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Title: Quantum Calculations on Plant Cell Wall Component Interactions

Abstract

In this paper, density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M0 5-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in explicit H 2O, and in polarized continuum models (PCM) of solvation. PCMs were used to represent water, methanol, and chloroform. The results predict the relative ranges of each type of interaction and when specific configurations will be strongly preferred. Finally, structures and energies are useful as a basis for testing classical force fields and as guidance for coarse-grained models of PCWs.

Authors:
 [1];  [2];  [3];  [3];  [4];  [1];  [2]
  1. Pennsylvania State Univ., University Park, PA (United States). Dept. of Biology
  2. Univ. of Texas, El Paso, TX (United States). Dept. of Geological Sciences
  3. Pennsylvania State Univ., University Park, PA (United States). Dept. of Geological Sciences
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pennsylvania State Univ., University Park, PA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1474698
Grant/Contract Number:  
AC05-00OR22725; SC0001090
Resource Type:
Accepted Manuscript
Journal Name:
Interdisciplinary Sciences: Computational Life Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 3; Journal ID: ISSN 1913-2751
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; interaction energies; quantum chemistry; cellulose; xylan; lignin; pectin

Citation Formats

Yang, Hui, Watts, Heath D., Gibilterra, Virgil, Weiss, T. Blake, Petridis, Loukas, Cosgrove, Daniel J., and Kubicki, James D. Quantum Calculations on Plant Cell Wall Component Interactions. United States: N. p., 2018. Web. doi:10.1007/s12539-018-0293-4.
Yang, Hui, Watts, Heath D., Gibilterra, Virgil, Weiss, T. Blake, Petridis, Loukas, Cosgrove, Daniel J., & Kubicki, James D. Quantum Calculations on Plant Cell Wall Component Interactions. United States. doi:10.1007/s12539-018-0293-4.
Yang, Hui, Watts, Heath D., Gibilterra, Virgil, Weiss, T. Blake, Petridis, Loukas, Cosgrove, Daniel J., and Kubicki, James D. Mon . "Quantum Calculations on Plant Cell Wall Component Interactions". United States. doi:10.1007/s12539-018-0293-4. https://www.osti.gov/servlets/purl/1474698.
@article{osti_1474698,
title = {Quantum Calculations on Plant Cell Wall Component Interactions},
author = {Yang, Hui and Watts, Heath D. and Gibilterra, Virgil and Weiss, T. Blake and Petridis, Loukas and Cosgrove, Daniel J. and Kubicki, James D.},
abstractNote = {In this paper, density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M05-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in explicit H2O, and in polarized continuum models (PCM) of solvation. PCMs were used to represent water, methanol, and chloroform. The results predict the relative ranges of each type of interaction and when specific configurations will be strongly preferred. Finally, structures and energies are useful as a basis for testing classical force fields and as guidance for coarse-grained models of PCWs.},
doi = {10.1007/s12539-018-0293-4},
journal = {Interdisciplinary Sciences: Computational Life Sciences},
number = 3,
volume = 11,
place = {United States},
year = {2018},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
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Figures / Tables:

Figure 1 Figure 1: Tetramers of 84 glucuronic acid, where 3 of the 4 COOH groups were methyl esterified, were used to represent 85 pectin.

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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

Mechanism of lignin inhibition of enzymatic biomass deconstruction
journal, December 2015

  • Vermaas, Josh V.; Petridis, Loukas; Qi, Xianghong
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0379-8

Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-binding Module on Cellulose
journal, April 2012

  • Nimlos, Mark R.; Beckham, Gregg T.; Matthews, James F.
  • Journal of Biological Chemistry, Vol. 287, Issue 24
  • DOI: 10.1074/jbc.M112.358184

Water–Polysaccharide Interactions in the Primary Cell Wall of Arabidopsis thaliana from Polarization Transfer Solid-State NMR
journal, July 2014

  • White, Paul B.; Wang, Tuo; Park, Yong Bum
  • Journal of the American Chemical Society, Vol. 136, Issue 29
  • DOI: 10.1021/ja504108h

The ORCA program system: The ORCA program system
journal, June 2011

  • Neese, Frank
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 1
  • DOI: 10.1002/wcms.81

Comparative structure and biomechanics of plant primary and secondary cell walls
journal, January 2012


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

Carbohydrate–aromatic π interactions: a test of density functionals and the DFT-D method
journal, January 2009

  • Raju, Rajesh K.; Ramraj, Anitha; Hillier, Ian H.
  • Physical Chemistry Chemical Physics, Vol. 11, Issue 18
  • DOI: 10.1039/b822877a

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

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
journal, May 2009

  • Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 18, p. 6378-6396
  • DOI: 10.1021/jp810292n

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

Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules
journal, January 1971

  • Ditchfield, R.; Hehre, W. J.; Pople, J. A.
  • The Journal of Chemical Physics, Vol. 54, Issue 2
  • DOI: 10.1063/1.1674902

Relaxation dynamics of surface-adsorbed water molecules in nanoporous silica probed by terahertz spectroscopy
journal, August 2015

  • Huang, Yu-Ru; Liu, Kao-Hsiang; Mou, Chung-Yuan
  • Applied Physics Letters, Vol. 107, Issue 8
  • DOI: 10.1063/1.4929767

Accuracy of AH n equilibrium geometries by single determinant molecular orbital theory
journal, January 1974


A Revised Architecture of Primary Cell Walls Based on Biomechanical Changes Induced by Substrate-Specific Endoglucanases
journal, February 2012


Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
conference, November 2006

  • Bowers, Kevin J.; Chow, David E.; Xu, Huafeng
  • SC 2006 Proceedings Supercomputing 2006, ACM/IEEE SC 2006 Conference (SC'06)
  • DOI: 10.1109/SC.2006.54

Theoretical Study of the Remarkably Diverse Linkages in Lignin
journal, October 2011

  • Parthasarathi, R.; Romero, Raymond A.; Redondo, Antonio
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 20
  • DOI: 10.1021/jz201201q

Towards lignin-protein crosslinking: amino acid adducts of a lignin model quinone methide
journal, January 2014


Additive empirical force field for hexopyranose monosaccharides
journal, November 2008

  • Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh
  • Journal of Computational Chemistry, Vol. 29, Issue 15
  • DOI: 10.1002/jcc.21004

Modelling of xyloglucan, pectins and pectic side chains binding onto cellulose microfibrils
journal, October 2008


Competitive binding of pectin and xyloglucan with primary cell wall cellulose
journal, November 2008


Structure and Interactions of Plant Cell-Wall Polysaccharides by Two- and Three-Dimensional Magic-Angle-Spinning Solid-State NMR
journal, February 2011

  • Dick-Pérez, Marilú; Zhang, Yuan; Hayes, Jennifer
  • Biochemistry, Vol. 50, Issue 6
  • DOI: 10.1021/bi101795q

A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
journal, August 1997

  • Cancès, E.; Mennucci, B.; Tomasi, J.
  • The Journal of Chemical Physics, Vol. 107, Issue 8
  • DOI: 10.1063/1.474659

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


Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions
journal, January 2006

  • Zhao, Yan; Schultz, Nathan E.; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 2, Issue 2
  • DOI: 10.1021/ct0502763

A comparison of ab initio quantum-mechanical and experimental D 0 binding energies of eleven H-bonded and eleven dispersion-bound complexes
journal, January 2015

  • Haldar, Susanta; Gnanasekaran, Ramachandran; Hobza, Pavel
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 40
  • DOI: 10.1039/C5CP04427H

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


Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965


Cellulose-Pectin Spatial Contacts Are Inherent to Never-Dried Arabidopsis Primary Cell Walls: Evidence from Solid-State Nuclear Magnetic Resonance
journal, June 2015

  • Wang, Tuo; Park, Yong Bum; Cosgrove, Daniel J.
  • Plant Physiology, Vol. 168, Issue 3
  • DOI: 10.1104/pp.15.00665

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
journal, January 2005

  • Weigend, Florian; Ahlrichs, Reinhart
  • Physical Chemistry Chemical Physics, Vol. 7, Issue 18, p. 3297-3305
  • DOI: 10.1039/b508541a

Hartree–Fock exchange fitting basis sets for H to Rn
journal, January 2007

  • Weigend, Florian
  • Journal of Computational Chemistry, Vol. 29, Issue 2
  • DOI: 10.1002/jcc.20702

Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993

  • Becke, Axel D.
  • The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
  • DOI: 10.1063/1.464913

Insights into Hydrogen Bonding and Stacking Interactions in Cellulose
journal, December 2011

  • Parthasarathi, R.; Bellesia, G.; Chundawat, S. P. S.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 49
  • DOI: 10.1021/jp203620x

Common processes drive the thermochemical pretreatment of lignocellulosic biomass
journal, January 2014

  • Langan, Paul; Petridis, Loukas; O'Neill, Hugh M.
  • Green Chem., Vol. 16, Issue 1
  • DOI: 10.1039/C3GC41962B

Control of thickness of collenchyma cell walls by pectins
journal, May 1992


Solvation of hydrocarbons in aqueous-organic mixtures
journal, May 2016

  • Sedov, I. A.; Magsumov, T. I.; Solomonov, B. N.
  • The Journal of Chemical Thermodynamics, Vol. 96
  • DOI: 10.1016/j.jct.2015.12.034

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

Assessment of In Vitro Binding of Isolated Pectic Domains to Cellulose by Adsorption Isotherms, Electron Microscopy, and X-ray Diffraction Methods
journal, January 2007

  • Zykwinska, Agata; Gaillard, Cédric; Buléon, Alain
  • Biomacromolecules, Vol. 8, Issue 1
  • DOI: 10.1021/bm060292h

Molecular domains of the cellulose/xyloglucan network in the cell walls of higher plants
journal, December 1999


Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18
journal, May 1980

  • McLean, A. D.; Chandler, G. S.
  • The Journal of Chemical Physics, Vol. 72, Issue 10, p. 5639-5648
  • DOI: 10.1063/1.438980

Optimized accurate auxiliary basis sets for RI-MP2 and RI-CC2 calculations for the atoms Rb to Rn
journal, January 2007

  • Hellweg, Arnim; Hättig, Christof; Höfener, Sebastian
  • Theoretical Chemistry Accounts, Vol. 117, Issue 4
  • DOI: 10.1007/s00214-007-0250-5

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

Inhomogeneous Electron Gas
journal, November 1964


The xyloglucan–cellulose assembly at the atomic scale
journal, January 2006

  • Hanus, Jaroslav; Mazeau, Karim
  • Biopolymers, Vol. 82, Issue 1
  • DOI: 10.1002/bip.20460

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses
journal, August 2009

  • Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct900242e

Self‐consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets
journal, April 1984

  • Frisch, Michael J.; Pople, John A.; Binkley, J. Stephen
  • The Journal of Chemical Physics, Vol. 80, Issue 7
  • DOI: 10.1063/1.447079

A molecular mechanics force field for lignin
journal, February 2009

  • Petridis, Loukas; Smith, Jeremy C.
  • Journal of Computational Chemistry, Vol. 30, Issue 3
  • DOI: 10.1002/jcc.21075

Note on an Approximation Treatment for Many-Electron Systems
journal, October 1934


Dynamics of Water Confined in Reversed Micelles: Multidimensional Vibrational Spectroscopy Study
journal, September 2013

  • Bakulin, Artem A.; Cringus, Dan; Pieniazek, Piotr A.
  • The Journal of Physical Chemistry B, Vol. 117, Issue 49
  • DOI: 10.1021/jp405853j

Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F
journal, October 1983

  • Clark, Timothy; Chandrasekhar, Jayaraman; Spitznagel, G�nther W.
  • Journal of Computational Chemistry, Vol. 4, Issue 3
  • DOI: 10.1002/jcc.540040303

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

Re-constructing our models of cellulose and primary cell wall assembly
journal, December 2014


Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules
journal, March 1972

  • Hehre, W. J.; Ditchfield, R.; Pople, J. A.
  • The Journal of Chemical Physics, Vol. 56, Issue 5, p. 2257-2261
  • DOI: 10.1063/1.1677527

Blow-up criteria for the inhomogeneous nonlinear Schrödinger equation
journal, February 2014