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

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Abstract

The B3LYP/6–31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li+, Na+, K+) and divalent (Mg2+) metal counterions in interaction with the charged PO2− 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 (6H2O) and the hybrid model (6H2O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li+, Na+, K+, Mg2+) 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 Mg2+) 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 Mg2+. 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 6H2O/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 6H2O/Continuum for the g+g+ conformer and experimental value measured in an aqueous solution of the DMP-Na+ complex, is <1.07% for the PO2− (asymmetric and symmetric) stretching modes and <2.03% for the O5′-C5′ and O3′-C3′ stretching modes.

dDSMP-(OO)− Mg2+/6W/Continuum

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  1. Department of Physics, Higher Teachers’ Training College, University of Maroua, PO Box 46, Maroua, Cameroon

    Alain Minguirbara & Mama Nsangou

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  1. Alain Minguirbara
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  2. Mama Nsangou
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Correspondence to Mama Nsangou.

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Minguirbara, A., Nsangou, M. DFT study of geometrical and vibrational features of a 3′,5′-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent. J Mol Model 24, 88 (2018). https://doi.org/10.1007/s00894-018-3629-4

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