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(2+)) 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 Mg(2+)) 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