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Computational methods such as molecular dynamics (MD) have illuminated how single-atom ions permeate membrane channels and how selectivity among them is achieved. Much less is understood about molecular permeation through eukaryotic channels that mediate the flux of small molecules (e.g. connexins, pannexins, LRRC8s, CALHMs). Here we describe computational methods that have been profitably employed to explore the movements of molecules through wide pores, revealing mechanistic insights, guiding experiments, and suggesting testable hypotheses. This review illustrates MD techniques such as voltage-driven flux, potential of mean force, and mean first-passage-time calculations, as applied to molecular permeation through wide pores. These techniques have enabled detailed and quantitative modeling of molecular interactions and movement of permeants at the atomic level. We highlight novel contributors to the transit of molecules through these wide pathways. In particular, the flexibility and anisotropic nature of permeant molecules, coupled with the dynamics of pore-lining residues, lead to bespoke permeation dynamics. As more eukaryotic large-pore channel structures and functional data become available, these insights and approaches will be important for understanding the physical principles underlying molecular permeation and as guides for experimental design., (© 2024 The Authors. The Journal of Physiology © 2024 The Physiological Society.)

Pillared paddle-wheel-based metal-organic framework (MOF) materials are an attractive target as they offer a reliable method for constructing well-defined, multifunctional materials. A drawback of these materials, which has limited their application, is their tendency to form catenated frameworks with little accessible volume. To eliminate this disadvantage, it is necessary to investigate strategies for constructing non-catenated pillared paddle-wheel MOFs. Hydrogen-bonding substituents on linkers have been postulated to prevent catenation in certain frameworks and, in this work, we present a new MOF to further bolster this theory. Using 2,2'-diamino-[1,1'-biphenyl]-4,4'-dicarboxylic acid, BPDC-(NH 2 ) 2 , linkers and dipyridyl glycol, DPG, pillars, we assembled a MOF with pcu topology. The new material is non-catenated, exhibiting large accessible pores and low density. To the best of our knowledge, this material constitutes the pcu framework with the largest pore volume and lowest density. We attribute the lack of catenation to the presence of H-bonding substituents on both linkers.