Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach

Year 2024, Volume: 13 Issue: 3, 553 - 563, 26.09.2024

Deniz Karataş

https://doi.org/10.17798/bitlisfen.1451774

Abstract

In this study, the molecular interactions of sepiolite, a biocompatibility clay mineral with known as biomaterial, and purine and pyrimidine molecules forming the bases of DNA and RNA molecules were modeled by Density Functional Theory. In addition to the geometry optimization, interaction energy, bond critical point, and electrostatic potential calculations revealed that essential molecules for our source of life interact with the basal surface of the clay. For example, the best interaction energies between bases / sepiolite were found to be -127.47, -121.35 kJ / mol for guanine and cytosine, respectively. Looking at the modeling results, one of the most important factors affecting the interaction energies is H-bond. In order to reveal this, bond critical points analyze were performed and it was computed that a large amount of intermolecular interaction energies came from H-bonds. For example, it has been calculated that close to 70% of the total energy in the guanine/TOT model is from H-bonds. Besides, this value of the cytosine/TOT model was found to be around 72%. The most effective indexes in these two models are 145 and 135, and the H-bond energies were recorded as -22.41 and 31.41 kJ/mol, respectively. Considering all the analyzes run, it can be concluded that the basal surfaces of the sepiolite are a suitable host for the nitrogenous bases, which are the main sources of life.

Keywords

Bond critical points, DFT, H-bonds, Sepiolite basal surfaces, Nucleobases

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