Coupled Surface and Pore Diffusion of Neutral Organic Molecules in Nanopores

Abstract The transport of neutral organic molecules through nanoscale pores is central to a wide range of processes, yet the molecular factors governing their mobility remain difficult to predict. Here, we use all-atom molecular dynamics simulations under a nonpolarizable force field to examine the diffusion of 1,4-dioxane, phenol, ethanol, and acetonitrile in anodic aluminum oxide nanopores with diameters of 4 and 8 nm. On the basis of the decay of molecule-wall potential energy and the molecular size, we establish a 1 nm boundary to separate surface-associated diffusion from pore-interior diffusion. Additionally, our simulation results show that surface diffusion is controlled by molecule-specific wall affinity and confinement-enhanced contact, whereas pore diffusion is governed by rotation–translation coupling. Molecules with higher polarity rotate faster, which reduces the persistent axial displacement and slows pore diffusion. The overall diffusivity emerges from the weighted contributions of the surface residence, interfacial mobility, and pore-interior dynamics. The results from this study provide mechanistic insights into neutral organic transport in nanofluidics and nanoporous membranes.