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Title: Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers

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 π–π interactions, and conserve their 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 cis or 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 with the cis-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 dimers of triazine trimers. Here, we found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures,more » rather than that of the side chains, which can help researchers design more robust materials.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Stanford Univ., Stanford, CA (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1543277
Alternate Identifier(s):
OSTI ID: 1458796
Report Number(s):
PNNL-SA-132292
Journal ID: ISSN 0021-9606
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 149; Journal Issue: 7; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; polymer; biomimetic; simulation; dynamics

Citation Formats

Ahn, Surl -Hee, Grate, Jay W., and Darve, Eric F. Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers. United States: N. p., 2018. Web. doi:10.1063/1.5024552.
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Ahn, Surl -Hee, Grate, Jay W., & Darve, Eric F. Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers. United States. https://doi.org/10.1063/1.5024552
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Ahn, Surl -Hee, Grate, Jay W., and Darve, Eric F. Tue . "Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers". United States. https://doi.org/10.1063/1.5024552. https://www.osti.gov/servlets/purl/1543277.
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@article{osti_1543277,
title = {Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers},
author = {Ahn, Surl -Hee and Grate, Jay W. and Darve, Eric F.},
abstractNote = {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 π–π interactions, and conserve their 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 cis or 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 with the cis-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 dimers of triazine trimers. Here, 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.},
doi = {10.1063/1.5024552},
journal = {Journal of Chemical Physics},
number = 7,
volume = 149,
place = {United States},
year = {Tue Jul 03 00:00:00 EDT 2018},
month = {Tue Jul 03 00:00:00 EDT 2018}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1063/1.5024552
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Cited by: 7 works
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Figures / Tables:

FIG. 1 FIG. 1: Diagram of how resampling is carried out in the CAS algorithm. U(x) denotes the energy in terms of the reaction coordinate x. The simulation time is set to $τ$, and the target number of walkers per macrostate is set to 2. The walkers, represented as circles, carry weightsmore » that are represented by the black portion in the circle. The walkers are first split into two walkers for each of the visited macrostates at t = $τ$ and are merged where there are three walkers and split where there is one walker at t = 2$τ$. The WE method resampling diagram from Ref. 31 was modified to incorporate the resampling method from the CAS algorithm.« less
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