Electronic Properties of a Graphene Device with Peptide Adsorption: Insight from Simulation

Abstract

In this work, to explain doping behavior of single-layer graphene upon HSSYWYAFNNKT (P1) and HSSAAAAFNNKT (P1-3A) adsorption in field-effect transistors (GFETs), we applied a combined computational approach, whereby peptide adsorption was modeled by molecular dynamics simulations, and the lowest energy configuration was confirmed by density functional theory calculations. On the basis of the resulting structures of the hybrid materials, electronic structure and transport calculations were investigated. We demonstrate that π-π stacking of the aromatic residues and proximate peptide backbone to the graphene surface in P1 have a role in the p-doping. These results are consistent with our experimental observation of the GFET's p-doping even after a 24-h annealing procedure. Upon substitution of three of the aromatic residues to Ala in (P1-3A), a considerable decrease from p-doping is observed experimentally, demonstrating n-doping as compared to the nonadsorbed device, yet not explained based on the atomistic MD simulation structures. To gain a qualitative understanding of P1-3A's adsorption over a longer simulation time, which may differ from aromatic amino acid residues' swift anchoring on the surface, we analyzed equilibrated coarse-grain simulations performed for 500 ns. Desorption of the Ala residues from the surface was shown computationally, which could in turn affect charge transfer, yet a full explanation of the mechanism of n-doping will require elucidation of differences between various aromatic residues as dependent on peptide composition, and inclusion of effects of the substrate and environment, to be considered in future work.

Modeling and simulation of protein–surface interactions: achievements and challenges

“…The interaction of quartz and aluminosilicate structures with phospholipids was also studied by DFT to understand why the enzyme phospholipase A2 digests phospholipids faster in the presence of quartz than aluminosilicates (Snyder & Madura, 2008). The interaction of amino-acids with graphene has also been the subject of recent DFT studies (Akdim et al 2013;Wang et al 2014).…”

“…They discussed the driving force for the adsorption and the role of the surface in determining the peptide folding. A system of similar size (a dodecapeptide on a graphene sheet) has also been investigated by Akdim et al (2013) to confirm by DFT the adsorbed peptide geometries obtained with a classical force-field.…”

“…Various corrections have been proposed to solve this problem (Tkatchenko et al 2010), and some of them have also been tested in the framework of protein-surface interactions with encouraging results. In particular, the DFT-Dn methods (Grimme, 2004;Grimme et al 2010;Wu et al 2001) (that add to the DFT energy, empirical atom-atom d −6 terms, where d is the pairwise interatomic distance, suitably damped for small d) have been used for amino acid and peptide adsorption on mineral surfaces (Folliet et al 2013;Rimola et al 2009) and on graphene (Akdim et al 2013). The f xc functional, vdW-DF, which does not contain empirical terms (Dion et al 2004), has been tested against experimental desorption energy data for some small molecules on Au(111) (Wright et al 2013a).…”

“…The behavior of water on different types of TiO 2 surfaces, including partial dissociation of water, was investigated using the reactive FF ReaxFF Kim et al 2013) and AIMD (Carravetta et al 2009;Schneider & Colombi Ciacchi, 2011). More details on theoretical studies of titania-water interactions can be found in the review by Sun et al (2010).…”

Aqueous Peptide–TiO2 Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

“…[1][2][3][4] Use of bioinspired approaches to realize the nucleation, growth and functionalization of materials in aqueous media, principally by the addition of peptides [5][6] shows exciting promise, and has become the subject of intense scrutiny for a range of materials 7 , such as noble metals, [8][9] graphene [10][11] and silica, 12 in addition to titania (TiO2).…”