However, the novel energy sources extraction and storage technologies, although efficient and green, are complex to fabricate and utilize. [1][2][3][4] Among fuel cells, direct methanol fuel cells (DMFC) show great promise; they use liquid methanol as fuel, which is plentiful and low in cost, and they have a relatively simple and reliable design. [5,6] A key element in the new DMFC fuel cells is the proton exchanging membranes that play a critical role in their performance. These fuel cells are highly susceptible to cathode poisoning, a corrosive phenomenon that happens as undesirable species cross over membranes and reach the cathode, diminishing its potential. As a remedy, selective nanomembranes were introduced which hinder, or completely block the movement of undesirable species. Selective gateways are not a novel phenomenon, as they are present in living organisms and are more suitable for larger ions. Proton-selective channels, on the other hand, can help boost the performance of the new fuel cells deemed to the key to the future of the energy industry and the development of novel fuel cell technologies.The selectivity of a channel is mainly attributed to the function of nanopores geometry, surface chemistry, and environmental conditions that control the ion transport. [7][8][9] These factors were discussed by Razmjou et al. for extracting larger cations in membranes. [10] The key-controlling factors are the dehydration degree of the ions and the nature of the interaction between ions and the inner surface of the channel. Ion movement is facilitated by the existence of water molecules, both as vehicle and as a jumping stage for different ions, making it indispensable for efficient ion conduction. [1] Reducing the channel height, which refers to the smallest dimension of the channel entry, creates an energy barrier that is a direct realization of the spatial obstruction that acts against the hydration shell of the ions. [11,12] Decreasing the channel size, not only creates an energy obstacle against the entering ions, but it also affects the formation of the water molecules inside. The main vehicle for ion transport in this scale is water which is prone to significant phase and behavioral change [13][14][15] under confinement. [16][17][18] This alteration also extends to the ice like formation water under nanoconfinement. [19,20] Under high pressures, water molecules that are trapped inside confinement rearrange their formation and stabilize with unconventional Balancing ionic selectivity against permeability in filters made from graphene remains a challenge today. Interlayer distance, as the most important factor, dominates nearly all aspects of the flow inside the channel, from the formation of water molecules to the hydration shell of the ions. Unraveling the effects of the interlayer distance on the proton diffusion process helps lay a foundation for the cutting-edge proton conduction technology. Here, the reactive molecular dynamics simulations are used to probe the proton flow through a series of hydra...