Hydration of agarose double helix: A monte carlo simulation

Abstract

The structure of the water around agarose double helix is analyzed with ab initio quantum mechanical calculations and Monte Carlo simulations. The potential surface is sampled by computing the interaction energy between fragments of agarose and a water molecule placed at 221 different orientations and/or positions. These energy values are fitted to a simple analytical expression representing atom-atom pair potentials for a water molecule interacting with agarose. A preliminary understanding of the agarose-water interaction is obtained from isoenergy contour maps at planar cross sections, perpendicular to the long axis of the double helix, and for cylindrical surfaces enclosing the double helix. A more detailed understanding is obtained from Monte Carlo simulations on a system composed of 600 water molecules surrounding a three-turn fragment of agarose double helix at a temperature of 300 K. The most probable position for agarose hydrogen atoms, the coordination numbers for the water molecules hydrating agarose atoms, and the structures of water molecules surrounding the agarose double helix are discussed in detail.