Computer simulations of self-assembling nanofibers from thiophene-peptide oligomers

Abstract

Polythiophenes are conductive polymers with outstanding semiconducting, optical, electroluminescent and processing properties making them a promising compound class for applications in organic electronics, sensor design, etc. The ability to organize molecules into various functional structures at micro and nano scale in a controlled fashion is now seen as an important challenge which will contribute to the ongoing technological revolution in the field of nanotechnology. A perspective approach towards the design of such structures is the chemical conjugation of synthetic polymers with specific biopolymers which are known to self-assemble into well ordered supramolecular aggregates. Several new hybrid compounds have been recently synthesized containing the oligothiophene moiety conjugated with a beta-sheet forming peptide, which are known to self-assemble into amyloid-like fibrillar structures similar to those featured in many human diseases (Alzheimer, type II diabetes, etc.). These compounds were indeed shown to self-assemble into fibrillar aggregates (molecular nanowires) in organic solvent. However, the structure of the aggregates as well as the rational understanding of the self-assembly principles and their properties remained elusive. In this thesis we aimed at applying an arsenal of theoretical approaches, including molecular mechanics, molecular dynamics, crystalline packing prediction, dissipative particle dynamics, quantum chemistry calculations, etc. to deduce the possible atomistic models for the arrangement of the molecules in the observed fibrils, to study their morphological, conformational and conducting properties, as well as to develop a methodology for computer simulations of these complex systems.