Foundations of Molecular Modeling and Simulation

Part of the series Molecular Modeling and Simulation pp 21-35


Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation

  • K. G. SprengerAffiliated withDepartment of Chemical Engineering, University of Washington
  • , Yi HeAffiliated withCollege of Chemical and Biological Engineering, Zhejiang University
  • , Jim PfaendtnerAffiliated withDepartment of Chemical Engineering, University of Washington Email author 

* Final gross prices may vary according to local VAT.

Get Access


Due to their flexible chemical functionality and simple formulation, self-assembled monolayer (SAM) surfaces have become an ideal choice for a multitude of wide-ranging applications. However, a major issue in the preparation of SAM surfaces is naturally occurring defects that manifest in a number of different ways, including depressions in the underlying gold substrate that cause surface roughness or through incorrect self-assembly of the chains that causes domain boundary effects. Molecular simulations can provide valuable insight into the origins of these defects and the effect they have on biological and other processes. Molecular dynamics (MD) simulations have been performed on a SAM surface with a carboxylic acid/carboxylate terminal functionality and induced with two types of experimentally observed defects. The enhanced sampling method PTMetaD-WTE has been used to model the adsorption of LKα14 onto the two types of defective SAM surfaces and onto a control SAM surface with no defective chains. An advanced clustering algorithm has been used to elucidate the effect of the surface defects on the conformations of the adsorbed peptide. Results show significant structural differences arise as a result of the defects. Specifically, both types of defects lead to a near-complete loss of secondary structure of the adsorbed peptide as compared to the control simulation, in which LKα14 adopts a perfect helical structure at the SAM/water interface. On the surface with domain boundary effects, extended conformations of the peptide are stabilized, whereas on the SAM with surface roughness (i.e., chains of various lengths), random coil conformations dominate the ensemble of surface-bound structures.


Self-assembled monolayers Surface defects Peptide adsorption Molecular dynamics Enhanced sampling