Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP).

The effects of the interaction of the monovalent (Li, Na, K) and divalent (Mg) counterions hexahydrated (6HO), with the PO group, on the geometrical and vibrational characteristics of 3', 5'-dDCMP, were studied using the DFT/B3LYP/6-31++G(d) method. These calculations were performed using the explicit (6HO) and hybrid (6HO/Continuum) solvation models. The optimizations reveal that in the conformation gg and in the explicit model of solvation, the small ions (Li, Na) deviate from the bisector plane of the angle O1-P-O2 and the large ions (K and Mg) remain in this plane, whereas in the hybrid model of solvation, the counterions deviate from this plane. However, when the conformer is gg, the monovalent counterions deviate and divide the remainder of the plane regardless of the type of solvation model. In addition, the gg conformer is the most stable in the presence of the explicit solvent, while the gg conformer is the most stable in the presence of the hybrid solvent. Finally, the normal modes of the conformers gg and gg in the presence of the counterions in the hybrid model show a better agreement with the available experimental data of the DNA forms A, B (gg), and Z (gg) relatively to the explicit model. This very good agreement is illustrated by the very small deviations ≤ 0.08% (gg) and ≤ 0.41% (gg) observed between the calculated and experimental data for the PO (asymmetric) stretching mode in the presence of the counterion K in the hybrid model. Graphical abstract.