Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. I. Structures of acetic acid, glycine, H2SO4, H3PO4, Si(OH)4, and Al(OH)4?

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Abstract
Activation of amino acids appears to have played a crucial role in prebiotic peptide bond formation. As a model of this process in living systems, phosphates have been used as amino acid activators. The possible role of clay and other minerals has also been investigated. We are presently using ab initio methods to investigate the activation of amino acids by these agents, as an initial step in peptide bond formation. A model of this activation process is described by the reaction: The first step in such an investigation, reported here, was to determine the lowest energy structures of a suitable set of reactants. As initial models of amino acids, Z was chosen to be H and NH2, corresponding to acetic acid and glycine, respectively. XO4Hn+1 = H3PO4 represents a phosphate group, while Si(OH)4 describes an edge tetrahedral site of a clay mineral. Al(OH) was also included to represent a tetrahedral edge site where the silicon is replaced by an aluminum. Finally, to complete the series XO4Hn+1, H2SO4 was added to the set of reactants. All species were optimized using the STO‐3G and STO‐3G* basis sets. For H3PO4 and Al(OH) , STO‐3G* full optimizations were not possible. In these cases, certain torsional angles were optimized separately, then held at the optimized value, while the rest of the bond lengths and angles were optimized. All structures were compared to other calculations and to experimental geometries when available.