# Investigating the Role of Non-Covalent Interactions in Conformation and Assembly of Triazine-Based Sequence-Defined Polymers

## TL;DR

This study uses advanced molecular dynamics simulations to explore how non-covalent interactions influence the conformation and assembly of triazine-based polymers, revealing the importance of backbone hydrogen bonding in nanostructure formation.

## Contribution

It introduces the use of REMD and CAS algorithms to analyze conformational dynamics and assembly pathways of triazine polymers, highlighting the role of backbone interactions.

## Key findings

- Backbone hydrogen bonding is crucial for nanorod assembly.
- Side chain variations have less impact on self-assembly.
- Conformational stability depends on backbone structure.

## 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 structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and $\pi$-$\pi$ interactions, and conserve their \emph{cis/trans} conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the \emph{cis} or \emph{trans} conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated to the \emph{cis}-\emph{trans} isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimer of triazine trimers. We found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.