The dihydrogen-bonded complexes of methane and its fluoro and chloro derivatives with lithium hydride are analyzed using ab initio methods as well as the Bader theory. All calculations were performed using Pople's basis sets (6-311++G(d,p), 6-311++G(2df,2pd), and 6-311++G(3df,3pd)) and the Dunning bases (aug-cc-pVDZ and aug-cc-pVTZ) within the MP2 method. The results of the calculations show that the binding energy for the analyzed complexes increases with the increase of the number of fluoro or chloro substituents, up to ∼7 kcal/mol. In the same order there is an increase of the electrostatic energy term, showing that for the CF3H···HLi complex the dihydrogen bond interaction is similar in nature as for the water dimer where a conventional O−H···O hydrogen bond exists, while for the CCl3H···HLi dimer the exchange energy term outweighs the electrostatic energy. Hence, the other attractive energy terms are important. A topological analysis based on the Bader theory supports the results of the ab initio calculations since the electron densities at the H···H bond critical points and the other topological parameters are similar to those calculated for moderate conventional hydrogen bonds.

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.

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