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 protonvia 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.

The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3–C4/N1–C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1–C2/C5–C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH₃ or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.

The fragmentation process of the uracil RNA base has been investigated via DFT calculations in order to assign fragments to the ionisation mass spectrum obtained after dissociation induced by collision experiments. The analysis of the electronic distribution and geometry parameters of the cation allows selection of several bonds that may be cleaved and lead to the formation of various fragments. Differences are observed in the electronic behaviour of the bond breaking as well as the energy required for the cleavage. It is reported that N₃–C₄ and N₁–C₂ bonds are more easily cleaved than the C₅–C₆ bond, since the corresponding energy barriers amount to ΔG = +1.627, +1.710, +5.459 eV, respectively, which makes the C₅–C₆ bond cleavage almost prohibited. Among all possible formed fragments, the formation of the OCN⁺ fragment for the peak at m/z = 42 Da is excluded because of an intermediate that was not observed experimentally and too a large free energy barrier. Based on the required free energy, it is observed that two fragment derivatives: C₂H₄N⁺ and C₂H₂O˙⁺ may be formed, with a small preference for C₂H₄N⁺. This latter product is not formed through a retro Diels Alder reaction in contrast to C₂H₂O˙⁺. The following sequence is proposed for the peak at 42 Da: C₂H₄N⁺ (from N₁–C₂, C₄–C₅ cleavages) > C₂H₂O˙⁺ (from N₃–C₄, N₁–C₂ and C₅–C₆ cleavages) > C₂H₄N⁺ (from N₁–C₂, N₃–C₄ and C₄–C₅) > C₂H₂O˙⁺ (from C₅–C₆, N₁–C₂ and N₃–C₄ cleavages) > NCO⁺ (from N₁–C₂, C₄–C₅ and N₃–C₄ cleavages). Finally the peak at 28 Da is assigned to CNH₂ ⁺ derivatives that can be formed through two different paths, the easiest one requiring 5.4 eV.

The adsorption of two pharmaceuticals, carbamazepine and paracetamol, onto the expandable clay mineral saponite has been studied through the combination of kinetic experiments, X-ray diffraction, and theoretical modeling. Kinetic experiments indicate low adsorption for carbamazepine and paracetamol on expandable smectite clay. Accordingly, X-ray diffraction experiments show that neither compound enters smectite interlayer space. Molecular dynamics simulations were carried out to understand the interactions between the two pharmaceuticals and the saponite basal surface in the presence of Na⁺ cations. Calculations reveal that paracetamol almost does not coordinate solution cations, whereas a rather low coordination to cation is observed for carbamazepine. As a result, the adsorption onto the clay surface results mainly from van der Waals interactions for both pharmaceuticals. Carbamazepine does adsorb the surface via two configurations, one involving cation coordination, which corresponds to a rather stable adsorption compared to paracetamol. This is confirmed by structural analyses completed with desorption free energy profile.