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

Title: Systematic Parameterization of Lignin for the CHARMM Force Field

Journal Article · · Green Chemistry
DOI:https://doi.org/10.1039/C8GC03209B· OSTI ID:1495650
 [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)

We develop a comprehensive molecular mechanics force field for lignin and evaluate its performance in terms of thermodynamics and structure with respect to experimental observables. The developed force field can be used to model lignin polymers, including their covalent linkages to carbohydrates, and their interaction with other biomolecules.

Research Organization:
National Renewable Energy Laboratory (NREL), Golden, CO (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
SC0018409; AC36-08GO2830; FWP ERKP752; TG-MCB09015; AC05-00OR22725
OSTI ID:
1495650
Alternate ID(s):
OSTI ID: 1484813; OSTI ID: 1502519; OSTI ID: 1506678
Report Number(s):
NREL/JA-2700-70925; GRCHFJ
Journal Information:
Green Chemistry, Vol. 21, Issue 1; ISSN 1463-9262
Publisher:
Royal Society of ChemistryCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 46 works
Citation information provided by
Web of Science

References (125)

Profiling of diferulates (plant cell wall cross-linkers) using ultrahigh-performance liquid chromatography-tandem mass spectrometry journal January 2013
Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study journal April 2012
A polymer of caffeyl alcohol in plant seeds journal January 2012
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD journal May 2016
Mechanism of lignin inhibition of enzymatic biomass deconstruction journal December 2015
Redetermination of 4-hydroxybenzaldehyde journal December 2007
Bright Side of Lignin Depolymerization: Toward New Platform Chemicals journal January 2018
Thermochemical Study of the Methoxy- and Dimethoxyphenol Isomers journal May 2003
On the stereochemistry of lignin model compounds of the arylglycerol-?-aryl ether type: Crystal structure oferythro-1-(4-hydroxy-3,5-dimethoxyphenyl)-2-(4-hydroxymethyl-2,6-dimethoxyphenoxy)-1,3-propanediol, C20H26O9 journal April 1989
Continuous Co-Crystallization As a Separation Technology: The Study of 1:2 Co-Crystals of Phenazine–Vanillin journal November 2012
Di-hydroxybenzenes: Catechol, resorcinol, and hydroquinone journal May 2008
Quantification of lignin–carbohydrate linkages with high-resolution NMR spectroscopy journal February 2011
Reactive Molecular Dynamics Simulations of Biomass Pyrolysis and Combustion under Various Oxidative and Humidity Environments journal October 2017
Proof of the presence of racemic forms of arylglycerol-Β-aryl ether structure in lignin: studies on the stereo structure of lignin by ozonation journal October 2000
A second polymorph of (+)-pinoresinol–dioxane (1/1) journal December 2003
Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate journal July 2010
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers journal September 2015
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins journal April 1998
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 journal April 2017
Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis journal November 2017
4-Hydroxy-3,5-dimethoxybenzaldehyde (syringaldehyde) journal July 2004
Constant pressure molecular dynamics simulation: The Langevin piston method journal September 1995
Radical Nature of C-Lignin journal May 2016
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Mass Spectrometry-Based Sequencing of Lignin Oligomers journal June 2010
Empirical force fields for biological macromolecules: Overview and issues journal January 2004
A Stochastic Method to Generate Libraries of Structural Representations of Lignin journal June 2016
Inhibition of lignin-derived phenolic compounds to cellulase journal March 2016
From Tree to Tape: Direct Synthesis of Pressure Sensitive Adhesives from Depolymerized Raw Lignocellulosic Biomass journal May 2018
Robustness in the fitting of molecular mechanics parameters journal March 2015
Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics journal January 2016
Stereochemistry oflignin structures of the ß-0-4 type journal January 1994
The impact of alterations in lignin deposition on cellulose organization of the plant cell wall journal June 2016
The Crystal Structure of trans-2,3-Dihydro-2-(4-hydroxy-3-methoxyphenyl)-3-hydroxymethyl-7-methoxybenzofuran. journal January 1987
Ab initio quantum chemistry: Methodology and applications journal May 2005
Feruloylation in Grasses: Current and Future Perspectives journal September 2009
The Origin of Biological Homochirality journal March 2010
Molecular dynamics with coupling to an external bath journal October 1984
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose journal September 2009
Are Lignins Optically Active? journal August 1999
Determination of vaporization enthalpies of simple organic molecules by correlations of changes in gas chromatographic net retention times journal January 1995
A Simplification of the Hartree-Fock Method journal February 1951
Large historical growth in global terrestrial gross primary production journal April 2017
Molecular simulation as a tool for studying lignin journal December 2011
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin journal March 1988
Computational Generation of Lignin Libraries from Diverse Biomass Sources journal July 2017
Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of Vaporization journal June 2011
Lignin Composition and Structure Differs between Xylem, Phloem and Phellem in Quercus suber L. journal October 2016
A (sub)graph isomorphism algorithm for matching large graphs journal October 2004
Matplotlib: A 2D Graphics Environment journal January 2007
threo -2-(2,6-Dimethoxyphenoxy)-1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,3-diol: a conformational study journal March 2005
Machine Learning Force Fields: Construction, Validation, and Outlook journal December 2016
A molecular mechanics force field for lignin journal February 2009
Determining the Composition of Lignins in Different Tissues of Silver Birch journal April 2015
Note on an Approximation Treatment for Many-Electron Systems journal October 1934
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling journal August 2011
Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C–H···O Hydrogen Bond journal November 2012
The NumPy Array: A Structure for Efficient Numerical Computation journal March 2011
Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification journal December 2014
Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies journal November 2010
VMD: Visual molecular dynamics journal February 1996
Building Force Fields: An Automatic, Systematic, and Reproducible Approach journal May 2014
Lignin Biosynthesis journal June 2003
Tricin, a Flavonoid Monomer in Monocot Lignification journal February 2015
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits journal January 2017
Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem journal July 2014
Studies on Lignin Model Compounds of the beta-O-4 Type: Crystal Structures of threo-1-(4-Hydroxy-3,5-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol and 3-Hydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1-propanone--Methanol (1/1). journal January 1988
Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance journal November 2016
Cell-wall carbohydrates and their modification as a resource for biofuels journal May 2008
Structural Analysis of Wheat Straw Lignin by Quantitative 31 P and 2D NMR Spectroscopy. The Occurrence of Ester Bonds and α-O-4 Substructures journal April 1997
The Cambridge Structural Database
  • 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 https://doi.org/10.1107/S2052520616003954
journal April 2016
Scalable molecular dynamics with NAMD journal January 2005
GROMACS: Fast, flexible, and free journal January 2005
Understanding the role of water during ionic liquid pretreatment of lignocellulose: co-solvent or anti-solvent? journal January 2014
P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation journal December 2007
The Nose–Hoover thermostat journal October 1985
erythro -2-(2,6-Dimethoxyphenoxy)-1-(4-hydroxy-3,5-dimethoxyphenyl)-1,3-propanediol journal December 2001
XSEDE: Accelerating Scientific Discovery journal September 2014
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing journal November 2012
Significance of Lignin S/G Ratio in Biomass Recalcitrance of Populus trichocarpa Variants for Bioethanol Production journal December 2017
Additive empirical force field for hexopyranose monosaccharides journal November 2008
5,5′-Bis(hydroxymethyl)-3,3′-dimethoxybiphenyl-2,2′-diol with a new three-dimensional 3-modal topology of synthons journal November 2010
VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems journal March 2016
Stereochemistry of lignin structures of the arylglycerol ß-aryl ether type journal January 1996
Rapid parameterization of small molecules using the force field toolkit journal September 2013
Development and testing of a general amber force field journal January 2004
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges journal November 2012
Quantification of Lignin and Its Structural Features in Plant Biomass Using 13 C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS journal October 2017
Biomolecular Simulation: A Computational Microscope for Molecular Biology journal June 2012
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins journal December 2015
Complexes with lignin model compound vanillic acid. Two different carboxylate ligands in the same dinuclear tetracarboxylate complex [Cu2(C8H7O4)2(O2CCH3)2(CH3OH)2] journal March 2006
Machine Learning Force Field Parameters from Ab Initio Data journal August 2017
Lignin Radicals in the Plant Cell Wall Probed by Kerr-Gated Resonance Raman Spectroscopy journal April 2006
Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals journal August 2017
Lignin Biosynthesis and Structure journal May 2010
Computational ‘microscopy’ of cellular membranes journal January 2016
Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny journal November 2016
Lignin Valorization: Improving Lignin Processing in the Biorefinery journal May 2014
Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration journal March 2014
Additive CHARMM force field for naturally occurring modified ribonucleotides: CHARMM Potential Energy Function journal February 2016
Synthesis and crystal structure determination of model compounds for the dibenzodioxocine structure occurring in wood lignins journal January 1996
On the Occurrence of Structural Elements of the Lignan Type (ß—ß Structures) in Lignins - The Crystal Structures of (+)-Pinoresinol and (±)- trans -3,4-Divanillyltetrahydrofuran journal January 1988
Variation in susceptibility to microbial lignin oxidation in a set of wheat straw cultivars: influence of genetic, seasonal and environmental factors - OPEN ACCESS journal December 2017
Constant temperature simulations using the Langevin equation with velocity Verlet integration journal September 1998
Scalable parallel programming with CUDA journal March 2008
Lignin-derived inhibition of monocomponent cellulases and a xylanase in the hydrolysis of lignocellulosics journal May 2017
Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization journal December 1997
Superior plant based carbon fibers from electrospun poly-(caffeyl alcohol) lignin journal July 2016
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses journal August 2009
Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity journal December 2016
(+)-Pinoresinol–dioxane (1/1) journal November 2003
Cellulase–lignin interactions—The role of carbohydrate-binding module and pH in non-productive binding journal October 2013
A smooth particle mesh Ewald method journal November 1995
Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant journal March 2014
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data journal July 2013
Crystal structure of 2,3,4,5,6-pentaacetyl-(N-allyl)-D-gluconamide, C19H27NO11 journal April 1998
The origin of biological homochirality journal October 2011
Rational identification and characterisation of peptide ligands for targeting polysialic acid journal May 2020
NADPH levels affect cellular epigenetic state by inhibiting HDAC3–Ncor complex journal January 2021
The Origin of Biological Homochirality journal March 2019
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost text January 2017
Profiling of diferulates (plant cell wall cross-linkers) using ultrahigh-performance liquid chromatography-tandem mass spectrometry text January 2013
Scalable parallel programming with CUDA conference January 2008
Machine learning force fields: Construction, validation, and outlook preprint January 2016

Cited By (1)

Passive membrane transport of lignin-related compounds journal October 2019