Search for a reliable nucleic acid force field using neutron inelastic scattering and quantum mechanical calculations: Bases, nucleosides and nucleotides

Abstract

Neutron inelastic scattering (NIS), IR and Raman spectra of the RNA constituents: bases, nucleosides and nucleotides have been analyzed. The complementary aspects of these different experimental techniques makes them especially powerful for assigning the vibrational modes of the molecules of interest. Geometry optimization and harmonic force field calculations of these molecules have been undertaken by quantum mechanical calculations at several theoretical levels: Hartree-Fock (HF), Moller-plesset second-order perturbation (MP2) and Density Functional Theory (DFT). In all cases, it has been shown that HF calculations lead to insufficient results for assigning accurately the intramolecular vibrational modes. In the case of the nucleic bases, these discrepancies could be satisfactorily removed by introducing the correlation effects at MP2 level. However, the application of the MP2 procedure to the large size molecules such as nucleosides and nucleotides is absolutely impossible, taking into account the prohibitive computational time needed. On the basis of our results, the calculations at DFT levels using B3LYP exchange and correlation functional appear to be a cost-effective alternative in obtaining a reliable force field for the whole set of nucleic acid constituents.