In the genetic-first viewpoint of the origin of Life, the RNA molecule is proposed to play the role of protein and DNA, i.e. catalyze reactions and store the genetic information essential for life to begin the long path to cellular evolution. The RNA prebiotic synthesis remained, however, a problem that has been tackled for several years by Ferris et al. (Ferris, 2005). His idea is based on clay mineral catalysis of RNA, because clays and in particular Montmorillonite deposits, largely found in volcanic ash, can adsorb organic molecules and prevent them from decomposition. Moreover clay minerals are known for their ability to catalyze organic reactions through the action of bound metal cations. In that aim Ferris investigated the oligomerization of RNA on Montmorillonite for different conditions by using activating groups and mono-metal exchanged Na+-Montmorillonite that gave up to 50-mers in one day. Following these studies our goal is to shed light on the mechanism of the formation of the phosphodiester bond catalyzed by Na+-montmorillonite by using Quantum Chemical methods. As a starting point we investigated the adsorption of RNA bases on a surface of Na+-montmorillonite. Periodic plane wave DFT calculations were performed with VASP (Kresse, 1993) on an Ottay type montmorillonite model. The cell consists of 2 unit cells of pyrophilite where one Al3+ is substituted by Mg2+. The negative charge is compensated by Na+ adsorbed on the surface of the clay. The optimized structure is then used to investigate the adsorption modes of nucleobases. Adenine, Cytosine, Guanine, Uridine and Thymine were optimized in different configurations, considering the interaction via the nitrogen and/or oxygen hetero atoms, the Na+/pi interaction, the direct interaction with the surface, and no interaction with the surface. For each optimized structure we discuss the role of the cation and the role of the surface on the energies, and geometric parameters. The Grimme correction describing the dispersion contribution (Grimme, 2006) to the energy is included to the final energy of adsorption, which allows us to discuss the effect of the Van Der Waals forces. This study follows previous works on the role of mineral material in prebiotic chemistry, in particular the formation and catalysis of the peptide bond by aluminosilicate surface (Rimola, 2007).
Theoretical Study of the Adsorption of RNA Bases on a Surface of Na+-Montmorillonite
UGLIENGO, Piero;
2009-01-01
Abstract
In the genetic-first viewpoint of the origin of Life, the RNA molecule is proposed to play the role of protein and DNA, i.e. catalyze reactions and store the genetic information essential for life to begin the long path to cellular evolution. The RNA prebiotic synthesis remained, however, a problem that has been tackled for several years by Ferris et al. (Ferris, 2005). His idea is based on clay mineral catalysis of RNA, because clays and in particular Montmorillonite deposits, largely found in volcanic ash, can adsorb organic molecules and prevent them from decomposition. Moreover clay minerals are known for their ability to catalyze organic reactions through the action of bound metal cations. In that aim Ferris investigated the oligomerization of RNA on Montmorillonite for different conditions by using activating groups and mono-metal exchanged Na+-Montmorillonite that gave up to 50-mers in one day. Following these studies our goal is to shed light on the mechanism of the formation of the phosphodiester bond catalyzed by Na+-montmorillonite by using Quantum Chemical methods. As a starting point we investigated the adsorption of RNA bases on a surface of Na+-montmorillonite. Periodic plane wave DFT calculations were performed with VASP (Kresse, 1993) on an Ottay type montmorillonite model. The cell consists of 2 unit cells of pyrophilite where one Al3+ is substituted by Mg2+. The negative charge is compensated by Na+ adsorbed on the surface of the clay. The optimized structure is then used to investigate the adsorption modes of nucleobases. Adenine, Cytosine, Guanine, Uridine and Thymine were optimized in different configurations, considering the interaction via the nitrogen and/or oxygen hetero atoms, the Na+/pi interaction, the direct interaction with the surface, and no interaction with the surface. For each optimized structure we discuss the role of the cation and the role of the surface on the energies, and geometric parameters. The Grimme correction describing the dispersion contribution (Grimme, 2006) to the energy is included to the final energy of adsorption, which allows us to discuss the effect of the Van Der Waals forces. This study follows previous works on the role of mineral material in prebiotic chemistry, in particular the formation and catalysis of the peptide bond by aluminosilicate surface (Rimola, 2007).
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