DFT study of geometrical and vibrational features of a 3′,5′-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent

• Published in: Journal of molecular modeling 2018-04, Vol.24 (4), p.88-16, Article 88
• Main Authors: Minguirbara, Alain, 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; Crystallography; Deoxyribonucleic acid; DNA; Mathematical models; Molecular Medicine; Original Paper; Solvation; Solvents; Stretching; Theoretical and Computational Chemistry
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-018-3629-4

The B3LYP/6–31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li + , Na + , K + ) and divalent (Mg 2+ ) metal counterions in interaction with the charged PO 2 − group, on the geometrical and vibrational characteristics of the DNA fragments of 3′,5′-dDSMP, represented by four conformers (g + g + , g + t, g − g − and g − t). All complexes were optimized through two solvation models [the explicit model (6H 2 O) and the hybrid model (6H 2 O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li + , Na + , K + , Mg 2+ ) always remain in the bisector plane of the O1–P–O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li + , Na + ) deviate from the bisector plane, while the largest counterions (K + and Mg 2+ ) always remain in the same plane. On the other hand, the present calculations reveal that the g + g + conformer is the most stable in the presence of monovalent counterions, while conformers g + t and g − t are the most stable in the presence of the divalent counterion Mg 2+ . Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4′-C3′-O3′-PO − 2 -O5′-C5′-C4′ segment of all complexes of the g − g − conformer in 6H 2 O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g + g + conformer in the presence of the monovalent counterion and of g − t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H 2 O/Continuum for the g + g + conformer and experimental value measured in an aqueous solution of the DMP-Na + complex, is