Molecular dynamics simulations of DNA-inspired macromolecules from perylenediimide base surrogates

Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) have been extensively studied for organic electronics applications. Additionally, PTCDI-based supramolecular architectures have been used as platforms for the investigation of various charge transfer/transport phenomena. For these systems, the study of their structural characteristics and self-assembly behavior with molecular dynamics simulations has remained relatively limited. Herein, we describe a detailed molecular dynamics investigation of the intramolecular self-assembly of DNA-inspired columnar macromolecules, which consist of multiple hexaethyleneglycol-substituted PTCDIs that are covalently appended to a phosphoalkane backbone. By evaluating relevant geometric and energetic parameters obtained from our simulations, we determine the factors underpinning the dynamics of PTCDI stacking for our constructs. Our findings may shed insight into the structure of biomimetic one-dimensional molecular wires from PTCDIs and other related materials.