A DFT Analysis of NMR Scalar Interactions Across the Glycosidic Bond in DNA
| Authors | |
|---|---|
| Year of publication | 2003 |
| Type | Article in Periodical |
| Magazine / Source | Journal of the American Chemical Society |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | NUCLEIC-ACIDS; CONSTANTS; OLIGONUCLEOTIDES; NMR |
| Description | Abstract. The relationship between the glycosidic torsion angle c, the three-bond couplings 3JC2/4-H1' and 3JC6/8-H1', and the one-bond coupling 1JC1'-H1' in deoxyribonucleosides and a number of uracil cyclo-nucleosides has been analyzed using density functional theory. The influence of the sugar pucker and the hydroxymethyl conformation has also been considered. The parameters of the Karplus relationships between the three-bond couplings and c depend strongly on the aromatic base. 3JC2/4-H1' reveals different behavior for deoxyadenosine, deoxyguanosine, and deoxycytidine as compared to deoxythymidine and deoxyuridine. In the case of 3JC6/8-H1', an opposite trans to cis ratio of couplings is obtained for pyrimidine nucleosides in contrast to purine nucleosides. The extremes of the Karplus curves are shifted by ca. 10o with respect to syn and anti-periplanar orientations of the coupled nuclei. The change in the sugar pucker from S to N decreases 3JC2/4-H1' and 3JC6/8-H1' while increasing 1JC1'-H1' for the syn rotamers, whereas all of the trends are reversed for the anti rotamers. The influence of the sugar pucker on 1JC1'-H1' is interpreted in terms of interactions between the nO4', sigma C1'-H1' orbitals. The 1JC1'-H1' are related to chi through a generalized Karplus relationship, which combines cos(chi) and cos2(chi) functions with mutually different phase shifts that implicitly accounts for a significant portion of the related sugar pucker effects. Most of theoretical 3JC2/4-H1' and 3JC6/8-H1' for uracil cyclo-nucleosides compare well with available experimental data. 3JC6/8-H1' couplings for all C2-bridged nucleosides are up to 3 Hz smaller than in the genuine nucleosides with the corresponding chi, revealing a non-local aspect of the spin-spin interactions across the glycosidic bond. Theoretical 1JC1'-H1' are underestimated with respect to the experiment by ca. 10% but reproduce the trends in 1JC1'-H1' vs. chi. |
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