Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Abstract

Summary: 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.The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.imageThe probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.

Hydrothermal decomposition of various crystalline celluloses as treated by semi-flow hot-compressed water

“…The original publication is available at Springer via http://dx.doi.org/ 10.1007/s10570-014-0343-y increment of the temperatures. Queyroy et al (2004) studied the MD simulation of tetraose and octaose of cellulose and observed that most of the glucopyranose rings assumed a puckered un-chaired conformation at ~527 ˚C. As the decomposition of cellulose was considered to relate to the ring conformation change, the evaluation of the conformational changes would be important (Hosoya et al 2009).…”

Mechanism of microfibril contraction and anisotropic dimensional changes for cells in wood treated with aqueous NaOH solution

“…Thus, determination of DL/L can be reduced to Dl/l, which in turn can be evaluated from the end-to-end distance of the amorphous cellulose chain along the longitudinal axis of the microfibril. It is difficult to know the actual behavior of the cellulose chain when both ends may be bound to a crystalline region, though some researchers reported the simulation of conformation of single cellulose chain in this regard (for example Queyroy et al 2004). Additionally, the end-to-end distance of the cellulose chain appears to be slightly influenced by non-crystallization because of a non-flexible polymer chain.…”

“…The degree of contraction calculated from the ratio of end-to-end distance to contour length was about 0.10-0.20. According to analyses of single cellulose chains by Queyroy et al (2004), the end-toend distance of a chain consisting of eight glucose residues with a contour length of 4.4 nm is about 3.2 nm. This corresponds to a 0.30 contraction.…”

Electronically excited states and photochemical reaction mechanisms of β-glucose

“…1 For decades, carbohydrates have been the focus of many experimental, spectroscopic, and computational investigations. Studies include the exploration of the conformational space and structural properties of mono-, [2][3][4][5][6][7][8][9][10][11][12] di-, [13][14][15][16] oligo-, and polysaccharides, [17][18][19][20] chemical reactions (condensation and isomerization, [21][22][23][24][25][26] hydrogen abstraction 27 and (photo-)fragmentation [28][29][30][31] ) and the computation of vibrational spectra. [32][33][34] Progress has also been made in the computational simulation of the structure of biopolymers such as cellulose 35,36 as well as computations of their physical and chemical properties.…”