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

  • Alain Minguirbara
  • Mama Nsangou
Original Paper


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, gg and gt). 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 gt 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′-PO2-O5′-C5′-C4′ segment of all complexes of the gg 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 gt 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.

Graphical abstract

dDSMP-(OO) Mg2+/6W/Continuum


B3LYP/6–31++G* 3′,5′-deoxydisugar-monophosphate Vibrational features Counterions Solvent Mode assignment 

Supplementary material

894_2018_3629_MOESM1_ESM.docx (8.5 mb)
ESM 1 (DOCX 8715 kb)
894_2018_3629_MOESM2_ESM.docx (140 kb)
ESM 2 (DOCX 140 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Physics, Higher Teachers’ Training CollegeUniversity of MarouaMarouaCameroon

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