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

Title: An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose

Authors:
; ;
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Lignocellulose Structure and Formation (CLSF)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1470537
DOE Contract Number:  
SC0001090
Resource Type:
Journal Article
Journal Name:
Cellulose
Additional Journal Information:
Journal Volume: 25; Journal Issue: 7; Related Information: CLSF partners with Pennsylvania State University (lead); North Carolina State University; University of Rhode Island; Virginia Tech University; Journal ID: ISSN 0969-0239
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
biofuels (including algae and biomass), bio-inspired, membrane, carbon sequestration, materials and chemistry by design, synthesis (self-assembly)

Citation Formats

Oehme, Daniel P., Yang, Hui, and Kubicki, James D. An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose. United States: N. p., 2018. Web. doi:10.1007/s10570-018-1793-4.
Oehme, Daniel P., Yang, Hui, & Kubicki, James D. An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose. United States. doi:10.1007/s10570-018-1793-4.
Oehme, Daniel P., Yang, Hui, and Kubicki, James D. Tue . "An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose". United States. doi:10.1007/s10570-018-1793-4.
@article{osti_1470537,
title = {An evaluation of the structures of cellulose generated by the CHARMM force field: comparisons to in planta cellulose},
author = {Oehme, Daniel P. and Yang, Hui and Kubicki, James D.},
abstractNote = {},
doi = {10.1007/s10570-018-1793-4},
journal = {Cellulose},
issn = {0969-0239},
number = 7,
volume = 25,
place = {United States},
year = {2018},
month = {4}
}

Works referenced in this record:

Solid-state NMR investigations of cellulose structure and interactions with matrix polysaccharides in plant primary cell walls
journal, September 2015

  • Wang, Tuo; Hong, Mei
  • Journal of Experimental Botany, Vol. 67, Issue 2
  • DOI: 10.1093/jxb/erv416

Constraints on $${\rm I}\beta$$ I β cellulose twist from DFT calculations of $$^{13}\hbox {C}$$ 13 C NMR chemical shifts
journal, September 2014


Origin of the twist of cellulosic materials
journal, January 2016


Diffraction from nonperiodic models of cellulose crystals
journal, January 2012


Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ
journal, August 2013

  • Alekozai, Emal M.; GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.
  • Cellulose, Vol. 21, Issue 2
  • DOI: 10.1007/s10570-013-0026-0

6-31G* basis set for third-row atoms
journal, January 2001

  • Rassolov, Vitaly A.; Ratner, Mark A.; Pople, John A.
  • Journal of Computational Chemistry, Vol. 22, Issue 9
  • DOI: 10.1002/jcc.1058

Spatial organization of cellulose microfibrils and matrix polysaccharides in primary plant cell walls as imaged by multichannel atomic force microscopy
journal, January 2016

  • Zhang, Tian; Zheng, Yunzhen; Cosgrove, Daniel J.
  • The Plant Journal, Vol. 85, Issue 2
  • DOI: 10.1111/tpj.13102

Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs
journal, April 2011

  • Beckham, Gregg T.; Matthews, James F.; Peters, Baron
  • The Journal of Physical Chemistry B, Vol. 115, Issue 14
  • DOI: 10.1021/jp1106394

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields
journal, January 2012

  • Matthews, James F.; Beckham, Gregg T.; Bergenstråhle-Wohlert, Malin
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 2
  • DOI: 10.1021/ct2007692

Effects of Xylan Side-Chain Substitutions on Xylan–Cellulose Interactions and Implications for Thermal Pretreatment of Cellulosic Biomass
journal, March 2017


Comparison of Multistandard and TMS-Standard Calculated NMR Shifts for Coniferyl Alcohol and Application of the Multistandard Method to Lignin Dimers
journal, March 2011

  • Watts, Heath D.; Mohamed, Mohamed Naseer Ali; Kubicki, James D.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 9
  • DOI: 10.1021/jp110330q

Electron diffraction study on the two crystalline phases occurring in native cellulose from an algal cell wall
journal, July 1991

  • Sugiyama, Junji; Vuong, Roger; Chanzy, Henri
  • Macromolecules, Vol. 24, Issue 14
  • DOI: 10.1021/ma00014a033

Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride
journal, November 2011

  • Gross, Adam S.; Bell, Alexis T.; Chu, Jhih-Wei
  • The Journal of Physical Chemistry B, Vol. 115, Issue 46
  • DOI: 10.1021/jp202415v

Structural factors affecting 13C NMR chemical shifts of cellulose: a computational study
journal, November 2017


Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models
journal, January 1998

  • Adamo, Carlo; Barone, Vincenzo
  • The Journal of Chemical Physics, Vol. 108, Issue 2
  • DOI: 10.1063/1.475428

Diversity of potential hydrogen bonds in cellulose I revealed by molecular dynamics simulation
journal, October 2013


Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra
journal, November 2015

  • Lee, Christopher M.; Kubicki, James D.; Fan, Bingxin
  • The Journal of Physical Chemistry B, Vol. 119, Issue 49
  • DOI: 10.1021/acs.jpcb.5b08015

Ab Initio Studies of Cellulose I: Crystal Structure, Intermolecular Forces, and Interactions with Water
journal, May 2011

  • Li, Yan; Lin, Milo; Davenport, James W.
  • The Journal of Physical Chemistry C, Vol. 115, Issue 23
  • DOI: 10.1021/jp2006759

Native Cellulose: A Composite of Two Distinct Crystalline Forms
journal, January 1984


A DFT study of vibrational frequencies and 13C NMR chemical shifts of model cellulosic fragments as a function of size
journal, December 2013


The Shape and Size Distribution of Crystalline Nanoparticles Prepared by Acid Hydrolysis of Native Cellulose
journal, January 2008

  • Elazzouzi-Hafraoui, Samira; Nishiyama, Yoshiharu; Putaux, Jean-Luc
  • Biomacromolecules, Vol. 9, Issue 1
  • DOI: 10.1021/bm700769p

Studies of microstructure in native celluloses using solid-state carbon-13 NMR
journal, August 1984

  • VanderHart, David L.; Atalla, R. H.
  • Macromolecules, Vol. 17, Issue 8
  • DOI: 10.1021/ma00138a009

Unique Aspects of the Structure and Dynamics of Elementary I β Cellulose Microfibrils Revealed by Computational Simulations
journal, March 2015

  • Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.
  • Plant Physiology, Vol. 168, Issue 1
  • DOI: 10.1104/pp.114.254664

Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation
journal, September 2013

  • Lindner, Benjamin; Petridis, Loukas; Schulz, Roland
  • Biomacromolecules, Vol. 14, Issue 10
  • DOI: 10.1021/bm400442n

Characterization of crystalline cellulose in biomass: Basic principles, applications, and limitations of XRD, NMR, IR, Raman, and SFG
journal, October 2013

  • Kim, Seong H.; Lee, Christopher M.; Kafle, Kabindra
  • Korean Journal of Chemical Engineering, Vol. 30, Issue 12
  • DOI: 10.1007/s11814-013-0162-0

Dynamics of water bound to crystalline cellulose
journal, September 2017


A CP/MAS13C NMR investigation of molecular ordering in celluloses
journal, July 1997


Correlated C−C and C−O Bond Conformations in Saccharide Hydroxymethyl Groups:  Parametrization and Application of Redundant 1 H− 1 H, 13 C− 1 H, and 13 C− 13 C NMR J -Couplings
journal, December 2004

  • Thibaudeau, Christophe; Stenutz, Roland; Hertz, Brian
  • Journal of the American Chemical Society, Vol. 126, Issue 48
  • DOI: 10.1021/ja0306718

Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex
journal, June 2016

  • Nixon, B. Tracy; Mansouri, Katayoun; Singh, Abhishek
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep28696

Force Pulling of Single Cellulose Chains at the Crystalline Cellulose−Liquid Interface: A Molecular Dynamics Study
journal, April 2009

  • Bergenstråhle, Malin; Thormann, Esben; Nordgren, Niklas
  • Langmuir, Vol. 25, Issue 8
  • DOI: 10.1021/la803915c

Molecular deformation mechanisms in cellulose allomorphs and the role of hydrogen bonds
journal, October 2015


Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis
journal, March 2013

  • Zhao, Zhen; Shklyaev, Oleg E.; Nili, Abdolmajid
  • The Journal of Physical Chemistry A, Vol. 117, Issue 12
  • DOI: 10.1021/jp3089929

Cellulose-Builder: A toolkit for building crystalline structures of cellulose
journal, March 2012

  • Gomes, Thiago C. F.; Skaf, Munir S.
  • Journal of Computational Chemistry, Vol. 33, Issue 14
  • DOI: 10.1002/jcc.22959

High-Temperature Behavior of Cellulose I
journal, March 2011

  • Matthews, James F.; Bergenstråhle, Malin; Beckham, Gregg T.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 10
  • DOI: 10.1021/jp1106839

NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities
journal, October 1997

  • Gottlieb, Hugo E.; Kotlyar, Vadim; Nudelman, Abraham
  • The Journal of Organic Chemistry, Vol. 62, Issue 21
  • DOI: 10.1021/jo971176v

The DFT route to NMR chemical shifts
journal, January 1999


Computational Prediction of 1 H and 13 C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry
journal, November 2011

  • Lodewyk, Michael W.; Siebert, Matthew R.; Tantillo, Dean J.
  • Chemical Reviews, Vol. 112, Issue 3
  • DOI: 10.1021/cr200106v

Crystal Structure and Hydrogen Bonding System in Cellulose I α from Synchrotron X-ray and Neutron Fiber Diffraction
journal, November 2003

  • Nishiyama, Yoshiharu; Sugiyama, Junji; Chanzy, Henri
  • Journal of the American Chemical Society, Vol. 125, Issue 47
  • DOI: 10.1021/ja037055w

Peptide Recognition Capabilities of Cellulose in Molecular Dynamics Simulations
journal, October 2015

  • Nawrocki, Grzegorz; Cazade, Pierre-André; Thompson, Damien
  • The Journal of Physical Chemistry C, Vol. 119, Issue 43
  • DOI: 10.1021/acs.jpcc.5b07118

The Arabidopsis Cellulose Synthase Complex: A Proposed Hexamer of CESA Trimers in an Equimolar Stoichiometry
journal, December 2014

  • Hill, Joseph L.; Hammudi, Mustafa B.; Tien, Ming
  • The Plant Cell, Vol. 26, Issue 12
  • DOI: 10.1105/tpc.114.131193

Calculation of NMR Shielding Tensors Using Gauge-Including Atomic Orbitals and Modern Density Functional Theory
journal, January 1995

  • Schreckenbach, Georg; Ziegler, Tom
  • The Journal of Physical Chemistry, Vol. 99, Issue 2
  • DOI: 10.1021/j100002a024

Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption
journal, October 2015


CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling
journal, August 2011

  • Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 10
  • DOI: 10.1021/ct200328p

Coarse-Grain Model for Natural Cellulose Fibrils in Explicit Water
journal, March 2014

  • Srinivas, Goundla; Cheng, Xiaolin; Smith, Jeremy C.
  • The Journal of Physical Chemistry B, Vol. 118, Issue 11
  • DOI: 10.1021/jp407953p

On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils
journal, October 2010

  • Gross, Adam S.; Chu, Jhih-Wei
  • The Journal of Physical Chemistry B, Vol. 114, Issue 42
  • DOI: 10.1021/jp106452m

Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction
journal, August 2002

  • Nishiyama, Yoshiharu; Langan, Paul; Chanzy, Henri
  • Journal of the American Chemical Society, Vol. 124, Issue 31
  • DOI: 10.1021/ja0257319

Diffraction evidence for the structure of cellulose microfibrils in bamboo, a model for grass and cereal celluloses
journal, June 2015


Stereoelectronic and Solvation Effects Determine Hydroxymethyl Conformational Preferences in Monosaccharides
journal, December 2008

  • Barnett, Christopher B.; Naidoo, Kevin J.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 48
  • DOI: 10.1021/jp8067409

Conversion of cellulose Iα to Iβ via a high temperature intermediate (I-HT) and other cellulose phase transformations
journal, November 2011


Ab Initio Study of Molecular Interactions in Cellulose Iα
journal, August 2013

  • Devarajan, Ajitha; Markutsya, Sergiy; Lamm, Monica H.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 36
  • DOI: 10.1021/jp406266u

Cellulose Aggregation under Hydrothermal Pretreatment Conditions
journal, July 2016

  • Silveira, Rodrigo L.; Stoyanov, Stanislav R.; Kovalenko, Andriy
  • Biomacromolecules, Vol. 17, Issue 8
  • DOI: 10.1021/acs.biomac.6b00603

Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
journal, July 2015

  • Angles d’Ortoli, Thibault; Sjöberg, Nils A.; Vasiljeva, Polina
  • The Journal of Physical Chemistry B, Vol. 119, Issue 30
  • DOI: 10.1021/acs.jpcb.5b02866

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

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations
journal, April 2011

  • Paavilainen, Sami; Róg, Tomasz; Vattulainen, Ilpo
  • The Journal of Physical Chemistry B, Vol. 115, Issue 14
  • DOI: 10.1021/jp111459b

Dynamics of cello-oligosaccharides on a cellulose crystal surface
journal, September 2012


Conformational features of crystal-surface cellulose from higher plants
journal, June 2002


Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
journal, May 2013

  • Zhao, Gongpu; Perilla, Juan R.; Yufenyuy, Ernest L.
  • Nature, Vol. 497, Issue 7451
  • DOI: 10.1038/nature12162

Effect of Solvation on the Rotation of Hydroxymethyl Groups in Carbohydrates
journal, October 1998

  • Rockwell, Glen D.; Grindley, T. Bruce
  • Journal of the American Chemical Society, Vol. 120, Issue 42
  • DOI: 10.1021/ja981958l

A Multi-standard Approach for GIAO 13 C NMR Calculations
journal, October 2009

  • Sarotti, Ariel M.; Pellegrinet, Silvina C.
  • The Journal of Organic Chemistry, Vol. 74, Issue 19
  • DOI: 10.1021/jo901234h

Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
journal, October 2002

  • Kuttel, Michelle; Brady, J. W.; Naidoo, Kevin J.
  • Journal of Computational Chemistry, Vol. 23, Issue 13
  • DOI: 10.1002/jcc.10119

Hydration Control of the Mechanical and Dynamical Properties of Cellulose
journal, October 2014

  • Petridis, Loukas; O’Neill, Hugh M.; Johnsen, Mariah
  • Biomacromolecules, Vol. 15, Issue 11
  • DOI: 10.1021/bm5011849

Structural changes of native cellulose crystals induced by annealing in aqueous alkaline and acidic solutions at high temperatures
journal, October 1989

  • Yamamoto, Hiroyuki; Horii, Fumitaka; Odani, Hisashi
  • Macromolecules, Vol. 22, Issue 10
  • DOI: 10.1021/ma00200a058

A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers
journal, November 2015

  • Vandavasi, Venu Gopal; Putnam, Daniel K.; Zhang, Qiu
  • Plant Physiology, Vol. 170, Issue 1
  • DOI: 10.1104/pp.15.01356

Structure of Cellulose Microfibrils in Primary Cell Walls from Collenchyma
journal, November 2012

  • Thomas, Lynne H.; Forsyth, V. Trevor; Šturcová, Adriana
  • Plant Physiology, Vol. 161, Issue 1
  • DOI: 10.1104/pp.112.206359

Solid-state 13C-NMR study of conformations of oligosaccharides and cellulose: Conformation of CH2OH group about the exo-cyclic C-C bond
journal, September 1983

  • Horii, Fumitaka; Hirai, Asako; Kitamaru, Ryozo
  • Polymer Bulletin, Vol. 10, Issue 7-8
  • DOI: 10.1007/BF00281948

Hybrid Density Functional Methods Empirically Optimized for the Computation of 13 C and 1 H Chemical Shifts in Chloroform Solution
journal, May 2006

  • Wiitala, Keith W.; Hoye, Thomas R.; Cramer, Christopher J.
  • Journal of Chemical Theory and Computation, Vol. 2, Issue 4
  • DOI: 10.1021/ct6001016

Nanostructure of cellulose microfibrils in spruce wood
journal, November 2011

  • Fernandes, A. N.; Thomas, L. H.; Altaner, C. M.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 47
  • DOI: 10.1073/pnas.1108942108

A comparison of models for calculating nuclear magnetic resonance shielding tensors
journal, April 1996

  • Cheeseman, James R.; Trucks, Gary W.; Keith, Todd A.
  • The Journal of Chemical Physics, Vol. 104, Issue 14
  • DOI: 10.1063/1.471789

Effect of microfibril twisting on theoretical powder diffraction patterns of cellulose Iβ
journal, September 2013


Quantum mechanical modeling of the structures, energetics and spectral properties of Iα and Iβ cellulose
journal, February 2013


Atomistic Modeling of the Adsorption of Benzophenone onto Cellulosic Surfaces
journal, March 2002


3D Electron Tomography of Pretreated Biomass Informs Atomic Modeling of Cellulose Microfibrils
journal, August 2013

  • Ciesielski, Peter N.; Matthews, James F.; Tucker, Melvin P.
  • ACS Nano, Vol. 7, Issue 9
  • DOI: 10.1021/nn4031542

Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations
journal, November 1990

  • Wolinski, Krzysztof; Hinton, James F.; Pulay, Peter
  • Journal of the American Chemical Society, Vol. 112, Issue 23
  • DOI: 10.1021/ja00179a005

Ab Initio Study of Structure and Interconversion of Native Cellulose Phases
journal, September 2011

  • Bučko, Tomáš; Tunega, Daniel; Ángyán, János G.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 35
  • DOI: 10.1021/jp205827y

Unraveling Cellulose Microfibrils: A Twisted Tale: Unraveling Cellulose Microfibrils
journal, July 2013

  • Hadden, Jodi A.; French, Alfred D.; Woods, Robert J.
  • Biopolymers, Vol. 99, Issue 10
  • DOI: 10.1002/bip.22279

The molecular origins of twist in cellulose I-beta
journal, July 2015


Water Structuring over the Hydrophobic Surface of Cellulose
journal, November 2014

  • Miyamoto, Hitomi; Schnupf, Udo; Brady, John W.
  • Journal of Agricultural and Food Chemistry, Vol. 62, Issue 46
  • DOI: 10.1021/jf501763r

Different Conformations of Surface Cellulose Molecules in Native Cellulose Microfibrils Revealed by Layer-by-Layer Peeling
journal, October 2017


Hydrogen bonds and twist in cellulose microfibrils
journal, November 2017


Hydroxymethyl Group Conformation in Saccharides: Structural Dependencies of 2 J HH , 3 J HH , and 1 J CH Spin−Spin Coupling Constants
journal, February 2002

  • Stenutz, Roland; Carmichael, Ian; Widmalm, Göran
  • The Journal of Organic Chemistry, Vol. 67, Issue 3
  • DOI: 10.1021/jo010985i

Line shapes in CP/MAS 13C NMR spectra of cellulose I
journal, November 2005

  • Larsson, Per Tomas; Westlund, Per-Olof
  • Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Vol. 62, Issue 1-3
  • DOI: 10.1016/j.saa.2005.01.021

Solid-State 13C Nuclear Magnetic Resonance Characterization of Cellulose in the Cell Walls of Arabidopsis thaliana Leaves
journal, June 1996

  • Newman, R. H.; Davies, L. M.; Harris, P. J.
  • Plant Physiology, Vol. 111, Issue 2
  • DOI: 10.1104/pp.111.2.475

Monitoring Meso-Scale Ordering of Cellulose in Intact Plant Cell Walls Using Sum Frequency Generation Spectroscopy
journal, August 2013


Comparison of the interface between water and four surfaces of native crystalline cellulose by molecular dynamics simulations
journal, January 1998


Decrystallization of Oligosaccharides from the Cellulose Iβ Surface with Molecular Simulation
journal, June 2011

  • Payne, Christina M.; Himmel, Michael E.; Crowley, Michael F.
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 13
  • DOI: 10.1021/jz2005122

Molecular simulation of surface reorganization and wetting in crystalline cellulose I and II
journal, February 2013