Ground state properties of the nucleic acid constituents studied by density functional calculations. 2. Comparison between calculated and experimental vibrational spectra of uridine and cytidine

Vibrational spectra of two ribonucleosides containing pyrimidine bases, i.e ., uridine and cytidine, were analyzed in the solid state at low temperatur e by neutron inelastic scattering (NIS) and in an aqueous solution at room temperature by Raman scattering and Fourier transform infrared absorption ( FT-IR). Analysis of all these experimental spectra, measured on both native and deuterated (on labile hydrogens) species, allows a complete set of inf ormation on the vibrational modes arising from the base residues and ribose to be obtained. To interpret the vibrational spectra, a harmonic force fie ld has been estimated for isolated ribonucleosides at the Hartree-Fock (HF) and density functional theory (DFT) levels. All these calculations have be en performed by means of the Becke-Lee-Yang-Parr (B3LYP) local exchange and correlation functional (for DFT calculations) and the split valence basis sets, 631G(()*()), including nonstandard polarization functions on heavy at oms (for DFT and HF calculations). The lowest energy conformers of these ri bonucleosides, i.e., C3'-endo/ anti and C2'-endo/anti have been used in the vibrational mode calculations, where C3'-endo and C2'-endo refer to the N- type and S-type ribose puckering, respectively, and anti designates the ori entation of base with respect to the sugar. The absence of any imaginary fr equencies in the vibrational calculations confirms that the optimized geome try of the ribonucleosides well corresponds to their local mimima. The addi tion of the zero-point vibrational energy (ZPVE) to the electronic energy d oes not, however, change the energy order of the conformers. In both ribonu cleosides, the C3'-endo/anti conformer has a lower energy than the C2'-endo / anti one. It has been shown that NIS intensities calculated at the DFT/B3 LYP/631G(()*()) level account more accurately for the characteristics of th e experimental spectra. Therefore, the assignment of the observed vibration al modes has been extensively discussed in this paper on the basis of the r esults calculated by means of the DFT method. On the other hand, comparison between observed and calculated NIS spectra of native and deuterated speci es can give insight on the effect of intermolecular hydrogen bonding in the solid phase. Finally, the calculated results seem to be able to interpret the Raman marker shifts observed upon the A-Z helix transitions of poly- an d oligonucleotides (C3'-endo/anti to C2/-endo/anti conformational transitio n of the cytosine residue), as well as those related to the UUCG tetraloop hairpin, involving C2'-endo/anti uridine and cytidine residues found in the middle positions of this highly stable tetraloop.