Molecular dynamics simulation of ion selectivity process in nanopores

How chemical defects influence the charging of nanoporous carbon supercapacitors

Nanoporous carbon texture makes fundamental understanding of the electrochemical processes challenging. Based on density functional theory (DFT) results, the proposed atomistic approach takes into account topological and chemical defects of the electrodes and attributes to them a partial charge that depends on the applied voltage. Using a realistic carbon nanotexture, a model is developed to simulate the ionic charge both at the surface and in the subnanometric pores of the electrodes of a supercapacitor. Before entering the smallest pores, ions dehydrate at the external surface of the electrodes, leading to asymmetric adsorption behavior. Ions in subnanometric pores are mostly fully dehydrated. The simulated capacitance is in qualitative agreement with experiments. Part of these ions remain irreversibly trapped upon discharge.

Ion desolvation and confinement are key physical processes in porous carbon-based supercapacitors undergoing charging and discharging cycles. We investigate electrolyte interactions between polarized porous carbon with subnanometer pore sizes and aqueous sodium chloride electrolyte, using molecular dynamics. Inspired by recent first-principles calculations, we develop a scheme accounting for chemical defects in electrodes where only the non-sp2 carbons species carry an extra negative charge (on the anode) and an extra positive charge (on the cathode) due to voltage polarization. This drives electrolyte species (ions and solvent molecules; water, in this work) to adsorb at the electrode surface and in subnanometric pores upon polarization. First, we observe an asymmetrical desolvation process of sodium and chloride ions at the external surface of the electrodes. The ionic distribution at the external surface of the electrodes is consistent with the Debye–Hückel electric potential equation and empirical trends observed for nonporous electrodes. In a second stage, we demonstrate that the nanoporosity of the electrodes is filled with ions and scarce water molecules and contributes to about 20% of the overall capacitance. A fraction of desolvated ions are irreversibly trapped in the core of electrodes during discharge. While maintaining the overall electroneutrality of the simulation cell, we find that anodes and cathodes do not carry the same amount of ions at all time steps, leading to charge imbalance.

Reverse Translocation of Nucleotides through a Carbon Nanotube

We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K⁺ ions, in contrast to a negligible and opposing current of Cl^- ions. The K⁺ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K⁺ ions and water molecules, and the nucleotide is driven in the same direction as the K⁺ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K⁺ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.

Nanoporous carbon for electrochemical capacitive energy storage

This review summarizes the recent advances of nanoporous carbon materials in the application of EDLCs, including a better understanding of the charge storage mechanisms by combining the advanced techniques and simulations methods.

Cytotoxicity effects and ionic diffusion of single-wall carbon nanotubes in cell membrane

While carbon nanotubes have been put into massive practical industrial, environmental and biomedicine applications, the cytotoxicity effects or the effect to the ionic channels they bring into the living cells need to be thoroughly investigated. In this work, molecular dynamic simulations have been carried out to investigate the ionic diffusion through the single wall armchair carbon nanotube embedded right inside the cell membrane. By modeling a two-membrane system, we build a virtual cytoplasm environment including a cell chamber and an extracellular space, in which a certain amount of solute is dissolved. The system is first brought to its equilibrium by deployment of minimization and then simulated. The results suggested that carbon nanotubes (CNTs) with size less than (12, 12) shall be less cytotoxic since it does not bring any ionic diffusion through the CNT channel, so as to maintain active cytoplasm environment. Another phenomenon we observed is a notable shifting angle of the carbon nanotube which was normal to the surface of cell membrane initially. In general, the inclination angle of the carbon nanotube increases with its radius.

Codeposition Modification of Cation Exchange Membranes with Dopamine and Crown Ether To Achieve High K+ Electrodialysis Selectivity

Surface modification has been proven to be an effective approach for ion exchange membranes to achieve separation of counterions with different valences by altering interfacial construction of membranes to improve ion transfer performance. In this work, we have fabricated a series of novel cation exchange membranes (CEMs) by modifying sulfonated polysulfone (SPSF) membranes via codeposition of mussel-inspired dopamine (DA) and 4'-aminobenzo-15-crown-5 (ACE), followed by glutaraldehyde cross-linking, aiming at achieving selective separation of specific cations. The as-prepared membranes before and after modification were systematically characterized in terms of their structural, physicochemical, electrochemical, and electrodialytic properties. In the electrodialysis process, the modified membranes exhibit distinct perm selectivity to K⁺ ions in binary (K⁺/Li⁺, K⁺/Na⁺, K⁺/Mg²⁺) and ternary (K⁺/Li⁺/Mg²⁺) systems. In particular, at a constant current density of 5.0 mA·cm^-2, modified membrane M-co-0.50 shows significantly prominent perm selectivity [Formula: see text] in the K⁺/Mg²⁺ system and M-co-0.75 exhibits remarkable performance in the K⁺/Li⁺ system [Formula: see text], superior to commercial monovalent-selective CEM (CIMS, [Formula: see text], [Formula: see text]). Besides, in the K⁺/Li⁺/Mg²⁺ ternary system, K⁺ flux reaches 30.8 nmol·cm^-2·s^-1 for M-co-0.50, while it reaches 25.8 nmol·cm^-2·s^-1 for CIMS. It possibly arises from the effects of pore-size sieving and the synergistic action of electric field driving and host-guest molecular recognition of ACE and K⁺ ions. This study can provide new insights into the separation of specific alkali metal ions, especially on reducing influence of coexisting cations K⁺ and Na⁺ on Li⁺ ion recovery from salt lake and seawater.

Sensitive Detection of a Modified Base in Single-Stranded DNA by a Single-Walled Carbon Nanotube

In this work, we use molecular dynamics simulations to study the responses of the configuration of single-strand DNA (ssDNA) within a carbon nanotube (CNT) and the concomitant ion flow to a single modified base, i.e., benzoimidazole (Bzim)-modified 5-hydroxymethyl cytosine (5hmC). Our simulation results show the Bzim-modified 5hmC can considerably increase the ion flow through a single-walled carbon nanotube (SWCNT), despite its larger size, which is consistent with prior experimental results. This phenomenon is attributed to enhanced adsorption of DNA to the interior wall of the CNT driven by the Bzim-modified 5hmC, leading to a reduced steric effect on ion transport through the CNT. As revealed in this work, the distribution of ssDNA can be affected by limited change in the interactions with the CNT surface. Such behavior of ssDNA within small-sized CNTs can be exploited to further improve the sensitivity of nanopore detection.

A mechanical nanogate based on a carbon nanotube for reversible control of ion conduction

Control of mass transport through nanochannels is of critical importance in many nanoscale devices and nanofiltration membranes. The gates in biological channels, which control the transport of substances across cell membranes, can provide inspiration for this purpose. Gates in many biological channels are formed by a constriction ringed with hydrophobic residues which can prevent ion conduction even when they are not completely physically occluded. In this work, we use molecular dynamics simulations to design a nanogate inspired by this hydrophobic gating mechanism. Deforming a carbon nanotube (12,12) with an external force can form a hydrophobic constriction in the centre of the tube that controls ion conduction. The simulation results show that increasing the magnitude of the applied force narrows the constriction and lowers the fluxes of K(+) and Cl(-) found under an electric field. With the exerted force larger than 5 nN, the constriction blocks the conduction of K(+) and Cl(-) due to partial dehydration while allowing for a noticeable water flux. Ion conduction can revert back to the unperturbed level upon force retraction, suggesting the reversibility of the nanogate. The force can be exerted by available experimental facilities, such as atomic force microscope (AFM) tips. It is found that partial dehydration in a continuous water-filled hydrophobic constriction is enough to close the channel, while full dewetting is not necessarily required. This mechanically deformed nanogate has many potential applications, such as a valve in nanofluidic systems to reversibly control ion conduction and a high-performance nanomachine for desalination and water treatment.

Competitive entry of sodium and potassium into nanoscale pores

We have studied the competitive entry of potassium and sodium into carbon nanotubes using molecular dynamics simulations. Our results demonstrate how a combination of strong sodium hydration coupled with strong potassium-chlorine interaction leads to enhanced potassium selectivity at certain diameters. We detail the reasons behind this, and show how variation of nanotube diameter can cause a switch to sodium selectivity, or even cause a decrease in overall ion entry despite an increase in diameter. These results demonstrate the importance of considering inter-ion dependence in the theoretical study of pore selectivity and show that, with careful design, the practical separation of sodium and potassium is possible using diameter variation alone.

pH-tunable ion selectivity in carbon nanotube pores

The selectivity of ion transport in nanochannels is of primary importance for a number of physical, chemical, and biological processes ranging from fluid separation to ion-channel-regulated cellular processes. Fundamental understanding of these phenomena requires model nanochannels with well-defined and controllable structural properties. Carbon nanotubes provide an ideal choice for nanofluidic studies because of their simple chemistry and structure, the atomic scale smoothness and chemical inertness of the graphitic walls, and the tunability of their diameter and length. Here, we investigate the selectivity of single and, for the first time, binary salt mixtures transport through narrow carbon nanotubes that act as the only pores in a silicon nitride membrane. We demonstrate that negatively charged carboxylic groups are responsible for the ion rejection performance of carbon nanotube pores and that ion permeation of small salts can be tuned by varying solution pH. Investigation of the effect of solution composition and ion valences for binary electrolytes with common cation in a pressure-driven flow reveals that the addition of slower diffusing multivalent anions to a solution of faster diffusing monovalent anions favors permeation of the monovalent anion. Larger fractions and valences of the added multivalent anions lower the rejection of the monovalent anion. In some cases, we observe negative rejection at low monovalent ion content.

Boron nitride nanotubes selectively permeable to cations or anions

Biological ion channels in membranes are selectively permeable to specific ionic species. They maintain the resting membrane potential, generate propagated action potentials, and control a wide variety of cell functions. Here it is demonstrated theoretically that boron nitride nanotubes have the ability to carry out some of the important functions of biological ion channels. Boron nitride nanotubes with radii of 4.83 and 5.52 A embedded in a silicon nitride membrane are selectively permeable to cations and anions, respectively. They broadly mimic some of the permeation characteristics of gramicidin and chloride channels. Using distributional molecular dynamics, which is a combination of molecular and stochastic dynamics simulations, the properties of these engineered nanotubes are characterized, such as the free energy encountered by charged particles, the water-ion structure within the pore, and the current-voltage and current-concentration profiles. These engineered nanotubes have potential applications as sensitive biosensors, antibiotics, or filtration devices.