Synthetic chloride-selective carbon nanotubes examined by using molecular and stochastic dynamics

Abstract

Synthetic channels, such as nanotubes, offer the possibility of ion-selective nanoscale pores which can broadly mimic the functions of various biological ion channels, and may one day be used as antimicrobial agents, or for treatment of cystic fibrosis. We have designed a carbon nanotube that is selectively permeable to anions. The virtual nanotubes are constructed from a hexagonal array of carbon atoms (graphene) rolled up to form a tubular structure, with an effective radius of 4.53 Å and length of 34 Å. The pore ends are terminated with polar carbonyl groups. The nanotube thus formed is embedded in a lipid bilayer and a reservoir containing ionic solutions is added at each end of the pore. The conductance properties of these synthetic channels are then examined with molecular and stochastic dynamics simulations. Profiles of the potential of mean force at 0 mM reveal that a cation moving across the pore encounters an insurmountable free energy barrier of ∼25 kT in height. In contrast, for anions, there are two energy wells of ∼12 kT near each end of the tube, separated by a central free energy barrier of 4 kT. The conductance of the pore, with symmetrical 500 mM solutions in the reservoirs, is 72 pS at 100 mV. The current saturates with an increasing ionic concentration, obeying a Michaelis-Menten relationship. The pore is normally occupied by two ions, and the rate-limiting step in conduction is the time taken for the resident ion near the exit gate to move out of the energy well.

Figure 1

Schematic of the (9, 9) carbon nanotube with (A) oxygen-terminated ends (shown in red) and (B) embedded in a lipid bilayer. Note that for clarity, water in the reservoirs is not shown.

Figure 2

Distributional molecular dynamics parameters for chloride in the (9, 9) carbon nanotube. (A) Variation in the diffusion coefficient. (B) Inverse decay time of the friction memory kernel, κ. (Solid line) Average value.

Figure 3

Free energy profile as a function of the z distance between the nanotube and lipid bilayer centers-of-mass. Note that the pulling speed of 2.5 and 5 Å/ns is shown.

Figure 4

Free energy profile of (A) sodium (Na⁺) and (B) chloride (Cl⁻) ions for the (9, 9) carbon nanotube with a length of 34 Å at 0 mM ionic concentration and using the carbonyl charge from the CHARMM27 force field (±0.51 e) and GROMOS force field (±0.38 e).

Figure 5

Current-voltage-concentration profiles for (9, 9) carbon nanotube 34 Å in length. (A) Current-voltage profile generated at an ionic concentration of 500 mM, and (B) current-concentration profile generated at a voltage of 200 mV of chloride ions. Each data point represents the average of five sets of simulations, each simulation lasting 8 × 10⁶ timesteps (0.8 μs). Error bars represent two standard errors of the mean and error bars smaller than the data points are not shown.

Figure 6

Binding sites of chloride ions for the (9, 9) carbon nanotube in the absence of an applied potential and using the carbonyl charge from the CHARMM27 force field (±0.51 e).