Ab initio study of molecular interactions in cellulose Iα

Journal of Physical Chemistry B

Volumn 117, Issue 36, 2013, Pages 10430-10443

  Devarajan, Ajitha ^a,b   Markutsya, Sergiy ^a,c   Lamm, Monica H ^a,c   Cheng, Xiaolin ^d   Smith, Jeremy C ^d,e   Baluyut, John Y ^a,b   Kholod, Yana ^a,b   Gordon, Mark S ^a,b   Windus, Theresa L ^a,b  

^a IOWA STATE UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c Iowa State University   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF TENNESSEE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMASS RECALCITRANCES; CRYSTALLINE CELLULOSE; CRYSTALLINE STRUCTURE; FRAGMENT MOLECULAR ORBITAL METHODS; HYDROGEN BOND NETWORKS; INTERCHAIN HYDROGEN BONDS; PAIR INTERACTION ENERGIES; SECOND ORDER PERTURBATION;

CELLULOSE; CHAINS; MOLECULAR ORBITALS; PERTURBATION TECHNIQUES;

HYDROGEN BONDS;

CELLULOSE;

ARTICLE; CHEMISTRY; CONFORMATION; CRYSTALLIZATION; HYDROGEN BOND; STATIC ELECTRICITY; THERMODYNAMICS;

CELLULOSE; CRYSTALLIZATION; HYDROGEN BONDING; MOLECULAR CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84884197198     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp406266u     Document Type: Article

References (55)

1. Himmel, M. E.; Ding, S. Y.; Johnson, D. K.; Adney, W. S.; Nimlos, M. R.; Brady, J. W.; Foust, T. D. Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production Science 2007, 315, 804-807
2. Stephanopoulos, G. Challenges in Engineering Microbes for Biofuels Production Science 2007, 315, 801-804
3. Hu, S.-Q.; Gao, Y.-G.; Tajima, K.; Sunagawa, N.; Zhou, Y.; Kavano, S.; Fujiwara, T.; Yoda, T.; Shimura, D.; Satoh, Y. Structure of bacterial cellulose synthase subunit D octamer with four inner passageways Proc. Natl. Acad. Sci. U.S.A. 2007, 107, 17957-61
4. Zhu, J. Y.; Verril, S. P.; Liu, H.; Herian, V. L.; Pan, X.; Rockwood, D. L. On Polydispersity of Plant Biomass Recalcitrance and Its Effects on Pretreatment Optimization for Sugar Production. et al BioEnergy Res. 2011, 4, 201-210
5. Matthews, J. F.; Skopec, C. E.; Mason, P. E.; Zuccato, P.; Torget, R. W.; Sugiyama, J.; Himmel, M. E.; Brady, J. W. Computer Simulation Studies of Microcrystalline Cellulose Iβ Carbohydr. Res. 2006, 341, 138-152
6. BergenstraÌŠhle, M.; Wohlert, J.; Himmel, M. E.; Brady, J. W. Simulation Studies of the Insolubility of Cellulose Carbohydr. Res. 2010, 345, 2060-2066
7. Shen, T.; Langan, P.; French, A. D.; Johnson, G. P.; Gnanakaran, S. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence J. Am. Chem. Soc. 2009, 131, 14786-14794
8. Shen, T.; Gnanakaran, S. The Stability of Cellulose: A Statistical Perspective from a Coarse-Grained Model of Hydrogen-Bond Networks J. Biophys. 2009, 8, 3032-3040
9. Nishiyama, Y.; Sugiyama, J.; Chanzy, H.; Langan, P. Crystal Structure and Hydrogen Bonding System in Cellulose Iα from Synchrotron X-ray and Neutron Fiber Diffraction J. Am. Chem. Soc. 2003, 125, 14300-14306
10. Matthews, J. F.; Beckham, G. T.; Bergenstrahle, M.; Brady, J. W.; Himmel, M. E.; Crowley, M. F. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields J. Chem. Theory Comput. 2012, 8, 735-748
11. Guvench, O.; Greene, S. N.; Kamath, G.; Brady, J. W.; Venable, R. M.; Pastor, R. W.; MacKerell, A. D., Jr. Additive Empirical Force Field for Hexopyranose Monosaccharides J. Comput. Chem. 2008, 29, 2543-2564
12. Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; Gonzalez-Outeirino, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates J. Comput. Chem. 2008, 29, 622-655
13. Lins, R. D.; Hunenberger, P. H. A New GROMOS Force Field for Hexopyranose-based Carbohydrates J. Comput. Chem. 2005, 26, 1400-1412
14. Parthasarathi, R.; Bellesia, G.; Chundawat, S. P.; Dale, B. E.; Langan, P.; Gnanakaran, S. Insights into Hydrogen Bonding and Stacking Interactions in Cellulose J. Phys. Chem. A 2011, 115, 14191-14200
15. Gordon, M. S.; Mullin, J. M.; Pruitt, S. R.; Roskop, L. B.; Slipchenko, L. V.; Boatz, J. A. Accurate Methods for Large Molecular Systems J. Phys. Chem. B 2009, 113, 9646-9663 (Invited Centennial Feature Article)
16. Pranami, G.; Slipchenko, L. V.; Lamm, M. H.; Gordon, M. S. Coarse-Grained Intermolecular Potentials Derived from the Effective Fragment Potential: Application to Water, Benzene, and Carbon Tetrachloride. In Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications; York, D.M.; Lee, T.-S., Eds.; Springer-Verlag: London, 2009.
17. Devarajan, A.; Windus, T. L.; Gordon, M. S. Implementation of Dynamical Nucleation Theory Effective Fragment Potentials Method for Modeling Aerosol Chemistry J. Phys. Chem. A 2011, 115, 13987-13996
18. Gordon, M. S.; Fedorov, D. G.; Pruitt, S. R.; Slipchenko, L. V. Fragmentation Methods: A Route to Accurate Calculations on Large Systems Chem. Rev. 2012, 112, 632-672
19. Fedorov, D. G.; Kitaura, K. Second order Moeller-Plesset Perturbation Theory Based Upon the Fragment Molecular Orbital Method J. Chem. Phys. 2004, 121, 2483-2490
20. Fedorov, D. G.; Olson, R. M.; Kitaura, K.; Gordon, M. S.; Koseki, S. A New Hierarchical Parallelization Scheme: Generalized Distributed Data Interface (GDDI), and an Application to the Fragment Molecular Orbital Method (FMO) J. Comput. Chem. 2004, 25, 872-80
21. Bekker, H.; Berendsen, H. J. C.; Dijkstra, E. J.; Achterop, S.; van Drunen, R.; van der Spoel, D.; Sijbers, A.; Keegstra, H.; Reitsma, B.; Renardus, M. K. R. Gromacs: A parallel computer for molecular dynamics simulations. In Physics Computing 92; de Groot, R. A.; Nadrchal, J., Eds.; World Scientific: Singapore, 1993.
22. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
23. Guvench, O.; Hatcher, E. R.; Venable, R. M.; Pastor, R. W.; MacKerell, A. D. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses J. Chem. Theory Comput. 2009, 5, 2353-2370
24. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1987.
25. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A Generalized Reaction Field Method for Molecular Dynamics Simulations J. Chem. Phys. 1995, 102, 5451-5459
26. Schulz, R.; Lindner, B.; Petridis, L.; Smith, J. C. Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer J. Chem. Theory Comput. 2009, 5, 2798-2808
27. Nose, S. A Molecular Dynamics Method for Simulations in the Canonical Ensemble Mol. Phys. 1984, 52, 255-268
28. Hanley, S. J.; Revol, J. F.; Godbout, L.; Gray, D. G. Atomic Force Microscopy and Transmission Electron Microscopy of Cellulose from Micrasterias Denticulata; Evidence for a Chiral Helical Microfibril Twist Cellulose 1997, 4, 209-220
29. Zhao, Z.; Shklyaev, O. E.; Nili, A.; Mohamed, M. N. A. Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis J. Phys. Chem. A 2013, 117, 2580-2589
30. Matthews, J. F.; Bergenstrahle, M.; Beckham, G. T.; Himmel, M. E.; Nimlos, M. R.; Brady, J. W.; Crowley, M. F. High-Temperature Behavior of Cellulose I J. Phys. Chem. B 2011, 115, 2155-2166
31. Benziman, M.; Haigler, C. H.; Brown, R. M.; White, A. R.; Cooper, K. M. Cellulose Biogenesis: Polymerization and Crystallization are Coupled Processes in Acetobacter Xylinum Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 6678-6682
32. Haigler, C. H.; White, A. R.; Brown, R. M.; Cooper, K. M. Alteration of In Vivo Cellulose Ribbon Assembly by Carboxymethylcellulose and Other Cellulose Derivatives J. Cell Biol. 1982, 94, 64-69
33. Bowling, A. J.; Amano, Y.; Lindstrom, R.; Brown, R. M. Rotation of Cellulose Ribbons During Degradation with Fungal Cellulase Cellulose 2001, 8, 91-97
34. Koyama, M.; Helbert, W.; Imai, T.; Sugiyama, J.; Henrissat, B. Parallel-up Structure Evidences the Molecular Directionality During Biosynthesis of Bacterial Cellulose Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 9091-9095
35. Koyama, M.; Sugiyama, J.; Itoh, T. Systematic Survey on Crystalline Features of Algal Celluloses Cellulose 1997, 4, 147-160
36. Lee, H.; Brown, R. J. A Comparative Structural Characterization of Two Cellobiohydrolases from Trichoderma Reesei: a High Resolution Electron Microscopy Study Biotechnol. 1997, 57, 127-136
37. Brown, R., Jr. Cellulose and wood: chemistry and technology; John Wiley and Sons: New York, 1995; pp 639-657.
38. Haigler, C. H.; Chanzy, H. J. Electron Diffraction Analysis of the Altered Cellulose Synthesized by Acetobacter Xylinum in the Presence of Fluorescent Brightening Agents and Direct Dyes J. Ultrastruct. Mol. Struct. Res. 1988, 98, 299-311
39. Shibazaki, H.; Kuga, S.; Okano, T. Mercerization and Acid Hydrolysis of Bacterial Cellulose Cellulose 1997, 4, 75-87
40. Kondo, T.; Nojiri, M.; Hishikawa, Y.; Togawa, E.; Romanovicz, D.; Brown, R. M. Biodirected Epitaxial Nanodeposition of Polymers on Oriented Macromolecular Templates Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 14008-14013
41. Nobles, D.; Romanovicz, D.; Brown, R., Jr. Cellulose in Cyanobacteria. Origin of Vascular Plant Cellulose Synthase? Plant Physiol. 2001, 127, 529-542
42. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
43. 2O J. Chem. Phys. 1971, 55, 1236-1244
44. Kitaura, K.; Morokuma, K. A New Energy Decomposition Scheme for Molecular Interactions within the Hartree-Fock Approximation Int. J. Quantum Chem. 1976, 10, 325-340
45. Chen, W.; Gordon, M. S. Energy Decomposition Analyses for Many-Body Interaction and Applications to Water Complexes J. Chem. Phys. 1996, 100, 14316-14328
46. Fedorov, D. G.; Kitaura, K. Pair Interaction Energy Decomposition Analysis J. Comput. Chem. 2007, 28, 222-237
47. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. General atomic and molecular electronic structure system J. Comput. Chem. 1993, 14, 1347-1363
48. Gordon, M. S.; Schmidt, M. W. In Theory and Applications of Computational Chemistry; Dykstra, C. E.; Frenking, G.; Kim, K. S.; Scuseria, G. E.; Eds.; Elsevier: New York, 2005; Ch. 41.
49. Gross, A. S.; Chu, J. W. On the Molecular Origins of Biomass Recalcitrance: The Interaction network and solvation Structures of Cellulose Microfibrils J. Phys. Chem. B 2010, 114, 13333-13341
50. French, A. D.; Miller, D. P.; Aabloo, A. Miniature Crystal Models of Cellulose Polymorphs and Other Carbohydrates Int. J. Biol. Macromol. 1993, 15, 30-36
51. Beckham, G. T.; Matthews, J. F.; Peters, B.; Bomble, Y. J.; Himmel, M. E.; Crowley, M. F. Molecular-level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs J. Phys. Chem. B 2011, 115, 4118-4127
52. α Fibrils Describes the Recalcitrance to Thermal Deconstruction J. Chem. Phys. 2011, 135, 085106
53. I Biomacromolecules 2007, 8, 817-824
54. Cho, H. M.; Gross, A. S.; Chu, J.-W. J. Am. Chem. Soc. 2011, 133, 14033-14041
55. Chang, R.; Gross, A. S.; J-W. J. Phys. Chem. B 2012, 116, 8074-8083