Molecular Dynamics Simulation of Dextran Extension at Constant Pulling Speed

A dextran monomer and a 10mer under constant pulling speed were studied using the atomistic simulations. Molecular dynamics (MD) with the new Amber‐Glycam04 forcefield were performed. The main result of the present Amber‐based MD simulations is that the experimental plateau of the force‐extension dependence for dextran can be explained by a transition of the glucopyranose rings in the dextran monomers from a chair (4C1) to a inverted chair (1C4) conformation whereas chair to boat transitions occur at higher forces. Density functional (DFT) calculations of monomer were also performed for a monomer at different fixed end‐to‐end distances (lengths) to clarify the molecular mechanism of dextran extension. These DFT calculations confirm the existence of an inverted chair (1C4) conformation at intermediate extensions and its possible important contribution to the plateau in the experimental force‐extension dependence of dextran.