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

• Published in: Journal of molecular modeling 2020-04, Vol.26 (5), p.99-99, Article 99
• Main Authors: Minguirbara, Alain, Vamhindi, Berthelot Saïd Duvalier Ramlina, Koyambo-Konzapa, Stève Jonathan, Nsangou, Mama
• Format: Article
• Language: English
• Subjects: Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Deoxycytosine Nucleotides - chemistry; Ions - chemistry; Models, Molecular; Molecular Conformation; Molecular Medicine; Original Paper; Sodium; Solvation; Solvents; Solvents - chemistry; Theoretical and Computational Chemistry; Vibration; Water - chemistry
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-020-04369-6

The effects of the interaction of the monovalent (Li + , Na + , K + ) and divalent (Mg 2+ ) counterions hexahydrated (6H 2 O), with the PO 2 − 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 (6H 2 O) and hybrid (6H 2 O/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 ≤ 0.08% (g − g − ) and ≤ 0.41% (g + g + ) observed between the calculated and experimental data for the PO 2 − (asymmetric) stretching mode in the presence of the counterion K + in the hybrid model. Graphical abstract