Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite

Abstract

In the present study, DFT periodic plane wave calculations, at the PBE-D level of theory, were carried out to investigate the interaction of DNA nucleobases with acidic montmorillonite. The surface model was considered in its octahedral (Osub) and tetrahedral (Tsub) substituted forms, known to have different acidic properties. The adsorption of adenine, guanine and cytosine was considered in both orthogonal and coplanar orientations with the surface, interacting with the proton via a given heteroatom. In almost all considered cases, adsorption involved the spontaneous proton transfer to the nucleobase, with a more pronounced character in the Osub structures. The binding energy is about 10 kcal mol(-1) larger for Osub than for Tsub complexes mainly due to the larger acidity in Osub surfaces and due to the better stabilization by H-bond contacts between the negatively charged surface and the protonated base. The binding energy of coplanar orientations of the base is observed to be as large as the orthogonal ones due to a balance between electrostatic and dispersion contributions. Finally the binding of guanine and adenine on the acidic surface amounts to 50 kcal mol(-1) while that of cytosine rises to 44 kcal mol(-1).

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

“…412,728 The same is also true for studies dealing with phospholipids as model of cell membranes in which only one paper has been published. 729 Both fields should be explored in depth, among other reasons because of the importance of DNA in developing nano-devices within a bottom-up approach.…”

How do Nucleotides Adsorb Onto Clays?

“…Most of them considered the stability and/or polymerization of bases in the interlayer [27,87,88,89] and did not consider the fact that the interlayer of clay minerals is unlikely to be available for the adsorption in seawater, as shown in the previous sections. The few studies that examined adsorption on the external basal surfaces of clay minerals considered a low ionic strength environment [90,91].…”

Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca2+-montmorillonite clay surfaces

“…Because of environmental issues but also for their interesting chemistry, several authors got interested into organic chemicals interacting with clay minerals, in particular montmorillonite by using computational chemistry methods . For instance, DNA bases on acidic external surface of montmorillonite has been studied by P. Mignon and M. Sodupe . V. Aggarwal et al have investigated adsorption of polar organic compounds onto montmorillonite.…”