Single-file Chain Research Articles

One-dimensionally confined ammonia molecules: A theoretical study

We examine a single-file chain of ammonia molecules in a carbon nanotube. To this end, we use i) molecular dynamics simulations (combined with the charges for ammonia nitrogen and hydrogen obtained from quantum chemistry) and ii) lattice-model calculations by M. Druchok et al. (2023) [7]. Our findings demonstrate the occurrence of the orientational quasiorder of the ammonia dipoles, which become parallel to the tube axis, at intermediate temperatures below 100 K.

Toward a quasiphase transition in the single-file chain of water molecules: Simple lattice model.

Recently, Ma et al. [Phys. Rev. Lett. 118, 027402 (2017)] have suggested that water molecules encapsulated in (6,5) single-wall carbon nanotube experience a temperature-induced quasiphase transition around 150K interpreted as changes in the water dipoles orientation. We discuss further this temperature-driven quasiphase transition performing quantum chemical calculations and molecular dynamics simulations and, most importantly, suggesting a simple lattice model to reproduce the properties of the one-dimensional confined finite arrays of water molecules. The lattice model takes into account not only the short-range and long-range interactions but also the rotations in a narrow tube, and both ingredients provide an explanation for a temperature-driven orientational ordering of the water molecules, which persists within a relatively wide temperature range.

Ultrasonic chaining of emulsion droplets

Emulsion droplets trapped in an ultrasonic levitator organize themselves in a way that solid spheres do not. Rather than coalescing into planar colloidal crystals, monodisperse emulsion droplets instead form single-file chains. These chains' collective behavior and their influence on nearby droplets suggest that their constituent droplets are spinning rapidly around their common axis. Such acoustically induced spinning also distinguishes fluid droplets from solid spheres and naturally accounts for the droplets' propensity to form chains. In this interpretation, solid spheres do not form chains because they do not spin. We demonstrate the chain-to-crystal transition with a model system in which fluid emulsion droplets can be photopolymerized into solid spheres without significantly changing other material properties. The behavior of this experimental system is quantitatively consistent with an acoustohydrodynamic model for spinning spheres in an acoustic levitator. This study therefore introduces acoustically driven spinning as a mechanism for guiding self-organization of acoustically levitated matter.

Formation of a Stable Bridge between Two Disjoint Nanotubes with Single-File Chains of Water.

It was recently demonstrated that stable water bridges can form between two relatively large disjoint nanochannels, such as carbon nanotubes (CNTs), under an applied pressure drop. Such bridges are relevant to fabrication of nanostructured materials, drug delivery, water desalination devices, hydrogen fuel cells, dip-pen nanolithography, and several other applications. If the nanotubes are small enough, however, then one has only single-file hydrogen-bonded chains of water molecules. The distribution of water in such nanotubes manifests unusual physical properties that are attributed to the low number of hydrogen bonds (HBs) formed in the channel since, on average, each water molecule in a single-file chain forms only 1.7 HBs, almost half of the value for bulk water. Using extensive molecular dynamics simulations, we demonstrate that stable bridges can form even between two small disjoint CNTs that contain single-file chains of water. The structure, stability, and properties of such bridges and their dependence on the applied pressure drop and the length of the gap between the two CNTs are studied in detail, as is the distribution of the HBs. We demonstrate, in particular, that the efficiency of flow through the bridge is at maximum at a specific pressure difference.

Two-state diffusive mobility of slow and fast transport of water in narrow nanochannels.

Transport of water in narrow nanochannels as a single-file chain is involved in various biological activities and nanofluidic applications. However, although the consistent dipole orientation of the water molecules is intensively studied, its effect upon the transport behavior is still unknown. In this Rapid Communication, we find two states of slow and fast transport coexist in the single-file water in the presence of channel defects that break the collective dipole orientation. A low diffusive mobility is found for the dipole orientation inconsistent configurations while mobility approximately two times higher is found for the consistent ones. The two-state diffusion process relies on the different hydrogen bond connections, which possess overlapped structures, enabling a spontaneous transition. The slow state is insensitive to the increased defect number while the fast state is reduced accordingly. The two states exhibit different lifetime and temperature dependences that demonstrate a possibility for manipulation. Our result implies the possibility of two-state diffusion process of water in nanofluid phenomena due to the common presence of defects in nanochannels.

Deformation Effect on Water Transport through Nanotubes

In this study, we used non-equilibrium molecular dynamics to study the transport of water through deformed (6,6) Carbon Nanotubes (CNTs) and Boron Nitride Nanotubes (BNNTs). The results were then compared with that of the perfect nanotubes. The main aim of this study was to get a better insight into the deformation effect on water transport through nanotubes rather than directly comparing the CNTs and BNNTs. As the diameters of both types of nanotubes differ from each other for the same chiral value, they are not directly comparable. We carried out our study on deformations such as screw distortion, XY-distortion, and Z-distortion. XY-distortion of value 2 shows a change from single-file water transport to near-Fickian diffusion. The XY-distortions of higher value shows a notable negative effect on water transport when their distortion values get larger. These suggest that the degree of deformation plays a crucial role in water transport through deformed nanotubes. The Z-distortion of 2 showed discontinuous single-file chain formation inside the nanotubes. Similar phenomena are observed in both nanotubes, irrespective of their type, while the magnitudes of their effects vary.

High-Precision Size Recognition and Separation in Synthetic 1D Nanochannels.

Covalent organic frameworks (COFs) allow elaborate manufacture of ordered one-dimensional channels in the crystal. We defined a superlattice of COFs by engineering channels with a persistent triangular shape and discrete pore size. We observed a size-recognition regime that is different from the characteristic adsorption of COFs, whereby pore windows and walls were cooperative so that triangular apertures sorted molecules of one-atom difference and notch nanogrooves confined them into single-file molecular chains. The recognition and confinement were accurately described by sensitive spectroscopy and femtosecond dynamic simulations. The resulting COFs enabled instantaneous separation of mixtures at ambient temperature and pressure. This study offers an approach to merge precise recognition, selective transport, and instant separation in synthetic 1D channels.

Soliton-like propagation of dipole reorientation in confined single-file water chains

Water molecules confined in a narrow nanotube channel orient themselves into a uniformly ordered single-file chain. Here, we report by means of comprehensive molecular dynamics simulations and soliton-model-based theoretical analysis that the reorientation (i.e., rotation) of a single water molecule in this dipole chain, triggered for example by an external charge, can induce successive reorientation of the rest of the water molecules, which propagates in a soliton-like manner. The resulting local potential energy peak separating the reoriented and the pending reorientation subsections moves with an unweakened peak intensity at a constant velocity in the ambient environment, and particularly, can penetrate or make a turn through a crossed nanotube junction. The propagation velocity depends on the strength of the external charge, in agreement with our sine-Gordon soliton-based theoretical analysis. We further show that this unidirectional propagation originates from the partially inhibited fluctuation in dipole orientation of reoriented water with respect to that of original ones. These findings may be helpful in the development of high-efficiency information transmitting, processing and storage devices and the understanding of functioning of biological water channels.

Selective Transport through the Ultrashort Carbon Nanotubes Embedded in Lipid Bilayers

Carbon nanotubes (CNTs) have shown growing potential applications in the fields of biotechnology and biomedicine because of their unique structure and properties. The hollow channels can be used to deliver drug molecules. However, the transport properties of small molecules through the CNT hollow channels are not yet clear. In this study, we will investigate the transport properties of small polar molecules in the ultrashort CNTs embedded in the lipid bilayer using molecular dynamics simulations. By varying the diameter of the CNTs, we find that only water molecules can enter the (6, 6) CNT. Furthermore, the (7, 7) tube exhibits selectivity between dimethyl sulfoxide (DMSO) and urea, whereas both DMSO and water or urea and water can flow in the (8, 8) CNT. Potential of mean force (PMF) calculations confirm that DMSO in the (7, 7) CNT possesses a lower free energy compared with urea. Because of the strong dipolar interaction, DMSO molecules form a single-file chain in (7, 7) CNT, but they are not well orde...

Structure and kinetics of water in highly confined conditions: A molecular dynamics simulation study

In this work, we carried out a systematic and detailed study of water under severely confined conditions, based on atomistic molecular dynamics (MD) simulations. Specifically, MD simulations were performed for water confined in single-walled capped carbon nanotubes of chiral indices between (4,4) and (10,10). The structure and dynamics of confined water, and its dependence on the diameter and length of the capped carbon nanotubes (CCNTs) was examined, alongside with the influence of the latter on water immersion. Our results show that the axial water density decreases with increasing distance from the open face of the CCNTs, and that water forms well-defined shells along the radius of the CCNTs. The confined water molecules closer to the water–wall interfacial region tend to orient themselves pointing their OH bonds towards the wall. This trend becomes less evident in the inner regions of the CCNTs, so that the water molecules in the central region of the (10,10) CCNT are almost randomly oriented. On the other hand, the water molecules inside the (6,6) CCNT form a single-file chain along the CCNT's axis. Furthermore, the average number of hydrogen bonds per water molecule decreases with increasing length of the CCNT and decreasing diameter. Hydrogen bonding and water orientations in the CCNTs significantly affect the mobility of water, being the mobility of water faster in the (7,7) CCNT than in other CCNTs of the same length.

Enhanced water permeability and tunable ion selectivity in subnanometer carbon nanotube porins.

Fast water transport through carbon nanotube pores has raised the possibility to use them in the next generation of water treatment technologies. We report that water permeability in 0.8-nanometer-diameter carbon nanotube porins (CNTPs), which confine water down to a single-file chain, exceeds that of biological water transporters and of wider CNT pores by an order of magnitude. Intermolecular hydrogen-bond rearrangement, required for entry into the nanotube, dominates the energy barrier and can be manipulated to enhance water transport rates. CNTPs block anion transport, even at salinities that exceed seawater levels, and their ion selectivity can be tuned to configure them into switchable ionic diodes. These properties make CNTPs a promising material for developing membrane separation technologies.

(Invited) Quasi Phase Transition in a Single File of Water Molecules Encapsulated inside (6,5) Carbon Nanotubes

The confinement of water molecules in one-dimensional channels leads to fascinating new properties which are of critical importance for many processes in biology, geology, catalysis and nanofluidics. Single-walled carbon nanotubes (SWCNTs) are one of the most promising model systems to investigate molecules under confinement. They combined atomically-precise diameters that deliver the necessary level of confinement with a weak interaction of the water molecules with their smooth inner walls. Despite significant efforts, theoretical predictions of the behavior and peculiar properties of a single-file chain of water water molecules (e.g. interesting for ultrafast proton transport) have proven to be very hard to validate experimentally. In this work, we present temperature-dependent (4.2K up to room temperature) photoluminescence (PL) spectra of water-filled and empty chirality-sorted (6,5) SWCNTs. Superimposed on a linear temperature-depenent PL spectral shift of the empty tubes, an additional stepwise PL shift of the water-filled SWCNTs is observed at around 150K. With the empty SWCNTs serving as the ideal reference system, we can assign this observation to temperature-induced changes occuring within the single file molecular chain. Supported by new Molecular Dynamics simulations, we obtain the first experimental evidence of a quasi phase transition of the orientation of the molecular dipoles within such a one-dimensional single file chain of water molecules.

Quasiphase Transition in a Single File of Water Molecules Encapsulated in (6,5) Carbon Nanotubes Observed by Temperature-Dependent Photoluminescence Spectroscopy.

Molecules confined inside single-walled carbon nanotubes (SWCNTs) behave quite differently from their bulk analogues. In this Letter we present temperature-dependent (4.2K up to room temperature) photoluminescence (PL) spectra of water-filled and empty single-chirality (6,5) SWCNTs. Superimposed on a linear temperature-dependent PL spectral shift of the empty SWCNTs, an additional stepwise PL spectral shift of the water-filled SWCNTs is observed at ∼150 K. With the empty SWCNTs serving as an ideal reference system, we assign this shift to temperature-induced changes occurring in the single-file chain of water molecules encapsulated in the tubes. Our molecular dynamics simulations further support the occurrence of a quasiphase transition of the orientational order of the water dipoles in the single-file chain.

Fast mass transport of oil and supercritical carbon dioxide through organic nanopores in shale

Hydrocarbon production from shale has grown dramatically in North America, and has the potential to do so globally. Nanoporous organic matter is probably the dominant mode of porosity occurrence in productive shale systems, but the physics of liquid transport through organic-hosted pores is still ambiguous. In the present work, molecular dynamics simulations were conducted to study the static properties and pressure-driven flow behavior of pure liquid hydrocarbons (octane) and supercritical carbon dioxide (scCO2) confined in slit-shaped organic nanopores. Carbonaceous slits having apertures ranging from 1.5 to 11.2nm were explored. A range of thermodynamic conditions, corresponding to the sedimentary reservoirs, were examined. Equilibrium molecular dynamics (EMD) enabled us to determine the density profile, from which we observed the layering structure of confined fluid and the preferential adsorption of scCO2 relative to C8H18 and CH4. As the pore size increases, the structure of the adsorbed phase transforms from a single-file chain to four and three dense monolayers for C8H18 and scCO2, respectively. Then we calculated, using nonequilibrium molecular dynamics (NEMD), their velocity profiles and studied the hydrodynamics under a pressure gradient. We found that the velocity profiles in an organic slit tend to be pluglike, which deviates significantly from the parabolic profile in inorganic nanopores, and the flow exceeds predictions of the no-slip Poiseuille equation by 1–3 orders of magnitude. We proposed two models to characterize the flow behavior, each of which can be integrated into a bottom-up framework to mimic fluid transport in shale and estimate the apparent liquid permeability. The parameters in our models, slip length and apparent viscosity, are exponentially dependent on driving force, pore size, and temperature. Our results, which highlight the need for taking into account the different nature of organic matter and inorganic minerals in flow modeling, will shed light on the development of shale resources and, more generally, mass transfer in nanoporous materials.

Clusters of circulating tumor cells traverse capillary-sized vessels

Multicellular aggregates of circulating tumor cells (CTC clusters) are potent initiators of distant organ metastasis. However, it is currently assumed that CTC clusters are too large to pass through narrow vessels to reach these organs. Here, we present evidence that challenges this assumption through the use of microfluidic devices designed to mimic human capillary constrictions and CTC clusters obtained from patient and cancer cell origins. Over 90% of clusters containing up to 20 cells successfully traversed 5- to 10-μm constrictions even in whole blood. Clusters rapidly and reversibly reorganized into single-file chain-like geometries that substantially reduced their hydrodynamic resistances. Xenotransplantation of human CTC clusters into zebrafish showed similar reorganization and transit through capillary-sized vessels in vivo. Preliminary experiments demonstrated that clusters could be disrupted during transit using drugs that affected cellular interaction energies. These findings suggest that CTC clusters may contribute a greater role to tumor dissemination than previously believed and may point to strategies for combating CTC cluster-initiated metastasis.

Confinement effects on liquid-flow characteristics in carbon nanotubes

Liquid flow dynamics through the armchair (6,6)-(160,160) carbon nanotubes (CNTs) is elucidated by molecular dynamics simulations. The liquid is modeled by nonpolar argon atoms to understand the fundamental flow physics. The velocity profiles and slip lengths are discussed considering the radial distributions of the fluid density by the presently proposed finite difference-based velocity fitting method. It is found that as the CNT diameter D increases, the slip length and the flow rate enhancement show three-step transitional profiles in the region of D≤2.3 nm. The slip length and the flow rate stepwise increase at the first transition while they drop at the second and third transitions. The first transition corresponds to the structural change from the single-file chain to single-ring structures of the molecule cluster. The second and third transitions take place when the ring structure starts to develop another inner layer.

Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes.

Classical molecular dynamics simulations have been performed to investigate the dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes (CPNTs) with various radii, i.e., 8×(WL¯)n=3,4,5/POPE. The results show that ethanol molecules spontaneously fill the octa- and deca-CPNTs, but not the hexa-CPNT. In the octa-CPNT, ethanol molecules are trapped at individual gaps with their carbon skeletons perpendicular to the tube axis and hydroxyl groups towards the tube wall, forming a broken single-file chain. As the channel radius increases, ethanol molecules inside the deca-CPNT tend to form a tubular layer and the hydroxyl groups mainly stretch towards the tube axis. Computations of diffusion coefficients indicate that ethanol molecules in the octa-CPNT nearly lost their diffusion abilities, while those in the deca-CPNT diffuse as 4.5 times as in a (8, 8) carbon nanotube with a similar tube diameter. The osmotic and diffusion permeabilities (pf and pd, respectively) of the octa- and deca-CPNTs transporting ethanol were deduced for the first time. The distributions of the gauche and trans conformers of ethanol molecules in two CPNTs are quite similar, both with approximately 57% gauche conformers. The non-bonded interactions of channel ethanol with a CPNT wall and surrounding ethanol were explored. The potential of mean force elucidates the mechanism underlying the transporting characteristics of channel ethanol in a transmembrane CPNT.

Water permeability in carbon nanotube arrays

The membrane composed of carbon nanotube arrays may be widely used in biological molecular devices, image display area and optoelectronic devices. In this paper, the water permeability of the (11, 11) carbon nanotube arrays is simulated by using the SPC/E water model and the molecular dynamics program LAMMPS at 300 K. It is found that the distance between carbon nanotubes has a significant impact on water density distribution and the electric dipole moment orientation. Regardless of the distance between the neighboring tubes, water molecules will get into the nanotubes and form a double-layer cylindrical ring structure inside the nanotubes. However, water molecules can fill into the interstitial space of the nanotube array only when the nearest distance between the neighbor the tubes is greater than 3.4 Å, or the interstitial cross area becomes greater than 57.91 Å2. As the interstitial space increases, the structure of water molecules in the interstitial space will evolve from disconnected single-file chains to boundary-shared close-packing-like columnar circles. Meanwhile, the radius of the water ring inside the nanotube will increase and its boundary becomes more sharp due to the attractions from those water molecules filled in the interstitial space. Relative to the tube axis, the distributions of the water molecular electric dipole moments in the interstitial space depend upon water structures. Under the condition of single-file chain, the distribution exhibits a bimodal characteristic, which is very similar to the distribution of water dipole moments inside the nanotube. Whereas, for the boundary-shared close-packing-like water columnar circle, the distribution of dipole moments shows a unimodal characteristic and the peak corresponds to the angle 90°. This indicates that the preferred orientation of the water dipoles points to the direction perpendicular to the tube axis. These conclusions are helpful in the understanding of the water transport properties in carbon nanotube arrays.

Mathematical models of ion transport through cell membrane channels

We discuss various models of ion transport through cell membrane channels. Recent experimental data shows that sizes of some ion channels are compared to those of ions and that only few ions may be simultaneously in any single channel. Theoretical description of ion transport in such channels should therefore take into account stochastic fluctuations and interactions between ions and between ions and channel proteins. This is not satisfied by macroscopic continuum models based on the Poisson-Nernst-Planck equations. More realistic descriptions of ion transport are offered by microscopic molecular and Brownian dynamics. We present a derivation of the Poisson-Nernst-Planck equations. We also review some recent models such as single-file diffusion and Markov chains of interacting ions (boundary driven lattice gases). Such models take into account discrete and stochastic nature of ion transport and specifically interactions between ions in ion channels.

Atomic Mechanisms and Equation of State of Methane Adsorption in Carbon Nanopores

Adsorption is an important issue both in the estimation of natural gas reserves and efficient storage of methane. In this study, we focus on the mechanisms of methane adsorption in carbon nanopores and endeavor to establish the equation of state for the adsorbed phase through molecular dynamics simulations and theoretical analyses. Here, the nanopores were modeled by carbon nanotubes (CNTs). The higher storage capacity of the CNT compared to the bulk phase was attributed to the additional pressure exerted by the CNT wall on the adsorbed phase, considering which, the equation of state for the adsorbed phase was established. As the CNT diameter increases, the adsorption structure transforms from a single-file chain to two adsorption layers. Moreover, it was found that there exists an optimal CNT diameter that maximizes the adsorption, which is due to the competition between the curvature effect and the size effect. In the explanation of this phenomenon, the nanostructure of the CNT wall plays an important role, without considering which, the adsorption density would monotonically decrease as the CNT diameter rises. Our findings and related analyses may help reveal the underlying mechanisms behind the adsorption phenomena, which is not only of theoretical importance, but may also help estimate the natural gas reserves and design nanoporous materials with higher storage capacity.