Does Silica Surface Catalyse Peptide Bond Formation? New Insights from First‐Principles Calculations

Abstract

The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6-31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen-bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Si(surf)-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6-31+G(d,p) calculations show that formation of the surface mixed anhydride Si(surf)-O-C(=O)-R is disfavoured (delta(r)G298 approximately 6 kcal mol(-1)), and that the surface bond only moderately lowers the free-energy barrier of the nucleophilic attack responsible for peptide bond formation (deltaG298(double dagger) approximately 48 kcal mol(-1)) in comparison with the uncatalysed reaction (deltaG298(double dagger) approximately 52 kcal mol(-1)). A further decrease of the free-energy barrier of peptide bond formation (deltaG298(double dagger) approximately 41 kcal mol(-1)) is achieved by a single water molecule close to the reaction centre acting as a proton-transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride Si(surf)-O-C(=O)-R has also been addressed.

Mechanism of promoted dipeptide formation on hydroxyapatite crystal surfaces

“…Furthermore, the role of silica has been already highlighted in previous studies on mineral-assisted condensation. In comparison, it was reported that the adsorption of Gly on silica reduced the E a by only 10% [40]. In our experiment, HAP decreased the E a of Gly condensation by more than 60%.…”

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

“…Drawn from data of Refs. 74,223 The value of 1699 cm -1 represents the maximum bathochromic shift (-85 cm -1 ) of the (C=O) fingerprint mode and results from the H-bonding with two different terminal silanol groups (see "double H-bonding" interaction pattern in Figure 62). Theoretical results indicate that the interaction of Gly with silica surfaces may also take place with only one SiOH group through the "single H-bonding" interaction pattern (see Figure 62).…”

Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

“…Due to the relatively small size of such systems, ab initio and DFT calculations could be carried out for these computational studies. [15][16][17] Of particular interest to the present contribution is the work of Rimola et al [16] These authors claimed that a direct glycine-silica interaction is possible without the need of having water molecules as a solvent. Moreover, the hydroxylated silica surface was shown to stabilize the glycine zwitterionic form.…”