Ground state properties of the nucleic acid constituents studied by density functional calculations.: I.: Conformational features of ribose, dimethyl phosphate, uridine, cytidine, 5′-methyl phosphate-uridine, and 3′-methyl phosphate-uridine

Ground state energies and geometries have been determined at the DFT/B3LYP level for different model compounds such as ribose, dimethyl phosphate, uridine, cytidine, 3'-methyl phosphate-uridine, and 5'-methyl phosphate-uridine as a function of the most prominent conformations adopted by each of them. The counterion used for neutralizing the phosphate negative charge was an ammonium ion (NH4+). This systematic study allowed us to analyze the stability of a ribonucleotide (base+ribsse+phosphate) which is the chemical repeating unit of RNA. In the dimethyl phosphate model, the lowest energy corresponds to the gauche(-)-gauche(-) conformation, as also predicted by previous calculations on this motif at different theoretical levels. In the ribose model, the C2'-endo (S-type) conformer has a lower energy than the C3'-endo (N-type) one. When a pyrimidine base (uracil or cytosine) is added to the ribose to form a ribonucleoside, the electronic energies of the three optimized conformers with the C3'-endo and C3'-endo sugar puckers as well as the anti and syn orientations of the base with respect to the sugar are located in the following order: C3'-endo/anti < C2'-endo/anti < C3'-endo/syn. However, the energy difference between these conformers depends on the type of the pyrimidine base connected to the ribose. The optimization of the ribonucleotides confirms the stability of the conformers containing A- and Z-form conformational angles. The role of the intramolecular O-H ... O and C-H ... O hydrogen bonds in the overall stability of ribose, nucleosides, and ribonucleotides has been discussed.