Elucidating the role of catalytic amino acid residues in the peptide-mediated silica oligomerization reaction mechanism.

Understanding the detailed mechanism by which the proteins of marine diatoms such as silaffins are able to control the morphology of silica oligomers has eluded synthetic chemists and materials scientists for decades. In this study, we use DFT calculations to determine how individual amino acid residues of silaffin catalyze silica dimerization. The reaction network for formation of a silica dimer was explored using several different small molecules, including water, guanidinium ions, and methylammonium ions, the latter two molecules representing analogs of arginine and lysine, both of which are known to play critical roles in enabling the catalytic function of naturally occurring protein and synthetic analogs of silaffin. It was found that the lysine analog selectively lowers the energy of a direct water removal pathway for silicate dimerization. Comparing the energy landscapes and mechanisms for various catalysts for this reaction provides direct evidence for the role of lysine side chains of silaffins in the oligmerization of silica.