonucleosides) have been recorded in solid phase by means of neutron inelastic scattering (NIS) at low temperature (T=15 K). The NIS technique has been chosen for its particular use in the analysis of the vibrational modes in which hydrogen atom motions are involved. Moreover, in order to assign as accurately as possible the observed vibrational modes, the effect of the H–D isotopic exchange on the labile hydrogens of sugar and bases has also been studied by recording the NIS spectra of deuterated species. To interpret all the above-mentioned set of experimental data, the harmonic force fields of isolated bases and ribonucleosides have been calculated after full geometry optimisation at the density functional theory level. To test the ability of the theoretical force field to reproduce NIS intensities, first-order spectra of all the above-mentioned molecular compounds have been calculated with the unscaled ab initio force field estimated for isolated molecules. In the spectral region above 900 cm−1, a satisfactory agreement has been obtained between the calculated and observed NIS spectra of the native molecular species. Below 900 cm−1, where the vibrational modes arising from the N–H and NH2 wagging modes are located, some discrepancies have however been found on the comparison between the experimental and theoretical results. This disagreement is mainly related to the intermolecular hydrogen bonding occurring in solid phase in which the labile hydrogens are mainly involved. We have verified this fact by analysing the NIS spectra of the labile hydrogen deuterated species of bases and ribonucleosides which reveal a better agreement with the theoretical spectra in the spectral region below 900 cm−1.