Prebiotic Chemistry and Sepiolite: A Density Functional Theory Approach

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

References

1. [1] G. Biddeci, G. Spinelli, P. Colomba, and F. Di Blasi, "Halloysite Nanotubes and Sepiolite for Health Applications," Int J Mol Sci, vol. 24, Mar 2 2023.
2. [2] M. C. Hermosin, J. Cornejo, J. L. White, and S. L. Hem, "Sepiolite, a potential excipient for drugs subject to oxidative degradation," J Pharm Sci, vol. 70, pp. 189-92, Feb 1981.
3. [3] C. Aguzzi, P. Cerezo, C. Viseras, and C. Caramella, "Use of clays as drug delivery systems: Possibilities and limitations," Applied Clay Science, vol. 36, pp. 22-36, 2007.
4. [4] D. E. Bayraktepe, K. Polat, C. Yıldız, and Z. Yazan, "Electrochemical detection of bicalutamide in sepiolite clay sensing platform: Its possible electrooxidation mechanism, determination, and DNA interaction," Electroanalysis,vol. 36, no. 7, pp.1-12, 2024.
5. [5] M. D. Eduardo Ruiz-Hitzky, Francisco M. Fernandes, Bernd Wicklein, Ana C. S. Alcântara, and Pilar Aranda, "Bionanocomposites of sepiolite and palygorskite and their Medical issues," in Natural Mineral Nanotubes: Properties and Applications, G. J. C. Pooria Pasbakhsh, Ed., 1st Edition ed New York: Taylor & Francis Group, 2015.
6. [6] F. A. Castro-Smirnov, O. Pietrement, P. Aranda, J. R. Bertrand, J. Ayache, E. Le Cam, et al., "Physical interactions between DNA and sepiolite nanofibers, and potential application for DNA transfer into mammalian cells," Sci Rep, vol. 6, p. 36341, Nov 3 2016.
7. [7] F. A. Castro-Smirnov, J. Ayache, J. R. Bertrand, E. Dardillac, E. Le Cam, O. Pietrement, et al., "Cellular uptake pathways of sepiolite nanofibers and DNA transfection improvement," Sci Rep, vol. 7, p. 5586, Jul 17 2017.
8. [8] E. Gonzalez-Tortuero, J. Rodriguez-Beltran, R. Radek, J. Blazquez, and A. Rodriguez-Rojas, "Clay-induced DNA breaks as a path for genetic diversity, antibiotic resistance, and asbestos carcinogenesis," Sci Rep, vol. 8, p. 8504, May 31 2018.

9. [9] P. Mignon, G. Corbin, S. Le Crom, V. Marry, J. Hao, and I. Daniel, "Adsorption of nucleotides on clay surfaces: Effects of mineral composition, pH and solution salts," Applied Clay Science, vol. 190, p. 105544, 2020.
10. [10] T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski, "Hydrogen bonding of thymine and uracil with surface of dickite: An ab initio study," Journal of Molecular Structure, vol. 844-845, pp. 48-58, 2007.
11. [11] P. Mignon, P. Ugliengo, and M. Sodupe, "Theoretical Study of the Adsorption of RNA/DNA Bases on the External Surfaces of Na+-Montmorillonite," The Journal of Physical Chemistry C, vol. 113, pp. 13741-13749, 2009.
12. [12] S. A. Villafane-Barajas, J. P. T. Bau, M. Colin-Garcia, A. Negron-Mendoza, A. Heredia-Barbero, T. Pi-Puig, et al., "Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment," Orig Life Evol Biosph, vol. 48, pp. 181-200, Jun 2018.
13. [13] P. Mignon and M. Sodupe, "Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite," Phys Chem Chem Phys, vol. 14, pp. 945-54, Jan 14 2012.
14. [14] A. Michalkova, T. L. Robinson, and J. Leszczynski, "Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water," Phys Chem Chem Phys, vol. 13, pp. 7862-81, May 7 2011.
15. [15] P. Bhatt, C. K. Pant, P. Pandey, Y. Pandey, S. C. Sati, and M. S. Mehata, "Adsorption of cytosine on prebiotic siliceous clay surface induced with metal dications: Relevance to origin of life," Materials Chemistry and Physics, vol. 291, p. 126720, 2022.
16. [16] U. Pedreira-Segade, C. Feuillie, M. Pelletier, L. J. Michot, and I. Daniel, "Adsorption of nucleotides onto ferromagnesian phyllosilicates: Significance for the origin of life," Geochimica et Cosmochimica Acta, vol. 176, pp. 81-95, 2016.
17. [17] U. Pedreira-Segade, J. Hao, A. Razafitianamaharavo, M. Pelletier, V. Marry, S. Le Crom, et al., "How do Nucleotides Adsorb Onto Clays?," Life (Basel), vol. 8, Nov 27 2018.
18. [18] U. Pedreira-Segade, L. J. Michot, and I. Daniel, "Effects of salinity on the adsorption of nucleotides onto phyllosilicates," Phys Chem Chem Phys, vol. 20, pp. 1938-1952, Jan 17 2018.
19. [19] J. E. Post, D. L. Bish, and P. J. Heaney, "Synchrotron powder X-ray diffraction study of the structure and dehydration behavior of sepiolite," American Mineralogist, vol. 92, pp. 91-97, 2007.
20. [20] D. Karataş, D. Senol-Arslan, and O. Ozdemir, "Experimental and Atomic Modeling of the Adsorption of Acid Azo Dye 57 to Sepiolite," Clays and Clay Minerals, vol. 66, pp. 426-437, 2018.
21. [21] D. Karataş, A. Tekin, and M. S. Çelik, "Adsorption of quaternary amine surfactants and their penetration into the intracrystalline cavities of sepiolite," New Journal of Chemistry, vol. 37, p. 3936, 2013.
22. [22] D. Karataş, A. Tekin, and M. Sabri Çelik, "Density functional theory computation of organic compound penetration into sepiolite tunnels," Clays and Clay Minerals, vol. 65, pp. 1-13, 2017.
23. [23] S. G. Balasubramani, G. P. Chen, S. Coriani, M. Diedenhofen, M. S. Frank, Y. J. Franzke, et al., "TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations," J Chem Phys, vol. 152, p. 184107, May 14 2020.
24. [24] S. F. Boys and F. Bernardi, "The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors," Molecular Physics, vol. 19, pp. 553-566, 2006.
25. [25] J. Villard, M. P. Bircher, and U. Rothlisberger, "Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit," J Chem Theory Comput, vol. 19, pp. 9211-9227, Dec 26 2023.
26. [26] C. Steffen, K. Thomas, U. Huniar, A. Hellweg, O. Rubner, and A. Schroer, "TmoleX--a graphical user interface for TURBOMOLE," J Comput Chem, vol. 31, pp. 2967-70, Dec 2010.
27. [27] T. Lu and F. Chen, "Multiwfn: a multifunctional wavefunction analyzer," J Comput Chem, vol. 33, pp. 580-92, Feb 15 2012.
28. [28] L. Ismahan, N. Leila, M. Fatiha, G. Abdelkrim, C. Mouna, B. Nada, et al., "Computational study of inclusion complex of l-Glutamine/beta-Cycldextrin: Electronic and intermolecular interactions investigations," Journal of Molecular Structure, vol. 1206, p. 127740, 2020.
29. [29] A. Mehranfar, M. Izadyar, and A. N. Shamkhali, "A joint MD/QM study on the possibility of alkaloids detection by cucurbiturils and graphene oxide-cucurbituril composites," Journal of Molecular Liquids, vol. 272, pp. 963-972, 2018.
30. [30] S. Emamian, T. Lu, H. Kruse, and H. Emamian, "Exploring Nature and Predicting Strength of Hydrogen Bonds: A Correlation Analysis Between Atoms-in-Molecules Descriptors, Binding Energies, and Energy Components of Symmetry-Adapted Perturbation Theory," J Comput Chem, vol. 40, pp. 2868-2881, Dec 15 2019.
31. [31] E. Espinosa, E. Molins, and C. Lecomte, "Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities," Chemical Physics Letters, vol. 285, pp. 170-173, 1998.
32. [32] H. Yang, P. Boulet, and M.-C. Record, "A rapid method for analyzing the chemical bond from energy densities calculations at the bond critical point," Computational and Theoretical Chemistry, vol. 1178, p. 112784, 2020.
33. [33] W. F. Bleam, "The Nature of Cation-Substitution Sites in Phyllosilicates," Clays and Clay Minerals, vol. 38, no. 5, pp. 527-536, 1990.
34. [34] C. Nomicisio, M. Ruggeri, E. Bianchi, B. Vigani, C. Valentino, C. Aguzzi, et al., "Natural and Synthetic Clay Minerals in the Pharmaceutical and Biomedical Fields," Pharmaceutics, vol. 15, no. 5, pp. 1368, Apr 29 2023.