Does silica surface catalyse peptide bond formation? New insights from first-principles calculations

Albert Rimola, Sergio Tosoni, Mariona Sodupe, Piero Ugliengo

Research output: Contribution to journalArticleResearchpeer-review

66 Citations (Scopus)

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. Hydrogenbond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Sisurf-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nudeophilic 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 Sisurf-O-C(=O)-R is disfavoured (ΔrG298≈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 (ΔG 298≠≈48 kcal mol-1) in comparison with the uncatalysed reaction (ΔG298≠≈52 kcal mol-1). A further decrease of the free-energy barrier of peptide bond formation (ΔG298≠≈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. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.
Original languageEnglish
Pages (from-to)157-163
JournalChemPhysChem
Volume7
Issue number1
DOIs
Publication statusPublished - 16 Jan 2006

Keywords

  • Density functional calculations
  • Hydrogen bonds
  • Peptides
  • Reaction mechanisms
  • Silicates

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