Behavior of Water in 3-D Confinement: Implications for Macromolecular Function

Abstract

It has long been known that water near surfaces and in channels behaves in some significant ways differently from bulk water. In this work we report on computational studies of water in 3-D confinement. The long-range goal of the work is to elucidate the extent to which confinement in nanoscale cavities in biological cells modifies macromolecular function through modification of the solvation environmentl, leading to differences between in vivo and in vitro behavior. The systems we explore consist of cavities of various sizes computationally “carved out” of a block of amorphous silica and filled with water. Because of evidence that both polar-lined and non-polar lined cavities exist in biological cells, we explore both polar and nonpolar cavities by adjusting the partial charges on the atoms in the silica molecules. In polar cavities, with diameters ranging from 0.8 nm-2.8 nm, water exhibits limited translational and rotational motion, compared to bulk. This emerges from hydrogen bonding between water molecules and the cavity surface. In non-polar cavities, translational motion is low but rotational diffusion is anomalously high relative to bulk. At a critical diameter of 1.2 nm, the water freezes into an immobile block. We note this is the same diameter at which our group observed anomalous freezing in carbon nanotubes. However the structure of the water frozen by 3-D confinement is more complex than the anomalously frozen water in the nanotube. In ongoing related work we are exploring structure and dynamics of waters of solvation around proteins, and the proteins themselves, in bulk and confined in cavities.