This work analyzes the adsorption of RNA/DNA nucleobases on the external surfaces of Na+-montmorillonite by using periodic plane wave calculations based on the PBE functional. The adsorption energies were corrected by a posteriori added empirical term to account for purely dispersive interactions. Adsorption has been considered either on the side comprising the Na+ counterion or on the opposite side, where only siloxane bonds are present, Different orientations of the nucleobases (parallel and orthogonal to the surface plane) have been considered. The results show that guanine and cytosine, for which the metal cation interacts with two basic centers (N and O), are the ones with larger adsorption energies (-27.6 kcal mol(-1) for G(O6N7) and -27.0 kcal mol(-1) for C-O2N3). The remaining three bases present smaller adsorption energies (-21.7 for T-pi(O4), -21.2 for U-pi(O4) and -20.2 kcal mol(-1) for A(N3)). On the other hand, adsorption of the nucleobase on the surface free from Na+, either in a face-to-face or orthogonal orientation, was found to be sizable for all bases (from -3.7 to -11.3 kcal mol(-1)), due to the stabilizing effect of dispersion interactions.

Theoretical Study of the Adsorption of RNA/DNA Bases on the External Surfaces of Na+-Montmorillonite

UGLIENGO, Piero;
2009-01-01

Abstract

This work analyzes the adsorption of RNA/DNA nucleobases on the external surfaces of Na+-montmorillonite by using periodic plane wave calculations based on the PBE functional. The adsorption energies were corrected by a posteriori added empirical term to account for purely dispersive interactions. Adsorption has been considered either on the side comprising the Na+ counterion or on the opposite side, where only siloxane bonds are present, Different orientations of the nucleobases (parallel and orthogonal to the surface plane) have been considered. The results show that guanine and cytosine, for which the metal cation interacts with two basic centers (N and O), are the ones with larger adsorption energies (-27.6 kcal mol(-1) for G(O6N7) and -27.0 kcal mol(-1) for C-O2N3). The remaining three bases present smaller adsorption energies (-21.7 for T-pi(O4), -21.2 for U-pi(O4) and -20.2 kcal mol(-1) for A(N3)). On the other hand, adsorption of the nucleobase on the surface free from Na+, either in a face-to-face or orthogonal orientation, was found to be sizable for all bases (from -3.7 to -11.3 kcal mol(-1)), due to the stabilizing effect of dispersion interactions.
2009
113
31
13741
13749
http://pubs.acs.org/doi/abs/10.1021/jp901699q
RNA bases; DNA bases; layered materials
P. Mignon; P. Ugliengo; M. Sodupe
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2318/61236
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