Molecular dynamics study of lignin constituents in water

Holzforschung

Volumn 59, Issue 3, 2005, Pages 253-262

  Xiao, Yi Li ^a   Eriksson, Leif A ^a,b  

^a ÖREBRO UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Coniferyl alcohol; Coumaryl alcohol; Lignin; Molecular dynamics; Polymerization

Indexed keywords

ALCOHOLS; COMPUTER SIMULATION; DIMERS; MOLECULAR DYNAMICS; MONOMERS; PHENOLS; SOLUTIONS; WATER;

Β-04 DIMERS; BOND FORMATION; DIMER-DIMER ASSOCIATION; MONOLIGNOLS;

LIGNIN;

CONIFERYL ALCOHOL; COUMARYL ALCOHOL; DIMERS; LIGNINS; MONOMERS; PHENOLS; SIMULATION; WATER;

EID: 21844445056     PISSN: 00183830     EISSN: None     Source Type: Trade Journal    
DOI: 10.1515/HF.2005.042     Document Type: Article

References (40)

1. Ban, F., Lundqvist, M.J., Boyd, R.J., Eriksson, L.A. (2002) Theoretical studies of the cross-linking mechanism between cytosine and tyrosine. J. Am. Chem. Soc. 124:2753-2761.
2. Baucher, M., Monties, B., van Montagu, M., Boerjan, W. (1998) Biosynthesis and genetic engineering of lignin. Crit. Rev. Plant Sci. 17:125-197.
3. Becke, A.D. (1993) A new mixing of Hartree-Fock and local density functional theories. J. Chem. Phys. 98:1372-1377.
4. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Hermans, J. (1981) Intermolecular Forces. Reidel, Dordrecht, The Netherlands.
5. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren,W.F., DiNola, A., Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
6. Berendsen, H.J.C., van der Spoel, D., van Drunen, R. (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Commun. 91:43-56.
7. Berger, O., Edholm, O., Jähnig, F. (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophysical J. 72:2002-2013.
8. Chioccara, F., Poli, S., Rindone, B., Pilati, T., Brunow, G., Pietikäinen, P., Setälä, H. (1993) Regio- and diastereo-selective synthesis of dimeric lignins using oxidative coupling. Acta Chem. Scand. 47:610-616.
9. Durbeej, B., Eriksson, L.A. (2003a) 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.
10. Durbeej, B., Eriksson, L.A. (2003b) Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals. Holzforschung 57:59-61.
11. Durbeej, B., Eriksson, L.A. (2003c) Formation of β-O4 lignin models - a theoretical study. Holzforschung 57:466-478.
12. Elder, T.J., Ede, R.M. (1995) Coupling of coniferyl alcohol in the formation of dilignols. A molecular orbital study. In: Proceedings of the 8th International Symposium on Wood and Pulping Chemistry, Vol. 1. Gummerus Kirjapaino Oy, Helsinki. pp. 115-122.
13. Elder, T.J., McKee, M.L., Worley, S.D. (1988) The application of molecular orbital calculations to wood chemistry V. The formation and reactivity of quinone methide intermediates. Holzforschung 42:233-240.
14. Faulon, J.L., Hatcher, P.G. (1994) Is there any order in the structure of lignin? Energy Fuels 8:402-407.
15. Freudenberg, K. (1965) Lignin: its constitution and formation from p-hydroxycinnamyl alcohols. Science 148:595-600.
16. Frisch, M.J. et al. Gaussian 03 Rev. A.3. Gaussian Inc, Pittsburgh, PA, 2003.
17. Glasser, W.G., Glasser, H.R. (1974) Simulation of reactions with lignin by computer (SIMREL). 1. Polymerization of coniferyl alcohol monomers. Macromolecules 7:17-27.
18. Glasser, W.G., Glasser, H.R. (1981) The evaluation of lignin's chemical structure by experimental and computer simulation techniques. Pap. Puu 2:71-83.
19. Glasser, W.G., Glasser, H.R., Morohoshi, N. (1981) Simulation of reactions with lignin by computer (SIMREL). 6. Interpretation of primary experimental analysis data ("Analysis program"). Macromolecules 14:253-262.
20. Higuchi, T. (1985) In: Biosynthesis and Biodegradation of Wood Components. Academic Press, Orlando, FL. p. 141.
21. Houtman, C.J. (1999) What factors control dimerization of coniferyl alcohol? Holzforschung 53:585-589.
22. Houtman, C.J., Atalla, R.H. (1995) Cellulose-lignin interactions. Plant Physiol. 107:977-984.
23. Lange, H., Wagner, B., Yan, J.F., Kaler, E.W., McCarthy, J.L. (1992) Computer modeling of gymnosperm lignins: synthesis and characterization. In: Proceedings of the 7th International Symposium on Wood and Pulping Chemistry. Vol. 1. Beijing. pp. 111-122.
24. Lee, C., Yang, W., Parr, R.G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37:785-789.
25. Lindahl, E., Hess, B., van der Spoel. D. (2001) Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
26. Lundquist, K. (1992) Proton (1H) NMR spectroscopy. In: Methods in Lignin Chemistry. Eds. Lin, S.Y., Dence, C.W. Springer-Verlag, Berlin. pp. 242-249.
27. Monties, B. (1989a) Lignins. In: Methods in Plant Biochemistry: Plant Phenolics. Eds. Dey, P.M., Harborne, J.B. Vol. 1. Academic Press, New York. pp. 113-157
28. Monties, B. (1989b) Lignins. In: Methods in Plant Biochemistry: Plant Phenolics. Eds. Dey, P.M., Harborne, J.B. Vol. 1. Academic Press, New York. p. 161.
29. Monties, B. (1998) Novel structures and properties of lignins in relation to their natural and induced variability in ecotypes, mutants and transgenic plants. Polym. Degrad. Stabil. 59:53-64.
30. Robert, D. 1992. Carbon-13 nuclear magnetic resonance spectroscopy. In: Methods in Lignin Chemistry. Eds. Lin, S.Y., Dence, C.W. Springer-Verlag, Berlin. pp. 250-273.
31. Roussel, M.R., Lim, C. (1995a) Dynamic model of lignin growing in restricted spaces. Macromolecules 28:370-376.
32. Roussel, M.R., Lim, C. (1995b) Discrete, dynamic polymer modeling: a pseudo-diatomic model of lignin. J. Comput. Chem. 16:1181-1191.
33. Simon, J.P., Eriksson, K.-E. (1995) A molecular mechanics investigation of lignin structure I. Conformational analysis of 1-pheny1-2-phenoxy-1,3- propanediol using MM3. Holzforschung 49:429-438.
34. Simon, J.P., Eriksson, K.-E. (1996) The significance of intramolecular hydrogen bonding in the β-O4 linkage of lignin. J. Mol. Struct. 384:1-7.
35. Simon, J.P., Eriksson, K.-E. (1998) Computational studies of the three-dimensional structure of gualacyl β-O4 lignin models. Holzforschung 52:287-296.
36. Stomberg, R., Lundquist, K. (1986) Stereochemical assignment of the diastereomers of 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol from X-ray analysis. Acta Chem. Scand. A 40:705-710.
37. Stomberg, R., Hauteville, M., Lundquist, K. (1988) Studies on lignin model compounds of the β-O4 type: crystal structures of threo-1-(4-hydroxy-3,5-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol and 3-hydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1-propanone- methanol (1/1). Acta Chem. Scand. B 42:697-707.
38. Tanahashi, M., Takeuchi, H., Higuchi, T. (1976) Dehydrogenative polymerisation of 3,5-disubstituted p-coumaryl alcohols. Wood res. 61:44-53.
39. Terashima, N., Atalla, R.H. (1995) formation and structure of lignified cell wall - factors controlling lignin structure during its formation. In: Proceedings of the 8th International Symposium on Wood and Pulping chemistry, Vol. 1. Gummerus Kirjapaina Oy, Helsinki. pp. 69-76.
40. van der Spoel, D., Lindahl, E. Hess, B., Van Buuren, A.R., Apol, E, Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., Feenstra, K.A., Van Drunen, R., Berendsen, H.J.C. (2004) Gromacs User Manual version 3.2. www.gromacs.org.