Electric-field-controlled water and ion permeation of a hydrophobic nanopore

The permeation of hydrophobic, cylindrical nanopores by water molecules and ions is investigated under equilibrium and out-of-equilibrium conditions by extensive molecular-dynamics simulations. Neglecting the chemical structure of the confining pore surface, we focus on the effects of pore radius and electric field on permeation. The simulations confirm the intermittent filling of the pore by water, reported earlier under equilibrium conditions for pore radii larger than a critical radius R(c). Below this radius, water can still permeate the pore under the action of a strong electric field generated by an ion concentration imbalance at both ends of the pore embedded in a structureless membrane. The water driven into the channel undergoes considerable electrostriction characterized by a mean density up to twice the bulk density and by a dramatic drop in dielectric permittivity which can be traced back to a considerable distortion of the hydrogen-bond network inside the pore. The free-energy barrier to ion permeation is estimated by a variant of umbrella sampling for Na(+), K(+), Ca(2+), and Cl(-) ions, and correlates well with known solvation free energies in bulk water. Starting from an initial imbalance in ion concentration, equilibrium is gradually restored by successive ion passages through the water-filled pore. At each passage the electric field across the pore drops, reducing the initial electrostriction, until the pore, of radius less than R(c), closes to water and hence to ion transport, thus providing a possible mechanism for voltage-dependent gating of hydrophobic pores.     

Synthetic cation-selective nanotube: permeant cations chaperoned by anions

The ability to design ion-selective, synthetic nanotubes which mimic biological ion channels may have significant implications for the future treatment of bacteria, diseases, and as ultrasensitive biosensors. We present the design of a synthetic nanotube made from carbon atoms that selectively allows monovalent cations to move across and rejects all anions. The cation-selective nanotube mimics some of the salient properties of biological ion channels. Before practical nanodevices are successfully fabricated it is vital that proof-of-concept computational studies are performed. With this in mind we use molecular and stochastic dynamics simulations to characterize the dynamics of ion permeation across a single-walled (10, 10), 36 A? long, carbon nanotube terminated with carboxylic acid with an effective radius of 5.08 A?. Although cations encounter a high energy barrier of 7 kT, its height is drastically reduced by a chloride ion in the nanotube. The presence of a chloride ion near the pore entrance thus enables a cation to enter the pore and, once in the pore, it is chaperoned by the resident counterion across the narrow pore. The moment the chaperoned cation transits the pore, the counterion moves back to the entrance to ferry another ion. The synthetic nanotube has a high sodium conductance of 124 pS and shows linear current-voltage and current-concentration profiles. The cation-anion selectivity ratio ranges from 8 to 25, depending on the ionic concentrations in the reservoirs.     

Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family

Understanding the mechanisms of gating and ion permeation in biological channels and receptors has been a long-standing challenge in biophysics. Recent advances in structural biology have revealed the architecture of a number of transmembrane channels and allowed detailed, molecular-level insight into these systems. Herein, we have examined the barriers to ion conductance and origins of ion selectivity in models of the cationic human alpha7 nicotinic acetylcholine receptor (nAChR) and the anionic alpha1 glycine receptor (GlyR), based on the structure of Torpedo nAChR. Molecular dynamics simulations were used to determine water density profiles along the channel length, and they established that both receptor pores were fully hydrated. The very low water density in the middle of the nAChR pore indicated the existence of a hydrophobic constriction. By contrast, the pore of GlyR was lined with hydrophilic residues and remained well-hydrated throughout. Adaptive biasing force simulations allowed us to reconstruct potentials of mean force (PMFs) for chloride and sodium ions in the two receptors. For the nicotinic receptor we observed barriers to ion translocation associated with rings of hydrophobic residues-Val13' and Leu9'-in the middle of the transmembrane domain. This finding further substantiates the hydrophobic gating hypothesis for nAChR. The PMF revealed no significant hydrophobic barrier for chloride translocation in GlyR. For both receptors nonpermeant ions displayed considerable barriers. Thus, the overall electrostatics and the presence of rings of charged residues at the entrance and exit of the channels were sufficient to explain the experimentally observed anion and cation selectivity.     

Non-equilibrium molecular dynamics simulation study on permeation phenomena of LJ particles in slit-shaped membranes with periodic belt-like heterogeneous surfaces

In order to make clear the relationship between the pore structure and the diffusivity, we have carried out permeation simulations of pure gases through simple model membranes by using the external-field non-equilibrium molecular dynamics method. As the membrane, we model slit-shaped pores with periodic belt-like heterogeneous pore surfaces which are caused by the upheaval of surface atoms. Applying simulation results for membranes with several upheaval interval distances to Maxwell–Stefan (MS) theory, we calculate the effects of the molecular loading of permeating molecules in the pores on MS diffusivity (D_MS). In addition, the permeation potential barrier is estimated as the difference between the maximum and minimum permeation potential energies. The effect of the molecular loading on the permeation potential barrier and the D_MS are in inverse proportion. It is noted that, when the width of the adsorption area in the permeation direction is not common multiples of the molecular diameter, the permeation potential barrier decreases with the increase in the molecular loading. This is because the positive force against the permeation direction is caused to the permeating molecules by interactions with permeating molecules in the adsorpton area between adjacent upheavals. Therefore, we could suggest that the key factor for controlling diffusion property is the structural relationship between the adsorption area and the permeating molecules.     

Chloride ion conduction without water coordination in the pore of ClC protein

In the present work, we have found by an atomistic molecular dynamics simulation that hydrogen atoms originating from the residues of a prokaryotic ClC protein (EcClC) stabilize the chloride ion without water molecules in the pore of ClC protein. When the chloride ion conduction is simulated by pulling a chloride ion along the pore axis, the free energy barrier for chloride ion conduction is calculated to be low (4 kcal/mol), although the chloride ion is stripped of its hydration shell as it passes through the dehydrated pore region. The calculation of the number of hydrogen atoms surrounding the chloride ion reveals that water molecules hydrating the chloride ion are replaced by polar and non‐polar hydrogen atoms protruding from the protein residues. From the analysis of the pair interaction energy between the chloride ion and these hydrogen atoms, it is realized that the hydrogen atoms from the protein residues stabilize the chloride ion at the dehydrated region instead of water molecules, by which the energetic penalty for detaching water molecules from the permeating ion is compensated. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Quantifying barriers to monovalent anion transport in narrow non-polar pores

The transport of anionic drinking water contaminants (fluoride, chloride, nitrate and nitrite) through narrow pores ranging in effective radius from 2.5 to 6.5 ? was systematically evaluated using molecular dynamics simulations to elucidate the magnitude and origin of energetic barriers encountered in nanofiltration. Free energy profiles for ion transport through the pores show that energy barriers depend on pore size and ion properties and that there are three key regimes that affect transport. The first is where the ion can fit in the pore with its full inner hydration shell, the second is where the pore size is between the bare ion and hydrated radius, and the third is where the ion size approaches that of the pore. Energy barriers in the first regime are relatively small and due to rearrangement of the inner hydration shell and/or displacement of further hydration shells. Energy barriers in the second regime are due to partial dehydration and are larger than barriers seen in the first regime. In the third regime, the pore becomes too small for bare ions to fit regardless of hydration and thus energy barriers are very high. In the second regime where partial dehydration controls transport, the trend in the slopes of the change in energy barrier with pore size corresponds to the hydration strength of the anions.     

The role of hydrophobic surfaces in altering water-mediated peptide-peptide interactions in an aqueous environment

Using Born-Oppenheimer molecular dynamics within the density functional framework, we calculated the effective force acting on water-mediated peptide-peptide interaction between antiparallel β-sheets in an aqueous environment and also in the vicinity of a hydrophobic surface. From the magnitude of the effective force (corresponding to the slope of the free energy as a function of the interpeptide distance) and its sign (a negative value indicates an effective attraction, whereas a positive value indicates an effective repulsion) we can elucidate the fundamental differences of the water-mediated peptide-peptide interactions in those two environments. The computed effective forces indicate that the water-mediated interaction between peptides in an aqueous environment is attractive in the range of interpeptide distance d = 7-8 ? when hydrophobic surfaces are not nearby. Due to the stabilization of the water molecules bridging between the two β-sheets, a free energy barrier exists between the direct and indirect (water-mediated) interpeptide interactions. However, when the peptides are in the proximity of hydrophobic surfaces, this free energy barrier decreases because the hydrophobic surfaces enhance the interpeptide attraction by the destabilization and ease-to-libration of the bridging water molecules between them.     

Development of a molecular recognition ion gating membrane and estimation of its pore size control

We have fabricated a molecular recognition ion gating membrane. This synthetic membrane spontaneously opens and closes its pores in response to specific solvated ions. In addition to this switching function, we found that this membrane could control its pore size in response to a known concentration of a specific ion. The membrane was prepared by plasma graft copolymerization, which filled the pores of porous polyethylene film with a copolymer of NIPAM (N-isopropylacrylamide) and BCAm (benzo[18]crown-6-acrylamide). NIPAM is well-known to have an LCST (lower critical solution temperature), at which its volume changes dramatically in water. The crown receptor of the BCAm traps a specific ion, and causes a shift in the LCST. Therefore, selectively responding to either K(+) or Ba(2+), the grafted copolymer swelled and shrank in the pores at a constant temperature between two LCSTs. The solution flux in the absence of Ba(2+) decreased by about 2 orders of magnitude over a solution flux containing Ba(2+). The pore size was estimated by the filtration of aqueous dextran solutions with various solute sizes. This revealed that the membrane changed its pore size between 5 and 27 nm in response to the Ba(2+) concentration changes. No such change was observed for Ca(2+) solutions. Furthermore, this pore size change occurred uniformly in all pores, as a clear cut-off value for a solute size that could pass through pores was always present. This membrane may be useful not only as a molecular recognition ion gate, but also as a device for spontaneously controlling the permeation flux and solute size.     

Cooperative transport in a potassium ion channel

Our current understanding of ion permeation through the selectivity filter of the KcsA potassium channel is based on the concept of a multi-ion transport mechanism. The details of this concerted movement, however, are not well understood. In the present paper we report on molecular dynamics simulations which provides new insights. It is shown that ion translocation is based on the collective hopping of ions and water molecules which is mediated by the flexible charged carbonyl groups lining the backbone of the pore. In particular, there is strong evidence for pairwise translocations where one ion and one water molecule form a bound state. We suggest a physical explanation of the observed phenomena employing a simple lattice model. It is argued that the water molecules can act as rectifiers during the hopping of ion-water pairs.     

How to make the Cassie wetting state stable?

Wetting of rough hydrophilic and hydrophobic surfaces is discussed. The stability of the Cassie state, with air trapped in relief details under the droplet, is necessary for the design of true superhydrophobic surfaces. The potential barrier separating the Cassie state and the Wenzel state, for which the substrate is completely wetted, is calculated for both hydrophobic and hydrophilic surfaces. When the surface is hydrophobic, the multiscaled roughness of pillars constituting the surface increases the potential barrier separating the Cassie and Wenzel states. When water fills the hydrophilic pore, the energy gain due to the wetting of the pore hydrophilic wall is overcompensated by the energy increase because of the growth of the high-energetic liquid-air interface. The potential barrier separating the Cassie and Wenzel states is calculated for various topographies of surfaces. Structural features of reliefs favoring enhanced hydrophobicity are elucidated.     

Electric field-controlled water permeation coupled to ion transport through a nanopore

We report molecular dynamics simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na(+) concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium conditions, but the strong electric field caused by the ionic concentration gradient drives water molecules in. The density and structure of water in the pore are highly field dependent. In a typical simulation run, we observe a succession of cation passages through the pore, characterized by approximately bulk mobility. These ion passages reduce the electric field, until the pore empties of water and closes to further ion transport, thus providing a possible mechanism for biological ion channel gating.     

Is the mobility of the pore walls and water molecules in the selectivity filter of KcsA channel functionally important?

We performed in-depth analysis of the forces which act on the K(+) ions in the selectivity filter of the KcsA channel in order to estimate the relative importance of static and dynamic influence of the filter wall and water molecules on ion permeation and selectivity. The forces were computed using the trajectories of all-atom molecular dynamics simulations. It is shown that the dynamics of the selectivity filter contributes about 3% to the net force acting on the ions and can be neglected in the studies focused on the macroscopic properties of the channel, such as the current. Among the filter atoms, only the pore-forming carbonyl groups can be considered as dynamic in the studies of microscopic events of conduction, while the dynamic effects from all other atoms are negligible. We also show that the dynamics of the water molecules in the filter can not be neglected. The fluctuating forces from the water molecules can be as strong as net forces from the pore walls and can effectively drive the ions through the local energy barriers in the filter.     

The competitive adsorption of water and toluene on KU-2-8 ion exchanger in the presence of aromatic amino acids

The Weitkamp procedure was used to calculate hydrophobicity indices for several ion exchange systems, including adsorbed aromatic amino acids. The determination of hydrophobicity indices was based on the competitive adsorption of water and toluene from their mixture. Strongly acid KU-2 ion exchanger with hydrophilic properties predominantly sorbed water molecules in the competitive adsorption from their mixture with toluene vapor. The saturation of the ion exchanger with aromatic amino acids substantially decreased its sorption ability because of amino acid structuring and a decrease in permeability. The conclusion was drawn that the saturation of the ion exchanger with amino acids caused not only a decrease in the sorption of water but also a decrease in the sorption of hydrophobic toluene. This contradicted the assertion of an increase in hydrophobicity as a whole.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

Insights into the effect of combustion-generated carbon nanoparticles on biological membranes: a computer simulation study

Classical molecular dynamics simulations of atomistic models of combustion-generated carbon nanoparticles and lipid bilayers have been performed to explore their possible structural, dynamical, and thermodynamic effects on biological membranes. The DREIDING generic force field is used for the carbonaceous nanoparticles of different morphologies, as produced from combustion sources, and the united atom model was employed for the dimyristoylphosphatidylcholine (DMPC) bilayer. It is observed that particle shape and structure have significant effects on solvation, mobility, adsorption, and permeation behavior of the particles. While combustion-generated carbon nanoparticles with an aspect ratio close to unity prefer to stay near the membrane center, precursors with other shapes mostly reside within the hydrocarbon tail region of the membrane. Carbon nanoparticles are not trapped in a local region even inside the membranes but move freely with a speed depending on their molecular weight. The adsorption of the particles on the surface of the biological membrane is comparable to thermal fluctuations because the weak segregation effect by water molecules is the main driving force to the adsorption behavior. The bigger the precursors are, the stronger they are bound to the membrane surface. The presence of combustion-generated nanoparticles inside the membrane perturbs local lipid density by pushing the neighboring lipid molecules away from the nanoparticles. This, coupled with thermal fluctuations, can induce an instantaneous membrane pore to allow water protrusion. From the umbrella sampling method, the potential of mean force for the permeation of carbona nanoparticles into the bilayer was also obtained. Surprisingly, elongated particles have a free energy barrier an order of magnitude smaller compared with more round ones. In addition, the round carbon nanoparticles showed strong hysteresis due to the local trapping of water molecules. Although the carbon soot precursors studied in this work are not the well-known carbon nanoparticles such as fullerenes or carbon nanotubes, the qualitative features of this study may be applicable to them as well.     

Preparation of hydrophilic/hydrophobic porous materials

A novel porous material was designed and prepared in this work. A hydrophobic open-celled porous polystyrene (PS) was first synthesized via a concentrated emulsion polymerization of water in styrene. Subsequently the porous polystyrene was saturated with an aqueous solution of acrylamide (AM) and an initiator, which was subjected to another polymerization and the resulted polyacrylamide (PAM) penetrated in the cells and intercellular pores of the PS matrix. The PAM would change its volume according to the environmental humidity and thus adjusted the permeation of the material. The morphology, pore size distributions, water absorption, and vapor permeation of the materials were investigated.     

Free Energy of Bare and Capped Gold Nanoparticles Permeating through a Lipid Bilayer

Herein, we study the permeation free energy of bare and octane‐thiol‐capped gold nanoparticles (AuNPs) translocating through a lipid membrane. To investigate this, we have pulled the bare and capped AuNPs from bulk water to the membrane interior and estimated the free energy cost. The adsorption of the bare AuNP on the bilayer surface is energetically favorable but further loading inside it requires energy. However, the estimated free‐energy barrier for loading the capped AuNP into the lipid membrane is much higher compared to bare AuNP. We also demonstrate the details of the permeation process of bare and capped AuNPs. Bare AuNP induces the curvature in the lipid membrane whereas capped AuNP creates an opening in the interacting monolayer and get inserted into the membrane. The insertion of capped AuNP induces a partial unzipping of the lipid bilayer, which results in the ordering of the local lipids interacting with the nanoparticle. However, bare AuNP disrupts the lipid membrane by pushing the lipid molecules inside the membrane. We also analyze pore formation due to the insertion of capped AuNP into the membrane, which results in water molecules penetrating the hydrophobic region.     

Molecular origin of anticooperativity in hydrophobic association

The structuring of water molecules in the vicinity of nonpolar solutes is responsible for hydrophobic hydration and association thermodynamics in aqueous solutions. Here, we studied the potential of mean force (PMF) for the formation of a dimer and trimers of methane molecules in three specific configurations in explicit water to explain multibody effects in hydrophobic association on a molecular level. We analyzed the packing and orientation of water molecules in the vicinity of the solute to explain the effect of ordering of the water around nonpolar solutes on many-body interactions. Consistent with previous theoretical studies, we observed cooperativity, manifested as a reduction of the height of the desolvation barrier for the trimer in an isosceles triangle geometry, but for linear trimers, we observed only anticooperativity. A simple mechanistic picture of hydrophobic association is drawn. The free energy of hydrophobic association depends primarily on the difference in the number of water molecules in the first solvation shell of a cluster and that in the monomers of a cluster; this can be approximated by the molecular surface area. However, there are unfavorable electrostatic interactions between the water molecules from different parts of the solvation shell of a trimer because of their increased orientation induced by the nonpolar solute. These electrostatic interactions make an anticooperative contribution to the PMF, which is clearly manifested for the linear trimer where the multibody contribution due to changes in the molecular surface area is equal to zero. The information theory model of hydrophobic interactions of Hummer et al. also explains the anticooperativity of hydrophobic association of the linear trimers; however, it predicts anticooperativity with a qualitatively identical distance dependence for nonlinear trimers, which disagrees with the results of simulations.     

Transport of hydrated nitrate and nitrite ions through graphene nanopores in aqueous medium

Nitrate () and nitrite () ions are naturally occurring inorganic ions that are part of the nitrogen cycle. High doses of these ions in drinking water impose a potential risk to public health. In this work, molecular dynamics simulations are carried out to study the passage of nitrate and nitrite ions from water through graphene nanosheets (GNS) with hydrogen-functionalized narrow pores in presence of an external electric field. The passage of ions through the pores is investigated through calculations of ion flux, and the results are analyzed through calculations of various structural and thermodynamic properties such as the density of ions and water, ion–water radial distribution functions, two-dimensional density distribution functions, and the potentials of mean force of the ions. Current simulations show that the nitrite ions can pass more in numbers than the nitrate ions in a given time through GNS hydrogen-functionalized pore of different geometry. It is found that the nitrite ions can permeate faster than the nitrate ions despite the former having higher hydration energy in the bulk. This can be explained in terms of the competition between the number density of the ions along the pore axis and the free energy barrier calculated from the potential of mean force. Also, an externally applied electric field is found to be important for faster permeation of the nitrite over the nitrate ions. The current study suggests that graphene nanosheets with carefully created pores can be effective in achieving selective passage of ions from aqueous solutions.     

苯基修饰的疏水微孔二氧化硅膜的制备与表征

采用苯基三乙氧基硅烷(PTES)和正硅酸乙酯(TEOS)作为前驱体,通过溶胶-凝胶法制备了苯基修饰的SiO2膜材料。利用扫描电镜、N2吸附、视频光学接触角测量仪、热重分析、红外光谱等测试手段对膜的孔结构以及疏水性能进行了表征,最后还研究了修饰后膜材料在室温条件下的单组份气体渗透和分离性能。结果表明,随着PTES加入量的增大,膜材料的疏水性逐渐增强,当PTES/TEOS和H2O/TEOS的化学计量比分别达到0.6和9.6时,膜材料对水的接触角达到115±0.5°,仍保持良好的微孔结构,其孔体积为0.17cm3/g,孔径为0.4-0.5nm。室温下氢气在修饰后SiO2膜的输运既遵循发生在微孔孔道的表面扩散机理也遵循发生在较大孔道或者微缺陷的努森扩散机理,膜材料的H2渗透率达到1.49×10-6mol?m-2?Pa-1?s-1,H2/CO2 和H2/SF6的理想分离系数分别达到4.64和365.59