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 (Mg2+) counterions hexahydrated (6H2O), with the PO2- 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 (6H2O) and hybrid (6H2O/Continuum) solvation models. The optimizations reveal that in the conformation g-g- 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 Mg2+) remain in this plane, whereas in the hybrid model of solvation, the counterions deviate from this plane. However, when the conformer is g+g+, the monovalent counterions deviate and divide the remainder of the plane regardless of the type of solvation model. In addition, the g-g- conformer is the most stable in the presence of the explicit solvent, while the g+g+ conformer is the most stable in the presence of the hybrid solvent. Finally, the normal modes of the conformers g-g- and g+g+ 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 (g-g-), and Z (g+g+) relatively to the explicit model. This very good agreement is illustrated by the very small deviations ≤ 0.08% (g-g-) and ≤ 0.41% (g+g+) observed between the calculated and experimental data for the PO2- (asymmetric) stretching mode in the presence of the counterion K+ in the hybrid model. Graphical abstract.