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[Preprint]. 2024 Aug 8:2023.11.14.567055. Originally published 2023 Nov 14. [Version 2] doi: 10.1101/2023.11.14.567055

Figure 4: Analysis of the partially open state.

Figure 4:

Trajectories of water (cyan), sodium (green) and Cl− (orange) ions in z-coordinates as a function of time within the neck region of the partially open state pore (PDB ID 8D1K) using A the AMOEBA forcefield or B c36m forcefield. The red box in A highlights a Cl− that can occupy locations above F84 in the neck whereas nearly no ions can be seen in B with c36m. C Bottom-up view of F84 of the partially open state neck. The volume that Cl− may occupy over the simulation is represented by the orange mesh. D Side-view of the neck region. F84 of the neck may accommodate for Cl−; however, the neck is not permeable to Cl−. E Bottom-up view of F84. Cl− can be seen to interact with the aromatic ring through edgewise anion-π interactions. The coordinating atoms within the first solvation shell of the Cl− (orange sphere) are represented as spheres.