Systematic Parameterization of Lignin for the CHARMM Force Field

Vermaas, Josh V.; Petridis, Loukas; Ralph, John; Crowley, Michael F.; Beckham, Gregg T.

doi:10.1039/C8GC03209B

Title: Systematic Parameterization of Lignin for the CHARMM Force Field

Journal Article · 27 November 2018 · Green Chemistry

DOI: https://doi.org/10.1039/C8GC03209B · OSTI ID:1495650

Vermaas, Josh V. ^[1]; Petridis, Loukas ^[2]; Ralph, John ^[3]; Crowley, Michael F. ^[1]; Beckham, Gregg T. ^[4]

National Renewable Energy Lab. (NREL), Golden, CO (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of Wisconsin, Madison, WI (United States)
Univ. of Wisconsin, Madison, WI (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)

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.

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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

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Cited by: 46 works

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References (125)

Profiling of diferulates (plant cell wall cross-linkers) using ultrahigh-performance liquid chromatography-tandem mass spectrometry Vismeh, Ramin; Lu, Fachuang; Chundawat, Shishir P. S. The Analyst, Vol. 138, Issue 21 https://doi.org/10.1039/c3an36709f	journal	January 2013
Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study Sangha, Amandeep K.; Parks, Jerry M.; Standaert, Robert F. The Journal of Physical Chemistry B, Vol. 116, Issue 16 https://doi.org/10.1021/jp2122449	journal	April 2012
A polymer of caffeyl alcohol in plant seeds Chen, F.; Tobimatsu, Y.; Havkin-Frenkel, D. Proceedings of the National Academy of Sciences, Vol. 109, Issue 5 https://doi.org/10.1073/pnas.1120992109	journal	January 2012
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD Vermaas, Josh V.; Hardy, David J.; Stone, John E. Journal of Chemical Information and Modeling, Vol. 56, Issue 6 https://doi.org/10.1021/acs.jcim.6b00103	journal	May 2016
Mechanism of lignin inhibition of enzymatic biomass deconstruction Vermaas, Josh V.; Petridis, Loukas; Qi, Xianghong Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0379-8	journal	December 2015
Redetermination of 4-hydroxybenzaldehyde Jasinski, Jerry P.; Butcher, Ray J.; Narayana, B. Acta Crystallographica Section E Structure Reports Online, Vol. 64, Issue 1 https://doi.org/10.1107/S1600536807063659	journal	December 2007
Bright Side of Lignin Depolymerization: Toward New Platform Chemicals Sun, Zhuohua; Fridrich, Bálint; de Santi, Alessandra Chemical Reviews, Vol. 118, Issue 2 https://doi.org/10.1021/acs.chemrev.7b00588	journal	January 2018
Thermochemical Study of the Methoxy- and Dimethoxyphenol Isomers Matos, M. Agostinha R.; Miranda, Margarida S.; Morais, Victor M. F. Journal of Chemical & Engineering Data, Vol. 48, Issue 3 https://doi.org/10.1021/je025641j	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 Stomberg, Rolf; Lundquist, Knut Journal of Crystallographic and Spectroscopic Research, Vol. 19, Issue 2 https://doi.org/10.1007/BF01194128	journal	April 1989
Continuous Co-Crystallization As a Separation Technology: The Study of 1:2 Co-Crystals of Phenazine–Vanillin Lee, Tu; Chen, Hsin Rong; Lin, Hong Yu Crystal Growth & Design, Vol. 12, Issue 12 https://doi.org/10.1021/cg300763t	journal	November 2012
Di-hydroxybenzenes: Catechol, resorcinol, and hydroquinone Verevkin, Sergey P.; Kozlova, Svetlana A. Thermochimica Acta, Vol. 471, Issue 1-2 https://doi.org/10.1016/j.tca.2008.02.016	journal	May 2008
Quantification of lignin–carbohydrate linkages with high-resolution NMR spectroscopy Balakshin, Mikhail; Capanema, Ewellyn; Gracz, Hanna Planta, Vol. 233, Issue 6 https://doi.org/10.1007/s00425-011-1359-2	journal	February 2011
Reactive Molecular Dynamics Simulations of Biomass Pyrolysis and Combustion under Various Oxidative and Humidity Environments Chen, Chao; Zhao, Lingling; Wang, Jingfan Industrial & Engineering Chemistry Research, Vol. 56, Issue 43 https://doi.org/10.1021/acs.iecr.7b01714	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 Akiyama, Takuya; Magara, Kengo; Matsumoto, Yuji Journal of Wood Science, Vol. 46, Issue 5 https://doi.org/10.1007/BF00776407	journal	October 2000
A second polymorph of (+)-pinoresinol–dioxane (1/1) Stomberg, Rolf; Langer, Vratislav; Lundquist, Knut Acta Crystallographica Section E Structure Reports Online, Vol. 60, Issue 1 https://doi.org/10.1107/S1600536803027806	journal	December 2003
Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate Beer, C.; Reichstein, M.; Tomelleri, E. Science, Vol. 329, Issue 5993 https://doi.org/10.1126/science.1184984	journal	July 2010
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 Wang, Lee-Ping; McKiernan, Keri A.; Gomes, Joseph The Journal of Physical Chemistry B, Vol. 121, Issue 16 https://doi.org/10.1021/acs.jpcb.7b02320	journal	April 2017
Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis Smith, Micholas Dean; Cheng, Xiaolin; Petridis, Loukas Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-15048-7	journal	November 2017
4-Hydroxy-3,5-dimethoxybenzaldehyde (syringaldehyde) Kolev, Tsonko; Wortmann, Rüdiger; Spiteller, Michael Acta Crystallographica Section E Structure Reports Online, Vol. 60, Issue 8 https://doi.org/10.1107/S1600536804017015	journal	July 2004
Constant pressure molecular dynamics simulation: The Langevin piston method Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W. The Journal of Chemical Physics, Vol. 103, Issue 11 https://doi.org/10.1063/1.470648	journal	September 1995
Radical Nature of C-Lignin Berstis, Laura; Elder, Thomas; Crowley, Michael ACS Sustainable Chemistry & Engineering, Vol. 4, Issue 10 https://doi.org/10.1021/acssuschemeng.6b00520	journal	May 2016
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Mass Spectrometry-Based Sequencing of Lignin Oligomers Morreel, Kris; Dima, Oana; Kim, Hoon Plant Physiology, Vol. 153, Issue 4 https://doi.org/10.1104/pp.110.156489	journal	June 2010
Empirical force fields for biological macromolecules: Overview and issues Mackerell, Alexander D. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20082	journal	January 2004
A Stochastic Method to Generate Libraries of Structural Representations of Lignin Yanez, Abraham J.; Li, Wenjun; Mabon, Ross Energy & Fuels, Vol. 30, Issue 7 https://doi.org/10.1021/acs.energyfuels.6b00966	journal	June 2016
Inhibition of lignin-derived phenolic compounds to cellulase Qin, Lei; Li, Wen-Chao; Liu, Li Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0485-2	journal	March 2016
From Tree to Tape: Direct Synthesis of Pressure Sensitive Adhesives from Depolymerized Raw Lignocellulosic Biomass Wang, Shu; Shuai, Li; Saha, Basudeb ACS Central Science, Vol. 4, Issue 6 https://doi.org/10.1021/acscentsci.8b00140	journal	May 2018
Robustness in the fitting of molecular mechanics parameters Vanommeslaeghe, Kenno; Yang, Mingjun; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 36, Issue 14 https://doi.org/10.1002/jcc.23897	journal	March 2015
Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics Smith, Micholas Dean; Mostofian, Barmak; Cheng, Xiaolin Green Chemistry, Vol. 18, Issue 5 https://doi.org/10.1039/C5GC01952D	journal	January 2016
Stereochemistry oflignin structures of the ß-0-4 type Stomberg, Rolf; Lundquist, Knut Nordic Pulp & Paper Research Journal, Vol. 9, Issue 1 https://doi.org/10.3183/NPPRJ-1994-09-01-p037-043	journal	January 1994
The impact of alterations in lignin deposition on cellulose organization of the plant cell wall Liu, Jiliang; Kim, Jeong Im; Cusumano, Joanne C. Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0540-z	journal	June 2016
The Crystal Structure of trans-2,3-Dihydro-2-(4-hydroxy-3-methoxyphenyl)-3-hydroxymethyl-7-methoxybenzofuran. Stomberg, Rolf; Lundquist, Knut; Koziol, Jacek Acta Chemica Scandinavica, Vol. 41b https://doi.org/10.3891/acta.chem.scand.41b-0304	journal	January 1987
Ab initio quantum chemistry: Methodology and applications Friesner, R. A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 19 https://doi.org/10.1073/pnas.0408036102	journal	May 2005
Feruloylation in Grasses: Current and Future Perspectives de O. Buanafina, Marcia M. Molecular Plant, Vol. 2, Issue 5 https://doi.org/10.1093/mp/ssp067	journal	September 2009
The Origin of Biological Homochirality Blackmond, D. G. Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 5 https://doi.org/10.1101/cshperspect.a002147	journal	March 2010
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	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 Best, Robert B.; Zhu, Xiao; Shim, Jihyun Journal of Chemical Theory and Computation, Vol. 8, Issue 9 https://doi.org/10.1021/ct300400x	journal	August 2012
CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D. The Journal of Physical Chemistry B, Vol. 113, Issue 37 https://doi.org/10.1021/jp905496e	journal	September 2009
Are Lignins Optically Active? Ralph, John; Peng, Junpeng; Lu, Fachuang Journal of Agricultural and Food Chemistry, Vol. 47, Issue 8 https://doi.org/10.1021/jf9901136	journal	August 1999
Determination of vaporization enthalpies of simple organic molecules by correlations of changes in gas chromatographic net retention times Chickos, James S.; Hosseini, Sarah; Hesse, Donald G. Thermochimica Acta, Vol. 249 https://doi.org/10.1016/0040-6031(95)90670-3	journal	January 1995
A Simplification of the Hartree-Fock Method Slater, J. C. Physical Review, Vol. 81, Issue 3 https://doi.org/10.1103/PhysRev.81.385	journal	February 1951
Large historical growth in global terrestrial gross primary production Campbell, J. E.; Berry, J. A.; Seibt, U. Nature, Vol. 544, Issue 7648 https://doi.org/10.1038/nature22030	journal	April 2017
Molecular simulation as a tool for studying lignin Sangha, Amandeep K.; Petridis, Loukas; Smith, Jeremy C. Environmental Progress & Sustainable Energy, Vol. 31, Issue 1 https://doi.org/10.1002/ep.10628	journal	December 2011
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin Jorgensen, William L.; Tirado-Rives, Julian Journal of the American Chemical Society, Vol. 110, Issue 6 https://doi.org/10.1021/ja00214a001	journal	March 1988
Computational Generation of Lignin Libraries from Diverse Biomass Sources Dellon, Lauren D.; Yanez, Abraham J.; Li, Wenjun Energy & Fuels, Vol. 31, Issue 8 https://doi.org/10.1021/acs.energyfuels.7b01150	journal	July 2017
Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of Vaporization Wang, Junmei; Hou, Tingjun Journal of Chemical Theory and Computation, Vol. 7, Issue 7 https://doi.org/10.1021/ct200142z	journal	June 2011
Lignin Composition and Structure Differs between Xylem, Phloem and Phellem in Quercus suber L. Lourenço, Ana; Rencoret, Jorge; Chemetova, Catarina Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01612	journal	October 2016
A (sub)graph isomorphism algorithm for matching large graphs Cordella, L. P.; Foggia, P.; Sansone, C. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 26, Issue 10 https://doi.org/10.1109/TPAMI.2004.75	journal	October 2004
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
threo -2-(2,6-Dimethoxyphenoxy)-1-(4-hydroxy-3,5-dimethoxyphenyl)propane-1,3-diol: a conformational study Lundquist, Knut; Li, Shiming; Langer, Vratislav Acta Crystallographica Section C Crystal Structure Communications, Vol. 61, Issue 4 https://doi.org/10.1107/S0108270105006359	journal	March 2005
Machine Learning Force Fields: Construction, Validation, and Outlook Botu, V.; Batra, R.; Chapman, J. The Journal of Physical Chemistry C, Vol. 121, Issue 1 https://doi.org/10.1021/acs.jpcc.6b10908	journal	December 2016
A molecular mechanics force field for lignin Petridis, Loukas; Smith, Jeremy C. Journal of Computational Chemistry, Vol. 30, Issue 3 https://doi.org/10.1002/jcc.21075	journal	February 2009
Determining the Composition of Lignins in Different Tissues of Silver Birch Fagerstedt, Kurt; Saranpää, Pekka; Tapanila, Tarja Plants, Vol. 4, Issue 2 https://doi.org/10.3390/plants4020183	journal	April 2015
Note on an Approximation Treatment for Many-Electron Systems Møller, Chr.; Plesset, M. S. Physical Review, Vol. 46, Issue 7 https://doi.org/10.1103/PhysRev.46.618	journal	October 1934
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu Journal of Chemical Theory and Computation, Vol. 7, Issue 10 https://doi.org/10.1021/ct200328p	journal	August 2011
Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C–H···O Hydrogen Bond Thomas, Sajesh P.; Pavan, Mysore S.; Guru Row, Tayur N. Crystal Growth & Design, Vol. 12, Issue 12 https://doi.org/10.1021/cg301211h	journal	November 2012
The NumPy Array: A Structure for Efficient Numerical Computation van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël Computing in Science & Engineering, Vol. 13, Issue 2 https://doi.org/10.1109/MCSE.2011.37	journal	March 2011
Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification Gao, Dahai; Haarmeyer, Carolyn; Balan, Venkatesh Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/s13068-014-0175-x	journal	December 2014
Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies Lemkul, Justin A.; Allen, William J.; Bevan, David R. Journal of Chemical Information and Modeling, Vol. 50, Issue 12 https://doi.org/10.1021/ci100335w	journal	November 2010
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Building Force Fields: An Automatic, Systematic, and Reproducible Approach Wang, Lee-Ping; Martinez, Todd J.; Pande, Vijay S. The Journal of Physical Chemistry Letters, Vol. 5, Issue 11 https://doi.org/10.1021/jz500737m	journal	May 2014
Lignin Biosynthesis Boerjan, Wout; Ralph, John; Baucher, Marie Annual Review of Plant Biology, Vol. 54, Issue 1, p. 519-546 https://doi.org/10.1146/annurev.arplant.54.031902.134938	journal	June 2003
Tricin, a Flavonoid Monomer in Monocot Lignification Lan, Wu; Lu, Fachuang; Regner, Matthew Plant Physiology, Vol. 167, Issue 4 https://doi.org/10.1104/pp.114.253757	journal	February 2015
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits Biazzi, Elisa; Nazzicari, Nelson; Pecetti, Luciano PLOS ONE, Vol. 12, Issue 1 https://doi.org/10.1371/journal.pone.0169234	journal	January 2017
Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem Hopkins, Chad W.; Roitberg, Adrian E. Journal of Chemical Information and Modeling, Vol. 54, Issue 7 https://doi.org/10.1021/ci500112w	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). Stomberg, Rolf; Hauteville, Marcelle; Lundquist, Knut Acta Chemica Scandinavica, Vol. 42b https://doi.org/10.3891/acta.chem.scand.42b-0697	journal	January 1988
Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance Li, Mi; Pu, Yunqiao; Ragauskas, Arthur J. Frontiers in Chemistry, Vol. 4 https://doi.org/10.3389/fchem.2016.00045	journal	November 2016
Cell-wall carbohydrates and their modification as a resource for biofuels Pauly, Markus; Keegstra, Kenneth The Plant Journal, Vol. 54, Issue 4, p. 559-568 https://doi.org/10.1111/j.1365-313X.2008.03463.x	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 Crestini, Claudia; Argyropoulos, Dimitris S. Journal of Agricultural and Food Chemistry, Vol. 45, Issue 4 https://doi.org/10.1021/jf960568k	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 Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
GROMACS: Fast, flexible, and free Van Der Spoel, David; Lindahl, Erik; Hess, Berk Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20291	journal	January 2005
Understanding the role of water during ionic liquid pretreatment of lignocellulose: co-solvent or anti-solvent? Shi, Jian; Balamurugan, Kanagasabai; Parthasarathi, Ramakrishnan Green Chem., Vol. 16, Issue 8 https://doi.org/10.1039/C4GC00373J	journal	January 2014
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation Hess, Berk Journal of Chemical Theory and Computation, Vol. 4, Issue 1 https://doi.org/10.1021/ct700200b	journal	December 2007
The Nose–Hoover thermostat Evans, D. J.; Holian, B. L. The Journal of Chemical Physics, Vol. 83, Issue 8 https://doi.org/10.1063/1.449071	journal	October 1985
erythro -2-(2,6-Dimethoxyphenoxy)-1-(4-hydroxy-3,5-dimethoxyphenyl)-1,3-propanediol Langer, Vratislav; Li, Shiming; Lundquist, Knut Acta Crystallographica Section E Structure Reports Online, Vol. 58, Issue 1 https://doi.org/10.1107/S1600536801021146	journal	December 2001
XSEDE: Accelerating Scientific Discovery Towns, John; Cockerill, Timothy; Dahan, Maytal Computing in Science & Engineering, Vol. 16, Issue 5 https://doi.org/10.1109/MCSE.2014.80	journal	September 2014
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing Vanommeslaeghe, K.; MacKerell, A. D. Journal of Chemical Information and Modeling, Vol. 52, Issue 12 https://doi.org/10.1021/ci300363c	journal	November 2012
Significance of Lignin S/G Ratio in Biomass Recalcitrance of Populus trichocarpa Variants for Bioethanol Production Yoo, Chang Geun; Dumitrache, Alexandru; Muchero, Wellington ACS Sustainable Chemistry & Engineering, Vol. 6, Issue 2 https://doi.org/10.1021/acssuschemeng.7b03586	journal	December 2017
Additive empirical force field for hexopyranose monosaccharides Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh Journal of Computational Chemistry, Vol. 29, Issue 15 https://doi.org/10.1002/jcc.21004	journal	November 2008
5,5′-Bis(hydroxymethyl)-3,3′-dimethoxybiphenyl-2,2′-diol with a new three-dimensional 3-modal topology of synthons Langer, Vratislav; Lundquist, Knut Acta Crystallographica Section C Crystal Structure Communications, Vol. 66, Issue 12 https://doi.org/10.1107/S0108270110046913	journal	November 2010
VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems Zheng, Suqing; Tang, Qing; He, Jian Journal of Chemical Information and Modeling, Vol. 56, Issue 4 https://doi.org/10.1021/acs.jcim.5b00687	journal	March 2016
Stereochemistry of lignin structures of the arylglycerol ß-aryl ether type Lundquist, Knut; Li, Shiming; Stomberg, Ralf Nordic Pulp & Paper Research Journal, Vol. 11, Issue 1 https://doi.org/10.3183/NPPRJ-1996-11-01-p043-047	journal	January 1996
Rapid parameterization of small molecules using the force field toolkit Mayne, Christopher G.; Saam, Jan; Schulten, Klaus Journal of Computational Chemistry, Vol. 34, Issue 32 https://doi.org/10.1002/jcc.23422	journal	September 2013
Development and testing of a general amber force field Wang, Junmei; Wolf, Romain M.; Caldwell, James W. Journal of Computational Chemistry, Vol. 25, Issue 9 https://doi.org/10.1002/jcc.20035	journal	January 2004
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D. Journal of Chemical Information and Modeling, Vol. 52, Issue 12 https://doi.org/10.1021/ci3003649	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 van Erven, Gijs; de Visser, Ries; Merkx, Donny W. H. Analytical Chemistry, Vol. 89, Issue 20 https://doi.org/10.1021/acs.analchem.7b02632	journal	October 2017
Biomolecular Simulation: A Computational Microscope for Molecular Biology Dror, Ron O.; Dirks, Robert M.; Grossman, J. P. Annual Review of Biophysics, Vol. 41, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155245	journal	June 2012
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins Harder, Edward; Damm, Wolfgang; Maple, Jon Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00864	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] Kozlevčar, Bojan; Odlazek, Darja; Golobič, Amalija Polyhedron, Vol. 25, Issue 5 https://doi.org/10.1016/j.poly.2005.08.031	journal	March 2006
Machine Learning Force Field Parameters from Ab Initio Data Li, Ying; Li, Hui; Pickard, Frank C. Journal of Chemical Theory and Computation, Vol. 13, Issue 9 https://doi.org/10.1021/acs.jctc.7b00521	journal	August 2017
Lignin Radicals in the Plant Cell Wall Probed by Kerr-Gated Resonance Raman Spectroscopy Barsberg, Søren; Matousek, Pavel; Towrie, Mike Biophysical Journal, Vol. 90, Issue 8 https://doi.org/10.1529/biophysj.105.070391	journal	April 2006
Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals Wu, Weihua; Dutta, Tanmoy; Varman, Arul M. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-07895-1	journal	August 2017
Lignin Biosynthesis and Structure Vanholme, R.; Demedts, B.; Morreel, K. Plant Physiology, Vol. 153, Issue 3, p. 895-905 https://doi.org/10.1104/pp.110.155119	journal	May 2010
Computational ‘microscopy’ of cellular membranes Ingólfsson, Helgi I.; Arnarez, Clément; Periole, Xavier Journal of Cell Science, Vol. 129, Issue 2 https://doi.org/10.1242/jcs.176040	journal	January 2016
Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny Lan, Wu; Rencoret, Jorge; Lu, Fachuang The Plant Journal, Vol. 88, Issue 6 https://doi.org/10.1111/tpj.13315	journal	November 2016
Lignin Valorization: Improving Lignin Processing in the Biorefinery Ragauskas, A. J.; Beckham, G. T.; Biddy, M. J. Science, Vol. 344, Issue 6185, p. 1246843-1246843 https://doi.org/10.1126/science.1246843	journal	May 2014
Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration Jämbeck, Joakim P. M.; Lyubartsev, Alexander P. The Journal of Physical Chemistry B, Vol. 118, Issue 14 https://doi.org/10.1021/jp4111234	journal	March 2014
Additive CHARMM force field for naturally occurring modified ribonucleotides: CHARMM Potential Energy Function Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey Journal of Computational Chemistry, Vol. 37, Issue 10 https://doi.org/10.1002/jcc.24307	journal	February 2016
Synthesis and crystal structure determination of model compounds for the dibenzodioxocine structure occurring in wood lignins Karhunen, Pirkko; Rummakko, Petteri; Pajunen, Aarne Journal of the Chemical Society, Perkin Transactions 1, Issue 18 https://doi.org/10.1039/p19960002303	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 Lundquist, Knut; Rolf, Stomberg Holzforschung, Vol. 42, Issue 6 https://doi.org/10.1515/hfsg.1988.42.6.375	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 Konstantopoulou, Marina; Slator, Patrick J.; Taylor, Charles R. Nordic Pulp and Paper Research Journal, Vol. 32, Issue 04 https://doi.org/10.3183/NPPRJ-2017-32-04-p493-507	journal	December 2017
Constant temperature simulations using the Langevin equation with velocity Verlet integration Paterlini, M. Germana; Ferguson, David M. Chemical Physics, Vol. 236, Issue 1-3 https://doi.org/10.1016/S0301-0104(98)00214-6	journal	September 1998
Scalable parallel programming with CUDA Nickolls, John; Buck, Ian; Garland, Michael Queue, Vol. 6, Issue 2 https://doi.org/10.1145/1365490.1365500	journal	March 2008
Lignin-derived inhibition of monocomponent cellulases and a xylanase in the hydrolysis of lignocellulosics Kellock, Miriam; Rahikainen, Jenni; Marjamaa, Kaisa Bioresource Technology, Vol. 232 https://doi.org/10.1016/j.biortech.2017.01.072	journal	May 2017
Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization Zhu, Ciyou; Byrd, Richard H.; Lu, Peihuang ACM Transactions on Mathematical Software, Vol. 23, Issue 4 https://doi.org/10.1145/279232.279236	journal	December 1997
Superior plant based carbon fibers from electrospun poly-(caffeyl alcohol) lignin Nar, Mangesh; Rizvi, Hussain R.; Dixon, Richard A. Carbon, Vol. 103 https://doi.org/10.1016/j.carbon.2016.02.053	journal	July 2016
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M. Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900242e	journal	August 2009
Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity Johnson, Christopher W.; Salvachúa, Davinia; Khanna, Payal Metabolic Engineering Communications, Vol. 3 https://doi.org/10.1016/j.meteno.2016.04.002	journal	December 2016
(+)-Pinoresinol–dioxane (1/1) Stomberg, Rolf; Ibrahim, Wilson; Langer, Vratislav Acta Crystallographica Section E Structure Reports Online, Vol. 59, Issue 12 https://doi.org/10.1107/S1600536803026114	journal	November 2003
Cellulase–lignin interactions—The role of carbohydrate-binding module and pH in non-productive binding Rahikainen, Jenni Liisa; Evans, James David; Mikander, Saara Enzyme and Microbial Technology, Vol. 53, Issue 5 https://doi.org/10.1016/j.enzmictec.2013.07.003	journal	October 2013
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant Bonawitz, Nicholas D.; Kim, Jeong Im; Tobimatsu, Yuki Nature, Vol. 509, Issue 7500, p. 376-380 https://doi.org/10.1038/nature13084	journal	March 2014
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data Huang, Lei; Roux, Benoît Journal of Chemical Theory and Computation, Vol. 9, Issue 8 https://doi.org/10.1021/ct4003477	journal	July 2013
Crystal structure of 2,3,4,5,6-pentaacetyl-(N-allyl)-D-gluconamide, C19H27NO11 Braunmühl, V. von; Stadler, R.; Schollmeyer, D. Zeitschrift für Kristallographie - New Crystal Structures, Vol. 213, Issue 1-4 https://doi.org/10.1524/ncrs.1998.213.14.421	journal	April 1998
The origin of biological homochirality Blackmond, Donna G. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 366, Issue 1580 https://doi.org/10.1098/rstb.2011.0130	journal	October 2011
Rational identification and characterisation of peptide ligands for targeting polysialic acid Shastry, Divya G.; Irudayanathan, Flaviyan Jerome; Williams, Asher Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-64088-z	journal	May 2020
NADPH levels affect cellular epigenetic state by inhibiting HDAC3–Ncor complex Li, Wei; Kou, Junjie; Qin, Junying Nature Metabolism, Vol. 3, Issue 1 https://doi.org/10.1038/s42255-020-00330-2	journal	January 2021
The Origin of Biological Homochirality Blackmond, Donna G. Cold Spring Harbor Perspectives in Biology, Vol. 11, Issue 3 https://doi.org/10.1101/cshperspect.a032540	journal	March 2019
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/bhbf-9r93	text	January 2017
Profiling of diferulates (plant cell wall cross-linkers) using ultrahigh-performance liquid chromatography-tandem mass spectrometry Vismeh, Ramin; Lu, Fachuang; Chundawat, Shishir P. S. Rutgers University https://doi.org/10.7282/t3pc34pv	text	January 2013
Scalable parallel programming with CUDA Nickolls, John; Buck, Ian; Garland, Michael ACM SIGGRAPH 2008 classes on - SIGGRAPH '08 https://doi.org/10.1145/1401132.1401152	conference	January 2008
Machine learning force fields: Construction, validation, and outlook Botu, Venkatesh; Batra, Rohit; Chapman, James arXiv https://doi.org/10.48550/arxiv.1610.02098	preprint	January 2016

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