Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP)
| Autor: | Alain Minguirbara, Berthelot Saïd Duvalier Ramlina Vamhindi, Mama Nsangou, Steve Jonathan Koyambo-Konzapa |
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| Rok vydání: | 2020 |
| Předmět: |
Models
Molecular Molecular Conformation 010402 general chemistry 01 natural sciences Vibration Catalysis Ion Divalent Inorganic Chemistry Normal mode 0103 physical sciences Physical and Theoretical Chemistry Conformational isomerism chemistry.chemical_classification Ions 010304 chemical physics Organic Chemistry Small deviations Solvation Water 0104 chemical sciences Computer Science Applications Solvent Crystallography Computational Theory and Mathematics chemistry Deoxycytosine Nucleotides Solvents Counterion |
| Zdroj: | Journal of molecular modeling. 26(5) |
| ISSN: | 0948-5023 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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