DFT study of geometrical and vibrational features of a 3',5'-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent.

The B3LYP/6-31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li, Na, K) and divalent (Mg) metal counterions in interaction with the charged PO group, on the geometrical and vibrational characteristics of the DNA fragments of 3',5'-dDSMP, represented by four conformers (gg, gt, gg and gt). All complexes were optimized through two solvation models [the explicit model (6HO) and the hybrid model (6HO/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li, Na, K, Mg) always remain in the bisector plane of the O1-P-O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li, Na) deviate from the bisector plane, while the largest counterions (K and Mg) always remain in the same plane. On the other hand, the present calculations reveal that the gg conformer is the most stable in the presence of monovalent counterions, while conformers gt and gt are the most stable in the presence of the divalent counterion Mg. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4'-C3'-O3'-PO-O5'-C5'-C4' segment of all complexes of the gg conformer in 6HO/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the gg conformer in the presence of the monovalent counterion and of gt conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6HO/Continuum for the gg conformer and experimental value measured in an aqueous solution of the DMP-Na complex, is <1.07% for the PO (asymmetric and symmetric) stretching modes and <2.03% for the O5'-C5' and O3'-C3' stretching modes. Graphical abstract dDSMP-(OO) Mg/6W/Continuum.