Liquid–vapor oscillations of water in hydrophobic nanopores

Abstract

Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one-dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular dynamics simulations of water in short (0.8 nm) hydrophobic pores the water density in the pore fluctuates on a nanosecond time scale. In long simulations (460 ns in total) at pore radii ranging from 0.35 to 1.0 nm we quantify the kinetics of oscillations between a liquid-filled and a vapor-filled pore. This behavior can be explained as capillary evaporation alternating with capillary condensation, driven by pressure fluctuations in the water outside the pore. The freeenergy difference between the two states depends linearly on the radius. The free-energy landscape shows how a metastable liquid state gradually develops with increasing radius. For radii > Ϸ0.55 nm it becomes the globally stable state and the vapor state vanishes. One-dimensional confinement affects the dynamic behavior of the water molecules and increases the self diffusion by a factor of 2-3 compared with bulk water. Permeabilities for the narrow pores are of the same order of magnitude as for biological water pores. Water flow is not continuous but occurs in bursts. Our results suggest that simulations aimed at collective phenomena such as hydrophobic effects may require simulation times >50 ns. For water in confined geometries, it is not possible to extrapolate from bulk or short time behavior to longer time scales. C hannel and transporter proteins control flow of water, ions, and other solutes across cell membranes. In recent years several channel and pore structures have been solved at near atomic resolution (1-6), which together with three decades of physiological data (7) and theoretical and simulation approaches (8) allow us to describe transport of ions, water, or other small molecules at a molecular level. Water plays a special role here: it either solvates the inner surfaces of the pore and the permeators (for example, ions and small molecules like glycerol), or it is the permeant species itself as in the aquaporin family of water pores (9-11) or in the bacterial peptide channel gramicidin A, whose water transport properties are well studied (12-14). Thus, a better characterization of the behavior of water would improve our understanding of the biological function of a wide range of transporters. The remarkable water transport properties of aquaporins [water is conducted through a long (Ϸ2 nm) and narrow (Ϸ0.3 nm diameter) pore at bulk diffusion rates while at the same time protons are strongly selected against] are the topic of recent simulation studies (15, 16).The shape and dimensions of biological pores and the nature of the pore-lining atoms are recognized as major determinants of function. How the behavior of water depends on these factors is far from understood (17). Water is not a simple liquid because of its strong hydrogen bond network. When confined to narrow geometries like slits or pores ...

Self-assembling subnanometer pores with unusual mass-transport properties

“…We noted recent studies on carbon nanotubes showing that water can spontaneously fill small hydrophobic nanopores 36,37 , especially those with small pore diameters [36][37][38][39][40][41][42] , leading to enhanced mass flow or resonance 40,43 . The observed ion conductance of the hydrophobic channel formed by 1a implies that this sub-nm pore may also be filled with water molecules.…”

Strong correlations and Fickian water diffusion in narrow carbon nanotubes

“…The interest in studying such systems arises from the importance of understanding the properties of confined water and from the possibility of extrapolating the conclusions to other physical situations of similar nature, such as water adsorbed in nanopores in biological and geological systems. In recent years, Molecular Dynamics (MD) simulations have been used to study various aspects of these systems in microscopic detail [2,3,4,5,6,7,8]. Such studies complement experimental investigations by providing detailed microscopic understanding of some of the experimentally observed features.…”

“…They found that clusters of water molecules are transferred through the nanotube in the form of occasional bursts arising due to pressure fluctuations occurring outside the nanotube. Beckstein et al [3,4] have extended such simulations to 2 study the density fluctuations of water inside other hydrophobic pores. Transport of oxygen and organic molecules such as methane, ethane and ethylene through carbon nanotubes has also been studied [13,14,15,16] through MD simulations.…”

Interface dynamics of microscopic cavities in water

“…3 Furthermore, water, which is close to the liquid-vapor transition at normal conditions, can minimize interface area by locally evaporating and forming a 'nanobubble' within hydrophobic confinement. Evidence of bubble formation in confined geometry has been given early by computer simulations of smooth plate-like solutes, 4 but more recently it has been demonstrated in varying degrees in atomistically resolved plate-like solutes, 5,6 hydrophobic tubes and ion channels, 7,8 and in the collapse of proteins, 9,10 suggesting that it plays a key role in the stabilization and folding dynamics of certain classes of biomolecules. 11,12 Experimental evidence of nanobubbles in strong confinement (in contrast to bubbles at a single planar surface 3 ) has been given for instance in studies of water between hydrophobic surfaces, 13 in zeolites and silica nanotubes, 14,15 and on a subnanometer scale in nonpolar protein cavities.…”