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Grate and co-workers at Pacific Northwest National Laboratory recentlydeveloped high information content triazine-based sequence-defined polymersthat are robust by not having hydrolyzable bonds and can encode structure andfunctionality by having various side chains. Through molecular dynamics (MD)simulations, the triazine polymers have been shown to form particularsequential stacks, have stable backbone-backbone interactions through hydrogenbonding and $\pi$-$\pi$ interactions, and conserve their \emph{cis/trans}conformations throughout the simulation. However, we do not know the effects ofhaving different side chains and backbone structures on the entire conformationand whether the \emph{cis} or \emph{trans} conformation is more stable for thetriazine polymers. For this reason, we investigate the role of non-covalentinteractions for different side chains and backbone structures on theconformation and assembly of triazine polymers in MD simulations. Since thereis a high energy barrier associated to the \emph{cis}-\emph{trans}isomerization, we use replica exchange molecular dynamics (REMD) to samplevarious conformations of triazine hexamers. To obtain rates and intermediateconformations, we use the recently developed concurrent adaptive sampling (CAS)algorithm for dimer of triazine trimers. We found that the hydrogen bondingability of the backbone structure is critical for the triazine polymers toself-assemble into nanorod-like structures, rather than that of the sidechains, which can help researchers design more robust materials.

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