Molecular dynamics of zigzag single walled carbon nanotube immersion in water

The results of enthalpy of immersion in water for finite single-walled carbon nanotubes are reported. Using molecular dynamics simulation, we discuss the relation between the value of this enthalpy and tube diameters showing that the obtained plot can be divided into three regions. The structure of water inside tubes in all three regions is discussed and it is shown that the existence of the strong maximum of enthalpy observed for tube diameter ca. 1.17 nm is due to freezing of water under confinement. The calculations of hydrogen bond statistics and water density profiles inside tubes are additionally reported to confirm the obtained results. Next, we show the results of calculation for the same tubes but containing surface carbonyl oxygen groups at pore entrances. A remarkable rise in the value of enthalpy of immersion in comparison to the initial tubes is observed. We also discuss the influence of charge distribution between oxygen and carbon atom forming surface carbonyls on the structure of confined water. It is concluded for the first time that the presence of surface oxygen atoms at the pore entrances remarkably influences the structure and stability of ice created inside nanotubes, and surface carbonyls appear to be chaotropic (i.e. structure breaking) for confined water. This effect is explained by the pore blocking leading to a decrease (compared to initial structure) in the number of confined water molecules after introduction of surface oxygen groups at pore entrances.     

Role of water molecules in the KcsA protein channel by molecular dynamics calculations

Molecular dynamics simulations supported by electrostatic calculations have been conducted on the KcsA channel to determine the role of water molecules in the pore. Starting from the X-ray structure of the KcsA channel in its closed state at 2.0 angstroms resolution, the opening of the pore towards a conformation built on the basis of EPR results is studied. We show that water molecules act as a structural element for the K+ ions inside the filter and the hydrophobic cavity of the channel. In the filter, water tends to enhance the depth of the wells occupied by the K+ ions, while in the cavity there is a strong correlation between the water molecules and the cavity ion. As a consequence, the protein remains very stable in the presence of three K+ ions in the selectivity filter and one in the cavity. The analysis of the dynamics of water molecules in the cavity reveals preferred orientations of the dipoles along the pore axis, and a correlated behavior between this dipole orientation and the displacement of the K+ ion during the gating process.     

Analysis of swelling process of protein by positron annihilation lifetime spectroscopy and differential scanning calorimetry

The change in the nanoscopic structure and bound state of water in the protein gel were investigated using positron annihilation lifetime spectroscopy (PALS) and differential scanning calorimetry (DSC). Gelatin was used as a protein. To examine the bound state of water in gelatin gel, the amount of freezing and nonfreezing water in gelatin gels were evaluated by fusion enthalpy of DSC curves. Below water content of 40% (w/w), the whole amount of water was nonfreezing water, whereas above water content of 40% (w/w), the amount of freezing water increased according to increase in water content. To investigate the nanoscopic spatial structure under coexistence of polymer and water, positron annihilation lifetime measurement was performed. The lifetime of o‐Ps or the pore size increased according to increase in water content, particularly below the water content of 40% (w/w). When the water penetrates into the gelatin network, the water molecules form hydrogen bonds with hydrophilic groups inside the helical structure in gelatin gel. The water molecules inside the helical structure expand the structure outward, leading to increase in pore size. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2031–2037, 2007.     

Structure of the hydration shell of the Na+ ion in a planar nanopore with hydrophobic walls

The effect of steric hindrances in extremely narrow planar pores on the structure of the hydration shell of the single-charged sodium cation in water vapors at room temperature was studied by computer simulation. The deficiency of empty space for the motion in the slit-like pore was shown to slightly affect the radial distribution of molecules around the ion. The integrated (over the directions) numbers of ion-oxygen atom bonds of molecules in the ion’s hydration shell did not change despite the change in the shape of the hydration cluster from three- to two-dimensional. It was concluded that the changes in the positions of molecules relative to the ion were mainly reduced to azimuthal displacements; as a result, the local bulk density of molecules in the pore was higher than at the same distances outside the pore for the same total number of molecules. The distribution of molecules over layers inside the pore demonstrates the effect of molecules spread over the walls. The effect of ion displacement from its own hydration shell found earlier for the free chloride ion is steadily reproduced under the pore conditions. An alternative explanation to this effect was proposed that does not suggest high ion polarizability.     

Titanosilicate molecular sieve for size-screening photocatalytic conversion

Titanosilicate molecular sieves, when activated by ultraviolet light irradiation in water in the presence of molecular oxygen, catalyze a conversion of molecules having a size close to the pore of the catalysts but are inactive for molecules having much larger or smaller size. This unprecedented size-screening photocatalytic activity is triggered by a combination of H2O-induced shortened lifetime of active species (charge-transfer excited state of tetrahedrally coordinated titanium oxide) and restricted diffusion of a molecule inside the pore. This catalytic property demonstrates a potential utility of the catalyst for selective transformation of molecules that is associated with a size reduction of molecules, so-labeled "molecular shave" transformation.     

Strong correlations and Fickian water diffusion in narrow carbon nanotubes

The authors have used atomistic molecular dynamics (MD) simulations to study the structure and dynamics of water molecules inside an open ended carbon nanotube placed in a bath of water molecules. The size of the nanotube allows only a single file of water molecules inside the nanotube. The water molecules inside the nanotube show solidlike ordering at room temperature, which they quantify by calculating the pair correlation function. It is shown that even for the longest observation times, the mode of diffusion of the water molecules inside the nanotube is Fickian and not subdiffusive. They also propose a one-dimensional random walk model for the diffusion of the water molecules inside the nanotube. They find good agreement between the mean-square displacements calculated from the random walk model and from MD simulations, thereby confirming that the water molecules undergo normal mode diffusion inside the nanotube. They attribute this behavior to strong positional correlations that cause all the water molecules inside the nanotube to move collectively as a single object. The average residence time of the water molecules inside the nanotube is shown to scale quadratically with the nanotube length.     

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.     

Structure of a Na<Superscript>+</Superscript> cation hydration shell on heating in a planar nanopore

Resistance to heating above the boiling point of water of the molecular structure of a single-charged sodium cation hydration shell growing under the conditions of a model planar nanopore with a width of 5 Å is studied by computer simulation. Monte Carlo calculations of spatial correlation functions are performed in a detailed model with regard to many-body interactions between the ion and water molecules. The system demonstrates an increased resistance to thermal fluctuations along the pore plane and a decreased one in the transverse direction. The heating is accompanied by an enhanced coating effect of molecules around the ion and a diminished effect of extruding the ion out of its own hydration shell. The orientational molecular order due to strong spatial anisotropy inside the nanopore is much more stable than the hydrogen bonds between the molecules.     

Ab Initio H2O in Realistic Hydrophilic Confinement

A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long‐range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized.     

Neutron scattering study on dynamics of water molecules in MCM-41. 2. Determination of translational diffusion coefficient

Quasielastic neutron scattering (QENS) spectra of water-filled MCM-41 samples (pore diameters: 21.4 and 28.4 Angstrom) were measured over the temperature range 238-298 K and the momentum transfer range 0.31-0.99 A(-1) to investigate the dynamics of confined water molecules. The spectra, which consist mainly of contributions from the translational diffusion of water molecules, were analyzed by using the Lorentzian and the stretched exponential functions. Comparison of the fits indicated that the latter analysis is more reliable than the former one. The fraction of immobile water molecules located in the vicinity of the pore walls, which give an elastic component, was found to be 0.044-0.061 in both pores. The stretch exponent beta was determined as 0.66-0.80. It was shown that the translational diffusion of water molecules in the pores is decelerated by confinement and that the deceleration becomes marked with a decrease in pore size. The ratios of the translational diffusion coefficient D(T) of confined water to that of bulk water at room temperature were within a range of 0.47-0.63.     

Regioselective competitive adsorption of water and organic vapor mixtures on pristine single-walled carbon nanotube bundles

Sequential adsorption of water and organic vapor mixtures onto single-walled carbon nanotube (SWNT) bundles is studied experimentally and by grand canonical Monte Carlo (GCMC) simulation to elucidate the distinct interactions between select adsorbates and the nanoporous structure of SWNTs. Experimental adsorption isotherms on SWNT bundles for hexane, methyl ethyl ketone, cyclohexane, and toluene individually mixed in carrier gases that were nearly saturated with water vapor are compared with the GCMC-simulated isotherms for hexane, as a representative organic, on the external surface of the heterogeneous SWNT bundles. From the nearly perfect overlap between the experimental and simulated isotherms, it is concluded that until near saturation only the internal pore volume of pristine SWNT bundles fills with water. The adsorption of water vapor on the peripheral surface of the bundles remains insignificant, if not negligible, in comparison to the adsorption of water in the internal volume of the bundles. This is in contrast with the adsorption of pure hexane, which exhibits appreciable adsorption both inside the bundles and on their external surface. It is also suggested that during competitive adsorption, water molecules take precedence over small nonpolar and polar organic molecules for adsorption inside SWNTs and leave unoccupied the hydrophobic external surface of the bundles for other more compatible adsorbates.     

Melting and freezing of water in cylindrical silica nanopores

Freezing and melting of H(2)O and D(2)O in the cylindrical pores of well-characterized MCM-41 silica materials (pore diameters from 2.5 to 4.4 nm) was studied by differential scanning calorimetry (DSC) and (1)H NMR cryoporometry. Well-resolved DSC melting and freezing peaks were obtained for pore diameters down to 3.0 nm, but not in 2.5 nm pores. The pore size dependence of the melting point depression DeltaT(m) can be represented by the Gibbs-Thomson equation when the existence of a layer of nonfreezing water at the pore walls is taken into account. The DSC measurements also show that the hysteresis connected with the phase transition, and the melting enthalpy of water in the pores, both vanish near a pore diameter D* approximately equal to 2.8 nm. It is concluded that D* represents a lower limit for first-order melting/freezing in the pores. The NMR spin echo measurements show that a transition from low to high mobility of water molecules takes place in all MCM-41 materials, including the one with 2.5 nm pores, but the transition revealed by NMR occurs at a higher temperature than indicated by the DSC melting peaks. The disagreement between the NMR and DSC transition temperatures becomes more pronounced as the pore size decreases. This is attributed to the fact that with decreasing pore size an increasing fraction of the water molecules is situated in the first and second molecular layers next to the pore wall, and these molecules have slower dynamics than the molecules in the core of the pore.     

Confined water inside single-walled carbon nanotubes: global phase diagram and effect of finite length

Studies on confined water are important not only from the viewpoint of scientific interest but also for the development of new nanoscale devices. In this work, we aimed to clarify the properties of confined water in the cylindrical pores of single-walled carbon nanotubes (SWCNTs) that had diameters in the range of 1.46 to 2.40 nm. A combination of x-ray diffraction (XRD), nuclear magnetic resonance, and electrical resistance measurements revealed that water inside SWCNTs with diameters between 1.68 and 2.40 nm undergoes a wet-dry type transition with the lowering of temperature; below the transition temperature T(wd), water was ejected from the SWCNTs. T(wd) increased with increasing SWCNT diameter D. For the SWCNTs with D = 1.68, 2.00, 2.18, and 2.40 nm, T(wd) obtained by the XRD measurements were 218, 225, 236, and 237 K, respectively. We performed a systematic study on finite length SWCNT systems using classical molecular dynamics calculations to clarify the effect of open ends of the SWCNTs and water content on the water structure. It was found that ice structures that were formed at low temperatures were strongly affected by the bore diameter, a = D - σ(OC), where σ(OC) is gap distance between the SWCNT and oxygen atom in water, and the number of water molecules in the system. In small pores (a < 1.02 nm), tubule ices or the so-called ice nanotubes (ice NTs) were formed irrespective of the water content. On the other hand, in larger pores (a > 1.10 nm) with small water content, filled water clusters were formed leaving some empty space in the SWCNT pore, which grew to fill the pore with increasing water content. For pores with sizes in between these two regimes (1.02 < a < 1.10 nm), tubule ice also appeared with small water content and grew with increasing water content. However, once the tubule ice filled the entire SWCNT pore, further increase in the water content resulted in encapsulation of the additional water molecules inside the tubule ice. Corresponding XRD measurements on SWCNTs with a mean diameter of 1.46 nm strongly suggested the presence of such a filled structure.     

Frequency‐dependent NMR relaxation of liquids confined inside porous media containing an increased amount of magnetic impurities

Frequency‐dependent NMR relaxation studies have been carried out on water (polar) and cyclohexane (nonpolar) molecules confined inside porous ceramics containing variable amounts of iron oxide (III). The porous ceramics were prepared by compression of powders mixed with iron oxide followed by thermal treatment. The pore size distribution was estimated using a technique based on diffusion in internal fields that exposed a narrow distribution of macropore sizes with an average pore dimension independent of iron oxide content. The relaxation dispersion curves were obtained at room temperature using a fast field cycling NMR instrument. They display an increase of the relaxation rate proportional to the iron oxide concentration. This behavior is more prominent at low Larmor frequencies and is independent of the polar character of the confined molecules. The results reported here can be fitted well with a relaxation model considering exchange between molecules in the close vicinity of the paramagnetic centers located in the surface and bulk‐like molecules inside the pores. This model allows the extraction of the transverse diffusional correlation time that can be related to the polar character of the confined molecules. Copyright © 2013 John Wiley & Sons, Ltd.     

Water inside a hydrophobic cavitand molecule

The structure and dynamics of water inside a water-soluble, bowl-shaped cavitand molecule with a hydrophobic interior are studied using molecular dynamics computer simulations. The simulations find that the number of inside water molecules is about 4.5, but it fluctuates from being completely empty to full on a time scale of tens of nanoseconds. The transition from empty to full is energetically favorable and entropically unfavorable. The water molecules inside have fewer hydrogen bonds than the bulk and in general weaker interactions; the lower energy results from the nearest-neighbor interactions with the cavitand atoms and the water molecules at the entrance of the cavitand, interactions that are lost upon dewetting. An analysis of translational and rotational motion suggests that the lower entropy of the inside water molecules is due to decreased translational entropy, which outweighs an increased orientational entropy. The cavitand molecule acts as a host binding hydrophobic guests, and dewetting can be induced by the presence of a hydrophobic guest molecule about 3 A above the entrance. At this position, the guest displaces the water molecules which stabilize the inside water molecules and the empty cavitand becomes more stable than the full.     

Density functional description of adsorption in slitlike pores modified with chain molecules: a simple model for pillaredlike materials

We propose a density functional theory to describe adsorption of Lennard-Jones fluid in slitlike pores modified by chain molecules. Specifically, the chains are bonded by their ends to the opposite pore walls, so they can form pillaredlike structure. Two models are studied. In the first model, the nonterminating segments of chains can change their configuration inside the pore upon adsorption of spherical species. In the second model, the chains configuration remains fixed, so that the system is similar to a nonuniform quenched-annealed mixture. We study capillary condensation of fluid species inside such modified pores and compare the results obtained for two models.     

Effect of salts on water viscosity in narrow membrane pores

The effect of various salts on the viscosity, and by implication structure, of water in polymeric membrane pores of radius approximately 1.69 nm and low charge density has been studied. Permeation of pure water and various electrolyte solutions was analyzed using the Hagen-Poiseuille equation expressed in a ratio form to exclude membrane-specific quantities such as pore radius and length. The analysis produced viscosity ratios of electrolyte to pure water inside the membrane pores. Comparing the viscosity ratios inside the pores with their bulk counterparts showed that confinement significantly increased the sensitivity of water structure to the presence of ions. It has been found that, in relative terms in the pores, Cl- was a strong structure breaker, K+ was a moderately strong structure breaker, Na+ was a weak structure breaker, SO4(2-) was a weak structure maker, and Mg2+ was a strong structure maker. Predictive modeling of membrane separation performance would benefit from such effects being taken into account in cases where the pore ion concentrations may be high.     

On the nature of antimicrobial activity: a model for protegrin-1 pores

We conducted over 150 ns of simulation of a protegrin-1 octamer pore in a lipid bilayer composed of palmitoyloleoyl-phosphatidylethanolamine (POPE) and palmitoyloleoyl-phosphatidylglycerol (POPG) lipids mimicking the inner membrane of a bacterial cell. The simulations improve on a model of a pore proposed from recent NMR experiments and provide a coherent understanding of the molecular mechanism of antimicrobial activity. Although lipids tilt somewhat toward the peptides, the simulated protegrin-1 pore more closely follows the barrel-stave model than the toroidal-pore model. The movement of ions is investigated through the pore. The pore selectively allows negatively charged chloride ions to pass through at an average rate of one ion every two nanoseconds. Only two events are observed of sodium ions crossing through the pore. The potential of mean force is calculated for the water and both ion types. It is determined that the chloride ions move through the pore with ease, similarly to the water molecules with the exception of a zone of restricted movement midway through the pore. In bacteria, ions moving through the pore will compromise the integrity of the transmembrane potential. Without the transmembrane potential as a countermeasure, water will readily flow inside the higher osmolality cytoplasm. We determine that the diffusivity of water through a single PG-1 pore is sufficient to cause fast cell death by osmotic lysis.     

Phase behavior and local structure of a binary mixture in pores: mean-field lattice model calculations for analyzing neutron scattering data

We investigate the phase behavior of an asymmetric binary liquid A-W mixture confined between two planar homogenous substrates (slit pore). Molecules of species W interact preferentially with the solid walls via a long-range potential. Assuming nearest-neighbor attractions between the liquid molecules, we employ a lattice-gas model and a mean-field approximation for the grand potential. Minimization of this potential yields the density profiles of thermodynamically stable phases for fixed temperature, chemical potentials of both species, pore width and strengths of attraction. This model is used to analyze experimental small-angle neutron-scattering (SANS) data on the microscopic structure of the binary system isobutyric acid (iBA)+heavy water (D2O) inside a mesoscopic porous matrix (controlled-pore glass of about 10 nm mean pore width). Confinement-independent model parameters are adjusted so that the theoretical liquid-liquid coexistence curve in the bulk matches its experimental counterpart. By choosing appropriate values of the pore width and the attraction strength between substrates and water we analyze the effect of confinement on the phase diagram. In addition to a depression of the liquid-liquid critical point we observe surface induced phase transitions as well as water-film adsorption near the walls. The temperature dependence of the structure of water-rich and iBA-rich phases of constant composition are discussed in detail. The theoretical predictions are consistent with results of the SANS study and assist their interpretation.     

Adsorption and calorimetric studies of hydrothermally modified carbosils

The article presents the studies of effects of hydrothermal treatment (HTT) (in saturated water vapours or under the liquid water layer) using various sources of thermal energy (classical autoclave or high pressure microwave reactor) on structural and surface properties of initial and modified silica gels and carbon–silica adsorbents. The porous structure of the initial and modified materials was characterised by the low-temperature nitrogen adsorption/desorption method as well as by determining pore volume distribution curves from the calorimetric data (DSC) using the thermal effects of liquid (water) phase transitions previously brought inside the pores of the studied materials. Large compatibility of the characteristics obtained using the above methods was found. The microscopic investigations (SEM, TEM) were also conducted to evaluate the morphology and topography of the samples. It was proved that during HTT, the carbon deposit on the silica surface screens it against the access of water molecules, in this way affecting decrease in intensity of dissolution and condensation of polysilicic acids. At the same time, owing to oxidizing properties of water molecules under hydrothermal conditions, development of porous structure in the carbon deposit is observed. Extent of these changes depends on both the applied system (water vapour/liquid water) and kind of the used energy (classical/microwave).