The role of weak interactions in lignin polymerization

  • Ángel Sánchez-González
  • Francisco J. Martín-Martínez
  • J. A. Dobado
Original Paper


Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose. This work presents a complete computational study on some of the key steps of lignin polymerization mechanisms. Density functional theory (DFT) calculations have been performed to evaluate the most appropriate methodology and to compute the chemical structures and reaction enthalpies for the monolignol dimerization, the simplest key step that controls the polymerization. Quantum theory of atoms in molecules (QTAIM) has been applied to understand the coupling reaction mechanisms, for which the radical species and transition states (TSs) involved have been characterized. The coupling that leads to the formation of the β–O–4 linkage has been theoretically reproduced according to proposed mechanisms, for which weak interactions have been found to play a key role in the arrangement of reactants. The hydrogen bond formed between the oxygen of the phenoxy radical, and the alcohol of the aliphatic chain, together with the interaction between aromatic rings, locates the reactants in a position that favors such β–O–4 linkage.

Graphical Abstract

QTAIM analysis of the complex between coumaryl and coniferyl alcohols. It emphasizes the importance of weak interactions during the formation of beta-O-4 linkages in the polymerization of lignin.


Density functional theory Lignin polymerization QTAIM Monolignols 



This work was financed by Proyecto Prometeo, Secretaría de Educación Superior, Ciencia, Tecnología e Innovación of the Republic of Ecuador. We also thank the “Centro de Servicios de Informática y Redes de Comunicaciones” (CSIRC) (UGRGrid), University of Granada and Universidad Técnica Particular de Loja for providing computing time. Mr. David Nesbitt reviewed the English version of the manuscript. We want to thank Dr. Santiago Melchor for his help in the management of computing resources.

Supplementary material

894_2017_3257_MOESM1_ESM.docx (3.6 mb)
(DOCX 3.55 MB)


  1. 1.
    Calvo-Flores FG, Dobado JA, Isac-Garcia J, Martin-Martinez FJ (2015) Lignin and lignans as renewable raw materials: chemistry technology and applications. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  2. 2.
    O’Sullivan AC (1997) Cellulose: the structure slowly unravels. Cellulose 4:173–207. doi: 10.1023/A:1018431705579 CrossRefGoogle Scholar
  3. 3.
    Bonawitz ND, Chaple C (2010) The genetics of lignin biosynthesis: connecting genotype to phenotype. Annu Rev Genet 44:337–363. doi: 10.1146/annurev-genet-102209-163508 CrossRefGoogle Scholar
  4. 4.
    Whetten RW, MacKay JJ, Sederoff RR (1998) Recent advances in understanding lignin biosynthesis. Annu Rev Plant Physiol Plant Mol Biol 49:585–609. doi: 10.1146/annurev.arplant.49.1.585 CrossRefGoogle Scholar
  5. 5.
    Balakshin M, Capanema E, Gracz H, Chang HM, Jameel H (2011) Quantification of lignin-carbohydrate linkages with high-resolution NMR spectroscopy. Planta 233:1097–1110. doi: 10.1007/s00425-011-1359-2 CrossRefGoogle Scholar
  6. 6.
    Freudenberg K (1965) Lignin: its constitution and formation from p-hydroxycinnamyl alcohols. Science 148:595–600. doi: 10.1126/science.148.3670.595 CrossRefGoogle Scholar
  7. 7.
    Aoyama W, Sasaki S, Matsumura S, Mitsunaga T, Hirai H, Tsutsumi Y, Nishida T (2002) Sinapyl alcohol-specific peroxidase isoenzyme catalyzes the formation of the dehydrogenative polymer from sinapyl alcohol. J Wood Sci 48:497–504. doi: 10.1007/BF00766646 CrossRefGoogle Scholar
  8. 8.
    Kobayashi T, Taguchi H, Shigematsu M, Tanahashi M (2005) Substituent effects of 3,5-disubstituted p-coumaryl alcohols on their oxidation using horseradish peroxidase– H2O2 as the oxidant. J Wood Sci 51:607–614. doi: 10.1007/s10086-005-0702-2 CrossRefGoogle Scholar
  9. 9.
    Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Plant Biol 54:519–546. doi: 10.1146/annurev.arplant.54.031902.134938 CrossRefGoogle Scholar
  10. 10.
    Chakar FS, Ragaukas AJ (2004) Review of current and future softwood kraft lignin process chemistry. Ind Crops Prod 20:131–141. doi: 10.1016/j.indcrop.2004.04.016 CrossRefGoogle Scholar
  11. 11.
    Sakakibara A (1980) A structural model of softwood lignin. Wood Sci Technol 14:89–100. doi: 10.1007/BF00584038 CrossRefGoogle Scholar
  12. 12.
    Harton SE, Pingali SV, Nunnery GA (2012) Evidence for complex molecular architectures for solvent-extracted lignins. ACS Macro Lett 1:568–573. doi: 10.1021/mz300045e CrossRefGoogle Scholar
  13. 13.
    Petridis L, Pingali SV, Urban V, Heller WT, O’Neill HM, Foston M, Ragauskas A, Smith JC (2011) Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Phys Rev E83:061911. doi: 10.1103/PhysRevE.83.061911 Google Scholar
  14. 14.
    Besombes S, Robert D, Utille J, Taravel FR, Mazeau K (2003) Molecular modeling of lignin β–O–4 model compounds. Comparative study of the computed and experimental conformational properties for a guaiacyl β–O–4 dimer. Holzforschung 57:266–274. doi: 10.1515/HF.2003.040 CrossRefGoogle Scholar
  15. 15.
    Besombes S, Robert D, Utille J, Taravel FR, Mazeau K (2003) Molecular modeling of syringyl and p-hydroxyphenyl β–O–4 dimers. Comparative study of the computed and experimental conformational properties of lignin β–O–4 model compounds. J Agric Food Chem 51:34–42. doi: 10.1021/jf0206668 CrossRefGoogle Scholar
  16. 16.
    Durbeej B, Eriksson LA (2003) A density functional theory study of coniferyl alcohol intermonomeric cross linkages in lignin: three-dimensional structures, stabilities and the thermodynamic control hypothesis. Holzforschung 57:150–164. doi: 10.1515/HF.2003.024 Google Scholar
  17. 17.
    Besombes S, Utille J, Mazeau K, Robert D, Taravel FR (2004) Conformational study of a guaiacyl β-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution. Magn Reson Chem 42:337–347. doi: 10.1002/mrc.1317 CrossRefGoogle Scholar
  18. 18.
    Besombes S, Mazeau K (2004) Molecular dynamics simulations of a guaiacyl β–O–4 lignin model compound: examination of intramolecular hydrogen bonding and conformational flexibility. Biopolymers 73:301–315. doi: 10.1002/bip.10587 CrossRefGoogle Scholar
  19. 19.
    Beste A, Buchanan III AC (2009) Computational study of bond dissociation enthalpies for lignin model compounds. Substituent effects in phenethyl phenyl ethers. J Org Chem 74:2837–2841. doi: 10.1021/jo9001307 CrossRefGoogle Scholar
  20. 20.
    Elder T (2010) A computational study of pyrolysis reactions of lignin model compounds. Holzforschung 64:435–440. doi: 10.1515/hf.2010.086 CrossRefGoogle Scholar
  21. 21.
    Younker JM, Beste A, Buchanan III AC (2011) Computational study of bond dissociation enthalpies for substituted β–O–4 lignin model compounds. ChemPhysChem 12:3556–3565. doi: 10.1002/cphc.201100477 CrossRefGoogle Scholar
  22. 22.
    Kim S, Chmely SC, Nimlos MR, Bomble YJ, Foust TD, Paton RS, Beckham GT (2011) Computational study of bond dissociation enthalpies for a large range of native and modified lignins. J Phys Chem Lett 2:2846–2852. doi: 10.1021/jz201182w CrossRefGoogle Scholar
  23. 23.
    Beste A, Buchanan III AC (2013) Computational investigation of the pyrolysis product selectivity for α–hydroxy phenethyl phenyl ether and phenethyl phenyl ether: analysis of substituent effects and reactant conformer selection. J Phys Chem A 117:3235–3242. doi: 10.1021/jp4015004 CrossRefGoogle Scholar
  24. 24.
    Huang J, Liu C, Tong H, Li W, Wu D (2014) A density functional theory study on formation mechanism of CO, CO2 and CH4 in pyrolysis of lignin. Comput Theor Chem 1045:1–9. doi: 10.1016/j.comptc.2014.06.009 CrossRefGoogle Scholar
  25. 25.
    Huang J, Liu C, Wu D, Tong H, Ren L (2014) Density functional theory studies on pyrolysis mechanism of β–O–4 type lignin dimer model compound. J Anal Appl Pyrolysis 109:98–106. doi: 10.1016/j.jaap.2014.07.007 CrossRefGoogle Scholar
  26. 26.
    Janesko BG (2014) Acid-catalyzed hydrolysis of lignin β–O–4 linkages in ionic liquid solvents: a computational mechanistic study. Phys Chem Chem Phys 16:5423–5433. doi: 10.1039/C3CP53836B CrossRefGoogle Scholar
  27. 27.
    Younker JM, Beste A, Buchanan III AC (2012) Computational study of bond dissociation enthalpies for lignin model compounds: β–5 arylcoumaran. Chem Phys Lett 545:100–106. doi: 10.1016/j.cplett.2012.07.017 CrossRefGoogle Scholar
  28. 28.
    Huang J, He C, Liu C, Tong H, Wu L, Wu S (2015) A computational study on thermal decomposition mechanism of β–1 linkage lignin dimer. Comput Theor Chem 1054:80–87. doi: 10.1016/j.comptc.2014.12.007 CrossRefGoogle Scholar
  29. 29.
    Beste A (2014) ReaxFF study of the oxidation of lignin model compounds for the most common linkages in softwood in view of carbon fiber production. J Phys Chem A 118:803–814. doi: 10.1021/jp410454q CrossRefGoogle Scholar
  30. 30.
    Beste A, Buchanan III AC (2011) Kinetic analysis of the phenyl-shift reaction in β–O–4 lignin model compounds: a computational study. J Org Chem 76:2195–2203. doi: 10.1021/jo2000385 CrossRefGoogle Scholar
  31. 31.
    Watts HD, Mohamed MNA, Kubicki JD (2011) Evaluation of potential reaction mechanisms leading to the formation of coniferyl alcohol α–linkages in lignin: a density functional theory study. Phys Chem Chem Phys 13:20974–20985. doi: 10.1039/c1cp21906e CrossRefGoogle Scholar
  32. 32.
    Ayers PW, Yang W, Bartolotti LJ (2009) The Fukui function in chemical reactivity theory: a density functional view. (Ed: Chattaraj PK). CRC Press, New York, pp 255–267Google Scholar
  33. 33.
    Durbeej B, Erikson LA (2003) Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals. Holzforschung 57:59–61. doi: 10.1515/HF.2003.009 Google Scholar
  34. 34.
    Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, Smith JC (2012) Relative binding affinities of monolignols to horseradish peroxidase. J Phys Chem B 116:4760–4768. doi: 10.1021/acs.jpcb.6b00789 CrossRefGoogle Scholar
  35. 35.
    Durbeej B, Eriksson LA (2003) Formation of β–O–4 lignin models–a theoretical study. Holzforschung 57:466–478. doi: 10.1515/HF.2003.070 Google Scholar
  36. 36.
    Chen Y, Sarkanen S (2010) Macromolecular replication during lignin biosynthesis. Phytochem 71:453–462. doi: 10.1016/j.phytochem.2009.11.012 CrossRefGoogle Scholar
  37. 37.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin A J, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö , Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09 revision B.01. Gaussian Inc., WallingfordGoogle Scholar
  38. 38.
    Henderson TM, Izmaylov AF, Scalmani G, Scuseria GE (2009) Can short-range hybrids describe long-range-dependent properties? J Chem Phys 131:044108. doi: 10.1063/1.3185673 CrossRefGoogle Scholar
  39. 39.
    Remya K, Suresh CH (2013) Which density functional is close to CCSD accuracy to describe geometry and interaction energy of small noncovalent dimers? A benchmark study using Gaussian09. J Comput Chem 34:1341–1353. doi: 10.1002/jcc.23263 CrossRefGoogle Scholar
  40. 40.
    Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652. doi: 10.1063/1.464913 CrossRefGoogle Scholar
  41. 41.
    Lee C, Yang W, Parr RG (1988) Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789. doi: 10.1103/PhysRevB.37.785 CrossRefGoogle Scholar
  42. 42.
    Zhao Y, Truhlar DG (2008) The m06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four m06-class functionals and 12 other functionals. Theor Chem Account 120:215–241. doi: 10.1007/s00214-007-0310-x CrossRefGoogle Scholar
  43. 43.
    Chai JD, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys 10:6615–6620. doi: 10.1039/b810189b CrossRefGoogle Scholar
  44. 44.
    Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88:889–926. doi: 10.1021/cr00088a005 CrossRefGoogle Scholar
  45. 45.
    AIMALl (version 15.09.27), Todd AK, gristmill TK software, Overland Park KS, USA, 2015 (
  46. 46.
    Young D (2001) Computational chemistry: a practical guide for applying techniques to real world problems. Wiley Interscience, New YorkGoogle Scholar
  47. 47.
    Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010) Revealing noncovalent interactions. J Amer Chem Soc 132:6498–6506. doi: 10.1021/ja100936w CrossRefGoogle Scholar
  48. 48.
    Bader RFW (1990) Atoms in molecules: a quantum theory. Clarendon Press, Oxford, UKGoogle Scholar
  49. 49.
    Sjöström E (1981) Wood chemistry: fundamentals and applications. Academic Press, New YorkGoogle Scholar
  50. 50.
    Setälä H, Pajunen A, Rummakko P, Sipilä J, Brunow G (1999) A novel type of spiro compound formed by oxidative cross coupling of methyl sinapate with a syringyl lignin model compound. a model system for the β–1 pathway in lignin biosynthesis. J Chem Soc Perkin Trans 1:461–464. doi: 10.1039/A808884E CrossRefGoogle Scholar
  51. 51.
    Alkorta I, Blanco F, Elguero J, Dobado JA, Melchor A, Vidal I (2009) Carbon ⋯carbon weak interactions. J Phys Chem A 113:8387–8393. doi: 10.1021/jp903016e CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Ángel Sánchez-González
    • 1
  • Francisco J. Martín-Martínez
    • 2
  • J. A. Dobado
    • 3
  1. 1.Dpto. Química AplicadaUniversidad Técnica Particular de LojaLojaEcuador
  2. 2.Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  3. 3.Grupo de Modelización y Diseño Molecular, Dpto. Química Orgánica, Facultad de CienciasUniversidad de GranadaGranadaSpain

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