AM‐1 molecular orbital calculations of silica–alanine–nitrogen interaction

Chemical binding of proteins with bioactive surfaces is modeled using a semi-empirical molecular orbital theory (AM-1). The model calculates the optimized molecular structures of an amino acid (L-alanine) interacting with a cyclotetrasiloxane silica cluster (a four-membered hydrated silica ring). The calculated heats of formation for various orientations of alanine show +5 kcal/mol difference for binding via the -NH2 group following a condensation reaction with a pentacoordinate Si intermediate. Hydrogen bonding of the alanine via the -COOH group occurs with +13 to +15 kcal/mole differences in heats of formation and imposes a highly specific geometric orientation on the amino acid. Association of a diatomic N2 molecule with the silica cluster before interaction with alanine inhibits formation of an intermolecular bond, as is observed experimentally in studies of silica-alanine epitaxy.