Source: https://cmb.ornl.gov/index.php/research/bioenergy/dynamic-visualization-of-lignocellulose
Timestamp: 2019-04-22 15:15:15+00:00

Document:
Our aim is to provide fundamental knowledge about how solvents alter the structure and arrangement of critical biomolecule assemblies that comprise plant cell walls and microbial membranes. The focus is on how these structures are affected by the presence of solvents and what physical and molecular forces drive these effects. Recent work aimed at improving the conversion of biomass to advanced biofuels and bioproducts has highlighted the critical importance of solvent effects. These effects are important both in the efficient solvent-based deconstruction of biomass and in the product titer limitations of fermentations due to the solvent-based destabilization of microbial membranes.
For both processing steps, the presence of nonaqueous co-solvents can disrupt the structures of key biological systems. In the case of biomass, this disruption is desirable, as it facilitates the solubilization and fractionation of lignocellulosic polymers for subsequent cellulosic conversion and lignin valorization. In contrast, the presence of nonaqueous solvents can be detrimental to fermentative microbes, as they can disrupt cell membranes, inhibiting microbial fermentation. Gaining a predictive understanding of these solvent effects will provide a fundamental understanding that can be used to develop optimized industrial biomass conversions. [Loukas Petridis, Sai Venkatesh Pingali, Micholas D. Smith, Takat B. Rawal, Shih-Hsien Liu, Derya Vural, Marcella Berg, Riddhi Shah, Yunqiao Pu, Volker Urban, Barbara R. Evans, Hugh M. O’Neill, Art Ragauskas, Paul Langan, Jeremy C. Smith, and Brian H. Davison].
Cellulase enzyme (orange) hydrolyzing cellulose (green) despite the presence of lignin (brown).
BER Biofuels SFA: Patent Issued for "High-Throughput Reproducible Cantilever Functionalization"
60. Vermaas, J. V., Petridis, L., Ralph, J., Crowley, M. F., Beckham, G. T., "Systematic parameterization of lignin for the CHARMM force field", Green Chem. (2019) 21, 109-122.
59. Shah, R., Huan, S., Pingali, S. V., Sawada, D., Kim, S., Evans, B. R., Davison, B. H., O’Neill, H. “Hemicellulose-cellulose composites reveal differences in cellulose organization after dilute acid pretreatment”, Biomacromolecules (2019) 20, 893–903.
58. Petridis, L; Smith, J.C., "Molecular-level driving forces in the assembly of lignocellulosic biomass and its deconstruction for biofuels and bioproducts", Nat. Rev. Chem. (2018) 2, 382-389.
57. Vural, D., Smith, J. C., Petridis, L., "Dynamics of the lignin glass transition", Phys. Chem. Chem. Phys. (2018) 20, 20504-20512.
56. Satlewal A., Agrawal R., Bhagia S., Sangoro J., and Ragauskas A.J., "Deep eutectic solvents for lignocellulosic biomass pretreatment: Recent developments, challenges and novel opportunities", Biotechnology advances, (2018) 36, 2032-2050.
55. Bhagia, S., Pu, Y., Evans, B. R., Davison, B. H., Ragauskas, A. J., “Hemicellulose characterization of deuterated switchgrass”, Bioresource Technology, (2018) 269, 569-570.
54. Bhagia, S., Meng, X., Evans, B. R., Dunlap, J. R., Bali, G., Chen, J., Reeves, K. S., Ho, H. C. H., Davison, B. H., and Ragauskas, A. J. "Ultrastructure and Enzymatic Hydrolysis of Deuterated Switchgrass.”, Scientific Reports (2018) 8, 13226.
53. Vural, D., Gainaru, C., O’Neill, H., Pu, Y., Smith, M. D., Pingali, S. V., Mamontov, E., Davison, B. H., Sokolov, A. P., Ragauskas, A. J., Smith, J. C., Petridis, L. “Impact of hydration and temperature history on the structure and dynamics of lignin.”, Green Chemistry (2018) 20, 1602-1611.
52. Smith, M. D., Cai, C.; Cheng, X., Petridis, L., Smith, J. C. “Phase-dependent solvation of xylan in tetrahydrofuran-water enables synergistic processing of lignocellulosic biomass.”, Green Chemistry, (2018) 20, 1612-1620.
51. Vural, D., Smith, J.C., Glyde, H. “Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins.”, Biophysical Journal, (2018) 114, 2397-2407.
50. Kumar, R., Bhagia, S., Smith, M. D., Petridis, L., Ong, R., Cai, C. M., Mittal, A., Himmel, M. E., Balan, V., Dale, B. D., Ragauskas, A., Smith, J. C., Wyman, C. E. "Cellulose-Hemicellulose Interactions at Elevated Temperatures Increase Cellulose Recalcitrance to Biological Conversion", Green Chemistry, (2018) 20, 921-934.
49. Sawada. D., Kalluri, U., O'Neill, H., Urban, V., Langan, P., Davison, B., Pingali, S. V. "Tension wood structure and morphology conducive for better enzymatic digestion", Biotechnology for Biofuels, (2018) 11, 44.
48. Smith, J. C., Tan, P., Petridis, L. and Hong, L. "Dynamic Neutron Scattering by Biological Systems." Annual Review of Biophysics, (2018) 47, 335-354.
47. Moyer, P., Smith, M. D., Abdoulmoumine, M., Chmely, S. C., Smith, J. C., Petridis, L., and Labbé, N. "Relationship between lignocellulosic biomass solubilization and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions", Physical Chemistry Chemical Physics (2018) 20(4),2508-2516.
46. Meng, X., Pu, Y., Sannigrahi, P., Li, M., Cao, S., Ragauskas, A. J. "The nature of hololignin." ACS Sustainable Chemistry & Engineering, (2018) 6(1), 957-964.
45. Smith, M. D., Cheng, X., Petridis, L., Mostofian, B., Smith, J. C. "Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis." Scientific Reports (2017) 7(1), 14494.
44. Evans, B. R., Bali, G., Ragauskas, A., Shah, R., O'Neill, H., Howard, C., Lavenhouse, F., Ramirez, D., Weston, K., Ramey, K., Cangemi, V., Kinney, B., Partee, C., Ware, T., and Davison, B. "Alleopathic effects of exogenous phenylalanine: A comparison of four monocot species." Planta (2017) 246 (4), 673-685.
43. Meng, X., Evans, B. R., Yoo, C. G., Pu, Y., Davison, B. H., Ragauskas, A. J. "Effect of in Vivo Deuteration on Structure of Switchgrass Lignin." ACS Sustainable Chemistry & Engineering, (2017) 5(9), 8004-8010.
42. O'Neill, H.M.; Pingali, S.V.; Petridis, L.; He, J.; Evans, B.; Mamontov, E.; Hong, L. Urban, V.; Langan, P.; Smith, J.C.; Davison, B. "Dynamics of water bound to crystalline cellulose." Scientific Reports (2017) 7, 11840.
41. Goodell, B., Zhu, Y., Kim, S., Kafle, K., Eastwood, D., Daniel, G., Jellison, J., Yoshida, M., Groom, L., Pingali, S. V. O'Neill, H. "Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown-rot wood decay fungi." Biotechnol. for Biofuels, (2017) 10, 179.
40. Pingali, S. V., Urban, V. S., Heller, W. T., McGaughey, J., O'Neill, H., Foston, M. B., Li, H., Wyman, C. E., Myles, D. A., Langan, P., Ragauskas, A., Davison, B., Evans, B. R. "Understanding Multiscale Structural Changes During Dilute Acid Pretreatment of Switchgrass and Poplar.", ACS Sustainable Chemistry & Engineering (2017) 5(1), 426-435.
39. Sawada, D., Ogawa, Y., Nishiyama,Y., Togawa, E., Kimura, S., Langan, P. "Molecular interactions in an ɑ-chitin/hydrazine complex: Dynamic hydrogen bonds and improvement of polymeric crystallinity.", Crystal Growth & Design, (2016) 16(6), 3345-3352.
38. Plaza, N. Z., Qian, S., Heller, W. T., Pingali, S. V., Jakes, J. E. "Informing the improvement of forest products durability using small angle neutron scattering.", Cellulose, (2016) 23(3), 1593 - 1607.
37. Petridis, L., and Smith, J. C. "Conformations of low-molecular weight lignin polymers in water.", ChemSusChem (2016) 9(3), 289-295.
36. Evans, B. R., & Shah, R., "Development of Approaches for Deuterium Labeling in Plants", in Methods in Enzymology: Volume 565 Isotope Labeling of Biomolecules, ed. Kelman, Z., Chapter 10, Elsevier Ltd., Oxford, Great Britain (2015), pp. 213-243.
35. O'Neill, H., Shah, R., Evans, B., He, J., Pingali, S. V., Chundawat, S. P. S., Jones, A. D., Langan, P., Davison, B. H., Urban, V., "Production of Bacterial Cellulose with Controlled Deuterium-Hydrogen Substitution for Neutron Scattering Studies" in Methods in Enzymology: Volume 565 Isotope Labeling of Biomolecules, ed. Kelman, Z., Volume 565, Chapter 6, Elsevier Ltd., Oxford, Great Britain (2015), pp. 123-146.
34. Vermaas, J. V., Petridis, L., Qi, X., Schulz, R., Lindner, B., Smith, J. C. "Mechanism of Lignin Inhibition of Enzymatic Biomass Deconstruction." Biotechnol. Biofuels, (2015) 8(1), 1-16.
33. G. Bali, X. Meng, J.I. Deneff, Q. Sun, A.J. Ragauskas,; “The Effect of Alkaline Pretreatment Methods on Cellulose Structure and Accessibility in Milled Populus””, Chem. Sus. Chem., (2015) 8(2), 275-279.
32. I. Lee, B. Evans, G. Bali, M. Foston, A.J. Ragauskas,; “Silicon cantilever functionalization for cellulose-specific chemical force imaging of switchgrass””, Analytical Methods, (2015) 7, 4541.
31. B. Evans, G. Bali, M. Foston, A.J. Ragauskas, H.M. O'Neil, R. Shah, J. McGaughey, D. Reeves, C.S. Rempe, B.H. Davison ; “Production of deuterated switchgrass by hydroponic cultivation”, Planta, (2015) 242(1), 215-222.
30. B. Lindner, L. Petridis, P. Langan and J. C. Smith; “Cellulose Crystallinity and Powder Diffraction Diagrams”, Biopolymers, (2015) 203, 67-73.
29. L. Petridis, H. M. O’Neill, M. Johnsen, B. Fan, R. Schulz, E. Mamontov, J. Maranas, P. Langan and J.C. Smith “Hydration Control of the Mechanical and Dynamical Properties of Cellulose” Biomacromolecules (2014) 15, 4152–59.
28. L. Hong, L. Petridis and J. C. Smith; “Biomolecular Structure and Dynamics: The View from Simulation”, Israel Journal of Chemistry, (2014) 54, 1264-1273.
27. Q. Sun, M. Foston, D. Sawada, S.V. Pingali, H.M. O’Neill, H. Li, C.E. Wyman, P. Langan, Y. Pu and A.J. Ragauskas, "Comparison of Changes in Cellulose Ultrastructure During Different Pretreatments of Poplar”, Cellulose, (2014) 21, 2419-31.
26. D. Sawada, L. Hanson, M. Wada, Y. Nishiyama and P. Langan, “The Initial Structure of Cellulose During Ammonia Pretreatment”, Cellulose, (2014) 21, 1117-1126.
25. A.J. Ragauskas, G.T. Beckham, M.J. Biddy, R. Chandra, F. Chen, M.F. Davis, B.H. Davison, R.A. Dixon, P. Gilna, M. Keller, P. Langan, A.K. Naskar, J. N. Saddler, T. J. Tschaplinski, G.A. Tuskan and C.E. Wyman, “Lignin Valorization in the Biorefinery”, Science, (2014) 16, 709.
24. E. M. Alekozai, P. K. Ghattyvenkatakrishna, E. C. Uberbacher, M. F. Crowley, J. C. Smith and X. Cheng,“Simulation Analysis of the Cellulase Cel7A Carbohydrate Binding Module on the Surface of the Cellulose Iβ”, Cellulose, (2014) 21(2): 951–971.
23. D. Sawada, Y. Ogawa, S. Kimura, Y. Nishiyama, P. Langan, and M. Wada, “Solid-Solvent Molecular Interactions Observed in Crystal Structures of Beta-Chitin Complexes”, Cellulose, (2014) 21(2), 1007-1014.
22. J. He, S.V. Pingali, S.P.S. Chundawat, A. Pack, A. D. Jones, P. Langan, B.H. Davison, V. Urban, B. Evans and H. O’Neill, “Controlled Incorporation of Deuterium into Bacterial Cellulose”, Cellulose, (2014) 21(2), 927–936.
21. Y. Nishiyama, P. Langan, H. O'Neill, S.V. Pingali and S. Harton, “Structural Coarsening of Aspen Wood by Hydrothermal Pretreatment Monitored by Small- and Wide-Angle Scattering of X-ray and Neutrons on Oriented Specimens”, Cellulose 21(2), 1015–1024 (2014).
20. S. V. Pingali, H. M. O’Neill, L. He, Y. Nishiyama, Y. Melnichenko, V. S. Urban, L. Petridis, B. Davison, and P. Langan, “Morphological Changes in the Cellulose and Lignin Components of Biomass Occur at Different Stages During Steam Pretreatment”, Cellulose 21(2), 873–878 (2014).
19. H. Wang, G. Gurau, S. V. Pingali, H. O'Neill, B. Evans, V. Urban, W. Heller, and R. Rogers, “Physical Insight into Switchgrass Dissolution in the Ionic Liquid 1-Ethyl-3-Methylimidazolium Acetate”, ACS Sustainable Chemistry & Engineering (April 13, 2014) 1264–1269 (2014).
18. B. Evans, G. Bali, D. Reeves, H. O'Neill, Q. Sun, R. Shah, and A. Ragauskas, A., “Effect of D2O on Growth Properties and Chemical Structure of Annual Ryegrass (Lolium multiflorum)”, Journal of Agricultural and Food Chemistry, (2014) 62(12), 2592–2604.
17. P. Langan, L. Petridis, H. M. O’Neill, S.V. Pingali, M. Foston, Y. Nishiyama, R. Schulz, B. Lindner, B.L. Hanson, S. Harton, W.T. Heller, V. Urban, B.R. Evans, S. Gnanakaran, A.J. Ragauskas, J.C. Smith and B.H. Davison, “Common Processes Driving the Thermochemical Pretreatment of Lignocellulosic Biomass”, Green Chemistry, (2014) 16, 63–68.
16. B. Lindner, L. Petridis, R. Schulz and J. C. Smith; “Solvent-Driven Preferential Association of Lignin with Crystalline Cellulose Regions in Multimillion Atom Molecular Dynamics Simulation”, Biomacromolecules, (2013) 14(10), 3390–3398.
15. D. Sawada, Y. Nishiyama, L. Petridis, R. Parthasarathi, S. Gnanakaran, V. T. Forsyth, M. Wada, P. Langan, “Structure and dynamics of a complex of cellulose with EDA: insights into the action of amines on cellulose”, Cellulose, (2013) 20 1563-1571.
14. G. Bali, M. Foston, B. R. Evans, J. He, A. J. Ragauskas, "The effect of deuteration on the structure of bacterial cellulose” Carbohydrate Research, (2013) 347, 82-88.
13. P. Langan, B. R. Evans, M. Foston, W. T. Heller, H. M. O’Neill, L. Petridis, S. V. Pingali, A. J. Ragauskas, J. C. Smith, B. Davison, “Neutron Technologies for Bioenergy Research.”, Industrial Biotechnology, (2012) 8, 209.
12. S. E, Harton, S. V., Pingali, G. A. Nunnery, D. A. Baker, S. H. Walker, D. C. Muddiman, T. Koga, T. G. Rials, V. S. Urban, and P. Langan “Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins.”, ACS Macro Lett., (2012) 1, 568-573.
11. Foston, M.B.; McGaughey, J.; O’Neill, H.; Barbara R. Evans, B.R.; Ragauskas, A.J - “Deuterium Incorporation in Biomass Cell Wall Components by NMR Analysis”, Analyst, (2012) 137, 1090-1093.
10. Petridis, R. Schulz, J.C. Smith – “Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics", J. Am. Chem. Soc. (2011) 133, 20277-20287.
9. Petridis, S.V. Pingali, V. Urban, W.T. Heller, H.M. O' Neill, M. Foston, A. Ragauskas, and J.C. Smith “Self-Similar Multiscale Structure of Lignin Revealed by Neutron Scattering and Molecular Dynamics Simulation, Phys. Rev. E, (2011) 83, 061911.
8. S.V. Pingali, H.M. O'Neill, J. McGaughey, V.S. Urban, C.S. Rempe, L. Petridis, J.C. Smith, B.R. Evans, and W.T. Heller “Small-angle neutron scattering reveals a pH-dependent conformational change in Trichoderma reesei cellobiohydrolase I: Implications for enzymatic activity.”, J. Biol. Chem., (2011) 286, 32801-32809.
7. M. Foston, C.A. Hubbel, A.J. Ragauskas – “Cellulose isolation methodology for NMR analysis of cellulose ultrastructure,” Materials, (2011) 4, 1985-2002.
6. J.C. Smith, M. Krishnan, L. Petridis, N. Smolin – “Structure and dynamics of biological systems: Integration of Neutron Scattering with Computer Simulation,” Dynamics of Soft Matter, (2011).
5. S.V. Pingali, V. Urban, W.T. Heller, J. McGaughey, H.M. O' Neill, M. Foston, D. Myles, A. Ragauskas, B.R. Evans “Breakdown of Cell Wall Nanostructure in Dilute Acid Pretreated Biomass.", Biomacromolecules, (2010) 11, 2329-2335.
4. S.V. Pingali, V. Urban, W.T. Heller, J. McGaughey, H.M. O' Neill, M. Foston, D. Myles, A. Ragauskas, B.R. Evans “SANS Study of Cellulose Extracted from Switchgrass.”, ActaCryst. (2010) D66, 1189-1193.
3. Foston, M; Ragauskas, AJ, “Changes in lignocellulosic supramolecular and ultrastructure during dilute acid pretreatment of Populus and switchgrass", Biomass & Bioenergy, (2010) 34, 1885-1895.
2. Schulz, R.; Lindner, B.; Petridis, L.; Smith, J.C. “Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Computer.”, J.Chem. Theory Comput. (2009) 5, 2798–2808.
1. Petridis, L., and Smith, J.C. “A molecular mechanics force field for lignin.”, J. Comp. Chem., (2009) 30(3), 457-67.
This research (ORNL Biofuels SFA) is funded by the Genomic Science Program, Office of Biological and Environmental Research, U.S. Department of Energy.

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