A coarse-grain force-field for xylan and its interaction with cellulose

Carbohydrate Polymers

Volumn 127, Issue , 2015, Pages 438-450

  Li, Liang ^a   Pérré, Patrick ^b   Frank, Xavier ^c   Mazeau, Karim ^d,e  

^a LERFoB   (France)

^b ECOLE CENTRALE PARIS   (France)

^c CIRAD   (France)

^d UNIV GRENOBLE ALPES   (France)

^e CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

Author keywords

Adsorption; Cellulose; Coarse grain; Composite; Interaction; Molecular dynamics; Xylan

Indexed keywords

ADSORPTION; COMPOSITE MATERIALS; CRYSTALLINE MATERIALS; MOLECULAR DYNAMICS;

CELLULOSE SURFACES; COARSE GRAINS; CRYSTALLINE CELLULOSE; FORCE FIELD PARAMETERS; FORCE FIELDS; INTERACTION; SINGLE GRAINS; XYLAN;

CELLULOSE;

ADSORPTION; CELLULOSE; WATER REPELLENCE; XYLANS;

CELLULOSE; XYLAN;

ADSORPTION; CHEMISTRY; MOLECULAR DYNAMICS; SURFACE PROPERTY;

ADSORPTION; CELLULOSE; MOLECULAR DYNAMICS SIMULATION; SURFACE PROPERTIES; XYLANS;

EID: 84928468065     PISSN: 01448617     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.carbpol.2015.04.003     Document Type: Article

References (84)

1. D.C. Adler, and M.J. Buehler Mesoscale mechanics of wood cell walls under axial strain Soft Matter 9 29 2013 7138 7144
2. P.D.A. Albersheim, K. Roberts, R. Seferoff, and A. Staehelin Plant cell walls 2010 Garland Science; Taylor and Francis Group; LLC New York
3. A. Asztalos, M. Daniels, A. Sethi, T. Shen, P. Langan, and A. Redondo A coarse-grained model for synergistic action of multiple enzymes on cellulose Biotechnology for Biofuels 5 2012 55 70
4. R.H. Atalla, J.M. Hackney, I. Uhlin, and N.S. Thompson Hemicelluloses as structure regulators in the aggregation of native cellulose International Journal of Biological Macromolecules 15 2 1993 109 112
5. F. Bazooyar, F.A. Momany, and K. Bolton Validating empirical force fields for molecular-level simulation of cellulose dissolution Computational and Theoretical Chemistry 984 2012 119 127
6. G. Bellesia, S.P.S. Chundawat, P. Langan, A. Redondo, B.E. Dale, and S. Gnanakaran Coarse-grained model for the interconversion between native and liquid ammonia-treated crystalline cellulose The Journal of Physical Chemistry B 116 28 2012 8031 8037
7. M. Bergenstrahle, J. Wohlert, P.T. Larsson, K. Mazeau, and L.A. Berglund Dynamics of cellulose-water interfaces: NMR spin-lattice relaxation times calculated from atomistic computer simulations The Journal of Physical Chemistry B 112 9 2008 2590 2595
8. L. Bu, G.T. Beckham, M.F. Crowley, C.H. Chang, J.F. Matthews, and Y.J. Bomble The energy landscape for the interaction of the family 1 carbohydrate-binding module and the cellulose surface is altered by hydrolyzed glycosidic bonds The Journal of Physical Chemistry B 113 31 2009 10994 11002
9. L. Bu, M.E. Himmel, and M.R. Nimlos Meso-scale modeling of polysaccharides in plant cell walls: An application to translation of CBMs on the cellulose surface ACS Symp. Ser. 1052 2010 99 117 (Computational Modeling in Lignocellulosic Biofuel Production)
10. N.C. Carpita, and M.C. McCann The functions of cell wall polysaccharides in composition and architecture revealed through mutations Plant Soil 247 1 2002 71 80
11. D.F. Caulfield Questioning X-ray evidence of crystallizability of xylan in situ Tappi 51 8 1968 371 372
12. G. Dervilly-Pinel, J.F. Thibault, and L. Saulnier Experimental evidence for a semi-flexible conformation for arabinoxylans Carbohydrate Research 330 3 2001 365 372
13. A. Ebringerova, and T. Heinze Xylan and xylan derivatives - biopolymers with valuable properties. 1. Naturally occurring xylans structures, isolation procedures and properties Macromolecular Rapid Communications 21 2000 542 556
14. B. Ensing, S.O. Nielsen, P.B. Moore, M.L. Klein, and M. Parrinello Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics Journal of Chemical Theory and Computation 3 2007 1100 1105
15. D.J. Evans, and B.L. Holian The Nose-Hoover thermostat The Journal of Chemical Physics 83 8 1985 4069 4074
16. D. Fritz, V.A. Harmandaris, K. Kremer, and N.F.A. van der Vegt Coarse-grained polymer melts based on isolated atomistic chains: Simulation of polystyrene of different tacticities Macromolecules 42 2009 7579 7588
17. D.C. Glass, K. Moritsugu, X. Cheng, and J.C. Smith REACH coarse-grained simulation of a cellulose fiber Biomacromolecules 13 9 2012 2634 2644
18. O. Gordobil, I. Egues, I. Urruzola, and J. Labidi Xylan-cellulose films: Improvement of hydrophobicity, thermal and mechanical properties Carbohydrate Polymers 112 2014 56 62
19. G.S. Grest, B. Dünweg, and K. Kremer Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles Computer Physics Communications 55 3 1989 269 285
20. A.S. Gross, A.T. Bell, and J.-W. Chu Preferential interactions between lithium chloride and glucan chains in N,N-dimethylacetamide drive cellulose dissolution The Journal of Physical Chemistry B 117 12 2013 3280 3286
21. S.L. Heikkinen, K.S. Mikkonen, K. Pirkkalainen, R. Serimaa, C. Joly, and M. Tenkanen Specific enzymatic tailoring of wheat arabinoxylan reveals the role of substitution on xylan film properties Carbohydrate Polymers 92 2013 733 740
22. L. Henao, and K. Mazeau The molecular basis of the adsorption of bacterial exopolysaccharides on montmorillonite mineral surface Molecular Simulation 34 2008 1185 1195
23. L.J. Henao, and K. Mazeau Molecular modeling studies of clay-exopolysaccharide complexes: Soil aggregation and water retention phenomena Materials Science and Engineering C 29 2009 2326 2332
24. A. Henriksson, and P. Gatenholm Controlled assembly of glucuronoxylans onto cellulose fibers Holzforschung 55 5 2001 494 502
25. A. Hoeije, E. Sternemalm, S. Heikkinen, M. Tenkanen, and P. Gatenholm Material properties of films from enzymatically tailored arabinoxylans Biomacromolecules 9 2008 2042 2047
26. S. Izvekov, and G.A. Voth A multiscale coarse-graining method for biomolecular systems The Journal of Physical Chemistry B 109 2005 2469 2473
27. M.A. Kabel, H. van den Borne, J.-P. Vincken, A.G.J. Voragen, and H.A. Schols Structural differences of xylans affect their interaction with cellulose Carbohydrate Polymers 69 1 2007 94 105
28. K. Keegstra Plant cell walls Plant Physiology 154 2 2010 483 486
29. T. Koehnke, A. Lin, T. Elder, H. Theliander, and A.J. Ragauskas Nanoreinforced xylan-cellulose composite foams by freeze-casting Green Chemistry 14 2012 1864 1869
30. T. Koehnke, A. Oestlund, and H. Brelid Adsorption of arabinoxylan on cellulosic surfaces: Influence of degree of substitution and substitution pattern on adsorption characteristics Biomacromolecules 12 7 2011 2633 2641
31. T. Kohnke, T. Elder, H. Theliander, and A.J. Ragauskas Ice templated and cross-linked xylan/nanocrystalline cellulose hydrogels Carbohydrate Polymers 100 2014 24 30
32. P.T. Larsson Interaction between cellulose I and hemicelluloses studied by spectral fitting of CP/MAS 13C-NMR spectra ACS Symposium Series 864 2004 254L 268 (Hemicelluloses)
33. P.T. Larsson, E.L. Hult, K. Wickholm, E. Pettersson, and T. Iversen CP/MAS 13C-NMR spectroscopy applied to structure and interaction studies on cellulose I Solid State Nuclear Magnetic Resonance 15 1 1999 31 40
34. X. Li, X. Ma, L. Huang, and H. Liang Developing coarse-grained force fields for cis-poly(1,4-butadiene) from the atomistic simulation Polymer 46 2005 6507 6512
35. C.Y. Liang, K.H. Bassett, E.A. McGinnes, and R.H. Marchessault Infrared spectra of crystalline polysaccharides. VII. Thin wood sections Tappi 43 1960 1017 1024
36. Y. Lin, G.T. Beckham, M.E. Himmel, M.F. Crowley, and J.-W. Chu Endoglucanase peripheral loops facilitate complexation of glucan chains on cellulose via adaptive coupling to the emergent substrate structures The Journal of Physical Chemistry B 117 37 2013 10750 10758
37. A.P. Linder, R. Bergman, A. Bodin, and P. Gatenholm Mechanism of assembly of xylan onto cellulose surfaces Langmuir 19 12 2003 5072 5077
38. O.V. Manyuhina, A. Fasolino, and M.I. Katsnelson Slow dynamics in a model of the cellulose network Los Alamos Natl. Lab., Prepr. Arch., Condens. Matter 1-13 2007 arXiv:07060997v0701
39. R.H. Marchessault, and C.Y. Liang The infrared spectra of crystalline polysaccharides. VIII. Xylans Journal of Polymer Science 59 1962 357 378
40. R.H. Marchessault, W.J. Settineri, and W. Winter Crystallization of xylan in the presence of cellulose Tappi 50 2 1967 55 59
41. G.J. Martyna, M.L. Klein, and M. Tuckerman Nosé-Hoover chains: The canonical ensemble via continuous dynamics The Journal of Chemical Physics 97 1992 2635 2643
42. K. Mazeau Structural micro-heterogeneities of crystalline Iβ-cellulose Cellulose 12 2005 339 349
43. K. Mazeau On the external morphology of native cellulose microfibrils Carbohydrate Polymers 84 1 2011 524 532
44. K. Mazeau, and L. Charlier The molecular basis of the adsorption of xylans on cellulose surface Cellulose 19 2 2012 337 349
45. K. Mazeau, C. Moine, P. Krausz, and V. Gloaguen Conformational analysis of xylan chains Carbohydrate Research 340 18 2005 2752 2760
46. K.S. Mikkonen, L. Pitkaenen, V. Liljestroem, E. Mabasa Bergstroem, R. Serimaa, and L. Salmen Arabinoxylan structure affects the reinforcement of films by microfibrillated cellulose Cellulose 19 2012 467 480
47. F. Mora, K. Ruel, J. Comtat, and J.P. Joseleau Aspect of native and redeposited xylans at the surface of cellulose microfibrils Holzforschung 40 2 1986 85 91
48. S. Morris, S. Hanna, and M.J. Miles The self-assembly of plant cell wall components by single-molecule force spectroscopy and Monte Carlo modelling Nanotechnology 15 9 2004 1296 1301
49. F. Muller-Plathe Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back ChemPhysChem 3 9 2002 755 769
50. I. Nieduszynski, and R.H. Marchessault Structure of β-d-(1 → 4) xylan hydrate Nature 232 5305 1971 46 47
51. J. Nieuwland, R. Feron, B.A.H. Huisman, A. Fasolino, C.W. Hilbers, and J. Derksen Lipid transfer proteins enhance cell wall extension in tobacco Plant Cell 17 2005 2009 2019
52. Y. Nishiyama, P. Langan, and H. Chanzy Crystal structure and hydrogen-bonding system in cellulose Iβ from synchrotron X-ray and neutron fiber diffraction Journal of the American Chemical Society 124 31 2002 9074 9082
53. W.G. Noid Perspective: Coarse-grained models for biomolecular systems The Journal of Chemical Physics 139 9 2013 090901/090901-090901/090925
54. K. Ohgren, R. Bura, J. Saddler, and G. Zacchi Effect of hemicellulose and lignin removal on enzymatic hydrolysis of steam pretreated corn stover Bioresource Technology 98 13 2007 2503 2510
55. A.-M. Olsson, I. Bjurhager, L. Gerber, B. Sundberg, and L. Salmen Ultra-structural organisation of cell wall polymers in normal and tension wood of aspen revealed by polarisation FTIR microspectroscopy Planta 233 6 2011 1277 1286
56. D.H. Page A note on the cell-wall structure of softwood tracheids Wood Fiber 7 4 1976 246 248
57. X.-W. Peng, J.-L. Ren, L.-X. Zhong, and R.-C. Sun Nanocomposite films based on xylan-rich hemicelluloses and cellulose nanofibers with enhanced mechanical properties Biomacromolecules 12 2011 3321 3329
58. P.A. Penttila, A. Varnai, J. Pere, T. Tammelin, L. Salmen, and M. Siika-aho Xylan as limiting factor in enzymatic hydrolysis of nanocellulose Bioresource Technology 129 2013 135 141
59. S. Queyroy, S. Neyertz, D. Brown, and F. Mueller-Plathe Preparing relaxed systems of amorphous polymers by multiscale simulation: Application to cellulose Macromolecules 37 19 2004 7338 7350
60. A.K. Rappe, C.J. Casewit, K.S. Colwell, W.A. Goddard III, and W.M. Skiff UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations Journal of the American Chemical Society 114 1992 10024 10035
61. A.K. Rappé, and W.A. Goddard III Charge equilibration for molecular dynamics simulations The Journal of Physical Chemistry 95 8 1991 3358 3363
62. D. Reith, H. Meyer, and F. Mueller-Plathe Mapping atomistic to coarse-grained polymer models using automatic simplex optimization to fit structural properties Macromolecules 34 2001 2335 2345
63. D. Reith, M. Puetz, and F. Mueller-Plathe Deriving effective mesoscale potentials from atomistic simulations Journal of Computational Chemistry 24 2003 1624 1636
64. J.C. Roberts, and S.A. El-Karim The behavior of surface adsorbed xylans during the beating of a bleached kraft pine pulp Cellulose Chemistry and Technology 17 4 1983 379 386
65. M.G. Saunders, and G.A. Voth Coarse-graining methods for computational biology Annual Review of Biophysics 42 2013 73 93
66. A. Saxena, T.J. Elder, S. Pan, and A.J. Ragauskas Novel nanocellulosic xylan composite film Composites Part B 40B 2009 727 730
67. A. Saxena, M. Foston, M. Kassaee, T.J. Elder, and A.J. Ragauskas Biopolymer nanocomposite films reinforced with nanocellulose whiskers Journal of Nanoscience and Nanotechnology 12 2012 218 226
68. T. Shen, and S. Gnanakaran The stability of cellulose: A statistical perspective from a coarse-grained model of hydrogen-bond networks Biophysics Journal 96 8 2009 3032 3040
69. Q. Shi, S. Izvekov, and G.A. Voth Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel The Journal of Physical Chemistry B 110 2006 15045 15048
70. Q. Shi, P. Liu, and G.A. Voth Coarse-graining in interaction space: An analytical approximation for the effective short-ranged electrostatics The Journal of Physical Chemistry B 112 2008 16230 16237
71. G. Srinivas, X. Cheng, and J.C. Smith A solvent-free coarse grain model for crystalline and amorphous cellulose fibrils Journal of Chemical Theory and Computation 7 8 2011 2539 2548
72. E. Sternemalm, A. Hoeije, and P. Gatenholm Effect of arabinose substitution on the material properties of arabinoxylan films Carbohydrate Research 343 2008 753 757
73. J.S. Stevanic, C. Joly, K.S. Mikkonen, K. Pirkkalainen, R. Serimaa, and C. Remond Bacterial nanocellulose-reinforced arabinoxylan films Journal of Applied Polymer Science 122 2011 1030 1039
74. J.S. Stevanic, and L. Salmen Orientation of the wood polymers in the cell wall of spruce wood fibers Holzforschung 63 5 2009 497 503
75. Q. Sun, A. Mandalika, T. Elder, S.S. Nair, X. Meng, and F. Huang Nanocomposite film prepared by depositing xylan on cellulose nanowhiskers matrix Green Chemistry 16 2014 3458 3462
76. N. Terashima, K. Kitano, M. Kojima, M. Yoshida, H. Yamamoto, and U. Westermark Nanostructural assembly of cellulose, hemicellulose, and lignin in the middle layer of secondary wall of ginkgo tracheid Journal of Wood Science 55 6 2009 409 416
77. C. Tokoh, K. Takabe, J. Sugiyama, and M. Fujita Cellulose synthesized by Acetobacter xylinum in the presence of plant cell wall polysaccharides Cellulose 9 1 2002 65 74
78. M. Tuckerman, B.J. Berne, and G.J. Martyna Reversible multiple time scale molecular dynamics The Journal of Chemical Physics 97 1992 1990 2001
79. J.E. Varner, and L.S. Lin Plant cell wall architecture Cell 56 2 1989 231 239
80. L. Verlet Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules Physical Review 159 1 1967 98 103
81. J. Wohlert, and L.A. Berglund A coarse-grained model for molecular dynamics simulations of native cellulose Journal of Chemical Theory and Computation 7 3 2011 753 760
82. S. Wu, H.-y. Zhan, H.-m. Wang, and Y. Ju Secondary structure analysis of native cellulose by molecular dynamics simulations with coarse-grained model Chinese Journal of Chemical Physics 25 2 2012 191 198
83. S. Yllner, and B. Enstrom Adsorption of xylan on cellulose fibers during the sulfate cook Svensk Papperstidning-Nordisk Cellulosa 59 1956 229 232
84. Y.-L. Zhu, H. Liu, Z.-W. Li, H.-J. Qian, G. Milano, and Z.-Y. Lu GALAMOST: GPU-accelerated large-scale molecular simulation toolkit Journal of Computational Chemistry 34 2013 2197 2211