Solution Properties of Hemicellulose Polysaccharides with Four Common Carbohydrate Force Fields

• Published in: Journal of chemical theory and computation 2015-04, Vol.11 (4), p.1765-1774
• Main Authors: Sauter, Jörg, Grafmüller, Andrea
• Format: Article
• Language: English
• Subjects: Diffusion; Hydrogen Bonding; Molecular Dynamics Simulation; Polysaccharides - chemistry; Thermodynamics; Water - chemistry
• ISSN: 1549-9618; 1549-9626
• DOI: 10.1021/ct500924f

Hemicellulose polysaccharides play an important role in the swelling behavior of the primary plant cell wall, and molecular dynamics simulations provide the means of gaining a concise understanding of the interactions of hemicellulose polysaccharides with water. Here, we compare four of the main polysaccharide force fields (CHARMM36 TIP3P, GROMOS56A6CARBO SPC, GLYCAM06h TIP3P, and GLYCAM06h TIP5P) for the most abundant hemicellulose backbone components. In particular, we compare aggregation, diffusion coefficients, system density, and investigate the free energy of hydration of saccharides in water. We find that the saccharides show nonphysical aggregation at low concentrations with the GLYCAM06h TIP3P force field, which can be rectified by the use of the TIP5P water model. As a result of the aggregation, GLYCAM06h TIP3P does not lead to reasonable diffusion coefficients whereas the diffusion coefficients, as well as the system density, agrees best with experimental data for the GLYCAM06h TIP5P force field. Overall, GLYCAM06h TIP5P gives good agreement with experimental free energy of hydration data for small saccharides. In addition, the free energy of hydration for short polysaccharides calculated with the GLYCAM06h TIP5P force field is consistent with the radial distribution functions between the polysaccharides and water, the hydration number of the polysaccharides, and the hydrogen bonds formed in the system.