Ground-State Properties of Nucleic Acid Constituents Studied by Density Functional Calculations. 3. Role of Sugar Puckering and Base Orientation on the Energetics and Geometry of 2‘-Deoxyribonucleosides and Ribonucleosides

Abstract

In the present paper, we have analyzed the conformational energy and geometrical parameters of the isolated 2′-deoxyribonucleosides and ribonucleosides. Geometry optimization of these nucleic acid constituents has been undertaken by means of density functional theory with the Becke-Lee-Yang-Parr exchange and correlation functional and split valence basis sets, 6-31G (/) , including nonstandard polarization functions on carbon, nitrogen, and oxygen atoms. For each nucleoside, three major conformers, i.e., C2′-endo/anti, C3′endo/anti, and C3′-endo/syn, have been taken into consideration, where C3′-endo and C2′-endo refer to the north (N)-type and south (S)-type sugar puckering, respectively, and anti and syn designate the orientation of the base with respect to the sugar. In both families (2′-deoxyribonucleosides and ribonucleosides) the anti orientation of the base stabilized by an intramolecular C-H‚‚‚O hydrogen bond formed between the base and the O5′ atom of the sugar moiety corresponds to the lowest energy states. In the 2′-deoxyribonucleosides including uracil, guanine, and adenine bases the lowest energy conformer is C2′-endo/anti, whereas in 2′deoxycytidine the most stable conformer is C3′-endo/anti. In ribonucleosides, the C3′-endo/anti and C2′endo/anti conformers nearly have the same energy, except in cytidine, where the most stable conformer is C3′-endo/anti. Therefore, a general discussion has been devoted to the exceptional cases of 2′-deoxycytidine and cytidine compared to the other nucleosides. The present calculated results have also been compared with those recently reported at the MP2 level by other authors on the 2′-deoxyribonucleosides or smaller model compounds on one hand, and with the experimental results based on a statistical survey of nucleoside crystal structures on the other hand.

Estimation of gas-phase acidities of deoxyribonucleosides: An experimental and theoretical study

“…There was a good agreement of high level calculations results with the measured values; thus, they concluded the DFT methods represent the best tools for obtaining ⌬H acid values for medium to large sized molecular systems. Ground state geometries for the studied deoxyribonucleosides were taken from the earlier study [18], in which C3=-endo/anticonformer for dC and C2=-endo/anti for the remaining deoxyribonucleosides were considered. The reoptimized geometries of the molecules obtained at the B3LYP/6-311G** level of theory were in good agreement with the earlier reported data [18].…”

“…Most stable structures of deoxyribonucleosides were taken from the earlier reports [18]. Geometrical optimizations and the vibrational frequencies of the neutral and deprotonated forms of all deoxyribonucleosides were carried out with B3LYP method using 6-311G(d,p) basis set.…”

Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

“…However, recently it has become possible to analyze these conformational properties using highlevel ab initio QM methods. 55,[75][76][77][78][79][80][81][82][83][84][85] In this paper, we attempt to gain insight into the complexity, modeling, and conformational flexibility of the DNA backbone. This is achieved by calculations on two model systems mimicking the basic building block of the DNA phosphodiester backbone.…”

Peptide release on the ribosome depends critically on the 2′ OH of the peptidyl–tRNA substrate

“…) (Hocquet et al 2000) and fA76 is expected to favor the C39-endo conformation favored by the wild-type rA76 variant (Uesugi et al 1979). In addition, structural studies have demonstrated that rA76 and dA76 substrates bind the P site in identical conformations (Schmeing et al 2005).…”