Molecular dynamics study of lignin constituents in water

References

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.124:2753–2761.10.1021/ja011528mSearch in Google Scholar

Baucher, M., Monties, B., van Montagu, M., Boerjan, W. (1998) Biosynthesis and genetic engineering of lignin. Crit. Rev. Plant Sci.17:125–197.10.1080/07352689891304203Search in Google Scholar

Becke, A.D. (1993) A new mixing of Hartree-Fock and local density functional theories. J. Chem. Phys.98:1372–1377.10.1063/1.464304Search in Google Scholar

Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Hermans, J. (1981) Intermolecular Forces. Reidel, Dordrecht, The Netherlands.Search in Google Scholar

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.81:3684–3690.10.1063/1.448118Search in Google Scholar

Berendsen, H.J.C., van der Spoel, D., van Drunen, R. (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Commun.91:43–56.10.1016/0010-4655(95)00042-ESearch in Google Scholar

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.:722002–2013.10.1016/S0006-3495(97)78845-3Search in Google Scholar

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.47:610–616.10.3891/acta.chem.scand.47-0610Search in Google Scholar

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. Holzforschung57:150–164.10.1515/HF.2003.024Search in Google Scholar

Durbeej, B., Eriksson, L.A. (2003b) Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals. Holzforschung57:59–61.10.1515/HF.2003.009Search in Google Scholar

Durbeej, B., Eriksson, L.A. (2003c) Formation of β-O4 lignin models – a theoretical study. Holzforschung57:466–478.10.1515/HF.2003.070Search in Google Scholar

Elder, T.J., Ede, R.M. (1995) Coupling of coniferyl alcohol in the formation of dilignols. A molecular orbital study. In: Proceedings of the 8^th International Symposium on Wood and Pulping Chemistry, Vol. 1. Gummerus Kirjapaino Oy, Helsinki. pp. 115–122.Search in Google Scholar

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. Holzforschung42:233–240.Search in Google Scholar

Faulon, J.L., Hatcher, P.G. (1994) Is there any order in the structure of lignin?Energy Fuels8:402–407.10.1021/ef00044a018Search in Google Scholar

Freudenberg, K. (1965) Lignin: its constitution and formation from p-hydroxycinnamyl alcohols. Science148:595–600.10.1126/science.148.3670.595Search in Google Scholar

Frisch, M.J. et al. (2003) Gaussian 03 Rev. A.3. Gaussian Inc, Pittsburgh, PA.Search in Google Scholar

Glasser, W.G., Glasser, H.R. (1974) Simulation of reactions with lignin by computer (SIMREL). 1. Polymerization of coniferyl alcohol monomers. Macromolecules7:17–27.Search in Google Scholar

Glasser, W.G., Glasser, H.R. (1981) The evaluation of lignin's chemical structure by experimental and computer simulation techniques. Pap. Puu2:71–83.Search in Google Scholar

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”). Macromolecules14:253–262.Search in Google Scholar

Higuchi, T. (1985) In: Biosynthesis and Biodegradation of Wood Components. Academic Press, Orlando, FL. p. 141.Search in Google Scholar

Houtman, C.J. (1999) What factors control dimerization of coniferyl alcohol?Holzforschung53:585–589.10.1515/HF.1999.097Search in Google Scholar

Houtman, C.J., Atalla, R.H. (1995) Cellulose-lignin interactions. Plant Physiol.107:977–984.10.1104/pp.107.3.977Search in Google Scholar

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 7^th International Symposium on Wood and Pulping Chemistry. Vol. 1. Beijing. pp. 111–122.Search in Google Scholar

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. B37:785–789.10.1103/PhysRevB.37.785Search in Google Scholar

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.Search in Google Scholar

Lundquist, K. (1992) Proton (1H) NMR spectroscopy. In: Methods in Lignin Chemistry. Eds. S. Y. Lin, C.W. Dence. Springer-Verlag, Berlin. pp. 242–249.10.1007/978-3-642-74065-7_17Search in Google Scholar

Monties, B. (1989a) Lignins. In: Methods in Plant Biochemistry: Plant Phenolics, Vol. 1. Eds. P.M. Dey, J.B. Harborne. Academic Press, New York. pp. 113–15710.1016/B978-0-12-461011-8.50010-XSearch in Google Scholar

Monties, B. (1989b) Lignins. In: Methods in Plant Biochemistry: Plant Phenolics, Vol. 1. Eds. P.M. Dey, J.B. Harborne. Academic Press, New York. p. 161.10.1016/B978-0-12-461011-8.50010-XSearch in Google Scholar

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.59:53–64.10.1016/S0141-3910(97)00166-3Search in Google Scholar

Robert, D. 1992. Carbon-13 nuclear magnetic resonance spectroscopy. In: Methods in Lignin Chemistry. Eds. S.Y. Lin, C.W. Dence. Springer-Verlag, Berlin. pp. 250–273.Search in Google Scholar

Roussel, M.R., Lim, C. (1995a) Dynamic model of lignin growing in restricted spaces. Macromolecules28:370–376.10.1021/ma00105a052Search in Google Scholar

Roussel, M.R., Lim, C. (1995b) Discrete, dynamic polymer modeling: a pseudo-diatomic model of lignin. J. Comput. Chem.16:1181–1191.10.1002/jcc.540161002Search in Google Scholar

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. Holzforschung49:429–438.Search in Google Scholar

Simon, J.P., Eriksson, K.-E. (1996) The significance of intra-molecular hydrogen bonding in the β-O4 linkage of lignin. J. Mol. Struct.384:1–7.Search in Google Scholar

Simon, J.P., Eriksson, K.-E. (1998) Computational studies of the three-dimensional structure of guaiacyl β-O4 lignin models. Holzforschung52:287–296.10.1515/hfsg.1998.52.3.287Search in Google Scholar

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. A40:705–710.10.3891/acta.chem.scand.40a-0705Search in Google Scholar

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-me-thanol (1/1). Acta Chem. Scand. B42:697–707.10.3891/acta.chem.scand.42b-0697Search in Google Scholar

Tanahashi, M., Takeuchi, H., Higuchi, T. (1976) Dehydrogenative polymerisation of 3,5-disubstituted p-coumarye alcohols. Wood res.61:44–53.Search in Google Scholar

Terashima, N., Atalla, R.H. (1995) formation and structure of lignified cell wall – factors controlling lignin structure during its formation. In: Proceedings of the 8^th International Symposium on Wood and Pulping chemistry, Vol. 1. Gummerus Kirjapaina Oy, Helsinki. pp. 69–76.Search in Google Scholar

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.Search in Google Scholar