Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube

Abstract

The effects of geometric restraints and frictional parameters on the energetics and dynamics of ion transport through a synthetic ion channel are investigated using molecular dynamics (MD) simulations for several different ions. To do so, potential of mean force profiles and position‐dependent diffusion coefficients for Na+, K+, Ca2+, and Cl− transport through a simple cyclic peptide nanotube, which is composed of 4× cyclo[−(D‐Ala‐Glu‐D‐Ala‐Gln)2−] rings, are calculated via an adaptive biasing force MD simulation method and a Baysian inference/Monte Carlo algorithm. Among the restraints and parameters examined in this work, the radius parameter used in the flat‐bottom half‐harmonic restraint at the entrance and exit to channel has a great effect on the energetics of ion transport through the variation of entropy in the outside of the channel. The diffusivity profiles for the ions show a strong dependence on the damping coefficient, but the dependence on the coefficient becomes minimal inside the channel, indicating that the most important factor which affects the diffusivity of ions inside the channel is local interactions of ions with the structured channel water molecules through confinement.

Extended kinetic lattice grand canonical Monte Carlo simulation method for transport of multicomponent ion mixtures through a model nanopore system

“…We chose R c ¼ 10Å because previous MD simulation studies revealed that the diffusion coefficients of ions begin to decrease nearly 10 Å away from the channel entrance of cyclic peptide nanotubes (CPNs) that possess a similar structure to the model nanopore in this study. 29,30 Then, the ion current for ion i can be evaluated as…”

“…21,[34][35][36][37] Ion-related parameters such as the LJ parameters and diffusion coefficients in bulk water and inside the nanopore are presented in Table 1 where the values of D chn i are set to be 0.4 D blk i for K + , Na + , and Cl À on a basis of the molecular dynamics (MD) simulation results for the position-dependent diffusion coefficients of ions inside a cyclic peptide nanotube (CPN). 29,30 We used the ion radii from the Chemistry at Harvard Macromolecular Mechanics (CHARMM) force field instead of the hydrodynamic radii of ions because our previous MD simulations showed that the ions are partially dehydrated inside a small nanopore like the model system we used in this study. 10,42 A two-dimensional contour map and a one-dimensional profile for the relative position-dependent diffusion coefficient of ion i used in our simulations are illustrated in Figure 2.…”

“…The inhomogeneous diffusivity of ions is observed in the translocation of ions inside a small nanopore as well as among different kinds of ions in bulk water. [26][27][28][29][30] Unlike the original KLGCMC/MF simulation method that is unable to treat inhomogeneous ion diffusion, the extended version can handle the inhomogeneous diffusivity of ions by using a diffusion probability algorithm that was proposed for a lattice-based KMC simulation method. 31 In the original KLGCMC/MF simulation, Legendre polynomials were used as a basis set for the BSE method.…”

Quantum‐Chemical Modeling of Cyclic Peptide‐Selenium Nanoparticle as an Anticancer Drug Nanocarrier

“…Cyclic compounds have been the center of attention of many chemists . Recently, cyclic peptides (CPs) have been noted for their application in chemistry and biology . They are useful in many fields of applications such as antibacterial agents, molecular transport systems, electronics, and other applications .…”