Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes

Designing a hydrophobic barrier within biomimetic nanopores

Nanopores in membranes have a range of potential applications. Biomimetic design of nanopores aims to mimic key functions of biological pores within a stable template structure. Molecular dynamics simulations have been used to test whether a simple β-barrel protein nanopore can be modified to incorporate a hydrophobic barrier to permeation. Simulations have been used to evaluate functional properties of such nanopores, using water flux as a proxy for ionic conductance. The behavior of these model pores has been characterized as a function of pore size and of the hydrophobicity of the amino acid side chains lining the narrow central constriction of the pore. Potential of mean force calculations have been used to calculate free energy landscapes for water and for ion permeation in selected models. These studies demonstrate that a hydrophobic barrier can indeed be designed into a β-barrel protein nanopore, and that the height of the barrier can be adjusted by modifying the number of consecutive rings of hydrophobic side chains. A hydrophobic barrier prevents both water and ion permeation even though the pore is sterically unoccluded. These results both provide insights into the nature of hydrophobic gating in biological pores and channels, and furthermore demonstrate that simple design features may be computationally transplanted into β-barrel membrane proteins to generate functionally complex nanopores.

Electrostatic field-exposed water in nanotube at constant axial pressure

Water confined within nanoscale geometries under external field has many interesting properties which is very important for its application in biological processes and engineering. Using molecular dynamics simulations, we investigate the effect of external fields on polarization and structure as well as phase transformations of water confined within carbon nanotubes. We find that dipoles of water molecules tend to align along external field in nanoscale cylindrical confinement. Such alignment directly leads to the longitudinal electrostriction and cross-sectional dilation of water in nanotube. It also influences the stability of ice structures. As the electrostatic field strengthens, the confined water undergoes phase transitions from a prism structure to a helical one to a single chain as the electrostatic field strengthens. These results imply a rich phase diagram of the confined water due to the presence of external electriostatic field, which can be of importance for the industrial applications in nanopores.

Electricity resonance-induced fast transport of water through nanochannels

We performed molecular dynamics simulations to study water permeation through a single-walled carbon nanotube with electrical interference. It was found that the water net flux across the nanochannel is greatly affected by the external electrical interference, with the maximal net flux occurred at an electrical interference frequency of 16670 GHz being about nine times as high as the net flux at the low or high frequency range of (<1000 GHz or >80,000 GHz). The above phenomena can be attributed to the breakage of hydrogen bonds as the electrical interference frequency approaches to the inherent resonant frequency of hydrogen bonds. The new mechanism of regulating water flux across nanochannels revealed in this study provides an insight into the water transportation through biological water channels and has tremendous potential in the design of high-flux nanofluidic systems.

Model atomistic protrusions favouring the ordering and retention of water

The ordering of water molecules near model linear atomistic protrusions is studied using classical molecular dynamics simulations.

On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations

Single-file water chains confined in carbon nanotubes are studied using molecular dynamics simulations and free energy calculations to characterize the pore loading in terms of energy, entropy and free energy.

Functional understanding of solvent structure in GroEL cavity through dipole field analysis

Solvent plays a ubiquitous role in all biophysical phenomena. Yet, just how the molecular nature of water impacts processes in biology remains an important question. While one can simulate the behavior of water near biomolecules such as proteins, it is challenging to gauge the potential structural role solvent plays in mediating both kinetic and equilibrium processes. Here, we propose an analysis scheme for understanding the nature of solvent structure at a local level. We first calculate coarse-grained dipole vector fields for an explicitly solvated system simulated through molecular dynamics. We then analyze correlations between these vector fields to characterize water structure under biologically relevant conditions. In applying our method to the interior of the wild type chaperonin complex GroEL+ES, along with nine additional mutant GroEL complexes, we find that dipole field correlations are strongly related to chaperonin function.

Pore waters regulate ion permeation in a calcium release-activated calcium channel

The recent crystal structure of Orai, the pore unit of a calcium release-activated calcium (CRAC) channel, is used as the starting point for molecular dynamics and free-energy calculations designed to probe this channel's conduction properties. In free molecular dynamics simulations, cations localize preferentially at the extracellular channel entrance near the ring of Glu residues identified in the crystal structure, whereas anions localize in the basic intracellular half of the pore. To begin to understand ion permeation, the potential of mean force (PMF) was calculated for displacing a single Na(+) ion along the pore of the CRAC channel. The computed PMF indicates that the central hydrophobic region provides the major hindrance for ion diffusion along the permeation pathway, thereby illustrating the nonconducting nature of the crystal structure conformation. Strikingly, further PMF calculations demonstrate that the mutation V174A decreases the free energy barrier for conduction, rendering the channel effectively open. This seemingly dramatic effect of mutating a nonpolar residue for a smaller nonpolar residue in the pore hydrophobic region suggests an important role for the latter in conduction. Indeed, our computations show that even without significant channel-gating motions, a subtle change in the number of pore waters is sufficient to reshape the local electrostatic field and modulate the energetics of conduction, a result that rationalizes recent experimental findings. The present work suggests the activation mechanism for the wild-type CRAC channel is likely regulated by the number of pore waters and hence pore hydration governs the conductance.

Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions

The structure and properties of water at biological interfaces differ drastically from bulk due to effects including confinement and the presence of complicated charge distributions. This non-bulk-like behavior generally arises from water frustration, wherein all favorable interactions among water molecules cannot be simultaneously satisfied. While the frustration of interfacial water is ubiquitous in the cell, the role this frustration plays in mediating biophysical processes like protein folding is not well understood. To investigate the impact of frustration at interfaces, we here derive a general field theoretic model for the interaction of bulk and disordered vector fields at an embedded surface. We calculate thermodynamic and correlation functions for the model in two and three dimensions, and we compare our results to Monte Carlo simulations of lattice system analogs. In our analysis, we see that field-field cross correlations near the interface in the model give rise to a loss in entropy like that seen in glassy systems. We conclude by assessing our theory's utility as a coarse-grained model for water at polar biological interfaces.

Hydroxide ion can move faster than an excess proton through one-dimensional water chains in hydrophobic narrow pores

Carbon nanotubes (CNT) are known to provide a hydrophobic, confined environment for water where its structure and dynamics can be very different from those of bulk water. In particular, narrow CNTs of the type (6,6) allow only a single one-dimensional (1D) chain of water molecules inside them, thus providing an idealized scenario to study motion in 1D along water chains. In the present study, we have investigated structural and dynamic behavior of water and also of an excess proton and hydroxide ion in water-filled narrow CNTs by means of ab initio molecular dynamics and combined quantum-classical simulations. The main focus of the present work is on the molecular mechanism and kinetics of hydronium and hydroxide ion migration along 1D water chains of different lengths in confinement. It is found that the hydrogen-bonded structures of water and the excess proton and hydroxide ion in CNTs can be very different from those in bulk, and these altered solvation structures play critical roles in determining the proton-transfer (PT) rates along water chains. For the present 1D chain systems, the hydroxide ion is found to migrate at a slightly faster rate than the excess proton, unlike their relative mobilities in bulk water. This faster migration of the hydroxide ion is found not only in CNTs with periodicity along the tube axis but also in isolated CNTs where the excess proton and the hydroxide ion are allowed to move under the influence of an electric field of an oppositely charged ion. The roles of rotational jumps and hydrogen-bond fluctuations in the PT events are discussed. In addition, the significance of hydrogen-bonding defects on the dynamics of an excess proton and hydroxide ion is also discussed for varying chain lengths.

Entropy of single-file water in (6,6) carbon nanotubes

We used molecular dynamics simulations to investigate the thermodynamics of filling of a (6,6) open carbon nanotube (diameter D = 0.806 nm) solvated in TIP3P water over a temperature range from 280 K to 320 K at atmospheric pressure. In simulations of tubes with slightly weakened carbon-water attractive interactions, we observed multiple filling and emptying events. From the water occupancy statistics, we directly obtained the free energy of filling, and from its temperature dependence the entropy of filling. We found a negative entropy of about -1.3 k(B) per molecule for filling the nanotube with a hydrogen-bonded single-file chain of water molecules. The entropy of filling is nearly independent of the strength of the attractive carbon-water interactions over the range studied. In contrast, the energy of transfer depends strongly on the carbon-water attraction strength. These results are in good agreement with entropies of about -0.5 k(B) per water molecule obtained from grand-canonical Monte Carlo calculations of water in quasi-infinite tubes in vacuum under periodic boundary conditions. Overall, for realistic carbon-water interactions we expect that at ambient conditions filling of a (6,6) carbon nanotube open to a water reservoir is driven by a favorable decrease in energy, and opposed by a small loss of water entropy.

Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction

The theoretical prediction of water drying transitions near nonpolar surfaces has stimulated an intensive search for biological processes exploiting this extreme form of hydrophobicity. Here we quantitatively demonstrate that drying of a hydrophobic constriction is the major determinant of ion conductance in the GLIC pentameric ion channel. Molecular-dynamics simulations show that in the closed state, the channel conductance is ∼12 orders-of-magnitude lower than in the open state. This large drop in conductance is remarkable because even in the functionally closed conformation the pore constriction remains wide enough for the passage of sodium ions, aided by a continuous bridge of ∼12 water molecules. However, we find that the free energy cost of hydrating the hydrophobic gate is large, accounting almost entirely for the energetic barrier blocking ion passage. The free energies of transferring a sodium ion into a prehydrated gate in functionally closed and open states differ by only 1.2 kcal/mol, compared to an 11 kcal/mol difference in the costs of hydrating the hydrophobic gate. Conversely, ion desolvation effects play only minor roles in GLIC ion channel gating. Our simulations help rationalize experiments probing the gating kinetics of the nicotinic acetylcholine receptor in response to mutations of pore-lining residues. The molecular character and phase behavior of water should thus be included in quantitative descriptions of ion channel gating.

Effect of nanochannel dimension on the transport of water molecules

From the perspectives of biological applications and material sciences, it is essential to understand the transport properties of water molecules through nanochannels. Although considerable effort and progress has been made in recent years, a systematic understanding of the effect of nanochannel dimension is still lacking. In this paper, we use molecular dynamics (MD) simulations to study the transport of water molecules through carbon nanotubes (CNTs) with various dimensions under pressure differences. We find an exponential decay describing the relation of the water flow and CNT lengths (L) for different pressures. The average translocation time of individual water molecules yields to a power law relation with L. We also exploit these results by comparing with the single-file transport, where some interesting relations were figured. Meanwhile, for a given CNT length, the water flow vs CNT diameters (R) can be depicted by a power law, which is found to be relevant to the water occupancy inside the nanochannel. In addition, we compare our MD results with predictions from the no-slip Hagen-Poisseuille (HP) relation. The dependence of the enhancement of the simulated water flux over the HP prediction on the CNT length and diameter supports previous MD and experimental studies. Actually, the effect of nanotube dimension is not only originated from the motion of water molecules inside the CNT but also related to thermal fluctuations in the bulk water outside the CNT. These results enrich our knowledge about the channel size effect on the water transportation, which should have deep implications for the design of nanofluidic devices.

Electric-field-induced wetting and dewetting in single hydrophobic nanopores

The behaviour of water in nanopores is very different from that of bulk water. Close to hydrophobic surfaces, the water density has been found to be lower than in the bulk, and if confined in a sufficiently narrow hydrophobic nanopore, water can spontaneously evaporate. Molecular dynamics simulations have suggested that a nanopore can be switched between dry and wet states by applying an electric potential across the nanopore membrane. Nanopores with hydrophobic walls could therefore create a gate system for water, and also for ionic and neutral species. Here, we show that single hydrophobic nanopores can undergo reversible wetting and dewetting due to condensation and evaporation of water inside the pores. The reversible process is observed as fluctuations between conducting and non-conducting ionic states and can be regulated by a transmembrane electric potential.

Single-file water in nanopores

Water molecules confined to pores with sub-nanometre diameters form single-file hydrogen-bonded chains. In such nanoscale confinement, water has unusual physical properties that are exploited in biology and hold promise for a wide range of biomimetic and nanotechnological applications. The latter can be realized by carbon and boron nitride nanotubes which confine water in a relatively non-specific way and lend themselves to the study of intrinsic properties of single-file water. As a consequence of strong water-water hydrogen bonds, many characteristics of single-file water are conserved in biological and synthetic pores despite differences in their atomistic structures. Charge transport and orientational order in water chains depend sensitively on and are mainly determined by electrostatic effects. Thus, mimicking functions of biological pores with apolar pores and corresponding external fields gives insight into the structure-function relation of biological pores and allows the development of technical applications beyond the molecular devices found in living systems. In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores.

Phase transition of nanotube-confined water driven by electric field

The effects of electric field on the phase behaviors of water encapsulated in a thick single-walled carbon nanotube (SWCNT) (diameter = 1.2 nm) have been studied by performing extensive molecular dynamics simulations at atmospheric pressure. We found that liquid water can freeze continuously into either pentagonal or helical solidlike ice nanotube in SWCNT, depending on the strengths of the external electric field applied along the tube axis. Remarkably, the helical one is new ice phase which was not observed previously in the same size of SWCNT in the absence of electric field. Furthermore, a discontinuous solid-solid phase transition is observed between pentagonal and helical ice nanotubes as the strengths of the external electric field changes. The mechanism of electric-field-induced phase transition is discussed. The dependence of ice structures on the chiralities of SWCNTs is also investigated. Finally, we present a phase diagram of confined water in the electric field-temperature plane.

Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Brønsted slopes of one and zero, respectively.

Entropy and the driving force for the filling of carbon nanotubes with water

The spontaneous filling of hydrophobic carbon nanotubes (CNTs) by water observed both experimentally and from simulations is counterintuitive because confinement is generally expected to decrease both entropy and bonding, and remains largely unexplained. Here we report the entropy, enthalpy, and free energy extracted from molecular dynamics simulations of water confined in CNTs from 0.8 to 2.7-nm diameters. We find for all sizes that water inside the CNTs is more stable than in the bulk, but the nature of the favorable confinement of water changes dramatically with CNT diameter. Thus we find (i) an entropy (both rotational and translational) stabilized, vapor-like phase of water for small CNTs (0.8-1.0 nm), (ii) an enthalpy stabilized, ice-like phase for medium-sized CNTs (1.1-1.2 nm), and (iii) a bulk-like liquid phase for tubes larger than 1.4 nm, stabilized by the increased translational entropy as the waters sample a larger configurational space. Simulations with structureless coarse-grained water models further reveal that the observed free energies and sequence of transitions arise from the tetrahedral structure of liquid water. These results offer a broad theoretical basis for understanding water transport through CNTs and other nanostructures important in nanofluidics, nanofiltrations, and desalination.

Control of unidirectional transport of single-file water molecules through carbon nanotubes in an electric field

The transport of water molecules through nanopores is not only crucial to biological activities but also useful for designing novel nanofluidic devices. Despite considerable effort and progress that has been made, a controllable and unidirectional water flow is still difficult to achieve and the underlying mechanism is far from being understood. In this paper, using molecular dynamics simulations, we systematically investigate the effects of an external electric field on the transport of single-file water molecules through a carbon nanotube (CNT). We find that the orientation of water molecules inside the CNT can be well-tuned by the electric field and is strongly coupled to the water flux. This orientation-induced water flux is energetically due to the asymmetrical water-water interaction along the CNT axis. The wavelike water density profiles are disturbed under strong field strengths. The frequency of flipping for the water dipoles will decrease as the field strength is increased, and the flipping events vanish completely for the relatively large field strengths. Most importantly, a critical field strength E(c) related to the water flux is found. The water flux is increased as E is increased for E ≤ E(c), while it is almost unchanged for E > E(c). Thus, the electric field offers a level of governing for unidirectional water flow, which may have some biological applications and provides a route for designing efficient nanopumps.

Water in the polar and nonpolar cavities of the protein interleukin-1β

Water in the protein interior serves important structural and functional roles and is also increasingly recognized as a relevant factor in drug binding. The nonpolar cavity in the protein interleukin-1β has been reported to be filled by water on the basis of some experiments and simulations and to be empty on the basis of others. Here we study the thermodynamics of filling the central nonpolar cavity and the four polar cavities of interleukin-1β by molecular dynamics simulation. We use different water models (TIP3P and SPC/E) and protein force fields (amber94 and amber03) to calculate the semigrand partition functions term by term that quantify the hydration equilibria. We consistently find that water in the central nonpolar cavity is thermodynamically unstable, independent of force field and water model. The apparent reason is the relatively small size of the cavity, with a volume less than ∼80 Å(3). Our results are consistent with the most recent X-ray crystallographic and simulation studies but disagree with an earlier interpretation of nuclear magnetic resonance (NMR) experiments probing protein-water interactions. We show that, at least semiquantitatively, the measured nuclear Overhauser effects indicating the proximity of water to the methyl groups lining the nonpolar cavity can, in all likelihood, be attributed to interactions with buried and surface water molecules near the cavity. The same methods applied to determine the occupancy of the polar cavities show that they are filled by the same number of water molecules observed in crystallography, thereby validating the theoretical and simulation methods used to study the water occupancy in the nonpolar protein cavity.

Single-file water as a one-dimensional Ising model

We show that single-file water in nanopores can be viewed as a one-dimensional Ising model and investigate, on this basis, the static dielectric response of a chain of hydrogen-bonded water molecules to an external field. To this end, we use a recently developed dipole lattice model which accurately captures the free energetics of nanopore water. In this model, the total energy of the system can be expressed as a sum of effective interactions of chain ends and orientational defects. Neglecting these interactions, we essentially obtain the one-dimensional Ising model which allows us to derive analytical expressions for the free energy as a function of the total dipole moment and for the dielectric susceptibility. Our expressions, which agree very well with simulation results, provide the basis for the interpretation of future dielectric spectroscopy experiments on water-filled nanopore membranes.

Electrolyte solution transport in electropolar nanotubes

Electrolyte transport in nanochannels plays an important role in a number of emerging areas. Using non-equilibrium molecular dynamics (NEMD) simulations, the fundamental transport behavior of an electrolyte/water solution in a confined model nanoenvironment is systematically investigated by varying the nanochannel dimension, solid phase, electrolyte phase, ion concentration and transport rate. It is found that the shear resistance encountered by the nanofluid strongly depends on these material/system parameters; furthermore, several effects are coupled. The mechanisms of the nanofluidic transport characteristics are explained by considering the unique molecular/ion structure formed inside the nanochannel. The lower shear resistance observed in some of the systems studies could be beneficial for nanoconductors, while the higher shear resistance (or higher effective viscosity) observed in other systems might enhance the performance of energy dissipation devices.

Binary mixture adsorbed in a slit pore: Field-induced population inversion near the bulk instability

The recently proposed method for modulating through an external field the composition of a binary fluid mixture adsorbed in a slit pore is discussed. The population inversion near the bulk (demixing) instability is first analyzed in the case of a symmetric mixture of nonadditive hard spheres, without field. It is next investigated for a mixture comprising dipolar particles subject to an external field. The influence of several factors on the adsorption curves including bulk composition, pore width, field direction, polarizability versus permanent dipoles, and temperature on this field induced population inversion is shown by Monte Carlo simulation.

Role of dissolved gas in optical breakdown of water: differences between effects due to helium and other gases

It is shown that water contains defects in the form of heterogeneous optical breakdown centers. Long-living complexes composed of gas and liquid molecules may serve as nuclei for such centers. A new technique for removing dissolved gas from water is developed. It is based on a "helium washing" routine. The structure of helium-washed water is very different from that of water containing dissolved atmospheric gas. It is able to withstand higher optical intensities and temperatures of superheating compared with the nonprocessed ones. The characteristics of plasma spark and values of the breakdown thresholds for processed and nonprocessed samples are given.

Explicit and implicit modeling of nanobubbles in hydrophobic confinement

Water at normal conditions is a fluid thermodynamically close to the liquid-vapor phase coexistence and features a large surface tension. This combination can lead to interesting capillary phenomena on microscopic scales. Explicit water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capillary evaporation on nanometer scales, i.e., the formation of nanometer-sized vapor bubbles (nanobubbles) between confining hydrophobic surfaces. This phenomenon has been exemplified for solutes with varying complexity, e.g., paraffin plates, coarse-grained homopolymers, biological and solid-state channels, and atomistically resolved proteins. It has been argued that nanobubbles strongly impact interactions in nanofluidic devices, translocation processes, and even in protein stability, function, and folding. As large-scale MD simulations are computationally expensive, the efficient multiscale modeling of nanobubbles and the prediction of their stability poses a formidable task to the'nanophysical' community. Recently, we have presented a conceptually novel and versatile implicit solvent model, namely, the variational implicit solvent model (VISM), which is based on a geometric energy functional. As reviewed here, first solvation studies of simple hydrophobic solutes using VISM coupled with the numerical level-set scheme show promising results, and, in particular, capture nanobubble formation and its subtle competition to local energetic potentials in hydrophobic confinement.

Orientational dynamics and dielectric response of nanopore water

We present numerical calculations, simulation results, and analytical considerations for the frequency-dependent dielectric constant of single-file water in narrow nanopores, described by a recently developed dipole lattice model. We find Debye relaxation over all length scales with relaxation times that strongly depend on pore length. This behavior is analyzed in terms of the dynamics of orientational defects leading to simple quantitative expressions for the static dielectric susceptibility and the relaxation time in the limits of short and long pores. Based on these formulas, we suggest how the predicted macroscopic order of nanopore water can be probed via dielectric spectroscopy and explain how the excitation energy, diffusion constant, and effective interaction of the defects that destroy the order can be extracted from such measurements.

Effect of induced electric field on single-file reverse osmosis

We investigated the effect of the electric field on single-file reverse osmosis (RO) water flux using molecular dynamics simulations. The electric field is generated by introducing oppositely charged biomolecules to the salt solution and pure water chambers attached to the nanopore. Simulation results indicate that an electric field in the direction of RO enhances the water flux while in the direction opposite to RO it suppresses the water flux. When the RO water flux is enhanced, the single-file water dipoles are aligned in the direction of the electric field. The addition of an electric field in the direction of RO led to a flux of 3 water molecules ns(-1) by constantly maintaining water dipole vectors in the direction of the electric field, and this water flux is superimposed on the pressure driven water flux.