Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. II. Structures and thermodynamics of the activated complex species.

Abstract

Amino acid activation by anhydride formation in model tetrahedral silicate and aluminate sites in clays and neutral phosphates have been studied by semi-empirical molecular orbital calculations. The results have been compared to previous ab initio studies on the reactant species and were found to be in good agreement. The geometries of all species were totally optimized and heats of formation obtained. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be A1 greater than Si greater than P which is the same order as the stability of hydrolysis. The relative efficacy of the anhydrides in promoting peptide bond formation has been evaluated using both thermodynamic and chemical reactivity criteria. Heats of reaction for model reactions were calculated from calculated enthalpies of formation of the products and reactants. The electrophilicity of the carbonyl carbon and the nucleophilicity of the oxygen were specifically used as indicators of chemical reactivity towards dipeptide formation by the activated amino acids. Our results indicate that if the reaction mechanism is dominated by the nucleophilic character of the oxygen, tetrahedral A1 sites should be more active than Si, and if the electrophilic character dominates, the order would be reversed.