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Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods.

08:00 EDT 11th October 2019 | BioPortfolio

Summary of "Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods."

Triazine-based sequence-defined polymers have recently been developed that are biomimetic and robust. In molecular dynamics (MD) simulations, the triazine polymers were shown to form linear nanorod foldamers through hydrogen bonding and pi-pi interactions. The nanorod foldamers have motifs resembling those of DNA, alpha-helices, and beta-sheets, and have potential to be useful building blocks for new macromolecules and materials. To understand the formation of nanorod foldamers, we investigate how linker structures in the middle of the triazine polymers lead to folding using MD simulations. We found that a variety of linkers can participate in folding, but that specific linker structures are more favorable than others, depending on the polymer length. Folding of hexamers into well-defined nanorod foldamers was most favorable with pentanediamine and ortho-xylenediamine linkers in the center of the polymers. Foldamers with ortho-xylenediamine linkers in the center were investigated for longer polymers, i.e., octamers and decamers, using two different enhanced sampling methods, since regular MD simulations had failed to show any folding for these longer polymers. In particular, the recently developed concurrent adaptive sampling (CAS) algorithm and replica exchange molecular dynamics (REMD) were used. We found that the two enhanced sampling methods did lead to the observation of foldamers, and that REMD revealed new foldamer architectures where cis-trans isomerizations had occurred. Foldamer formation, diversity, and the strengths and limitations of simulation techniques are discussed. These findings provide new insights into the diversity of foldamer architectures for a new type of biomimetic synthetic polymer.

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Name: The journal of physical chemistry. B
ISSN: 1520-5207
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