Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap

Smith, Micholas Dean; Petridis, Loukas; Cheng, Xiaolin; Mostofian, Barmak; Smith, Jeremy C.

doi:10.1039/C5CP07088K

Title: Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap

Abstract

Using temperature replica-exchange molecular dynamics, we characterize a globule-to-coil transition for a softwood-like lignin biopolymer in a tetrahydrofuran (THF)-water cosolvent system at temperatures at which the cosolvent undergoes a de-mixing transition. The lignin is found to be in a coil state, similar to that in the high-temperature miscible region. Analysis of the transition kinetics indicates that THF acts in a surfactant-like fashion. In conclusion, the present study thus suggests that THF-water based pretreatments may efficiently remove lignin from biomass even at relatively low (non-water boiling) temperatures.

Authors:

Smith, Micholas Dean ^[1]; Petridis, Loukas ^[1]; Cheng, Xiaolin ^[1]; Mostofian, Barmak ^[1]; Smith, Jeremy C. ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

Publication Date:: Tue Jan 26 00:00:00 EST 2016

Research Org.:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1327652

Grant/Contract Number:: AC05-00OR22725

Resource Type:: Accepted Manuscript

Journal Name:: Physical Chemistry Chemical Physics. PCCP

Additional Journal Information:: Journal Volume: 18; Journal Issue: 9; Journal ID: ISSN 1463-9076

Publisher:: Royal Society of Chemistry

Country of Publication:: United States

Language:: English

Subject:: 09 BIOMASS FUELS

Citation Formats


                    Smith, Micholas Dean, Petridis, Loukas, Cheng, Xiaolin, Mostofian, Barmak, and Smith, Jeremy C. Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap.  United States: N. p., 2016. 
Web.  doi:10.1039/C5CP07088K.

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                    Smith, Micholas Dean, Petridis, Loukas, Cheng, Xiaolin, Mostofian, Barmak, & Smith, Jeremy C. Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap.  United States.  https://doi.org/10.1039/C5CP07088K

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                    Smith, Micholas Dean, Petridis, Loukas, Cheng, Xiaolin, Mostofian, Barmak, and Smith, Jeremy C. Tue .  
"Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap".  United States.  https://doi.org/10.1039/C5CP07088K.  https://www.osti.gov/servlets/purl/1327652.

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@article{osti_1327652,

  title        = {Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap},

  author       = {Smith, Micholas Dean and Petridis, Loukas and Cheng, Xiaolin and Mostofian, Barmak and Smith, Jeremy C.},

  abstractNote = {Using temperature replica-exchange molecular dynamics, we characterize a globule-to-coil transition for a softwood-like lignin biopolymer in a tetrahydrofuran (THF)-water cosolvent system at temperatures at which the cosolvent undergoes a de-mixing transition. The lignin is found to be in a coil state, similar to that in the high-temperature miscible region. Analysis of the transition kinetics indicates that THF acts in a surfactant-like fashion. In conclusion, the present study thus suggests that THF-water based pretreatments may efficiently remove lignin from biomass even at relatively low (non-water boiling) temperatures.},

  doi          = {10.1039/C5CP07088K},

  journal      = {Physical Chemistry Chemical Physics. PCCP},

  number       = 9,

  volume       = 18,

  place        = {United States},

  year         = {Tue Jan 26 00:00:00 EST 2016},

  month        = {Tue Jan 26 00:00:00 EST 2016}

}

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https://doi.org/10.1039/C5CP07088K

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Works referencing / citing this record:

Performances of Several Solvents on the Cleavage of Inter- and Intramolecular Linkages of Lignin in Corncob Residue
journal, April 2018

Zhang, Hui; Liu, Xudong; Li, Jianmei
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Title: Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap

Abstract

Citation Formats

Bioenergy and Sustainable Development? journal, November 2007

Enzymatic conversion of lignocellulose into fermentable sugars: challenges and opportunities journal, October 2007

Propensity of Lignin to Associate: Light Scattering Photometry Study with Native Lignins journal, December 2008

Milled Wood Lignin: A Linear Oligomer journal, November 2011

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Coupling metal halides with a co-solvent to produce furfural and 5-HMF at high yields directly from lignocellulosic biomass as an integrated biofuels strategy journal, January 2014

THF co-solvent enhances hydrocarbon fuel precursor yields from lignocellulosic biomass journal, January 2013

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Co-solvent Pretreatment Reduces Costly Enzyme Requirements for High Sugar and Ethanol Yields from Lignocellulosic Biomass journal, February 2015

Phase equilibria and excess molar volumes of tetrahydrofuran (1) + deuterium oxide (2) journal, October 1975

Phase equilibria in the system tetrahydrofuran(1)-water(2) journal, January 1972

Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics journal, January 2016

Multidimensional replica-exchange method for free-energy calculations journal, October 2000

Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation journal, June 2011

Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics journal, December 2011

A molecular mechanics force field for lignin journal, February 2009

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers journal, March 2007

Comparison of simple potential functions for simulating liquid water journal, July 1983

Molecular dynamics with coupling to an external bath journal, October 1984

Canonical sampling through velocity rescaling journal, January 2007

Polymorphic transitions in single crystals: A new molecular dynamics method journal, December 1981

LINCS: A linear constraint solver for molecular simulations journal, September 1997

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation journal, December 2007

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models journal, October 1992

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5 journal, April 2011

GROMACS: A message-passing parallel molecular dynamics implementation journal, September 1995

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal, February 2008

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit journal, February 2013

GROMACS: Fast, flexible, and free journal, January 2005

Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity journal, January 2009

VMD: Visual molecular dynamics journal, February 1996

Globule-to-Coil Transition of a Single Homopolymer Chain in Solution journal, May 1998

Polymer–surfactant complexes: solubilization of polymeric globule by surfactants journal, March 2000

Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths † journal, April 2005

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations journal, November 2006

Theory of binless multi-state free energy estimation with applications to protein-ligand binding journal, April 2012

Protein Folding Kinetics and Thermodynamics from Atomistic Simulations journal, June 2006

Performances of Several Solvents on the Cleavage of Inter- and Intramolecular Linkages of Lignin in Corncob Residue journal, April 2018

Bioenergy and Sustainable Development?
journal, November 2007

Enzymatic conversion of lignocellulose into fermentable sugars: challenges and opportunities
journal, October 2007

Propensity of Lignin to Associate: Light Scattering Photometry Study with Native Lignins
journal, December 2008

Milled Wood Lignin: A Linear Oligomer
journal, November 2011

Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins
journal, April 2012

Coupling metal halides with a co-solvent to produce furfural and 5-HMF at high yields directly from lignocellulosic biomass as an integrated biofuels strategy
journal, January 2014

THF co-solvent enhances hydrocarbon fuel precursor yields from lignocellulosic biomass
journal, January 2013

Integrated furfural production as a renewable fuel and chemical platform from lignocellulosic biomass: Furfural production from lignocellulosic biomass
journal, August 2013

Co-solvent Pretreatment Reduces Costly Enzyme Requirements for High Sugar and Ethanol Yields from Lignocellulosic Biomass
journal, February 2015

Phase equilibria and excess molar volumes of tetrahydrofuran (1) + deuterium oxide (2)
journal, October 1975

Phase equilibria in the system tetrahydrofuran(1)-water(2)
journal, January 1972

Cosolvent pretreatment in cellulosic biofuel production: effect of tetrahydrofuran-water on lignin structure and dynamics
journal, January 2016

Multidimensional replica-exchange method for free-energy calculations
journal, October 2000

Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation
journal, June 2011

Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics
journal, December 2011

A molecular mechanics force field for lignin
journal, February 2009

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers
journal, March 2007

Comparison of simple potential functions for simulating liquid water
journal, July 1983

Molecular dynamics with coupling to an external bath
journal, October 1984

Canonical sampling through velocity rescaling
journal, January 2007

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
journal, December 2007

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5
journal, April 2011

GROMACS: A message-passing parallel molecular dynamics implementation
journal, September 1995

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

GROMACS: Fast, flexible, and free
journal, January 2005

Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity
journal, January 2009

VMD: Visual molecular dynamics
journal, February 1996

Globule-to-Coil Transition of a Single Homopolymer Chain in Solution
journal, May 1998

Polymer–surfactant complexes: solubilization of polymeric globule by surfactants
journal, March 2000

Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths ^†
journal, April 2005

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
journal, November 2006

Theory of binless multi-state free energy estimation with applications to protein-ligand binding
journal, April 2012

Protein Folding Kinetics and Thermodynamics from Atomistic Simulations
journal, June 2006

Performances of Several Solvents on the Cleavage of Inter- and Intramolecular Linkages of Lignin in Corncob Residue
journal, April 2018