PNNL

Abstract

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode information by having various side chains (Grate et al., Angewandte Chemie 2016;55.12;3925-3930). Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particu- lar sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and p - p interactions, and conserve their cis/trans conformations through- out the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we in- vestigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simula- tions. Since there is a high energy barrier associated to the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conforma- tions of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm (Ahn et al., JCP 2017;147.7;074115) for dimer of triazine trimers. We found that REMD and the CAS algorithm are suitable enhanced sampling methods for this problem and that the hydrogen bonding ability of the backbone structure is essential for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains. This can help researchers design more robust materials.