skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on November 27, 2019

Title: Systematic Parameterization of Lignin for the CHARMM Force Field

Abstract

Lignin is an abundant aromatic biopolymer within plant cell walls formed through radical coupling chemistry, whose composition and topology can vary greatly depending on the biomass source. Computational modeling provides a complementary approach to traditional experimental techniques to probe lignin interactions, lignin structure, and lignin material properties. However, current modeling approaches are limited based on the subset of lignin chemistries covered by existing lignin force fields. To fill the gap, we developed a comprehensive lignin force field that accounts for more lignin-lignin and lignin-carbohydrate interlinkages than existing lignin force fields, and also greatly expands the lignin monomer chemistries that can be modeled beyond simple alcohols and into the rich mixture of natural lignin varieties. The development of this force field utilizes recent developments in parameterization methodology, and synthesizes them into a workflow that combines target data from multiple molecules simultaneously into a single consistent and comprehensive parameter set. The parameter set represents a significant improvement to alternatives for atomic modeling of diverse lignin topologies, more accurately reproducing experimental observables while also significantly reducing the error relative to quantum calculations. The improved energetics, as well as the rigid adherence to CHARMM parameterization philosophy, enables simulation of lignin within its biological contextmore » with greater accuracy than was previously possible. The lignin force field presented here is therefore a crucial first step towards modeling lignin structure across a broad range of environments, including within plant cell walls where lignin is complexed with carbohydrates and deconstructed by bacterial or fungal enzymes, or as it exists within industrial solvent mixtures. Future simulations enabled by this updated lignin force field will thus lead to better chemical and structural understanding of lignin, providing new insight into its role in biomass recalcitrance or probing the potential for lignin to be used within industrial processes.« less

Authors:
 [1];  [2];  [3];  [1];  [4]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of Wisconsin, Madison, WI (United States)
  4. Univ. of Wisconsin, Madison, WI (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1495650
Alternate Identifier(s):
OSTI ID: 1484813; OSTI ID: 1502519; OSTI ID: 1506678
Report Number(s):
NREL/JA-2700-70925
Journal ID: ISSN 1463-9262; GRCHFJ
Grant/Contract Number:  
SC0018409; AC36-08GO2830; FWP ERKP752; TG-MCB09015; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Green Chemistry
Additional Journal Information:
Journal Volume: 21; Journal Issue: 1; Journal ID: ISSN 1463-9262
Publisher:
Royal Society of Chemistry
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; molecular dynamics; force field parameterization; lignin

Citation Formats

Vermaas, Josh V., Petridis, Loukas, Ralph, John, Crowley, Michael F., and Beckham, Gregg T. Systematic Parameterization of Lignin for the CHARMM Force Field. United States: N. p., 2018. Web. doi:10.1039/C8GC03209B.
Vermaas, Josh V., Petridis, Loukas, Ralph, John, Crowley, Michael F., & Beckham, Gregg T. Systematic Parameterization of Lignin for the CHARMM Force Field. United States. doi:10.1039/C8GC03209B.
Vermaas, Josh V., Petridis, Loukas, Ralph, John, Crowley, Michael F., and Beckham, Gregg T. Tue . "Systematic Parameterization of Lignin for the CHARMM Force Field". United States. doi:10.1039/C8GC03209B.
@article{osti_1495650,
title = {Systematic Parameterization of Lignin for the CHARMM Force Field},
author = {Vermaas, Josh V. and Petridis, Loukas and Ralph, John and Crowley, Michael F. and Beckham, Gregg T.},
abstractNote = {Lignin is an abundant aromatic biopolymer within plant cell walls formed through radical coupling chemistry, whose composition and topology can vary greatly depending on the biomass source. Computational modeling provides a complementary approach to traditional experimental techniques to probe lignin interactions, lignin structure, and lignin material properties. However, current modeling approaches are limited based on the subset of lignin chemistries covered by existing lignin force fields. To fill the gap, we developed a comprehensive lignin force field that accounts for more lignin-lignin and lignin-carbohydrate interlinkages than existing lignin force fields, and also greatly expands the lignin monomer chemistries that can be modeled beyond simple alcohols and into the rich mixture of natural lignin varieties. The development of this force field utilizes recent developments in parameterization methodology, and synthesizes them into a workflow that combines target data from multiple molecules simultaneously into a single consistent and comprehensive parameter set. The parameter set represents a significant improvement to alternatives for atomic modeling of diverse lignin topologies, more accurately reproducing experimental observables while also significantly reducing the error relative to quantum calculations. The improved energetics, as well as the rigid adherence to CHARMM parameterization philosophy, enables simulation of lignin within its biological context with greater accuracy than was previously possible. The lignin force field presented here is therefore a crucial first step towards modeling lignin structure across a broad range of environments, including within plant cell walls where lignin is complexed with carbohydrates and deconstructed by bacterial or fungal enzymes, or as it exists within industrial solvent mixtures. Future simulations enabled by this updated lignin force field will thus lead to better chemical and structural understanding of lignin, providing new insight into its role in biomass recalcitrance or probing the potential for lignin to be used within industrial processes.},
doi = {10.1039/C8GC03209B},
journal = {Green Chemistry},
number = 1,
volume = 21,
place = {United States},
year = {2018},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on November 27, 2019
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Lignin Biosynthesis
journal, June 2003


Cell-wall carbohydrates and their modification as a resource for biofuels
journal, May 2008


The Cambridge Structural Database
journal, April 2016

  • Groom, Colin R.; Bruno, Ian J.; Lightfoot, Matthew P.
  • Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials, Vol. 72, Issue 2, p. 171-179
  • DOI: 10.1107/S2052520616003954

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Lignin Biosynthesis and Structure
journal, May 2010

  • Vanholme, R.; Demedts, B.; Morreel, K.
  • Plant Physiology, Vol. 153, Issue 3, p. 895-905
  • DOI: 10.1104/pp.110.155119

Lignin Valorization: Improving Lignin Processing in the Biorefinery
journal, May 2014

  • Ragauskas, A. J.; Beckham, G. T.; Biddy, M. J.
  • Science, Vol. 344, Issue 6185, p. 1246843-1246843
  • DOI: 10.1126/science.1246843

Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant
journal, March 2014

  • Bonawitz, Nicholas D.; Kim, Jeong Im; Tobimatsu, Yuki
  • Nature, Vol. 509, Issue 7500, p. 376-380
  • DOI: 10.1038/nature13084