Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach

Abstract

Sepiolite, a natural clay mineral, offers a large surface area due to its fibrous structure, allowing it to exhibit adsorption properties. In this study, the molecular interactions of sepiolite, a biocompatible clay mineral known as a biomaterial, and purine and pyrimidine molecules forming the bases of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules were modeled by Density Functional Theory. In addition to geometry optimization, calculations of interaction energy, bond critical points, and electrostatic potential revealed that essential molecules for our source of life interact with basal surface of the clay. For example, the best interaction energies between bases/sepiolite were found to be -127.47 kJ/mol for guanine and -121.35 kJ/mol for cytosine, respectively. Looking at the modeling results, one of the most important factors affecting the interaction energies is hydrogen bonding. To reveal this, bond critical point analysis was performed, and it was computed that a large amount of intermolecular interaction energies came from hydrogen bonds. For example, it was calculated that approximately 70% of the total energy in the guanine/TOT (two tetrahedra and one octahedron) model comes from hydrogen bonds. Furthermore, this value for the cytosine/TOT model was found to be around 72%. The most effective indices in these two models are 145 and 135, with the Hbond energies recorded as -22.41 and -31.41 kJ/mol, respectively. Considering all analyses, it can be concluded that basal surfaces of sepiolite serve as suitable hosts for nitrogenous bases, which are the basic components of life. The aim of this study is to show that sepiolite offers an important surface feature to protect and stabilize DNA and RNA nucleic acid bases, which are necessary for the existence of living organisms, and to reveal the existence of a robust adsorption interaction between sepiolite and bases, thanks to the surface and chemical properties of sepiolite.