Molecular dynamics simulations were used to explore the distribution of linkages in coumaryl alcohol and coniferyl alcohol systems, including monomeric systems and monomers interacting with b-O4 dimers, respectively. Studying the interactions of two monolignols and the corresponding dimers sheds light on the preferred mechanism of reaction of the growing lignin polymer from the view of kinetic factors. The energy change upon association was quantified, and the distances between the centers of mass of different molecules, and the relative orientations between the phenol groups were calculated for all the systems. Using a cut-off threshold of 4 Å to indicate association leading to bond formation, it is concluded that the presence of the additional methoxy group on coniferyl alcohol assists in promoting interaction of the O4 group with the second moiety. Based on the computed data it is furthermore concluded that in aqueous solution, the most likely model of polymerization is that involving initial dimer formation, followed by dimer-dimer association.
The concerted photoreaction between trimethyl psoralen (TMP) and isomeric model compounds of oleic acid methyl ester (OAME) and eadilic acid methyl ester (EAME) are explored using density functional theory. The S(1) surfaces all reveal large barriers (25-31 kcal/mol) to reach the decay channels, whereas the S(2) surfaces differ considerably between the furan and pyrone side adducts. For the pyrone side adducts, a small barrier to reach the intersection between the S(1) and S(2) states is found, followed by a small second barrier on the S(1) surface to the low-lying decay channel. For the furan-side adducts, no such intersection between S(1) and S(2) is seen, which thus prevents these products from being formed in high yields. The photoinduced cycloaddition is more favorable between OAME and the pyrone side double bond of TMP than for any of the other systems, which agrees with the experimental findings that this is formed in the highest yield. The computed UV absorption spectra of TMP and the TMP(pyrone)-OAME cycloadduct agree well with the experimental spectra.
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