Computer simulations to explore prebiotic chemical processes
RNA production and its subsequent accumulation and polymerization in the primitive Earth are part of the key events behind the RNA World hypothesis. In this regard, many efforts have been dedicated to explore RNA synthesis under different plausible prebiotic conditions, comprising the catalytic function of mineral surfaces, the role of salts or lipid compounds, the exposure to drying/wetting cycles, and so forth [1]. However, one of the main challenges is to achieve the formation of RNA monomers (ribonucleotides) that subsequently polymerize to constitute larger RNA oligomers potentially able to perform more complex chemical systems. In this work, we provide quantitative new insights on the chemical reactions of ribonucleotides synthesis under hydrothermal prebiotic environments, performing ab initio molecular dynamics simulations explicitly taking into account water molecules and in presence of a biological pentose phosphate precursor (PRPP). Additionally, we exploit free-energy methods [2,3] in combination with a topological approach that accurately tracks the chemical bond network along a reaction path [4]. From this framework, we are able to unveil a mechanism of ribonucleotide synthesis, as well as to quantitatively assess the thermodynamic properties of this chemical process [5]. Additionally, we performed Mass Spectroscopy experiments to monitor the formation of ribonucleotides under hydrothermal conditions explored by the in-silico approaches. From this framework we identified a common precursor of ribonucleotide synthesis for both current biological systems and primitive hydrothermal conditions.
[1] Forsythe JG et al (2015) Angewandte Chemie 127:10009–10013.
[2] Laio, Parrinello (2002) PNAS 99:12562–12566.
[3] Torrie GM and Valleau JP (1977) J Comp Phys 23:187–199.
[4] Pietrucci, Saitta (2015) PNAS 112:15030–15035.
[5] Pérez-Villa A et al. (2018) JPCL 9 (17), 4981-4987