Large-scale atomistic simulation of a nanosized fibril formed by thiophene–peptide “molecular chimeras”

Abstract

We present the results of an extensive molecular dynamics simulation aimed at investigating the structural organization of a nanosized fibrillar aggregate formed by bioinspired diblock copolymers consisting of oligothiophene and β-sheet-forming peptide parts. The main motivation of our study is that those supramolecular structures can be promising for nanoelectronic and other advanced technological applications. In order to construct the initial fibril configuration, a rational approach based on predicting the likely polymorphic structures that are favorable to the formation of fibrils is used. We demonstrate that the system simulated in this work is very stable, at least on the nanosecond timescale, and can be viewed globally as a linear “super-polymer” that exhibits a large length-to-thickness ratio (∼20). The average content of secondary structure elements (β-sheets, bridges, turns, and coils) in the peptide-containing domains as well as the fraction of the thiophene rings participating in π–π-stacking interactions is also analyzed.