Molecular dynamics study of polygalacturonic acid chains in aqueous solution

Molecular dynamics (MD) simulations were performed on a system consisting of polygalacturonic acid (PGA) chains. MD experiments were conducted both in vacuo and in the presence of water. The PGA chains were formed by 12 GalA units and each chain had a molecular weight of 2132. Three chains were enclosed in the simulation cells. NPT runs, carried out either in the absence and in the presence of water molecules, evidenced the collapse of the chains which aggregate due to the formation of hydrogen bonds. NVT trajectories performed in the presence of water molecules show that the solvent moves in channels which separate the PGA aggregates, These findings well agree with experimental results about gel formation by PGA and other pectins in strong acid media.