Multiscale theory, modelling, and simulation of hemicellulose and lignin in solution

Authors

DOI:

https://doi.org/10.5488/CMP.29.13802

Keywords:

cellulose nanocrystals, hemicellulose, lignin, molecular solvation theory, solvation thermodynamics, molecular simulations

Abstract

This review examines multiscale modelling approaches for cellulose nanocrystals (CNCs) and lignocellulosic plant cell walls, with a focus on hemicellulose and lignin interactions in aqueous environments. The threedimensional reference interaction site model with the Kovalenko–Hirata closure (3D-RISM-KH) is highlighted as a powerful molecular solvation theory applied in nanochemistry and biomolecular simulations. The method has been successfully employed to investigate hemicellulose hydrogels, the influence of hemicellulose composition on nanoscale forces in primary cell walls, and lignin-lignin and lignin-hemicellulose interactions. Findings indicate that these interactions are predominantly hydrophobic and entropy-driven, arising from water exclusion effects. Insights gained through this modeling framework deepen the understanding of molecular-scale forces in plant cell walls and inform strategies for biomass valorization, including genetic engineering and pretreatment technologies aimed at enhancing cellulose extraction and utilization.

References

Gerez G., di Remigio Eikås R., Rune Jensen S., Bjørgve M., Frediani L., J. Chem. Theory Comput., 2023, 19, 1986–1997.

Skyner R. E., McDonagh J. L., Groom C. R., van Mourik T., Mitchell J. B. O., Phys. Chem. Chem. Phys., 2015, 17, 6174–6191.

Vyboishchikov S. F.,Voityuk A. A., J. Chem. Inf. Model., 2021, 61, 4544–4553.

Klamt A., Diedenhofen M., J. Phys. Chem. A, 2015, 119, 5439–5445.

Chaudhari M. I., Vanegas J. M., Pratt L. R., Muralidharan A., Rempe S. B., Annu. Rev. Phys. Chem., 2020, 71, 461.

Pratt L. R., Rempe S. B., AIP Conf. Proc., 1999, 492, 172–201.

Asthagiri D., Dixit P., Merchant S., Paulaitis M., Pratt L., Rempe S. B., Varma S., Chem. Phys. Lett., 2010, 485, 1–7.

Rogers D. M., Rempe S. B., Phys. Chem. B, 2011, 115, 911––9129.

Rogers D. M., Jiao D., Pratt L. R., Rempe S. B., Annu. Rep. Comput. Chem., 2012, 8, 71–127.

Himmel M. E., Ding S., Johnson D. K., Adney W. S., Nimlos M. R., Brady J. W., Foust T. D., Science, 2007, 315, 804–807.

Chundawat S. P. S., Beckham G. T., Himmel M. E., Dale B. E., Annu. Rev. Chem. Biomol. Eng., 2011, 2, 121–145.

Abolore R. S., Jaiswal S., Jaiswal A. K., Carbohydr. Polym. Technol. Appl., 2024, 7, 100396.

Mortimer J. C., Miles G. P., Brown D. M., Zhang Z., Segura M. P.,Weimar T., Yu X., Seffen K. A., Stephens E., Turner S. R., Dupree P., Proc.Natl.Acad. Sci.U.S.A., 2010, 107, 17409–17414.

Clark J. H., Green Chem., 2019, 21, 1168–1170.

Abolore R. S., Jaiswal S., Jaiswal A. K., Carbohydr. Polym. Technol. Appl., 2024, 7, 100396.

Mazumder S., Golbabaei M. H., Zhang N., Biomimetics, 2025, 10, 802.

Kong Y., Fu S., BioResources, 2022, 17, 7135–7166.

Mazumder S., Zhang N., Biomimetics, 2023, 8, 188.

Luo X., Li Q., Fuel Process. Technol., 2024, 258, 108093.

Mensah M., Tia R., Adei E., Nora H. de Leeuw N. H., Front. Chem., 2022, 10, 793759.

Zhang Y., He H., Dong K., Fan M., Zhang S., RSC Adv., 2017, 7, 12670–12681.

Kostetskyy P., Broadbelt L.J., Energy Fuels, 2020, 34, 15195–15216.

Wang W., Xu Y., Zhu B., Ge H., Wang S., Li B., Xu H., Bioresour. Technol., 2023, 385, 129401.

Hirata F. (Ed.), Molecular Theory of Solvation, Understanding Chemical Reactivity, Kluwer, Dordrech, 2003, 358.

Roy D., Kovalenko A., Int. J. Mol. Sci., 2021, 22, 5061.

Hansen J.-P., McDonald I. R., In: Theory of Simple Liquids: With Applications to Soft Matter, Academic Press, Oxford, fourth edn., 2013, 455–510.

Verlet L., Mol. Phys., 1980, 41, 183–190.

Verlet L., Levesque D., Mol. Phys., 1982, 46, 969–980.

Martynov G. A., Sarkisov G. N., Mol. Phys., 1983, 49, 1495–1504.

Rogers F. J., Young D. A., Phys. Rev. A, 1984, 30, 999–1007.

Zerah G., Hansen J., J. Chem. Phys., 1986, 84, 2336–2343.

Ballone P., Pastore G., Galli G., Gazzillo D., Mol. Phys., 1986, 59, 275–290.

Martynov G. A., Vompe A. G., Phys. Rev. E, 1993, 47, 1012.

Duh D., Haymet A. D. J., J. Chem. Phys., 1995, 103, 2625–2633.

Lee L. L., J. Chem. Phys., 1995, 103, 9388–9396.

Kovalenko A., Hirata F., J. Chem. Phys., 1999, 110, 10095–10112.

Kast S. M., Phys. Rev. E, 2003, 67, 041203.

Kast S. M., Kloss T., J. Chem. Phys., 2008, 129, 236101.

Tsednee T., Luchko T., Phys. Rev. E, 2019, 99, 032130.

Johnson J., Case D.A., Yamazaki T., Gusarov S., Kovalenko A., Luchko T., J. Phys.: Condens. Matter, 2016, 28, 344002.

Imai T., Hiraoka R., Kovalenko A., Hirata F., J. Am. Chem. Soc., 2005, 127, 15334–15335.

Kondratenko M., Stoyanov S. R., Gusarov S., Kovalenko A., McCreery R. L., J. Phys. Chem. C, 2015, 119, 11286–11295.

Stoyanov S. R., Gusarov S., Kuznicki S. M., Kovalenko A., J. Phys. Chem. C, 2008, 112, 6794–6810.

da Costa L. M., Stoyanov S. R., Gusarov S., Seidl P. R., de M. Carneiro J. W., Kovalenko A., J. Phys. Chem. A, 2014, 118, 896–908.

Fafard J., Lyubimova O., Stoyanov S. R., Dedzo G. K., Gusarov S., Kovalenko A., Detellier C., J. Phys. Chem. C, 2013, 117, 18556–185662.

Genheden S., Luchko T., Gusarov S., Kovalenko A., Ryde U., J. Phys. Chem. B, 2010, 114, 8505–8516.

Imai T., Miyashita N., Sugita Y., Kovalenko A., Hirata F., Kidera A., J. Phys. Chem. B, 2011, 115, 8288–8295.

Malvaldi M., Bruzzone S., Chiappe C., Gusarov S., Kovalenko A., J. Phys. Chem. B, 2009, 113, 3536–3542.

Omelyan I., Kovalenko A., J. Chem. Theory Comput., 2015, 11, 1875–1895.

Kovalenko A., Kobryn A. E., Gusarov S., Lyubimova O., Liu X., Blinov N., Yoshida M., Soft Matter, 2012, 8, 1508–1520.

Blinov N., Dorosh L., Wishart D., Kovalenko A., Biophys. J., 2010, 98, 282–296.

Casanova D., Gusarov S., Kovalenko A., Ziegler T., J. Chem. Theory Comput., 2007, 3, 458–476.

Carpita N. C., McCann M. C., J. Biol. Chem., 2020, 295, 15144–15157.

Roman M., Cannizzo C., Pinault T., Isare B., Andrioletti B., van der Schoot P., Boutellier L., J. Am. Chem. Soc., 2010, 132, 16818–16824.

Aida T., Meijer E. W., Stupp S. I., Science, 2012, 335, 813–817.

Varki A., Cummings R. D., Esko J. D., Stanley P., Hart G.W.,Aebi M., Darvill A. G., Kinoshita T., PackerN. H., Prestegard J. H., Schnaar R. L., Seeberger P. H. (Eds.), Essentials of Glycobiology, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (NY), 3rd edn., 2015.

Dong C., Beis K., Nasper J., Brunkan-LaMontagne A. L., Clarke B. R., Whitfield C., Naismith J. H., Nature, 2006, 444, 226–229.

Gama C. I., Tully S. E., Sotogaku N., Clark P. M., Pawat M., Vaidehi N., Goddard W. A. III, Nishi A., Hsieh-Wilson L. C., Nature Chem. Biol., 2006, 2, 467–473.

Silveira R. L., Stoyanov S. R., Gusarov S., Skaf M. S., Kovalenko A., J. Am. Chem. Soc., 2013, 135, 19048–19051.

Silveira R. L., Stoyanov S. R., Gusarov S., Skaf M. S., Kovalenko A., J. Phys. Chem. Lett., 2015, 6, 206–211.

Kovalenko A., In: Springer Handbook of Electrochemical Energy, Breitkopf C., Swider-Lyons K. (Eds.), Springer Berlin Heidelberg, Berlin, Heidelberg, 2017, 95–139.

Kovalenko A., Gusarov S., Phys. Chem. Chem. Phys., 2018, 20, 2947–2969.

Gusarov S., Pujari B. S., Kovalenko A., J. Comput. Chem., 2012, 33, 1478–1494.

Kovalenko A., In: Molecular Theory of Solvation, Understanding Chemical Reactivity, Vol. 24, Hirata F. (Ed.), Kluwer Academic Publishers, Dordrecht, 2004, 169–275.

Kovalenko A., Hirata F., J. Chem. Phys., 2000, 112, 10391–10402.

Kovalenko A., Hirata F., J. Chem. Phys., 2000, 112, 10403–10417.

Kovalenko A., Hirata F., Chem. Phys. Lett., 1998, 290, 237–244.

Perkyns J. S., Pettitt B. M., J. Chem. Phys., 1992, 97, 7656–7666.

Kirkwood J. G., Buff F. P., J. Chem. Phys., 1951, 19, 774–777.

Harano Y., Imai T., Kovalenko A., Kinoshita M., Hirata F., J. Chem. Phys., 2001, 114, 9506–9511.

Imai T., Harano Y., Kovalenko A., Hirata F., Biopolymers, 2001, 59, 512–519.

Palmer D. S., Frolov A. I., Ratkova E. L., Fedorov M. V., J. Phys.: Condens. Matter, 2010, 22, 492101.

Kovalenko A., Ten-no S., Hirata F., J. Comput. Chem., 1999, 20, 928–936.

Pulay P., Chem. Phys. Lett., 1980, 73, 393–398.

Saad Y., Schultz M. H., SIAM J. Sci. Stat. Comput., 1986, 7, 856–869.

Howard J. J., Perkyns J. S., Choudhury N., Pettitt B. M., J. Chem. Theory Comput., 2008, 4, 1928–1939.

Minezawa N., Kato S., J. Chem. Phys., 2007, 126, 054511.

Pauly M., Keegstra M., Plant J., 2008, 54, 559–568.

Chen F., Dixon R. A., Nat. Biotechnol., 2007, 25, 759–761.

Ding S.-Y., Liu Y.-S., Zeng Y., Himmel M. E., Baker J. O., Bayer E. A., Science, 2012, 338, 1055–1060.

Habibi Y., Lucia L. A., Rojas O. J., Chem. Rev., 2010, 110, 3479–3500.

Shishir P. S., Chundawat S. P. S., Bellesia G., Uppugundla N., da Costa Sousa L., Gao D., Cheh A. M., Agarwal U. P., Bianchetti C. M., Phillips Jr. G. N., Langan P., Balan. V., Gnanakaran S., Dale B. E., J. Am. Chem. Soc., 2011, 133, 11163–11174.

Gomes T. C. F., Skaf M. S., J. Comput. Chem., 2012, 33, 1338–1346.

Yoshida N., Phongphanphanee S., Maruyama Y., Imai T., Hirata F., J. Am. Chem. Soc., 2006, 128, 12042–12043.

Agbor V. B., Cicek N., Sparling R., Berlin A., Levin D. B., Biotechnol. Adv., 2011, 29, 675–685.

Nishiyama Y., Sugiyama J., Chanzy H., Langan P., J. Am. Chem. Soc., 2003, 125, 14300–14306.

Achyuthan K. E., Achyuthan A. M., Adams P. D., Dirk S. M., Harper J. C., Simmons B. A., Singh A. K., Molecules, 2010, 15, 8641–8688.

Ragauskas A. J., Beckham G. T., Biddy M. J., Chandra R., Chen F., Davis M. F., Davison B. H., Dixon R. A., Gilna P., Keller M., Langan P., Naskar A. K., Saddler J. N., Tschaplinski T. J., Tuskan G. A., Wyman C. E., Science, 2014, 344, No. 6185, 1246843.

Tuck C. O., Pérez E., Horávth I. T., Sheldon R. A., Poliakoff M., Science, 2012, 337, 695–699.

Scheller H. V., Ulvskov P., Annu. Rev. Plant Biol., 2010, 61, 263–289.

Petridis L., Pingali S. V., Urban V., Heller W. T., O’Neill H. M., Foston M., Ragauskas A., Smith J. C., Phys. Rev. E, 2011, 83, 061911.

Petridis L., Schulz R., Smith J. C., J. Am. Chem. Soc., 2011, 133, 20277–20287.

Charlier L., Mazeau K., J. Phys. Chem. B, 2012, 116, 4163–4174.

Boerjan W, Ralph J., Baucher M., Annu. Rev. Plant Biol., 2003, 54, 519–546.

PuY., Hu F., Huang F., Davison B. H., Ragauskas A. J., Biotechnol. Biofuels, 2013, 6, 15–13.

Guvench O., Greene S. N., Kamath G., Brady J. W., Venable R. M., Pastor R. W., MacKerell A. D. Jr., J. Comput. Chem., 2008, 29, 2543–2564.

Petridis L., Smith J. C., J. Comput. Chem., 2009, 30, 457–467.

Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R.W., Klein M. L., J. Chem. Phys., 1983, 79, 926–935.

MacKerell A. D. Jr., Bashford D., Bellott R. L., Dunbrack R. L. Jr., Evanseck J. D., Field M. J., Fischer S., Gao J., Guo H., Ha S., et al., J. Phys. Chem. B, 1998, 102, 3586–3616.

Donohoe B. S., Decker S. R., Tucker M. P., Himmel M. E., Vinzant T. B., Biotechnol. Bioeng., 2008, 101, 913–925.

Jung J. H., Fouad W. M, Vermerris W., Gallo M., Altpeter F., Plant Biotechnol. J., 2012, 10, 1067–1076.

Fu C., Mielenz J. R., Xiao X., Ge Y., Hamilton C. Y., Rodriguez M. Jr., Chen F., Foston M., Ragauskas A., Bouton J., Dixon R.A., Wang Z.-Y., Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 3803–3808.

Bonawitz N. D., Kim J. I., Tobimatsu Y., Ciesielski P. N., Anderson N. A., Ximenes E., Maeda J., Ralph J., Donohoe B. S., Ladisch M., Chapple C., Nature, 2014, 509, 376–380.

Ziebell A., Gracom K., Katahira R., Chen F., Pu Y., Ragauskas A., Dixon R. A., Davis M., J. Biol. Chem., 2010, 285, 38961–38968.

Li X., Weng J.-K., Chapple C., Plant J., 2008, 54, 569–581.

Mansfield S. D., Curr. Opin. Biotechnol., 2009, 20, 286–294.

DeMartini J. D., Pattathil S., Miller J. S., Li H., Hahn M. G., Wyman C. E., Energy Environ. Sci., 2013, 6, 898–909.

Published

2026-03-30

How to Cite

[1]
A. Kovalenko, “Multiscale theory, modelling, and simulation of hemicellulose and lignin in solution”, Condens. Matter Phys., vol. 29, no. 1, p. 13802, Mar. 2026, doi: 10.5488/CMP.29.13802.

Similar Articles

41-50 of 98

You may also start an advanced similarity search for this article.