Molecular dynamics Simulations of cellulose oligomers:: Conformational analysis

The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end-to-end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end-to-end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.