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Title: Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder

Abstract

Lignin is an abundant aromatic heteropolymer found in secondary plant cell walls and is a potential feedstock for conversion into bioderived fuels and chemicals. Lignin chemical diversity complicates traditional structural studies, and so, relatively little experimental evidence exists for how lignin structure exists in aqueous solution or how lignin polymers respond to changes in their chemical environment. Molecular modeling can address these concerns; however, prior computational structural lignin models typically did not capture lignin heterogeneity, as only a few polymers were considered. LigninBuilder creates a framework for building structural libraries for lignin from existing topological libraries, permitting significantly greater diversity of lignin structures to be sampled at atomic detail. As a demonstration of its capabilities, LigninBuilder was applied to three libraries of lignin from hardwood, softwood, and grass, and the resulting polymer structures were simulated in an aqueous environment. The lignins adopted compact globular structures, as would be expected for polymers in poor solvents. The differences between the libraries were largest when quantifying the packing of nonadjacent aromatic residues, with greater branching within the polymer resulting in poorer aromatic packing. Individual lignin polymers were also found to undergo rapid conformational changes, with the dwell time within a state growing asmore » the square of the molecular weight. This first application of LigninBuilder demonstrates the potential for atomic-level insight into lignin interactions. LigninBuilder is distributed as a plugin to the visualization software VMD, lowering the barrier for modeling lignin structure in diverse environments.« less

Authors:
 [1];  [2];  [2];  [1];  [1]
+ Show Author Affiliations
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  2. Northwestern Univ., Evanston, IL (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office
OSTI Identifier:
1494729
Report Number(s):
NREL/JA-2700-72983
Journal ID: ISSN 2168-0485
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
ACS Sustainable Chemistry & Engineering
Additional Journal Information:
Journal Volume: 7; Journal Issue: 3; Journal ID: ISSN 2168-0485
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; atomic structure; lignin modeling; molecular dynamics; polymer power laws

Citation Formats

Vermaas, Josh V., Dellon, Lauren D., Broadbelt, Linda J., Beckham, Gregg T., and Crowley, Michael F. Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder. United States: N. p., 2018. Web. doi:10.1021/acssuschemeng.8b05665.
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Vermaas, Josh V., Dellon, Lauren D., Broadbelt, Linda J., Beckham, Gregg T., & Crowley, Michael F. Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder. United States. https://doi.org/10.1021/acssuschemeng.8b05665
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Vermaas, Josh V., Dellon, Lauren D., Broadbelt, Linda J., Beckham, Gregg T., and Crowley, Michael F. Tue . "Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder". United States. https://doi.org/10.1021/acssuschemeng.8b05665. https://www.osti.gov/servlets/purl/1494729.
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@article{osti_1494729,
title = {Automated Transformation of Lignin Topologies into Atomic Structures with LigninBuilder},
author = {Vermaas, Josh V. and Dellon, Lauren D. and Broadbelt, Linda J. and Beckham, Gregg T. and Crowley, Michael F.},
abstractNote = {Lignin is an abundant aromatic heteropolymer found in secondary plant cell walls and is a potential feedstock for conversion into bioderived fuels and chemicals. Lignin chemical diversity complicates traditional structural studies, and so, relatively little experimental evidence exists for how lignin structure exists in aqueous solution or how lignin polymers respond to changes in their chemical environment. Molecular modeling can address these concerns; however, prior computational structural lignin models typically did not capture lignin heterogeneity, as only a few polymers were considered. LigninBuilder creates a framework for building structural libraries for lignin from existing topological libraries, permitting significantly greater diversity of lignin structures to be sampled at atomic detail. As a demonstration of its capabilities, LigninBuilder was applied to three libraries of lignin from hardwood, softwood, and grass, and the resulting polymer structures were simulated in an aqueous environment. The lignins adopted compact globular structures, as would be expected for polymers in poor solvents. The differences between the libraries were largest when quantifying the packing of nonadjacent aromatic residues, with greater branching within the polymer resulting in poorer aromatic packing. Individual lignin polymers were also found to undergo rapid conformational changes, with the dwell time within a state growing as the square of the molecular weight. This first application of LigninBuilder demonstrates the potential for atomic-level insight into lignin interactions. LigninBuilder is distributed as a plugin to the visualization software VMD, lowering the barrier for modeling lignin structure in diverse environments.},
doi = {10.1021/acssuschemeng.8b05665},
journal = {ACS Sustainable Chemistry & Engineering},
number = 3,
volume = 7,
place = {United States},
year = {Tue Dec 11 00:00:00 EST 2018},
month = {Tue Dec 11 00:00:00 EST 2018}
}
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https://doi.org/10.1021/acssuschemeng.8b05665
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