The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions

Molecular dynamics simulations are carried out to determine the effects of channel wall structure on water and ion properties. We compare hydrophobic (Lennard-Jones 5-3 and atomic) and molecular-hydrophilic cylindrical pores of 2-6 Å in effective radius, relevant to the study of most significant biological ion channels including gramicidin A, ACh, and potassium channels, and to the study of many microporous materials. Large variations in levels of self-diffusion and rotational correlation within hydrophobic channels are explained in terms of water geometry, hydrogen bonding, and dipole correlation. The differing levels of water structure and self-diffusion in hydrophobic and hydrophilic pores arise because of marked differences in the preferred orientation of water dipole moments, and due to hydrogen bonding with molecules on the pore lining. Axial sodium ion diffusion does not experience large variations with pore size, despite anomalous stability in moderate-sized hydrophobic pores. We attribute this to the ability of ions to diffuse along troughs of water density. Ion diffusion along the pore axis exhibits a general increase with channel radius in hydrophobic channels but remains fairly low in hydrophilic channels.